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BMC Bioinformatics
ISSN: 14712105
Subject:
Biology
Publisher: BioMed Central
Country: United Kingdom
Language: English
Keywords: bioinformatics, biology
Start Year: 2000
License: 
Year: 2006 - Volume:
7 - Issue: 1
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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