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Learning Interpretable SVMs for Biological Sequence Classification
Author: Rätsch Gunnar ; Sonnenburg Sören ; Schäfer Christin Journal: BMC Bioinformatics Year: 2006 Vol: 7 Issue: Suppl 1 Pages/record No.: S9
Discrete profile comparison using information bottleneck
Author: O'Rourke Sean ; Chechik Gal ; Friedman Robin ; Eskin Eleazar Journal: BMC Bioinformatics Year: 2006 Vol: 7 Issue: Suppl 1 Pages/record No.: S8
ARACNE: An Algorithm for the Reconstruction of Gene Regulatory Networks in a Mammalian Cellular Context
Author: Margolin Adam ; Nemenman Ilya ; Basso Katia ; Wiggins Chris ; Stolovitzky Gustavo ; Favera Riccardo ; Califano Andrea Journal: BMC Bioinformatics Year: 2006 Vol: 7 Issue: Suppl 1 Pages/record No.: S7
The Secrets of a Functional Synapse – From a Computational and Experimental Viewpoint
Author: Linial Michal Journal: BMC Bioinformatics Year: 2006 Vol: 7 Issue: Suppl 1 Pages/record No.: S6
A classification-based framework for predicting and analyzing gene regulatory response
Author: Kundaje Anshul ; Middendorf Manuel ; Shah Mihir ; Wiggins Chris ; Freund Yoav ; Leslie Christina Journal: BMC Bioinformatics Year: 2006 Vol: 7 Issue: Suppl 1 Pages/record No.: S5
Network-based de-noising improves prediction from microarray data
Author: Kato Tsuyoshi ; Murata Yukio ; Miura Koh ; Asai Kiyoshi ; Horton Paul ; Tsuda Koji ; Fujibuchi Wataru Journal: BMC Bioinformatics Year: 2006 Vol: 7 Issue: Suppl 1 Pages/record No.: S4
PepDist: A New Framework for Protein-Peptide Binding Prediction based on Learning Peptide Distance Functions
Author: Hertz Tomer ; Yanover Chen Journal: BMC Bioinformatics Year: 2006 Vol: 7 Issue: Suppl 1 Pages/record No.: S3
Choosing negative examples for the prediction of protein-protein interactions
Author: Ben-Hur Asa ; Noble William Journal: BMC Bioinformatics Year: 2006 Vol: 7 Issue: Suppl 1 Pages/record No.: S2
A Regression-based K nearest neighbor algorithm for gene function prediction from heterogeneous data
Author: Yao Zizhen ; Ruzzo Walter Journal: BMC Bioinformatics Year: 2006 Vol: 7 Issue: Suppl 1 Pages/record No.: S11
Protein Ranking by Semi-Supervised Network Propagation
Author: Weston Jason ; Kuang Rui ; Leslie Christina ; Noble William Journal: BMC Bioinformatics Year: 2006 Vol: 7 Issue: Suppl 1 Pages/record No.: S10
The Cluster Variation Method for Efficient Linkage Analysis on Extended Pedigrees
Author: Albers Cornelis ; Leisink Martijn ; Kappen Hilbert Journal: BMC Bioinformatics Year: 2006 Vol: 7 Issue: Suppl 1 Pages/record No.: S1
The relationship between protein sequences and their gene ontology functions
Author: Duan Zhong-Hui ; Hughes Brent ; Reichel Lothar ; Perez Dianne ; Shi Ting Journal: BMC Bioinformatics Year: 2006 Vol: 7 Issue: Suppl 4 Pages/record No.: S11
SEQOPTICS: a protein sequence clustering system
Author: Chen Yonghui ; Reilly Kevin ; Sprague Alan ; Guan Zhijie Journal: BMC Bioinformatics Year: 2006 Vol: 7 Issue: Suppl 4 Pages/record No.: S10
Development of computations in bioscience and bioinformatics and its application: review of the Symposium of Computations in Bioinformatics and Bioscience (SCBB06)
Author: Deng Youping ; Ni Jun ; Zhang Chaoyang Journal: BMC Bioinformatics Year: 2006 Vol: 7 Issue: Suppl 4 Pages/record No.: S1
Parallelization of multicategory support vector machines (PMC-SVM) for classifying microarray data
Author: Zhang Chaoyang ; Li Peng ; Rajendran Arun ; Deng Youping ; Chen Dequan Journal: BMC Bioinformatics Year: 2006 Vol: 7 Issue: Suppl 4 Pages/record No.: S15
Improved Chou-Fasman method for protein secondary structure prediction
Author: Chen Hang ; Gu Fei ; Huang Zhengge Journal: BMC Bioinformatics Year: 2006 Vol: 7 Issue: Suppl 4 Pages/record No.: S14
Determination of the minimum number of microarray experiments for discovery of gene expression patterns
Author: Wu Fang-Xiang ; Zhang WJ ; Kusalik Anthony Journal: BMC Bioinformatics Year: 2006 Vol: 7 Issue: Suppl 4 Pages/record No.: S13
Towards a better solution to the shortest common supersequence problem: the deposition and reduction algorithm
Author: Ning Kang ; Leong Hon Journal: BMC Bioinformatics Year: 2006 Vol: 7 Issue: Suppl 4 Pages/record No.: S12
Frequency distribution of TATA Box and extension sequences on human promoters
Author: Shi Wei ; Zhou Wanlei Journal: BMC Bioinformatics Year: 2006 Vol: 7 Issue: Suppl 4 Pages/record No.: S2
Clustering of gene expression data: performance and similarity analysis
Author: Yin Longde ; Huang Chun-Hsi ; Ni Jun Journal: BMC Bioinformatics Year: 2006 Vol: 7 Issue: Suppl 4 Pages/record No.: S19
GenomeBlast: a web tool for small genome comparison
Author: Lu Guoqing ; Jiang Liying ; Helikar Resa ; Rowley Thaine ; Zhang Luwen ; Chen Xianfeng ; Moriyama Etsuko Journal: BMC Bioinformatics Year: 2006 Vol: 7 Issue: Suppl 4 Pages/record No.: S18
Evaluation of clustering algorithms for gene expression data
Author: Datta Susmita ; Datta Somnath Journal: BMC Bioinformatics Year: 2006 Vol: 7 Issue: Suppl 4 Pages/record No.: S17
Identification of new members of hydrophobin family using primary structure analysis
Author: Yang Kuan ; Deng Youping ; Zhang Chaoyang ; Elasri Mohamed Journal: BMC Bioinformatics Year: 2006 Vol: 7 Issue: Suppl 4 Pages/record No.: S16
Systematic gene function prediction from gene expression data by using a fuzzy nearest-cluster method
Author: Li Xiao-Li ; Tan Yin-Chet ; Ng See-Kiong Journal: BMC Bioinformatics Year: 2006 Vol: 7 Issue: Suppl 4 Pages/record No.: S23
Comparison of transcriptional responses in liver tissue and primary hepatocyte cell cultures after exposure to hexahydro-1, 3, 5-trinitro-1, 3, 5-triazine
Author: Perkins Edward ; Bao Wenjun ; Guan Xin ; Ang Choo-Yaw ; Wolfinger Russell ; Chu Tzu-Ming ; Meyer Sharon ; Inouye Laura Journal: BMC Bioinformatics Year: 2006 Vol: 7 Issue: Suppl 4 Pages/record No.: S22
Combining comparative genomics with de novo motif discovery to identify human transcription factor DNA-binding motifs
Author: Mao Linyong ; Zheng W Jim Journal: BMC Bioinformatics Year: 2006 Vol: 7 Issue: Suppl 4 Pages/record No.: S21
Particle simulation approach for subcellular dynamics and interactions of biological molecules
Author: Azuma Ryuzo ; Kitagawa Tetsuji ; Kobayashi Hiroshi ; Konagaya Akihiko Journal: BMC Bioinformatics Year: 2006 Vol: 7 Issue: Suppl 4 Pages/record No.: S20
An improved ant colony algorithm with diversified solutions based on the immune strategy
Author: Qin Ling ; Pan Yi ; Chen Ling ; Chen Yixin Journal: BMC Bioinformatics Year: 2006 Vol: 7 Issue: Suppl 4 Pages/record No.: S3
In silico modelling of hormone response elements
Author: Stepanova Maria ; Lin Feng ; Lin Valerie Journal: BMC Bioinformatics Year: 2006 Vol: 7 Issue: Suppl 4 Pages/record No.: S27
AffyMiner: mining differentially expressed genes and biological knowledge in GeneChip microarray data
Author: Lu Guoqing ; Nguyen The ; Xia Yuannan ; Fromm Michael Journal: BMC Bioinformatics Year: 2006 Vol: 7 Issue: Suppl 4 Pages/record No.: S26
A novel approach to phylogenetic tree construction using stochastic optimization and clustering
Author: Qin Ling ; Chen Yixin ; Pan Yi ; Chen Ling Journal: BMC Bioinformatics Year: 2006 Vol: 7 Issue: Suppl 4 Pages/record No.: S24
SVM Classifier – a comprehensive java interface for support vector machine classification of microarray data
Author: Pirooznia Mehdi ; Deng Youping Journal: BMC Bioinformatics Year: 2006 Vol: 7 Issue: Suppl 4 Pages/record No.: S25
The impact of sample imbalance on identifying differentially expressed genes
Author: Yang Kun ; Li Jianzhong ; Gao Hong Journal: BMC Bioinformatics Year: 2006 Vol: 7 Issue: Suppl 4 Pages/record No.: S8
FM-test: a fuzzy-set-theory-based approach to differential gene expression data analysis
Author: Liang Lily ; Lu Shiyong ; Wang Xuena ; Lu Yi ; Mandal Vinay ; Patacsil Dorrelyn ; Kumar Deepak Journal: BMC Bioinformatics Year: 2006 Vol: 7 Issue: Suppl 4 Pages/record No.: S7
Maximum common subgraph: some upper bound and lower bound results
Author: Huang Xiuzhen ; Lai Jing ; Jennings Steven Journal: BMC Bioinformatics Year: 2006 Vol: 7 Issue: Suppl 4 Pages/record No.: S6
Estimate haplotype frequencies in pedigrees
Author: Zhang Qiangfeng ; Zhao Yuzhong ; Chen Guoliang ; Xu Yun Journal: BMC Bioinformatics Year: 2006 Vol: 7 Issue: Suppl 4 Pages/record No.: S5
A fast parallel algorithm for finding the longest common sequence of multiple biosequences
Author: Chen Yixin ; Wan Andrew ; Liu Wei Journal: BMC Bioinformatics Year: 2006 Vol: 7 Issue: Suppl 4 Pages/record No.: S4
Degenerated primer design to amplify the heavy chain variable region from immunoglobulin cDNA
Author: Wang Ying ; Chen Wei ; Li Xu ; Cheng Bing Journal: BMC Bioinformatics Year: 2006 Vol: 7 Issue: Suppl 4 Pages/record No.: S9
Curation of viral genomes: challenges, applications and the way forward
Author: Kulkarni-Kale Urmila ; Bhosle Shriram ; Manjari G Sunitha ; Joshi Manali ; Bansode Sandeep ; Kolaskar Ashok Journal: BMC Bioinformatics Year: 2006 Vol: 7 Issue: Suppl 5 Pages/record No.: S12
NERBio: using selected word conjunctions, term normalization, and global patterns to improve biomedical named entity recognition
Author: Tsai Richard ; Sung Cheng-Lung ; Dai Hong-Jie ; Hung Hsieh-Chuan ; Sung Ting-Yi ; Hsu Wen-Lian Journal: BMC Bioinformatics Year: 2006 Vol: 7 Issue: Suppl 5 Pages/record No.: S11
Trends in life science grid: from computing grid to knowledge grid
Author: Konagaya Akihiko Journal: BMC Bioinformatics Year: 2006 Vol: 7 Issue: Suppl 5 Pages/record No.: S10
Modelling study of dimerization in mammalian defensins
Author: Suresh Anita ; Verma Chandra Journal: BMC Bioinformatics Year: 2006 Vol: 7 Issue: Suppl 5 Pages/record No.: S17
SPIDer: Saccharomyces protein-protein interaction database
Author: Wu Xiaomei ; Zhu Lei ; Guo Jie ; Fu Cong ; Zhou Hongjun ; Dong Dong ; Li Zhenbo ; Zhang Da-Yong ; Lin Kui Journal: BMC Bioinformatics Year: 2006 Vol: 7 Issue: Suppl 5 Pages/record No.: S16
Splice site identification using probabilistic parameters and SVM classification
Author: Baten AKMA ; Chang BCH ; Halgamuge SK ; Li Jason Journal: BMC Bioinformatics Year: 2006 Vol: 7 Issue: Suppl 5 Pages/record No.: S15
Prediction of the functional class of metal-binding proteins from sequence derived physicochemical properties by support vector machine approach
Author: Lin HH ; Han LY ; Zhang HL ; Zheng CJ ; Xie B ; Cao ZW ; Chen YZ Journal: BMC Bioinformatics Year: 2006 Vol: 7 Issue: Suppl 5 Pages/record No.: S13
SVM-based prediction of caspase substrate cleavage sites
Author: Wee Lawrence ; Tan Tin ; Ranganathan Shoba Journal: BMC Bioinformatics Year: 2006 Vol: 7 Issue: Suppl 5 Pages/record No.: S14
Asymptotic behaviour and optimal word size for exact and approximate word matches between random sequences
Author: Forêt Sylvain ; Kantorovitz Miriam ; Burden Conrad Journal: BMC Bioinformatics Year: 2006 Vol: 7 Issue: Suppl 5 Pages/record No.: S21
MicroTar: predicting microRNA targets from RNA duplexes
Author: Thadani Rahul ; Tammi Martti Journal: BMC Bioinformatics Year: 2006 Vol: 7 Issue: Suppl 5 Pages/record No.: S20
An evaluation of human protein-protein interaction data in the public domain
Author: Mathivanan Suresh ; Periaswamy Balamurugan ; Gandhi TKB ; Kandasamy Kumaran ; Suresh Shubha ; Mohmood Riaz ; Ramachandra YL ; Pandey Akhilesh Journal: BMC Bioinformatics Year: 2006 Vol: 7 Issue: Suppl 5 Pages/record No.: S19
Comparative genomics in cyprinids: common carp ESTs help the annotation of the zebrafish genome
Author: Christoffels Alan ; Bartfai Richard ; Srinivasan Hamsa ; Komen Hans ; Orban Laszlo Journal: BMC Bioinformatics Year: 2006 Vol: 7 Issue: Suppl 5 Pages/record No.: S2
Fly-DPI: database of protein interactomes for D. melanogaster in the approach of systems biology
Author: Lin Chung-Yen ; Chen Shu-Hwa ; Cho Chi-Shiang ; Chen Chia-Ling ; Lin Fan-Kai ; Lin Chieh-Hua ; Chen Pao-Yang ; Lo Chen-Zen ; Hsiung Chao Journal: BMC Bioinformatics Year: 2006 Vol: 7 Issue: Suppl 5 Pages/record No.: S18
Improving the performance of DomainDiscovery of protein domain boundary assignment using inter-domain linker index
Author: Sikder Abdur ; Zomaya Albert Journal: BMC Bioinformatics Year: 2006 Vol: 7 Issue: Suppl 5 Pages/record No.: S6
Projections for fast protein structure retrieval
Author: Bhattacharya Sourangshu ; Bhattacharyya Chiranjib ; Chandra Nagasuma Journal: BMC Bioinformatics Year: 2006 Vol: 7 Issue: Suppl 5 Pages/record No.: S5
Large-scale analysis of antigenic diversity of T-cell epitopes in dengue virus
Author: Khan Asif ; Heiny AT ; Lee Kenneth ; Srinivasan KN ; Tan Tin ; August J Thomas ; Brusic Vladimir Journal: BMC Bioinformatics Year: 2006 Vol: 7 Issue: Suppl 5 Pages/record No.: S4
Evaluation and comparison of mammalian subcellular localization prediction methods
Author: Sprenger Josefine ; Fink J Lynn ; Teasdale Rohan Journal: BMC Bioinformatics Year: 2006 Vol: 7 Issue: Suppl 5 Pages/record No.: S3
Selecting effective siRNA sequences by using radial basis function network and decision tree learning
Author: Takasaki Shigeru ; Kawamura Yoshihiro ; Konagaya Akihiko Journal: BMC Bioinformatics Year: 2006 Vol: 7 Issue: Suppl 5 Pages/record No.: S22
Establishing bioinformatics research in the Asia Pacific
Author: Ranganathan Shoba ; Tammi Martti ; Gribskov Michael ; Tan Tin Wee Journal: BMC Bioinformatics Year: 2006 Vol: 7 Issue: Suppl 5 Pages/record No.: S1
MycoperonDB: a database of computationally identified operons and transcriptional units in Mycobacteria
Author: Ranjan Sarita ; Gundu Ranjit ; Ranjan Akash Journal: BMC Bioinformatics Year: 2006 Vol: 7 Issue: Suppl 5 Pages/record No.: S9
Computational promoter analysis of mouse, rat and human antimicrobial peptide-coding genes
Author: Brahmachary Manisha ; Schönbach Christian ; Yang Liang ; Huang Enli ; Tan Sin ; Chowdhary Rajesh ; Krishnan SPT ; Lin Chin-Yo ; Hume David ; Kai Chikatoshi ; Kawai Jun ; Carninci Piero ; Hayashizaki Yoshihide ; Bajic Vladimir Journal: BMC Bioinformatics Year: 2006 Vol: 7 Issue: Suppl 5 Pages/record No.: S8
Prediction of desmoglein-3 peptides reveals multiple shared T-cell epitopes in HLA DR4- and DR6- associated Pemphigus vulgaris
Author: Tong Joo ; Tan Tin ; Sinha Animesh ; Ranganathan Shoba Journal: BMC Bioinformatics Year: 2006 Vol: 7 Issue: Suppl 5 Pages/record No.: S7
An environment for relation mining over richly annotated corpora: the case of GENIA
Author: Rinaldi Fabio ; Schneider Gerold ; Kaljurand Kaarel ; Hess Michael ; Romacker Martin Journal: BMC Bioinformatics Year: 2006 Vol: 7 Issue: Suppl 3 Pages/record No.: S3
Proceedings of the Second International Symposium for Semantic Mining in Biomedicine
Author: Ananiadou Sophia ; Fluck Juliane Journal: BMC Bioinformatics Year: 2006 Vol: 7 Issue: Suppl 3 Pages/record No.: S1
Lexical adaptation of link grammar to the biomedical sublanguage: a comparative evaluation of three approaches
Author: Pyysalo Sampo ; Salakoski Tapio ; Aubin Sophie ; Nazarenko Adeline Journal: BMC Bioinformatics Year: 2006 Vol: 7 Issue: Suppl 3 Pages/record No.: S2
A critical review of PASBio's argument structures for biomedical verbs
Author: Cohen K Bretonnel ; Hunter Lawrence Journal: BMC Bioinformatics Year: 2006 Vol: 7 Issue: Suppl 3 Pages/record No.: S5
Mapping data elements to terminological resources for integrating biomedical data sources
Author: Mougin Fleur ; Burgun Anita ; Bodenreider Olivier Journal: BMC Bioinformatics Year: 2006 Vol: 7 Issue: Suppl 3 Pages/record No.: S6
Automatic recognition of topic-classified relations between prostate cancer and genes using MEDLINE abstracts
Author: Chun Hong-Woo ; Tsuruoka Yoshimasa ; Kim Jin-Dong ; Shiba Rie ; Nagata Naoki ; Hishiki Teruyoshi ; Tsujii Jun'ichi Journal: BMC Bioinformatics Year: 2006 Vol: 7 Issue: Suppl 3 Pages/record No.: S4
Fast-Find: A novel computational approach to analyzing combinatorial motifs
Author: Hamady Micah ; Peden Erin ; Knight Rob ; Singh Ravinder Journal: BMC Bioinformatics Year: 2006 Vol: 7 Issue: 1 Pages/record No.: 1
Cluster analysis of networks generated through homology: automatic identification of important protein communities involved in cancer metastasis
Author: Jonsson Pall ; Cavanna Tamara ; Zicha Daniel ; Bates Paul Journal: BMC Bioinformatics Year: 2006 Vol: 7 Issue: 1 Pages/record No.: 2
Gene selection and classification of microarray data using random forest
Author: Díaz-Uriarte Ramón ; Alvarez de Andrés Sara Journal: BMC Bioinformatics Year: 2006 Vol: 7 Issue: 1 Pages/record No.: 3
Application of machine learning in SNP discovery
Author: Matukumalli Lakshmi ; Grefenstette John ; Hyten David ; Choi Ik-Young ; Cregan Perry ; Van Tassell Curtis Journal: BMC Bioinformatics Year: 2006 Vol: 7 Issue: 1 Pages/record No.: 4
The comprehensive updated regulatory network of Escherichia coli K-12
Author: Salgado Heladia ; Santos-Zavaleta Alberto ; Gama-Castro Socorro ; Peralta-Gil Martín ; Peñaloza-Spínola Mónica ; Martínez-Antonio Agustino ; Karp Peter ; Collado-Vides Julio Journal: BMC Bioinformatics Year: 2006 Vol: 7 Issue: 1 Pages/record No.: 5
Finding biological process modifications in cancer tissues by mining gene expression correlations
Author: Gamberoni Giacomo ; Storari Sergio ; Volinia Stefano Journal: BMC Bioinformatics Year: 2006 Vol: 7 Issue: 1 Pages/record No.: 6
OligoSpawn: a software tool for the design of overgo probes from large unigene datasets
Author: Zheng Jie ; Svensson Jan ; Madishetty Kavitha ; Close Timothy ; Jiang Tao ; Lonardi Stefano Journal: BMC Bioinformatics Year: 2006 Vol: 7 Issue: 1 Pages/record No.: 7
Approximation properties of haplotype tagging
Author: Vinterbo Staal ; Dreiseitl Stephan ; Ohno-Machado Lucila Journal: BMC Bioinformatics Year: 2006 Vol: 7 Issue: 1 Pages/record No.: 8
ZCURVE_V: a new self-training system for recognizing protein-coding genes in viral and phage genomes
Author: Guo Feng-Biao ; Zhang Chun-Ting Journal: BMC Bioinformatics Year: 2006 Vol: 7 Issue: 1 Pages/record No.: 9
A high level interface to SCOP and ASTRAL implemented in Python
Author: Casbon James ; Crooks Gavin ; Saqi Mansoor Journal: BMC Bioinformatics Year: 2006 Vol: 7 Issue: 1 Pages/record No.: 10
SuperMimic – Fitting peptide mimetics into protein structures
Author: Goede Andrean ; Michalsky Elke ; Schmidt Ulrike ; Preissner Robert Journal: BMC Bioinformatics Year: 2006 Vol: 7 Issue: 1 Pages/record No.: 11
Utilization of two sample t-test statistics from redundant probe sets to evaluate different probe set algorithms in GeneChip studies
Author: Hu Zihua ; Willsky Gail Journal: BMC Bioinformatics Year: 2006 Vol: 7 Issue: 1 Pages/record No.: 12
Construction of a nasopharyngeal carcinoma 2D/MS repository with Open Source XML Database – Xindice
Author: Li Feng ; Li Maoyu ; Xiao Zhiqiang ; Zhang Pengfei ; Li Jianling ; Chen Zhuchu Journal: BMC Bioinformatics Year: 2006 Vol: 7 Issue: 1 Pages/record No.: 13
Local protein structure prediction using discriminative models
Author: Sander Oliver ; Sommer Ingolf ; Lengauer Thomas Journal: BMC Bioinformatics Year: 2006 Vol: 7 Issue: 1 Pages/record No.: 14
An improved procedure for gene selection from microarray experiments using false discovery rate criterion
Author: Yang James ; Yang Mark Journal: BMC Bioinformatics Year: 2006 Vol: 7 Issue: 1 Pages/record No.: 15
Automatic discovery of cross-family sequence features associated with protein function
Author: Brameier Markus ; Haan Josien ; Krings Andrea ; MacCallum Robert Journal: BMC Bioinformatics Year: 2006 Vol: 7 Issue: 1 Pages/record No.: 16
An approach for clustering gene expression data with error information
Author: Tjaden Brian Journal: BMC Bioinformatics Year: 2006 Vol: 7 Issue: 1 Pages/record No.: 17
In silico discovery of human natural antisense transcripts
Author: Li Yuan-Yuan ; Qin Lei ; Guo Zong-Ming ; Liu Lei ; Xu Hao ; Hao Pei ; Su Jiong ; Shi Yixiang ; He Wei-Zhong ; Li Yi-Xue Journal: BMC Bioinformatics Year: 2006 Vol: 7 Issue: 1 Pages/record No.: 18
OpWise: Operons aid the identification of differentially expressed genes in bacterial microarray experiments
Author: Price Morgan ; Arkin Adam ; Alm Eric Journal: BMC Bioinformatics Year: 2006 Vol: 7 Issue: 1 Pages/record No.: 19
Prediction of protein structural class with Rough Sets
Author: Cao Youfang ; Liu Shi ; Zhang Lida ; Qin Jie ; Wang Jiang ; Tang Kexuan Journal: BMC Bioinformatics Year: 2006 Vol: 7 Issue: 1 Pages/record No.: 20
GenoLink: a graph-based querying and browsing system for investigating the function of genes and proteins
Author: Durand Patrick ; Labarre Laurent ; Meil Alain ; Divo1 Jean-Louis ; Vandenbrouck Yves ; Viari Alain ; Wojcik Jérôme Journal: BMC Bioinformatics Year: 2006 Vol: 7 Issue: 1 Pages/record No.: 21
preAssemble: a tool for automatic sequencer trace data processing
Author: Adzhubei Alexei ; Laerdahl Jon ; Vlasova Anna Journal: BMC Bioinformatics Year: 2006 Vol: 7 Issue: 1 Pages/record No.: 22
Evaluation of methods for oligonucleotide array data via quantitative real-time PCR
Author: Qin Li-Xuan ; Beyer Richard ; Hudson Francesca ; Linford Nancy ; Morris Daryl ; Kerr Kathleen Journal: BMC Bioinformatics Year: 2006 Vol: 7 Issue: 1 Pages/record No.: 23
Metabolic pathways variability and sequence/networks comparisons
Author: Tun Kyaw ; Dhar Pawan ; Palumbo Maria ; Giuliani Alessandro Journal: BMC Bioinformatics Year: 2006 Vol: 7 Issue: 1 Pages/record No.: 24
Analysis and visualization of chromosomal abnormalities in SNP data with SNPscan
Author: Ting Jason ; Ye Ying ; Thomas George ; Ruczinski Ingo ; Pevsner Jonathan Journal: BMC Bioinformatics Year: 2006 Vol: 7 Issue: 1 Pages/record No.: 25
Discovery of time-delayed gene regulatory networks based on temporal gene expression profiling
Author: Li Xia ; Rao Shaoqi ; Jiang Wei ; Li Chuanxing ; Xiao Yun ; Guo Zheng ; Zhang Qingpu ; Wang Lihong ; Du Lei ; Li Jing ; Li Li ; Zhang Tianwen ; Wang Qing Journal: BMC Bioinformatics Year: 2006 Vol: 7 Issue: 1 Pages/record No.: 26
NOXclass: prediction of protein-protein interaction types
Author: Zhu Hongbo ; Domingues Francisco ; Sommer lngolf ; Lengauer Thomas Journal: BMC Bioinformatics Year: 2006 Vol: 7 Issue: 1 Pages/record No.: 27
A new pooling strategy for high-throughput screening: the Shifted Transversal Design
Author: Thierry-Mieg Nicolas Journal: BMC Bioinformatics Year: 2006 Vol: 7 Issue: 1 Pages/record No.: 28
Recrafting the neighbor-joining method
Author: Mailund Thomas ; Brodal Gerth ; Fagerberg Rolf ; Pedersen Christian ; Phillips Derek Journal: BMC Bioinformatics Year: 2006 Vol: 7 Issue: 1 Pages/record No.: 29
WholePathwayScope: a comprehensive pathway-based analysis tool for high-throughput data
Author: Yi Ming ; Horton Jay ; Cohen Jonathan ; Hobbs Helen ; Stephens Robert Journal: BMC Bioinformatics Year: 2006 Vol: 7 Issue: 1 Pages/record No.: 30
Similarity-based gene detection: using COGs to find evolutionarily-conserved ORFs
Author: Powell Bradford ; Hutchison Clyde Journal: BMC Bioinformatics Year: 2006 Vol: 7 Issue: 1 Pages/record No.: 31
Missing value estimation for DNA microarray gene expression data by Support Vector Regression imputation and orthogonal coding scheme
Author: Wang Xian ; Li Ao ; Jiang Zhaohui ; Feng Huanqing Journal: BMC Bioinformatics Year: 2006 Vol: 7 Issue: 1 Pages/record No.: 32
Djinn Lite: a tool for customised gene transcript modelling, annotation-data enrichment and exploration
Author: Teber Erdahl ; Crawford Edward ; Bolton Kent ; Van Dyk Derek ; Schofield Peter ; Kapoor Vimal ; Church W Bret Journal: BMC Bioinformatics Year: 2006 Vol: 7 Issue: 1 Pages/record No.: 33
A domain-oriented approach to the reduction of combinatorial complexity in signal transduction networks
Author: Conzelmann Holger ; Saez-Rodriguez Julio ; Sauter Thomas ; Kholodenko Boris ; Gilles Ernst Journal: BMC Bioinformatics Year: 2006 Vol: 7 Issue: 1 Pages/record No.: 34
A proposed metric for assessing the measurement quality of individual microarrays
Author: Kim Kyoungmi ; Page Grier ; Beasley T Mark ; Barnes Stephen ; Scheirer Katherine ; Allison David Journal: BMC Bioinformatics Year: 2006 Vol: 7 Issue: 1 Pages/record No.: 35
MitoRes: a resource of nuclear-encoded mitochondrial genes and their products in Metazoa
Author: Catalano Domenico ; Licciulli Flavio ; Turi Antonio ; Grillo Giorgio ; Saccone Cecilia ; D'Elia Domenica Journal: BMC Bioinformatics Year: 2006 Vol: 7 Issue: 1 Pages/record No.: 36
CoSMoS: Conserved Sequence Motif Search in the proteome
Author: Liu Xiao ; Korde Neeraj ; Jakob Ursula ; Leichert Lars Journal: BMC Bioinformatics Year: 2006 Vol: 7 Issue: 1 Pages/record No.: 37
A reinforced merging methodology for mapping unique peptide motifs in members of protein families
Author: Chang Hao-Teng ; Pai Tun-Wen ; Fan Tan-chi ; Su Bo-Han ; Wu Pei-Chih ; Tang Chuan-Yi ; Chang Chun-Tien ; Liu Shi-Hwei ; Chang Margaret Journal: BMC Bioinformatics Year: 2006 Vol: 7 Issue: 1 Pages/record No.: 38
GPNN: Power studies and applications of a neural network method for detecting gene-gene interactions in studies of human disease
Author: Motsinger Alison ; Lee Stephen ; Mellick George ; Ritchie Marylyn Journal: BMC Bioinformatics Year: 2006 Vol: 7 Issue: 1 Pages/record No.: 39
Protein structure similarity from principle component correlation analysis
Author: Zhou Xiaobo ; Chou James ; Wong Stephen Journal: BMC Bioinformatics Year: 2006 Vol: 7 Issue: 1 Pages/record No.: 40
Discovering semantic features in the literature: a foundation for building functional associations
Author: Chagoyen Monica ; Carmona-Saez Pedro ; Shatkay Hagit ; Carazo Jose ; Pascual-Montano Alberto Journal: BMC Bioinformatics Year: 2006 Vol: 7 Issue: 1 Pages/record No.: 41
MassSorter: a tool for administrating and analyzing data from mass spectrometry experiments on proteins with known amino acid sequences
Author: Barsnes Harald ; Mikalsen Svein-Ole ; Eidhammer Ingvar Journal: BMC Bioinformatics Year: 2006 Vol: 7 Issue: 1 Pages/record No.: 42
SynTReN: a generator of synthetic gene expression data for design and analysis of structure learning algorithms
Author: Van den Bulcke Tim ; Van Leemput Koenraad ; Naudts Bart ; van Remortel Piet ; Ma Hongwu ; Verschoren Alain ; De Moor Bart ; Marchal Kathleen Journal: BMC Bioinformatics Year: 2006 Vol: 7 Issue: 1 Pages/record No.: 43
An improved distance measure between the expression profiles linking co-expression and co-regulation in mouse
Author: Kim Ryung ; Ji Hongkai ; Wong Wing Journal: BMC Bioinformatics Year: 2006 Vol: 7 Issue: 1 Pages/record No.: 44
Querying the public databases for sequences using complex keywords contained in the feature lines
Author: Croce Olivier ; Lamarre Michaël ; Christen Richard Journal: BMC Bioinformatics Year: 2006 Vol: 7 Issue: 1 Pages/record No.: 45
Rapid and asymmetric divergence of duplicate genes in the human gene coexpression network
Author: Chung Wen-Yu ; Albert Reka ; Albert Istvan ; Nekrutenko Anton ; Makova Kateryna Journal: BMC Bioinformatics Year: 2006 Vol: 7 Issue: 1 Pages/record No.: 46
Protein kinases associated with the yeast phosphoproteome
Author: Brinkworth Ross ; Munn Alan ; Kobe Boštjan Journal: BMC Bioinformatics Year: 2006 Vol: 7 Issue: 1 Pages/record No.: 47
On single and multiple models of protein families for the detection of remote sequence relationships
Author: Casbon James ; Saqi Mansoor Journal: BMC Bioinformatics Year: 2006 Vol: 7 Issue: 1 Pages/record No.: 48
Effects of filtering by Present call on analysis of microarray experiments
Author: McClintick Jeanette ; Edenberg Howard Journal: BMC Bioinformatics Year: 2006 Vol: 7 Issue: 1 Pages/record No.: 49
Assessing stability of gene selection in microarray data analysis
Author: Qiu Xing ; Xiao Yuanhui ; Gordon Alexander ; Yakovlev Andrei Journal: BMC Bioinformatics Year: 2006 Vol: 7 Issue: 1 Pages/record No.: 50
Detection of compound mode of action by computational integration of whole-genome measurements and genetic perturbations
Author: Hallén Kristofer ; Björkegren Johan ; Tegnér Jesper Journal: BMC Bioinformatics Year: 2006 Vol: 7 Issue: 1 Pages/record No.: 51
On the attenuation and amplification of molecular noise in genetic regulatory networks
Author: Chen Bor-Sen ; Wang Yu-Chao Journal: BMC Bioinformatics Year: 2006 Vol: 7 Issue: 1 Pages/record No.: 52
PDB-UF: database of predicted enzymatic functions for unannotated protein structures from structural genomics
Author: von Grotthuss Marcin ; Plewczynski Dariusz ; Ginalski Krzysztof ; Rychlewski Leszek ; Shakhnovich Eugene Journal: BMC Bioinformatics Year: 2006 Vol: 7 Issue: 1 Pages/record No.: 53
Integrated analysis of gene expression by association rules discovery
Author: Carmona-Saez Pedro ; Chagoyen Monica ; Rodriguez Andres ; Trelles Oswaldo ; Carazo Jose ; Pascual-Montano Alberto Journal: BMC Bioinformatics Year: 2006 Vol: 7 Issue: 1 Pages/record No.: 54
PathSys: integrating molecular interaction graphs for systems biology
Author: Baitaluk Michael ; Qian Xufei ; Godbole Shubhada ; Raval Alpan ; Ray Animesh ; Gupta Amarnath Journal: BMC Bioinformatics Year: 2006 Vol: 7 Issue: 1 Pages/record No.: 55
A methodology for the structural and functional analysis of signaling and regulatory networks
Author: Klamt Steffen ; Saez-Rodriguez Julio ; Lindquist Jonathan ; Simeoni Luca ; Gilles Ernst Journal: BMC Bioinformatics Year: 2006 Vol: 7 Issue: 1 Pages/record No.: 56
FastGroupII: A web-based bioinformatics platform for analyses of large 16S rDNA libraries
Author: Yu Yanan ; Breitbart Mya ; McNairnie Pat ; Rohwer Forest Journal: BMC Bioinformatics Year: 2006 Vol: 7 Issue: 1 Pages/record No.: 57
Identifying biological concepts from a protein-related corpus with a probabilistic topic model
Author: Zheng Bin ; McLean David ; Lu Xinghua Journal: BMC Bioinformatics Year: 2006 Vol: 7 Issue: 1 Pages/record No.: 58
BAMarray™: Java software for Bayesian analysis of variance for microarray data
Author: Ishwaran Hemant ; Rao J Sunil ; Kogalur Udaya Journal: BMC Bioinformatics Year: 2006 Vol: 7 Issue: 1 Pages/record No.: 59
JLIN: A java based linkage disequilibrium plotter
Author: Carter Kim ; McCaskie Pamela ; Palmer Lyle Journal: BMC Bioinformatics Year: 2006 Vol: 7 Issue: 1 Pages/record No.: 60
Comparative analysis of haplotype association mapping algorithms
Author: McClurg Phillip ; Pletcher Mathew ; Wiltshire Tim ; Su Andrew Journal: BMC Bioinformatics Year: 2006 Vol: 7 Issue: 1 Pages/record No.: 61
Gene prediction in eukaryotes with a generalized hidden Markov model that uses hints from external sources
Author: Stanke Mario ; Schöffmann Oliver ; Morgenstern Burkhard ; Waack Stephan Journal: BMC Bioinformatics Year: 2006 Vol: 7 Issue: 1 Pages/record No.: 62
Bayesian detection of periodic mRNA time profiles without use of training examples
Author: Andersson Claes ; Isaksson Anders ; Gustafsson Mats Journal: BMC Bioinformatics Year: 2006 Vol: 7 Issue: 1 Pages/record No.: 63
HotSwap for bioinformatics: A STRAP tutorial
Author: Gille Christoph ; Robinson Peter Journal: BMC Bioinformatics Year: 2006 Vol: 7 Issue: 1 Pages/record No.: 64
Computational models with thermodynamic and composition features improve siRNA design
Author: Shabalina Svetlana ; Spiridonov Alexey ; Ogurtsov Aleksey Journal: BMC Bioinformatics Year: 2006 Vol: 7 Issue: 1 Pages/record No.: 65
RibAlign: a software tool and database for eubacterial phylogeny based on concatenated ribosomal protein subunits
Author: Teeling Hanno ; Gloeckner Frank Journal: BMC Bioinformatics Year: 2006 Vol: 7 Issue: 1 Pages/record No.: 66
Algebraic comparison of metabolic networks, phylogenetic inference, and metabolic innovation
Author: Forst Christian ; Flamm Christoph ; Hofacker Ivo ; Stadler Peter Journal: BMC Bioinformatics Year: 2006 Vol: 7 Issue: 1 Pages/record No.: 67
Prediction of protein continuum secondary structure with probabilistic models based on NMR solved structures
Author: Bodén Mikael ; Yuan Zheng ; Bailey Timothy Journal: BMC Bioinformatics Year: 2006 Vol: 7 Issue: 1 Pages/record No.: 68
In search of functional association from time-series microarray data based on the change trend and level of gene expression
Author: He Feng ; Zeng An-Ping Journal: BMC Bioinformatics Year: 2006 Vol: 7 Issue: 1 Pages/record No.: 69
BIOZON: a system for unification, management and analysis of heterogeneous biological data
Author: Birkland Aaron ; Yona Golan Journal: BMC Bioinformatics Year: 2006 Vol: 7 Issue: 1 Pages/record No.: 70
Hubs of knowledge: using the functional link structure in Biozon to mine for biologically significant entities
Author: Shafer Paul ; Isganitis Timothy ; Yona Golan Journal: BMC Bioinformatics Year: 2006 Vol: 7 Issue: 1 Pages/record No.: 71
GO-Diff: Mining functional differentiation between EST-based transcriptomes
Author: Chen Zuozhou ; Wang Weilin ; Ling Xuefeng ; Liu Jane ; Chen Liangbiao Journal: BMC Bioinformatics Year: 2006 Vol: 7 Issue: 1 Pages/record No.: 72
Instance-based concept learning from multiclass DNA microarray data
Author: Berrar Daniel ; Bradbury Ian ; Dubitzky Werner Journal: BMC Bioinformatics Year: 2006 Vol: 7 Issue: 1 Pages/record No.: 73
Spectral embedding finds meaningful (relevant) structure in image and microarray data
Author: Higgs Brandon ; Weller Jennifer ; Solka Jeffrey Journal: BMC Bioinformatics Year: 2006 Vol: 7 Issue: 1 Pages/record No.: 74
Detecting overlapping coding sequences in virus genomes
Author: Firth Andrew ; Brown Chris Journal: BMC Bioinformatics Year: 2006 Vol: 7 Issue: 1 Pages/record No.: 75
BIPAD: A web server for modeling bipartite sequence elements
Author: Bi Chengpeng ; Rogan Peter Journal: BMC Bioinformatics Year: 2006 Vol: 7 Issue: 1 Pages/record No.: 76
Quantitative comparison of EST libraries requires compensation for systematic biases in cDNA generation
Author: Liu Donglin ; Graber Joel Journal: BMC Bioinformatics Year: 2006 Vol: 7 Issue: 1 Pages/record No.: 77
Biclustering of gene expression data by non-smooth non-negative matrix factorization
Author: Carmona-Saez Pedro ; Pascual-Marqui Roberto ; Tirado F ; Carazo Jose ; Pascual-Montano Alberto Journal: BMC Bioinformatics Year: 2006 Vol: 7 Issue: 1 Pages/record No.: 78
Taxonomic colouring of phylogenetic trees of protein sequences
Author: Palidwor Gareth ; Reynaud Emmanuel ; Andrade-Navarro Miguel Journal: BMC Bioinformatics Year: 2006 Vol: 7 Issue: 1 Pages/record No.: 79
Gene annotation and network inference by phylogenetic profiling
Author: Wu Jie ; Hu Zhenjun ; DeLisi Charles Journal: BMC Bioinformatics Year: 2006 Vol: 7 Issue: 1 Pages/record No.: 80
Transcriptomic response to differentiation induction
Author: Patton GW ; Stephens R ; Sidorov IA ; Xiao X ; Lempicki RA ; Dimitrov DS ; Shoemaker RH ; Tudor G Journal: BMC Bioinformatics Year: 2006 Vol: 7 Issue: 1 Pages/record No.: 81
PhosphoregDB: The tissue and sub-cellular distribution of mammalian protein kinases and phosphatases
Author: Forrest Alistair ; Taylor Darrin ; Fink J Lynn ; Gongora M Milena ; Flegg Cameron ; Teasdale Rohan ; Suzuki Harukazu ; Kanamori Mutsumi ; Kai Chikatoshi ; Hayashizaki Yoshihide ; Grimmond Sean Journal: BMC Bioinformatics Year: 2006 Vol: 7 Issue: 1 Pages/record No.: 82
CARAT: A novel method for allelic detection of DNA copy number changes using high density oligonucleotide arrays
Author: Huang Jing ; Wei Wen ; Chen Joyce ; Zhang Jane ; Liu Guoying ; Di Xiaojun ; Mei Rui ; Ishikawa Shumpei ; Aburatani Hiroyuki ; Jones Keith ; Shapero Michael Journal: BMC Bioinformatics Year: 2006 Vol: 7 Issue: 1 Pages/record No.: 83
The PowerAtlas: a power and sample size atlas for microarray experimental design and research
Author: Page Grier ; Edwards Jode ; Gadbury Gary ; Yelisetti Prashanth ; Wang Jelai ; Trivedi Prinal ; Allison David Journal: BMC Bioinformatics Year: 2006 Vol: 7 Issue: 1 Pages/record No.: 84
Statistical analysis of real-time PCR data
Author: Yuan Joshua ; Reed Ann ; Chen Feng ; Stewart C Neal Journal: BMC Bioinformatics Year: 2006 Vol: 7 Issue: 1 Pages/record No.: 85
BayGO: Bayesian analysis of ontology term enrichment in microarray data
Author: Vêncio Ricardo ; Koide Tie ; Gomes Suely ; de B Pereira Carlos Journal: BMC Bioinformatics Year: 2006 Vol: 7 Issue: 1 Pages/record No.: 86
Phase analysis of circadian-related genes in two tissues
Author: Liu Delong ; Peddada Shyamal ; Li Leping ; Weinberg Clarice Journal: BMC Bioinformatics Year: 2006 Vol: 7 Issue: 1 Pages/record No.: 87
SIMMAP: Stochastic character mapping of discrete traits on phylogenies
Author: Bollback Jonathan Journal: BMC Bioinformatics Year: 2006 Vol: 7 Issue: 1 Pages/record No.: 88
Integrating protein structures and precomputed genealogies in the Magnum database: Examples with cellular retinoid binding proteins
Author: Bradley Michael ; Benner Steven Journal: BMC Bioinformatics Year: 2006 Vol: 7 Issue: 1 Pages/record No.: 89
A graphical model approach to automated classification of protein subcellular location patterns in multi-cell images
Author: Chen Shann-Ching ; Murphy Robert Journal: BMC Bioinformatics Year: 2006 Vol: 7 Issue: 1 Pages/record No.: 90
Bias in error estimation when using cross-validation for model selection
Author: Varma Sudhir ; Simon Richard Journal: BMC Bioinformatics Year: 2006 Vol: 7 Issue: 1 Pages/record No.: 91
Various criteria in the evaluation of biomedical named entity recognition
Author: Tsai Richard Tzong-Han ; Wu Shih-Hung ; Chou Wen-Chi ; Lin Yu-Chun ; He Ding ; Hsiang Jieh ; Sung Ting-Yi ; Hsu Wen-Lian Journal: BMC Bioinformatics Year: 2006 Vol: 7 Issue: 1 Pages/record No.: 92
Multiscale Hy3S: Hybrid stochastic simulation for supercomputers
Author: Salis Howard ; Sotiropoulos Vassilios ; Kaznessis Yiannis Journal: BMC Bioinformatics Year: 2006 Vol: 7 Issue: 1 Pages/record No.: 93
GONOME: measuring correlations between GO terms and genomic positions
Author: Stanley Stefan ; Bailey Timothy ; Mattick John Journal: BMC Bioinformatics Year: 2006 Vol: 7 Issue: 1 Pages/record No.: 94
Gene selection algorithms for microarray data based on least squares support vector machine
Author: Tang E Ke ; Suganthan PN ; Yao Xin Journal: BMC Bioinformatics Year: 2006 Vol: 7 Issue: 1 Pages/record No.: 95
Microarray image analysis: background estimation using quantile and morphological filters
Author: Bengtsson Anders ; Bengtsson Henrik Journal: BMC Bioinformatics Year: 2006 Vol: 7 Issue: 1 Pages/record No.: 96
The Ontology Lookup Service, a lightweight cross-platform tool for controlled vocabulary queries
Author: Côté Richard ; Jones Philip ; Apweiler Rolf ; Hermjakob Henning Journal: BMC Bioinformatics Year: 2006 Vol: 7 Issue: 1 Pages/record No.: 97
REtools: A laboratory program for restriction enzyme work: enzyme selection and reaction condition assistance
Author: Martin Patrick ; Boulukos Kim ; Pognonec Philippe Journal: BMC Bioinformatics Year: 2006 Vol: 7 Issue: 1 Pages/record No.: 98
Determination of strongly overlapping signaling activity from microarray data
Author: Bidaut Ghislain ; Suhre Karsten ; Claverie Jean-Michel ; Ochs Michael Journal: BMC Bioinformatics Year: 2006 Vol: 7 Issue: 1 Pages/record No.: 99
Methodological study of affine transformations of gene expression data with proposed robust non-parametric multi-dimensional normalization method
Author: Bengtsson Henrik ; Hössjer Ola Journal: BMC Bioinformatics Year: 2006 Vol: 7 Issue: 1 Pages/record No.: 100
A multivariate prediction model for microarray cross-hybridization
Author: Chen Yian ; Chou Cheng-Chung ; Lu Xinghua ; Slate Elizabeth ; Peck Konan ; Xu Wenying ; Voit Eberhard ; Almeida Jonas Journal: BMC Bioinformatics Year: 2006 Vol: 7 Issue: 1 Pages/record No.: 101
SimArray: a user-friendly and user-configurable microarray design tool
Author: Auburn Richard ; Russell Roslin ; Fischer Bettina ; Meadows Lisa ; Sevillano Matilla Santiago ; Russell Steven Journal: BMC Bioinformatics Year: 2006 Vol: 7 Issue: 1 Pages/record No.: 102
SinicView: A visualization environment for comparisons of multiple nucleotide sequence alignment tools
Author: Shih Arthur ; Lee DT ; Lin Laurent ; Peng Chin-Lin ; Chen Shiang-Heng ; Wu Yu-Wei ; Wong Chun-Yi ; Chou Meng-Yuan ; Shiao Tze-Chang ; Hsieh Mu-Fen Journal: BMC Bioinformatics Year: 2006 Vol: 7 Issue: 1 Pages/record No.: 103
SCOWLP: a web-based database for detailed characterization and visualization of protein interfaces
Author: Teyra Joan ; Doms Andreas ; Schroeder Michael ; Pisabarro M Teresa Journal: BMC Bioinformatics Year: 2006 Vol: 7 Issue: 1 Pages/record No.: 104
The effect of oligonucleotide microarray data pre-processing on the analysis of patient-cohort studies
Author: Verhaak Roel ; Staal Frank ; Valk Peter ; Lowenberg Bob ; Reinders Marcel ; de Ridder Dick Journal: BMC Bioinformatics Year: 2006 Vol: 7 Issue: 1 Pages/record No.: 105
A simple method for assessing sample sizes in microarray experiments
Author: Tibshirani Robert Journal: BMC Bioinformatics Year: 2006 Vol: 7 Issue: 1 Pages/record No.: 106
Evaluation of absolute quantitation by nonlinear regression in probe-based real-time PCR
Author: Goll Rasmus ; Olsen Trine ; Cui Guanglin ; Florholmen Jon Journal: BMC Bioinformatics Year: 2006 Vol: 7 Issue: 1 Pages/record No.: 107
A quantitative analysis of secondary RNA structure using domination based parameters on trees
Author: Haynes Teresa ; Knisley Debra ; Seier Edith ; Zou Yue Journal: BMC Bioinformatics Year: 2006 Vol: 7 Issue: 1 Pages/record No.: 108
VANTED: A system for advanced data analysis and visualization in the context of biological networks
Author: Junker Björn ; Klukas Christian ; Schreiber Falk Journal: BMC Bioinformatics Year: 2006 Vol: 7 Issue: 1 Pages/record No.: 109
IsoSVM – Distinguishing isoforms and paralogs on the protein level
Author: Spitzer Michael ; Lorkowski Stefan ; Cullen Paul ; Sczyrba Alexander ; Fuellen Georg Journal: BMC Bioinformatics Year: 2006 Vol: 7 Issue: 1 Pages/record No.: 110
Metabolite coupling in genome-scale metabolic networks
Author: Becker Scott ; Price Nathan ; Palsson Bernhard Journal: BMC Bioinformatics Year: 2006 Vol: 7 Issue: 1 Pages/record No.: 111
Lower expression of genes near microRNA in C. elegans germline
Author: Inaoka Hidenori ; Fukuoka Yutaka ; Kohane Isaac Journal: BMC Bioinformatics Year: 2006 Vol: 7 Issue: 1 Pages/record No.: 112
An improved map of conserved regulatory sites for Saccharomyces cerevisiae
Author: MacIsaac Kenzie ; Wang Ting ; Gordon D Benjamin ; Gifford David ; Stormo Gary ; Fraenkel Ernest Journal: BMC Bioinformatics Year: 2006 Vol: 7 Issue: 1 Pages/record No.: 113
Genome-wide analysis of core promoter elements from conserved human and mouse orthologous pairs
Author: Jin Victor ; Singer Gregory ; Agosto-Pérez Francisco ; Liyanarachchi Sandya ; Davuluri Ramana Journal: BMC Bioinformatics Year: 2006 Vol: 7 Issue: 1 Pages/record No.: 114
MAGIC-SPP: a database-driven DNA sequence processing package with associated management tools
Author: Liang Chun ; Sun Feng ; Wang Haiming ; Qu Junfeng ; Freeman Robert ; Pratt Lee ; Cordonnier-Pratt Marie-Michèle Journal: BMC Bioinformatics Year: 2006 Vol: 7 Issue: 1 Pages/record No.: 115
Machine learning approaches to supporting the identification of photoreceptor-enriched genes based on expression data
Author: Wang Haiying ; Zheng Huiru ; Simpson David ; Azuaje Francisco Journal: BMC Bioinformatics Year: 2006 Vol: 7 Issue: 1 Pages/record No.: 116
Microbial identification by mass cataloging
Author: Zhang Zhengdong ; Jackson George ; Fox George ; Willson Richard Journal: BMC Bioinformatics Year: 2006 Vol: 7 Issue: 1 Pages/record No.: 117
Low degree metabolites explain essential reactions and enhance modularity in biological networks
Author: Samal Areejit ; Singh Shalini ; Giri Varun ; Krishna Sandeep ; Raghuram Nandula ; Jain Sanjay Journal: BMC Bioinformatics Year: 2006 Vol: 7 Issue: 1 Pages/record No.: 118
Discovering functional gene expression patterns in the metabolic network of Escherichia coli with wavelets transforms
Author: König Rainer ; Schramm Gunnar ; Oswald Marcus ; Seitz Hanna ; Sager Sebastian ; Zapatka Marc ; Reinelt Gerhard ; Eils Roland Journal: BMC Bioinformatics Year: 2006 Vol: 7 Issue: 1 Pages/record No.: 119
TF Target Mapper: A BLAST search tool for the identification of Transcription Factor target genes
Author: Horsman Sebastiaan ; Moorhouse Michael ; de Jager Victor ; van der Spek Peter ; Grosveld Frank ; Strouboulis John ; Katsantoni Eleni Journal: BMC Bioinformatics Year: 2006 Vol: 7 Issue: 1 Pages/record No.: 120
An unsupervised classification scheme for improving predictions of prokaryotic TIS
Author: Tech Maike ; Meinicke Peter Journal: BMC Bioinformatics Year: 2006 Vol: 7 Issue: 1 Pages/record No.: 121
Selection of antisense oligonucleotides based on multiple predicted target mRNA structures
Author: Bo Xiaochen ; Lou Shaoke ; Sun Daochun ; Shu Wenjie ; Yang Jing ; Wang Shengqi Journal: BMC Bioinformatics Year: 2006 Vol: 7 Issue: 1 Pages/record No.: 122
Detecting outliers when fitting data with nonlinear regression – a new method based on robust nonlinear regression and the false discovery rate
Author: Motulsky Harvey ; Brown Ronald Journal: BMC Bioinformatics Year: 2006 Vol: 7 Issue: 1 Pages/record No.: 123
Prediction of cis/trans isomerization in proteins using PSI-BLAST profiles and secondary structure information
Author: Song Jiangning ; Burrage Kevin ; Yuan Zheng ; Huber Thomas Journal: BMC Bioinformatics Year: 2006 Vol: 7 Issue: 1 Pages/record No.: 124
Optimized Particle Swarm Optimization (OPSO) and its application to artificial neural network training
Author: Meissner Michael ; Schmuker Michael ; Schneider Gisbert Journal: BMC Bioinformatics Year: 2006 Vol: 7 Issue: 1 Pages/record No.: 125
A two-sample Bayesian t-test for microarray data
Author: Fox Richard ; Dimmic Matthew Journal: BMC Bioinformatics Year: 2006 Vol: 7 Issue: 1 Pages/record No.: 126
Improved variance estimation of classification performance via reduction of bias caused by small sample size
Author: Wickenberg-Bolin Ulrika ; Göransson Hanna ; Fryknäs Mårten ; Gustafsson Mats ; Isaksson Anders Journal: BMC Bioinformatics Year: 2006 Vol: 7 Issue: 1 Pages/record No.: 127
Protein protein interactions, evolutionary rate, abundance and age
Author: Saeed Ramazan ; Deane Charlotte Journal: BMC Bioinformatics Year: 2006 Vol: 7 Issue: 1 Pages/record No.: 128
SNA – a toolbox for the stoichiometric analysis of metabolic networks
Author: Urbanczik Robert Journal: BMC Bioinformatics Year: 2006 Vol: 7 Issue: 1 Pages/record No.: 129
Extraction of phylogenetic network modules from the metabolic network
Author: Yamada Takuji ; Kanehisa Minoru ; Goto Susumu Journal: BMC Bioinformatics Year: 2006 Vol: 7 Issue: 1 Pages/record No.: 130
EpiJen: a server for multistep T cell epitope prediction
Author: Doytchinova Irini ; Guan Pingping ; Flower Darren Journal: BMC Bioinformatics Year: 2006 Vol: 7 Issue: 1 Pages/record No.: 131
Network-level analysis of metabolic regulation in the human red blood cell using random sampling and singular value decomposition
Author: Barrett Christian ; Price Nathan ; Palsson Bernhard Journal: BMC Bioinformatics Year: 2006 Vol: 7 Issue: 1 Pages/record No.: 132
Choosing the best heuristic for seeded alignment of DNA sequences
Author: Sun Yanni ; Buhler Jeremy Journal: BMC Bioinformatics Year: 2006 Vol: 7 Issue: 1 Pages/record No.: 133
Effect of data normalization on fuzzy clustering of DNA microarray data
Author: Kim Seo ; Lee Jae ; Bae Jong Journal: BMC Bioinformatics Year: 2006 Vol: 7 Issue: 1 Pages/record No.: 134
Gene functional similarity search tool (GFSST)
Author: Zhang Peisen ; Zhang Jinghui ; Sheng Huitao ; Russo James ; Osborne Brian ; Buetow Kenneth Journal: BMC Bioinformatics Year: 2006 Vol: 7 Issue: 1 Pages/record No.: 135
Identification and evolutionary analysis of novel exons and alternative splicing events using cross-species EST-to-genome comparisons in human, mouse and rat
Author: Chen Feng-Chi ; Chen Chuang-Jong ; Ho Jar-Yi ; Chuang Trees-Juen Journal: BMC Bioinformatics Year: 2006 Vol: 7 Issue: 1 Pages/record No.: 136
How to decide? Different methods of calculating gene expression from short oligonucleotide array data will give different results
Author: Millenaar Frank ; Okyere John ; May Sean ; van Zanten Martijn ; Voesenek Laurentius ; Peeters Anton Journal: BMC Bioinformatics Year: 2006 Vol: 7 Issue: 1 Pages/record No.: 137
A joint model for nonparametric functional mapping of longitudinal trajectory and time-to-event
Author: Lin Min ; Wu Rongling Journal: BMC Bioinformatics Year: 2006 Vol: 7 Issue: 1 Pages/record No.: 138
mGrid: A load-balanced distributed computing environment for the remote execution of the user-defined Matlab code
Author: Karpievitch Yuliya ; Almeida Jonas Journal: BMC Bioinformatics Year: 2006 Vol: 7 Issue: 1 Pages/record No.: 139
Exploring supervised and unsupervised methods to detect topics in biomedical text
Author: Lee Minsuk ; Wang Weiqing ; Yu Hong Journal: BMC Bioinformatics Year: 2006 Vol: 7 Issue: 1 Pages/record No.: 140
A computational approach to discovering the functions of bacterial phytochromes by analysis of homolog distributions
Author: Lamparter Tilman Journal: BMC Bioinformatics Year: 2006 Vol: 7 Issue: 1 Pages/record No.: 141
Score-based prediction of genomic islands in prokaryotic genomes using hidden Markov models
Author: Waack Stephan ; Keller Oliver ; Asper Roman ; Brodag Thomas ; Damm Carsten ; Fricke Wolfgang ; Surovcik Katharina ; Meinicke Peter ; Merkl Rainer Journal: BMC Bioinformatics Year: 2006 Vol: 7 Issue: 1 Pages/record No.: 142
Sigma: multiple alignment of weakly-conserved non-coding DNA sequence
Author: Siddharthan Rahul Journal: BMC Bioinformatics Year: 2006 Vol: 7 Issue: 1 Pages/record No.: 143
The 3of5 web application for complex and comprehensive pattern matching in protein sequences
Author: Seiler Markus ; Mehrle Alexander ; Poustka Annemarie ; Wiemann Stefan Journal: BMC Bioinformatics Year: 2006 Vol: 7 Issue: 1 Pages/record No.: 144
Genetic algorithm learning as a robust approach to RNA editing site prediction
Author: Thompson James ; Gopal Shuba Journal: BMC Bioinformatics Year: 2006 Vol: 7 Issue: 1 Pages/record No.: 145
INTEGRATOR: interactive graphical search of large protein interactomes over the Web
Author: Chang Aaron ; McDermott Jason ; Frazier Zachary ; Guerquin Michal ; Samudrala Ram Journal: BMC Bioinformatics Year: 2006 Vol: 7 Issue: 1 Pages/record No.: 146
Ensemble attribute profile clustering: discovering and characterizing groups of genes with similar patterns of biological features
Author: Semeiks JR ; Rizki A ; Bissell MJ ; Mian IS Journal: BMC Bioinformatics Year: 2006 Vol: 7 Issue: 1 Pages/record No.: 147
Identification of physicochemical selective pressure on protein encoding nucleotide sequences
Author: Wong Wendy ; Sainudiin Raazesh ; Nielsen Rasmus Journal: BMC Bioinformatics Year: 2006 Vol: 7 Issue: 1 Pages/record No.: 148
CARMA: A platform for analyzing microarray datasets that incorporate replicate measures
Author: Greer Kevin ; McReynolds Matthew ; Brooks Heddwen ; Hoying James Journal: BMC Bioinformatics Year: 2006 Vol: 7 Issue: 1 Pages/record No.: 149
Development of an unbiased statistical method for the analysis of unigenic evolution
Author: Behrsin Colleen ; Brandl Chris ; Litchfield David ; Shilton Brian ; Wahl Lindi Journal: BMC Bioinformatics Year: 2006 Vol: 7 Issue: 1 Pages/record No.: 150
GOurmet: A tool for quantitative comparison and visualization of gene expression profiles based on gene ontology (GO) distributions
Author: Doherty Jason ; Carmichael Lynn ; Mills Jason Journal: BMC Bioinformatics Year: 2006 Vol: 7 Issue: 1 Pages/record No.: 151
Domain-based small molecule binding site annotation
Author: Snyder Kevin ; Feldman Howard ; Dumontier Michel ; Salama John ; Hogue Christopher Journal: BMC Bioinformatics Year: 2006 Vol: 7 Issue: 1 Pages/record No.: 152
Predicting population coverage of T-cell epitope-based diagnostics and vaccines
Author: Bui Huynh-Hoa ; Sidney John ; Dinh Kenny ; Southwood Scott ; Newman Mark ; Sette Alessandro Journal: BMC Bioinformatics Year: 2006 Vol: 7 Issue: 1 Pages/record No.: 153
Empirical validation of the S-Score algorithm in the analysis of gene expression data
Author: Kennedy Richard ; Archer Kellie ; Miles Michael Journal: BMC Bioinformatics Year: 2006 Vol: 7 Issue: 1 Pages/record No.: 154
DNPTrapper: an assembly editing tool for finishing and analysis of complex repeat regions
Author: Arner Erik ; Tammi Martti ; Tran Anh-Nhi ; Kindlund Ellen ; Andersson Bjorn Journal: BMC Bioinformatics Year: 2006 Vol: 7 Issue: 1 Pages/record No.: 155
Predicting survival outcomes using subsets of significant genes in prognostic marker studies with microarrays
Author: Matsui Shigeyuki Journal: BMC Bioinformatics Year: 2006 Vol: 7 Issue: 1 Pages/record No.: 156
Modeling Sage data with a truncated gamma-Poisson model
Author: Thygesen Helene ; Zwinderman Aeilko Journal: BMC Bioinformatics Year: 2006 Vol: 7 Issue: 1 Pages/record No.: 157
2DDB – a bioinformatics solution for analysis of quantitative proteomics data
Author: Malmström Lars ; Marko-Varga György ; Westergren-Thorsson Gunilla ; Laurell Thomas ; Malmström Johan Journal: BMC Bioinformatics Year: 2006 Vol: 7 Issue: 1 Pages/record No.: 158
Amplification of the Gene Ontology annotation of Affymetrix probe sets
Author: Muro Enrique ; Perez-Iratxeta Carolina ; Andrade-Navarro Miguel Journal: BMC Bioinformatics Year: 2006 Vol: 7 Issue: 1 Pages/record No.: 159
More robust detection of motifs in coexpressed genes by using phylogenetic information
Author: Monsieurs Pieter ; Thijs Gert ; Fadda Abeer ; De Keersmaecker Sigrid ; Vanderleyden Jozef ; De Moor Bart ; Marchal Kathleen Journal: BMC Bioinformatics Year: 2006 Vol: 7 Issue: 1 Pages/record No.: 160
GOPET: A tool for automated predictions of Gene Ontology terms
Author: Vinayagam Arunachalam ; del Val Coral ; Schubert Falk ; Eils Roland ; Glatting Karl-Heinz ; Suhai Sándor ; König Rainer Journal: BMC Bioinformatics Year: 2006 Vol: 7 Issue: 1 Pages/record No.: 161
An application of statistics to comparative metagenomics
Author: Rodriguez-Brito Beltran ; Rohwer Forest ; Edwards Robert Journal: BMC Bioinformatics Year: 2006 Vol: 7 Issue: 1 Pages/record No.: 162
PPSP: prediction of PK-specific phosphorylation site with Bayesian decision theory
Author: Xue Yu ; Li Ao ; Wang Lirong ; Feng Huanqing ; Yao Xuebiao Journal: BMC Bioinformatics Year: 2006 Vol: 7 Issue: 1 Pages/record No.: 163
Application of a sensitive collection heuristic for very large protein families: Evolutionary relationship between adipose triglyceride lipase (ATGL) and classic mammalian lipases
Author: Schneider Georg ; Neuberger Georg ; Wildpaner Michael ; Tian Sun ; Berezovsky Igor ; Eisenhaber Frank Journal: BMC Bioinformatics Year: 2006 Vol: 7 Issue: 1 Pages/record No.: 164
Unraveling condition specific gene transcriptional regulatory networks in Saccharomyces cerevisiae
Author: Kim Hyunsoo ; Hu William ; Kluger Yuval Journal: BMC Bioinformatics Year: 2006 Vol: 7 Issue: 1 Pages/record No.: 165
SNPs3D: Candidate gene and SNP selection for association studies
Author: Yue Peng ; Melamud Eugene ; Moult John Journal: BMC Bioinformatics Year: 2006 Vol: 7 Issue: 1 Pages/record No.: 166
Prediction of indirect interactions in proteins
Author: Prusis Peteris ; Uhlén Staffan ; Petrovska Ramona ; Lapinsh Maris ; Wikberg Jarl Journal: BMC Bioinformatics Year: 2006 Vol: 7 Issue: 1 Pages/record No.: 167
GEM System: automatic prototyping of cell-wide metabolic pathway models from genomes
Author: Arakawa Kazuharu ; Yamada Yohei ; Shinoda Kosaku ; Nakayama Yoichi ; Tomita Masaru Journal: BMC Bioinformatics Year: 2006 Vol: 7 Issue: 1 Pages/record No.: 168
AltTrans: Transcript pattern variants annotated for both alternative splicing and alternative polyadenylation
Author: Le Texier Vincent ; Riethoven Jean-Jack ; Kumanduri Vasudev ; Gopalakrishnan Chellappa ; Lopez Fabrice ; Gautheret Daniel ; Thanaraj Thangavel Alphonse Journal: BMC Bioinformatics Year: 2006 Vol: 7 Issue: 1 Pages/record No.: 169
BioWarehouse: a bioinformatics database warehouse toolkit
Author: Lee Thomas ; Pouliot Yannick ; Wagner Valerie ; Gupta Priyanka ; Stringer-Calvert David ; Tenenbaum Jessica ; Karp Peter Journal: BMC Bioinformatics Year: 2006 Vol: 7 Issue: 1 Pages/record No.: 170
Automatic pathway building in biological association networks
Author: Yuryev Anton ; Mulyukov Zufar ; Kotelnikova Ekaterina ; Maslov Sergei ; Egorov Sergei ; Nikitin Alexander ; Daraselia Nikolai ; Mazo Ilya Journal: BMC Bioinformatics Year: 2006 Vol: 7 Issue: 1 Pages/record No.: 171
GENOMEMASKER package for designing unique genomic PCR primers
Author: Andreson Reidar ; Reppo Eric ; Kaplinski Lauris ; Remm Maido Journal: BMC Bioinformatics Year: 2006 Vol: 7 Issue: 1 Pages/record No.: 172
Detection of non-coding RNAs on the basis of predicted secondary structure formation free energy change
Author: Uzilov Andrew ; Keegan Joshua ; Mathews David Journal: BMC Bioinformatics Year: 2006 Vol: 7 Issue: 1 Pages/record No.: 173
UVPAR: fast detection of functional shifts in duplicate genes
Author: Arnau Vicente ; Gallach Miguel ; Lucas J Ignasi ; Marín Ignacio Journal: BMC Bioinformatics Year: 2006 Vol: 7 Issue: 1 Pages/record No.: 174
LS-NMF: A modified non-negative matrix factorization algorithm utilizing uncertainty estimates
Author: Wang Guoli ; Kossenkov Andrew ; Ochs Michael Journal: BMC Bioinformatics Year: 2006 Vol: 7 Issue: 1 Pages/record No.: 175
The Gaggle: An open-source software system for integrating bioinformatics software and data sources
Author: Shannon Paul ; Reiss David ; Bonneau Richard ; Baliga Nitin Journal: BMC Bioinformatics Year: 2006 Vol: 7 Issue: 1 Pages/record No.: 176
Identifying metabolic enzymes with multiple types of association evidence
Author: Kharchenko Peter ; Chen Lifeng ; Freund Yoav ; Vitkup Dennis ; Church George Journal: BMC Bioinformatics Year: 2006 Vol: 7 Issue: 1 Pages/record No.: 177
Protein secondary structure prediction for a single-sequence using hidden semi-Markov models
Author: Aydin Zafer ; Altunbasak Yucel ; Borodovsky Mark Journal: BMC Bioinformatics Year: 2006 Vol: 7 Issue: 1 Pages/record No.: 178
AtRTPrimer: database for Arabidopsis genome-wide homogeneous and specific RT-PCR primer-pairs
Author: Han Sangjo ; Kim Dongsup Journal: BMC Bioinformatics Year: 2006 Vol: 7 Issue: 1 Pages/record No.: 179
A two-stage approach for improved prediction of residue contact maps
Author: Vullo Alessandro ; Walsh Ian ; Pollastri Gianluca Journal: BMC Bioinformatics Year: 2006 Vol: 7 Issue: 1 Pages/record No.: 180
Detection of divergent genes in microbial aCGH experiments
Author: Snipen Lars ; Repsilber Dirk ; Nyquist Ludvig ; Ziegler Andreas ; Aakra Ågot ; Aastveit Are Journal: BMC Bioinformatics Year: 2006 Vol: 7 Issue: 1 Pages/record No.: 181
Quantitative prediction of mouse class I MHC peptide binding affinity using support vector machine regression (SVR) models
Author: Liu Wen ; Meng Xiangshan ; Xu Qiqi ; Flower Darren ; Li Tongbin Journal: BMC Bioinformatics Year: 2006 Vol: 7 Issue: 1 Pages/record No.: 182
Exploiting the full power of temporal gene expression profiling through a new statistical test: Application to the analysis of muscular dystrophy data
Author: Vinciotti Veronica ; Liu Xiaohui ; Turk Rolf ; de Meijer Emile ; 't Hoen Peter Journal: BMC Bioinformatics Year: 2006 Vol: 7 Issue: 1 Pages/record No.: 183
Use of physiological constraints to identify quantitative design principles for gene expression in yeast adaptation to heat shock
Author: Vilaprinyo Ester ; Alves Rui ; Sorribas Albert Journal: BMC Bioinformatics Year: 2006 Vol: 7 Issue: 1 Pages/record No.: 184
Ebbie: automated analysis and storage of small RNA cloning data using a dynamic web server
Author: Ebhardt H Alexander ; Wiese Kay ; Unrau Peter Journal: BMC Bioinformatics Year: 2006 Vol: 7 Issue: 1 Pages/record No.: 185
Quantitative elementary mode analysis of metabolic pathways: the example of yeast glycolysis
Author: Schwartz Jean-Marc ; Kanehisa Minoru Journal: BMC Bioinformatics Year: 2006 Vol: 7 Issue: 1 Pages/record No.: 186
Classification of protein quaternary structure by functional domain composition
Author: Yu Xiaojing ; Wang Chuan ; Li Yixue Journal: BMC Bioinformatics Year: 2006 Vol: 7 Issue: 1 Pages/record No.: 187
Bio++: a set of C++ libraries for sequence analysis, phylogenetics, molecular evolution and population genetics
Author: Dutheil Julien ; Gaillard Sylvain ; Bazin Eric ; Glémin Sylvain ; Ranwez Vincent ; Galtier Nicolas ; Belkhir Khalid Journal: BMC Bioinformatics Year: 2006 Vol: 7 Issue: 1 Pages/record No.: 188
Algorithms for incorporating prior topological information in HMMs: application to transmembrane proteins
Author: Bagos Pantelis ; Liakopoulos Theodore ; Hamodrakas Stavros Journal: BMC Bioinformatics Year: 2006 Vol: 7 Issue: 1 Pages/record No.: 189
MIMAS: an innovative tool for network-based high density oligonucleotide microarray data management and annotation
Author: Hermida Leandro ; Schaad Olivier ; Demougin Philippe ; Descombes Patrick ; Primig Michael Journal: BMC Bioinformatics Year: 2006 Vol: 7 Issue: 1 Pages/record No.: 190
STEM: a tool for the analysis of short time series gene expression data
Author: Ernst Jason ; Bar-Joseph Ziv Journal: BMC Bioinformatics Year: 2006 Vol: 7 Issue: 1 Pages/record No.: 191
AbMiner: A bioinformatic resource on available monoclonal antibodies and corresponding gene identifiers for genomic, proteomic, and immunologic studies
Author: Major Sylvia ; Nishizuka Satoshi ; Morita Daisaku ; Rowland Rick ; Sunshine Margot ; Shankavaram Uma ; Washburn Frank ; Asin Daniel ; Kouros-Mehr Hosein ; Kane David ; Weinstein John Journal: BMC Bioinformatics Year: 2006 Vol: 7 Issue: 1 Pages/record No.: 192
An interactive tool for visualization of relationships between gene expression profiles
Author: Ruzanov Peter ; Jones Steven Journal: BMC Bioinformatics Year: 2006 Vol: 7 Issue: 1 Pages/record No.: 193
Mining gene expression data by interpreting principal components
Author: Roden Joseph ; King Brandon ; Trout Diane ; Mortazavi Ali ; Wold Barbara ; Hart Christopher Journal: BMC Bioinformatics Year: 2006 Vol: 7 Issue: 1 Pages/record No.: 194
A database and tool, IM Browser, for exploring and integrating emerging gene and protein interaction data for Drosophila
Author: Pacifico Svetlana ; Liu Guozhen ; Guest Stephen ; Parrish Jodi ; Fotouhi Farshad ; Finley Russell Journal: BMC Bioinformatics Year: 2006 Vol: 7 Issue: 1 Pages/record No.: 195
A case study in pathway knowledgebase verification
Author: Racunas Stephen ; Shah Nigam ; Fedoroff Nina Journal: BMC Bioinformatics Year: 2006 Vol: 7 Issue: 1 Pages/record No.: 196
Recursive SVM feature selection and sample classification for mass-spectrometry and microarray data
Author: Zhang Xuegong ; Lu Xin ; Shi Qian ; Xu Xiu-qin ; Leung Hon-chiu ; Harris Lyndsay ; Iglehart James ; Miron Alexander ; Liu Jun ; Wong Wing Journal: BMC Bioinformatics Year: 2006 Vol: 7 Issue: 1 Pages/record No.: 197
Correlation analysis of two-dimensional gel electrophoretic protein patterns and biological variables
Author: Van Belle Werner ; Ånensen Nina ; Haaland Ingvild ; Bruserud Øystein ; Høgda Kjell-Arild ; Gjertsen Bjørn Tore Journal: BMC Bioinformatics Year: 2006 Vol: 7 Issue: 1 Pages/record No.: 198
QPath: a method for querying pathways in a protein-protein interaction network
Author: Shlomi Tomer ; Segal Daniel ; Ruppin Eytan ; Sharan Roded Journal: BMC Bioinformatics Year: 2006 Vol: 7 Issue: 1 Pages/record No.: 199
Biologically relevant effects of mRNA amplification on gene expression profiles
Author: van Haaften Rachel ; Schroen Blanche ; Janssen Ben ; van Erk Arie ; Debets Jacques ; Smeets Hubert ; Smits Jos ; van den Wijngaard Arthur ; Pinto Yigal ; Evelo Chris Journal: BMC Bioinformatics Year: 2006 Vol: 7 Issue: 1 Pages/record No.: 200
A phylogenomic gene cluster resource: the Phylogenetically Inferred Groups (PhIGs) database
Author: Dehal Paramvir ; Boore Jeffrey Journal: BMC Bioinformatics Year: 2006 Vol: 7 Issue: 1 Pages/record No.: 201
Profiling alternatively spliced mRNA isoforms for prostate cancer classification
Author: Zhang Chaolin ; Li Hai-Ri ; Fan Jian-Bing ; Wang-Rodriguez Jessica ; Downs Tracy ; Fu Xiang-Dong ; Zhang Michael Journal: BMC Bioinformatics Year: 2006 Vol: 7 Issue: 1 Pages/record No.: 202
Integrative investigation of metabolic and transcriptomic data
Author: Pir Pınar ; Kırdar Betül ; Hayes Andrew ; Önsan Z Ýlsen ; Ülgen Kutlu ; Oliver Stephen Journal: BMC Bioinformatics Year: 2006 Vol: 7 Issue: 1 Pages/record No.: 203
Dissecting trait heterogeneity: a comparison of three clustering methods applied to genotypic data
Author: Thornton-Wells Tricia ; Moore Jason ; Haines Jonathan Journal: BMC Bioinformatics Year: 2006 Vol: 7 Issue: 1 Pages/record No.: 204
SIMAGE: simulation of DNA-microarray gene expression data
Author: Albers Casper ; Jansen Ritsert ; Kok Jan ; Kuipers Oscar ; van Hijum Sacha Journal: BMC Bioinformatics Year: 2006 Vol: 7 Issue: 1 Pages/record No.: 205
ROC and confusion analysis of structure comparison methods identify the main causes of divergence from manual protein classification
Author: Sam Vichetra ; Tai Chin-Hsien ; Garnier Jean ; Gibrat Jean-Francois ; Lee Byungkook ; Munson Peter Journal: BMC Bioinformatics Year: 2006 Vol: 7 Issue: 1 Pages/record No.: 206
Development and implementation of an algorithm for detection of protein complexes in large interaction networks
Author: Altaf-Ul-Amin Md ; Shinbo Yoko ; Mihara Kenji ; Kurokawa Ken ; Kanaya Shigehiko Journal: BMC Bioinformatics Year: 2006 Vol: 7 Issue: 1 Pages/record No.: 207
Length-dependent prediction of protein intrinsic disorder
Author: Peng Kang ; Radivojac Predrag ; Vucetic Slobodan ; Dunker A Keith ; Obradovic Zoran Journal: BMC Bioinformatics Year: 2006 Vol: 7 Issue: 1 Pages/record No.: 208
PedGenie: an analysis approach for genetic association testing in extended pedigrees and genealogies of arbitrary size
Author: Allen-Brady Kristina ; Wong Jathine ; Camp Nicola Journal: BMC Bioinformatics Year: 2006 Vol: 7 Issue: 1 Pages/record No.: 209
An integrated system for genetic analysis
Author: Fiddy Simon ; Cattermole David ; Xie Dong ; Duan Xiao ; Mott Richard Journal: BMC Bioinformatics Year: 2006 Vol: 7 Issue: 1 Pages/record No.: 210
Assessment of the relationship between pre-chip and post-chip quality measures for Affymetrix GeneChip expression data
Author: Jones Lesley ; Goldstein Darlene ; Hughes Gareth ; Strand Andrew ; Collin Francois ; Dunnett Stephen ; Kooperberg Charles ; Aragaki Aaron ; Olson James ; Augood Sarah ; Faull Richard ; Luthi-Carter Ruth ; Moskvina Valentina ; Hodges Angela Journal: BMC Bioinformatics Year: 2006 Vol: 7 Issue: 1 Pages/record No.: 211
Quality control for terms and definitions in ontologies and taxonomies
Author: Köhler Jacob ; Munn Katherine ; Rüegg Alexander ; Skusa Andre ; Smith Barry Journal: BMC Bioinformatics Year: 2006 Vol: 7 Issue: 1 Pages/record No.: 212
An analysis of the Sargasso Sea resource and the consequences for database composition
Author: Tress Michael ; Cozzetto Domenico ; Tramontano Anna ; Valencia Alfonso Journal: BMC Bioinformatics Year: 2006 Vol: 7 Issue: 1 Pages/record No.: 213
Correction: versatile and declarative dynamic programming using pair algebras
Author: Steffen Peter ; Giegerich Robert Journal: BMC Bioinformatics Year: 2006 Vol: 7 Issue: 1 Pages/record No.: 214
The statistics of identifying differentially expressed genes in Expresso and TM4: a comparison
Author: Sioson Allan ; Mane Shrinivasrao ; Li Pinghua ; Sha Wei ; Heath Lenwood ; Bohnert Hans ; Grene Ruth Journal: BMC Bioinformatics Year: 2006 Vol: 7 Issue: 1 Pages/record No.: 215
A factor analysis model for functional genomics
Author: Kustra Rafal ; Shioda Romy ; Zhu Mu Journal: BMC Bioinformatics Year: 2006 Vol: 7 Issue: 1 Pages/record No.: 216
Predicting deleterious nsSNPs: an analysis of sequence and structural attributes
Author: Dobson Richard ; Munroe Patricia ; Caulfield Mark ; Saqi Mansoor Journal: BMC Bioinformatics Year: 2006 Vol: 7 Issue: 1 Pages/record No.: 217
XcisClique: analysis of regulatory bicliques
Author: Pati Amrita ; Vasquez-Robinet Cecilia ; Heath Lenwood ; Grene Ruth ; Murali TM Journal: BMC Bioinformatics Year: 2006 Vol: 7 Issue: 1 Pages/record No.: 218
Exploration of biological network centralities with CentiBiN
Author: Junker Björn ; Koschützki Dirk ; Schreiber Falk Journal: BMC Bioinformatics Year: 2006 Vol: 7 Issue: 1 Pages/record No.: 219
Retrieval with gene queries
Author: Sehgal Aditya ; Srinivasan Padmini Journal: BMC Bioinformatics Year: 2006 Vol: 7 Issue: 1 Pages/record No.: 220
RNAmute: RNA secondary structure mutation analysis tool
Author: Churkin Alexander ; Barash Danny Journal: BMC Bioinformatics Year: 2006 Vol: 7 Issue: 1 Pages/record No.: 221
A novel scoring schema for peptide identification by searching protein sequence databases using tandem mass spectrometry data
Author: Zhang Zhuo ; Sun Shiwei ; Zhu Xiaopeng ; Chang Suhua ; Liu Xiaofei ; Yu Chungong ; Bu Dongbo ; Chen Runsheng Journal: BMC Bioinformatics Year: 2006 Vol: 7 Issue: 1 Pages/record No.: 222
Support vector machine for classification of meiotic recombination hotspots and coldspots in Saccharomyces cerevisiae based on codon composition
Author: Zhou Tong ; Weng Jianhong ; Sun Xiao ; Lu Zuhong Journal: BMC Bioinformatics Year: 2006 Vol: 7 Issue: 1 Pages/record No.: 223
IMGT/GeneInfo: T cell receptor gamma TRG and delta TRD genes in database give access to all TR potential V(D)J recombinations
Author: Baum Thierry-Pascal ; Hierle Vivien ; Pasqual Nicolas ; Bellahcene Fatena ; Chaume Denys ; Lefranc Marie-Paule ; Jouvin-Marche Evelyne ; Marche Patrice ; Demongeot Jacques Journal: BMC Bioinformatics Year: 2006 Vol: 7 Issue: 1 Pages/record No.: 224
JColorGrid: software for the visualization of biological measurements
Author: Joachimiak Marcin ; Weisman Jennifer ; May Barnaby Journal: BMC Bioinformatics Year: 2006 Vol: 7 Issue: 1 Pages/record No.: 225
GNU polyxmass: a software framework for mass spectrometric simulations of linear (bio-)polymeric analytes
Author: Rusconi Filippo Journal: BMC Bioinformatics Year: 2006 Vol: 7 Issue: 1 Pages/record No.: 226
MIDAS: software for analysis and visualisation of interallelic disequilibrium between multiallelic markers
Author: Gaunt Tom ; Rodriguez Santiago ; Zapata Carlos ; Day Ian Journal: BMC Bioinformatics Year: 2006 Vol: 7 Issue: 1 Pages/record No.: 227
A stable gene selection in microarray data analysis
Author: Yang Kun ; Cai Zhipeng ; Li Jianzhong ; Lin Guohui Journal: BMC Bioinformatics Year: 2006 Vol: 7 Issue: 1 Pages/record No.: 228
Meta-analysis discovery of tissue-specific DNA sequence motifs from mammalian gene expression data
Author: Huber Bertrand ; Bulyk Martha Journal: BMC Bioinformatics Year: 2006 Vol: 7 Issue: 1 Pages/record No.: 229
Parameter estimation for stiff equations of biosystems using radial basis function networks
Author: Matsubara Yoshiya ; Kikuchi Shinichi ; Sugimoto Masahiro ; Tomita Masaru Journal: BMC Bioinformatics Year: 2006 Vol: 7 Issue: 1 Pages/record No.: 230
Simplifying gene trees for easier comprehension
Author: Lott Paul-Ludwig ; Mundry Marvin ; Sassenberg Christoph ; Lorkowski Stefan ; Fuellen Georg Journal: BMC Bioinformatics Year: 2006 Vol: 7 Issue: 1 Pages/record No.: 231
Design of microarray probes for virus identification and detection of emerging viruses at the genus level
Author: Chou Cheng-Chung ; Lee Te-Tsui ; Chen Chun-Houh ; Hsiao Hsiang-Yun ; Lin Yi-Ling ; Ho Mei-Shang ; Yang Pan-Chyr ; Peck Konan Journal: BMC Bioinformatics Year: 2006 Vol: 7 Issue: 1 Pages/record No.: 232
PDA: Pooled DNA analyzer
Author: Yang Hsin-Chou ; Pan Chia-Ching ; Lin Chin-Yu ; Fann Cathy Journal: BMC Bioinformatics Year: 2006 Vol: 7 Issue: 1 Pages/record No.: 233
Metabolomic database annotations via query of elemental compositions: Mass accuracy is insufficient even at less than 1 ppm
Author: Kind Tobias ; Fiehn Oliver Journal: BMC Bioinformatics Year: 2006 Vol: 7 Issue: 1 Pages/record No.: 234
A comparison of univariate and multivariate gene selection techniques for classification of cancer datasets
Author: Lai Carmen ; Reinders Marcel ; van't Veer Laura ; Wessels Lodewyk Journal: BMC Bioinformatics Year: 2006 Vol: 7 Issue: 1 Pages/record No.: 235
Characterizing disease states from topological properties of transcriptional regulatory networks
Author: Tuck David ; Kluger Harriet ; Kluger Yuval Journal: BMC Bioinformatics Year: 2006 Vol: 7 Issue: 1 Pages/record No.: 236
Components of the antigen processing and presentation pathway revealed by gene expression microarray analysis following B cell antigen receptor (BCR) stimulation
Author: Lee Jamie ; Sinkovits Robert ; Mock Dennis ; Rab Eva ; Cai Jennifer ; Yang Peng ; Saunders Brian ; Hsueh Robert ; Choi Sangdun ; Subramaniam Shankar ; Scheuermann Richard Journal: BMC Bioinformatics Year: 2006 Vol: 7 Issue: 1 Pages/record No.: 237
K-SPMM: a database of murine spermatogenic promoters modules & motifs
Author: Lu Yi ; Platts Adrian ; Ostermeier G Charles ; Krawetz Stephen Journal: BMC Bioinformatics Year: 2006 Vol: 7 Issue: 1 Pages/record No.: 238
A hidden Markov model approach for determining expression from genomic tiling micro arrays
Author: Munch Kasper ; Gardner Paul ; Arctander Peter ; Krogh Anders Journal: BMC Bioinformatics Year: 2006 Vol: 7 Issue: 1 Pages/record No.: 239
Evaluation of sequence alignments and oligonucleotide probes with respect to three-dimensional structure of ribosomal RNA using ARB software package
Author: Kumar Yadhu ; Westram Ralf ; Kipfer Peter ; Meier Harald ; Ludwig Wolfgang Journal: BMC Bioinformatics Year: 2006 Vol: 7 Issue: 1 Pages/record No.: 240
Combining evidence, biomedical literature and statistical dependence: new insights for functional annotation of gene sets
Author: Aubry Marc ; Monnier Annabelle ; Chicault Celine ; de Tayrac Marie ; Galibert Marie-Dominique ; Burgun Anita ; Mosser Jean Journal: BMC Bioinformatics Year: 2006 Vol: 7 Issue: 1 Pages/record No.: 241
Multipolar representation of protein structure
Author: Gramada Apostol ; Bourne Philip Journal: BMC Bioinformatics Year: 2006 Vol: 7 Issue: 1 Pages/record No.: 242
Chaos game representation for comparison of whole genomes
Author: Joseph Jijoy ; Sasikumar Roschen Journal: BMC Bioinformatics Year: 2006 Vol: 7 Issue: 1 Pages/record No.: 243
Identification of consensus RNA secondary structures using suffix arrays
Author: Anwar Mohammad ; Nguyen Truong ; Turcotte Marcel Journal: BMC Bioinformatics Year: 2006 Vol: 7 Issue: 1 Pages/record No.: 244
Identification of gene expression patterns using planned linear contrasts
Author: Li Hao ; Wood Constance ; Liu Yushu ; Getchell Thomas ; Getchell Marilyn ; Stromberg Arnold Journal: BMC Bioinformatics Year: 2006 Vol: 7 Issue: 1 Pages/record No.: 245
Optimizing amino acid substitution matrices with a local alignment kernel
Author: Saigo Hiroto ; Vert Jean-Philippe ; Akutsu Tatsuya Journal: BMC Bioinformatics Year: 2006 Vol: 7 Issue: 1 Pages/record No.: 246
Bayesian models for pooling microarray studies with multiple sources of replications
Author: Conlon Erin ; Song Joon ; Liu Jun Journal: BMC Bioinformatics Year: 2006 Vol: 7 Issue: 1 Pages/record No.: 247
Promoter prediction and annotation of microbial genomes based on DNA sequence and structural responses to superhelical stress
Author: Wang Huiquan ; Benham Craig Journal: BMC Bioinformatics Year: 2006 Vol: 7 Issue: 1 Pages/record No.: 248
Applying dynamic Bayesian networks to perturbed gene expression data
Author: Dojer Norbert ; Gambin Anna ; Mizera Andrzej ; Wilczyński Bartek ; Tiuryn Jerzy Journal: BMC Bioinformatics Year: 2006 Vol: 7 Issue: 1 Pages/record No.: 249
Statistical modeling of biomedical corpora: mining the Caenorhabditis Genetic Center Bibliography for genes related to life span
Author: Blei DM ; Franks K ; Jordan MI ; Mian IS Journal: BMC Bioinformatics Year: 2006 Vol: 7 Issue: 1 Pages/record No.: 250
Correction of scaling mismatches in oligonucleotide microarray data
Author: Barenco Martino ; Stark Jaroslav ; Brewer Daniel ; Tomescu Daniela ; Callard Robin ; Hubank Michael Journal: BMC Bioinformatics Year: 2006 Vol: 7 Issue: 1 Pages/record No.: 251
Phylophenetic properties of metabolic pathway topologies as revealed by global analysis
Author: Zhang Yong ; Li Shaojuan ; Skogerbø Geir ; Zhang Zhihua ; Zhu Xiaopeng ; Zhang Zefeng ; Sun Shiwei ; Lu Hongchao ; Shi Baochen ; Chen Runsheng Journal: BMC Bioinformatics Year: 2006 Vol: 7 Issue: 1 Pages/record No.: 252
Regularized binormal ROC method in disease classification using microarray data
Author: Ma Shuangge ; Song Xiao ; Huang Jian Journal: BMC Bioinformatics Year: 2006 Vol: 7 Issue: 1 Pages/record No.: 253
Bounded search for de novo identification of degenerate cis-regulatory elements
Author: Carlson Jonathan ; Chakravarty Arijit ; Khetani Radhika ; Gross Robert Journal: BMC Bioinformatics Year: 2006 Vol: 7 Issue: 1 Pages/record No.: 254
Prediction of amphipathic in-plane membrane anchors in monotopic proteins using a SVM classifier
Author: Sapay Nicolas ; Guermeur Yann ; Deléage Gilbert Journal: BMC Bioinformatics Year: 2006 Vol: 7 Issue: 1 Pages/record No.: 255
The development and validation of the Virtual Tissue Matrix, a software application that facilitates the review of tissue microarrays on line
Author: Conway Catherine ; O'Shea Deirdre ; O'Brien Sallyann ; Lawler Darragh ; Dodrill Graham ; O'Grady Anthony ; Barrett Helen ; Gulmann Christian ; O'Driscoll Lorraine ; Gallagher William ; Kay Elaine ; O'Shea Daniel Journal: BMC Bioinformatics Year: 2006 Vol: 7 Issue: 1 Pages/record No.: 256
Use of a multi-way method to analyze the amino acid composition of a conserved group of orthologous proteins in prokaryotes
Author: Pasamontes Alberto ; Garcia-Vallve Santiago Journal: BMC Bioinformatics Year: 2006 Vol: 7 Issue: 1 Pages/record No.: 257
Haplotype-based quantitative trait mapping using a clustering algorithm
Author: Li Jing ; Zhou Yingyao ; Elston Robert Journal: BMC Bioinformatics Year: 2006 Vol: 7 Issue: 1 Pages/record No.: 258
The effects of multiple features of alternatively spliced exons on the KA/KS ratio test
Author: Chen Feng-Chi ; Chuang Trees-Juen Journal: BMC Bioinformatics Year: 2006 Vol: 7 Issue: 1 Pages/record No.: 259
On the persistence of supplementary resources in biomedical publications
Author: Anderson Nicholas ; Tarczy-Hornoch Peter ; Bumgarner Roger Journal: BMC Bioinformatics Year: 2006 Vol: 7 Issue: 1 Pages/record No.: 260
Empirical array quality weights in the analysis of microarray data
Author: Ritchie Matthew ; Diyagama Dileepa ; Neilson Jody ; van Laar Ryan ; Dobrovic Alexander ; Holloway Andrew ; Smyth Gordon Journal: BMC Bioinformatics Year: 2006 Vol: 7 Issue: 1 Pages/record No.: 261
Predicting DNA-binding sites of proteins from amino acid sequence
Author: Yan Changhui ; Terribilini Michael ; Wu Feihong ; Jernigan Robert ; Dobbs Drena ; Honavar Vasant Journal: BMC Bioinformatics Year: 2006 Vol: 7 Issue: 1 Pages/record No.: 262
Automatic generation of gene finders for eukaryotic species
Author: Munch Kasper ; Krogh Anders Journal: BMC Bioinformatics Year: 2006 Vol: 7 Issue: 1 Pages/record No.: 263
Spatial normalization of array-CGH data
Author: Neuvial Pierre ; Hupé Philippe ; Brito Isabel ; Liva Stéphane ; Manié Élodie ; Brennetot Caroline ; Radvanyi François ; Aurias Alain ; Barillot Emmanuel Journal: BMC Bioinformatics Year: 2006 Vol: 7 Issue: 1 Pages/record No.: 264
A jumping profile Hidden Markov Model and applications to recombination sites in HIV and HCV genomes
Author: Schultz Anne-Kathrin ; Zhang Ming ; Leitner Thomas ; Kuiken Carla ; Korber Bette ; Morgenstern Burkhard ; Stanke Mario Journal: BMC Bioinformatics Year: 2006 Vol: 7 Issue: 1 Pages/record No.: 265
Phylogeny based discovery of regulatory elements
Author: Gertz Jason ; Fay Justin ; Cohen Barak Journal: BMC Bioinformatics Year: 2006 Vol: 7 Issue: 1 Pages/record No.: 266
The use of concept maps during knowledge elicitation in ontology development processes – the nutrigenomics use case
Author: Castro Alexander ; Rocca-Serra Philippe ; Stevens Robert ; Taylor Chris ; Nashar Karim ; Ragan Mark ; Sansone Susanna-Assunta Journal: BMC Bioinformatics Year: 2006 Vol: 7 Issue: 1 Pages/record No.: 267
Genome wide prediction of protein function via a generic knowledge discovery approach based on evidence integration
Author: Xiong Jianghui ; Rayner Simon ; Luo Kunyi ; Li Yinghui ; Chen Shanguang Journal: BMC Bioinformatics Year: 2006 Vol: 7 Issue: 1 Pages/record No.: 268
An integrated approach to the prediction of domain-domain interactions
Author: Lee Hyunju ; Deng Minghua ; Sun Fengzhu ; Chen Ting Journal: BMC Bioinformatics Year: 2006 Vol: 7 Issue: 1 Pages/record No.: 269
Improving the specificity of high-throughput ortholog prediction
Author: Fulton Debra ; Li Yvonne ; Laird Matthew ; Horsman Benjamin ; Roche Fiona ; Brinkman Fiona Journal: BMC Bioinformatics Year: 2006 Vol: 7 Issue: 1 Pages/record No.: 270
Demonstration of two novel methods for predicting functional siRNA efficiency
Author: Jia Peilin ; Shi Tieliu ; Cai Yudong ; Li Yixue Journal: BMC Bioinformatics Year: 2006 Vol: 7 Issue: 1 Pages/record No.: 271
Epigenetic acquisition of inducibility of type III cytotoxicity in P. aeruginosa
Author: Filopon Didier ; Mérieau Annabelle ; Bernot Gilles ; Comet Jean-Paul ; LeBerre Rozenne ; Guery Benoit ; Polack Benoit ; Guespin-Michel Janine Journal: BMC Bioinformatics Year: 2006 Vol: 7 Issue: 1 Pages/record No.: 272
Agile methods in biomedical software development: a multi-site experience report
Author: Kane David ; Hohman Moses ; Cerami Ethan ; McCormick Michael ; Kuhlmman Karl ; Byrd Jeff Journal: BMC Bioinformatics Year: 2006 Vol: 7 Issue: 1 Pages/record No.: 273
Noise-injected neural networks show promise for use on small-sample expression data
Author: Hua Jianping ; Lowey James ; Xiong Zixiang ; Dougherty Edward Journal: BMC Bioinformatics Year: 2006 Vol: 7 Issue: 1 Pages/record No.: 274
AceTree: a tool for visual analysis of Caenorhabditis elegans embryogenesis
Author: Boyle Thomas ; Bao Zhirong ; Murray John ; Araya Carlos ; Waterston Robert Journal: BMC Bioinformatics Year: 2006 Vol: 7 Issue: 1 Pages/record No.: 275
Hybridization interactions between probesets in short oligo microarrays lead to spurious correlations
Author: Okoniewski Michał ; Miller Crispin Journal: BMC Bioinformatics Year: 2006 Vol: 7 Issue: 1 Pages/record No.: 276
EVEREST: automatic identification and classification of protein domains in all protein sequences
Author: Portugaly Elon ; Harel Amir ; Linial Nathan ; Linial Michal Journal: BMC Bioinformatics Year: 2006 Vol: 7 Issue: 1 Pages/record No.: 277
Automated functional classification of experimental and predicted protein structures
Author: Wang Kai ; Samudrala Ram Journal: BMC Bioinformatics Year: 2006 Vol: 7 Issue: 1 Pages/record No.: 278
Optimized mixed Markov models for motif identification
Author: Huang Weichun ; Umbach David ; Ohler Uwe ; Li Leping Journal: BMC Bioinformatics Year: 2006 Vol: 7 Issue: 1 Pages/record No.: 279
Integrated biclustering of heterogeneous genome-wide datasets for the inference of global regulatory networks
Author: Reiss David ; Baliga Nitin ; Bonneau Richard Journal: BMC Bioinformatics Year: 2006 Vol: 7 Issue: 1 Pages/record No.: 280
MeMo: a hybrid SQL/XML approach to metabolomic data management for functional genomics
Author: Spasić Irena ; Dunn Warwick ; Velarde Giles ; Tseng Andy ; Jenkins Helen ; Hardy Nigel ; Oliver Stephen ; Kell Douglas Journal: BMC Bioinformatics Year: 2006 Vol: 7 Issue: 1 Pages/record No.: 281
Automated in-silico detection of cell populations in flow cytometry readouts and its application to leukemia disease monitoring
Author: Toedling Joern ; Rhein Peter ; Ratei Richard ; Karawajew Leonid ; Spang Rainer Journal: BMC Bioinformatics Year: 2006 Vol: 7 Issue: 1 Pages/record No.: 282
The bovine QTL viewer: a web accessible database of bovine Quantitative Trait Loci
Author: Polineni Pavana ; Aragonda Prathyusha ; Xavier Suresh ; Furuta Richard ; Adelson David Journal: BMC Bioinformatics Year: 2006 Vol: 7 Issue: 1 Pages/record No.: 283
Construction of phylogenetic trees by kernel-based comparative analysis of metabolic networks
Author: Oh S June ; Joung Je-Gun ; Chang Jeong-Ho ; Zhang Byoung-Tak Journal: BMC Bioinformatics Year: 2006 Vol: 7 Issue: 1 Pages/record No.: 284
Gene Designer: a synthetic biology tool for constructing artificial DNA segments
Author: Villalobos Alan ; Ness Jon ; Gustafsson Claes ; Minshull Jeremy ; Govindarajan Sridhar Journal: BMC Bioinformatics Year: 2006 Vol: 7 Issue: 1 Pages/record No.: 285
SBEAMS-Microarray: database software supporting genomic expression analyses for systems biology
Author: Marzolf Bruz ; Deutsch Eric ; Moss Patrick ; Campbell David ; Johnson Michael ; Galitski Timothy Journal: BMC Bioinformatics Year: 2006 Vol: 7 Issue: 1 Pages/record No.: 286
BLISS: biding site level identification of shared signal-modules in DNA regulatory sequences
Author: Meng Hailong ; Banerjee Arunava ; Zhou Lei Journal: BMC Bioinformatics Year: 2006 Vol: 7 Issue: 1 Pages/record No.: 287
High throughput profile-profile based fold recognition for the entire human proteome
Author: McGuffin Liam ; Smith Richard ; Bryson Kevin ; Sørensen Søren-Aksel ; Jones David Journal: BMC Bioinformatics Year: 2006 Vol: 7 Issue: 1 Pages/record No.: 288
Cell_motility: a cross-platform, open source application for the study of cell motion paths
Author: Martens Lennart ; Monsieur Geert ; Ampe Christophe ; Gevaert Kris ; Vandekerckhove Joël Journal: BMC Bioinformatics Year: 2006 Vol: 7 Issue: 1 Pages/record No.: 289
Independent component analysis reveals new and biologically significant structures in micro array data
Author: Frigyesi Attila ; Veerla Srinivas ; Lindgren David ; Höglund Mattias Journal: BMC Bioinformatics Year: 2006 Vol: 7 Issue: 1 Pages/record No.: 290
Argument-predicate distance as a filter for enhancing precision in extracting predications on the genetic etiology of disease
Author: Masseroli Marco ; Kilicoglu Halil ; Lang François-Michel ; Rindflesch Thomas Journal: BMC Bioinformatics Year: 2006 Vol: 7 Issue: 1 Pages/record No.: 291
MCALIGN2: Faster, accurate global pairwise alignment of non-coding DNA sequences based on explicit models of indel evolution
Author: Wang Jun ; Keightley Peter ; Johnson Toby Journal: BMC Bioinformatics Year: 2006 Vol: 7 Issue: 1 Pages/record No.: 292
Representation of target-bound drugs by computed conformers: implications for conformational libraries
Author: Günther Stefan ; Senger Christian ; Michalsky Elke ; Goede Andrean ; Preissner Robert Journal: BMC Bioinformatics Year: 2006 Vol: 7 Issue: 1 Pages/record No.: 293
ROKU: a novel method for identification of tissue-specific genes
Author: Kadota Koji ; Ye Jiazhen ; Nakai Yuji ; Terada Tohru ; Shimizu Kentaro Journal: BMC Bioinformatics Year: 2006 Vol: 7 Issue: 1 Pages/record No.: 294
Analysis of circular genome rearrangement by fusions, fissions and block-interchanges
Author: Lu Chin Lung ; Huang Yen Lin ; Wang Tsui Ching ; Chiu Hsien-Tai Journal: BMC Bioinformatics Year: 2006 Vol: 7 Issue: 1 Pages/record No.: 295
Accelerating the reconstruction of genome-scale metabolic networks
Author: Notebaart Richard ; van Enckevort Frank ; Francke Christof ; Siezen Roland ; Teusink Bas Journal: BMC Bioinformatics Year: 2006 Vol: 7 Issue: 1 Pages/record No.: 296
Impact of RNA structure on the prediction of donor and acceptor splice sites
Author: Marashi Sayed-Amir ; Eslahchi Changiz ; Pezeshk Hamid ; Sadeghi Mehdi Journal: BMC Bioinformatics Year: 2006 Vol: 7 Issue: 1 Pages/record No.: 297
Predicting protein subcellular locations using hierarchical ensemble of Bayesian classifiers based on Markov chains
Author: Bulashevska Alla ; Eils Roland Journal: BMC Bioinformatics Year: 2006 Vol: 7 Issue: 1 Pages/record No.: 298
Kernel-based distance metric learning for microarray data classification
Author: Xiong Huilin ; Chen Xue-wen Journal: BMC Bioinformatics Year: 2006 Vol: 7 Issue: 1 Pages/record No.: 299
Evaluation of microarray data normalization procedures using spike-in experiments
Author: Rydén Patrik ; Andersson Henrik ; Landfors Mattias ; Näslund Linda ; Hartmanová Blanka ; Noppa Laila ; Sjöstedt Anders Journal: BMC Bioinformatics Year: 2006 Vol: 7 Issue: 1 Pages/record No.: 300
Improving the accuracy of protein secondary structure prediction using structural alignment
Author: Montgomerie Scott ; Sundararaj Shan ; Gallin Warren ; Wishart David Journal: BMC Bioinformatics Year: 2006 Vol: 7 Issue: 1 Pages/record No.: 301
A new measure for functional similarity of gene products based on Gene Ontology
Author: Schlicker Andreas ; Domingues Francisco ; Rahnenführer Jörg ; Lengauer Thomas Journal: BMC Bioinformatics Year: 2006 Vol: 7 Issue: 1 Pages/record No.: 302
A model-based approach to selection of tag SNPs
Author: Nicolas Pierre ; Sun Fengzhu ; Li Lei Journal: BMC Bioinformatics Year: 2006 Vol: 7 Issue: 1 Pages/record No.: 303
Association algorithm to mine the rules that govern enzyme definition and to classify protein sequences
Author: Chiu Shih-Hau ; Chen Chien-Chi ; Yuan Gwo-Fang ; Lin Thy-Hou Journal: BMC Bioinformatics Year: 2006 Vol: 7 Issue: 1 Pages/record No.: 304
Taking U out, with two nucleases?
Author: Mian I Saira ; Worthey Elizabeth ; Salavati Reza Journal: BMC Bioinformatics Year: 2006 Vol: 7 Issue: 1 Pages/record No.: 305
Improving missing value imputation of microarray data by using spot quality weights
Author: Johansson Peter ; Häkkinen Jari Journal: BMC Bioinformatics Year: 2006 Vol: 7 Issue: 1 Pages/record No.: 306
Array2BIO: from microarray expression data to functional annotation of co-regulated genes
Author: Loots Gabriela ; Chain Patrick ; Mabery Shalini ; Rasley Amy ; Garcia Emilio ; Ovcharenko Ivan Journal: BMC Bioinformatics Year: 2006 Vol: 7 Issue: 1 Pages/record No.: 307
Identification of QTLs controlling gene expression networks defined a priori
Author: Kliebenstein Daniel ; West Marilyn ; van Leeuwen Hans ; Loudet Olivier ; Doerge RW ; St Clair Dina Journal: BMC Bioinformatics Year: 2006 Vol: 7 Issue: 1 Pages/record No.: 308
In silico identification of putative promoter motifs of White Spot Syndrome Virus
Author: Marks Hendrik ; Ren Xin-Ying ; Sandbrink Hans ; van Hulten Mariëlle ; Vlak Just Journal: BMC Bioinformatics Year: 2006 Vol: 7 Issue: 1 Pages/record No.: 309
Docking protein domains in contact space
Author: Lise Stefano ; Walker-Taylor Alice ; Jones David Journal: BMC Bioinformatics Year: 2006 Vol: 7 Issue: 1 Pages/record No.: 310
Web-based analysis of the mouse transcriptome using Genevestigator
Author: Laule Oliver ; Hirsch-Hoffmann Matthias ; Hruz Tomas ; Gruissem Wilhelm ; Zimmermann Philip Journal: BMC Bioinformatics Year: 2006 Vol: 7 Issue: 1 Pages/record No.: 311
Prediction of catalytic residues using Support Vector Machine with selected protein sequence and structural properties
Author: Petrova Natalia ; Wu Cathy Journal: BMC Bioinformatics Year: 2006 Vol: 7 Issue: 1 Pages/record No.: 312
Subfamily logos: visualization of sequence deviations at alignment positions with high information content
Author: Beitz Eric Journal: BMC Bioinformatics Year: 2006 Vol: 7 Issue: 1 Pages/record No.: 313
AgdbNet – antigen sequence database software for bacterial typing
Author: Jolley Keith ; Maiden Martin Journal: BMC Bioinformatics Year: 2006 Vol: 7 Issue: 1 Pages/record No.: 314
PHY·FI: fast and easy online creation and manipulation of phylogeny color figures
Author: Fredslund Jakob Journal: BMC Bioinformatics Year: 2006 Vol: 7 Issue: 1 Pages/record No.: 315
CAVER: a new tool to explore routes from protein clefts, pockets and cavities
Author: Petřek Martin ; Otyepka Michal ; Banáš Pavel ; Košinová Pavlína ; Koča Jaroslav ; Damborský Jiří Journal: BMC Bioinformatics Year: 2006 Vol: 7 Issue: 1 Pages/record No.: 316
PSMIX: an R package for population structure inference via maximum likelihood method
Author: Wu Baolin ; Liu Nianjun ; Zhao Hongyu Journal: BMC Bioinformatics Year: 2006 Vol: 7 Issue: 1 Pages/record No.: 317
MACSIMS : multiple alignment of complete sequences information management system
Author: Thompson Julie ; Muller Arnaud ; Waterhouse Andrew ; Procter Jim ; Barton Geoffrey ; Plewniak Frédéric ; Poch Olivier Journal: BMC Bioinformatics Year: 2006 Vol: 7 Issue: 1 Pages/record No.: 318
Protein disorder prediction by condensed PSSM considering propensity for order or disorder
Author: Su Chung-Tsai ; Chen Chien-Yu ; Ou Yu-Yen Journal: BMC Bioinformatics Year: 2006 Vol: 7 Issue: 1 Pages/record No.: 319
Differential prioritization between relevance and redundancy in correlation-based feature selection techniques for multiclass gene expression data
Author: Ooi Chia ; Chetty Madhu ; Teng Shyh Journal: BMC Bioinformatics Year: 2006 Vol: 7 Issue: 1 Pages/record No.: 320
Bacterial genotyping by 16S rRNA mass cataloging
Author: Jackson George ; McNichols Roger ; Fox George ; Willson Richard Journal: BMC Bioinformatics Year: 2006 Vol: 7 Issue: 1 Pages/record No.: 321
SPODOBASE : an EST database for the lepidopteran crop pest Spodoptera
Author: Nègre Vincent ; Hôtelier Thierry ; Volkoff Anne-Nathalie ; Gimenez Sylvie ; Cousserans François ; Mita Kazuei ; Sabau Xavier ; Rocher Janick ; López-Ferber Miguel ; d'Alençon Emmanuelle ; Audant Pascaline ; Sabourault Cécile ; Bidegainberry Vincent ; Hilliou Frédérique ; Fournier Philippe Journal: BMC Bioinformatics Year: 2006 Vol: 7 Issue: 1 Pages/record No.: 322
Identification of putative domain linkers by a neural network – application to a large sequence database
Author: Miyazaki Satoshi ; Kuroda Yutaka ; Yokoyama Shigeyuki Journal: BMC Bioinformatics Year: 2006 Vol: 7 Issue: 1 Pages/record No.: 323
Novel knowledge-based mean force potential at the profile level
Author: Dong Qiwen ; Wang Xiaolong ; Lin Lei Journal: BMC Bioinformatics Year: 2006 Vol: 7 Issue: 1 Pages/record No.: 324
The Autoimmune Disease Database: a dynamically compiled literature-derived database
Author: Karopka Thomas ; Fluck Juliane ; Mevissen Heinz-Theodor ; Glass Änne Journal: BMC Bioinformatics Year: 2006 Vol: 7 Issue: 1 Pages/record No.: 325
A maximum likelihood framework for protein design
Author: Kleinman Claudia ; Rodrigue Nicolas ; Bonnard Cécile ; Philippe Hervé ; Lartillot Nicolas Journal: BMC Bioinformatics Year: 2006 Vol: 7 Issue: 1 Pages/record No.: 326
Using ESTs to improve the accuracy of de novo gene prediction
Author: Wei Chaochun ; Brent Michael Journal: BMC Bioinformatics Year: 2006 Vol: 7 Issue: 1 Pages/record No.: 327
Computational expression deconvolution in a complex mammalian organ
Author: Wang Min ; Master Stephen ; Chodosh Lewis Journal: BMC Bioinformatics Year: 2006 Vol: 7 Issue: 1 Pages/record No.: 328
An interactive visualization tool to explore the biophysical properties of amino acids and their contribution to substitution matrices
Author: Bulka Blazej ; desJardins Marie ; Freeland Stephen Journal: BMC Bioinformatics Year: 2006 Vol: 7 Issue: 1 Pages/record No.: 329
PROMPT: a protein mapping and comparison tool
Author: Schmidt Thorsten ; Frishman Dmitrij Journal: BMC Bioinformatics Year: 2006 Vol: 7 Issue: 1 Pages/record No.: 331
A joint model of regulatory and metabolic networks
Author: Yeang Chen-Hsiang ; Vingron Martin Journal: BMC Bioinformatics Year: 2006 Vol: 7 Issue: 1 Pages/record No.: 332
A methodology for global validation of microarray experiments
Author: Miron Mathieu ; Woody Owen ; Marcil Alexandre ; Murie Carl ; Sladek Robert ; Nadon Robert Journal: BMC Bioinformatics Year: 2006 Vol: 7 Issue: 1 Pages/record No.: 333
Machine learning and word sense disambiguation in the biomedical domain: design and evaluation issues
Author: Xu Hua ; Markatou Marianthi ; Dimova Rositsa ; Liu Hongfang ; Friedman Carol Journal: BMC Bioinformatics Year: 2006 Vol: 7 Issue: 1 Pages/record No.: 334
AMDA: an R package for the automated microarray data analysis
Author: Pelizzola Mattia ; Pavelka Norman ; Foti Maria ; Ricciardi-Castagnoli Paola Journal: BMC Bioinformatics Year: 2006 Vol: 7 Issue: 1 Pages/record No.: 335
ProtRepeatsDB: a database of amino acid repeats in genomes
Author: Kalita Mridul ; Ramasamy Gowthaman ; Duraisamy Sekhar ; Chauhan Virander ; Gupta Dinesh Journal: BMC Bioinformatics Year: 2006 Vol: 7 Issue: 1 Pages/record No.: 336
HeatMapper: powerful combined visualization of gene expression profile correlations, genotypes, phenotypes and sample characteristics
Author: Verhaak Roel ; Sanders Mathijs ; Bijl Maarten ; Delwel Ruud ; Horsman Sebastiaan ; Moorhouse Michael ; van der Spek Peter ; Löwenberg Bob ; Valk Peter Journal: BMC Bioinformatics Year: 2006 Vol: 7 Issue: 1 Pages/record No.: 337
Cluster analysis of protein array results via similarity of Gene Ontology annotation
Author: Wolting Cheryl ; McGlade C Jane ; Tritchler David Journal: BMC Bioinformatics Year: 2006 Vol: 7 Issue: 1 Pages/record No.: 338
Tools for integrated sequence-structure analysis with UCSF Chimera
Author: Meng Elaine ; Pettersen Eric ; Couch Gregory ; Huang Conrad ; Ferrin Thomas Journal: BMC Bioinformatics Year: 2006 Vol: 7 Issue: 1 Pages/record No.: 339
Quaternary structure predictions of transmembrane proteins starting from the monomer: a docking-based approach
Author: Casciari D ; Seeber M ; Fanelli F Journal: BMC Bioinformatics Year: 2006 Vol: 7 Issue: 1 Pages/record No.: 340
Curation of complex, context-dependent immunological data
Author: Vita Randi ; Vaughan Kerrie ; Zarebski Laura ; Salimi Nima ; Fleri Ward ; Grey Howard ; Sathiamurthy Muthu ; Mokili John ; Bui Huynh-Hoa ; Bourne Philip ; Ponomarenko Julia ; de Castro Romulo ; Chan Russell ; Sidney John ; Wilson Stephen ; Stewart Scott ; Way Scott ; Peters Bjoern ; Sette Alessandro Journal: BMC Bioinformatics Year: 2006 Vol: 7 Issue: 1 Pages/record No.: 341
EMD: an ensemble algorithm for discovering regulatory motifs in DNA sequences
Author: Hu Jianjun ; Yang Yifeng ; Kihara Daisuke Journal: BMC Bioinformatics Year: 2006 Vol: 7 Issue: 1 Pages/record No.: 342
Multivariate curve resolution of time course microarray data
Author: Wentzell Peter ; Karakach Tobias ; Roy Sushmita ; Martinez M Juanita ; Allen Christopher ; Werner-Washburne Margaret Journal: BMC Bioinformatics Year: 2006 Vol: 7 Issue: 1 Pages/record No.: 343
Optimised amino acid specific weighting factors for unbound protein docking
Author: Heuser Philipp ; Schomburg Dietmar Journal: BMC Bioinformatics Year: 2006 Vol: 7 Issue: 1 Pages/record No.: 344
Individualized markers optimize class prediction of microarray data
Author: Pavlidis Pavlos ; Poirazi Panayiota Journal: BMC Bioinformatics Year: 2006 Vol: 7 Issue: 1 Pages/record No.: 345
Structure alignment based on coding of local geometric measures
Author: Chang Peter ; Rinne Andrew ; Dewey T Gregory Journal: BMC Bioinformatics Year: 2006 Vol: 7 Issue: 1 Pages/record No.: 346
BBP: Brucella genome annotation with literature mining and curation
Author: Xiang Zuoshuang ; Zheng Wenjie ; He Yongqun Journal: BMC Bioinformatics Year: 2006 Vol: 7 Issue: 1 Pages/record No.: 347
Simulation of microarray data with realistic characteristics
Author: Nykter Matti ; Aho Tommi ; Ahdesmäki Miika ; Ruusuvuori Pekka ; Lehmussola Antti ; Yli-Harja Olli Journal: BMC Bioinformatics Year: 2006 Vol: 7 Issue: 1 Pages/record No.: 349
Genome BLAST distance phylogenies inferred from whole plastid and whole mitochondrion genome sequences
Author: Auch Alexander ; Henz Stefan ; Holland Barbara ; Göker Markus Journal: BMC Bioinformatics Year: 2006 Vol: 7 Issue: 1 Pages/record No.: 350
MANET: tracing evolution of protein architecture in metabolic networks
Author: Kim Hee ; Mittenthal Jay ; Caetano-Anollés Gustavo Journal: BMC Bioinformatics Year: 2006 Vol: 7 Issue: 1 Pages/record No.: 351
Discovery of cancer vaccination protocols with a genetic algorithm driving an agent based simulator
Author: Lollini Pier-Luigi ; Motta Santo ; Pappalardo Francesco Journal: BMC Bioinformatics Year: 2006 Vol: 7 Issue: 1 Pages/record No.: 352
A combined approach to data mining of textual and structured data to identify cancer-related targets
Author: Pospisil Pavel ; Iyer Lakshmanan ; Adelstein S James ; Kassis Amin Journal: BMC Bioinformatics Year: 2006 Vol: 7 Issue: 1 Pages/record No.: 354
Functional clustering of yeast proteins from the protein-protein interaction network
Author: Sen Taner ; Kloczkowski Andrzej ; Jernigan Robert Journal: BMC Bioinformatics Year: 2006 Vol: 7 Issue: 1 Pages/record No.: 355
New directions in biomedical text annotation: definitions, guidelines and corpus construction
Author: Wilbur W John ; Rzhetsky Andrey ; Shatkay Hagit Journal: BMC Bioinformatics Year: 2006 Vol: 7 Issue: 1 Pages/record No.: 356
Improved alignment quality by combining evolutionary information, predicted secondary structure and self-organizing maps
Author: Ohlson Tomas ; Aggarwal Varun ; Elofsson Arne ; MacCallum Robert Journal: BMC Bioinformatics Year: 2006 Vol: 7 Issue: 1 Pages/record No.: 357
Identification of biomarkers from mass spectrometry data using a "common" peak approach
Author: Fushiki Tadayoshi ; Fujisawa Hironori ; Eguchi Shinto Journal: BMC Bioinformatics Year: 2006 Vol: 7 Issue: 1 Pages/record No.: 358
Comparison and evaluation of methods for generating differentially expressed gene lists from microarray data
Author: Jeffery Ian ; Higgins Desmond ; Culhane Aedín Journal: BMC Bioinformatics Year: 2006 Vol: 7 Issue: 1 Pages/record No.: 359
A direct comparison of protein interaction confidence assignment schemes
Author: Suthram Silpa ; Shlomi Tomer ; Ruppin Eytan ; Sharan Roded ; Ideker Trey Journal: BMC Bioinformatics Year: 2006 Vol: 7 Issue: 1 Pages/record No.: 360
Cluster analysis for DNA methylation profiles having a detection threshold
Author: Marjoram Paul ; Chang Jing ; Laird Peter ; Siegmund Kimberly Journal: BMC Bioinformatics Year: 2006 Vol: 7 Issue: 1 Pages/record No.: 361
PIPE: a protein-protein interaction prediction engine based on the re-occurring short polypeptide sequences between known interacting protein pairs
Author: Pitre Sylvain ; Dehne Frank ; Chan Albert ; Cheetham Jim ; Duong Alex ; Emili Andrew ; Gebbia Marinella ; Greenblatt Jack ; Jessulat Mathew ; Krogan Nevan ; Luo Xuemei ; Golshani Ashkan Journal: BMC Bioinformatics Year: 2006 Vol: 7 Issue: 1 Pages/record No.: 365
bioNMF: a versatile tool for non-negative matrix factorization in biology
Author: Pascual-Montano Alberto ; Carmona-Saez Pedro ; Chagoyen Monica ; Tirado Francisco ; Carazo Jose ; Pascual-Marqui Roberto Journal: BMC Bioinformatics Year: 2006 Vol: 7 Issue: 1 Pages/record No.: 366
Prediction of a key role of motifs binding E2F and NR2F in down-regulation of numerous genes during the development of the mouse hippocampus
Author: Dabrowski Michal ; Aerts Stein ; Kaminska Bozena Journal: BMC Bioinformatics Year: 2006 Vol: 7 Issue: 1 Pages/record No.: 367
G-InforBIO: integrated system for microbial genomics
Author: Tanaka Naoto ; Abe Takashi ; Miyazaki Satoru ; Sugawara Hideaki Journal: BMC Bioinformatics Year: 2006 Vol: 7 Issue: 1 Pages/record No.: 368
Robust computational reconstitution – a new method for the comparative analysis of gene expression in tissues and isolated cell fractions
Author: Hoffmann Martin ; Pohlers Dirk ; Koczan Dirk ; Thiesen Hans-Jürgen ; Wölfl Stefan ; Kinne Raimund Journal: BMC Bioinformatics Year: 2006 Vol: 7 Issue: 1 Pages/record No.: 369
Automatic document classification of biological literature
Author: Chen David ; Müller Hans-Michael ; Sternberg Paul Journal: BMC Bioinformatics Year: 2006 Vol: 7 Issue: 1 Pages/record No.: 370
UniFrac – An online tool for comparing microbial community diversity in a phylogenetic context
Author: Lozupone Catherine ; Hamady Micah ; Knight Rob Journal: BMC Bioinformatics Year: 2006 Vol: 7 Issue: 1 Pages/record No.: 371
Gene and protein nomenclature in public databases
Author: Fundel Katrin ; Zimmer Ralf Journal: BMC Bioinformatics Year: 2006 Vol: 7 Issue: 1 Pages/record No.: 372
Text mining of full-text journal articles combined with gene expression analysis reveals a relationship between sphingosine-1-phosphate and invasiveness of a glioblastoma cell line
Author: Natarajan Jeyakumar ; Berrar Daniel ; Dubitzky Werner ; Hack Catherine ; Zhang Yonghong ; DeSesa Catherine ; Van Brocklyn James ; Bremer Eric Journal: BMC Bioinformatics Year: 2006 Vol: 7 Issue: 1 Pages/record No.: 373
Genome comparison using Gene Ontology (GO) with statistical testing
Author: Cai Zhaotao ; Mao Xizeng ; Li Songgang ; Wei Liping Journal: BMC Bioinformatics Year: 2006 Vol: 7 Issue: 1 Pages/record No.: 374
PeanutMap: an online genome database for comparative molecular maps of peanut
Author: Jesubatham Arun ; Burow Mark Journal: BMC Bioinformatics Year: 2006 Vol: 7 Issue: 1 Pages/record No.: 375
Detecting the limits of regulatory element conservation and divergence estimation using pairwise and multiple alignments
Author: Pollard Daniel ; Moses Alan ; Iyer Venky ; Eisen Michael Journal: BMC Bioinformatics Year: 2006 Vol: 7 Issue: 1 Pages/record No.: 376
A novel data mining method to identify assay-specific signatures in functional genomic studies
Author: Rollins Derrick ; Zhai Dongmei ; Joe Alrica ; Guidarelli Jack ; Murarka Abhishek ; Gonzalez Ramon Journal: BMC Bioinformatics Year: 2006 Vol: 7 Issue: 1 Pages/record No.: 377
Comprehensive quality control utilizing the prehybridization third-dye image leads to accurate gene expression measurements by cDNA microarrays
Author: Wang Xujing ; Jia Shuang ; Meyer Lisa ; Xiang Bixia ; Chen Li-Yen ; Jiang Nan ; Moreno Carol ; Jacob Howard ; Ghosh Soumitra ; Hessner Martin Journal: BMC Bioinformatics Year: 2006 Vol: 7 Issue: 1 Pages/record No.: 378
V-MitoSNP: visualization of human mitochondrial SNPs
Author: Chuang Li-Yeh ; Yang Cheng-Hong ; Cheng Yu-Huei ; Gu De-Leung ; Chang Phei-Lang ; Tsui Ke-Hung ; Chang Hsueh-Wei Journal: BMC Bioinformatics Year: 2006 Vol: 7 Issue: 1 Pages/record No.: 379
Validation and functional annotation of expression-based clusters based on gene ontology
Author: Steuer Ralf ; Humburg Peter ; Selbig Joachim Journal: BMC Bioinformatics Year: 2006 Vol: 7 Issue: 1 Pages/record No.: 380
Modelling the network of cell cycle transcription factors in the yeast Saccharomyces cerevisiae
Author: Cokus Shawn ; Rose Sherri ; Haynor David ; Grønbech-Jensen Niels ; Pellegrini Matteo Journal: BMC Bioinformatics Year: 2006 Vol: 7 Issue: 1 Pages/record No.: 381
MultiSeq: unifying sequence and structure data for evolutionary analysis
Author: Roberts Elijah ; Eargle John ; Wright Dan ; Luthey-Schulten Zaida Journal: BMC Bioinformatics Year: 2006 Vol: 7 Issue: 1 Pages/record No.: 382
Laboratory Information Management Software for genotyping workflows: applications in high throughput crop genotyping
Author: Jayashree B ; Reddy Praveen ; Leeladevi Y ; Crouch Jonathan ; Mahalakshmi V ; Buhariwalla Hutokshi ; Eshwar KE ; Mace Emma ; Folksterma Rolf ; Senthilvel S ; Varshney Rajeev ; Seetha K ; Rajalakshmi R ; Prasanth VP ; Chandra Subhash ; Swarupa L ; SriKalyani P ; Hoisington David Journal: BMC Bioinformatics Year: 2006 Vol: 7 Issue: 1 Pages/record No.: 383
Analysis of promoter regions of co-expressed genes identified by microarray analysis
Author: Veerla Srinivas ; Höglund Mattias Journal: BMC Bioinformatics Year: 2006 Vol: 7 Issue: 1 Pages/record No.: 384
Incorporating background frequency improves entropy-based residue conservation measures
Author: Wang Kai ; Samudrala Ram Journal: BMC Bioinformatics Year: 2006 Vol: 7 Issue: 1 Pages/record No.: 385
Hierarchical modularity of nested bow-ties in metabolic networks
Author: Zhao Jing ; Yu Hong ; Luo Jian-Hua ; Cao Zhi-Wei ; Li Yi-Xue Journal: BMC Bioinformatics Year: 2006 Vol: 7 Issue: 1 Pages/record No.: 386
On the statistical assessment of classifiers using DNA microarray data
Author: Ancona N ; Maglietta R ; Piepoli A ; D'Addabbo A ; Cotugno R ; Savino M ; Liuni S ; Carella M ; Pesole G ; Perri F Journal: BMC Bioinformatics Year: 2006 Vol: 7 Issue: 1 Pages/record No.: 387
Selecting normalization genes for small diagnostic microarrays
Author: Jaeger Jochen ; Spang Rainer Journal: BMC Bioinformatics Year: 2006 Vol: 7 Issue: 1 Pages/record No.: 388
Fast index based algorithms and software for matching position specific scoring matrices
Author: Beckstette Michael ; Homann Robert ; Giegerich Robert ; Kurtz Stefan Journal: BMC Bioinformatics Year: 2006 Vol: 7 Issue: 1 Pages/record No.: 389
PET-Tool: a software suite for comprehensive processing and managing of Paired-End diTag (PET) sequence data
Author: Chiu Kuo ; Wong Chee-Hong ; Chen Qiongyu ; Ariyaratne Pramila ; Ooi Hong ; Wei Chia-Lin ; Sung Wing-Kin ; Ruan Yijun Journal: BMC Bioinformatics Year: 2006 Vol: 7 Issue: 1 Pages/record No.: 390
GeneLibrarian: an effective gene-information summarization and visualization system
Author: Chiang Jung-Hsien ; Shin Jyh-Wei ; Liu Heng-Hui ; Chin Chong-Liang Journal: BMC Bioinformatics Year: 2006 Vol: 7 Issue: 1 Pages/record No.: 392
A probabilistic classifier for olfactory receptor pseudogenes
Author: Menashe Idan ; Aloni Ronny ; Lancet Doron Journal: BMC Bioinformatics Year: 2006 Vol: 7 Issue: 1 Pages/record No.: 393
Mining frequent patterns for AMP-activated protein kinase regulation on skeletal muscle
Author: Chen Qingfeng ; Chen Yi-Ping Journal: BMC Bioinformatics Year: 2006 Vol: 7 Issue: 1 Pages/record No.: 394
Probe set algorithms: is there a rational best bet?
Author: Seo Jinwook ; Hoffman Eric Journal: BMC Bioinformatics Year: 2006 Vol: 7 Issue: 1 Pages/record No.: 395
Predicting transcription factor binding sites using local over-representation and comparative genomics
Author: Defrance Matthieu ; Touzet Hélène Journal: BMC Bioinformatics Year: 2006 Vol: 7 Issue: 1 Pages/record No.: 396
Methods for evaluating clustering algorithms for gene expression data using a reference set of functional classes
Author: Datta Susmita ; Datta Somnath Journal: BMC Bioinformatics Year: 2006 Vol: 7 Issue: 1 Pages/record No.: 397
PhyloPat: phylogenetic pattern analysis of eukaryotic genes
Author: Hulsen Tim ; de Vlieg Jacob ; Groenen Peter Journal: BMC Bioinformatics Year: 2006 Vol: 7 Issue: 1 Pages/record No.: 398
Cancer diagnosis marker extraction for soft tissue sarcomas based on gene expression profiling data by using projective adaptive resonance theory (PART) filtering method
Author: Takahashi Hiro ; Nemoto Takeshi ; Yoshida Teruhiko ; Honda Hiroyuki ; Hasegawa Tadashi Journal: BMC Bioinformatics Year: 2006 Vol: 7 Issue: 1 Pages/record No.: 399
CRNPRED: highly accurate prediction of one-dimensional protein structures by large-scale critical random networks
Author: Kinjo Akira ; Nishikawa Ken Journal: BMC Bioinformatics Year: 2006 Vol: 7 Issue: 1 Pages/record No.: 401
Distill: a suite of web servers for the prediction of one-, two- and three-dimensional structural features of proteins
Author: Baú Davide ; Martin Alberto ; Mooney Catherine ; Vullo Alessandro ; Walsh Ian ; Pollastri Gianluca Journal: BMC Bioinformatics Year: 2006 Vol: 7 Issue: 1 Pages/record No.: 402
A database application for pre-processing, storage and comparison of mass spectra derived from patients and controls
Author: Titulaer Mark ; Siccama Ivar ; Dekker Lennard ; van Rijswijk Angelique ; Heeren Ron ; Sillevis Smitt Peter ; Luider Theo Journal: BMC Bioinformatics Year: 2006 Vol: 7 Issue: 1 Pages/record No.: 403
RDMAS: a web server for RNA deleterious mutation analysis
Author: Shu Wenjie ; Bo Xiaochen ; Liu Rujia ; Zhao Dongsheng ; Zheng Zhiqiang ; Wang Shengqi Journal: BMC Bioinformatics Year: 2006 Vol: 7 Issue: 1 Pages/record No.: 404
Predicting the effect of missense mutations on protein function: analysis with Bayesian networks
Author: Needham Chris ; Bradford James ; Bulpitt Andrew ; Care Matthew ; Westhead David Journal: BMC Bioinformatics Year: 2006 Vol: 7 Issue: 1 Pages/record No.: 405
Correction: genetic algorithm learning as a robust approach to RNA editing site site prediction
Author: Thompson James ; Gopal Shuba Journal: BMC Bioinformatics Year: 2006 Vol: 7 Issue: 1 Pages/record No.: 406
Identifying genes that contribute most to good classification in microarrays
Author: Baker Stuart ; Kramer Barnett Journal: BMC Bioinformatics Year: 2006 Vol: 7 Issue: 1 Pages/record No.: 407
Scanning sequences after Gibbs sampling to find multiple occurrences of functional elements
Author: Tharakaraman Kannan ; Mariño-Ramírez Leonardo ; Sheetlin Sergey ; Landsman David ; Spouge John Journal: BMC Bioinformatics Year: 2006 Vol: 7 Issue: 1 Pages/record No.: 408
Genome-wide DNA polymorphism analyses using VariScan
Author: Hutter Stephan ; Vilella Albert ; Rozas Julio Journal: BMC Bioinformatics Year: 2006 Vol: 7 Issue: 1 Pages/record No.: 409
Application of protein structure alignments to iterated hidden Markov model protocols for structure prediction
Author: Scheeff Eric ; Bourne Philip Journal: BMC Bioinformatics Year: 2006 Vol: 7 Issue: 1 Pages/record No.: 410
miTarget: microRNA target gene prediction using a support vector machine
Author: Kim Sung-Kyu ; Nam Jin-Wu ; Rhee Je-Keun ; Lee Wha-Jin ; Zhang Byoung-Tak Journal: BMC Bioinformatics Year: 2006 Vol: 7 Issue: 1 Pages/record No.: 411
Detecting recombination in evolving nucleotide sequences
Author: Chan Cheong ; Beiko Robert ; Ragan Mark Journal: BMC Bioinformatics Year: 2006 Vol: 7 Issue: 1 Pages/record No.: 412
Correlated fragile site expression allows the identification of candidate fragile genes involved in immunity and associated with carcinogenesis
Author: Re Angela ; Cora Davide ; Puliti Alda ; Caselle Michele ; Sbrana Isabella Journal: BMC Bioinformatics Year: 2006 Vol: 7 Issue: 1 Pages/record No.: 413
Quantification of the variation in percentage identity for protein sequence alignments
Author: Raghava GPS ; Barton Geoffrey Journal: BMC Bioinformatics Year: 2006 Vol: 7 Issue: 1 Pages/record No.: 415
Genomes as geography: using GIS technology to build interactive genome feature maps
Author: Dolan Mary ; Holden Constance ; Beard M Kate ; Bult Carol Journal: BMC Bioinformatics Year: 2006 Vol: 7 Issue: 1 Pages/record No.: 416
Searching for interpretable rules for disease mutations: a simulated annealing bump hunting strategy
Author: Jiang Rui ; Yang Hua ; Sun Fengzhu ; Chen Ting Journal: BMC Bioinformatics Year: 2006 Vol: 7 Issue: 1 Pages/record No.: 417
CROPPER: a metagene creator resource for cross-platform and cross-species compendium studies
Author: Paananen Jussi ; Storvik Markus ; Wong Garry Journal: BMC Bioinformatics Year: 2006 Vol: 7 Issue: 1 Pages/record No.: 418
A machine learning strategy to identify candidate binding sites in human protein-coding sequence
Author: Down Thomas ; Leong Bernard ; Hubbard Tim Journal: BMC Bioinformatics Year: 2006 Vol: 7 Issue: 1 Pages/record No.: 419
Comparative assessment of performance and genome dependence among phylogenetic profiling methods
Author: Snitkin Evan ; Gustafson Adam ; Mellor Joseph ; Wu Jie ; DeLisi Charles Journal: BMC Bioinformatics Year: 2006 Vol: 7 Issue: 1 Pages/record No.: 420
Computational reconstruction of transcriptional regulatory modules of the yeast cell cycle
Author: Wu Wei-Sheng ; Li Wen-Hsiung ; Chen Bor-Sen Journal: BMC Bioinformatics Year: 2006 Vol: 7 Issue: 1 Pages/record No.: 421
Analysis with respect to instrumental variables for the exploration of microarray data structures
Author: Baty Florent ; Facompré Michaël ; Wiegand Jan ; Schwager Joseph ; Brutsche Martin Journal: BMC Bioinformatics Year: 2006 Vol: 7 Issue: 1 Pages/record No.: 422
Detection of prokaryotic promoters from the genomic distribution of hexanucleotide pairs
Author: Jacques Pierre-Étienne ; Rodrigue Sébastien ; Gaudreau Luc ; Goulet Jean ; Brzezinski Ryszard Journal: BMC Bioinformatics Year: 2006 Vol: 7 Issue: 1 Pages/record No.: 423
PubFocus: semantic MEDLINE/PubMed citations analytics through integration of controlled biomedical dictionaries and ranking algorithm
Author: Plikus Maksim ; Zhang Zina ; Chuong Cheng-Ming Journal: BMC Bioinformatics Year: 2006 Vol: 7 Issue: 1 Pages/record No.: 424
Predicting residue-wise contact orders in proteins by support vector regression
Author: Song Jiangning ; Burrage Kevin Journal: BMC Bioinformatics Year: 2006 Vol: 7 Issue: 1 Pages/record No.: 425
Grouping Gene Ontology terms to improve the assessment of gene set enrichment in microarray data
Author: Lewin Alex ; Grieve Ian Journal: BMC Bioinformatics Year: 2006 Vol: 7 Issue: 1 Pages/record No.: 426
MICA: desktop software for comprehensive searching of DNA databases
Author: Stokes William ; Glick Benjamin Journal: BMC Bioinformatics Year: 2006 Vol: 7 Issue: 1 Pages/record No.: 427
XRate: a fast prototyping, training and annotation tool for phylo-grammars
Author: Klosterman Peter ; Uzilov Andrew ; Bendaña Yuri ; Bradley Robert ; Chao Sharon ; Kosiol Carolin ; Goldman Nick ; Holmes Ian Journal: BMC Bioinformatics Year: 2006 Vol: 7 Issue: 1 Pages/record No.: 428
Design of a combinatorial DNA microarray for protein-DNA interaction studies
Author: Mintseris Julian ; Eisen Michael Journal: BMC Bioinformatics Year: 2006 Vol: 7 Issue: 1 Pages/record No.: 429
Development of an open source laboratory information management system for 2-D gel electrophoresis-based proteomics workflow
Author: Morisawa Hiraku ; Hirota Mikako ; Toda Tosifusa Journal: BMC Bioinformatics Year: 2006 Vol: 7 Issue: 1 Pages/record No.: 430
The BiSearch web server
Author: Arányi Tamás ; Váradi András ; Simon István ; Tusnády Gábor E Journal: BMC Bioinformatics Year: 2006 Vol: 7 Issue: 1 Pages/record No.: 431
Feature selection using Haar wavelet power spectrum
Author: Subramani Prabakaran ; Sahu Rajendra ; Verma Shekhar Journal: BMC Bioinformatics Year: 2006 Vol: 7 Issue: 1 Pages/record No.: 432
M-GCAT: interactively and efficiently constructing large-scale multiple genome comparison frameworks in closely related species
Author: Treangen Todd ; Messeguer Xavier Journal: BMC Bioinformatics Year: 2006 Vol: 7 Issue: 1 Pages/record No.: 433
Rank-statistics based enrichment-site prediction algorithm developed for chromatin immunoprecipitation on chip experiments
Author: Ghosh Srinka ; Hirsch Heather ; Sekinger Edward ; Struhl Kevin ; Gingeras Thomas Journal: BMC Bioinformatics Year: 2006 Vol: 7 Issue: 1 Pages/record No.: 434
Coloring the Mu transpososome
Author: Darcy Isabel ; Chang Jeff ; Druivenga Nathan ; McKinney Colin ; Medikonduri Ram ; Mills Stacy ; Navarra-Madsen Junalyn ; Ponnusamy Arun ; Sweet Jesse ; Thompson Travis Journal: BMC Bioinformatics Year: 2006 Vol: 7 Issue: 1 Pages/record No.: 435
ORENZA: a web resource for studying ORphan ENZyme activities
Author: Lespinet Olivier ; Labedan Bernard Journal: BMC Bioinformatics Year: 2006 Vol: 7 Issue: 1 Pages/record No.: 436
STAR: predicting recombination sites from amino acid sequence
Author: Bauer Denis ; Bodén Mikael ; Thier Ricarda ; Gillam Elizabeth Journal: BMC Bioinformatics Year: 2006 Vol: 7 Issue: 1 Pages/record No.: 437
QualitySNP: a pipeline for detecting single nucleotide polymorphisms and insertions/deletions in EST data from diploid and polyploid species
Author: Tang Jifeng ; Vosman Ben ; Voorrips Roeland ; van der Linden C Gerard ; Leunissen Jack Journal: BMC Bioinformatics Year: 2006 Vol: 7 Issue: 1 Pages/record No.: 438
TreeDyn: towards dynamic graphics and annotations for analyses of trees
Author: Chevenet François ; Brun Christine ; Bañuls Anne-Laure ; Jacq Bernard ; Christen Richard Journal: BMC Bioinformatics Year: 2006 Vol: 7 Issue: 1 Pages/record No.: 439
A graph-search framework for associating gene identifiers with documents
Author: Cohen William ; Minkov Einat Journal: BMC Bioinformatics Year: 2006 Vol: 7 Issue: 1 Pages/record No.: 440
Exhaustive assignment of compositional bias reveals universally prevalent biased regions: analysis of functional associations in human and Drosophila
Author: Harrison Paul Journal: BMC Bioinformatics Year: 2006 Vol: 7 Issue: 1 Pages/record No.: 441
A simple method to combine multiple molecular biomarkers for dichotomous diagnostic classification
Author: Mamtani Manju ; Thakre Tushar ; Kalkonde Mrunal ; Amin Manik ; Kalkonde Yogeshwar ; Amin Amit ; Kulkarni Hemant Journal: BMC Bioinformatics Year: 2006 Vol: 7 Issue: 1 Pages/record No.: 442
GOLEM: an interactive graph-based gene-ontology navigation and analysis tool
Author: Sealfon Rachel ; Hibbs Matthew ; Huttenhower Curtis ; Myers Chad ; Troyanskaya Olga Journal: BMC Bioinformatics Year: 2006 Vol: 7 Issue: 1 Pages/record No.: 443
Testing statistical significance scores of sequence comparison methods with structure similarity
Author: Hulsen Tim ; de Vlieg Jacob ; Leunissen Jack ; Groenen Peter Journal: BMC Bioinformatics Year: 2006 Vol: 7 Issue: 1 Pages/record No.: 444
Analysis of optimal phenotypic space using elementary modes as applied to Corynebacterium glutamicum
Author: Gayen Kalyan ; Venkatesh KV Journal: BMC Bioinformatics Year: 2006 Vol: 7 Issue: 1 Pages/record No.: 445
CpGcluster: a distance-based algorithm for CpG-island detection
Author: Hackenberg Michael ; Previti Christopher ; Luque-Escamilla Pedro ; Carpena Pedro ; Martínez-Aroza José ; Oliver José Journal: BMC Bioinformatics Year: 2006 Vol: 7 Issue: 1 Pages/record No.: 446
Statistical inference of chromosomal homology based on gene colinearity and applications to Arabidopsis and rice
Author: Wang Xiyin ; Shi Xiaoli ; Li Zhe ; Zhu Qihui ; Kong Lei ; Tang Wen ; Ge Song ; Luo Jingchu Journal: BMC Bioinformatics Year: 2006 Vol: 7 Issue: 1 Pages/record No.: 447
Gene function classification using Bayesian models with hierarchy-based priors
Author: Shahbaba Babak ; Neal Radford Journal: BMC Bioinformatics Year: 2006 Vol: 7 Issue: 1 Pages/record No.: 448
Integrative missing value estimation for microarray data
Author: Hu Jianjun ; Li Haifeng ; Waterman Michael ; Zhou Xianghong Journal: BMC Bioinformatics Year: 2006 Vol: 7 Issue: 1 Pages/record No.: 449
Genepi: a blackboard framework for genome annotation
Author: Descorps-Declère Stéphane ; Ziébelin Danielle ; Rechenmann François ; Viari Alain Journal: BMC Bioinformatics Year: 2006 Vol: 7 Issue: 1 Pages/record No.: 450
MIMOX: a web tool for phage display based epitope mapping
Author: Huang Jian ; Gutteridge Alex ; Honda Wataru ; Kanehisa Minoru Journal: BMC Bioinformatics Year: 2006 Vol: 7 Issue: 1 Pages/record No.: 451
A fisheye viewer for microarray-based gene expression data
Author: Wu Min ; Thao Cheng ; Mu Xiangming ; Munson Ethan Journal: BMC Bioinformatics Year: 2006 Vol: 7 Issue: 1 Pages/record No.: 452
REEF: searching REgionally Enriched Features in genomes
Author: Coppe Alessandro ; Danieli Gian Antonio ; Bortoluzzi Stefania Journal: BMC Bioinformatics Year: 2006 Vol: 7 Issue: 1 Pages/record No.: 453
Whole genome association mapping by incompatibilities and local perfect phylogenies
Author: Mailund Thomas ; Besenbacher Søren ; Schierup Mikkel Journal: BMC Bioinformatics Year: 2006 Vol: 7 Issue: 1 Pages/record No.: 454
Building multiclass classifiers for remote homology detection and fold recognition
Author: Rangwala Huzefa ; Karypis George Journal: BMC Bioinformatics Year: 2006 Vol: 7 Issue: 1 Pages/record No.: 455
A framework for protein structure classification and identification of novel protein structures
Author: Kim You ; Patel Jignesh Journal: BMC Bioinformatics Year: 2006 Vol: 7 Issue: 1 Pages/record No.: 456
Comparison of protein interaction networks reveals species conservation and divergence
Author: Liang Zhi ; Xu Meng ; Teng Maikun ; Niu Liwen Journal: BMC Bioinformatics Year: 2006 Vol: 7 Issue: 1 Pages/record No.: 457
NBA-Palm: prediction of palmitoylation site implemented in Naïve Bayes algorithm
Author: Xue Yu ; Chen Hu ; Jin Changjiang ; Sun Zhirong ; Yao Xuebiao Journal: BMC Bioinformatics Year: 2006 Vol: 7 Issue: 1 Pages/record No.: 458
MannDB – A microbial database of automated protein sequence analyses and evidence integration for protein characterization
Author: Zhou Carol ; Lam Marisa ; Smith Jason ; Zemla Adam ; Dyer Matthew ; Kuczmarski Thomas ; Vitalis Elizabeth ; Slezak Thomas Journal: BMC Bioinformatics Year: 2006 Vol: 7 Issue: 1 Pages/record No.: 459
Representing and comparing protein structures as paths in three-dimensional space
Author: Zhi Degui ; Krishna S Sri ; Cao Haibo ; Pevzner Pavel ; Godzik Adam Journal: BMC Bioinformatics Year: 2006 Vol: 7 Issue: 1 Pages/record No.: 460
inGeno – an integrated genome and ortholog viewer for improved genome to genome comparisons
Author: Liang Chunguang ; Dandekar Thomas Journal: BMC Bioinformatics Year: 2006 Vol: 7 Issue: 1 Pages/record No.: 461
Java GUI for InterProScan (JIPS): A tool to help process multiple InterProScans and perform ortholog analysis
Author: Syed Aijazuddin ; Upton Chris Journal: BMC Bioinformatics Year: 2006 Vol: 7 Issue: 1 Pages/record No.: 462
SVRMHC prediction server for MHC-binding peptides
Author: Wan Ji ; Liu Wen ; Xu Qiqi ; Ren Yongliang ; Flower Darren ; Li Tongbin Journal: BMC Bioinformatics Year: 2006 Vol: 7 Issue: 1 Pages/record No.: 463
A summarization approach for Affymetrix GeneChip data using a reference training set from a large, biologically diverse database
Author: Katz Simon ; Irizarry Rafael ; Lin Xue ; Tripputi Mark ; Porter Mark Journal: BMC Bioinformatics Year: 2006 Vol: 7 Issue: 1 Pages/record No.: 464
Meta-All: a system for managing metabolic pathway information
Author: Weise Stephan ; Grosse Ivo ; Klukas Christian ; Koschützki Dirk ; Scholz Uwe ; Schreiber Falk ; Junker Björn Journal: BMC Bioinformatics Year: 2006 Vol: 7 Issue: 1 Pages/record No.: 465
ProFAT: a web-based tool for the functional annotation of protein sequences
Author: Bradshaw Charles ; Surendranath Vineeth ; Habermann Bianca Journal: BMC Bioinformatics Year: 2006 Vol: 7 Issue: 1 Pages/record No.: 466
Goulphar: rapid access and expertise for standard two-color microarray normalization methods
Author: Lemoine Sophie ; Combes Florence ; Servant Nicolas ; Le Crom Stéphane Journal: BMC Bioinformatics Year: 2006 Vol: 7 Issue: 1 Pages/record No.: 467
SNP-PHAGE – High throughput SNP discovery pipeline
Author: Matukumalli Lakshmi ; Grefenstette John ; Hyten David ; Choi Ik-Young ; Cregan Perry ; Van Tassell Curtis Journal: BMC Bioinformatics Year: 2006 Vol: 7 Issue: 1 Pages/record No.: 468
Evaluating different methods of microarray data normalization
Author: Fujita André ; Sato João ; Rodrigues Leonardo ; Ferreira Carlos ; Sogayar Mari Journal: BMC Bioinformatics Year: 2006 Vol: 7 Issue: 1 Pages/record No.: 469
GeneTools – application for functional annotation and statistical hypothesis testing
Author: Beisvag Vidar ; Jünge Frode ; Bergum Hallgeir ; Jølsum Lars ; Lydersen Stian ; Günther Clara-Cecilie ; Ramampiaro Heri ; Langaas Mette ; Sandvik Arne ; Lægreid Astrid Journal: BMC Bioinformatics Year: 2006 Vol: 7 Issue: 1 Pages/record No.: 470
The accuracy of several multiple sequence alignment programs for proteins
Author: Nuin Paulo ; Wang Zhouzhi ; Tillier Elisabeth Journal: BMC Bioinformatics Year: 2006 Vol: 7 Issue: 1 Pages/record No.: 471
CGAT: a comparative genome analysis tool for visualizing alignments in the analysis of complex evolutionary changes between closely related genomes
Author: Uchiyama Ikuo ; Higuchi Toshio ; Kobayashi Ichizo Journal: BMC Bioinformatics Year: 2006 Vol: 7 Issue: 1 Pages/record No.: 472
CAFTAN: a tool for fast mapping, and quality assessment of cDNAs
Author: del Val Coral ; Kuryshev Vladimir ; Glatting Karl-Heinz ; Ernst Peter ; Hotz-Wagenblatt Agnes ; Poustka Annemarie ; Suhai Sandor ; Wiemann Stefan Journal: BMC Bioinformatics Year: 2006 Vol: 7 Issue: 1 Pages/record No.: 473
Annotation, submission and screening of repetitive elements in Repbase: RepbaseSubmitter and Censor
Author: Kohany Oleksiy ; Gentles Andrew ; Hankus Lukasz ; Jurka Jerzy Journal: BMC Bioinformatics Year: 2006 Vol: 7 Issue: 1 Pages/record No.: 474
Normalization and expression changes in predefined sets of proteins using 2D gel electrophoresis: A proteomic study of L-DOPA induced dyskinesia in an animal model of Parkinson's disease using DIGE
Author: Kultima Kim ; Scholz Birger ; Alm Henrik ; Sköld Karl ; Svensson Marcus ; Crossman Alan ; Bezard Erwan ; Andrén Per ; Lönnstedt Ingrid Journal: BMC Bioinformatics Year: 2006 Vol: 7 Issue: 1 Pages/record No.: 475
Using the nucleotide substitution rate matrix to detect horizontal gene transfer
Author: Hamady Micah ; Betterton M ; Knight Rob Journal: BMC Bioinformatics Year: 2006 Vol: 7 Issue: 1 Pages/record No.: 476
Browsing repeats in genomes: Pygram and an application to non-coding region analysis
Author: Durand Patrick ; Mahé Frédéric ; Valin Anne-Sophie ; Nicolas Jacques Journal: BMC Bioinformatics Year: 2006 Vol: 7 Issue: 1 Pages/record No.: 477
Topological basis of signal integration in the transcriptional-regulatory network of the yeast, Saccharomyces cerevisiae
Author: Farkas Illés ; Wu Chuang ; Chennubhotla Chakra ; Bahar Ivet ; Oltvai Zoltán Journal: BMC Bioinformatics Year: 2006 Vol: 7 Issue: 1 Pages/record No.: 478
HybGFS: a hybrid method for genome-fingerprint scanning
Author: Shinoda Kosaku ; Yachie Nozomu ; Masuda Takeshi ; Sugiyama Naoyuki ; Sugimoto Masahiro ; Soga Tomoyoshi ; Tomita Masaru Journal: BMC Bioinformatics Year: 2006 Vol: 7 Issue: 1 Pages/record No.: 479
RiboSubstrates: a web application addressing the cleavage specificities of ribozymes in designated genomes
Author: Lucier Jean-François ; Bergeron Lucien ; Brière Francis ; Ouellette Rodney ; Elela Sherif ; Perreault Jean-Pierre Journal: BMC Bioinformatics Year: 2006 Vol: 7 Issue: 1 Pages/record No.: 480
Mining expressed sequence tags identifies cancer markers of clinical interest
Author: Campagne Fabien ; Skrabanek Lucy Journal: BMC Bioinformatics Year: 2006 Vol: 7 Issue: 1 Pages/record No.: 481
Application of Petri net based analysis techniques to signal transduction pathways
Author: Sackmann Andrea ; Heiner Monika ; Koch Ina Journal: BMC Bioinformatics Year: 2006 Vol: 7 Issue: 1 Pages/record No.: 482
Novel metaheuristic for parameter estimation in nonlinear dynamic biological systems
Author: Rodriguez-Fernandez Maria ; Egea Jose ; Banga Julio Journal: BMC Bioinformatics Year: 2006 Vol: 7 Issue: 1 Pages/record No.: 483
A statistical score for assessing the quality of multiple sequence alignments
Author: Ahola Virpi ; Aittokallio Tero ; Vihinen Mauno ; Uusipaikka Esa Journal: BMC Bioinformatics Year: 2006 Vol: 7 Issue: 1 Pages/record No.: 484
Machine learning techniques in disease forecasting: a case study on rice blast prediction
Author: Kaundal Rakesh ; Kapoor Amar ; Raghava Gajendra Journal: BMC Bioinformatics Year: 2006 Vol: 7 Issue: 1 Pages/record No.: 485
GibbsST: a Gibbs sampling method for motif discovery with enhanced resistance to local optima
Author: Shida Kazuhito Journal: BMC Bioinformatics Year: 2006 Vol: 7 Issue: 1 Pages/record No.: 486
Accurate and unambiguous tag-to-gene mapping in serial analysis of gene expression
Author: Malig Rodrigo ; Varela Cristian ; Agosin Eduardo ; Melo Francisco Journal: BMC Bioinformatics Year: 2006 Vol: 7 Issue: 1 Pages/record No.: 487
Evaluation of clustering algorithms for protein-protein interaction networks
Author: Brohée Sylvain ; van Helden Jacques Journal: BMC Bioinformatics Year: 2006 Vol: 7 Issue: 1 Pages/record No.: 488
A simple spreadsheet-based, MIAME-supportive format for microarray data: MAGE-TAB
Author: Rayner Tim ; Rocca-Serra Philippe ; Spellman Paul ; Causton Helen ; Farne Anna ; Holloway Ele ; Irizarry Rafael ; Liu Junmin ; Maier Donald ; Miller Michael ; Petersen Kjell ; Quackenbush John ; Sherlock Gavin ; Stoeckert Christian ; White Joseph ; Whetzel Patricia ; Wymore Farrell ; Parkinson Helen ; Sarkans Ugis ; Ball Catherine ; Brazma Alvis Journal: BMC Bioinformatics Year: 2006 Vol: 7 Issue: 1 Pages/record No.: 489
XML schemas for common bioinformatic data types and their application in workflow systems
Author: Seibel Philipp ; Krüger Jan ; Hartmeier Sven ; Schwarzer Knut ; Löwenthal Kai ; Mersch Henning ; Dandekar Thomas ; Giegerich Robert Journal: BMC Bioinformatics Year: 2006 Vol: 7 Issue: 1 Pages/record No.: 490
Assessing protein similarity with Gene Ontology and its use in subnuclear localization prediction
Author: Lei Zhengdeng ; Dai Yang Journal: BMC Bioinformatics Year: 2006 Vol: 7 Issue: 1 Pages/record No.: 491
Automated recognition of malignancy mentions in biomedical literature
Author: Jin Yang ; McDonald Ryan ; Lerman Kevin ; Mandel Mark ; Carroll Steven ; Liberman Mark ; Pereira Fernando ; Winters Raymond ; White Peter Journal: BMC Bioinformatics Year: 2006 Vol: 7 Issue: 1 Pages/record No.: 492
A method for rapid similarity analysis of RNA secondary structures
Author: Liu Na ; Wang Tianming Journal: BMC Bioinformatics Year: 2006 Vol: 7 Issue: 1 Pages/record No.: 493
Time scale and dimension analysis of a budding yeast cell cycle model
Author: Lovrics Anna ; Csikász-Nagy Attila ; Zsély István ; Zádor Judit ; Turányi Tamás ; Novák Béla Journal: BMC Bioinformatics Year: 2006 Vol: 7 Issue: 1 Pages/record No.: 494
DWARF – a data warehouse system for analyzing protein families
Author: Fischer Markus ; Thai Quan ; Grieb Melanie ; Pleiss Jürgen Journal: BMC Bioinformatics Year: 2006 Vol: 7 Issue: 1 Pages/record No.: 495
methBLAST and methPrimerDB: web-tools for PCR based methylation analysis
Author: Pattyn Filip ; Hoebeeck Jasmien ; Robbrecht Piet ; Michels Evi ; De Paepe Anne ; Bottu Guy ; Coornaert David ; Herzog Robert ; Speleman Frank ; Vandesompele Jo Journal: BMC Bioinformatics Year: 2006 Vol: 7 Issue: 1 Pages/record No.: 496
cPath: open source software for collecting, storing, and querying biological pathways
Author: Cerami Ethan ; Bader Gary ; Gross Benjamin ; Sander Chris Journal: BMC Bioinformatics Year: 2006 Vol: 7 Issue: 1 Pages/record No.: 497
4SALE – A tool for synchronous RNA sequence and secondary structure alignment and editing
Author: Seibel Philipp ; Müller Tobias ; Dandekar Thomas ; Schultz Jörg ; Wolf Matthias Journal: BMC Bioinformatics Year: 2006 Vol: 7 Issue: 1 Pages/record No.: 498
State of the art: refinement of multiple sequence alignments
Author: Chakrabarti Saikat ; Lanczycki Christopher ; Panchenko Anna ; Przytycka Teresa ; Thiessen Paul ; Bryant Stephen Journal: BMC Bioinformatics Year: 2006 Vol: 7 Issue: 1 Pages/record No.: 499
PathogenMIPer: a tool for the design of molecular inversion probes to detect multiple pathogens
Author: Thiyagarajan Sreedevi ; Karhanek Miloslav ; Akhras Michael ; Davis Ronald ; Pourmand Nader Journal: BMC Bioinformatics Year: 2006 Vol: 7 Issue: 1 Pages/record No.: 500
Predicting Class II MHC-Peptide binding: a kernel based approach using similarity scores
Author: Salomon Jesper ; Flower Darren Journal: BMC Bioinformatics Year: 2006 Vol: 7 Issue: 1 Pages/record No.: 501
A correlated motif approach for finding short linear motifs from protein interaction networks
Author: Tan Soon-Heng ; Hugo Willy ; Sung Wing-Kin ; Ng See-Kiong Journal: BMC Bioinformatics Year: 2006 Vol: 7 Issue: 1 Pages/record No.: 502
Predicting residue contacts using pragmatic correlated mutations method: reducing the false positives
Author: Kundrotas Petras ; Alexov Emil Journal: BMC Bioinformatics Year: 2006 Vol: 7 Issue: 1 Pages/record No.: 503
A comparative analysis of the information content in long and short SAGE libraries
Author: Li Yi-Ju ; Xu Puting ; Qin Xuejun ; Schmechel Donald ; Hulette Christine ; Haines Jonathan ; Pericak-Vance Margaret ; Gilbert John Journal: BMC Bioinformatics Year: 2006 Vol: 7 Issue: 1 Pages/record No.: 504
Using local gene expression similarities to discover regulatory binding site modules
Author: Wilczyński Bartek ; Hvidsten Torgeir ; Kryshtafovych Andriy ; Tiuryn Jerzy ; Komorowski Jan ; Fidelis Krzysztof Journal: BMC Bioinformatics Year: 2006 Vol: 7 Issue: 1 Pages/record No.: 505
Visual setup of logical models of signaling and regulatory networks with ProMoT
Author: Saez-Rodriguez Julio ; Mirschel Sebastian ; Hemenway Rebecca ; Klamt Steffen ; Gilles Ernst ; Ginkel Martin Journal: BMC Bioinformatics Year: 2006 Vol: 7 Issue: 1 Pages/record No.: 506
Novel methods for secondary structure determination using low wavelength (VUV) circular dichroism spectroscopic data
Author: Lees Jonathan ; Miles Andrew ; Janes Robert ; Wallace B Journal: BMC Bioinformatics Year: 2006 Vol: 7 Issue: 1 Pages/record No.: 507
IntNetDB v1.0: an integrated protein-protein interaction network database generated by a probabilistic model
Author: Xia Kai ; Dong Dong ; Han Jing-Dong Journal: BMC Bioinformatics Year: 2006 Vol: 7 Issue: 1 Pages/record No.: 508
CoXpress: differential co-expression in gene expression data
Author: Watson Michael Journal: BMC Bioinformatics Year: 2006 Vol: 7 Issue: 1 Pages/record No.: 509
Connectivity independent protein-structure alignment: a hierarchical approach
Author: Kolbeck Bjoern ; May Patrick ; Schmidt-Goenner Tobias ; Steinke Thomas ; Knapp Ernst-Walter Journal: BMC Bioinformatics Year: 2006 Vol: 7 Issue: 1 Pages/record No.: 510
Statistical analysis of an RNA titration series evaluates microarray precision and sensitivity on a whole-array basis
Author: Holloway Andrew ; Oshlack Alicia ; Diyagama Dileepa ; Bowtell David ; Smyth Gordon Journal: BMC Bioinformatics Year: 2006 Vol: 7 Issue: 1 Pages/record No.: 511
Systematic assignment of thermodynamic constraints in metabolic network models
Author: Kümmel Anne ; Panke Sven ; Heinemann Matthias Journal: BMC Bioinformatics Year: 2006 Vol: 7 Issue: 1 Pages/record No.: 512
JUICE: a data management system that facilitates the analysis of large volumes of information in an EST project workflow
Author: Latorre Mariano ; Silva Herman ; Saba Juan ; Guziolowski Carito ; Vizoso Paula ; Martinez Veronica ; Maldonado Jonathan ; Morales Andrea ; Caroca Rodrigo ; Cambiazo Veronica ; Campos-Vargas Reinaldo ; Gonzalez Mauricio ; Orellana Ariel ; Retamales Julio ; Meisel Lee Journal: BMC Bioinformatics Year: 2006 Vol: 7 Issue: 1 Pages/record No.: 513
A hierarchical Naïve Bayes Model for handling sample heterogeneity in classification problems: an application to tissue microarrays
Author: Demichelis Francesca ; Magni Paolo ; Piergiorgi Paolo ; Rubin Mark ; Bellazzi Riccardo Journal: BMC Bioinformatics Year: 2006 Vol: 7 Issue: 1 Pages/record No.: 514
SigFlux: A novel network feature to evaluate the importance of proteins in signal transduction networks
Author: Liu Wei ; Li Dong ; Zhang Jiyang ; Zhu Yunping ; He Fuchu Journal: BMC Bioinformatics Year: 2006 Vol: 7 Issue: 1 Pages/record No.: 515
Integrated siRNA design based on surveying of features associated with high RNAi effectiveness
Author: Gong Wuming ; Ren Yongliang ; Xu Qiqi ; Wang Yejun ; Lin Dong ; Zhou Haiyan ; Li Tongbin Journal: BMC Bioinformatics Year: 2006 Vol: 7 Issue: 1 Pages/record No.: 516
Correcting ligands, metabolites, and pathways
Author: Ott Martin ; Vriend Gert Journal: BMC Bioinformatics Year: 2006 Vol: 7 Issue: 1 Pages/record No.: 517
Prediction of protein submitochondria locations by hybridizing pseudo-amino acid composition with various physicochemical features of segmented sequence
Author: Du Pufeng ; Li Yanda Journal: BMC Bioinformatics Year: 2006 Vol: 7 Issue: 1 Pages/record No.: 518
Inferring topology from clustering coefficients in protein-protein interaction networks
Author: Friedel Caroline ; Zimmer Ralf Journal: BMC Bioinformatics Year: 2006 Vol: 7 Issue: 1 Pages/record No.: 519
An accurate and interpretable model for siRNA efficacy prediction
Author: Vert Jean-Philippe ; Foveau Nicolas ; Lajaunie Christian ; Vandenbrouck Yves Journal: BMC Bioinformatics Year: 2006 Vol: 7 Issue: 1 Pages/record No.: 520
Dynamic variable selection in SNP genotype autocalling from APEX microarray data
Author: Podder Mohua ; Welch William ; Zamar Ruben ; Tebbutt Scott Journal: BMC Bioinformatics Year: 2006 Vol: 7 Issue: 1 Pages/record No.: 521
Cis-motifs upstream of the transcription and translation initiation sites are effectively revealed by their positional disequilibrium in eukaryote genomes using frequency distribution curves
Author: Berendzen Kenneth ; Stüber Kurt ; Harter Klaus ; Wanke Dierk Journal: BMC Bioinformatics Year: 2006 Vol: 7 Issue: 1 Pages/record No.: 522
BioMoby extensions to the Taverna workflow management and enactment software
Author: Kawas Edward ; Senger Martin ; Wilkinson Mark Journal: BMC Bioinformatics Year: 2006 Vol: 7 Issue: 1 Pages/record No.: 523
Improvement in accuracy of multiple sequence alignment using novel group-to-group sequence alignment algorithm with piecewise linear gap cost
Author: Yamada Shinsuke ; Gotoh Osamu ; Yamana Hayato Journal: BMC Bioinformatics Year: 2006 Vol: 7 Issue: 1 Pages/record No.: 524
iHAP – integrated haplotype analysis pipeline for characterizing the haplotype structure of genes
Author: Song Chun Meng ; Yeo Boon Huat ; Tantoso Erwin ; Yang Yuchen ; Lim Yun Ping ; Li Kuo-Bin ; Rajagopal Gunaretnam Journal: BMC Bioinformatics Year: 2006 Vol: 7 Issue: 1 Pages/record No.: 525
Chromosomal patterns of gene expression from microarray data: methodology, validation and clinical relevance in gliomas
Author: Turkheimer Federico ; Roncaroli Federico ; Hennuy Benoit ; Herens Christian ; Nguyen Minh ; Martin Didier ; Evrard Annick ; Bours Vincent ; Boniver Jacques ; Deprez Manuel Journal: BMC Bioinformatics Year: 2006 Vol: 7 Issue: 1 Pages/record No.: 526
Logarithmic gap costs decrease alignment accuracy
Author: Cartwright Reed Journal: BMC Bioinformatics Year: 2006 Vol: 7 Issue: 1 Pages/record No.: 527
A specialized learner for inferring structured cis-regulatory modules
Author: Noto Keith ; Craven Mark Journal: BMC Bioinformatics Year: 2006 Vol: 7 Issue: 1 Pages/record No.: 528
Fast estimation of the difference between two PAM/JTT evolutionary distances in triplets of homologous sequences
Author: Dessimoz Christophe ; Gil Manuel ; Schneider Adrian ; Gonnet Gaston Journal: BMC Bioinformatics Year: 2006 Vol: 7 Issue: 1 Pages/record No.: 529
MathDAMP: a package for differential analysis of metabolite profiles
Author: Baran Richard ; Kochi Hayataro ; Saito Natsumi ; Suematsu Makoto ; Soga Tomoyoshi ; Nishioka Takaaki ; Robert Martin ; Tomita Masaru Journal: BMC Bioinformatics Year: 2006 Vol: 7 Issue: 1 Pages/record No.: 530
The NeuARt II system: a viewing tool for neuroanatomical data based on published neuroanatomical atlases
Author: Burns Gully ; Cheng Wei-Cheng ; Thompson Richard ; Swanson Larry Journal: BMC Bioinformatics Year: 2006 Vol: 7 Issue: 1 Pages/record No.: 531
Model-driven user interfaces for bioinformatics data resources: regenerating the wheel as an alternative to reinventing it
Author: Garwood Kevin ; Garwood Christopher ; Hedeler Cornelia ; Griffiths Tony ; Swainston Neil ; Oliver Stephen ; Paton Norman Journal: BMC Bioinformatics Year: 2006 Vol: 7 Issue: 1 Pages/record No.: 532
Effect of various normalization methods on Applied Biosystems expression array system data
Author: Barbacioru Catalin ; Wang Yulei ; Canales Roger ; Sun Yongming ; Keys David ; Chan Frances ; Poulter Karen ; Samaha Raymond Journal: BMC Bioinformatics Year: 2006 Vol: 7 Issue: 1 Pages/record No.: 533
iHOPerator: user-scripting a personalized bioinformatics Web, starting with the iHOP website
Author: Good Benjamin ; Kawas Edward ; Kuo Byron ; Wilkinson Mark Journal: BMC Bioinformatics Year: 2006 Vol: 7 Issue: 1 Pages/record No.: 534
PageMan: An interactive ontology tool to generate, display, and annotate overview graphs for profiling experiments
Author: Usadel Björn ; Nagel Axel ; Steinhauser Dirk ; Gibon Yves ; Bläsing Oliver ; Redestig Henning ; Sreenivasulu Nese ; Krall Leonard ; Hannah Matthew ; Poree Fabien ; Fernie Alisdair ; Stitt Mark Journal: BMC Bioinformatics Year: 2006 Vol: 7 Issue: 1 Pages/record No.: 535
TaxMan: a taxonomic database manager
Author: Jones Martin ; Blaxter Mark Journal: BMC Bioinformatics Year: 2006 Vol: 7 Issue: 1 Pages/record No.: 536
Empirical study of supervised gene screening
Author: Ma Shuangge Journal: BMC Bioinformatics Year: 2006 Vol: 7 Issue: 1 Pages/record No.: 537
Intensity-based hierarchical Bayes method improves testing for differentially expressed genes in microarray experiments
Author: Sartor Maureen ; Tomlinson Craig ; Wesselkamper Scott ; Sivaganesan Siva ; Leikauf George ; Medvedovic Mario Journal: BMC Bioinformatics Year: 2006 Vol: 7 Issue: 1 Pages/record No.: 538
A minimally invasive multiple marker approach allows highly efficient detection of meningioma tumors
Author: Keller Andreas ; Ludwig Nicole ; Comtesse Nicole ; Hildebrandt Andreas ; Meese Eckart ; Lenhof Hans-Peter Journal: BMC Bioinformatics Year: 2006 Vol: 7 Issue: 1 Pages/record No.: 539
A method for estimation of elasticities in metabolic networks using steady state and dynamic metabolomics data and linlog kinetics
Author: Nikerel I Emrah ; van Winden Wouter ; van Gulik Walter ; Heijnen Joseph Journal: BMC Bioinformatics Year: 2006 Vol: 7 Issue: 1 Pages/record No.: 540
How repetitive are genomes?
Author: Haubold Bernhard ; Wiehe Thomas Journal: BMC Bioinformatics Year: 2006 Vol: 7 Issue: 1 Pages/record No.: 541
HaploRec: efficient and accurate large-scale reconstruction of haplotypes
Author: Eronen Lauri ; Geerts Floris ; Toivonen Hannu Journal: BMC Bioinformatics Year: 2006 Vol: 7 Issue: 1 Pages/record No.: 542
Recursive gene selection based on maximum margin criterion: a comparison with SVM-RFE
Author: Niijima Satoshi ; Kuhara Satoru Journal: BMC Bioinformatics Year: 2006 Vol: 7 Issue: 1 Pages/record No.: 543
The Virtual Insect Brain protocol: creating and comparing standardized neuroanatomy
Author: Jenett Arnim ; Schindelin Johannes ; Heisenberg Martin Journal: BMC Bioinformatics Year: 2006 Vol: 7 Issue: 1 Pages/record No.: 544
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