Bioinformatics, Volume 22

Volume 22, Number 1, January 2006

• Alex Bateman:
  Bioinformatics - The new home for protein sequence motifs. 2
  

• Dorit Amikam, Michael Y. Galperin:
  PilZ domain is part of the bacterial c-di-GMP binding protein. 3-6
  

• Nusrat Rabbee, Terence P. Speed:
  A genotype calling algorithm for affymetrix SNP arrays. 7-12
  

• Miao Zhang, Warren Gish:
  Improved spliced alignment from an information theoretic approach. 13-20
  
• Kyle L. Jensen, Mark P. Styczynski, Isidore Rigoutsos, Gregory Stephanopoulos:
  A generic motif discovery algorithm for sequential data. 21-28
  
• Weichun Huang, David M. Umbach, Leping Li:
  Accurate anchoring alignment of divergent sequences. 29-34
  
• Zasha Weinberg, Walter L. Ruzzo:
  Sequence-based heuristics for faster annotation of non-coding RNA families. 35-39
  

• Yohan Kim, Mehmet Koyutürk, Umut Topkara, Ananth Grama, Shankar Subramaniam:
  Inferring functional information from domain co-evolution. 40-49
  

• Marta 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. 50-57
  
• Thomas Grotkjær, Ole Winther, Birgitte Regenberg, Jens Nielsen, Lars Kai Hansen:
  Robust multi-scale clustering of large DNA microarray datasets with the consensus algorithm. 58-67
  
• Xiaoyan Leng, Hans-Georg Müller:
  Classification using functional data analysis for temporal gene expression data. 68-76
  
• Yongxi 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. 77-87
  
• Hao Helen Zhang, Jeongyoun Ahn, Xiaodong Lin, Cheolwoo Park:
  Gene selection using support vector machines with non-convex penalty. 88-95
  

• Huai Li, Ming Zhan:
  Systematic intervention of transcription for identifying network response to disease and cellular phenotypes. 96-102
  

• Hongfang Liu, Zhang-Zhi Hu, Jian Zhang, Cathy H. Wu:
  BioThesaurus: a web-based thesaurus of protein and gene names. 103-105
  

• Ismael 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. 106-111
  

• Åsa Pérez-Bercoff, Johan Koch, Thomas R. Bürglin:
  LogoBar: bar graph visualization of protein logos with gaps. 112-114
  
• Colas Schretter, Michel C. Milinkovitch:
  OligoFaktory: a visual tool for interactive oligonucleotide design. 115-116
  

• Tom M. W. Nye, Pietro Liò, Walter R. Gilks:
  A novel algorithm and web-based tool for comparing two alternative phylogenetic trees. 117-119
  
• Vivek Gopalan, Wei-Gang Qiu, Michael Z. Chen, Arlin Stoltzfus:
  Nexplorer: phylogeny-based exploration of sequence family data. 120-121
  

• Alan R. Dabney:
  ClaNC: point-and-click software for classifying microarrays to nearest centroids. 122-123
  

• Xinglai Ji, Ying Xu:
  libSRES: a C library for stochastic ranking evolution strategy for parameter estimation. 124-126
  

Volume 22, Number 2, January 2006

• Victor de Lorenzo, Luis Serrano, Alfonso Valencia:
  Synthetic Biology: challenges ahead. 127-128
  

• Jean-Christophe Gelly, Alexandre G. de Brevern, Serge A. Hazout:
  'Protein Peeling': an approach for splitting a 3D protein structure into compact fragments. 129-133
  

• Aleksandr Morgulis, E. Michael Gertz, Alejandro A. Schäffer, Richa Agarwala:
  WindowMasker: window-based masker for sequenced genomes. 134-141
  
• James J. Gordon, Michael W. Towsey, James M. Hogan, Sarah A. Mathews, Peter Timms:
  Improved prediction of bacterial transcription start sites. 142-148
  

• I. Mihalek, I. Res, Olivier Lichtarge:
  A structure and evolution-guided Monte Carlo sequence selection strategy for multiple alignment-based analysis of proteins. 149-156
  
• Leelavati Narlikar, Alexander J. Hartemink:
  Sequence features of DNA binding sites reveal structural class of associated transcription factor. 157-163
  
• Jimin Pei, Wei Cai, Lisa N. Kinch, Nick V. Grishin:
  Prediction of functional specificity determinants from protein sequences using log-likelihood ratios. 164-171
  

• Hetunandan Kamisetty, Chris Bailey-Kellogg, Gopal Pandurangan:
  An efficient randomized algorithm for contact-based NMR backbone resonance assignment. 172-180
  
• Jan E. Gewehr, Ralf Zimmer:
  SSEP-Domain: protein domain prediction by alignment of secondary structure elements and profiles. 181-187
  
• Wei Xie, Nikolaos V. Sahinidis:
  Residue-rotamer-reduction algorithm for the protein side-chain conformation problem. 188-194
  
• Konstantin Arnold, Lorenza Bordoli, Jürgen Kopp, Torsten Schwede:
  The SWISS-MODEL workspace: a web-based environment for protein structure homology modelling. 195-201
  

• Francesca Martella:
  Classification of microarray data with factor mixture models. 202-208
  
• Anshuman Gupta, Costas D. Maranas, Réka Albert:
  Elucidation of directionality for co-expressed genes: predicting intra-operon termination sites. 209-214
  
• Mizanur R. Khondoker, Chris A. Glasbey, Bruce J. Worton:
  Statistical estimation of gene expression using multiple laser scans of microarrays. 215-219
  

• Zhaohui S. Qin, Shyam Gopalakrishnan, Gonçalo R. Abecasis:
  An efficient comprehensive search algorithm for tagSNP selection using linkage disequilibrium criteria. 220-225
  

• Ashish Choudhary, Aniruddha Datta, Michael L. Bittner, Edward R. Dougherty:
  Intervention in a family of Boolean networks. 226-232
  
• Barbara A. Novak, Ajay N. Jain:
  Pathway recognition and augmentation by computational analysis of microarray expression data. 233-241
  

• Do-Hoon Lee, Jeong-Hyeon Choi, Mehmet M. Dalkilic, Sun Kim:
  COMPAM : visualization of combining pairwise alignments for multiple genomes. 242-244
  

• Ljubomir J. Buturovic:
  PCP: a program for supervised classification of gene expression profiles. 245-247
  

• Anaïs 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. 248-250
  
• Jo Criel, Elena Tsiporkova:
  Gene Time Echipression Warper: a tool for alignment, template matching and visualization of gene expression time series. 251-252
  

• Mahender Kumar Singh, Shilpy Srivastava, G. P. S. Raghava, Grish C. Varshney:
  HaptenDB: a comprehensive database of haptens, carrier proteins and anti-hapten antibodies. 253-255
  

Volume 22, Number 3, February 2006

• Lakshminarayan 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. 257-263
  

• Matthew H. J. Cordes, Greta J. Binford:
  Lateral gene transfer of a dermonecrotic toxin between spiders and bacteria. 264-268
  

• Núria López-Bigas, Benjamin J. Blencowe, Christos A. Ouzounis:
  Highly consistent patterns for inherited human diseases at the molecular level. 269-277
  

• Susan 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. 278-284
  
• Qiwen Dong, Xiaolong Wang, Lei Lin:
  Application of latent semantic analysis to protein remote homology detection. 285-290
  
• S. Vishnu V. Deevi, Andrew C. R. Martin:
  An extensible automated protein annotation tool: standardizing input and output using validated XML. 291-296
  

• Eunhee Koh, Taehyo Kim, Hyun-soo Cho:
  Mean curvature as a major determinant of ß-sheet propensity. 297-302
  
• Baoqiang Cao, Aleksey A. Porollo, Rafal Adamczak, Mark Jarrell, Jaroslaw Meller:
  Enhanced recognition of protein transmembrane domains with prediction-based structural profiles. 303-309
  

• Earl F. Glynn, Jie Chen, Arcady R. Mushegian:
  Detecting periodic patterns in unevenly spaced gene expression time series using Lomb-Scargle periodograms. 310-316
  
• Wensheng 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. 317-325
  
• Dick de Ridder, Frank J. T. Staal, Jacques J. M. van Dongen, Marcel J. T. Reinders:
  Maximum significance clustering of oligonucleotide microarrays. 326-331
  
• Jianhua Ruan, Weixiong Zhang:
  A bi-dimensional regression tree approach to the modeling of gene expression regulation. 332-340
  

• Peter Beerli:
  Comparison of Bayesian and maximum-likelihood inference of population genetic parameters. 341-345
  

• Ravishankar Rao Vallabhajosyula, Vijay Chickarmane, Herbert M. Sauro:
  Conservation analysis of large biochemical networks. 346-353
  

• Mark 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. 354-355
  

• A. V. McDonnell, Taijiao Jiang, Amy E. Keating, B. Berger:
  Paircoil2: improved prediction of coiled coils from sequence. 356-358
  
• Tobias Dezulian, Michael Remmert, Javier F. Palatnik, Detlef Weigel, Daniel H. Huson:
  Identification of plant microRNA homologs. 359-360
  
• Tiago José P. Sobreira, Alan M. Durham, Arthur Gruber:
  TRAP: automated classification, quantification and annotation of tandemly repeated sequences. 361-362
  

• Nicolas Bortolussi, Eric Durand, Michael G. B. Blum, Olivier François:
  apTreeshape: statistical analysis of phylogenetic tree shape. 363-364
  

• Andreas Moll, Andreas Hildebrandt, Hans-Peter Lenhof, Oliver Kohlbacher:
  BALLView: a tool for research and education in molecular modeling. 365-366
  

• Elo Leung, Pierre R. Bushel:
  PAGE: phase-shifted analysis of gene expression. 367-368
  
• Giorgio Valentini:
  Clusterv: a tool for assessing the reliability of clusters discovered in DNA microarray data. 369-370
  

• Dumitru Brinza, Alexander Zelikovsky:
  2SNP: scalable phasing based on 2-SNP haplotypes. 371-373
  

• Ugur Dogrusöz, E. Z. Erson, Erhan Giral, Emek Demir, Ozgun Babur, Ahmet Cetintas, R. Colak:
  Patikaweb: a Web interface for analyzing biological pathways through advanced querying and visualization. 374-375
  

• Hu Chen, Ni Huang, Zhirong Sun:
  SubLoc: a server/client suite for protein subcellular location based on SOAP. 376-377
  
• Jing Ding, Laron M. Hughes, Daniel Berleant, Andy W. Fulmer, Eve Syrkin Wurtele:
  PubMed Assistant: a biologist-friendly interface for enhanced PubMed search. 378-380
  
• Steven M. Gallo, Long Li, Zihua Hu, Marc S. Halfon:
  REDfly: a Regulatory Element Database for Drosophila. 381-383
  

Volume 22, Number 4, February 2006

• Jiexin Zhang, Li Zhang, Kevin R. Coombes:
  Gene sequence signatures revealed by mining the UniGene affiliation network. 385-391
  
• Xiang Guo, Kay Tatsuoka, Rongxiang Liu:
  Histone acetylation and transcriptional regulation in the genome of Saccharomyces cerevisiae. 392-399
  
• Jussi Salmi, Robert Moulder, Jan-Jonas Filén, Olli Nevalainen, Tuula A. Nyman, Riitta Lahesmaa, Tero Aittokallio:
  Quality classification of tandem mass spectrometry data. 400-406
  

• András Kocsor, Attila Kertész-Farkas, László Kaján, Sándor Pongor:
  Application of compression-based distance measures to protein sequence classification: a methodological study. 407-412
  
• Yao-ming Huang, Christopher Bystroff:
  Improved pairwise alignments of proteins in the Twilight Zone using local structure predictions. 413-422
  
• Kenzie 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. 423-429
  
• Tilman Sauer, Ekaterina Shelest, Edgar Wingender:
  Evaluating phylogenetic footprinting for human-rodent comparisons. 430-437
  
• Joseph M. Volpe, Lindsay G. Cowell, Thomas B. Kepler:
  SoDA: implementation of a 3D alignment algorithm for inference of antigen receptor recombinations. 438-444
  
• Zizhen Yao, Zasha Weinberg, Walter L. Ruzzo:
  CMfinder - a covariance model based RNA motif finding algorithm. 445-452
  

• Elodie Duprat, Marie-Paule Lefranc, Olivier Gascuel:
  A simple method to predict protein-binding from aligned sequences - application to MHC superfamily and ß2-microglobulin. 453-459
  
• Simon W. Ginzinger, Johannes Fischer:
  SimShift: Identifying structural similarities from NMR chemical shifts. 460-465
  

• Lexin Li:
  Survival prediction of diffuse large-B-cell lymphoma based on both clinical and gene expression information. 466-471
  
• Baolin Wu:
  Differential gene expression detection and sample classification using penalized linear regression models. 472-476
  

• Eugene P. van Someren, B. L. T. Vaes, W. T. Steegenga, A. M. Sijbers, Koen J. Dechering, Marcel J. T. Reinders:
  Least absolute regression network analysis of the murine osteoblast differentiation network. 477-484
  

• Siddhartha Basu, Erich Bremer, Chun Zhou, Daniel F. Bogenhagen:
  MiGenes: a searchable interspecies database of mitochondrial proteins curated using gene ontology annotation. 485-492
  

• Jörg Rothgänger, Markus Weniger, Thomas Weniger, Alexander Mellmann, Dag Harmsen:
  Ridom TraceEdit: a DNA trace editor and viewer. 493-494
  
• Derek Huntley, Angela Baldo, Saurabh Johri, Marek J. Sergot:
  SEAN: SNP prediction and display program utilizing EST sequence clusters. 495-496
  
• Tiziana 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. 497-499
  
• Peter Steffen, Björn Voß, Marc Rehmsmeier, Jens Reeder, Robert Giegerich:
  RNAshapes: an integrated RNA analysis package based on abstract shapes. 500-503
  

• John Eargle, Dan Wright, Zaida Luthey-Schulten:
  Multiple Alignment of protein structures and sequences for VMD. 504-506
  

• Jeffrey T. Leek, Eva Monsen, Alan R. Dabney, John D. Storey:
  EDGE: extraction and analysis of differential gene expression. 507-508
  
• Michael Mueller, Anuj Goel, Manjula Thimma, Nicholas J. Dickens, Timothy J. Aitman, Jonathan Mangion:
  eQTL Explorer: integrated mining of combined genetic linkage and expression experiments. 509-511
  

• B. L. Browning:
  FLOSS: flexible ordered subset analysis for linkage mapping of complex traits. 512-513
  

• Henning Schmidt, Mats Jirstrand:
  Systems Biology Toolbox for MATLAB: a computational platform for research in systems biology. 514-515
  

Volume 22, Number 5, March 2006

• Daniel Dalevi, Devdatt P. Dubhashi, Malte Hermansson:
  Bayesian classifiers for detecting HGT using fixed and variable order markov models of genomic signatures. 517-522
  
• Guojun Yang, Timothy C. Hall:
  HideNseek, a post-genome approach to locate transgenes exemplified in Arabidopsis thaliana. 523-526
  

• Giuseppe D'Auria, Ravindra Pushker, Francisco Rodríguez-Valera:
  IWoCS: analyzing ribosomal intergenic transcribed spacers configuration and taxonomic relationships. 527-531
  
• Wolfgang P. Lehrach, Dirk Husmeier, Christopher K. I. Williams:
  A regularized discriminative model for the prediction of protein-peptide interactions. 532-540
  
• Matthew 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. 541-549
  

• Andreas Henschel, Wan Kyu Kim, Michael Schroeder:
  Equivalent binding sites reveal convergently evolved interaction motifs. 550-555
  

• Alexander Ploner, Stefano Calza, Arief Gusnanto, Yudi Pawitan:
  Multidimensional local false discovery rate for microarray studies. 556-565
  
• Johannes Tuikkala, Laura Elo, Olli Nevalainen, Tero Aittokallio:
  Improving missing value estimation in microarray data with gene ontology. 566-572
  

• Miguel Pérez-Enciso:
  Multiple association analysis via simulated annealing (MASSA). 573-580
  

• Yoram Louzoun, Lev Muchnik, Sorin Solomon:
  Copying nodes versus editing links: the source of the difference between genetic regulatory networks and the WWW. 581-588
  

• Roberto 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. 589-596
  
• Jung-jae Kim, Zhuo Zhang, Jong C. Park, See-Kiong Ng:
  BioContrasts: extracting and exploiting protein-protein contrastive relations from biomedical literature. 597-605
  
• Ofer Shai, Quaid Morris, Benjamin J. Blencowe, Brendan J. Frey:
  Inferring global levels of alternative splicing isoforms using a generative model of microarray data. 606-613
  

• Stephan H. F. Bernhart, Ivo L. Hofacker, Peter F. Stadler:
  Local RNA base pairing probabilities in large sequences. 614-615
  
• Leighton Pritchard, Jennifer A. White, Paul R. J. Birch, Ian K. Toth:
  GenomeDiagram: a python package for the visualization of large-scale genomic data. 616-617
  

• Andrew Smith, John-Marc Chandonia, Steven E. Brenner:
  ANDY: a general, fault-tolerant tool for database searching on computer clusters. 618-620
  

• Dominik Gront, Andrzej Kolinski:
  BioShell - a package of tools for structural biology computations. 621-622
  
• Mikhail A. Lomize, Andrei L. Lomize, Irina D. Pogozheva, Henry I. Mosberg:
  OPM: Orientations of Proteins in Membranes database. 623-625
  

• Bradley M. Hemminger, Billy Saelim, Patrick F. Sullivan:
  TAMAL: an integrated approach to choosing SNPs for genetic studies of human complex traits. 626-627
  

• Colin S. Gillespie, Darren J. Wilkinson, Carole J. Proctor, Daryl P. Shanley, Richard J. Boys, Thomas B. L. Kirkwood:
  Tools for the SBML Community. 628-629
  

• Guido Dieterich, Uwe Kärst, Jürgen Wehland, Lothar Jänsch:
  VIS-O-BAC: exploratory visualization of functional genome studies from bacteria. 630-631
  
• J. A. Falkner, J. W. Falkner, P. C. Andrews:
  ProteomeCommons.org JAF: reference information and tools for proteomics. 632-633
  
• Mikko Katajamaa, Jarkko Miettinen, Matej Oresic:
  MZmine: toolbox for processing and visualization of mass spectrometry based molecular profile data. 634-636
  

• Stephen 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. 637-640
  
• M. Dennis Prickett, Matt Page, Angela E. Douglas, Gavin H. Thomas:
  BuchneraBASE: a post-genomic resource for Buchnera sp. APS. 641-642
  

Volume 22, Number 6, March 2006

• Udo Hahn, Alfonso Valencia:
  Semantic Mining in Biomedicine (Introduction to the papers selected from the SMBM 2005 Symposium, Hinxton, U.K., April 2005). 643-644
  

• Jasmin Saric, Lars Juhl Jensen, Rossitza Ouzounova, Isabel Rojas, Peer Bork:
  Extraction of regulatory gene/protein networks from Medline. 645-650
  
• Ted Sandler, Andrew I. Schein, Lyle H. Ungar:
  Automatic term list generation for entity tagging. 651-657
  
• Patrick Ruch:
  Automatic assignment of biomedical categories: toward a generic approach. 658-664
  
• Jin-Bok Lee, Jung-jae Kim, Jong C. Park:
  Automatic extension of Gene Ontology with flexible identification of candidate terms. 665-670
  

• Elizabeta 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? 671-675
  

• Valentina Boeva, Mireille Régnier, Dmitri A. Papatsenko, Vsevolod Makeev:
  Short fuzzy tandem repeats in genomic sequences, identification, and possible role in regulation of gene expression. 676-684
  
• Chia-Jung Chang, Yao-Ting Huang, Kun-Mao Chao:
  A greedier approach for finding tag SNPs. 685-691
  

• Xiang Shao, Valery Shepelev, Alexei Fedorov:
  Bioinformatic analysis of exon repetition, exon scrambling and trans-splicing in humans. 692-698
  

• Joanna 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. 699-707
  
• Daniele Catanzaro, Raffaele Pesenti, Michel C. Milinkovitch:
  A non-linear optimization procedure to estimate distances and instantaneous substitution rate matrices under the GTR model. 708-715
  
• Tanja Gesell, Arndt von Haeseler:
  In silico sequence evolution with site-specific interactions along phylogenetic trees. 716-722
  

• Benjamin J. Polacco, Patricia C. Babbitt:
  Automated discovery of 3D motifs for protein function annotation. 723-730
  

• Kristin Missal, Michael A. Cross, Dirk Drasdo:
  Gene network inference from incomplete expression data: transcriptional control of hematopoietic commitment. 731-738
  
• Chiara Sabatti, Gareth M. James:
  Bayesian sparse hidden components analysis for transcription regulation networks. 739-746
  

• Zheng Li, Stephen M. Shaw, Matthew J. Yedwabnick, Christina Chan:
  Using a state-space model with hidden variables to infer transcription factor activities. 747-754
  

• Zuyi Wang, Yue Joseph 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. 755-761
  

• Wolfgang Gerlach, Robert Giegerich:
  GUUGle: a utility for fast exact matching under RNA complementary rules including G-U base pairing. 762-764
  

• Jonathon Blake, Christian Schwager, Misha Kapushesky, Alvis Brazma:
  ChroCoLoc: an application for calculating the probability of co-localization of microarray gene expression. 765-767
  

• Mary K. Kuhner:
  LAMARC 2.0: maximum likelihood and Bayesian estimation of population parameters. 768-770
  
• Alun Thomas, Nicola J. Camp:
  Maximum likelihood estimates of allele frequencies and error rates from samples of related individuals by gene counting. 771-772
  

• Euan A. Adie, Richard R. Adams, Kathryn L. Evans, David J. Porteous, Ben S. Pickard:
  SUSPECTS: enabling fast and effective prioritization of positional candidates. 773-774
  

Volume 22, Number 7, April 2006

• Marialuisa Pellegrini-Calace, Anna Tramontano:
  Identification of a novel putative mitogen-activated kinase cascade on human chromosome 21 by computational approaches. 775-778
  

• Raja Jothi, Elena Zotenko, Asba Tasneem, Teresa M. Przytycka:
  COCO-CL: hierarchical clustering of homology relations based on evolutionary correlations. 779-788
  

• Rafael A. Irizarry, Zhijin Wu, Harris A. Jaffee:
  Comparison of Affymetrix GeneChip expression measures. 789-794
  
• Wei Pan:
  Incorporating gene functions as priors in model-based clustering of microarray gene expression data. 795-801
  
• Hans-Peter Piepho, B. Keller, N. Hoecker, F. Hochholdinger:
  Combining signals from spotted cDNA microarrays obtained at different scanning intensities. 802-807
  
• Jinwook Seo, Heather Gordish-Dressman, Eric P. Hoffman:
  An interactive power analysis tool for microarray hypothesis testing and generation. 808-814
  

• Mukesh Bansal, Giusy Della Gatta, Diego di Bernardo:
  Inference of gene regulatory networks and compound mode of action from time course gene expression profiles. 815-822
  
• Haiyuan Yu, Alberto Paccanaro, Valery Trifonov, Mark Gerstein:
  Predicting interactions in protein networks by completing defective cliques. 823-829
  
• Zafer Barutçuoglu, Robert E. Schapire, Olga G. Troyanskaya:
  Hierarchical multi-label prediction of gene function. 830-836
  

• Ashish Choudhary, Marcel Brun, Jianping Hua, James Lowey, Edward Suh, Edward R. Dougherty:
  Genetic test bed for feature selection. 837-842
  
• Kazumi Hakamada, Masahiro Okamoto, Taizo Hanai:
  Novel technique for preprocessing high dimensional time-course data from DNA microarray: mathematical model-based clustering. 843-848
  
• Céline Rouveirol, Nicolas Stransky, Philippe Hupé, Philippe La Rosa, Eric Viara, Emmanuel Barillot, François Radvanyi:
  Computation of recurrent minimal genomic alterations from array-CGH data. 849-856
  

• Parantu K. Shah, Peer Bork:
  LSAT: learning about alternative transcripts in MEDLINE. 857-865
  
• Patricia 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, Joseph White, Christian J. Stoeckert Jr.:
  The MGED Ontology: a resource for semantics-based description of microarray experiments. 866-873
  
• Sandhya 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. 874-882
  

• E. Ryder, R. Jackson, A. Ferguson-Smith, Steven Russell:
  MAMMOT - a set of tools for the design, management and visualization of genomic tiling arrays. 883-884
  

• Payan Canaran, Lincoln Stein, Doreen Ware:
  Look-Align: an interactive web-based multiple sequence alignment viewer with polymorphism analysis support. 885-886
  
• Weizhong Li, Adam Godzik:
  VISSA: a program to visualize structural features from structure sequence alignment. 887-888
  
• Michael Sammeth, Thasso Griebel, Felix Tille, Jens Stoye:
  Panta rhei (QAlign2): an open graphical environment for sequence analysis. 889-890
  
• Avner Schlessinger, Guy Yachdav, Burkhard Rost:
  PROFbval: predict flexible and rigid residues in proteins. 891-893
  
• Fengfeng Zhou, Yu Xue, Xuebiao Yao, Ying Xu:
  CSS-Palm: palmitoylation site prediction with a clustering and scoring strategy (CSS). 894-896
  

• James M. Wettenhall, Ken M. Simpson, Keith Satterley, Gordon K. Smyth:
  affylmGUI: a graphical user interface for linear modeling of single channel microarray data. 897-899
  

• Sébastien Carrère, Jérôme Gouzy:
  REMORA: a pilot in the ocean of BioMoby web-services. 900-901
  
• Pedro Cipriano Feijão, Lissiene Silva Neiva, Ana Maria Lima de Azeredo-Espin, Ana Cláudia Lessinger:
  AMiGA: the arthropodan mitochondrial genomes accessible database. 902-903
  

Volume 22, Number 8, April 2006

• A. 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. 905-910
  

• Philippe Broët, Sylvia Richardson:
  Detection of gene copy number changes in CGH microarrays using a spatially correlated mixture model. 911-918
  
• Hao Xiong:
  Non-linear tests for identifying differentially expressed genes or genetic networks. 919-923
  

• Benjamin R. Jefferys, Lawrence A. Kelley, Marek J. Sergot, John Fox, Michael J. E. Sternberg:
  Capturing expert knowledge with argumentation: a case study in bioinformatics. 924-933
  
• Kay C. Wiese, Andrew Hendriks:
  Comparison of P-RnaPredict and mfold - algorithms for RNA secondary structure prediction. 934-942
  

• Sepp Hochreiter, Djork-Arné Clevert, Klaus Obermayer:
  A new summarization method for affymetrix probe level data. 943-949
  
• Ja-Yong Koo, Insuk Sohn, Sujong Kim, Jae Won Lee:
  Structured polychotomous machine diagnosis of multiple cancer types using gene expression. 950-958
  
• Peng Qiu, Z. Jane Wang, K. J. Ray Liu:
  Polynomial model approach for resynchronization analysis of cell-cycle gene expression data. 959-966
  

• Xiang Guo, Rongxiang Liu, Craig D. Shriver, Hai Hu, Michael N. Liebman:
  Assessing semantic similarity measures for the characterization of human regulatory pathways. 967-973
  
• Natasa Przulj, Derek G. Corneil, Igor Jurisica:
  Efficient estimation of graphlet frequency distributions in protein-protein interaction networks. 974-980
  

• Claudia Plant, Christian Böhm, Bernhard Tilg, Christian Baumgartner:
  Enhancing instance-based classification with local density: a new algorithm for classifying unbalanced biomedical data. 981-988
  
• Haiquan Li, Jinyan Li, Limsoon Wong:
  Discovering motif pairs at interaction sites from protein sequences on a proteome-wide scale. 989-996
  

• Philipp Pagel, Matthias Oesterheld, Volker Stümpflen, Dmitrij Frishman:
  The DIMA web resource - exploring the protein domain network. 997-998
  
• Voichita 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. 999-1001
  

• Martin Eisenacher, Jürgen de Braaf, Simone König:
  Mass Analysis Peptide Sequence Prediction (MAPSP). 1002-1003
  

• Michael J. Sanderson:
  Paloverde: an OpenGL 3D phylogeny browser. 1004-1006
  

• Surjit B. Dixit, David L. Beveridge:
  Structural bioinformatics of DNA: a web-based tool for the analysis of molecular dynamics results and structure prediction. 1007-1009
  

• Janko Dietzsch, Nils Gehlenborg, Kay Nieselt:
  Mayday-a microarray data analysis workbench. 1010-1012
  

• Jing Hua Zhao:
  Pedigree-drawing with R and graphviz. 1013-1014
  

• Ramon Aragues, Daniel Jaeggi, Baldo Oliva:
  PIANA: protein interactions and network analysis. 1015-1017
  
• Maria J. Schilstra, Lu Li, Joanne Matthews, Andrew Finney, Michael Hucka, Nicolas Le Novère:
  CellML2SBML: conversion of CellML into SBML. 1018-1020
  

• Balázs Adamcsek, Gergely Palla, Illés J. Farkas, Imre Derényi, Tamás Vicsek:
  CFinder: locating cliques and overlapping modules in biological networks. 1021-1023
  

• Adam Ameur, Vladimir Yankovski, Stefan Enroth, Ola Spjuth, Henryk Jan Komorowski:
  The LCB Data Warehouse. 1024-1026
  
• Yongliang Ren, Wuming Gong, Qiqi Xu, Xin Zheng, Dong Lin, Yejun Wang, Tongbin Li:
  siRecords: an extensive database of mammalian siRNAs with efficacy ratings. 1027-1028
  

• Baolin Wu:
  Differential gene expression detection and sample classification using penalized linear regression models. 1029
  

Volume 22, Number 9, May 2006

• Chris P. Ponting:
  A novel domain suggests a ciliary function for ASPM, a brain size determining gene. 1031-1035
  

• Fan Hsu, W. James Kent, Hiram Clawson, Robert M. Kuhn, Mark Diekhans, David Haussler:
  The UCSC Known Genes. 1036-1046
  

• Lawrence S. Hon, Ajay N. Jain:
  A deterministic motif finding algorithm with application to the human genome. 1047-1054
  
• Igor B. Kuznetsov, Seungwoo Hwang:
  A novel sensitive method for the detection of user-defined compositional bias in biological sequences. 1055-1063
  

• Jochen Maydt, Thomas Lengauer:
  Recco: recombination analysis using cost optimization. 1064-1071
  
• F. 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. 1072-1079
  

• Jessica Ebert, Douglas L. Brutlag:
  Development and validation of a consistency based multiple structure alignment algorithm. 1080-1087
  
• Violaine Moreau, Claude Granier, Sylvie Villard, Daniel Laune, Franck Molina:
  Discontinuous epitope prediction based on mimotope analysis. 1088-1095
  

• Ana Conesa, María José Nueda, Alberto Ferrer, Manuel Talón:
  maSigPro: a method to identify significantly differential expression profiles in time-course microarray experiments. 1096-1102
  
• Carlos 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. 1103-1110
  
• Lee Weng, Hongyue Dai, Yihui Zhan, Yudong D. He, Sergey B. Stepaniants, Douglas E. Bassett:
  Rosetta error model for gene expression analysis. 1111-1121
  
• Amela 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. 1122-1129
  

• Amanda Clare, Andreas Karwath, Helen Ougham, Ross D. King:
  Functional bioinformatics for Arabidopsis thaliana. 1130-1136
  

• Uwe 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. 1137-1143
  

• J. C. Marioni, Natalie P. Thorne, Simon Tavaré:
  BioHMM: a heterogeneous hidden Markov model for segmenting array CGH data. 1144-1146
  

• David 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. 1147-1149
  

• Dong-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. 1150-1151
  
• Sebastian Wernicke, Florian Rasche:
  FANMOD: a tool for fast network motif detection. 1152-1153
  

• Victor Trevino, Francesco Falciani:
  GALGO: an R package for multivariate variable selection using genetic algorithms. 1154-1156
  

Volume 22, Number 10, May 2006

• Andrew E. Torda, Thomas Lengauer:
  Editorial. 1157
  

• Annette 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. 1158-1165
  
• Hannes Luz, Martin Vingron:
  Family specific rates of protein evolution. 1166-1171
  

• Ivo L. Hofacker, Peter F. Stadler:
  Memory efficient folding algorithms for circular RNA secondary structures. 1172-1176
  
• Ulrike Mückstein, Hakim Tafer, Jörg Hackermüller, Stephan H. F. Bernhart, Peter F. Stadler, Ivo L. Hofacker:
  Thermodynamics of RNA-RNA binding. 1177-1182
  
• Jean-Christophe Nebel:
  Generation of 3D templates of active sites of proteins with rigid prosthetic groups. 1183-1189
  

• Alexander 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. 1190-1197
  

• Ari Rantanen, Taneli Mielikäinen, Juho Rousu, Hannu Maaheimo, Esko Ukkonen:
  Planning optimal measurements of isotopomer distributions for estimation of metabolic fluxes. 1198-1206
  

• Loris Nanni, Alessandra Lumini:
  An ensemble of K-local hyperplanes for predicting protein-protein interactions. 1207-1210
  

• Hideki 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. 1211-1216
  

• Anton Valouev, Yu Zhang, David C. Schwartz, Michael S. Waterman:
  Refinement of optical map assemblies. 1217-1224
  

• Faisal Ababneh, Lars S. Jermiin, Chunsheng Ma, John Robinson:
  Matched-pairs tests of homogeneity with applications to homologous nucleotide sequences. 1225-1231
  

• Joo 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. 1232-1238
  

• Ritesh Agrawal, Gary D. Stormo:
  Using mRNAs lengths to accurately predict the alternatively spliced gene products in Caenorhabditis elegans. 1239-1244
  
• Daniel P. Berrar, Ian Bradbury, Werner Dubitzky:
  Avoiding model selection bias in small-sample genomic datasets. 1245-1250
  
• Kristof Engelen, Bart Naudts, Bart De Moor, Kathleen Marchal:
  A calibration method for estimating absolute expression levels from microarray data. 1251-1258
  
• Desheng Huang, Wei Pan:
  Incorporating biological knowledge into distance-based clustering analysis of microarray gene expression data. 1259-1268
  

• Tijl De Bie, Nello Cristianini, Jeffery P. Demuth, Matthew W. Hahn:
  CAFE: a computational tool for the study of gene family evolution. 1269-1271
  

• Richard 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. 1272-1274
  

• Sarah M. Keating, Benjamin J. Bornstein, Andrew Finney, Michael Hucka:
  SBMLToolbox: an SBML toolbox for MATLAB users. 1275-1277
  
• Amanda M. White, Don Simone Daly, Susan M. Varnum, Kevin K. Anderson, Nikki Bollinger, Richard C. Zangar:
  ProMAT: protein microarray analysis tool. 1278-1279
  

• Jacek Sroka, Grzegorz Kaczor, Jerzy Tyszkiewicz, Andrzej M. Kierzek:
  XQTav: an XQuery processor for Taverna environment. 1280-1281
  
• Simon Barkow, Stefan Bleuler, Amela Prelic, Philip Zimmermann, Eckart Zitzler:
  BicAT: a biclustering analysis toolbox. 1282-1283
  

• Rasko Leinonen, Francesco Nardone, Weimin Zhu, Rolf Apweiler:
  UniSave: the UniProtKB Sequence/Annotation Version database. 1284-1285
  
• Ge Gao, Yingfu Zhong, Anyuan Guo, Qihui Zhu, Wen Tang, Wei-Mou Zheng, Xiaocheng Gu, Liping Wei, Jingchu Luo:
  DRTF: a database of rice transcription factors. 1286-1287
  

Volume 22, Number 11, June 2006

• Emmanuelle Becker, Vincent Meyer, Hocine Madaoui, Raphaël Guérois:
  Detection of a tandem BRCT in Nbs1 and Xrs2 with functional implications in the DNA damage response. 1289-1292
  

• Ute Müller, Günther Ernst, Christian Melle, Reinhard Guthke, Ferdinand von Eggeling:
  Convergence of the proteomic pattern in cancer. 1293-1296
  

• Kira 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. 1297-1301
  
• Florencia G. Leonardi:
  A generalization of the PST algorithm: modeling the sparse nature of protein sequences. 1302-1307
  
• Stephen McCauley, Jotun Hein:
  Using hidden Markov models and observed evolution to annotate viral genomes. 1308-1316
  
• Aleksey Y. Ogurtsov, Svetlana A. Shabalina, Alexey S. Kondrashov, Mikhail A. Roytberg:
  Analysis of internal loops within the RNA secondary structure in almost quadratic time. 1317-1324
  
• Malik 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. 1325-1334
  

• Nicholas J. Burgoyne, Richard M. Jackson:
  Predicting protein interaction sites: binding hot-spots in protein-protein and protein-ligand interfaces. 1335-1342
  
• Gilad 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. 1343-1352
  
• Konrad H. Paszkiewicz, Michael J. E. Sternberg, Michael Lappe:
  Prediction of viable circular permutants using a graph theoretic approach. 1353-1358
  

• Gaëlle 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. 1359-1366
  

• Xue-wen Chen, Gopalakrishna Anantha, Xinkun Wang:
  An effective structure learning method for constructing gene networks. 1367-1374
  
• Chao-Ping Hsu, Pei-Hsuan Lee, Ching-Wei Chang, Cheng-Tsung Lee:
  Constructing quantitative models from qualitative mutant phenotypes: preferences in selecting sensory organ precursors. 1375-1382
  
• Jacob 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. 1383-1390
  

• David P. De Souza, Eleanor C. Saunders, Malcolm J. McConville, Vladimir A. Likic:
  Progressive peak clustering in GC-MS Metabolomic experiments applied to Leishmania parasites. 1391-1396
  

• Christian X. Weichenberger, Manfred J. Sippl:
  NQ-Flipper: validation and correction of asparagine/glutamine amide rotamers in protein crystal structures. 1397-1398
  

• David L. Aylor, Eric W. Price, Ignazio Carbone:
  SNAP: Combine and Map modules for multilocus population genetic analysis. 1399-1401
  
• Claire Bardel, Vincent Danjean, Emmanuelle Génin:
  ALTree: association detection and localization of susceptibility sites using haplotype phylogenetic trees. 1402-1403
  
• Mario Falchi, Cesare Cappio Borlino:
  PowQ: a user-friendly package for the design of variance component multipoint linkage analysis studies. 1404-1405
  

• Rainer 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. 1406-1407
  
• Vladimir 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. 1408-1409
  

• Hyunsoo Kim, Gene H. Golub, Haesun Park:
  Missing value estimation for DNA microarray gene expression data: local least squares imputation. 1410-1411
  
• Jeffrey T. Leek, Eva Monsen, Alan R. Dabney, John D. Storey:
  EDGE: extraction and analysis of differential gene expression. 1412
  

Volume 22, Number 12, June 2006

• Alfonso Valencia, Alex Bateman:
  Software patents in Bioinformatics. 1415
  
• John Quackenbush, Steven Salzberg:
  It is time to end the patenting of software. 1416-1417
  

• Sophie Pasek, Jean-Loup Risler, Pierre Brézellec:
  Gene fusion/fission is a major contributor to evolution of multi-domain bacterial proteins. 1418-1423
  

• Martin G. Grigorov:
  Global dynamics of biological systems from time-resolved omics experiments. 1424-1430
  

• Radek Szklarczyk, Jaap Heringa:
  AuberGene - a sensitive genome alignment tool. 1431-1436
  
• Zhaolei Zhang, Nicholas Carriero, Deyou Zheng, John E. Karro, Paul M. Harrison, Mark Gerstein:
  PseudoPipe: an automated pseudogene identification pipeline. 1437-1439
  

• Florencio Pazos, Antonio Rausell, Alfonso Valencia:
  Phylogeny-independent detection of functional residues. 1440-1448
  

• Francesco Ortuso, Thierry Langer, Stefano Alcaro:
  GBPM: GRID-based pharmacophore model: concept and application studies to protein-protein recognition. 1449-1455
  
• Jianlin Cheng, Pierre Baldi:
  A machine learning information retrieval approach to protein fold recognition. 1456-1463
  
• Alison L. Cuff, Robert W. Janes, Andrew C. R. Martin:
  Analysing the ability to retain sidechain hydrogen-bonds in mutant proteins. 1464-1470
  

• S. E. Ahnert, K. Willbrand, F. C. S. Brown, T. M. A. Fink:
  Unbiased pattern detection in microarray data series. 1471-1476
  
• Philippe 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. 1477-1485
  
• Xin Gao:
  Construction of null statistics in permutation-based multiple testing for multi-factorial microarray experiments. 1486-1494
  
• Lars 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. 1495-1502
  

• Wentian Li, Mingyi Wang, Patricia Irigoyen, Peter K. Gregersen:
  Inferring causal relationships among intermediate phenotypes and biomarkers: a case study of rheumatoid arthritis. 1503-1507
  

• Quansong Ruan, Joshua A. Steele, Michael S. Schwalbach, Jed A. Fuhrman, Fengzhu Sun:
  A dynamic programming algorithm for binning microbial community profiles. 1508-1514
  

• Chuen Seng Tan, Alexander Ploner, Andreas Quandt, Janne Lehtiö, Yudi Pawitan:
  Finding regions of significance in SELDI measurements for identifying protein biomarkers. 1515-1523
  
• Smriti 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. 1524-1531
  

• Boris Adryan, Sarah A. Teichmann:
  FlyTF: a systematic review of site-specific transcription factors in the fruit fly Drosophila melanogaster. 1532-1533
  

• Yann Ponty, Michel Termier, Alain Denise:
  GenRGenS: software for generating random genomic sequences and structures. 1534-1535
  
• Vladimir Vacic, Lilia M. Iakoucheva, Predrag Radivojac:
  Two Sample Logo: a graphical representation of the differences between two sets of sequence alignments. 1536-1537
  

• Ryo Yoshida, Tomoyuki Higuchi, Seiya Imoto, Satoru Miyano:
  ArrayCluster: an analytic tool for clustering, data visualization and module finder on gene expression profiles. 1538-1539
  

• Ryota Suzuki, Hidetoshi Shimodaira:
  Pvclust: an R package for assessing the uncertainty in hierarchical clustering. 1540-1542
  

Volume 22, Number 13, July 2006

• Jonathan D. Wren:
  Theory and reality for software patents: good in concept, not so good in practice. 1543-1545
  

• Elhanan 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. 1546-1550
  

• Christina Toft, Mario A. Fares:
  GRAST: a new way of genome reduction analysis using comparative genomics. 1551-1561
  

• Burkhard Heil, Jost Ludwig, Hella Lichtenberg-Fraté, Thomas Lengauer:
  Computational recognition of potassium channel sequences. 1562-1568
  
• Kavitha Bhasi, Li Zhang, Daniel Brazeau, Aidong Zhang, Murali Ramanathan:
  VizStruct for visualization of genome-wide SNP analyses. 1569-1576
  
• Zhi Wei, Shane T. Jensen:
  GAME: detecting cis-regulatory elements using a genetic algorithm. 1577-1584
  

• Orhan Çamoglu, Tolga Can, Ambuj K. Singh:
  Integrating multi-attribute similarity networks for robust representation of the protein space. 1585-1592
  
• Deniz Dalli, Andreas Wilm, Indra Mainz, Gerhard Steger:
  StrAl: progressive alignment of non-coding RNA using base pairing probability vectors in quadratic time. 1593-1599
  

• Adrian Alexa, Jörg Rahnenführer, Thomas Lengauer:
  Improved scoring of functional groups from gene expression data by decorrelating GO graph structure. 1600-1607
  
• Geoffrey J. McLachlan, Richard Bean, Liat Ben-Tovim Jones:
  A simple implementation of a normal mixture approach to differential gene expression in multiclass microarrays. 1608-1615
  
• Golan Yona, William Dirks, Shafquat Rahman, David M. Lin:
  Effective similarity measures for expression profiles. 1616-1622
  

• Hon Nian Chua, Wing-Kin Sung, Limsoon Wong:
  Exploiting indirect neighbours and topological weight to predict protein function from protein-protein interactions. 1623-1630
  
• Dong-Yeon Cho, Kwang-Hyun Cho, Byoung-Tak Zhang:
  Identification of biochemical networks by S-tree based genetic programming. 1631-1640
  
• Lei 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. 1641-1647
  

• Shanfeng 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. 1648-1655
  

• I. Mihalek, I. Res, Olivier Lichtarge:
  Evolutionary trace report_maker: a new type of service for comparative analysis of proteins. 1656-1657
  
• Weizhong Li, Adam Godzik:
  Cd-hit: a fast program for clustering and comparing large sets of protein or nucleotide sequences. 1658-1659
  

• Olga Kirillova, Wladek Minor:
  Map2mod - a server for evaluation of crystallographic models and their agreement with electron density maps. 1660-1661
  

• Hiro 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. 1662-1664
  
• Fei Pan, Kiran Kamath, Kangyu Zhang, Sudip Pulapura, Avinash Achar, Juan Nunez-Iglesias, Yu Huang, 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. 1665-1667
  

• X. 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. 1668-1669
  
• Justin Klekota, Frederick P. Roth, Stuart L. Schreiber:
  Query Chem: a Google-powered web search combining text and chemical structures. 1670-1673
  

• Amanda Clare, Andreas Karwath, Helen Ougham, Ross D. King:
  Functional bioinformatics for Arabidopsis thaliana. 1674
  

Volume 22, Number 14, July 2006

Proceedings 14th International Conference on Intelligent Systems for Molecular Biology 2006, Fortaleza, Brazil, August 6-10, 2006. 2006
Contents

• Huai-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. 1675-1681
  
• Taesung Park, Sung-Gon Yi, Young Kee Shin, Seung Yeoun Lee:
  Combining multiple microarrays in the presence of controlling variables. 1682-1689
  

• K. H. Chu, C. P. Li, J. Qi:
  Ribosomal RNA as molecular barcodes: a simple correlation analysis without sequence alignment. 1690-1701
  

• Sebastien K. Gerega, Kevin M. Downard:
  PROXIMO - a new docking algorithm to model protein complexes using data from radical probe mass spectrometry (RP-MS). 1702-1709
  
• Katrin Stierand, Patrick C. Maaß, Matthias Rarey:
  Molecular complexes at a glance: automated generation of two-dimensional complex diagrams. 1710-1716
  
• Hong-Bin Shen, Kuo-Chen Chou:
  Ensemble classifier for protein fold pattern recognition. 1717-1722
  
• Yasuo Tabei, Koji Tsuda, Taishin Kin, Kiyoshi Asai:
  SCARNA: fast and accurate structural alignment of RNA sequences by matching fixed-length stem fragments. 1723-1729
  

• Sin-Ho Jung, Woncheol Jang:
  How accurately can we control the FDR in analyzing microarray data? 1730-1736
  
• Xiangdong 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. 1737-1744
  
• Shu-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. 1745-1752
  
• Guido Sanguinetti, Magnus Rattray, Neil D. Lawrence:
  A probabilistic dynamical model for quantitative inference of the regulatory mechanism of transcription. 1753-1759
  
• Suman 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. 1760-1766
  

• Syed Asad Rahman, Dietmar Schomburg:
  Observing local and global properties of metabolic pathways: "load points" and "choke points" in the metabolic networks. 1767-1774
  
• Ruiqi Wang, Luonan Chen, Kazuyuki Aihara:
  Synchronizing a multicellular system by external input: an artificial control strategy. 1775-1781
  

• Reinhard Engels, Tamara Yu, Chris Burge, Jill P. Mesirov, David DeCaprio, James E. Galagan:
  Combo: a whole genome comparative browser. 1782-1783
  

• Jian Guo, Yuanlie Lin:
  TSSub: eukaryotic protein subcellular localization by extracting features from profiles. 1784-1785
  

• Anne-Muriel Arigon, Guy Perrière, Manolo Gouy:
  HoSeqI: automated homologous sequence identification in gene family databases. 1786-1787
  
• Yoshio Nakano, Toru Takeshita, Yoshihisa Yamashita:
  TRFMA: a web-based tool for terminal restriction fragment length polymorphism analysis based on molecular weight. 1788-1789
  

• Isabel K. Darcy, Robert G. Scharein:
  TopoICE-R: 3D visualization modeling the topology of DNA recombination. 1790-1791
  
• Ricard García-Serna, Lulla Opatowski, Jordi Mestres:
  FCP: functional coverage of the proteome by structures. 1792-1793
  
• Yoichi Murakami, Susan Jones:
  SHARP²: protein-protein interaction predictions using patch analysis. 1794-1795
  
• Frank Mueller, Daniel J. Muller, Dirk Labudde:
  Analysis assistant for single-molecule force spectroscopy data on membrane proteins - MPTV. 1796-1799
  
• Jean Marc Kwasigroch, Marianne Rooman:
  Prelude&Fugue, predicting local protein structure, early folding regions and structural weaknesses. 1800-1802
  
• Montserrat 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. 1803-1804
  

• Laurence Calzone, François Fages, Sylvain Soliman:
  BIOCHAM: an environment for modeling biological systems and formalizing experimental knowledge. 1805-1807
  

Volume 22, Number 15, August 2006

• Mikael Bodén, Timothy L. Bailey:
  Identifying sequence regions undergoing conformational change via predicted continuum secondary structure. 1809-1814
  
• Isabelle Dupanloup, Henrik Kaessmann:
  Evolutionary simulations to detect functional lineage-specific genes. 1815-1822
  

• Anke Busch, Rolf Backofen:
  INFO-RNA - a fast approach to inverse RNA folding. 1823-1831
  
• Hyeon S. Son, Seung-Yeon Kim, Jooyoung Lee, Kyu-Kwang Han:
  Application of the multiensemble sampling to the equilibrium folding of proteins. 1832-1837
  
• Marc N. Offman, Paul W. Fitzjohn, Paul A. Bates:
  Developing a move-set for protein model refinement. 1838-1845
  
• Gennady Verkhivker:
  Imprint of evolutionary conservation and protein structure variation on the binding function of protein tyrosine kinases. 1846-1854
  

• De-Shuang Huang, Chun-Hou Zheng:
  Independent component analysis-based penalized discriminant method for tumor classification using gene expression data. 1855-1862
  
• David 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. 1863-1870
  

• Steven Carroll, Vladimir Pavlovic:
  Protein classification using probabilistic chain graphs and the Gene Ontology structure. 1871-1878
  
• Ralph Gauges, Ursula Rost, Sven Sahle, Katja Wegner:
  A model diagram layout extension for SBML. 1879-1885
  
• Simon J. Galbraith, Linh M. Tran, James C. Liao:
  Transcriptome network component analysis with limited microarray data. 1886-1894
  
• Jordi Vidal Rodríguez, Jaap A. Kaandorp, Maciej Dobrzynski, Joke G. Blom:
  Spatial stochastic modelling of the phosphoenolpyruvate-dependent phosphotransferase (PTS) pathway in Escherichia coli. 1895-1901
  

• Matthew Bellew, Marc Coram, Matthew Fitzgibbon, Mark Igra, Timothy W. 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. 1902-1909
  

• Joel 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. 1910-1916
  

• Karol Szafranski, Niels Jahn, Matthias Platzer:
  tuple_plot: Fast pairwise nucleotide sequence comparison with noise suppression. 1917-1918
  
• Wessel 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. 1919-1920
  

• M. M. Morin, Bernard M. E. Moret:
  NetGen: generating phylogenetic networks with diploid hybrids. 1921-1923
  

• Joshua Gould, Gad Getz, Stefano Monti, Michael Reich, Jill P. Mesirov:
  Comparative gene marker selection suite. 1924-1925
  

• Jin-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. 1926-1927
  
• Xavier Solé, Elisabet Guinó, Joan Valls, Raquel Iniesta, Víctor Moreno:
  SNPStats: a web tool for the analysis of association studies. 1928-1929
  

• Axel von Kamp, Stefan Schuster:
  Metatool 5.0: fast and flexible elementary modes analysis. 1930-1931
  

Volume 22, Number 16, August 2006

• María M. Abad-Grau, Rosana Montes, Paola Sebastiani:
  Building chromosome-wide LD maps. 1933-1934
  

• Pierre 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. 1935-1941
  
• Dan L. Nicolae, Xiaolin Wu, Kazuaki Miyake, Nancy J. Cox:
  GEL: a novel genotype calling algorithm using empirical likelihood. 1942-1947
  

• Sébastien Tempel, Mathieu Giraud, Dominique Lavenier, Israël-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. 1948-1954
  

• Jonathan G. Lees, Andrew J. Miles, Frank Wien, B. A. Wallace:
  A reference database for circular dichroism spectroscopy covering fold and secondary structure space. 1955-1962
  

• Wolfgang Huber, Joern Toedling, Lars M. Steinmetz:
  Transcript mapping with high-density oligonucleotide tiling arrays. 1963-1970
  
• Jun Liu, Jaaved Mohammed, James Carter, Sanjay Ranka, Tamer Kahveci, Michael Baudis:
  Distance-based clustering of CGH data. 1971-1978
  
• Stan Pounds, Cheng Cheng:
  Robust estimation of the false discovery rate. 1979-1987
  
• Zhaohui S. Qin:
  Clustering microarray gene expression data using weighted Chinese restaurant process. 1988-1997
  

• Jin Chen, Wynne Hsu, Mong-Li Lee, See-Kiong Ng:
  Increasing confidence of protein interactomes using network topological metrics. 1998-2004
  
• Je-Gun Joung, Dong-Ho Shin, Rho Hyun Seong, Byoung-Tak Zhang:
  Identification of regulatory modules by co-clustering latent variable models: stem cell differentiation. 2005-2011
  
• Julie L. Morrison, Rainer Breitling, Desmond J. Higham, David R. Gilbert:
  A lock-and-key model for protein-protein interactions. 2012-2019
  
• Simen Myhre, Henrik Tveit, Torulf Mollestad, Astrid Lægreid:
  Additional Gene Ontology structure for improved biological reasoning. 2020-2027
  
• Herbert 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. 2028-2036
  

• Jiexun 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. 2037-2043
  

• Todd 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. 2044-2046
  

• Marc A. Suchard, Benjamin D. Redelings:
  BAli-Phy: simultaneous Bayesian inference of alignment and phylogeny. 2047-2048
  

• Daniel H. Morgan, David M. Kristensen, David Mittelman, Olivier Lichtarge:
  ET viewer: an application for predicting and visualizing functional sites in protein structures. 2049-2050
  

• Christian Spieth, Jochen Supper, Felix Streichert, Nora Speer, Andreas Zell:
  JCell - a Java-based framework for inferring regulatory networks from time series data. 2051-2052
  
• Seong-Eui Hong, Seong-Hwan Rho, Young Il Yeom, Do Han Kim:
  HCNet: a database of heart and calcium functional network. 2053-2054
  

• G. 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. 2055-2057
  

Volume 22, Number 17, September 2006

• Pan Du, Warren A. Kibbe, Simon M. Lin:
  Improved peak detection in mass spectrum by incorporating continuous wavelet transform-based pattern matching. 2059-2065
  
• Philippe 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. 2066-2073
  
• P. Thébault, Simon de Givry, Thomas Schiex, Christine Gaspin:
  Searching RNA motifs and their intermolecular contacts with constraint networks. 2074-2080
  

• Kui Lin, Lei Zhu, Da-Yong Zhang:
  An initial strategy for comparing proteins at the domain architecture level. 2081-2086
  

• Yu Chen, Gordon M. Crippen:
  An iterative refinement algorithm for consistency based multiple structural alignment methods. 2087-2093
  
• Sjoerd J. de Vries, Alexandre M. J. J. Bonvin:
  Intramolecular surface contacts contain information about protein-protein interface regions. 2094-2098
  
• Mingyue 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. 2099-2106
  

• Xuejun Liu, Marta Milo, Neil D. Lawrence, Magnus Rattray:
  Probe-level measurement error improves accuracy in detecting differential gene expression. 2107-2113
  
• Andrea Malossini, Enrico Blanzieri, Raymond T. Ng:
  Detecting potential labeling errors in microarrays by data perturbation. 2114-2121
  

• Chun 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. 2122-2128
  

• Wentao Zhao, Erchin Serpedin, Edward R. Dougherty:
  Inferring gene regulatory networks from time series data using the minimum description length principle. 2129-2135
  

• Bo Han, Zoran Obradovic, Zhang-Zhi Hu, Cathy H. Wu, Slobodan Vucetic:
  Substring selection for biomedical document classification. 2136-2142
  
• Shao Li, Lijiang Wu, Zhongqi Zhang:
  Constructing biological networks through combined literature mining and microarray analysis: a LMMA approach. 2143-2150
  
• Rainer Malik, Lude Franke, Arno Siebes:
  Combination of text-mining algorithms increases the performance. 2151-2157
  

• Gill Bejerano:
  Branch and bound computation of exact p-values. 2158-2159
  
• Simon N. Jarman:
  Cleaver: software for identifying taxon specific restriction endonuclease recognition sites. 2160-2161
  

• Joshua 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. 2162-2163
  

• Nicolas Garnier, Anne Friedrich, Raphael Bolze, Emmanuel Bettler, Luc Moulinier, Christophe Geourjon, Julie Dawn Thompson, Gilbert Deléage, Olivier Poch:
  MAGOS: multiple alignment and modelling server. 2164-2165
  
• Rachel Kolodny, Barry Honig:
  VISTAL - a new 2D visualization tool of protein 3D structural alignments. 2166-2167
  
• Ali Mokdad, Neocles Leontis:
  Ribostral: an RNA 3D alignment analyzer and viewer based on basepair isostericities. 2168-2170
  
• Douglas L. Theobald, Deborah S. Wuttke:
  THESEUS: maximum likelihood superpositioning and analysis of macromolecular structures. 2171-2172