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Editor-in-Chief
Melissa Norton, MD Biology Editor
Penelope Webb, PhD In-house Editor
Danielle Burgess PhD
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| | BMC Bioinformatics, Volume 7 |
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Research article
  
Testing statistical significance scores of sequence comparison methods with structure similarity
Tim Hulsen, Jacob de Vlieg, Jack AM Leunissen, Peter MA Groenen
BMC Bioinformatics 2006, 7:444 (12October2006)
[Abstract] [Full text] [PDF] [PubMed] [Related articles] [Cited on BioMed Central]
Software
GOLEM: an interactive graph-based gene-ontology navigation and analysis tool
Rachel SG Sealfon, Matthew A Hibbs, Curtis Huttenhower, Chad L Myers, Olga G Troyanskaya
BMC Bioinformatics 2006, 7:443 (10October2006)
[Abstract] [Full text] [PDF] [PubMed] [Related articles] [Cited on BioMed Central]
Methodology article
A simple method to combine multiple molecular biomarkers for dichotomous diagnostic classification
Manju R Mamtani, Tushar P Thakre, Mrunal Y Kalkonde, Manik A Amin, Yogeshwar V Kalkonde, Amit P Amin, Hemant Kulkarni
BMC Bioinformatics 2006, 7:442 (10October2006)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
Research article
Exhaustive assignment of compositional bias reveals universally prevalent biased regions: analysis of functional associations in human and Drosophila
Paul M Harrison
BMC Bioinformatics 2006, 7:441 (10October2006)
[Abstract] [Full text] [PDF] [PubMed] [Related articles] [Cited on BioMed Central]
Methodology article
A graph-search framework for associating gene identifiers with documents
William W Cohen, Einat Minkov
BMC Bioinformatics 2006, 7:440 (10October2006)
[Abstract] [Full text] [PDF] [PubMed] [Related articles] [Cited on BioMed Central]
Software
TreeDyn: towards dynamic graphics and annotations for analyses of trees
Fran ois Chevenet, Christine Brun, Anne-Laure Ba uls, Bernard Jacq, Richard Christen
BMC Bioinformatics 2006, 7:439 (10October2006)
[Abstract] [Full text] [PDF] [PubMed] [Related articles] [Cited on BioMed Central]
Software
QualitySNP: a pipeline for detecting single nucleotide polymorphisms and insertions/deletions in EST data from diploid and polyploid species
Jifeng Tang, Ben Vosman, Roeland E Voorrips, C Gerard van der Linden, Jack AM Leunissen
BMC Bioinformatics 2006, 7:438 (9October2006)
[Abstract] [Full text] [PDF] [PubMed] [Related articles] [Cited on BioMed Central]
Software
STAR: predicting recombination sites from amino acid sequence
Denis C Bauer, Mikael Bod n, Ricarda Thier, Elizabeth M Gillam
BMC Bioinformatics 2006, 7:437 (8October2006)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
Database
ORENZA: a web resource for studying ORphan ENZyme activities
Olivier Lespinet, Bernard Labedan
BMC Bioinformatics 2006, 7:436 (6October2006)
[Abstract] [Full text] [PDF] [PubMed] [Related articles] [Cited on BioMed Central]
Methodology article
Coloring the Mu transpososome
Isabel K Darcy, Jeff Chang, Nathan Druivenga, Colin McKinney, Ram K Medikonduri, Stacy Mills, Junalyn Navarra-Madsen, Arun Ponnusamy, Jesse Sweet, Travis Thompson
BMC Bioinformatics 2006, 7:435 (5October2006)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
Methodology article
Rank-statistics based enrichment-site prediction algorithm developed for chromatin immunoprecipitation on chip experiments
Srinka Ghosh, Heather A Hirsch, Edward Sekinger, Kevin Struhl, Thomas R Gingeras
BMC Bioinformatics 2006, 7:434 (5October2006)
[Abstract] [Full text] [PDF] [PubMed] [Related articles] [Cited on BioMed Central]
Software
M-GCAT: interactively and efficiently constructing large-scale multiple genome comparison frameworks in closely related species
Todd J Treangen, Xavier Messeguer
BMC Bioinformatics 2006, 7:433 (5October2006)
[Abstract] [Full text] [PDF] [PubMed] [Related articles] [Cited on BioMed Central]
Research article
Feature selection using Haar wavelet power spectrum
Prabakaran Subramani, Rajendra Sahu, Shekhar Verma
BMC Bioinformatics 2006, 7:432 (5October2006)
[Abstract] [Full text] [PDF] [PubMed] [Related articles] [Cited on BioMed Central]
Software
The BiSearch web server
Tam s Arnyi, Andrs Vradi, Istvn Simon, Gbor E Tusndy
BMC Bioinformatics 2006, 7:431 (5October2006)
[Abstract] [Full text] [PDF] [PubMed] [Related articles] [Cited on BioMed Central]
Software
Development of an open source laboratory information management system for 2-D gel electrophoresis-based proteomics workflow
Hiraku Morisawa, Mikako Hirota, Tosifusa Toda
BMC Bioinformatics 2006, 7:430 (4October2006)
[Abstract] [Full text] [PDF] [PubMed] [Related articles] [Cited on BioMed Central]
Methodology article
Design of a combinatorial DNA microarray for protein-DNA interaction studies
Julian Mintseris, Michael B Eisen
BMC Bioinformatics 2006, 7:429 (3October2006)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
Software
XRate: a fast prototyping, training and annotation tool for phylo-grammars
Peter S Klosterman, Andrew V Uzilov, Yuri R Bendaa, Robert K Bradley, Sharon Chao, Carolin Kosiol, Nick Goldman, Ian Holmes
BMC Bioinformatics 2006, 7:428 (3October2006)
[Abstract] [Full text] [PDF] [PubMed] [Related articles] [Cited on BioMed Central]
Software
MICA: desktop software for comprehensive searching of DNA databases
William A Stokes, Benjamin S Glick
BMC Bioinformatics 2006, 7:427 (3October2006)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
Methodology article
Grouping Gene Ontology terms to improve the assessment of gene set enrichment in microarray data
Alex Lewin, Ian C Grieve
BMC Bioinformatics 2006, 7:426 (3October2006)
[Abstract] [Full text] [PDF] [PubMed] [Related articles] [Cited on BioMed Central]
Research article
Predicting residue-wise contact orders in proteins by support vector regression
Jiangning Song, Kevin Burrage
BMC Bioinformatics 2006, 7:425 (3October2006)
[Abstract] [Full text] [PDF] [PubMed] [Related articles] [Cited on BioMed Central]
Software
PubFocus: semantic MEDLINE/PubMed citations analytics through integration of controlled biomedical dictionaries and ranking algorithm
Maksim V Plikus, Zina Zhang, Cheng-Ming Chuong
BMC Bioinformatics 2006, 7:424 (2October2006)
[Abstract] [Full text] [PDF] [PubMed] [Related articles] [Cited on BioMed Central]
Research article
Detection of prokaryotic promoters from the genomic distribution of hexanucleotide pairs
Pierre- tienne Jacques, Sbastien Rodrigue, Luc Gaudreau, Jean Goulet, Ryszard Brzezinski
BMC Bioinformatics 2006, 7:423 (2October2006)
[Abstract] [Full text] [PDF] [PubMed] [Related articles] [Cited on BioMed Central]
Methodology article
Analysis with respect to instrumental variables for the exploration of microarray data structures
Florent Baty, Micha l Facompr, Jan Wiegand, Joseph Schwager, Martin H Brutsche
BMC Bioinformatics 2006, 7:422 (29September2006)
[Abstract] [Full text] [PDF] [PubMed] [Related articles] [Cited on BioMed Central]
Research article
Computational reconstruction of transcriptional regulatory modules of the yeast cell cycle
Wei-Sheng Wu, Wen-Hsiung Li, Bor-Sen Chen
BMC Bioinformatics 2006, 7:421 (29September2006)
[Abstract] [Full text] [PDF] [PubMed] [Related articles] [Cited on BioMed Central]
Research article
Comparative assessment of performance and genome dependence among phylogenetic profiling methods
Evan S Snitkin, Adam M Gustafson, Joseph Mellor, Jie Wu, Charles DeLisi
BMC Bioinformatics 2006, 7:420 (27September2006)
[Abstract] [Full text] [PDF] [PubMed] [Related articles] [Cited on BioMed Central]
Research article
A machine learning strategy to identify candidate binding sites in human protein-coding sequence
Thomas Down, Bernard Leong, Tim JP Hubbard
BMC Bioinformatics 2006, 7:419 (26September2006)
[Abstract] [Full text] [PDF] [PubMed] [Related articles] [Cited on BioMed Central]
Software
CROPPER: a metagene creator resource for cross-platform and cross-species compendium studies
Jussi Paananen, Markus Storvik, Garry Wong
BMC Bioinformatics 2006, 7:418 (22September2006)
[Abstract] [Full text] [PDF] [PubMed] [Related articles] [Cited on BioMed Central]
Research article
Searching for interpretable rules for disease mutations: a simulated annealing bump hunting strategy
Rui Jiang, Hua Yang, Fengzhu Sun, Ting Chen
BMC Bioinformatics 2006, 7:417 (19September2006)
[Abstract] [Full text] [PDF] [PubMed] [Related articles] [Cited on BioMed Central]
Methodology article
Genomes as geography: using GIS technology to build interactive genome feature maps
Mary E Dolan, Constance C Holden, M Kate Beard, Carol J Bult
BMC Bioinformatics 2006, 7:416 (19September2006)
[Abstract] [Full text] [PDF] [PubMed] [Related articles] [Cited on BioMed Central]
Correspondence
Quantification of the variation in percentage identity for protein sequence alignments
GPS Raghava, Geoffrey J Barton
BMC Bioinformatics 2006, 7:415 (19September2006)
[Abstract] [Full text] [PDF] [PubMed] [Related articles] [Cited on BioMed Central]
Methodology article
Semi-supervised discovery of differential genes
Shigeyuki Oba, Shin lshii
BMC Bioinformatics 2006, 7:414 (18September2006)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
Research article
Correlated fragile site expression allows the identification of candidate fragile genes involved in immunity and associated with carcinogenesis
Angela Re, Davide Cora, Alda Maria Puliti, Michele Caselle, Isabella Sbrana
BMC Bioinformatics 2006, 7:413 (18September2006)
[Abstract] [Full text] [PDF] [PubMed] [Related articles] [Cited on BioMed Central]
Research article
Detecting recombination in evolving nucleotide sequences
Cheong Xin Chan, Robert G Beiko, Mark A Ragan
BMC Bioinformatics 2006, 7:412 (18September2006)
[Abstract] [Full text] [PDF] [PubMed] [Related articles] [Cited on BioMed Central]
Software
miTarget: microRNA target gene prediction using a support vector machine
Sung-Kyu Kim, Jin-Wu Nam, Je-Keun Rhee, Wha-Jin Lee, Byoung-Tak Zhang
BMC Bioinformatics 2006, 7:411 (18September2006)
[Abstract] [Full text] [PDF] [PubMed] [Related articles] [Cited on BioMed Central]
Research article
Application of protein structure alignments to iterated hidden Markov model protocols for structure prediction
Eric D Scheeff, Philip E Bourne
BMC Bioinformatics 2006, 7:410 (14September2006)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
Software
Genome-wide DNA polymorphism analyses using VariScan
Stephan Hutter, Albert J Vilella, Julio Rozas
BMC Bioinformatics 2006, 7:409 (12September2006)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
Software
Scanning sequences after Gibbs sampling to find multiple occurrences of functional elements
Kannan Tharakaraman, Leonardo Mario-Ram rez, Sergey L Sheetlin, David Landsman, John L Spouge
BMC Bioinformatics 2006, 7:408 (8September2006)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
Research article
Identifying genes that contribute most to good classification in microarrays
Stuart G Baker, Barnett S Kramer
BMC Bioinformatics 2006, 7:407 (7September2006)
[Abstract] [Full text] [PDF] [PubMed] [Related articles] [Cited on BioMed Central]
Correction
Correction: genetic algorithm learning as a robust approach to RNA editing site site prediction
James Thompson, Shuba Gopal
BMC Bioinformatics 2006, 7:406 (6September2006)
[Abstract] [Full text] [PDF] [PubMed] [Related articles] [Cited on BioMed Central]
Research article
Predicting the effect of missense mutations on protein function: analysis with Bayesian networks
Chris J Needham, James R Bradford, Andrew J Bulpitt, Matthew A Care, David R Westhead
BMC Bioinformatics 2006, 7:405 (6September2006)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
Software
RDMAS: a web server for RNA deleterious mutation analysis
Wenjie Shu, Xiaochen Bo, Rujia Liu, Dongsheng Zhao, Zhiqiang Zheng, Shengqi Wang
BMC Bioinformatics 2006, 7:404 (6September2006)
[Abstract] [Full text] [PDF] [PubMed] [Related articles] [Cited on BioMed Central]
Software
A database application for pre-processing, storage and comparison of mass spectra derived from patients and controls
Mark K Titulaer, Ivar Siccama, Lennard J Dekker, Angelique LCT van Rijswijk, Ron MA Heeren, Peter A Sillevis Smitt, Theo M Luider
BMC Bioinformatics 2006, 7:403 (5September2006)
[Abstract] [Full text] [PDF] [PubMed] [Related articles] [Cited on BioMed Central]
Software
Distill: a suite of web servers for the prediction of one-, two- and three-dimensional structural features of proteins
Davide Ba , Alberto JM Martin, Catherine Mooney, Alessandro Vullo, Ian Walsh, Gianluca Pollastri
BMC Bioinformatics 2006, 7:402 (5September2006)
[Abstract] [Full text] [PDF] [PubMed] [Related articles] [Cited on BioMed Central]
Software
CRNPRED: highly accurate prediction of one-dimensional protein structures by large-scale critical random networks
Akira R Kinjo, Ken Nishikawa
BMC Bioinformatics 2006, 7:401 (5September2006)
[Abstract] [Full text] [PDF] [PubMed] [Related articles] [Cited on BioMed Central] [1 comment]
Methodology article
Efficient pairwise RNA structure prediction and alignment using sequence alignment constraints
Robin D Dowell, Sean R Eddy
BMC Bioinformatics 2006, 7:400 (4September2006)
[Abstract] [Full text] [PDF] [PubMed] [Related articles] [Cited on BioMed Central]
Research article
Cancer diagnosis marker extraction for soft tissue sarcomas based on gene expression profiling data by using projective adaptive resonance theory (PART) filtering method
Hiro Takahashi, Takeshi Nemoto, Teruhiko Yoshida, Hiroyuki Honda, Tadashi Hasegawa
BMC Bioinformatics 2006, 7:399 (4September2006)
[Abstract] [Full text] [PDF] [PubMed] [Related articles] [Cited on BioMed Central]
Database
PhyloPat: phylogenetic pattern analysis of eukaryotic genes
Tim Hulsen, Jacob de Vlieg, Peter MA Groenen
BMC Bioinformatics 2006, 7:398 (1September2006)
[Abstract] [Full text] [PDF] [PubMed] [Related articles] [Cited on BioMed Central]
Methodology article
Methods for evaluating clustering algorithms for gene expression data using a reference set of functional classes
Susmita Datta, Somnath Datta
BMC Bioinformatics 2006, 7:397 (31August2006)
[Abstract] [Full text] [PDF] [PubMed] [Related articles] [Cited on BioMed Central]
Software
Predicting transcription factor binding sites using local over-representation and comparative genomics
Matthieu Defrance, Hl ne Touzet
BMC Bioinformatics 2006, 7:396 (31August2006)
[Abstract] [Full text] [PDF] [PubMed] [Related articles] [Cited on BioMed Central]
Commentary
Probe set algorithms: is there a rational best bet?
Jinwook Seo, Eric P Hoffman
BMC Bioinformatics 2006, 7:395 (30August2006)
[Abstract] [Full text] [PDF] [PubMed] [Related articles] [Cited on BioMed Central]
Research article
Mining frequent patterns for AMP-activated protein kinase regulation on skeletal muscle
Qingfeng Chen, Yi-Ping Phoebe Chen
BMC Bioinformatics 2006, 7:394 (30August2006)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
Methodology article
A probabilistic classifier for olfactory receptor pseudogenes
Idan Menashe, Ronny Aloni, Doron Lancet
BMC Bioinformatics 2006, 7:393 (29August2006)
[Abstract] [Full text] [PDF] [PubMed] [Related articles] [Cited on BioMed Central]
Software
GeneLibrarian: an effective gene-information summarization and visualization system
Jung-Hsien Chiang, Jyh-Wei Shin, Heng-Hui Liu, Chong-Liang Chin
BMC Bioinformatics 2006, 7:392 (29August2006)
[Abstract] [Full text] [PDF] [PubMed] [Related articles] [Cited on BioMed Central]
Research article
Probe-level linear model fitting and mixture modeling results in high accuracy detection of differential gene expression
Sbastien Lemieux
BMC Bioinformatics 2006, 7:391 (25August2006)
[Abstract] [Full text] [PDF] [PubMed] [Related articles] [Cited on BioMed Central]
Software
PET-Tool: a software suite for comprehensive processing and managing of Paired-End diTag (PET) sequence data
Kuo Ping Chiu, Chee-Hong Wong, Qiongyu Chen, Pramila Ariyaratne, Hong Sain Ooi, Chia-Lin Wei, Wing-Kin Ken Sung, Yijun Ruan
BMC Bioinformatics 2006, 7:390 (25August2006)
[Abstract] [Full text] [PDF] [PubMed] [Related articles] [Cited on BioMed Central]
Methodology article
Fast index based algorithms and software for matching position specific scoring matrices
Michael Beckstette, Robert Homann, Robert Giegerich, Stefan Kurtz
BMC Bioinformatics 2006, 7:389 (24August2006)
[Abstract] [Full text] [PDF] [PubMed] [Related articles] [Cited on BioMed Central]
Methodology article
Selecting normalization genes for small diagnostic microarrays
Jochen Jaeger, Rainer Spang
BMC Bioinformatics 2006, 7:388 (22August2006)
[Abstract] [Full text] [PDF] [PubMed] [Related articles] [Cited on BioMed Central]
Research article
On the statistical assessment of classifiers using DNA microarray data
N Ancona, R Maglietta, A Piepoli, A D'Addabbo, R Cotugno, M Savino, S Liuni, M Carella, G Pesole, F Perri
BMC Bioinformatics 2006, 7:387 (19August2006)
[Abstract] [Full text] [PDF] [PubMed] [Related articles] [Cited on BioMed Central]
Research article
Hierarchical modularity of nested bow-ties in metabolic networks
Jing Zhao, Hong Yu, Jian-Hua Luo, Zhi-Wei Cao, Yi-Xue Li
BMC Bioinformatics 2006, 7:386 (18August2006)
[Abstract] [Full text] [PDF] [PubMed] [Related articles] [Cited on BioMed Central]
Methodology article
Incorporating background frequency improves entropy-based residue conservation measures
Kai Wang, Ram Samudrala
BMC Bioinformatics 2006, 7:385 (17August2006)
[Abstract] [Full text] [PDF] [PubMed] [Related articles] [Cited on BioMed Central]
Methodology article
Analysis of promoter regions of co-expressed genes identified by microarray analysis
Srinivas Veerla, Mattias H glund
BMC Bioinformatics 2006, 7:384 (17August2006)
[Abstract] [Full text] [PDF] [PubMed] [Related articles] [Cited on BioMed Central]
Software
Laboratory Information Management Software for genotyping workflows: applications in high throughput crop genotyping
B Jayashree, Praveen T Reddy, Y Leeladevi, Jonathan H Crouch, V Mahalakshmi, Hutokshi K Buhariwalla, KE Eshwar, Emma Mace, Rolf Folksterma, S Senthilvel, Rajeev K Varshney, K Seetha, R Rajalakshmi, VP Prasanth, Subhash Chandra, L Swarupa, P SriKalyani, David A Hoisington
BMC Bioinformatics 2006, 7:383 (17August2006)
[Abstract] [Full text] [PDF] [PubMed] [Related articles] [Cited on BioMed Central]
Software
MultiSeq: unifying sequence and structure data for evolutionary analysis
Elijah Roberts, John Eargle, Dan Wright, Zaida Luthey-Schulten
BMC Bioinformatics 2006, 7:382 (16August2006)
[Abstract] [Full text] [PDF] [PubMed] [Related articles] [Cited on BioMed Central]
Research article
Modelling the network of cell cycle transcription factors in the yeast Saccharomyces cerevisiae
Shawn Cokus, Sherri Rose, David Haynor, Niels Gr nbech-Jensen, Matteo Pellegrini
BMC Bioinformatics 2006, 7:381 (16August2006)
[Abstract] [Full text] [PDF] [PubMed] [Related articles] [Cited on BioMed Central]
Research article
Validation and functional annotation of expression-based clusters based on gene ontology
Ralf Steuer, Peter Humburg, Joachim Selbig
BMC Bioinformatics 2006, 7:380 (15August2006)
[Abstract] [Full text] [PDF] [PubMed] [Related articles] [Cited on BioMed Central]
Database
V-MitoSNP: visualization of human mitochondrial SNPs
Li-Yeh Chuang, Cheng-Hong Yang, Yu-Huei Cheng, De-Leung Gu, Phei-Lang Chang, Ke-Hung Tsui, Hsueh-Wei Chang
BMC Bioinformatics 2006, 7:379 (15August2006)
[Abstract] [Full text] [PDF] [PubMed] [Related articles] [Cited on BioMed Central]
Research article
Comprehensive quality control utilizing the prehybridization third-dye image leads to accurate gene expression measurements by cDNA microarrays
Xujing Wang, Shuang Jia, Lisa Meyer, Bixia Xiang, Li-Yen Chen, Nan Jiang, Carol Moreno, Howard J Jacob, Soumitra Ghosh, Martin J Hessner
BMC Bioinformatics 2006, 7:378 (14August2006)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
Methodology article
A novel data mining method to identify assay-specific signatures in functional genomic studies
Derrick K Rollins, Dongmei Zhai, Alrica L Joe, Jack W Guidarelli, Abhishek Murarka, Ramon Gonzalez
BMC Bioinformatics 2006, 7:377 (14August2006)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
Research article
Detecting the limits of regulatory element conservation and divergence estimation using pairwise and multiple alignments
Daniel A Pollard, Alan M Moses, Venky N Iyer, Michael B Eisen
BMC Bioinformatics 2006, 7:376 (14August2006)
[Abstract] [Full text] [PDF] [PubMed] [Related articles] [Cited on BioMed Central]
Database
PeanutMap: an online genome database for comparative molecular maps of peanut
Arun M Jesubatham, Mark D Burow
BMC Bioinformatics 2006, 7:375 (11August2006)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
Methodology article
Genome comparison using Gene Ontology (GO) with statistical testing
Zhaotao Cai, Xizeng Mao, Songgang Li, Liping Wei
BMC Bioinformatics 2006, 7:374 (11August2006)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
Research article
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
Jeyakumar Natarajan, Daniel Berrar, Werner Dubitzky, Catherine Hack, Yonghong Zhang, Catherine DeSesa, James R Van Brocklyn, Eric G Bremer
BMC Bioinformatics 2006, 7:373 (10August2006)
[Abstract] [Full text] [PDF] [PubMed] [Related articles] [Cited on BioMed Central]
Research article
Gene and protein nomenclature in public databases
Katrin Fundel, Ralf Zimmer
BMC Bioinformatics 2006, 7:372 (9August2006)
[Abstract] [Full text] [PDF] [PubMed] [Related articles] [Cited on BioMed Central]
Software
UniFrac  An online tool for comparing microbial community diversity in a phylogenetic context
Catherine Lozupone, Micah Hamady, Rob Knight
BMC Bioinformatics 2006, 7:371 (7August2006)
[Abstract] [Full text] [PDF] [PubMed] [Related articles] [F1000 Biology] [Cited on BioMed Central]
Methodology article
Automatic document classification of biological literature
David Chen, Hans-Michael M ller, Paul W Sternberg
BMC Bioinformatics 2006, 7:370 (7August2006)
[Abstract] [Full text] [PDF] [PubMed] [Related articles] [Cited on BioMed Central]
Methodology article
Robust computational reconstitution a new method for the comparative analysis of gene expression in tissues and isolated cell fractions
Martin Hoffmann, Dirk Pohlers, Dirk Koczan, Hans-Jrgen Thiesen, Stefan Wlfl, Raimund W Kinne
BMC Bioinformatics 2006, 7:369 (4August2006)
[Abstract] [Full text] [PDF] [PubMed] [Related articles] [Cited on BioMed Central]
Software
G-InforBIO: integrated system for microbial genomics
Naoto Tanaka, Takashi Abe, Satoru Miyazaki, Hideaki Sugawara
BMC Bioinformatics 2006, 7:368 (4August2006)
[Abstract] [Full text] [PDF] [PubMed] [Related articles] [Cited on BioMed Central]
Research article
Prediction of a key role of motifs binding E2F and NR2F in down-regulation of numerous genes during the development of the mouse hippocampus
Michal Dabrowski, Stein Aerts, Bozena Kaminska
BMC Bioinformatics 2006, 7:367 (2August2006)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
Software
bioNMF: a versatile tool for non-negative matrix factorization in biology
Alberto Pascual-Montano, Pedro Carmona-Saez, Monica Chagoyen, Francisco Tirado, Jose M Carazo, Roberto D Pascual-Marqui
BMC Bioinformatics 2006, 7:366 (28July2006)
[Abstract] [Full text] [PDF] [PubMed] [Related articles] [Cited on BioMed Central]
Research article
PIPE: a protein-protein interaction prediction engine based on the re-occurring short polypeptide sequences between known interacting protein pairs
Sylvain Pitre, Frank Dehne, Albert Chan, Jim Cheetham, Alex Duong, Andrew Emili, Marinella Gebbia, Jack Greenblatt, Mathew Jessulat, Nevan Krogan, Xuemei Luo, Ashkan Golshani
BMC Bioinformatics 2006, 7:365 (27July2006)
[Abstract] [Full text] [PDF] [PubMed] [Related articles] [Cited on BioMed Central]
Methodology article
Improving the quality of protein structure models by selecting from alignment alternatives
Ingolf Sommer, Stefano Toppo, Oliver Sander, Thomas Lengauer, Silvio CE Tosatto
BMC Bioinformatics 2006, 7:364 (27July2006)
[Abstract] [Full text] [PDF] [PubMed] [Related articles] [Cited on BioMed Central]
Methodology article
A literature-based similarity metric for biological processes
Monica Chagoyen, Pedro Carmona-Saez, Concha Gil, Jose M Carazo, Alberto Pascual-Montano
BMC Bioinformatics 2006, 7:363 (26July2006)
[Abstract] [Full text] [PDF] [PubMed] [Related articles] [Cited on BioMed Central]
Software
A fast SCOP fold classification system using content-based E-Predict algorithm
Pin-Hao Chi, Chi-Ren Shyu, Dong Xu
BMC Bioinformatics 2006, 7:362 (26July2006)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
Methodology article
Cluster analysis for DNA methylation profiles having a detection threshold
Paul Marjoram, Jing Chang, Peter W Laird, Kimberly D Siegmund
BMC Bioinformatics 2006, 7:361 (26July2006)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
Research article
A direct comparison of protein interaction confidence assignment schemes
Silpa Suthram, Tomer Shlomi, Eytan Ruppin, Roded Sharan, Trey Ideker
BMC Bioinformatics 2006, 7:360 (26July2006)
[Abstract] [Full text] [PDF] [PubMed] [Related articles] [Cited on BioMed Central]
Research article
Comparison and evaluation of methods for generating differentially expressed gene lists from microarray data
Ian B Jeffery, Desmond G Higgins, Aedn C Culhane
BMC Bioinformatics 2006, 7:359 (26July2006)
[Abstract] [Full text] [PDF] [PubMed] [Related articles] [Cited on BioMed Central]
Methodology article
Identification of biomarkers from mass spectrometry data using a "common" peak approach
Tadayoshi Fushiki, Hironori Fujisawa, Shinto Eguchi
BMC Bioinformatics 2006, 7:358 (26July2006)
[Abstract] [Full text] [PDF] [PubMed] [Related articles] [Cited on BioMed Central]
Methodology article
Improved alignment quality by combining evolutionary information, predicted secondary structure and self-organizing maps
Tomas Ohlson, Varun Aggarwal, Arne Elofsson, Robert M MacCallum
BMC Bioinformatics 2006, 7:357 (25July2006)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
Methodology article
New directions in biomedical text annotation: definitions, guidelines and corpus construction
W John Wilbur, Andrey Rzhetsky, Hagit Shatkay
BMC Bioinformatics 2006, 7:356 (25July2006)
[Abstract] [Full text] [PDF] [PubMed] [Related articles] [Cited on BioMed Central]
Research article
Functional clustering of yeast proteins from the protein-protein interaction network
Taner Z Sen, Andrzej Kloczkowski, Robert L Jernigan
BMC Bioinformatics 2006, 7:355 (24July2006)
[Abstract] [Full text] [PDF] [PubMed] [Related articles] [Cited on BioMed Central]
Methodology article
A combined approach to data mining of textual and structured data to identify cancer-related targets
Pavel Pospisil, Lakshmanan K Iyer, S James Adelstein, Amin I Kassis
BMC Bioinformatics 2006, 7:354 (20July2006)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
Research article
A powerful method for detecting differentially expressed genes from GeneChip arrays that does not require replicates
Anne-Mette K Hein, Sylvia Richardson
BMC Bioinformatics 2006, 7:353 (20July2006)
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Methodology article
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