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Editor-in-Chief Melissa Norton, MD Biology Editor Penelope Webb, PhD In-house Editor Tim Sands PhD
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| | BMC Bioinformatics, Volume 8 | |
Volume 8 Suppl 10
Proceedings
Whistler, Canada. 8 December 2006
Volume 8 Suppl 9
Proceedings
Arlington, VA, USA. 10 November 2006
Volume 8 Suppl 8
Meeting abstracts
Vienna, Austria. 21 July 2007
more supplements 
Research article
     Background frequencies for residue variability estimates: BLOSUM revisited I Mihalek, I Re , O Lichtarge BMC Bioinformatics 2007, 8:488 (27 December 2007) [Abstract] [Full text] [PDF] [PubMed] [Related articles] Software
     Userscripts for the Life Sciences Egon L Willighagen, Noel M O'Boyle, Harini Gopalakrishnan, Dazhi Jiao, Rajarshi Guha, Christoph Steinbeck, David J Wild BMC Bioinformatics 2007, 8:487 (21 December 2007) [Abstract] [Full text] [PDF] [PubMed] [Related articles] [Cited on BioMed Central] Methodology article
     h-Profile plots for the discovery and exploration of patterns in gene expression data with an application to time course data Yvonne E Pittelkow, Susan R Wilson BMC Bioinformatics 2007, 8:486 (20 December 2007) [Abstract] [Full text] [PDF] [PubMed] [Related articles] Research article
     Characterization and simulation of cDNA microarray spots using a novel mathematical model Hye Young Kim, Seo Eun Lee, Min Jung Kim, Jin Il Han, Bo Kyung Kim, Yong Sung Lee, Young Seek Lee, Jin Hyuk Kim BMC Bioinformatics 2007, 8:485 (20 December 2007) [Abstract] [Full text] [PDF] [PubMed] [Related articles] Research article
     Effective selection of informative SNPs and classification on the HapMap genotype data Nina Zhou, Lipo Wang BMC Bioinformatics 2007, 8:484 (20 December 2007) [Abstract] [Full text] [PDF] [PubMed] [Related articles] [Cited on BioMed Central] Database
     PARPs database: A LIMS systems for protein-protein interaction data mining or laboratory information management system Arnaud Droit, Joanna M Hunter, Mich le Rouleau, Chantal Ethier, Aude Picard-Cloutier, David Bourgais, Guy G Poirier BMC Bioinformatics 2007, 8:483 (19 December 2007) [Abstract] [Full text] [PDF] [PubMed] [Related articles] Research article
    Identifying protein complexes directly from high-throughput TAP data with Markov random fields Wasinee Rungsarityotin, Roland Krause, Arno Sch dl, Alexander Schliep BMC Bioinformatics 2007, 8:482 (19 December 2007) [Abstract] [Full text] [PDF] [PubMed] [Related articles] Research article
     Effective transcription factor binding site prediction using a combination of optimization, a genetic algorithm and discriminant analysis to capture distant interactions Victor G Levitsky, Elena V Ignatieva, Elena A Ananko, Igor I Turnaev, Tatyana I Merkulova, Nikolay A Kolchanov, TC Hodgman BMC Bioinformatics 2007, 8:481 (19 December 2007) [Abstract] [Full text] [PDF] [PubMed] [Related articles] Methodology article
    TABASCO: A single molecule, base-pair resolved gene expression simulator Sriram Kosuri, Jason R Kelly, Drew Endy BMC Bioinformatics 2007, 8:480 (19 December 2007) [Abstract] [Full text] [PDF] [PubMed] [Related articles] [Cited on BioMed Central] Software
     The Personal Sequence Database: a suite of tools to create and maintain web-accessible sequence databases Scott A Givan, Christopher M Sullivan, James C Carrington BMC Bioinformatics 2007, 8:479 (18 December 2007) [Abstract] [Full text] [PDF] [PubMed] [Related articles] Methodology article
     Ab initio identification of human microRNAs based on structure motifs Markus Brameier, Carsten Wiuf BMC Bioinformatics 2007, 8:478 (18 December 2007) [Abstract] [Full text] [PDF] [PubMed] [Related articles] [Cited on BioMed Central] Methodology article
     On the analysis of glycomics mass spectrometry data via the regularized area under the ROC curve Jingjing Ye, Hao Liu, Crystal Kirmiz, Carlito B Lebrilla, David M Rocke BMC Bioinformatics 2007, 8:477 (12 December 2007) [Abstract] [Full text] [PDF] [PubMed] [Related articles] Methodology article
    Penalized likelihood for sparse contingency tables with an application to full-length cDNA libraries Corinne Dahinden, Giovanni Parmigiani, Mark C Emerick, Peter B hlmann BMC Bioinformatics 2007, 8:476 (11 December 2007) [Abstract] [Full text] [PDF] [PubMed] [Related articles] Research article
     Predicting gene ontology functions from protein's regional surface structures Zhi-Ping Liu, Ling-Yun Wu, Yong Wang, Luonan Chen, Xiang-Sun Zhang BMC Bioinformatics 2007, 8:475 (11 December 2007) [Abstract] [Full text] [PDF] [PubMed] [Related articles] Software
     High-throughput sequence alignment using Graphics Processing Units Michael C Schatz, Cole Trapnell, Arthur L Delcher, Amitabh Varshney BMC Bioinformatics 2007, 8:474 (10 December 2007) [Abstract] [Full text] [PDF] [PubMed] [Related articles] [Cited on BioMed Central] Methodology article
     A systematic approach to detecting transcription factors in response to environmental stresses Li-Hsieh Lin, Hsiao-Ching Lee, Wen-Hsiung Li, Bor-Sen Chen BMC Bioinformatics 2007, 8:473 (8 December 2007) [Abstract] [Full text] [PDF] [PubMed] [Related articles] [Cited on BioMed Central] Research article
     Direct maximum parsimony phylogeny reconstruction from genotype data Srinath Sridhar, Fumei Lam, Guy E Blelloch, R Ravi, Russell Schwartz BMC Bioinformatics 2007, 8:472 (5 December 2007) [Abstract] [Full text] [PDF] [PubMed] [Related articles] Research article
     Predicting and improving the protein sequence alignment quality by support vector regression Minho Lee, Chan-seok Jeong, Dongsup Kim BMC Bioinformatics 2007, 8:471 (3 December 2007) [Abstract] [Full text] [PDF] [PubMed] [Related articles] Research article
     Domain motions of Argonaute, the catalytic engine of RNA interference Dengming Ming, Michael E Wall, Kevin Y Sanbonmatsu BMC Bioinformatics 2007, 8:470 (30 November 2007) [Abstract] [Full text] [PDF] [PubMed] [Related articles] Research article
    A structural analysis of in vitro catalytic activities of hammerhead ribozymes Yu Shao, Susan Wu, Chi Yu Chan, Jessie R Klapper, Erasmus Schneider, Ye Ding BMC Bioinformatics 2007, 8:469 (30 November 2007) [Abstract] [Full text] [PDF] [PubMed] [Related articles] [Cited on BioMed Central] Research article
    Statistical learning of peptide retention behavior in chromatographic separations: a new kernel-based approach for computational proteomics Nico Pfeifer, Andreas Leinenbach, Christian G Huber, Oliver Kohlbacher BMC Bioinformatics 2007, 8:468 (30 November 2007) [Abstract] [Full text] [PDF] [PubMed] [Related articles] [Cited on BioMed Central] Methodology article
     Generating confidence intervals on biological networks Thomas Thorne, Michael PH Stumpf BMC Bioinformatics 2007, 8:467 (30 November 2007) [Abstract] [Full text] [PDF] [PubMed] [Related articles] Research article
     Subcellular location prediction of proteins using support vector machines with alignment of block sequences utilizing amino acid composition Takeyuki Tamura, Tatsuya Akutsu BMC Bioinformatics 2007, 8:466 (30 November 2007) [Abstract] [Full text] [PDF] [PubMed] [Related articles] [Cited on BioMed Central] Software
    SAT, a flexible and optimized Web application for SSR marker development Alexis Dereeper, Xavier Argout, Claire Billot, Jean-Fran ois Rami, Manuel Ruiz BMC Bioinformatics 2007, 8:465 (29 November 2007) [Abstract] [Full text] [PDF] [PubMed] [Related articles] [Cited on BioMed Central] Research article
     Predicting RNA secondary structure by the comparative approach: how to select the homologous sequences St fan Engelen, Fariza Tahi BMC Bioinformatics 2007, 8:464 (28 November 2007) [Abstract] [Full text] [PDF] [PubMed] [Related articles] Research article
     Identification of DNA-binding proteins using support vector machines and evolutionary profiles Manish Kumar, Michael M Gromiha, Gajendra PS Raghava BMC Bioinformatics 2007, 8:463 (27 November 2007) [Abstract] [Full text] [PDF] [PubMed] [Related articles] [Cited on BioMed Central] Software
     Dynamic simulation of regulatory networks using SQUAD Alessandro Di Cara, Abhishek Garg, Giovanni De Micheli, Ioannis Xenarios, Luis Mendoza BMC Bioinformatics 2007, 8:462 (26 November 2007) [Abstract] [Full text] [PDF] [PubMed] [Related articles] [Cited on BioMed Central] Research article
     In situ analysis of cross-hybridisation on microarrays and the inference of expression correlation Tineke Casneuf, Yves Van de Peer, Wolfgang Huber BMC Bioinformatics 2007, 8:461 (26 November 2007) [Abstract] [Full text] [PDF] [PubMed] [Related articles] [Cited on BioMed Central] Software
     Dendroscope: An interactive viewer for large phylogenetic trees Daniel H Huson, Daniel C Richter, Christian Rausch, Tobias Dezulian, Markus Franz, Regula Rupp BMC Bioinformatics 2007, 8:460 (22 November 2007) [Abstract] [Full text] [PDF] [PubMed] [Related articles] [Cited on BioMed Central] Research article
     Predicting peptides binding to MHC class II molecules using multi-objective evolutionary algorithms Menaka Rajapakse, Bertil Schmidt, Lin Feng, Vladimir Brusic BMC Bioinformatics 2007, 8:459 (22 November 2007) [Abstract] [Full text] [PDF] [PubMed] [Related articles] [Cited on BioMed Central] Software
     Recodon: Coalescent simulation of coding DNA sequences with recombination, migration and demography Miguel Arenas, David Posada BMC Bioinformatics 2007, 8:458 (20 November 2007) [Abstract] [Full text] [PDF] [PubMed] [Related articles] [Cited on BioMed Central] Software
     GEDI: a user-friendly toolbox for analysis of large-scale gene expression data Andr Fujita, Jo o R Sato, Carlos E Ferreira, Mari C Sogayar BMC Bioinformatics 2007, 8:457 (19 November 2007) [Abstract] [Full text] [PDF] [PubMed] [Related articles] Software
     The Firegoose: two-way integration of diverse data from different bioinformatics web resources with desktop applications J Christopher Bare, Paul T Shannon, Amy K Schmid, Nitin S Baliga BMC Bioinformatics 2007, 8:456 (19 November 2007) [Abstract] [Full text] [PDF] [PubMed] [Related articles] Research article
    Use of genomic DNA control features and predicted operon structure in microarray data analysis: ArrayLeaRNA a Bayesian approach Carmen Pin, Mark Reuter BMC Bioinformatics 2007, 8:455 (19 November 2007) [Abstract] [Full text] [PDF] [PubMed] [Related articles] [Cited on BioMed Central] Methodology article
     Transcription factor target prediction using multiple short expression time series from Arabidopsis thaliana Henning Redestig, Daniel Weicht, Joachim Selbig, Matthew A Hannah BMC Bioinformatics 2007, 8:454 (18 November 2007) [Abstract] [Full text] [PDF] [PubMed] [Related articles] [Cited on BioMed Central] Methodology article
     Inferring biological functions and associated transcriptional regulators using gene set expression coherence analysis Tae-Min Kim, Yeun-Jun Chung, Mun-Gan Rhyu, Myeong Ho Jung BMC Bioinformatics 2007, 8:453 (17 November 2007) [Abstract] [Full text] [PDF] [PubMed] [Related articles] [Cited on BioMed Central] Methodology article
    Inferring activity changes of transcription factors by binding association with sorted expression profiles Chao Cheng, Xiting Yan, Fengzhu Sun, Lei M Li BMC Bioinformatics 2007, 8:452 (16 November 2007) [Abstract] [Full text] [PDF] [PubMed] [Related articles] [Cited on BioMed Central] Research article
     Peptide ligand screening of -synuclein aggregation modulators by in silico panning Koichi Abe, Natsuki Kobayashi, Koji Sode, Kazunori Ikebukuro BMC Bioinformatics 2007, 8:451 (16 November 2007) [Abstract] [Full text] [PDF] [PubMed] [Related articles] Software
     Predicting the phenotypic effects of non-synonymous single nucleotide polymorphisms based on support vector machines Jian Tian, Ningfeng Wu, Xuexia Guo, Jun Guo, Juhua Zhang, Yunliu Fan BMC Bioinformatics 2007, 8:450 (16 November 2007) [Abstract] [Full text] [PDF] [PubMed] [Related articles] [Cited on BioMed Central] Research article
     A comparison of Affymetrix gene expression arrays Mark D Robinson, Terence P Speed BMC Bioinformatics 2007, 8:449 (15 November 2007) [Abstract] [Full text] [PDF] [PubMed] [Related articles] [Cited on BioMed Central] Software
    PedGenie: meta genetic association testing in mixed family and case-control designs Karen Curtin, Jathine Wong, Kristina Allen-Brady, Nicola J Camp BMC Bioinformatics 2007, 8:448 (15 November 2007) [Abstract] [Full text] [PDF] [PubMed] [Related articles] [Cited on BioMed Central] Research article
    Application of a correlation correction factor in a microarray cross-platform reproducibility study Kellie J Archer, Catherine I Dumur, G Scott Taylor, Michael D Chaplin, Anthony Guiseppi-Elie, Geraldine Grant, Andrea Ferreira-Gonzalez, Carleton T Garrett BMC Bioinformatics 2007, 8:447 (15 November 2007) [Abstract] [Full text] [PDF] [PubMed] [Related articles] Software
    Novel definition files for human GeneChips based on GeneAnnot Francesco Ferrari, Stefania Bortoluzzi, Alessandro Coppe, Alexandra Sirota, Marilyn Safran, Michael Shmoish, Sergio Ferrari, Doron Lancet, Gian Antonio Danieli, Silvio Bicciato BMC Bioinformatics 2007, 8:446 (15 November 2007) [Abstract] [Full text] [PDF] [PubMed] [Related articles] [Cited on BioMed Central] Research article
    Predicting combinatorial binding of transcription factors to regulatory elements in the human genome by association rule mining Xochitl C Morgan, Shulin Ni, Daniel P Miranker, Vishwanath R Iyer BMC Bioinformatics 2007, 8:445 (15 November 2007) [Abstract] [Full text] [PDF] [PubMed] [Related articles] [Cited on BioMed Central] Research article
     Insertions and the emergence of novel protein structure: a structure-based phylogenetic study of insertions Haiyan Jiang, Christian Blouin BMC Bioinformatics 2007, 8:444 (15 November 2007) [Abstract] [Full text] [PDF] [PubMed] [Related articles] [Cited on BioMed Central] Correction
    Ringo an R/Bioconductor package for analyzing ChIP-chip readouts Joern Toedling, Oleg Skylar, Tammo Krueger, Jenny J Fischer, Silke Sperling, Wolfgang Huber BMC Bioinformatics 2007, 8:443 (15 November 2007) [Abstract] [Full text] [PDF] Methodology article
    A general strategy to determine the congruence between a hierarchical and a non-hierarchical classification Antonio Marco, Ignacio Mar n BMC Bioinformatics 2007, 8:442 (15 November 2007) [Abstract] [Full text] [PDF] [PubMed] [Related articles] [Cited on BioMed Central] Database
    A manually curated database of tetrapod mitochondrially encoded tRNA sequences and secondary structures Konstantin Yu Popadin, Leila A Mamirova, Fyodor A Kondrashov BMC Bioinformatics 2007, 8:441 (14 November 2007) [Abstract] [Full text] [PDF] [PubMed] [Related articles] [1 comment] Methodology article
    A general and efficient method for estimating continuous IBD functions for use in genome scans for QTL Francois Besnier, rjan Carlborg BMC Bioinformatics 2007, 8:440 (13 November 2007) [Abstract] [Full text] [PDF] [PubMed] [Related articles] Software
    BGX: a Bioconductor package for the Bayesian integrated analysis of Affymetrix GeneChips Ernest Turro, Natalia Bochkina, Anne-Mette K Hein, Sylvia Richardson BMC Bioinformatics 2007, 8:439 (12 November 2007) [Abstract] [Full text] [PDF] [PubMed] [Related articles] [Cited on BioMed Central] Research article
     Glycosylation site prediction using ensembles of Support Vector Machine classifiers Cornelia Caragea, Jivko Sinapov, Adrian Silvescu, Drena Dobbs, Vasant Honavar BMC Bioinformatics 2007, 8:438 (9 November 2007) [Abstract] [Full text] [PDF] [PubMed] [Related articles] [Cited on BioMed Central] Research article
     Identification of tissue-specific cis-regulatory modules based on interactions between transcription factors Xueping Yu, Jimmy Lin, Donald J Zack, Jiang Qian BMC Bioinformatics 2007, 8:437 (9 November 2007) [Abstract] [Full text] [PDF] [PubMed] [Related articles] [Cited on BioMed Central] Methodology article
     An open source infrastructure for managing knowledge and finding potential collaborators in a domain-specific subset of PubMed, with an example from human genome epidemiology Wei Yu, Ajay Yesupriya, Anja Wulf, Junfeng Qu, Muin J Khoury, Marta Gwinn BMC Bioinformatics 2007, 8:436 (9 November 2007) [Abstract] [Full text] [PDF] [PubMed] [Related articles] [Cited on BioMed Central] Research article
    Improving model construction of profile HMMs for remote homology detection through structural alignment Juliana S Bernardes, Alberto MR D vila, V tor S Costa, Gerson Zaverucha BMC Bioinformatics 2007, 8:435 (9 November 2007) [Abstract] [Full text] [PDF] [PubMed] [Related articles] Methodology article
    A Hidden Markov Model to estimate population mixture and allelic copy-numbers in cancers using Affymetrix SNP arrays Philippe Lamy, Claus L Andersen, Lars Dyrskjot, Niels Torring, Carsten Wiuf BMC Bioinformatics 2007, 8:434 (9 November 2007) [Abstract] [Full text] [PDF] [PubMed] [Related articles] [Cited on BioMed Central] Research article
     Incremental and unifying modelling formalism for biological interaction networks Anastasia Yartseva, Hanna Klaudel, Raymond Devillers, Fran ois K p s BMC Bioinformatics 2007, 8:433 (8 November 2007) [Abstract] [Full text] [PDF] [PubMed] [Related articles] Research article
     Identifications of conserved 7-mers in 3'-UTRs and microRNAs in Drosophila Jin Gu, Hu Fu, Xuegong Zhang, Yanda Li BMC Bioinformatics 2007, 8:432 (8 November 2007) [Abstract] [Full text] [PDF] [PubMed] [Related articles] Methodology article
     Comparative evaluation of gene-set analysis methods Qi Liu, Irina Dinu, Adeniyi J Adewale, John D Potter, Yutaka Yasui BMC Bioinformatics 2007, 8:431 (7 November 2007) [Abstract] [Full text] [PDF] [PubMed] [Related articles] [Cited on BioMed Central] Research article
    Analysis of feedback loops and robustness in network evolution based on Boolean models Yung-Keun Kwon, Kwang-Hyun Cho BMC Bioinformatics 2007, 8:430 (7 November 2007) [Abstract] [Full text] [PDF] [PubMed] [Related articles] Database
     CoryneRegNet 4.0 A reference database for corynebacterial gene regulatory networks Jan Baumbach BMC Bioinformatics 2007, 8:429 (6 November 2007) [Abstract] [Full text] [PDF] [PubMed] [Related articles] [Cited on BioMed Central] Software
    Cubic exact solutions for the estimation of pairwise haplotype frequencies: implications for linkage disequilibrium analyses and a web tool 'CubeX' Tom R Gaunt, Santiago Rodr guez, Ian NM Day BMC Bioinformatics 2007, 8:428 (2 November 2007) [Abstract] [Full text] [PDF] [PubMed] [Related articles] [Cited on BioMed Central] Research article
     Extracting gene expression patterns and identifying co-expressed genes from microarray data reveals biologically responsive processes Jeff W Chou, Tong Zhou, William K Kaufmann, Richard S Paules, Pierre R Bushel BMC Bioinformatics 2007, 8:427 (2 November 2007) [Abstract] [Full text] [PDF] [PubMed] [Related articles] [Cited on BioMed Central] Database
     DAVID Knowledgebase: a gene-centered database integrating heterogeneous gene annotation resources to facilitate high-throughput gene functional analysis Brad T Sherman, Da Wei Huang, Qina Tan, Yongjian Guo, Stephan Bour, David Liu, Robert Stephens, Michael W Baseler, H Clifford Lane, Richard A Lempicki BMC Bioinformatics 2007, 8:426 (2 November 2007) [Abstract] [Full text] [PDF] [PubMed] [Related articles] [Cited on BioMed Central] Research article
     SABERTOOTH: protein structural alignment based on a vectorial structure representation Florian Teichert, Ugo Bastolla, Markus Porto BMC Bioinformatics 2007, 8:425 (31 October 2007) [Abstract] [Full text] [PDF] [PubMed] [Related articles] [Cited on BioMed Central] Research article
    Large-scale validation of methods for cytotoxic T-lymphocyte epitope prediction Mette V Larsen, Claus Lundegaard, Kasper Lamberth, Soren Buus, Ole Lund, Morten Nielsen BMC Bioinformatics 2007, 8:424 (31 October 2007) [Abstract] [Full text] [PDF] [PubMed] [Related articles] Research article
     PubMed related articles: a probabilistic topic-based model for content similarity Jimmy Lin, W John Wilbur BMC Bioinformatics 2007, 8:423 (30 October 2007) [Abstract] [Full text] [PDF] [PubMed] [Related articles] [Cited on BioMed Central] Research article
    SIRAC: Supervised Identification of Regions of Aberration in aCGH datasets Carmen Lai, Hugo M Horlings, Marc J van de Vijver, Eric H van Beers, Petra M Nederlof, Lodewyk FA Wessels, Marcel JT Reinders BMC Bioinformatics 2007, 8:422 (30 October 2007) [Abstract] [Full text] [PDF] [PubMed] [Related articles] Methodology article
    A procedure for the estimation over time of metabolic fluxes in scenarios where measurements are uncertain and/or insufficient Francisco Llaneras, Jes s Pic BMC Bioinformatics 2007, 8:421 (30 October 2007) [Abstract] [Full text] [PDF] [PubMed] [Related articles] [Cited on BioMed Central] [1 comment] Methodology article
    'Unite and conquer': enhanced prediction of protein subcellular localization by integrating multiple specialized tools Yao Qing Shen, Gertraud Burger BMC Bioinformatics 2007, 8:420 (29 October 2007) [Abstract] [Full text] [PDF] [PubMed] [Related articles] [Cited on BioMed Central] Methodology article
     A dynamic programming approach for the alignment of signal peaks in multiple gas chromatography-mass spectrometry experiments Mark D Robinson, David P De Souza, Woon Wai Keen, Eleanor C Saunders, Malcolm J McConville, Terence P Speed, Vladimir A Liki BMC Bioinformatics 2007, 8:419 (29 October 2007) [Abstract] [Full text] [PDF] [PubMed] [Related articles] [Cited on BioMed Central] Software
     HeliCis: a DNA motif discovery tool for colocalized motif pairs with periodic spacing Erik Larsson, Per Lindahl, Petter Mostad BMC Bioinformatics 2007, 8:418 (28 October 2007) [Abstract] [Full text] [PDF] [PubMed] [Related articles] [Cited on BioMed Central] Research article
     How accurately is ncRNA aligned within whole-genome multiple alignments? Adrienne X Wang, Walter L Ruzzo, Martin Tompa BMC Bioinformatics 2007, 8:417 (26 October 2007) [Abstract] [Full text] [PDF] [PubMed] [Related articles] [Cited on BioMed Central] Research article
    ProCKSI: a decision support system for Protein (Structure) Comparison, Knowledge, Similarity and Information Daniel Barthel, Jonathan D Hirst, Jacek B a ewicz, Edmund K Burke, Natalio Krasnogor BMC Bioinformatics 2007, 8:416 (26 October 2007) [Abstract] [Full text] [PDF] [PubMed] [Related articles] [Cited on BioMed Central] Research article
     Prediction potential of candidate biomarker sets identified and validated on gene expression data from multiple datasets Michael Gormley, William Dampier, Adam Ertel, Bilge Karacali, Aydin Tozeren BMC Bioinformatics 2007, 8:415 (26 October 2007) [Abstract] [Full text] [PDF] [PubMed] [Related articles] [Cited on BioMed Central] Methodology article
     InPrePPI: an integrated evaluation method based on genomic context for predicting protein-protein interactions in prokaryotic genomes Jingchun Sun, Yan Sun, Guohui Ding, Qi Liu, Chuan Wang, Youyu He, Tieliu Shi, Yixue Li, Zhongming Zhao BMC Bioinformatics 2007, 8:414 (26 October 2007) [Abstract] [Full text] [PDF] [PubMed] [Related articles] [Cited on BioMed Central] Methodology article
    Identifying dynamical modules from genetic regulatory systems: applications to the segment polarity network David J Irons, Nicholas AM Monk BMC Bioinformatics 2007, 8:413 (25 October 2007) [Abstract] [Full text] [PDF] [PubMed] [Related articles] [F1000 Biology] [Cited on BioMed Central] Correspondence
     Reproducibility of microarray data: a further analysis of microarray quality control (MAQC) data James J Chen, Huey-Miin Hsueh, Robert R Delongchamp, Chien-Ju Lin, Chen-An Tsai BMC Bioinformatics 2007, 8:412 (25 October 2007) [Abstract] [Full text] [PDF] [PubMed] [Related articles] [Cited on BioMed Central] Methodology article
    Estimating genealogies from linked marker data: a Bayesian approach Dario Gasbarra, Matti Pirinen, Mikko J Sillanp , Elja Arjas BMC Bioinformatics 2007, 8:411 (25 October 2007) [Abstract] [Full text] [PDF] [PubMed] [Related articles] Research article
    Features generated for computational splice-site prediction correspond to functional elements Rezarta Islamaj Dogan, Lise Getoor, W John Wilbur, Stephen M Mount BMC Bioinformatics 2007, 8:410 (24 October 2007) [Abstract] [Full text] [PDF] [PubMed] [Related articles] Methodology article
    Absolute estimation of initial concentrations of amplicon in a real-time RT-PCR process Marjo V Smith, Chris R Miller, Michael Kohn, Nigel J Walker, Chris J Portier BMC Bioinformatics 2007, 8:409 (23 October 2007) [Abstract] [Full text] [PDF] [PubMed] [Related articles] [Cited on BioMed Central] Research article
    Growing functional modules from a seed protein via integration of protein interaction and gene expression data Ioannis A Maraziotis, Konstantina Dimitrakopoulou, Anastasios Bezerianos BMC Bioinformatics 2007, 8:408 (23 October 2007) [Abstract] [Full text] [PDF] [PubMed] [Related articles] [Cited on BioMed Central] Research article
    Bioinformatic identification of novel putative photoreceptor specific cis-elements Charles G Danko, Vera A McIlvain, Maochun Qin, Barry E Knox, Arkady M Pertsov BMC Bioinformatics 2007, 8:407 (22 October 2007) [Abstract] [Full text] [PDF] [PubMed] [Related articles] [Cited on BioMed Central] Software
     MetaLook: a 3D visualisation software for marine ecological genomics Thierry Lombardot, Renzo Kottmann, Gregory Giuliani, Andrea de Bono, Nans Addor, Frank Oliver Gl ckner BMC Bioinformatics 2007, 8:406 (22 October 2007) [Abstract] [Full text] [PDF] [PubMed] [Related articles] [Cited on BioMed Central] Software
    AxPcoords & parallel AxParafit: statistical co-phylogenetic analyses on thousands of taxa Alexandros Stamatakis, Alexander F Auch, Jan Meier-Kolthoff, Markus G ker BMC Bioinformatics 2007, 8:405 (22 October 2007) [Abstract] [Full text] [PDF] [PubMed] [Related articles] Methodology article
    Application of amino acid occurrence for discriminating different folding types of globular proteins Y-h Taguchi, M Michael Gromiha BMC Bioinformatics 2007, 8:404 (22 October 2007) [Abstract] [Full text] [PDF] [PubMed] [Related articles] [Cited on BioMed Central] Methodology article
    Modeling SAGE tag formation and its effects on data interpretation within a Bayesian framework Michael A Gilchrist, Hong Qin, Russell Zaretzki BMC Bioinformatics 2007, 8:403 (18 October 2007) [Abstract] [Full text] [PDF] [PubMed] [Related articles] [Cited on BioMed Central] Software
    Automated group assignment in large phylogenetic trees using GRUNT: GRouping, Ungrouping, Naming Tool Daniel Dalevi, Todd Z DeSantis, Jakob Fredslund, Gary L Andersen, Victor M Markowitz, Philip Hugenholtz BMC Bioinformatics 2007, 8:402 (18 October 2007) [Abstract] [Full text] [PDF] [PubMed] [Related articles] [Cited on BioMed Central] Software
     The Protein Identifier Cross-Referencing (PICR) service: reconciling protein identifiers across multiple source databases Richard G C t , Philip Jones, Lennart Martens, Samuel Kerrien, Florian Reisinger, Quan Lin, Rasko Leinonen, Rolf Apweiler, Henning Hermjakob BMC Bioinformatics 2007, 8:401 (18 October 2007) [Abstract] [Full text] [PDF] [PubMed] [Related articles] [Cited on BioMed Central] [1 comment] Research article
    CATMA, a comprehensive genome-scale resource for silencing and transcript profiling of Arabidopsis genes Gert Sclep, Joke Allemeersch, Robin Liechti, Bj rn De Meyer, Jim Beynon, Rishikesh Bhalerao, Yves Moreau, Wilfried Nietfeld, Jean-Pierre Renou, Philippe Reymond, Martin TR Kuiper, Pierre Hilson BMC Bioinformatics 2007, 8:400 (18 October 2007) [Abstract] [Full text] [PDF] [PubMed] [Related articles] Methodology article
    fREDUCE: Detection of degenerate regulatory elements using correlation with expression Randy Z Wu, Christina Chaivorapol, Jiashun Zheng, Hao Li, Shoudan Liang BMC Bioinformatics 2007, 8:399 (17 October 2007) [Abstract] [Full text] [PDF] [PubMed] [Related articles] [Cited on BioMed Central] Software
    Strainer: software for analysis of population variation in community genomic datasets John M Eppley, Gene W Tyson, Wayne M Getz, Jillian F Banfield BMC Bioinformatics 2007, 8:398 (17 October 2007) [Abstract] [Full text] [PDF] [PubMed] [Related articles] [Cited on BioMed Central] Research article
    Assessing the ability of sequence-based methods to provide functional insight within membrane integral proteins: a case study analyzing the neurotransmitter/Na+ symporter family Dennis R Livesay, Patrick D Kidd, Sepehr Eskandari, Usman Roshan BMC Bioinformatics 2007, 8:397 (17 October 2007) [Abstract] [Full text] [PDF] [PubMed] [Related articles] Research article
    Large scale clustering of protein sequences with FORCE -A layout based heuristic for weighted cluster editing Tobias Wittkop, Jan Baumbach, Francisco P Lobo, Sven Rahmann BMC Bioinformatics 2007, 8:396 (17 October 2007) [Abstract] [Full text] [PDF] [PubMed] [Related articles] [Cited on BioMed Central] Correction
    Permutation test for periodicity in short time series data Andrey A Ptitsyn, Sanjin Zvonic, Jeffrey M Gimble BMC Bioinformatics 2007, 8:395 (17 October 2007) [Abstract] [Full text] [PDF] Correspondence
    A response to Yu et al. "A forward-backward fragment assembling algorithm for the identification of genomic amplification and deletion breakpoints using high-density single nucleotide polymorphism (SNP) array", BMC Bioinformatics 2007, 8: 145 Oscar M Rueda, Ramon Diaz-Uriarte BMC Bioinformatics 2007, 8:394 (16 October 2007) [Abstract] [Full text] [PDF] [PubMed] [Related articles] Research article
     Local Renyi entropic profiles of DNA sequences Susana Vinga, Jonas S Almeida BMC Bioinformatics 2007, 8:393 (16 October 2007) [Abstract] [Full text] [PDF] [PubMed] [Related articles] [Cited on BioMed Central] Research article
    Improved human disease candidate gene prioritization using mouse phenotype Jing Chen, Huan Xu, Bruce J Aronow, Anil G Jegga BMC Bioinformatics 2007, 8:392 (16 October 2007) [Abstract] [Full text] [PDF] [PubMed] [Related articles] [Cited on BioMed Central] Research article
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