Journal: Bioinformatics

Volume 22, Issue 9

1031 -- 1035Chris P. Ponting. A novel domain suggests a ciliary function for ::::ASPM::::, a brain size determining gene
1036 -- 1046Fan Hsu, W. James Kent, Hiram Clawson, Robert M. Kuhn, Mark Diekhans, David Haussler. The UCSC Known Genes
1047 -- 1054Lawrence S. Hon, Ajay N. Jain. A deterministic motif finding algorithm with application to the human genome
1055 -- 1063Igor B. Kuznetsov, Seungwoo Hwang. A novel sensitive method for the detection of user-defined compositional bias in biological sequences
1064 -- 1071Jochen Maydt, Thomas Lengauer. Recco: recombination analysis using cost optimization
1072 -- 1079F. Collyn, L. Guy, M. Marceau, M. Simonet, Claude-Alain H. Roten. Describing ancient horizontal gene transfers at the nucleotide and gene levels by comparative pathogenicity island genometrics
1080 -- 1087Jessica Ebert, Douglas L. Brutlag. Development and validation of a consistency based multiple structure alignment algorithm
1088 -- 1095Violaine Moreau, Claude Granier, Sylvie Villard, Daniel Laune, Franck Molina. Discontinuous epitope prediction based on mimotope analysis
1096 -- 1102Ana Conesa, María José Nueda, Alberto Ferrer, Manuel Talón. maSigPro: a method to identify significantly differential expression profiles in time-course microarray experiments
1103 -- 1110Carlos Prieto, M. J. Rivas, J. M. Sánchez, J. López-Fidalgo, Javier De Las Rivas. Algorithm to find gene expression profiles of deregulation and identify families of disease-altered genes
1111 -- 1121Lee Weng, Hongyue Dai, Yihui Zhan, Yudong D. He, Sergey B. Stepaniants, Douglas E. Bassett. Rosetta error model for gene expression analysis
1122 -- 1129Amela Prelic, Stefan Bleuler, Philip Zimmermann, Anja Wille, Peter Bühlmann, Wilhelm Gruissem, Lars Hennig, Lothar Thiele, Eckart Zitzler. A systematic comparison and evaluation of biclustering methods for gene expression data
1130 -- 1136Amanda Clare, Andreas Karwath, Helen Ougham, Ross D. King. Functional bioinformatics for ::::Arabidopsis thaliana::::
1137 -- 1143Uwe Radetzki, Ulf Leser, S. C. Schulze-Rauschenbach, J. Zimmermann, Jens Lüssem, Thomas Bode, Armin B. Cremers. Adapters, shims, and glue - service interoperability for ::::in silico:::: experiments
1144 -- 1146J. C. Marioni, Natalie P. Thorne, Simon Tavaré. BioHMM: a heterogeneous hidden Markov model for segmenting array CGH data
1147 -- 1149David C. Walley, Ben W. Tripp, Young C. Song, Keith R. Walley, Scott J. Tebbutt. MACGT: multi-dimensional automated clustering genotyping tool for analysis of microarray-based mini-sequencing data
1150 -- 1151Dong-Yup Lee, Choamun Yun, Ayoun Cho, Bo Kyeng Hou, Sunwon Park, Sang Yup Lee. WebCell: a web-based environment for kinetic modeling and dynamic simulation of cellular networks
1152 -- 1153Sebastian Wernicke, Florian Rasche. FANMOD: a tool for fast network motif detection
1154 -- 1156Victor Trevino, Francesco Falciani. GALGO: an R package for multivariate variable selection using genetic algorithms

Volume 22, Issue 8

905 -- 910A. M. Quirke, F. Jerry Reen, Marcus J. Claesson, E. Fidelma Boyd. Genomic island identification in ::::Vibrio vulnificus:::: reveals significant genome plasticity in this human pathogen
911 -- 918Philippe Broët, Sylvia Richardson. Detection of gene copy number changes in CGH microarrays using a spatially correlated mixture model
919 -- 923Hao Xiong. Non-linear tests for identifying differentially expressed genes or genetic networks
924 -- 933Benjamin R. Jefferys, Lawrence A. Kelley, Marek J. Sergot, John Fox, Michael J. E. Sternberg. Capturing expert knowledge with argumentation: a case study in bioinformatics
934 -- 942Kay C. Wiese, Andrew Hendriks. Comparison of ::::P-RnaPredict:::: and ::::mfold:::: - algorithms for RNA secondary structure prediction
943 -- 949Sepp Hochreiter, Djork-Arné Clevert, Klaus Obermayer. A new summarization method for affymetrix probe level data
950 -- 958Ja-Yong Koo, Insuk Sohn, Sujong Kim, Jae-Won Lee. Structured polychotomous machine diagnosis of multiple cancer types using gene expression
959 -- 966Peng Qiu, Z. Jane Wang, K. J. Ray Liu. Polynomial model approach for resynchronization analysis of cell-cycle gene expression data
967 -- 973Xiang Guo, Rongxiang Liu, Craig D. Shriver, Hai Hu, Michael N. Liebman. Assessing semantic similarity measures for the characterization of human regulatory pathways
974 -- 980Natasa Przulj, Derek G. Corneil, Igor Jurisica. Efficient estimation of graphlet frequency distributions in protein-protein interaction networks
981 -- 988Claudia Plant, Christian Böhm, Bernhard Tilg, Christian Baumgartner. Enhancing instance-based classification with local density: a new algorithm for classifying unbalanced biomedical data
989 -- 996Haiquan Li, Jinyan Li, Limsoon Wong. Discovering motif pairs at interaction sites from protein sequences on a proteome-wide scale
997 -- 998Philipp Pagel, Matthias Oesterheld, Volker Stümpflen, Dmitrij Frishman. The DIMA web resource - exploring the protein domain network
999 -- 1001Voichita D. Marinescu, Isaac S. Kohane, Tae-Kyung Kim, David A. Harmin, Michael E. Greenberg, Alberto Riva. START: an automated tool for serial analysis of chromatin occupancy data
1002 -- 1003Martin Eisenacher, Jürgen de Braaf, Simone König. Mass Analysis Peptide Sequence Prediction (MAPSP)
1004 -- 1006Michael J. Sanderson. ::::Paloverde::::: an OpenGL 3D phylogeny browser
1007 -- 1009Surjit B. Dixit, David L. Beveridge. Structural bioinformatics of DNA: a web-based tool for the analysis of molecular dynamics results and structure prediction
1010 -- 1012Janko Dietzsch, Nils Gehlenborg, Kay Nieselt. Mayday-a microarray data analysis workbench
1013 -- 1014Jing Hua Zhao. Pedigree-drawing with R and graphviz
1015 -- 1017Ramon Aragues, Daniel Jaeggi, Baldo Oliva. PIANA: protein interactions and network analysis
1018 -- 1020Maria J. Schilstra, Lu Li, Joanne Matthews, Andrew Finney, Michael Hucka, Nicolas Le Novère. CellML2SBML: conversion of CellML into SBML
1021 -- 1023Balázs Adamcsek, Gergely Palla, Illés J. Farkas, Imre Derényi, Tamás Vicsek. CFinder: locating cliques and overlapping modules in biological networks
1024 -- 1026Adam Ameur, Vladimir Yankovski, Stefan Enroth, Ola Spjuth, Henryk Jan Komorowski. The LCB Data Warehouse
1027 -- 1028Yongliang Ren, Wuming Gong, Qiqi Xu, Xin Zheng, Dong Lin, Yejun Wang, Tongbin Li. siRecords: an extensive database of mammalian siRNAs with efficacy ratings
1029 -- 0Baolin Wu. Differential gene expression detection and sample classification using penalized linear regression models

Volume 22, Issue 7

775 -- 778Marialuisa Pellegrini-Calace, Anna Tramontano. Identification of a novel putative mitogen-activated kinase cascade on human chromosome 21 by computational approaches
779 -- 788Raja Jothi, Elena Zotenko, Asba Tasneem, Teresa M. Przytycka. COCO-CL: hierarchical clustering of homology relations based on evolutionary correlations
789 -- 794Rafael A. Irizarry, Zhijin Wu, Harris A. Jaffee. Comparison of Affymetrix GeneChip expression measures
795 -- 801Wei Pan. Incorporating gene functions as priors in model-based clustering of microarray gene expression data
802 -- 807H. P. Piepho, B. Keller, N. Hoecker, F. Hochholdinger. Combining signals from spotted cDNA microarrays obtained at different scanning intensities
808 -- 814Jinwook Seo, Heather Gordish-Dressman, Eric P. Hoffman. An interactive power analysis tool for microarray hypothesis testing and generation
815 -- 822Mukesh Bansal, Giusy Della Gatta, Diego di Bernardo. Inference of gene regulatory networks and compound mode of action from time course gene expression profiles
823 -- 829Haiyuan Yu, Alberto Paccanaro, Valery Trifonov, Mark Gerstein. Predicting interactions in protein networks by completing defective cliques
830 -- 836Zafer Barutçuoglu, Robert E. Schapire, Olga G. Troyanskaya. Hierarchical multi-label prediction of gene function
837 -- 842Ashish Choudhary, Marcel Brun, Jianping Hua, James Lowey, Edward Suh, Edward R. Dougherty. Genetic test bed for feature selection
843 -- 848Kazumi Hakamada, Masahiro Okamoto, Taizo Hanai. Novel technique for preprocessing high dimensional time-course data from DNA microarray: mathematical model-based clustering
849 -- 856Céline Rouveirol, Nicolas Stransky, Philippe Hupé, Philippe La Rosa, Eric Viara, Emmanuel Barillot, François Radvanyi. Computation of recurrent minimal genomic alterations from array-CGH data
857 -- 865Parantu K. Shah, Peer Bork. LSAT: learning about alternative transcripts in MEDLINE
866 -- 873Patricia L. Whetzel, Helen E. Parkinson, Helen C. Causton, Liju Fan, Jennifer Fostel, Gilberto Fragoso, Laurence Game, Mervi Heiskanen, Norman Morrison, Philippe Rocca-Serra, Susanna-Assunta Sansone, Chris J. Taylor 0002, Joseph White, Christian J. Stoeckert Jr.. The MGED Ontology: a resource for semantics-based description of microarray experiments
874 -- 882Sandhya Xirasagar, Scott F. Gustafson, Cheng-Cheng Huang, Qinyan Pan, Jennifer Fostel, Paul Boyer, B. Alex Merrick, Kenneth B. Tomer, Denny D. Chan, Kenneth J. Yost III, Danielle Choi, Nianqing Xiao, Stanley Stasiewicz, Pierre R. Bushel, Michael D. Waters. Chemical effects in biological systems (CEBS) object model for toxicology data, SysTox-OM: design and application
883 -- 884E. Ryder, R. Jackson, A. Ferguson-Smith, S. Russell. MAMMOT - a set of tools for the design, management and visualization of genomic tiling arrays
885 -- 886Payan Canaran, Lincoln Stein, Doreen Ware. Look-Align: an interactive web-based multiple sequence alignment viewer with polymorphism analysis support
887 -- 888Weizhong Li, Adam Godzik. VISSA: a program to visualize structural features from structure sequence alignment
889 -- 890Michael Sammeth, Thasso Griebel, Felix Tille, Jens Stoye. ::::Panta rhei:::: (QAlign2): an open graphical environment for sequence analysis
891 -- 893Avner Schlessinger, Guy Yachdav, Burkhard Rost. PROFbval: predict flexible and rigid residues in proteins
894 -- 896Fengfeng Zhou, Yu Xue, Xuebiao Yao, Ying Xu. CSS-Palm: palmitoylation site prediction with a clustering and scoring strategy (CSS)
897 -- 899James M. Wettenhall, Ken M. Simpson, Keith Satterley, Gordon K. Smyth. affylmGUI: a graphical user interface for linear modeling of single channel microarray data
900 -- 901Sébastien Carrère, Jérôme Gouzy. REMORA: a pilot in the ocean of BioMoby web-services
902 -- 903Pedro Cipriano Feijão, Lissiene Silva Neiva, Ana Maria Lima de Azeredo-Espin, Ana Cláudia Lessinger. AMiGA: the arthropodan mitochondrial genomes accessible database

Volume 22, Issue 6

643 -- 644Udo Hahn, Alfonso Valencia. Semantic Mining in Biomedicine ::::(Introduction to the papers selected from the SMBM 2005 Symposium, Hinxton, U.K., April 2005)::::
645 -- 650Jasmin Saric, Lars Juhl Jensen, Rossitza Ouzounova, Isabel Rojas, Peer Bork. Extraction of regulatory gene/protein networks from Medline
651 -- 657Ted Sandler, Andrew I. Schein, Lyle H. Ungar. Automatic term list generation for entity tagging
658 -- 664Patrick Ruch. Automatic assignment of biomedical categories: toward a generic approach
665 -- 670Jin-Bok Lee, Jung-jae Kim, Jong C. Park. Automatic extension of Gene Ontology with flexible identification of candidate terms
671 -- 675Elizabeta Bab-Dinitz, Hagay Shmuely, Julie Maupin-Furlow, Jerry Eichler, Boaz Shaanan. ::::Haloferax volcanii:::: PitA: an example of functional interaction between the Pfam chlorite dismutase and antibiotic biosynthesis monooxygenase families?
676 -- 684Valentina Boeva, Mireille Régnier, Dmitri A. Papatsenko, Vsevolod Makeev. Short fuzzy tandem repeats in genomic sequences, identification, and possible role in regulation of gene expression
685 -- 691Chia-Jung Chang, Yao-Ting Huang, Kun-Mao Chao. A greedier approach for finding tag SNPs
692 -- 698Xiang Shao, Valery Shepelev, Alexei Fedorov. Bioinformatic analysis of exon repetition, exon scrambling and trans-splicing in humans
699 -- 707Joanna C. Chiu, Ernest K. Lee, Mary G. Egan, Indra Neil Sarkar, Gloria M. Coruzzi, Robert DeSalle. OrthologID: automation of genome-scale ortholog identification within a parsimony framework
708 -- 715Daniele Catanzaro, Raffaele Pesenti, Michel C. Milinkovitch. A non-linear optimization procedure to estimate distances and instantaneous substitution rate matrices under the GTR model
716 -- 722Tanja Gesell, Arndt von Haeseler. ::::In silico:::: sequence evolution with site-specific interactions along phylogenetic trees
723 -- 730Benjamin J. Polacco, Patricia C. Babbitt. Automated discovery of 3D motifs for protein function annotation
731 -- 738Kristin Missal, Michael A. Cross, Dirk Drasdo. Gene network inference from incomplete expression data: transcriptional control of hematopoietic commitment
739 -- 746Chiara Sabatti, Gareth M. James. Bayesian sparse hidden components analysis for transcription regulation networks
747 -- 754Zheng Li, Stephen M. Shaw, Matthew J. Yedwabnick, Christina Chan. Using a state-space model with hidden variables to infer transcription factor activities
755 -- 761Zuyi Wang, Yue Wang, Jianhua Xuan, Yibin Dong, Marina Bakay, Yuanjian Feng, Robert Clarke, Eric P. Hoffman. Optimized multilayer perceptrons for molecular classification and diagnosis using genomic data
762 -- 764Wolfgang Gerlach, Robert Giegerich. GUUGle: a utility for fast exact matching under RNA complementary rules including G-U base pairing
765 -- 767Jonathon Blake, Christian Schwager, Misha Kapushesky, Alvis Brazma. ChroCoLoc: an application for calculating the probability of co-localization of microarray gene expression
768 -- 770Mary K. Kuhner. LAMARC 2.0: maximum likelihood and Bayesian estimation of population parameters
771 -- 772Alun Thomas, Nicola J. Camp. Maximum likelihood estimates of allele frequencies and error rates from samples of related individuals by gene counting
773 -- 774Euan A. Adie, Richard R. Adams, Kathryn L. Evans, David J. Porteous, Ben S. Pickard. SUSPECTS: enabling fast and effective prioritization of positional candidates

Volume 22, Issue 5

517 -- 522Daniel Dalevi, Devdatt P. Dubhashi, Malte Hermansson. Bayesian classifiers for detecting HGT using fixed and variable order markov models of genomic signatures
523 -- 526Guojun Yang, Timothy C. Hall. HideNseek, a post-genome approach to locate transgenes exemplified in ::::Arabidopsis thaliana::::
527 -- 531Giuseppe D Auria, Ravindra Pushker, Francisco Rodríguez-Valera. IWoCS: analyzing ribosomal intergenic transcribed spacers configuration and taxonomic relationships
532 -- 540Wolfgang P. Lehrach, Dirk Husmeier, Christopher K. I. Williams. A regularized discriminative model for the prediction of protein-peptide interactions
541 -- 549Matthew Rabinowitz, Lance Myers, Milena Banjevic, Albert Chan, Joshua Sweetkind-Singer, Jessica Haberer, Kelly McCann, Roland Wolkowicz. Accurate prediction of HIV-1 drug response from the reverse transcriptase and protease amino acid sequences using sparse models created by convex optimization
550 -- 555Andreas Henschel, Wan Kyu Kim, Michael Schroeder. Equivalent binding sites reveal convergently evolved interaction motifs
556 -- 565Alexander Ploner, Stefano Calza, Arief Gusnanto, Yudi Pawitan. Multidimensional local false discovery rate for microarray studies
566 -- 572Johannes Tuikkala, Laura Elo, Olli Nevalainen, Tero Aittokallio. Improving missing value estimation in microarray data with gene ontology
573 -- 580Miguel Pérez-Enciso. Multiple association analysis via simulated annealing (MASSA)
581 -- 588Yoram Louzoun, Lev Muchnik, Sorin Solomon. Copying nodes versus editing links: the source of the difference between genetic regulatory networks and the WWW
589 -- 596Roberto Amato, Angelo Ciaramella, N. Deniskina, Carmine Del Mondo, Diego di Bernardo, Ciro Donalek, Giuseppe Longo, Giuseppe Mangano, Gennaro Miele, Giancarlo Raiconi, Antonino Staiano, Roberto Tagliaferri. A multi-step approach to time series analysis and gene expression clustering
597 -- 605Jung-jae Kim, Zhuo Zhang, Jong C. Park, See-Kiong Ng. BioContrasts: extracting and exploiting protein-protein contrastive relations from biomedical literature
606 -- 613Ofer Shai, Quaid Morris, Benjamin J. Blencowe, Brendan J. Frey. Inferring global levels of alternative splicing isoforms using a generative model of microarray data
614 -- 615Stephan H. F. Bernhart, Ivo L. Hofacker, Peter F. Stadler. Local RNA base pairing probabilities in large sequences
616 -- 617Leighton Pritchard, Jennifer A. White, Paul R. J. Birch, Ian K. Toth. GenomeDiagram: a python package for the visualization of large-scale genomic data
618 -- 620Andrew Smith, John-Marc Chandonia, Steven E. Brenner. ANDY: a general, fault-tolerant tool for database searching on computer clusters
621 -- 622Dominik Gront, Andrzej Kolinski. BioShell - a package of tools for structural biology computations
623 -- 625Mikhail A. Lomize, Andrei L. Lomize, Irina D. Pogozheva, Henry I. Mosberg. OPM: Orientations of Proteins in Membranes database
626 -- 627Bradley M. Hemminger, Billy Saelim, Patrick F. Sullivan. TAMAL: an integrated approach to choosing SNPs for genetic studies of human complex traits
628 -- 629Colin S. Gillespie, Darren J. Wilkinson, Carole J. Proctor, Daryl P. Shanley, Richard J. Boys, Thomas B. L. Kirkwood. Tools for the SBML Community
630 -- 631Guido Dieterich, Uwe Kärst, Jürgen Wehland, Lothar Jänsch. VIS-O-BAC: exploratory visualization of functional genome studies from bacteria
632 -- 633J. A. Falkner, J. W. Falkner, P. C. Andrews. ProteomeCommons.org JAF: reference information and tools for proteomics
634 -- 636Mikko Katajamaa, Jarkko Miettinen, Matej Oresic. MZmine: toolbox for processing and visualization of mass spectrometry based molecular profile data
637 -- 640Stephen Montgomery, Obi L. Griffith, Monica C. Sleumer, Casey M. Bergman, Misha Bilenky, Erin Pleasance, Y. Prychyna, X. Zhang, Steven J. M. Jones. ORegAnno: an open access database and curation system for literature-derived promoters, transcription factor binding sites and regulatory variation
641 -- 642M. Dennis Prickett, Matt Page, Angela E. Douglas, Gavin H. Thomas. ::::Buchnera::::BASE: a post-genomic resource for ::::Buchnera:::: sp. APS

Volume 22, Issue 4

385 -- 391Jiexin Zhang, Li Zhang, Kevin R. Coombes. Gene sequence signatures revealed by mining the UniGene affiliation network
392 -- 399Xiang Guo, Kay Tatsuoka, Rongxiang Liu. Histone acetylation and transcriptional regulation in the genome of ::::Saccharomyces cerevisiae::::
400 -- 406Jussi Salmi, Robert Moulder, Jan-Jonas Filén, Olli Nevalainen, Tuula A. Nyman, Riitta Lahesmaa, Tero Aittokallio. Quality classification of tandem mass spectrometry data
407 -- 412András Kocsor, Attila Kertész-Farkas, László Kaján, Sándor Pongor. Application of compression-based distance measures to protein sequence classification: a methodological study
413 -- 422Yao-ming Huang, Christopher Bystroff. Improved pairwise alignments of proteins in the Twilight Zone using local structure predictions
423 -- 429Kenzie D. MacIsaac, D. Benjamin Gordon, Lena Nekludova, Duncan T. Odom, Joerg Schreiber, David K. Gifford, Richard A. Young, Ernest Fraenkel. A hypothesis-based approach for identifying the binding specificity of regulatory proteins from chromatin immunoprecipitation data
430 -- 437Tilman Sauer, Ekaterina Shelest, Edgar Wingender. Evaluating phylogenetic footprinting for human-rodent comparisons
438 -- 444Joseph M. Volpe, Lindsay G. Cowell, Thomas B. Kepler. SoDA: implementation of a 3D alignment algorithm for inference of antigen receptor recombinations
445 -- 452Zizhen Yao, Zasha Weinberg, Walter L. Ruzzo. CMfinder - a covariance model based RNA motif finding algorithm
453 -- 459Elodie Duprat, Marie-Paule Lefranc, Olivier Gascuel. A simple method to predict protein-binding from aligned sequences - application to MHC superfamily and ß2-microglobulin
460 -- 465Simon W. Ginzinger, Johannes Fischer. SimShift: Identifying structural similarities from NMR chemical shifts
466 -- 471Lexin Li. Survival prediction of diffuse large-B-cell lymphoma based on both clinical and gene expression information
472 -- 476Baolin Wu. Differential gene expression detection and sample classification using penalized linear regression models
477 -- 484Eugene P. van Someren, B. L. T. Vaes, W. T. Steegenga, A. M. Sijbers, K. J. Dechering, Marcel J. T. Reinders. Least absolute regression network analysis of the murine osteoblast differentiation network
485 -- 492Siddhartha Basu, Erich Bremer, Chun Zhou, Daniel F. Bogenhagen. MiGenes: a searchable interspecies database of mitochondrial proteins curated using gene ontology annotation
493 -- 494Jörg Rothgänger, Markus Weniger, Thomas Weniger, Alexander Mellmann, Dag Harmsen. Ridom TraceEdit: a DNA trace editor and viewer
495 -- 496Derek Huntley, Angela Baldo, Saurabh Johri, Marek J. Sergot. SEAN: SNP prediction and display program utilizing EST sequence clusters
497 -- 499Tiziana Castrignanò, Paolo D Onorio De Meo, Giorgio Grillo, Sabino Liuni, Flavio Mignone, Ivano Giuseppe Talamo, Graziano Pesole. GenoMiner: a tool for genome-wide search of coding and non-coding conserved sequence tags
500 -- 503Peter Steffen, Björn Voß, Marc Rehmsmeier, Jens Reeder, Robert Giegerich. RNAshapes: an integrated RNA analysis package based on abstract shapes
504 -- 506John Eargle, Dan Wright, Zaida Luthey-Schulten. ::::Multiple Alignment:::: of protein structures and sequences for VMD
507 -- 508Jeffrey T. Leek, Eva Monsen, Alan R. Dabney, John D. Storey. EDGE: extraction and analysis of differential gene expression
509 -- 511Michael Mueller, Anuj Goel, Manjula Thimma, Nicholas J. Dickens, Timothy J. Aitman, Jonathan Mangion. eQTL Explorer: integrated mining of combined genetic linkage and expression experiments
512 -- 513B. L. Browning. FLOSS: flexible ordered subset analysis for linkage mapping of complex traits
514 -- 515Henning Schmidt, Mats Jirstrand. Systems Biology Toolbox for MATLAB: a computational platform for research in systems biology

Volume 22, Issue 3

257 -- 263Lakshminarayan M. Iyer, A. Maxwell Burroughs, L. Aravind. The ASCH superfamily: novel domains with a fold related to the PUA domain and a potential role in RNA metabolism
264 -- 268Matthew H. J. Cordes, Greta J. Binford. Lateral gene transfer of a dermonecrotic toxin between spiders and bacteria
269 -- 277Núria López-Bigas, Benjamin J. Blencowe, Christos A. Ouzounis. Highly consistent patterns for inherited human diseases at the molecular level
278 -- 284Susan Idicula-Thomas, Abhijit J. Kulkarni, Bhaskar D. Kulkarni, Valadi K. Jayaraman, Petety V. Balaji. A support vector machine-based method for predicting the propensity of a protein to be soluble or to form inclusion body on overexpression in ::::Escherichia coli::::
285 -- 290Qiwen Dong, Xiaolong Wang, Lei Lin. Application of latent semantic analysis to protein remote homology detection
291 -- 296S. Vishnu V. Deevi, Andrew C. R. Martin. An extensible automated protein annotation tool: standardizing input and output using validated XML
297 -- 302Eunhee Koh, Taehyo Kim, Hyun-soo Cho. Mean curvature as a major determinant of ß-sheet propensity
303 -- 309Baoqiang Cao, Aleksey A. Porollo, Rafal Adamczak, Mark Jarrell, Jaroslaw Meller. Enhanced recognition of protein transmembrane domains with prediction-based structural profiles
310 -- 316Earl F. Glynn, Jie Chen, Arcady R. Mushegian. Detecting periodic patterns in unevenly spaced gene expression time series using Lomb-Scargle periodograms
317 -- 325Wensheng Zhang, Romdhane Rekaya, Keith Bertrand. A method for predicting disease subtypes in presence of misclassification among training samples using gene expression: application to human breast cancer
326 -- 331Dick de Ridder, Frank J. T. Staal, Jacques J. M. van Dongen, Marcel J. T. Reinders. Maximum significance clustering of oligonucleotide microarrays
332 -- 340Jianhua Ruan, Weixiong Zhang. A bi-dimensional regression tree approach to the modeling of gene expression regulation
341 -- 345Peter Beerli. Comparison of Bayesian and maximum-likelihood inference of population genetic parameters
346 -- 353Ravishankar Rao Vallabhajosyula, Vijay Chickarmane, Herbert M. Sauro. Conservation analysis of large biochemical networks
354 -- 355Mark W. E. J. Fiers, Huub van de Wetering, Tim H. J. M. Peeters, Jarke J. van Wijk, Jan Peter Nap. DNAVis: interactive visualization of comparative genome annotations
356 -- 358A. V. McDonnell, T. Jiang, A. E. Keating, B. Berger. Paircoil2: improved prediction of coiled coils from sequence
359 -- 360Tobias Dezulian, Michael Remmert, Javier F. Palatnik, Detlef Weigel, Daniel H. Huson. Identification of plant microRNA homologs
361 -- 362Tiago José P. Sobreira, Alan M. Durham, Arthur Gruber. TRAP: automated classification, quantification and annotation of tandemly repeated sequences
363 -- 364Nicolas Bortolussi, Eric Durand, Michael Blum, Olivier François. apTreeshape: statistical analysis of phylogenetic tree shape
365 -- 366Andreas Moll, Andreas Hildebrandt, Hans-Peter Lenhof, Oliver Kohlbacher. BALLView: a tool for research and education in molecular modeling
367 -- 368Elo Leung, Pierre R. Bushel. PAGE: phase-shifted analysis of gene expression
369 -- 370Giorgio Valentini. Clusterv: a tool for assessing the reliability of clusters discovered in DNA microarray data
371 -- 373Dumitru Brinza, Alexander Zelikovsky. 2SNP: scalable phasing based on 2-SNP haplotypes
374 -- 375Ugur Dogrusöz, E. Z. Erson, Erhan Giral, Emek Demir, Ozgun Babur, Ahmet Cetintas, R. Colak. Patika::::web::::: a Web interface for analyzing biological pathways through advanced querying and visualization
376 -- 377Hu Chen, Ni Huang, Zhirong Sun. SubLoc: a server/client suite for protein subcellular location based on SOAP
378 -- 380Jing Ding, Laron M. Hughes, Daniel Berleant, Andy W. Fulmer, Eve Syrkin Wurtele. PubMed Assistant: a biologist-friendly interface for enhanced PubMed search
381 -- 383Steven M. Gallo, Long Li, Zihua Hu, Marc S. Halfon. ::::REDfly: :::: a Regulatory Element Database for ::::Drosophila::::

Volume 22, Issue 24

2973 -- 2974Trey Ideker, Alfonso Valencia. Bioinformatics in the human interactome project
2975 -- 2979Koen Deforche, T. Silander, Ricardo Camacho, Z. Grossman, M. A. Soares, Kristel Van Laethem, R. Kantor, Yves Moreau, Anne-Mieke Vandamme. Analysis of HIV-1 ::::pol:::: sequences using Bayesian Networks: implications for drug resistance
2980 -- 2987Xuehui Li, Tamer Kahveci. A Novel algorithm for identifying low-complexity regions in a protein sequence
2988 -- 2995Stinus Lindgreen, Paul P. Gardner, Anders Krogh. Measuring covariation in RNA alignments: physical realism improves information measures
2996 -- 3002Nuno D. Mendes, Ana C. Casimiro, Pedro M. Santos, Isabel Sá-Correia, Arlindo L. Oliveira, Ana T. Freitas. MUSA: a parameter free algorithm for the identification of biologically significant motifs
3003 -- 3008Mireia Vilardell, Alex Sánchez-Pla. Hypothesis testing approaches to the exon prediction problem
3009 -- 3015Olav Zimmermann, Ulrich H. E. Hansmann. Support vector machines for prediction of dihedral angle regions
3016 -- 3024Jiang Du, Joel S. Rozowsky, Jan O. Korbel, Zhengdong D. Zhang, Thomas E. Royce, Martin H. Schultz, Michael Snyder, Mark Gerstein. A supervised hidden markov model framework for efficiently segmenting tiling array data in transcriptional and chIP-chip experiments: systematically incorporating validated biological knowledge
3025 -- 3031Yudi Pawitan, Stefano Calza, Alexander Ploner. Estimation of false discovery proportion under general dependence
3032 -- 3039Cathal Seoighe, Victoria Nembaware, Konrad Scheffler. Maximum likelihood inference of imprinting and allele-specific expression from EST data
3040 -- 3046Mark P. Brynildsen, Linh M. Tran, James C. Liao. A Gibbs sampler for the identification of gene expression and network connectivity consistency
3047 -- 3053János Z. Kelemen, Attila Kertész-Farkas, András Kocsor, László G. Puskás. Kalman filtering for disease-state estimation from microarray data
3054 -- 3060Daniel S. Yuan, Rafael A. Irizarry. High-resolution spatial normalization for microarrays containing embedded technical replicates
3061 -- 3066Paul Fearnhead. SequenceLDhot: detecting recombination hotspots
3067 -- 3074Stefan Hoops, Sven Sahle, Ralph Gauges, Christine Lee, Jürgen Pahle, Natalia Simus, Mudita Singhal, Liang Xu, Pedro Mendes, Ursula Kummer. COPASI - a COmplex PAthway SImulator
3075 -- 3081Claudio Eccher, Corrado Priami. Design and implementation of a tool for translating SBML into the biochemical stochastic pi-calculus
3082 -- 3088Fangping Mu, Pat J. Unkefer, Clifford J. Unkefer, William S. Hlavacek. Prediction of oxidoreductase-catalyzed reactions based on atomic properties of metabolites
3089 -- 3095Naoaki Okazaki, Sophia Ananiadou. Building an abbreviation dictionary using a term recognition approach
3096 -- 3098Sergei L. Kosakovsky Pond, David Posada, Michael B. Gravenor, Christopher H. Woelk, Simon D. W. Frost. GARD: a genetic algorithm for recombination detection
3099 -- 3100Jan Mrázek, Shaohua Xie. Pattern locator: a new tool for finding local sequence patterns in genomic DNA sequences
3101 -- 3102G. Andrew Woolley, En-shiun Lee, Fuzhong Zhang. sGAL: a computational method for finding surface exposed sites in proteins suitable for Cys-mediated cross-linking
3103 -- 3105Thomas Hoffmann, Christoph Lange. P:::2:::BAT: a massive parallel implementation of PBAT for genome-wide association studies in R
3106 -- 3108Jeongah Yoon, Anselm Blumer, Kyongbum Lee. An algorithm for modularity analysis of directed and weighted biological networks based on edge-betweenness centrality

Volume 22, Issue 23

2841 -- 2845Zoë Birtle, Chris P. Ponting. Meisetz and the birth of the KRAB motif
2846 -- 2850Melissa Da Silva, Ling Shen, Vasily Tcherepanov, Cristalle Watson, Chris Upton. Predicted function of the vaccinia virus G5R protein
2851 -- 2857Torben Friedrich, Birgit Pils, Thomas Dandekar, Jörg Schultz, Tobias Müller. Modelling interaction sites in protein domains with interaction profile hidden Markov models
2858 -- 2864Nora Pierstorff, Casey M. Bergman, Thomas Wiehe. Identifying ::::cis::::-regulatory modules by combining comparative and compositional analysis of DNA
2865 -- 2869László Kaján, Attila Kertész-Farkas, Dino Franklin, Neli Ivanova, András Kocsor, Sándor Pongor. Application of a simple likelihood ratio approximant to protein sequence classification
2870 -- 2875Nak-Kyeong Kim, Kannan Tharakaraman, John L. Spouge. Adding sequence context to a Markov background model improves the identification of regulatory elements
2876 -- 2882Qifang Xu, Adrian A. Canutescu, Zoran Obradovic, Roland L. Dunbrack Jr.. ProtBuD: a database of biological unit structures of protein families and superfamilies
2883 -- 2889Dong Wang, Yingli Lv, Zheng Guo, Xia Li, Yanhui Li, Jing Zhu, Da Yang, Jianzhen Xu, Chenguang Wang, Shaoqi Rao, Baofeng Yang. Effects of replacing the unreliable cDNA microarray measurements on the disease classification based on gene expression profiles and functional modules
2890 -- 2897Curtis Huttenhower, Matthew A. Hibbs, Chad L. Myers, Olga G. Troyanskaya. A scalable method for integration and functional analysis of multiple microarray datasets
2898 -- 2904Sukjoon Yoon, Young Yang, Jiwon Choi, Jeeweon Seong. Large scale data mining approach for gene-specific standardization of microarray gene expression data
2905 -- 2909Alexander Begun. Robust method for detecting differential gene expression in twin studies
2910 -- 2917Antti Lehmussola, Pekka Ruusuvuori, Olli Yli-Harja. Evaluating the performance of microarray segmentation algorithms
2918 -- 2925Chris Sanford, Matthew L. K. Yip, Carl White, John Parkinson. Cell++ - simulating biochemical pathways
2926 -- 2933Jeffrey T. Chang, Joseph Nevins. GATHER: a systems approach to interpreting genomic signatures
2934 -- 2939Sorin Draghici, Sivakumar Sellamuthu, Purvesh Khatri. Babel s tower revisited: a universal resource for cross-referencing across annotation databases
2940 -- 2944Agrawal Shipra, Kumar Chetan, M. R. S. Rao. CREMOFAC - a database of chromatin remodeling factors
2945 -- 2947Yan V. Sun, Douglas M. Jacobsen, Sharon L. R. Kardia. ChromoScan: a scan statistic application for identifying chromosomal regions in genomic studies
2948 -- 2949Oxana V. Galzitskaya, Sergiy O. Garbuzynskiy, Michail Yu. Lobanov. FoldUnfold: web server for the prediction of disordered regions in protein chain
2950 -- 2951James W. MacDonald, Debashis Ghosh. COPA - cancer outlier profile analysis
2952 -- 2954Xiaohui Chen, Ming Chen, Kaida Ning. ::::BNArray::::: an R package for constructing gene regulatory networks from microarray data by using Bayesian network
2955 -- 2957Xiangfeng Wang, Hang He, Lei Li, Runsheng Chen, Xing Wang Deng, Songgang Li. NMPP: a user-customized NimbleGen microarray data processing pipeline
2958 -- 2959Nicolas Goffard, Georg Weiller. Extending MapMan: application to legume genome arrays
2960 -- 2961Dale R. Nyholt. ssSNPer: identifying statistically similar SNPs to aid interpretation of genetic association studies
2962 -- 2965Boyke Bunk, Martin Kucklick, Rochus Jonas, Richard Münch, Max Schobert, Dieter Jahn, Karsten Hiller. MetaQuant: a tool for the automatic quantification of GC/MS-based metabolome data
2966 -- 2967Anastasia Deckard, Frank T. Bergmann, Herbert M. Sauro. Supporting the SBML layout extension
2968 -- 2970Kevin Y. Yip, Haiyuan Yu, Philip M. Kim, Martin H. Schultz, Mark Gerstein. The tYNA platform for comparative interactomics: a web tool for managing, comparing and mining multiple networks
2971 -- 2972S. Blair Hedges, Joel Dudley, Sudhir Kumar. TimeTree: a public knowledge-base of divergence times among organisms

Volume 22, Issue 22

2711 -- 2714Mensur Dlakic. DUF283 domain of Dicer proteins has a double-stranded RNA-binding fold
2715 -- 2721Usman Roshan, Dennis R. Livesay. Probalign: multiple sequence alignment using partition function posterior probabilities
2722 -- 2728Xudong Xie, Shuanhu Wu, Kin-Man Lam, Hong Yan. PromoterExplorer: an effective promoter identification method based on the AdaBoost algorithm
2729 -- 2734Emidio Capriotti, Remo Calabrese, Rita Casadio. Predicting the insurgence of human genetic diseases associated to single point protein mutations with support vector machines and evolutionary information
2735 -- 2738Anne E. Counterman Burba, Ursula Lehnert, Eric Z. Yu, Mark Gerstein. Helix Interaction Tool (HIT): a web-based tool for analysis of helix-helix interactions in proteins
2739 -- 2745J. E. Ecker-Passow, Ann L. Oberg, Terry M. Therneau, C. J. Mason, Douglas W. Mahoney, K. L. Johnson, J. E. Olson, H. R. Bergen III. Regression analysis for comparing protein samples with :::16:::O/:::18:::O stable-isotope labeled mass spectrometry
2746 -- 2752N. Morozova, J. Allers, J. Myers, Y. Shamoo. Protein-RNA interactions: exploring binding patterns with a three-dimensional superposition analysis of high resolution structures
2753 -- 2760Darrin P. Lewis, Tony Jebara, William Stafford Noble. Support vector machine learning from heterogeneous data: an empirical analysis using protein sequence and structure
2761 -- 2767Stewart T. Chang, Debashis Ghosh, Denise E. Kirschner, Jennifer J. Linderman. Peptide length-based prediction of peptide-MHC class II binding
2768 -- 2774Yong Zhao, Daniel Stoffler, Michel F. Sanner. Hierarchical and multi-resolution representation of protein flexibility
2775 -- 2781Guido Sanguinetti, Neil D. Lawrence, Magnus Rattray. Probabilistic inference of transcription factor concentrations and gene-specific regulatory activities
2782 -- 2789Mark Griffith, Tod Courtney, Jean Peccoud, William H. Sanders. Dynamic partitioning for hybrid simulation of the bistable HIV-1 transactivation network
2790 -- 2799Matthias Heinemann, Sven Panke. Synthetic biology - putting engineering into biology
2800 -- 2805Jianzhen Xu, Yongjin Li. Discovering disease-genes by topological features in human protein-protein interaction network
2806 -- 2812Vitaly A. Selivanov, Silvia Marin, Paul W.-N. Lee, Marta Cascante. Software for dynamic analysis of tracer-based metabolomic data: estimation of metabolic fluxes and their statistical analysis
2813 -- 2818Wei Zhou, Vetle I. Torvik, Neil R. Smalheiser. ADAM: another database of abbreviations in MEDLINE
2819 -- 2820A. Billion, Rohit Ghai, Trinad Chakraborty, Torsten Hain. Augur - a computational pipeline for whole genome microbial surface protein prediction and classification
2821 -- 2822Mario A. Fares, David McNally. CAPS: coevolution analysis using protein sequences
2823 -- 2824Luke Sheneman, Jason Evans, James A. Foster. Clearcut: a fast implementation of relaxed neighbor joining
2825 -- 2827Fangxin Hong, Rainer Breitling, Connor W. McEntee, Ben S. Wittner, Jennifer L. Nemhauser, Joanne Chory. RankProd: a bioconductor package for detecting differentially expressed genes in meta-analysis
2828 -- 2829Torsten Hothorn, Peter Bühlmann. Model-based boosting in high dimensions
2830 -- 2832Brendan MacLean, Jimmy K. Eng, Ronald C. Beavis, Martin McIntosh. General framework for developing and evaluating database scoring algorithms using the TANDEM search engine
2833 -- 2834Lei Zhang, Daiwen Yang. SCAssign: a sparky extension for the NMR resonance assignment of aliphatic side-chains of uniformly :::13:::C, :::15:::N-labeled large proteins
2835 -- 2837Eric J. Vallender, Justin E. Paschall, Christine M. Malcom, Bruce T. Lahn, Gerald J. Wyckoff. SPEED: a molecular-evolution-based database of mammalian orthologous groups
2838 -- 2840Kris Laukens, Rune Matthiesen, Filip Lemière, Eddy Esmans, Harry Van Onckelen, Ole Nørregaard Jensen, Erwin Witters. Integration of gel-based proteome data with pProRep

Volume 22, Issue 21

2581 -- 2584Kira S. Makarova, Nick V. Grishin, Eugene V. Koonin. The HicAB cassette, a putative novel, RNA-targeting toxin-antitoxin system in archaea and bacteria
2585 -- 2589Yu Wang, Tobias Hindemitt, Klaus F. X. Mayer. Significant sequence similarities in promoters and precursors of ::::Arabidopsis thaliana:::: non-conserved microRNAs
2590 -- 2596Chunlin Wang, Chris H. Q. Ding, Richard F. Meraz, Stephen R. Holbrook. PSoL: a positive sample only learning algorithm for finding non-coding RNA genes
2597 -- 2603Levon Budagyan, Ruben Abagyan. Weighted quality estimates in machine learning
2604 -- 2611Guohua Jin, Luay Nakhleh, Sagi Snir, Tamir Tuller. Maximum likelihood of phylogenetic networks
2612 -- 2618Dominique Douguet, Huei-Chi Chen, Andrey Tovchigrechko, Ilya A. Vakser. DOCKGROUND resource for studying protein-protein interfaces
2619 -- 2627Eran Eyal, Lee-Wei Yang, Ivet Bahar. Anisotropic network model: systematic evaluation and a new web interface
2628 -- 2634Fabian Birzele, Stefan Kramer. A new representation for protein secondary structure prediction based on frequent patterns
2635 -- 2642Ronglai Shen, Debashis Ghosh, Arul M. Chinnaiyan, Zhaoling Meng. Eigengene-based linear discriminant model for tumor classification using gene expression microarray data
2643 -- 2649Natasa Rajicic, Dianne M. Finkelstein, David A. Schoenfeld. Survival analysis of longitudinal microarrays
2650 -- 2657Chao Cheng, Xiaotu Ma, Xiting Yan, Fengzhu Sun, Lei M. Li. MARD: a new method to detect differential gene expression in treatment-control time courses
2658 -- 2666A. Callegaro, Dario Basso, Silvio Bicciato. A locally adaptive statistical procedure (LAP) to identify differentially expressed chromosomal regions
2667 -- 2673Joe Faith, Robert Mintram, Maia Angelova. Targeted projection pursuit for visualizing gene expression data classifications
2674 -- 2680Nicole Radde, Jutta Gebert, Christian V. Forst. Systematic component selection for gene-network refinement
2681 -- 2687Visakan Kadirkamanathan, Jing Yang, Stephen A. Billings, Phillip C. Wright. Markov Chain Monte Carlo Algorithm based metabolic flux distribution analysis on ::::Corynebacterium glutamicum::::
2688 -- 2690Alexandros Stamatakis. RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models
2691 -- 2692Brajesh Kumar Rai, Carlos J. Madrid-Aliste, J. Eduardo Fajardo, András Fiser. MMM: a sequence-to-structure alignment protocol
2693 -- 2694Shantanu Sharma, Feng Ding, Huifen Nie, Daniel Watson, Aditya Unnithan, Jameson Lopp, Diane Pozefsky, Nikolay V. Dokholyan. iFold: a platform for interactive folding simulations of proteins
2695 -- 2696Barry J. Grant, Ana P. C. Rodrigues, Karim M. ElSawy, J. Andrew McCammon, Leo S. D. Caves. Bio3d: an R package for the comparative analysis of protein structures
2697 -- 2698Tsun-Po Yang, Ting-Yu Chang, Chi-Hung Lin, Ming-Ta Hsu, Hsei-Wei Wang. ArrayFusion: a web application for multi-dimensional analysis of CGH, SNP and microarray data
2699 -- 2701Kellie J. Archer, Tobias Guennel. An application for assessing quality of RNA hybridized to Affymetrix GeneChips
2702 -- 2703Grégory Deceliere, Yann Letrillard, Sandrine Charles, Christian Biémont. TESD: a transposable element dynamics simulation environment
2704 -- 2705Zhike Zi, Edda Klipp. SBML-PET: a Systems Biology Markup Language-based parameter estimation tool
2706 -- 2708Ronald C. Taylor, Anuj Shah, Charles Treatman, Meridith Blevins. SEBINI: Software Environment for BIological Network Inference
2709 -- 2710Markus Ulrich, Constantin Kappel, Joël Beaudouin, Stefan Hezel, Jochen Ulrich, Roland Eils. Tropical - parameter estimation and simulation of reaction-diffusion models based on spatio-temporal microscopy images

Volume 22, Issue 20

2455 -- 2458Sunil Archak, Javaregowda Nagaraju. Eicosapentapeptide repeats (EPRs): novel repeat proteins specific to flowering plants
2459 -- 2462Dapeng Zhang, Christopher J. Martyniuk, Vance L. Trudeau. SANTA domain: a novel conserved protein module in ::::Eukaryota:::: with potential involvement in chromatin regulation
2463 -- 2465Michaël Bekaert, John F. Atkins, Pavel V. Baranov. ARFA: a program for annotating bacterial release factor genes, including prediction of programmed ribosomal frameshifting
2466 -- 2474Pekka Marttinen, Jukka Corander, Petri Törönen, Liisa Holm. Bayesian search of functionally divergent protein subgroups and their function specific residues
2475 -- 2479Xijin Ge, Qingfa Wu, Yong-Chul Jung, Jun Chen, San Ming Wang. A large quantity of novel human antisense transcripts detected by LongSAGE
2480 -- 2487Michiaki Hamada, Koji Tsuda, Taku Kudo, Taishin Kin, Kiyoshi Asai. Mining frequent stem patterns from unaligned RNA sequences
2488 -- 2492Tetsuya Sato, Yoshihiro Yamanishi, Katsuhisa Horimoto, Minoru Kanehisa, Hiroyuki Toh. Partial correlation coefficient between distance matrices as a new indicator of protein-protein interactions
2493 -- 2499Konrad Scheffler, Darren P. Martin, Cathal Seoighe. Robust inference of positive selection from recombining coding sequences
2500 -- 2506Theodora Manoli, Norbert Gretz, Hermann-Josef Gröne, Marc Kenzelmann, Roland Eils, Benedikt Brors. Group testing for pathway analysis improves comparability of different microarray datasets
2507 -- 2515Xin Zhou, K. Z. Mao. The ties problem resulting from counting-based error estimators and its impact on gene selection algorithms
2516 -- 2522Saumyadipta Pyne, Bruce Futcher, Steven Skiena. Meta-analysis based on control of false discovery rate: combining yeast ChIP-chip datasets
2523 -- 2531Adriano V. Werhli, Marco Grzegorczyk, Dirk Husmeier. Comparative evaluation of reverse engineering gene regulatory networks with relevance networks, graphical gaussian models and bayesian networks
2532 -- 2538Quansong Ruan, Debojyoti Dutta, Michael S. Schwalbach, Joshua A. Steele, Jed A. Fuhrman, Fengzhu Sun. Local similarity analysis reveals unique associations among marine bacterioplankton species and environmental factors
2539 -- 2546Gautier Stoll, Jacques Rougemont, Felix Naef. Few crucial links assure checkpoint efficiency in the yeast cell-cycle network
2547 -- 2553E. S. Motakis, G. P. Nason, P. Fryzlewicz, G. A. Rutter. Variance stabilization and normalization for one-color microarray data using a data-driven multiscale approach
2554 -- 2555Max Bylesjö, Andreas Sjödin, Daniel Eriksson, Henrik Antti, Thomas Moritz, Stefan Jansson, Johan Trygg. MASQOT-GUI: spot quality assessment for the two-channel microarray platform
2556 -- 2557Frédéric Guillaume, Jacques Rougemont. Nemo: an evolutionary and population genetics programming framework
2558 -- 2561Jingwu He, Alexander Zelikovsky. MLR-tagging: informative SNP selection for unphased genotypes based on multiple linear regression
2562 -- 2564Qi Zhao, Radka Stoyanova, Shuyan Du, Paul Sajda, Truman R. Brown. ::::HiRes:::: - a tool for comprehensive assessment and interpretation of metabolomic data
2565 -- 2566Roger M. Jarvis, David Broadhurst, Helen E. Johnson, Noel M. O Boyle, Royston Goodacre. PYCHEM: a multivariate analysis package for python
2567 -- 2569Julio Bonis, Laura Inés Furlong, Ferran Sanz. OSIRIS: a tool for retrieving literature about sequence variants
2570 -- 2571Luca Lenzi, Flavia Frabetti, Federica Facchin, Raffaella Casadei, Lorenza Vitale, Silvia Canaider, Paolo Carinci, Maria Zannotti, Pierluigi Strippoli. UniGene Tabulator: a full parser for the UniGene format
2572 -- 2573Dequan Li, Wen Gao, Charles X. Ling, Xiaobiao Wang, Ruixiang Sun, Simin He. IndexToolkit: an open source toolbox to index protein databases for high-throughput proteomics
2574 -- 2576Igor A. Gariev, Sergey D. Varfolomeev. Hierarchical classification of hydrolases catalytic sites
2577 -- 2579Florian Gnad, John Parsch. Sebida: a database for the functional and evolutionary analysis of genes with sex-biased expression

Volume 22, Issue 2

127 -- 128Victor de Lorenzo, Luis Serrano, Alfonso Valencia. Synthetic Biology: challenges ahead
129 -- 133Jean-Christophe Gelly, Alexandre G. de Brevern, Serge A. Hazout. Protein Peeling : an approach for splitting a 3D protein structure into compact fragments
134 -- 141Aleksandr Morgulis, E. Michael Gertz, Alejandro A. Schäffer, Richa Agarwala. WindowMasker: window-based masker for sequenced genomes
142 -- 148James J. Gordon, Michael W. Towsey, James M. Hogan, Sarah A. Mathews, Peter Timms. Improved prediction of bacterial transcription start sites
149 -- 156I. Mihalek, I. Res, Olivier Lichtarge. A structure and evolution-guided Monte Carlo sequence selection strategy for multiple alignment-based analysis of proteins
157 -- 163Leelavati Narlikar, Alexander J. Hartemink. Sequence features of DNA binding sites reveal structural class of associated transcription factor
164 -- 171Jimin Pei, Wei Cai, Lisa N. Kinch, Nick V. Grishin. Prediction of functional specificity determinants from protein sequences using log-likelihood ratios
172 -- 180Hetunandan Kamisetty, Chris Bailey-Kellogg, Gopal Pandurangan. An efficient randomized algorithm for contact-based NMR backbone resonance assignment
181 -- 187Jan E. Gewehr, Ralf Zimmer. SSEP-Domain: protein domain prediction by alignment of secondary structure elements and profiles
188 -- 194Wei Xie, Nikolaos V. Sahinidis. Residue-rotamer-reduction algorithm for the protein side-chain conformation problem
195 -- 201Konstantin Arnold, Lorenza Bordoli, Jürgen Kopp, Torsten Schwede. The SWISS-MODEL workspace: a web-based environment for protein structure homology modelling
202 -- 208Francesca Martella. Classification of microarray data with factor mixture models
209 -- 214Anshuman Gupta, Costas D. Maranas, Réka Albert. Elucidation of directionality for co-expressed genes: predicting intra-operon termination sites
215 -- 219Mizanur R. Khondoker, Chris A. Glasbey, Bruce J. Worton. Statistical estimation of gene expression using multiple laser scans of microarrays
220 -- 225Zhaohui S. Qin, Shyam Gopalakrishnan, Gonçalo R. Abecasis. An efficient comprehensive search algorithm for tagSNP selection using linkage disequilibrium criteria
226 -- 232Ashish Choudhary, Aniruddha Datta, Michael L. Bittner, Edward R. Dougherty. Intervention in a family of Boolean networks
233 -- 241Barbara A. Novak, Ajay N. Jain. Pathway recognition and augmentation by computational analysis of microarray expression data
242 -- 244Do-Hoon Lee, Jeong-Hyeon Choi, Mehmet M. Dalkilic, Sun Kim. COMPAM : visualization of combining pairwise alignments for multiple genomes
245 -- 247Ljubomir J. Buturovic. PCP: a program for supervised classification of gene expression profiles
248 -- 250Anaïs Baudot, David Martin, Pierre Mouren, François Chevenet, Alain Guénoche, Bernard Jacq, Marie-Christine Brun. PRODISTIN Web Site: a tool for the functional classification of proteins from interaction networks
251 -- 252Jo Criel, Elena Tsiporkova. Gene Time E::::chi::::pression Warper: a tool for alignment, template matching and visualization of gene expression time series
253 -- 255Mahender Kumar Singh, Shilpy Srivastava, G. P. S. Raghava, Grish C. Varshney. HaptenDB: a comprehensive database of haptens, carrier proteins and anti-hapten antibodies

Volume 22, Issue 19

2319 -- 0Alex Bateman, Alfonso Valencia. Structural genomics meets computational biology
2320 -- 2325Yiming Cheng, Robert M. Miura, Bin Tian. Prediction of mRNA polyadenylation sites by support vector machine
2326 -- 2332Bin Song, Jeong-Hyeon Choi, Guangyu Chen, Jacek Szymanski, Guo-Qiang Zhang, Anthony K. H. Tung, Jaewoo Kang, Sun Kim, Jiong Yang. ARCS: an aggregated related column scoring scheme for aligned sequences
2333 -- 2339Enrico Ferraro, Allegra Via, Gabriele Ausiello, Manuela Helmer-Citterich. A novel structure-based encoding for machine-learning applied to the inference of SH3 domain specificity
2340 -- 2347Aalt D. J. van Dijk, Alexandre M. J. J. Bonvin. Solvated docking: introducing water into the modelling of biomolecular complexes
2348 -- 2355Gavin C. Cawley, Nicola L. C. Talbot. Gene selection in cancer classification using sparse logistic regression with Bayesian regularization
2356 -- 2363Chad A. Davis, Fabian Gerick, Volker Hintermair, Caroline C. Friedel, Katrin Fundel, Robert Küffner, Ralf Zimmer. Reliable gene signatures for microarray classification: assessment of stability and performance
2364 -- 2372Darlene R. Goldstein. Partition resampling and extrapolation averaging: approximation methods for quantifying gene expression in large numbers of short oligonucleotide arrays
2373 -- 2380Sek Won Kong, William T. Pu, Peter J. Park. A multivariate approach for integrating genome-wide expression data and biological knowledge
2381 -- 2387Ann L. Oberg, Douglas W. Mahoney, Karla V. Ballman, Terry M. Therneau. Joint estimation of calibration and expression for high-density oligonucleotide arrays
2388 -- 2395Wei Pan, Xiaotong Shen, Aixiang Jiang, Robert P. Hebbel. Semi-supervised learning via penalized mixture model with application to microarray sample classification
2396 -- 2404Antonio Reverter, Aaron Ingham, Sigrid A. Lehnert, Siok-Hwee Tan, Yonghong Wang, Abhirami Ratnakumar, Brian P. Dalrymple. Simultaneous identification of differential gene expression and connectivity in inflammation, adipogenesis and cancer
2405 -- 2412Anbupalam Thalamuthu, Indranil Mukhopadhyay, Xiaojing Zheng, George C. Tseng. Evaluation and comparison of gene clustering methods in microarray analysis
2413 -- 2420Yong Wang, Trupti Joshi, Xiang-Sun Zhang, Dong Xu, Luonan Chen. Inferring gene regulatory networks from multiple microarray datasets
2421 -- 2429Carol Friedman, Tara Borlawsky, Lyudmila Shagina, H. Rosie Xing, Yves A. Lussier. Bio-Ontology and text: bridging the modeling gap
2430 -- 2436Chao Sima, Edward R. Dougherty. What should be expected from feature selection in small-sample settings
2437 -- 2438Nicholas Navin, Vladimir Grubor, Jim Hicks, Evan Leibu, Elizabeth Thomas, Jennifer Troge, Michael Riggs, Pär Lundin, Susanne Månér, Jonathan Sebat, Anders Zetterberg, Michael Wigler. PROBER: oligonucleotide FISH probe design software
2439 -- 2440Fabrice Armougom, Olivier Poirot, Sébastien Moretti, Desmond G. Higgins, Phillip Bucher, Vladimir Keduas, Cédric Notredame. APDB: a web server to evaluate the accuracy of sequence alignments using structural information
2441 -- 2443Karsten Hiller, Andreas Grote, Matthias Maneck, Richard Münch, Dieter Jahn. JVirGel 2.0: computational prediction of proteomes separated via two-dimensional gel electrophoresis under consideration of membrane and secreted proteins
2444 -- 2445Conrad Plake, Torsten Schiemann, Marcus Pankalla, Jörg Hakenberg, Ulf Leser. ALIBABA: PubMed as a graph
2446 -- 2451Xiao-Lin Wu, Larry J. Forney, Paul Joyce. Comments on Bayesian hierarchical error model for analysis of gene expression data
2452 -- 0HyungJun Cho, Jae K. Lee. Response to comments on Bayesian Hierarchical Error Model for Analysis of Gene Expression Data
2453 -- 0. Corrigendum

Volume 22, Issue 18

2187 -- 2188Wentian Li. The-more-the-better and the-less-the-better
2189 -- 2191Quan-Yuan He, Xiang-Hua Liu, Qiang Li, David J. Studholme, Xuan-Wen Li, Song-Ping Liang. G8: a novel domain associated with polycystic kidney disease and non-syndromic hearing loss
2192 -- 2195Jonathan W. Arthur, Angeles Sanchez-Perez, David I. Cook. Scoring of predicted GRK2 phosphorylation sites in Nedd4-2
2196 -- 2203Georgios S. Vernikos, Julian Parkhill. Interpolated variable order motifs for identification of horizontally acquired DNA: revisiting the ::::Salmonella:::: pathogenicity islands
2204 -- 2209Fang Fang, Shicai Fan, Xuegong Zhang, Michael Q. Zhang. Predicting methylation status of CpG islands in the human brain
2210 -- 2216Lang Li, Alfred S. L. Cheng, Victor X. Jin, Henry H. Paik, Meiyun Fan, Xiaoman Li, Wei Zhang, Jason Robarge, Curtis Balch, Ramana V. Davuluri, Sun Kim, Tim Hui-Ming Huang, Kenneth P. Nephew. A mixture model-based discriminate analysis for identifying ordered transcription factor binding site pairs in gene promoters directly regulated by estrogen receptor-alpha
2217 -- 2223Henry C. M. Leung, Francis Y. L. Chin. Finding motifs from all sequences with and without binding sites
2224 -- 2231Thomas Lingner, Peter Meinicke. Remote homology detection based on oligomer distances
2232 -- 2236Ketil Malde, Korbinian Schneeberger, Eivind Coward, Inge Jonassen. RBR: library-less repeat detection for ESTs
2237 -- 2243Jordi Espadaler, Enrique Querol, Francesc X. Avilés, Baldo Oliva. Identification of function-associated loop motifs and application to protein function prediction
2244 -- 2248Yifan Huang, Haiyan Xu, Violeta Calian, Jason C. Hsu. To permute or not to permute
2249 -- 2253Dougu Nam, Sang-Bae Kim, Seon-Kyu Kim, Sungjin Yang, Seon-Young Kim, In-Sun Chu. ADGO: analysis of differentially expressed gene sets using composite GO annotation
2254 -- 2261Ariadni Papana, Hemant Ishwaran. CART variance stabilization and regularization for high-throughput genomic data
2262 -- 2268Naijun Sha, Mahlet G. Tadesse, Marina Vannucci. Bayesian variable selection for the analysis of microarray data with censored outcomes
2269 -- 2275Andrew E. Teschendorff, Ali Naderi, Nuno L. Barbosa-Morais, Carlos H. Caldas. PACK: Profile Analysis using Clustering and Kurtosis to find molecular classifiers in cancer
2276 -- 2282Yu-Hsiang Chang, Yu-Chao Wang, Bor-Sen Chen. Identification of transcription factor cooperativity via stochastic system model
2283 -- 2290Jingchun Chen, Bo Yuan. Detecting functional modules in the yeast protein-protein interaction network
2291 -- 2297Pall F. Jonsson, Paul A. Bates. Global topological features of cancer proteins in the human interactome
2298 -- 2304James Lewis, Stephan Ossowski, Justin M. Hicks, Mounir Errami, Harold R. Garner. Text similarity: an alternative way to search MEDLINE
2305 -- 2307Eun-Kyung Lee, Sung-Gon Yi, Taesung Park. arrayQCplot: software for checking the quality of microarray data
2308 -- 2309Haiming Wang, Yanqi Su, Aaron J. Mackey, Eileen Kraemer, Jessica C. Kissinger. SynView: a GBrowse-compatible approach to visualizing comparative genome data
2310 -- 2312Rajesh Chowdhary, Sin-Lam Tan, R. Ayesha Ali, Brent Boerlage, Limsoon Wong, Vladimir B. Bajic. Dragon Promoter Mapper (DPM): a Bayesian framework for modelling promoter structures
2313 -- 2314Patricia Buendia, Giri Narasimhan. Serial NetEvolve: a flexible utility for generating serially-sampled sequences along a tree or recombinant network
2315 -- 2316Claudio Lottaz, Xinan Yang, Stefanie Scheid, Rainer Spang. ::::OrderedList:::: - a bioconductor package for detecting similarity in ordered gene lists
2317 -- 2318Thomas Mailund, Mikkel H. Schierup, Christian N. S. Pedersen, Jesper N. Madsen, Jotun Hein, Leif Schauser. GeneRecon - a coalescent based tool for fine-scale association mapping

Volume 22, Issue 17

2059 -- 2065Pan Du, Warren A. Kibbe, Simon M. Lin. Improved peak detection in mass spectrum by incorporating continuous wavelet transform-based pattern matching
2066 -- 2073Philippe La Rosa, Eric Viara, Philippe Hupé, Gaëlle Pierron, Stéphane Liva, Pierre Neuvial, Isabel Brito, Séverine Lair, Nicolas Servant, Nicolas Robine, Elodie Manié, Caroline Brennetot, Isabelle Janoueix-Lerosey, Virginie Raynal, Nadège Gruel, Céline Rouveirol, Nicolas Stransky, Marc-Henri Stern, Olivier Delattre, Alain Aurias, François Radvanyi, Emmanuel Barillot. VAMP: Visualization and analysis of array-CGH, transcriptome and other molecular profiles
2074 -- 2080P. Thébault, Simon de Givry, Thomas Schiex, Christine Gaspin. Searching RNA motifs and their intermolecular contacts with constraint networks
2081 -- 2086Kui Lin, Lei Zhu, Da-Yong Zhang. An initial strategy for comparing proteins at the domain architecture level
2087 -- 2093Yu Chen, Gordon M. Crippen. An iterative refinement algorithm for consistency based multiple structural alignment methods
2094 -- 2098Sjoerd J. de Vries, Alexandre M. J. J. Bonvin. Intramolecular surface contacts contain information about protein-protein interface regions
2099 -- 2106Mingyue Zheng, Zhiguo Liu, Chunxia Xue, Weiliang Zhu, Kaixian Chen, Xiaomin Luo, Hualiang Jiang. Mutagenic probability estimation of chemical compounds by a novel molecular electrophilicity vector and support vector machine
2107 -- 2113Xuejun Liu, Marta Milo, Neil D. Lawrence, Magnus Rattray. Probe-level measurement error improves accuracy in detecting differential gene expression
2114 -- 2121Andrea Malossini, Enrico Blanzieri, Raymond T. Ng. Detecting potential labeling errors in microarrays by data perturbation
2122 -- 2128Chun Zhang, Dione K. Bailey, Tarif Awad, Guoying Liu, Guoliang Xing, Manqiu Cao, Venu Valmeekam, Jacques Retief, Hajime Matsuzaki, Margaret Taub, Mark Seielstad, Giulia C. Kennedy. A whole genome long-range haplotype (WGLRH) test for detecting imprints of positive selection in human populations
2129 -- 2135Wentao Zhao, Erchin Serpedin, Edward R. Dougherty. Inferring gene regulatory networks from time series data using the minimum description length principle
2136 -- 2142Bo Han, Zoran Obradovic, Zhang-Zhi Hu, Cathy H. Wu, Slobodan Vucetic. Substring selection for biomedical document classification
2143 -- 2150Shao Li, Lijiang Wu, Zhongqi Zhang. Constructing biological networks through combined literature mining and microarray analysis: a LMMA approach
2151 -- 2157Rainer Malik, Lude Franke, Arno Siebes. Combination of text-mining algorithms increases the performance
2158 -- 2159Gill Bejerano. Branch and bound computation of exact ::::p::::-values
2160 -- 2161Simon N. Jarman. Cleaver: software for identifying taxon specific restriction endonuclease recognition sites
2162 -- 2163Joshua Wing Kei Ho, Cameron E. Adams, Jie Bin Lew, Timothy J. Matthews, Chiu Chin Ng, Arash Shahabi-Sirjani, Leng Hong Tan, Yu Zhao, Simon Easteal, Susan R. Wilson, Lars S. Jermiin. SeqVis: Visualization of compositional heterogeneity in large alignments of nucleotides
2164 -- 2165Nicolas Garnier, Anne Friedrich, Raphael Bolze, Emmanuel Bettler, Luc Moulinier, Christophe Geourjon, Julie Dawn Thompson, Gilbert Deléage, Olivier Poch. MAGOS: multiple alignment and modelling server
2166 -- 2167Rachel Kolodny, Barry Honig. VISTAL - a new 2D visualization tool of protein 3D structural alignments
2168 -- 2170Ali Mokdad, Neocles Leontis. Ribostral: an RNA 3D alignment analyzer and viewer based on basepair isostericities
2171 -- 2172Douglas L. Theobald, Deborah S. Wuttke. THESEUS: maximum likelihood superpositioning and analysis of macromolecular structures
2173 -- 2174William S. Bush, Scott M. Dudek, Marylyn D. Ritchie. Parallel multifactor dimensionality reduction: a tool for the large-scale analysis of gene-gene interactions
2175 -- 2177Zhi Liang, Meng Xu, Maikun Teng, Liwen Niu. NetAlign: a web-based tool for comparison of protein interaction networks
2178 -- 2179James Vlasblom, Samuel Wu, Shuye Pu, Mark Superina, Gina Liu, Chris Orsi, Shoshana J. Wodak. GenePro: a cytoscape plug-in for advanced visualization and analysis of interaction networks
2180 -- 2182Yun-Ching Chen, Chung-Der Hsiao, Wen-Dar Lin, Chung-Ming Hu, Pung-Pung Hwang, Jan-Ming Ho. ZooDDD: a cross-species database for digital differential display analysis
2183 -- 2185Joke Reumers, Sebastian Maurer-Stroh, Joost Schymkowitz, Frederic Rousseau. SNPeffect v2.0: a new step in investigating the molecular phenotypic effects of human non-synonymous SNPs

Volume 22, Issue 16

1933 -- 1934María M. Abad-Grau, Rosana Montes, Paola Sebastiani. Building chromosome-wide LD maps
1935 -- 1941Pierre Brézellec, Mark Hoebeke, Marie-Sophie Hiet, Sophie Pasek, Jean-Luc Ferat. DomainSieve: a protein domain-based screen that led to the identification of ::::dam::::-associated genes with potential link to DNA maintenance
1942 -- 1947Dan L. Nicolae, Xiaolin Wu, Kazuaki Miyake, Nancy J. Cox. GEL: a novel genotype calling algorithm using empirical likelihood
1948 -- 1954Sébastien Tempel, Mathieu Giraud, Dominique Lavenier, Israel-César Lerman, Anne-Sophie Valin, Ivan Couée, Abdelhak El Amrani, Jacques Nicolas. Domain organization within repeated DNA sequences: application to the study of a family of transposable elements
1955 -- 1962Jonathan G. Lees, Andrew J. Miles, Frank Wien, B. A. Wallace. A reference database for circular dichroism spectroscopy covering fold and secondary structure space
1963 -- 1970Wolfgang Huber, Joern Toedling, Lars M. Steinmetz. Transcript mapping with high-density oligonucleotide tiling arrays
1971 -- 1978Jun Liu, Jaaved Mohammed, James Carter, Sanjay Ranka, Tamer Kahveci, Michael Baudis. Distance-based clustering of CGH data
1979 -- 1987Stan Pounds, Cheng Cheng. Robust estimation of the false discovery rate
1988 -- 1997Zhaohui S. Qin. Clustering microarray gene expression data using weighted Chinese restaurant process
1998 -- 2004Jin Chen, Wynne Hsu, Mong-Li Lee, See-Kiong Ng. Increasing confidence of protein interactomes using network topological metrics
2005 -- 2011Je-Gun Joung, Dong-Ho Shin, Rho Hyun Seong, Byoung-Tak Zhang. Identification of regulatory modules by co-clustering latent variable models: stem cell differentiation
2012 -- 2019Julie L. Morrison, Rainer Breitling, Desmond J. Higham, David R. Gilbert. A lock-and-key model for protein-protein interactions
2020 -- 2027Simen Myhre, Henrik Tveit, Torulf Mollestad, Astrid Lægreid. Additional Gene Ontology structure for improved biological reasoning
2028 -- 2036Herbert Pang, Aiping Lin, Matthew Holford, Bradley E. Enerson, Bin Lu, Michael P. Lawton, Eugenia Floyd, Hongyu Zhao. Pathway analysis using random forests classification and regression
2037 -- 2043Jiexun Li, Xin Li, Hua Su, Hsinchun Chen, David W. Galbraith. A framework of integrating gene relations from heterogeneous data sources: an experiment on ::::Arabidopsis thaliana::::
2044 -- 2046Todd F. DeLuca, I-Hsien Wu, Jian Pu, Thomas Monaghan, Leonid Peshkin, Saurav Singh, Dennis P. Wall. Roundup: a multi-genome repository of orthologs and evolutionary distances
2047 -- 2048Marc A. Suchard, Benjamin D. Redelings. BAli-Phy: simultaneous Bayesian inference of alignment and phylogeny
2049 -- 2050Daniel H. Morgan, David M. Kristensen, David Mittelman, Olivier Lichtarge. ET viewer: an application for predicting and visualizing functional sites in protein structures
2051 -- 2052Christian Spieth, Jochen Supper, Felix Streichert, Nora Speer, Andreas Zell. JCell - a Java-based framework for inferring regulatory networks from time series data
2053 -- 2054Seong-Eui Hong, Seong-Hwan Rho, Young Il Yeom, Do Han Kim. HCNet: a database of heart and calcium functional network
2055 -- 2057G. R. Grimes, T. Q. Wen, Muriel Mewissen, Robert M. Baxter, Stuart L. Moodie, J. S. Beattie, Peter Ghazal. PDQ Wizard: automated prioritization and characterization of gene and protein lists using biomedical literature

Volume 22, Issue 15

1809 -- 1814Mikael Bodén, Timothy L. Bailey. Identifying sequence regions undergoing conformational change via predicted continuum secondary structure
1815 -- 1822Isabelle Dupanloup, Henrik Kaessmann. Evolutionary simulations to detect functional lineage-specific genes
1823 -- 1831Anke Busch, Rolf Backofen. INFO-RNA - a fast approach to inverse RNA folding
1832 -- 1837Hyeon S. Son, Seung-Yeon Kim, Jooyoung Lee, Kyu-Kwang Han. Application of the multiensemble sampling to the equilibrium folding of proteins
1838 -- 1845Marc N. Offman, Paul W. Fitzjohn, Paul A. Bates. Developing a move-set for protein model refinement
1846 -- 1854Gennady Verkhivker. Imprint of evolutionary conservation and protein structure variation on the binding function of protein tyrosine kinases
1855 -- 1862De-Shuang Huang, Chun-Hou Zheng. Independent component analysis-based penalized discriminant method for tumor classification using gene expression data
1863 -- 1870David S. Skibbe, Xiujuan Wang, Xuefeng Zhao, Lisa A. Borsuk, Dan Nettleton, Patrick S. Schnable. Scanning microarrays at multiple intensities enhances discovery of differentially expressed genes
1871 -- 1878Steven Carroll, Vladimir Pavlovic. Protein classification using probabilistic chain graphs and the Gene Ontology structure
1879 -- 1885Ralph Gauges, Ursula Rost, Sven Sahle, Katja Wegner. A model diagram layout extension for SBML
1886 -- 1894Simon J. Galbraith, Linh M. Tran, James C. Liao. Transcriptome network component analysis with limited microarray data
1895 -- 1901Jordi Vidal Rodríguez, Jaap A. Kaandorp, Maciej Dobrzynski, Joke G. Blom. Spatial stochastic modelling of the phosphoenolpyruvate-dependent phosphotransferase (PTS) pathway in ::::Escherichia coli::::
1902 -- 1909Matthew Bellew, Marc Coram, Matthew Fitzgibbon, Mark Igra, Tim Randolph, Pei Wang, Damon May, Jimmy K. Eng, Ruihua Fang, ChenWei Lin, Jinzhi Chen, David Goodlett, Jeffrey Whiteaker, Amanda G. Paulovich, Martin McIntosh. A suite of algorithms for the comprehensive analysis of complex protein mixtures using high-resolution LC-MS
1910 -- 1916Joel H. Saltz, Scott Oster, Shannon Hastings, Stephen Langella, Tahsin M. Kurç, William Sanchez, Manav Kher, Arumani Manisundaram, Krishnakant Shanbhag, Peter A. Covitz. caGrid: design and implementation of the core architecture of the cancer biomedical informatics grid
1917 -- 1918Karol Szafranski, Niels Jahn, Matthias Platzer. tuple_plot: Fast pairwise nucleotide sequence comparison with noise suppression
1919 -- 1920Wessel N. van Wieringen, Jeroen A. M. Belien, Sjoerd J. Vosse, Eskeatnaf M. Achame, Bauke Ylstra. ACE-it: a tool for genome-wide integration of gene dosage and RNA expression data
1921 -- 1923M. M. Morin, Bernard M. E. Moret. NetGen: generating phylogenetic networks with diploid hybrids
1924 -- 1925Joshua Gould, Gad Getz, Stefano Monti, Michael Reich, Jill P. Mesirov. Comparative gene marker selection suite
1926 -- 1927Jin-long Li, Miao-Xin Li, Yan-Fang Guo, H.-Y. Deng, Hong-Wen Deng. JADE: a distributed Java application for deleterious genomic mutation (DGM) estimation
1928 -- 1929Xavier Solé, Elisabet Guinó, Joan Valls, Raquel Iniesta, Víctor Moreno. SNPStats: a web tool for the analysis of association studies
1930 -- 1931Axel von Kamp, Stefan Schuster. Metatool 5.0: fast and flexible elementary modes analysis

Volume 22, Issue 14

1675 -- 1681Huai-Kuang Tsai, Grace Tzu-Wei Huang, Meng-Yuan Chou, Henry Horng-Shing Lu, Wen-Hsiung Li. Method for identifying transcription factor binding sites in yeast
1682 -- 1689Taesung Park, Sung-Gon Yi, Young Kee Shin, Seung Yeoun Lee. Combining multiple microarrays in the presence of controlling variables
1690 -- 1701K. H. Chu, C. P. Li, J. Qi. Ribosomal RNA as molecular barcodes: a simple correlation analysis without sequence alignment
1702 -- 1709Sebastien K. Gerega, Kevin M. Downard. PROXIMO - a new docking algorithm to model protein complexes using data from radical probe mass spectrometry (RP-MS)
1710 -- 1716Katrin Stierand, Patrick C. Maaß, Matthias Rarey. Molecular complexes at a glance: automated generation of two-dimensional complex diagrams
1717 -- 1722Hong-bin Shen, Kuo-Chen Chou. Ensemble classifier for protein fold pattern recognition
1723 -- 1729Yasuo Tabei, Koji Tsuda, Taishin Kin, Kiyoshi Asai. SCARNA: fast and accurate structural alignment of RNA sequences by matching fixed-length stem fragments
1730 -- 1736Sin-Ho Jung, Woncheol Jang. How accurately can we control the FDR in analyzing microarray data?
1737 -- 1744Xiangdong Liu, Siva Sivaganesan, Ka Yee Yeung, Junhai Guo, Roger Eugene Bumgarner, Mario Medvedovic. Context-specific infinite mixtures for clustering gene expression profiles across diverse microarray dataset
1745 -- 1752Shu-Kay Ng, Geoffrey J. McLachlan, Kui Wang, Liat Ben-Tovim Jones, S. W. Ng. A Mixture model with random-effects components for clustering correlated gene-expression profiles
1753 -- 1759Guido Sanguinetti, Magnus Rattray, Neil D. Lawrence. A probabilistic dynamical model for quantitative inference of the regulatory mechanism of transcription
1760 -- 1766Suman Sundaresh, Denise L. Doolan, Siddiqua Hirst, Yunxiang Mu, Berkay Unal, D. Huw Davies, Philip L. Felgner, Pierre Baldi. Identification of humoral immune responses in protein microarrays using DNA microarray data analysis techniques
1767 -- 1774Syed Asad Rahman, Dietmar Schomburg. Observing local and global properties of metabolic pathways: load points and choke points in the metabolic networks
1775 -- 1781Ruiqi Wang, Luonan Chen, Kazuyuki Aihara. Synchronizing a multicellular system by external input: an artificial control strategy
1782 -- 1783Reinhard Engels, Tamara Yu, Chris Burge, Jill P. Mesirov, David DeCaprio, James E. Galagan. Combo: a whole genome comparative browser
1784 -- 1785Jian Guo, Yuanlie Lin. TSSub: eukaryotic protein subcellular localization by extracting features from profiles
1786 -- 1787Anne-Muriel Arigon, Guy Perrière, Manolo Gouy. HoSeqI: automated homologous sequence identification in gene family databases
1788 -- 1789Yoshio Nakano, Toru Takeshita, Yoshihisa Yamashita. TRFMA: a web-based tool for terminal restriction fragment length polymorphism analysis based on molecular weight
1790 -- 1791Isabel K. Darcy, Robert G. Scharein. TopoICE-R: 3D visualization modeling the topology of DNA recombination
1792 -- 1793Ricard García-Serna, Lulla Opatowski, Jordi Mestres. FCP: functional coverage of the proteome by structures
1794 -- 1795Yoichi Murakami, Susan Jones. SHARP:::2:::: protein-protein interaction predictions using patch analysis
1796 -- 1799Frank Mueller, Daniel J. Muller, Dirk Labudde. Analysis assistant for single-molecule force spectroscopy data on membrane proteins - MPTV
1800 -- 1802Jean Marc Kwasigroch, Marianne Rooman. Prelude&Fugue, predicting local protein structure, early folding regions and structural weaknesses
1803 -- 1804Montserrat Vaqué, Anna Arola, Carles Aliagas, Gerard Pujadas. BDT: an easy-to-use front-end application for automation of massive docking tasks and complex docking strategies with AutoDock
1805 -- 1807Laurence Calzone, François Fages, Sylvain Soliman. BIOCHAM: an environment for modeling biological systems and formalizing experimental knowledge

Volume 22, Issue 13

1543 -- 1545Jonathan D. Wren. Theory and reality for software patents: good in concept, not so good in practice
1546 -- 1550Elhanan Magidovich, Sarel J. Fleishman, Ofer Yifrach. Intrinsically disordered C-terminal segments of voltage-activated potassium channels: a possible fishing rod-like mechanism for channel binding to scaffold proteins
1551 -- 1561Christina Toft, Mario A. Fares. GRAST: a new way of genome reduction analysis using comparative genomics
1562 -- 1568Burkhard Heil, Jost Ludwig, Hella Lichtenberg-Fraté, Thomas Lengauer. Computational recognition of potassium channel sequences
1569 -- 1576Kavitha Bhasi, Li Zhang, Daniel Brazeau, Aidong Zhang, Murali Ramanathan. VizStruct for visualization of genome-wide SNP analyses
1577 -- 1584Zhi Wei, Shane T. Jensen. GAME: detecting ::::cis::::-regulatory elements using a genetic algorithm
1585 -- 1592Orhan Çamoglu, Tolga Can, Ambuj K. Singh. Integrating multi-attribute similarity networks for robust representation of the protein space
1593 -- 1599Deniz Dalli, Andreas Wilm, Indra Mainz, Gerhard Steger. StrAl: progressive alignment of non-coding RNA using base pairing probability vectors in quadratic time
1600 -- 1607Adrian Alexa, Jörg Rahnenführer, Thomas Lengauer. Improved scoring of functional groups from gene expression data by decorrelating GO graph structure
1608 -- 1615Geoffrey J. McLachlan, Richard Bean, Liat Ben-Tovim Jones. A simple implementation of a normal mixture approach to differential gene expression in multiclass microarrays
1616 -- 1622Golan Yona, William Dirks, Shafquat Rahman, David M. Lin. Effective similarity measures for expression profiles
1623 -- 1630Hon Nian Chua, Wing-Kin Sung, Limsoon Wong. Exploiting indirect neighbours and topological weight to predict protein function from protein-protein interactions
1631 -- 1640Dong-Yeon Cho, Kwang-Hyun Cho, Byoung-Tak Zhang. Identification of biochemical networks by S-tree based genetic programming
1641 -- 1647Lei Nie, Gang Wu, Fred J. Brockman, Weiwen Zhang. Integrated analysis of transcriptomic and proteomic data of ::::Desulfovibrio vulgaris::::: zero-inflated Poisson regression models to predict abundance of undetected proteins
1648 -- 1655Shanfeng Zhu, Keiko Udaka, John Sidney, Alessandro Sette, Kiyoko F. Aoki-Kinoshita, Hiroshi Mamitsuka. Improving MHC binding peptide prediction by incorporating binding data of auxiliary MHC molecules
1656 -- 1657I. Mihalek, I. Res, Olivier Lichtarge. Evolutionary trace report_maker: a new type of service for comparative analysis of proteins
1658 -- 1659Weizhong Li, Adam Godzik. Cd-hit: a fast program for clustering and comparing large sets of protein or nucleotide sequences
1660 -- 1661Olga Kirillova, Wladek Minor. Map2mod - a server for evaluation of crystallographic models and their agreement with electron density maps
1662 -- 1664Hiro Takahashi, Hiroyuki Honda. Modified signal-to-noise: a new simple and practical gene filtering approach based on the concept of projective adaptive resonance theory (PART) filtering method
1665 -- 1667Fei Pan, Kiran Kamath, Kangyu Zhang, Sudip Pulapura, Avinash Achar, Juan Nunez-Iglesias, Yu Huang 0003, Xifeng Yan, Jiawei Han, Haiyan Hu, Min Xu, Jianjun Hu, Xianghong Jasmine Zhou. Integrative Array Analyzer: a software package for analysis of cross-platform and cross-species microarray data
1668 -- 1669X. Yuan, Zhang-Zhi Hu, H. T. Wu, Manabu Torii, Meenakshi Narayanaswamy, K. E. Ravikumar, K. Vijay-Shanker, Cathy H. Wu. An online literature mining tool for protein phosphorylation
1670 -- 1673Justin Klekota, Frederick P. Roth, Stuart L. Schreiber. Query Chem: a Google-powered web search combining text and chemical structures
1674 -- 0Amanda Clare, Andreas Karwath, Helen Ougham, Ross D. King. Functional bioinformatics for ::::Arabidopsis thaliana::::

Volume 22, Issue 12

1415 -- 0Alfonso Valencia, Alex Bateman. Software patents in Bioinformatics
1416 -- 1417John Quackenbush, Steven Salzberg. It is time to end the patenting of software
1418 -- 1423Sophie Pasek, Jean-Loup Risler, Pierre Brézellec. Gene fusion/fission is a major contributor to evolution of multi-domain bacterial proteins
1424 -- 1430Martin G. Grigorov. Global dynamics of biological systems from time-resolved omics experiments
1431 -- 1436Radek Szklarczyk, Jaap Heringa. AuberGene - a sensitive genome alignment tool
1437 -- 1439Zhaolei Zhang, Nicholas Carriero, Deyou Zheng, John E. Karro, Paul M. Harrison, Mark Gerstein. PseudoPipe: an automated pseudogene identification pipeline
1440 -- 1448Florencio Pazos, Antonio Rausell, Alfonso Valencia. Phylogeny-independent detection of functional residues
1449 -- 1455Francesco Ortuso, Thierry Langer, Stefano Alcaro. GBPM: GRID-based pharmacophore model: concept and application studies to protein-protein recognition
1456 -- 1463Jianlin Cheng, Pierre Baldi. A machine learning information retrieval approach to protein fold recognition
1464 -- 1470Alison L. Cuff, Robert W. Janes, Andrew C. R. Martin. Analysing the ability to retain sidechain hydrogen-bonds in mutant proteins
1471 -- 1476S. E. Ahnert, K. Willbrand, F. C. S. Brown, T. M. A. Fink. Unbiased pattern detection in microarray data series
1477 -- 1485Philippe Broët, Vladimir A. Kuznetsov, Jonas Bergh, Edison T. Liu, Lance D. Miller. Identifying gene expression changes in breast cancer that distinguish early and late relapse among uncured patients
1486 -- 1494Xin Gao. Construction of null statistics in permutation-based multiple testing for multi-factorial microarray experiments
1495 -- 1502Lars Kaderali, Thomas Zander, Ulrich Faigle, Jürgen Wolf, Joachim L. Schultze, Rainer Schrader. CASPAR: a hierarchical bayesian approach to predict survival times in cancer from gene expression data
1503 -- 1507Wentian Li, Mingyi Wang, Patricia Irigoyen, Peter K. Gregersen. Inferring causal relationships among intermediate phenotypes and biomarkers: a case study of rheumatoid arthritis
1508 -- 1514Quansong Ruan, Joshua A. Steele, Michael S. Schwalbach, Jed A. Fuhrman, Fengzhu Sun. A dynamic programming algorithm for binning microbial community profiles
1515 -- 1523Chuen Seng Tan, Alexander Ploner, Andreas Quandt, Janne Lehtiö, Yudi Pawitan. Finding regions of significance in SELDI measurements for identifying protein biomarkers
1524 -- 1531Smriti R. Ramakrishnan, Rui Mao, Aleksey A. Nakorchevskiy, John T. Prince, Willard S. Willard, Weijia Xu, Edward M. Marcotte, Daniel P. Miranker. A fast coarse filtering method for peptide identification by mass spectrometry
1532 -- 1533Boris Adryan, Sarah A. Teichmann. FlyTF: a systematic review of site-specific transcription factors in the fruit fly ::::Drosophila melanogaster::::
1534 -- 1535Yann Ponty, Michel Termier, Alain Denise. GenRGenS: software for generating random genomic sequences and structures
1536 -- 1537Vladimir Vacic, Lilia M. Iakoucheva, Predrag Radivojac. Two Sample Logo: a graphical representation of the differences between two sets of sequence alignments
1538 -- 1539Ryo Yoshida, Tomoyuki Higuchi, Seiya Imoto, Satoru Miyano. ArrayCluster: an analytic tool for clustering, data visualization and module finder on gene expression profiles
1540 -- 1542Ryota Suzuki, Hidetoshi Shimodaira. Pvclust: an R package for assessing the uncertainty in hierarchical clustering

Volume 22, Issue 11

1289 -- 1292Emmanuelle Becker, Vincent Meyer, Hocine Madaoui, Raphaël Guérois. Detection of a tandem BRCT in Nbs1 and Xrs2 with functional implications in the DNA damage response
1293 -- 1296Ute Müller, Günther Ernst, Christian Melle, Reinhard Guthke, Ferdinand von Eggeling. Convergence of the proteomic pattern in cancer
1297 -- 1301Kira S. Makarova, Eugene V. Koonin, Robert Haselkorn, Michael Y. Galperin. Cyanobacterial response regulator PatA contains a conserved N-terminal domain (PATAN) with an alpha-helical insertion
1302 -- 1307Florencia G. Leonardi. A generalization of the PST algorithm: modeling the sparse nature of protein sequences
1308 -- 1316Stephen McCauley, Jotun Hein. Using hidden Markov models and observed evolution to annotate viral genomes
1317 -- 1324Aleksey Y. Ogurtsov, Svetlana A. Shabalina, Alexey S. Kondrashov, Mikhail A. Roytberg. Analysis of internal loops within the RNA secondary structure in almost quadratic time
1325 -- 1334Malik Yousef, Michael Nebozhyn, Hagit Shatkay, Stathis Kanterakis, Louise C. Showe, Michael K. Showe. Combining multi-species genomic data for microRNA identification using a Naïve Bayes classifier
1335 -- 1342Nicholas J. Burgoyne, Richard M. Jackson. Predicting protein interaction sites: binding hot-spots in protein-protein and protein-ligand interfaces
1343 -- 1352Gilad Wainreb, Nurit Haspel, Haim J. Wolfson, Ruth Nussinov. A permissive secondary structure-guided superposition tool for clustering of protein fragments toward protein structure prediction via fragment assembly
1353 -- 1358Konrad H. Paszkiewicz, Michael J. E. Sternberg, Michael Lappe. Prediction of viable circular permutants using a graph theoretic approach
1359 -- 1366Gaëlle Lelandais, Pierre Vincens, Anne Badel-Chagnon, Stéphane Vialette, Claude Jacq, Serge A. Hazout. Comparing gene expression networks in a multi-dimensional space to extract similarities and differences between organisms
1367 -- 1374Xue-wen Chen, Gopalakrishna Anantha, Xinkun Wang. An effective structure learning method for constructing gene networks
1375 -- 1382Chao-Ping Hsu, Pei-Hsuan Lee, Ching-Wei Chang, Cheng-Tsung Lee. Constructing quantitative models from qualitative mutant phenotypes: preferences in selecting sensory organ precursors
1383 -- 1390Jacob Köhler, Jan Baumbach, Jan Taubert, Michael Specht, Andre Skusa, Alexander Rüegg, Christopher J. Rawlings, Paul Verrier, Stephan Philippi. Graph-based analysis and visualization of experimental results with ONDEX
1391 -- 1396David P. De Souza, Eleanor C. Saunders, Malcolm J. McConville, Vladimir A. Likic. Progressive peak clustering in GC-MS Metabolomic experiments applied to ::::Leishmania:::: parasites
1397 -- 1398Christian X. Weichenberger, Manfred J. Sippl. NQ-Flipper: validation and correction of asparagine/glutamine amide rotamers in protein crystal structures
1399 -- 1401David L. Aylor, Eric W. Price, Ignazio Carbone. SNAP: Combine and Map modules for multilocus population genetic analysis
1402 -- 1403Claire Bardel, Vincent Danjean, Emmanuelle Génin. ALTree: association detection and localization of susceptibility sites using haplotype phylogenetic trees
1404 -- 1405Mario Falchi, Cesare Cappio Borlino. PowQ: a user-friendly package for the design of variance component multipoint linkage analysis studies
1406 -- 1407Rainer Machné, Andrew Finney, Stefan Müller, James Lu, Stefanie Widder, Christoph Flamm. The SBML ODE Solver Library: a native API for symbolic and fast numerical analysis of reaction networks
1408 -- 1409Vladimir Makarenkov, Dmytro Kevorkov, Pablo Zentilli, Andrei V. Gagarin, Nathalie Malo, Robert Nadon. HTS-Corrector: software for the statistical analysis and correction of experimental high-throughput screening data
1410 -- 1411Hyunsoo Kim, Gene H. Golub, Haesun Park. Missing value estimation for DNA microarray gene expression data: local least squares imputation
1412 -- 0Jeffrey T. Leek, Eva Monsen, Alan R. Dabney, John D. Storey. EDGE: extraction and analysis of differential gene expression

Volume 22, Issue 10

1157 -- 0Andrew E. Torda, Thomas Lengauer. Editorial
1158 -- 1165Annette Höglund, Pierre Dönnes, Torsten Blum, Hans-Werner Adolph, Oliver Kohlbacher. MultiLoc: prediction of protein subcellular localization using N-terminal targeting sequences, sequence motifs and amino acid composition
1166 -- 1171Hannes Luz, Martin Vingron. Family specific rates of protein evolution
1172 -- 1176Ivo L. Hofacker, Peter F. Stadler. Memory efficient folding algorithms for circular RNA secondary structures
1177 -- 1182Ulrike Mückstein, Hakim Tafer, Jörg Hackermüller, Stephan H. F. Bernhart, Peter F. Stadler, Ivo L. Hofacker. Thermodynamics of RNA-RNA binding
1183 -- 1189Jean-Christophe Nebel. Generation of 3D templates of active sites of proteins with rigid prosthetic groups
1190 -- 1197Alexander E. Kel, Tatiana Konovalova, T. Waleev, Evgeny Cheremushkin, Olga V. Kel-Margoulis, Edgar Wingender. Composite Module Analyst: a fitness-based tool for identification of transcription factor binding site combinations
1198 -- 1206Ari Rantanen, Taneli Mielikäinen, Juho Rousu, Hannu Maaheimo, Esko Ukkonen. Planning optimal measurements of isotopomer distributions for estimation of metabolic fluxes
1207 -- 1210Loris Nanni, Alessandra Lumini. An ensemble of K-local hyperplanes for predicting protein-protein interactions
1211 -- 1216Hideki Nagasaki, Masanori Arita, Tatsuya Nishizawa, Makiko Suwa, Osamu Gotoh. Automated classification of alternative splicing and transcriptional initiation and construction of visual database of classified patterns
1217 -- 1224Anton Valouev, Yu Zhang, David C. Schwartz, Michael S. Waterman. Refinement of optical map assemblies
1225 -- 1231Faisal Ababneh, Lars S. Jermiin, Chunsheng Ma, John Robinson. Matched-pairs tests of homogeneity with applications to homologous nucleotide sequences
1232 -- 1238Joo Chuan Tong, Guanglan Zhang, Tin Wee Tan, J. Thomas August, Vladimir Brusic, Shoba Ranganathan. Prediction of HLA-DQ3.2ß Ligands: evidence of multiple registers in class II binding peptides
1239 -- 1244Ritesh Agrawal, Gary D. Stormo. Using mRNAs lengths to accurately predict the alternatively spliced gene products in ::::Caenorhabditis elegans::::
1245 -- 1250Daniel P. Berrar, Ian Bradbury, Werner Dubitzky. Avoiding model selection bias in small-sample genomic datasets
1251 -- 1258Kristof Engelen, Bart Naudts, Bart De Moor, Kathleen Marchal. A calibration method for estimating absolute expression levels from microarray data
1259 -- 1268Desheng Huang, Wei Pan. Incorporating biological knowledge into distance-based clustering analysis of microarray gene expression data
1269 -- 1271Tijl De Bie, Nello Cristianini, Jeffery P. Demuth, Matthew W. Hahn. CAFE: a computational tool for the study of gene family evolution
1272 -- 1274Richard E. Kennedy, Robnet T. Kerns, Xiangrong Kong, Kellie J. Archer, Michael F. Miles. ::::SScore::::: an R package for detecting differential gene expression without gene expression summaries
1275 -- 1277Sarah M. Keating, Benjamin J. Bornstein, Andrew Finney, Michael Hucka. SBMLToolbox: an SBML toolbox for MATLAB users
1278 -- 1279Amanda M. White, Don Simone Daly, Susan M. Varnum, Kevin K. Anderson, Nikki Bollinger, Richard C. Zangar. ProMAT: protein microarray analysis tool
1280 -- 1281Jacek Sroka, Grzegorz Kaczor, Jerzy Tyszkiewicz, Andrzej M. Kierzek. XQTav: an XQuery processor for Taverna environment
1282 -- 1283Simon Barkow, Stefan Bleuler, Amela Prelic, Philip Zimmermann, Eckart Zitzler. BicAT: a biclustering analysis toolbox
1284 -- 1285Rasko Leinonen, Francesco Nardone, Weimin Zhu, Rolf Apweiler. UniSave: the UniProtKB Sequence/Annotation Version database
1286 -- 1287Ge Gao, Yingfu Zhong, Anyuan Guo, Qihui Zhu, Wen Tang, Weimou Zheng, Xiaocheng Gu, Liping Wei, Jingchu Luo. DRTF: a database of rice transcription factors

Volume 22, Issue 1

2 -- 0Alex Bateman. Bioinformatics - The new home for protein sequence motifs
3 -- 6Dorit Amikam, Michael Y. Galperin. PilZ domain is part of the bacterial c-di-GMP binding protein
7 -- 12Nusrat Rabbee, Terence P. Speed. A genotype calling algorithm for affymetrix SNP arrays
13 -- 20Miao Zhang, Warren Gish. Improved spliced alignment from an information theoretic approach
21 -- 28Kyle L. Jensen, Mark P. Styczynski, Isidore Rigoutsos, Gregory Stephanopoulos. A generic motif discovery algorithm for sequential data
29 -- 34Weichun Huang, David M. Umbach, Leping Li. Accurate anchoring alignment of divergent sequences
35 -- 39Zasha Weinberg, Walter L. Ruzzo. Sequence-based heuristics for faster annotation of non-coding RNA families
40 -- 49Yohan Kim, Mehmet Koyutürk, Umut Topkara, Ananth Grama, Shankar Subramaniam. Inferring functional information from domain co-evolution
50 -- 57Marta Blangiardo, Simona Toti, Betti Giusti, Rosanna Abbate, Alberto Magi, Filippo Poggi, Luciana Rossi, Francesca Torricelli, Annibale Biggeri. Using a calibration experiment to assess gene-specific information: full Bayesian and empirical Bayesian models for two-channel microarray data
58 -- 67Thomas Grotkjær, Ole Winther, Birgitte Regenberg, Jens Nielsen, Lars Kai Hansen. Robust multi-scale clustering of large DNA microarray datasets with the consensus algorithm
68 -- 76Xiaoyan Leng, Hans-Georg Müller. Classification using functional data analysis for temporal gene expression data
77 -- 87Yongxi Tan, Leming M. Shi, Saber M. Hussain, Jun Xu, Weida Tong, John M. Frazier, Charles Wang. Integrating time-course microarray gene expression profiles with cytotoxicity for identification of biomarkers in primary rat hepatocytes exposed to cadmium
88 -- 95Hao Helen Zhang, Jeongyoun Ahn, Xiaodong Lin, Cheolwoo Park. Gene selection using support vector machines with non-convex penalty
96 -- 102Huai Li, Ming Zhan. Systematic intervention of transcription for identifying network response to disease and cellular phenotypes
103 -- 105Hongfang Liu, Zhang-Zhi Hu, Jian Zhang, Cathy H. Wu. BioThesaurus: a web-based thesaurus of protein and gene names
106 -- 111Ismael Navas Delgado, Maria del Mar Rojano-Muñoz, Sergio Ramírez, Antonio Jesús Pérez, Eduardo Andrés León, José Francisco Aldana Montes, Oswaldo Trelles. Intelligent client for integrating bioinformatics services
112 -- 114Åsa Pérez-Bercoff, Johan Koch, Thomas R. Bürglin. LogoBar: bar graph visualization of protein logos with gaps
115 -- 116Colas Schretter, Michel C. Milinkovitch. OligoFaktory: a visual tool for interactive oligonucleotide design
117 -- 119Tom M. W. Nye, Pietro Liò, Walter R. Gilks. A novel algorithm and web-based tool for comparing two alternative phylogenetic trees
120 -- 121Vivek Gopalan, Wei-Gang Qiu, Michael Z. Chen, Arlin Stoltzfus. Nexplorer: phylogeny-based exploration of sequence family data
122 -- 123Alan R. Dabney. ClaNC: point-and-click software for classifying microarrays to nearest centroids
124 -- 126Xinglai Ji, Ying Xu. libSRES: a C library for stochastic ranking evolution strategy for parameter estimation