Bioinformatics, Volume 22

Volume 22, Number 1, January 2006

Editorials

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

Discovery Note Sequence Analysis

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

Original Papers Genome Analysis

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

Sequence Analysis

• 
  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

Phylogenetics

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

Gene Expression

• 
  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

Systems Biology

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

Data and Text Mining

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

Databases and Ontologies

• 
  Ismael Navas-Delgado,Maria del Mar Rojano-Muñoz,Sergio Ramírez,Antonio J. Pérez-Pulido,Eduardo Andrés León,José Francisco Aldana Montes,Oswaldo Trelles:
  Intelligent client for integrating bioinformatics services.106-111

Applications Note Sequence Analysis

• 
  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

Phylogenetics

• 
  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

Gene Expression

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

Systems Biology

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

Volume 22, Number 2, January 2006

Editorials

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

Discovery Note Structural Bioinformatics

• 
  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

Original Papers Genome Analysis

• 
  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

Sequence Analysis

• 
  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

Structural Bioinformatics

• 
  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

Gene Expression

• 
  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

Genetics and Population Analysis

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

Systems Biology

• 
  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

Applications Note Genome Analysis

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

Gene Expression

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

Systems Biology

• 
  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

Databases and Ontologies

• 
  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

Discovery Note Sequence Analysis

• 
  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

Structural Bioinformatics

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

Data and Text Mining

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

Original Papers Sequence Analysis

• 
  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 inEscherichia 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

Structural Bioinformatics

• 
  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

Gene Expression

• 
  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

Genetics and Population Analysis

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

Systems Biology

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

Applications Note Genome Analysis

• 
  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

Sequence Analysis

• 
  A. V. McDonnell,Taijiao Jiang,Amy E. Keating,Bonnie 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

Phylogenetics

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

Structural Bioinformatics

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

Gene Expression

• 
  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

Genetics and Population Analysis

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

Systems Biology

• 
  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

Databases and Ontologies

• 
  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 forDrosophila.381-383

Volume 22, Number 4, February 2006

Original Papers Genome Analysis

• 
  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 ofSaccharomyces 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

Sequence Analysis

• 
  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

Structural Bioinformatics

• 
  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

Gene Expression

• 
  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

Systems Biology

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

Databases and Ontologies

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

Applications Note - Sequence Analysis

• 
  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

Structural Bioinformatics

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

Gene Expression

• 
  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

Genetics and Population Analysis

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

Systems Biology

• 
  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

Original Papers Genome Analysis

• 
  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 inArabidopsis thaliana.523-526

Sequence Analysis

• 
  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

Structural Bioinformatics

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

Gene Expression

• 
  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

Genetics and Population Analysis

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

Systems Biology

• 
  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

Data and Text Mining

• 
  Roberto Amato,Angelo Ciaramella,Natalia 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-Chan 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

Applications Note Genome Analysis

• 
  Stephan H. 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

Sequence Analysis

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

Structural Bioinformatics

• 
  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

Genetics and Population Analysis

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

Systems Biology

• 
  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

Data and Text Mining

• 
  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

Databases and Ontologies

• 
  Stephen B. 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 forBuchnera sp. APS.641-642

Volume 22, Number 6, March 2006

Editorials

• 
  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

Data and Text Mining

• 
  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-Chan Park:
  Automatic extension of Gene Ontology with flexible identification of candidate terms.665-670

Discovery Note - Sequence Analysis

• 
  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

Original Papers - Genome Analysis

• 
  Valentina Boeva,Mireille Régnier,Dmitri A. Papatsenko,Vsevolod J. 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

Sequence Analysis

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

Phylogenetics

• 
  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

Structural Bioinformatics

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

Gene Expression

• 
  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

Systems Biology

• 
  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

Data and Text Mining

• 
  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

Applications Note Sequence Analysis

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

Gene Expression

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

Genetics and Population Analysis

• 
  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

Data and Text Mining

• 
  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

Discovery Note - Sequence Analysis

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

Original Papers Genome Analysis

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

Gene Expression

• 
  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,Barbara Keller,Nadine Hoecker,Frank 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

Systems Biology

• 
  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

Data and Text Mining

• 
  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

Databases and Ontologies

• 
  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 F. 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

Applications Note Genome Analysis

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

Sequence Analysis

• 
  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

Gene Expression

• 
  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

Databases and Ontologies

• 
  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

Discovery Note Sequence Analysis

• 
  A. M. Quirke,F. Jerry Reen,Marcus J. Claesson,E. Fidelma Boyd:
  Genomic island identification inVibrio vulnificus reveals significant genome plasticity in this human pathogen.905-910

Original Papers Genome Analysis

• 
  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

Structural Bioinformatics

• 
  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 ofP-RnaPredict andmfold - algorithms for RNA secondary structure prediction.934-942

Gene Expression

• 
  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

Systems Biology

• 
  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

Data and Text Mining

• 
  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

Applications Note Genome Analysis

• 
  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

Sequence Analysis

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

Phylogenetics

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

Structural Bioinformatics

• 
  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

Gene Expression

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

Genetics and Population Analysis

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

Systems Biology

• 
  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

Data and Text Mining

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

Databases and Ontologies

• 
  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

Corrigendum

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

Volume 22, Number 9, May 2006

Discovery Note Sequence Analysis

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

Original Papers Genome Analysis

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

Sequence Analysis

• 
  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

Phylogenetics

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

Structural Bioinformatics

• 
  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

Gene Expression

• 
  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,Jesús 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

Data and Text Mining

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

Databases and Ontologies

• 
  Uwe Radetzki,Ulf Leser,S. C. Schulze-Rauschenbach,Jörg Zimmermann,Jens Lüssem,Thomas Bode,Armin B. Cremers:
  Adapters, shims, and glue - service interoperability forin silico experiments.1137-1143

Applications Note Genome Analysis

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

Sequence Analysis

• 
  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

Systems Biology

• 
  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

Data and Text Mining

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

Volume 22, Number 10, May 2006

Editorials

• 
  Andrew Ernest Torda,Thomas Lengauer:
  Editorial.1157

Sequence Analysis

• 
  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

Structural Bioinformatics

• 
  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. 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

Gene Expression

• 
  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

Systems Biology

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

Discovery Note Structural Bioinformatics

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

Original Papers Genome Analysis

• 
  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

Sequence Analysis

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

Phylogenetics

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

Structural Bioinformatics

• 
  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

Gene Expression

• 
  Ritesh Agrawal,Gary D. Stormo:
  Using mRNAs lengths to accurately predict the alternatively spliced gene products inCaenorhabditis 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

Applications Note Genome Analysis

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

Gene Expression

• 
  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

Systems Biology

• 
  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

Data and Text Mining

• 
  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

Databases and Ontologies

• 
  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

Discovery Notes Structural Bioinformatics

• 
  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

Systems Biology

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

Original Papers Sequence Analysis

• 
  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

Structural Bioinformatics

• 
  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

Gene Expression

• 
  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

Systems Biology

• 
  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

Data and Text Mining

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

Applications Note Structural Bioinformatics

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

Genetics and Population Analysis

• 
  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

Systems Biology

• 
  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

Corrigendum

• 
  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

Editorials

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

Discovery Notes Genome Analysis

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

Systems Biology

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

Original Papers Genome Analysis

• 
  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

Sequence Analysis

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

Structural Bioinformatics

• 
  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

Gene Expression

• 
  Sebastian E. Ahnert,Karen Willbrand,Francis C. S. Brown,Thomas 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

Genetics and Population Analysis

• 
  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

Systems Biology

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

Data and Text Mining

• 
  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

Applications Note Genome Analysis

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

Sequence Analysis

• 
  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

Gene Expression

• 
  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

Data and Text Mining

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

Volume 22, Number 13, July 2006

Editorials

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

Discovery Note Sequence Analysis

• 
  Elhanan Magidovich,Sarel Jacob 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

Original Papers Genome Analysis

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

Sequence Analysis

• 
  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: detectingcis-regulatory elements using a genetic algorithm.1577-1584

Structural Bioinformatics

• 
  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

Gene Expression

• 
  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 W. 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

Systems Biology

• 
  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 ofDesulfovibrio vulgaris: zero-inflated Poisson regression models to predict abundance of undetected proteins.1641-1647

Data and Text Mining

• 
  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

Applications Note Sequence Analysis

• 
  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

Structural Bioinformatics

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

Gene Expression

• 
  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

Data and Text Mining

• 
  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

Corrigendum

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

Volume 22, Number 14, July 2006

Original Papers - Genome Analysis

• 
  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

Sequence Analysis

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

Structural Bioinformatics

• 
  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

Gene Expression

• 
  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

Systems Biology

• 
  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

Applications Note - Genome Analysis

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

Sequence Analysis

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

Phylogenetics

• 
  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

Structural Bioinformatics

• 
  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

Systems Biology

• 
  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

Original Papers - Sequence Analysis

• 
  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

Structural Bioinformatics

• 
  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

Gene Expression

• 
  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

Systems Biology

• 
  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 inEscherichia coli.1895-1901

Data and Text Mining

• 
  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

Databases and Ontologies

• 
  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

Applications Note - Genome Analysis

• 
  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. Beliën,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

Phylogenetics

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

Gene Expression

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

Genetics and Population Analysis

• 
  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

Systems Biology

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

Volume 22, Number 16, August 2006

Discovery Note - Genetics and Population Analysis

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

Original Papers - Genome Analysis

• 
  Pierre Brézellec,Mark Hoebeke,Marie-Sophie Hiet,Sophie Pasek,Jean-Luc Ferat:
  DomainSieve: a protein domain-based screen that led to the identification ofdam-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

Sequence Analysis

• 
  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

Structural Bioinformatics

• 
  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

Gene Expression

• 
  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

Systems Biology

• 
  Jin Chen,Wynne Hsu,Mong-Li Lee,See-Kiong Ng:
  Increasing confidence of protein interactomes using network topological metrics.1998-2004
• 
  Je-Gun Joung,Dongho 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

Data and Text Mining

• 
  Jiexun Li,Xin Li,Hua Su,Hsinchun Chen,David W. Galbraith:
  A framework of integrating gene relations from heterogeneous data sources: an experiment onArabidopsis thaliana.2037-2043

Applications Note - Genome Analysis

• 
  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

Phylogenetics

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

Structural Bioinformatics

• 
  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

Systems Biology

• 
  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

Data and Text Mining

• 
  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

Original Papers - Genome Analysis

• 
  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
• 
  Patricia Thébault,Simon de Givry,Thomas Schiex,Christine Gaspin:
  Searching RNA motifs and their intermolecular contacts with constraint networks.2074-2080

Sequence Analysis

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

Structural Bioinformatics

• 
  Yu Chen,Gordon M. Crippen:
  An iterative refinement algorithm for consistency based multiple structural alignment methods.2087-2093
• 
  Sjoerd Jacob 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

Gene Expression

• 
  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

Genetics and Population Analysis

• 
  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

Systems Biology

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

Data and Text Mining

• 
  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

Applications Note - Sequence Analysis

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

Phylogenetics

• 
  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

Structural Bioinformatics

• 
  Nicolas B. 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

Genetics and Population Analysis

• 
  William S. Bush,Scott M. Dudek,Marylyn D. Ritchie:
  Parallel multifactor dimensionality reduction: a tool for the large-scale analysis of gene-gene interactions.2173-2174

Systems Biology

• 
  Zhi Liang,Meng Xu,Maikun Teng,Liwen Niu:
  NetAlign: a web-based tool for comparison of protein interaction networks.2175-2177
• 
  James 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.2178-2179

Databases and Ontologies

• 
  Yun-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.2180-2182
• 
  Joke 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.2183-2185

Volume 22, Number 18, September 2006

Editorials

• 
  Wentian Li:
  The-more-the-better and the-less-the-better.2187-2188

Discovery Note - Sequence Analysis

• 
  Quan-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.2189-2191

Structural Bioinformatics

• 
  Jonathan W. Arthur,Angeles Sanchez-Perez,David I. Cook:
  Scoring of predicted GRK2 phosphorylation sites in Nedd4-2.2192-2195

Original Papers - Genome Analysis

• 
  Georgios S. Vernikos,Julian Parkhill:
  Interpolated variable order motifs for identification of horizontally acquired DNA: revisiting theSalmonella pathogenicity islands.2196-2203

Sequence Analysis

• 
  Fang Fang,Shicai Fan,Xuegong Zhang,Michael Q. Zhang:
  Predicting methylation status of CpG islands in the human brain.2204-2209
• 
  Lang 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.2210-2216
• 
  Henry C. M. Leung,Francis Y. L. Chin:
  Finding motifs from all sequences with and without binding sites.2217-2223
• 
  Thomas Lingner,Peter Meinicke:
  Remote homology detection based on oligomer distances.2224-2231
• 
  Ketil Malde,Korbinian Schneeberger,Eivind Coward,Inge Jonassen:
  RBR: library-less repeat detection for ESTs.2232-2236

Structural Bioinformatics

• 
  Jordi Espadaler,Enrique Querol,Francesc X. Avilés,Baldo Oliva:
  Identification of function-associated loop motifs and application to protein function prediction.2237-2243

Gene Expression

• 
  Yifan Huang,Haiyan Xu,Violeta Calian,Jason C. Hsu:
  To permute or not to permute.2244-2248
• 
  Dougu 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.2249-2253
• 
  Ariadni Papana,Hemant Ishwaran:
  CART variance stabilization and regularization for high-throughput genomic data.2254-2261
• 
  Naijun Sha,Mahlet G. Tadesse,Marina Vannucci:
  Bayesian variable selection for the analysis of microarray data with censored outcomes.2262-2268
• 
  Andrew E. Teschendorff,Ali Naderi,Nuno L. Barbosa-Morais,Carlos Caldas:
  PACK: Profile Analysis using Clustering and Kurtosis to find molecular classifiers in cancer.2269-2275

Systems Biology

• 
  Yu-Hsiang Chang,Yu-Chao Wang,Bor-Sen Chen:
  Identification of transcription factor cooperativity via stochastic system model.2276-2282
• 
  Jingchun Chen,Bo Yuan:
  Detecting functional modules in the yeast protein-protein interaction network.2283-2290
• 
  Pall F. Jonsson,Paul A. Bates:
  Global topological features of cancer proteins in the human interactome.2291-2297

Data and Text Mining

• 
  James Lewis,Stephan Ossowski,Justin M. Hicks,Mounir Errami,Harold R. Garner:
  Text similarity: an alternative way to search MEDLINE.2298-2304

Applications Note - Genome Analysis

• 
  Eun-Kyung Lee,Sung-Gon Yi,Taesung Park:
  arrayQCplot: software for checking the quality of microarray data.2305-2307
• 
  Haiming Wang,Yanqi Su,Aaron J. Mackey,Eileen T. Kraemer,Jessica C. Kissinger:
  SynView: a GBrowse-compatible approach to visualizing comparative genome data.2308-2309

Sequence Analysis

• 
  Rajesh 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.2310-2312

Phylogenetics

• 
  Patricia Buendia,Giri Narasimhan:
  Serial NetEvolve: a flexible utility for generating serially-sampled sequences along a tree or recombinant network.2313-2314

Gene Expression

• 
  Claudio Lottaz,Xinan Yang,Stefanie Scheid,Rainer Spang:
  OrderedList - a bioconductor package for detecting similarity in ordered gene lists.2315-2316

Genetics and Population Analysis

• 
  Thomas 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.2317-2318

Volume 22, Number 19, October 2006

Editorials

• 
  Alex Bateman,Alfonso Valencia:
  Structural genomics meets computational biology.2319

Original Articles - Genome Analysis

• 
  Yiming Cheng,Robert M. Miura,Bin Tian:
  Prediction of mRNA polyadenylation sites by support vector machine.2320-2325

Sequence Analysis

• 
  Bin 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.2326-2332

Structural Bioinformatics

• 
  Enrico Ferraro,Allegra Via,Gabriele Ausiello,Manuela Helmer-Citterich:
  A novel structure-based encoding for machine-learning applied to the inference of SH3 domain specificity.2333-2339
• 
  Aalt D. J. van Dijk,Alexandre M. J. J. Bonvin:
  Solvated docking: introducing water into the modelling of biomolecular complexes.2340-2347

Gene Expression

• 
  Gavin C. Cawley,Nicola L. C. Talbot:
  Gene selection in cancer classification using sparse logistic regression with Bayesian regularization.2348-2355
• 
  Chad 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.2356-2363
• 
  Darlene R. Goldstein:
  Partition resampling and extrapolation averaging: approximation methods for quantifying gene expression in large numbers of short oligonucleotide arrays.2364-2372
• 
  Sek Won Kong,William T. Pu,Peter J. Park:
  A multivariate approach for integrating genome-wide expression data and biological knowledge.2373-2380
• 
  Ann L. Oberg,Douglas W. Mahoney,Karla V. Ballman,Terry M. Therneau:
  Joint estimation of calibration and expression for high-density oligonucleotide arrays.2381-2387
• 
  Wei Pan,Xiaotong Shen,Aixiang Jiang,Robert P. Hebbel:
  Semi-supervised learning via penalized mixture model with application to microarray sample classification.2388-2395
• 
  Antonio 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.2396-2404
• 
  Anbupalam Thalamuthu,Indranil Mukhopadhyay,Xiaojing Zheng,George C. Tseng:
  Evaluation and comparison of gene clustering methods in microarray analysis.2405-2412
• 
  Yong Wang,Trupti Joshi,Xiang-Sun Zhang,Dong Xu,Luonan Chen:
  Inferring gene regulatory networks from multiple microarray datasets.2413-2420

Data and Text Mining

• 
  Carol Friedman,Tara Borlawsky,Lyudmila Shagina,H. Rosie Xing,Yves A. Lussier:
  Bio-Ontology and text: bridging the modeling gap.2421-2429
• 
  Chao Sima,Edward R. Dougherty:
  What should be expected from feature selection in small-sample settings.2430-2436

Applications Note - Genome Analysis

• 
  Nicholas 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.2437-2438

Sequence Analysis

• 
  Fabrice 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.2439-2440
• 
  Karsten 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.2441-2443

Data and Text Mining

• 
  Conrad Plake,Torsten Schiemann,Marcus Pankalla,Jörg Hakenberg,Ulf Leser:
  ALIBABA: PubMed as a graph.2444-2445

Letter To Editor - Gene Expression

• 
  Xiaolin Wu,Larry J. Forney,Paul Joyce:
  Comments on "Bayesian hierarchical error model for analysis of gene expression data".2446-2451
• 
  HyungJun Cho,Jae K. Lee:
  Response to comments on "Bayesian Hierarchical Error Model for Analysis of Gene Expression Data".2452

Corrigendum

• 
  Corrigendum.2453

Volume 22, Number 20, October 2006

Discovery Note - Sequence Analysis

• 
  Sunil Archak,Javaregowda Nagaraju:
  Eicosapentapeptide repeats (EPRs): novel repeat proteins specific to flowering plants.2455-2458
• 
  Dapeng Zhang,Christopher J. Martyniuk,Vance L. Trudeau:
  SANTA domain: a novel conserved protein module inEukaryota with potential involvement in chromatin regulation.2459-2462

Original Papers - Genome Analysis

• 
  Michaël Bekaert,John F. Atkins,Pavel V. Baranov:
  ARFA: a program for annotating bacterial release factor genes, including prediction of programmed ribosomal frameshifting.2463-2465

Sequence Analysis

• 
  Pekka Marttinen,Jukka Corander,Petri Törönen,Liisa Holm:
  Bayesian search of functionally divergent protein subgroups and their function specific residues.2466-2474
• 
  Xijin Ge,Qingfa Wu,Yong-Chul Jung,Jun Chen,San Ming Wang:
  A large quantity of novel human antisense transcripts detected by LongSAGE.2475-2479
• 
  Michiaki Hamada,Koji Tsuda,Taku Kudo,Taishin Kin,Kiyoshi Asai:
  Mining frequent stem patterns from unaligned RNA sequences.2480-2487
• 
  Tetsuya Sato,Yoshihiro Yamanishi,Katsuhisa Horimoto,Minoru Kanehisa,Hiroyuki Toh:
  Partial correlation coefficient between distance matrices as a new indicator of protein-protein interactions.2488-2492

Phylogenetics

• 
  Konrad Scheffler,Darren P. Martin,Cathal Seoighe:
  Robust inference of positive selection from recombining coding sequences.2493-2499

Gene Expression

• 
  Theodora Manoli,Norbert Gretz,Hermann-Josef Gröne,Marc Kenzelmann,Roland Eils,Benedikt Brors:
  Group testing for pathway analysis improves comparability of different microarray datasets.2500-2506
• 
  Xin Zhou,Ke Zhi Mao:
  The ties problem resulting from counting-based error estimators and its impact on gene selection algorithms.2507-2515
• 
  Saumyadipta Pyne,Bruce Futcher,Steven Skiena:
  Meta-analysis based on control of false discovery rate: combining yeast ChIP-chip datasets.2516-2522

Systems Biology

• 
  Adriano Velasque Werhli,Marco Grzegorczyk,Dirk Husmeier:
  Comparative evaluation of reverse engineering gene regulatory networks with relevance networks, graphical gaussian models and bayesian networks.2523-2531
• 
  Quansong 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.2532-2538
• 
  Gautier Stoll,Jacques Rougemont,Felix Naef:
  Few crucial links assure checkpoint efficiency in the yeast cell-cycle network.2539-2546

Data and Text Mining

• 
  E. S. Motakis,Guy P. Nason,Piotr Fryzlewicz,G. A. Rutter:
  Variance stabilization and normalization for one-color microarray data using a data-driven multiscale approach.2547-2553

Applications Note - Gene Expression

• 
  Max Bylesjö,Andreas Sjödin,Daniel Eriksson,Henrik Antti,Thomas Moritz,Stefan Jansson,Johan Trygg:
  MASQOT-GUI: spot quality assessment for the two-channel microarray platform.2554-2555

Genetics and Population Analysis

• 
  Frédéric Guillaume,Jacques Rougemont:
  Nemo: an evolutionary and population genetics programming framework.2556-2557
• 
  Jingwu He,Alexander Zelikovsky:
  MLR-tagging: informative SNP selection for unphased genotypes based on multiple linear regression.2558-2561

Systems Biology

• 
  Qi Zhao,Radka Stoyanova,Shuyan Du,Paul Sajda,Truman R. Brown:
  HiRes - a tool for comprehensive assessment and interpretation of metabolomic data.2562-2564

Data and Text Mining

• 
  Roger M. Jarvis,David Broadhurst,Helen E. Johnson,Noel M. O'Boyle,Royston Goodacre:
  PYCHEM: a multivariate analysis package for python.2565-2566
• 
  Julio Bonis,Laura Inés Furlong,Ferran Sanz:
  OSIRIS: a tool for retrieving literature about sequence variants.2567-2569
• 
  Luca 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.2570-2571

Databases and Ontologies

• 
  Dequan 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.2572-2573
• 
  Igor A. Gariev,Sergey D. Varfolomeev:
  Hierarchical classification of hydrolases catalytic sites.2574-2576
• 
  Florian Gnad,John Parsch:
  Sebida: a database for the functional and evolutionary analysis of genes with sex-biased expression.2577-2579

Corrigendum

• 
  Corrigendum.2580

Volume 22, Number 21, November 2006

Discovery Note - Genome Analysis

• 
  Kira S. Makarova,Nick V. Grishin,Eugene V. Koonin:
  The HicAB cassette, a putative novel, RNA-targeting toxin-antitoxin system in archaea and bacteria.2581-2584

Sequence Analysis

• 
  Yu Wang,Tobias Hindemitt,Klaus F. X. Mayer:
  Significant sequence similarities in promoters and precursors ofArabidopsis thaliana non-conserved microRNAs.2585-2589

Original Papers - Genome Analysis

• 
  Chunlin Wang,Chris H. Q. Ding,Richard F. Meraz,Stephen R. Holbrook:
  PSoL: a positive sample only learning algorithm for finding non-coding RNA genes.2590-2596

Sequence Analysis

• 
  Levon Budagyan,Ruben Abagyan:
  Weighted quality estimates in machine learning.2597-2603

Phylogenetics

• 
  Guohua Jin,Luay Nakhleh,Sagi Snir,Tamir Tuller:
  Maximum likelihood of phylogenetic networks.2604-2611

Structural Bioinformatics

• 
  Dominique Douguet,Huei-Chi Chen,Andrey Tovchigrechko,Ilya A. Vakser:
  DOCKGROUND resource for studying protein-protein interfaces.2612-2618
• 
  Eran Eyal,Lee-Wei Yang,Ivet Bahar:
  Anisotropic network model: systematic evaluation and a new web interface.2619-2627
• 
  Fabian Birzele,Stefan Kramer:
  A new representation for protein secondary structure prediction based on frequent patterns.2628-2634

Gene Expression

• 
  Ronglai Shen,Debashis Ghosh,Arul M. Chinnaiyan,Zhaoling Meng:
  Eigengene-based linear discriminant model for tumor classification using gene expression microarray data.2635-2642
• 
  Natasa Rajicic,Dianne M. Finkelstein,David A. Schoenfeld:
  Survival analysis of longitudinal microarrays.2643-2649
• 
  Chao Cheng,Xiaotu Ma,Xiting Yan,Fengzhu Sun,Lei M. Li:
  MARD: a new method to detect differential gene expression in treatment-control time courses.2650-2657
• 
  A. Callegaro,Dario Basso,Silvio Bicciato:
  A locally adaptive statistical procedure (LAP) to identify differentially expressed chromosomal regions.2658-2666
• 
  Joe Faith,Robert Mintram,Maia Angelova:
  Targeted projection pursuit for visualizing gene expression data classifications.2667-2673

Systems Biology

• 
  Nicole Radde,Jutta Gebert,Christian V. Forst:
  Systematic component selection for gene-network refinement.2674-2680
• 
  Visakan Kadirkamanathan,Jing Yang,Stephen A. Billings,Phillip C. Wright:
  Markov Chain Monte Carlo Algorithm based metabolic flux distribution analysis onCorynebacterium glutamicum.2681-2687

Applications Note - Phylogenetics

• 
  Alexandros Stamatakis:
  RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models.2688-2690

Structural Bioinformatics

• 
  Brajesh Kumar Rai,Carlos J. Madrid-Aliste,J. Eduardo Fajardo,András Fiser:
  MMM: a sequence-to-structure alignment protocol.2691-2692
• 
  Shantanu 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.2693-2694
• 
  Barry J. Grant,Ana P. C. Rodrigues,Karim M. ElSawy,James Andrew McCammon,Leo S. D. Caves:
  Bio3d: an R package for the comparative analysis of protein structures.2695-2696

Gene Expression

• 
  Tsun-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.2697-2698
• 
  Kellie J. Archer,Tobias Guennel:
  An application for assessing quality of RNA hybridized to Affymetrix GeneChips.2699-2701

Genetics and Population Analysis

• 
  Grégory Deceliere,Yann Letrillard,Sandrine Charles,Christian Biémont:
  TESD: a transposable element dynamics simulation environment.2702-2703

Systems Biology

• 
  Zhike Zi,Edda Klipp:
  SBML-PET: a Systems Biology Markup Language-based parameter estimation tool.2704-2705
• 
  Ronald C. Taylor,Anuj Shah,Charles Treatman,Meridith Blevins:
  SEBINI: Software Environment for BIological Network Inference.2706-2708
• 
  Markus 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.2709-2710

Volume 22, Number 22, November 2006

Discovery Note - Sequence Analysis

• 
  Mensur Dlakic:
  DUF283 domain of Dicer proteins has a double-stranded RNA-binding fold.2711-2714

Original Papers - Sequence Analysis

• 
  Usman Roshan,Dennis R. Livesay:
  Probalign: multiple sequence alignment using partition function posterior probabilities.2715-2721
• 
  Xudong Xie,Shuanhu Wu,Kin-Man Lam,Hong Yan:
  PromoterExplorer: an effective promoter identification method based on the AdaBoost algorithm.2722-2728
• 
  Emidio 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.2729-2734

Structural Bioinformatics

• 
  Anne 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.2735-2738
• 
  Jeanette E. Eckel-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 with¹⁶O/¹⁸O stable-isotope labeled mass spectrometry.2739-2745
• 
  N. Morozova,J. Allers,Jeffrey C. Myers,Yousif Shamoo:
  Protein-RNA interactions: exploring binding patterns with a three-dimensional superposition analysis of high resolution structures.2746-2752
• 
  Darrin P. Lewis,Tony Jebara,William Stafford Noble:
  Support vector machine learning from heterogeneous data: an empirical analysis using protein sequence and structure.2753-2760
• 
  Stewart T. Chang,Debashis Ghosh,Denise E. Kirschner,Jennifer J. Linderman:
  Peptide length-based prediction of peptide-MHC class II binding.2761-2767
• 
  Yong Zhao,Daniel Stoffler,Michel F. Sanner:
  Hierarchical and multi-resolution representation of protein flexibility.2768-2774

Gene Expression

• 
  Guido Sanguinetti,Neil D. Lawrence,Magnus Rattray:
  Probabilistic inference of transcription factor concentrations and gene-specific regulatory activities.2775-2781

Systems Biology

• 
  Mark Griffith,Tod Courtney,Jean Peccoud,William H. Sanders:
  Dynamic partitioning for hybrid simulation of the bistable HIV-1 transactivation network.2782-2789
• 
  Matthias Heinemann,Sven Panke:
  Synthetic biology - putting engineering into biology.2790-2799
• 
  Jianzhen Xu,Yongjin Li:
  Discovering disease-genes by topological features in human protein-protein interaction network.2800-2805
• 
  Vitaly 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.2806-2812

Databases and Ontologies

• 
  Wei Zhou,Vetle I. Torvik,Neil R. Smalheiser:
  ADAM: another database of abbreviations in MEDLINE.2813-2818

Applications Note - Sequence Analysis

• 
  André Billion,Rohit Ghai,Trinad Chakraborty,Torsten Hain:
  Augur - a computational pipeline for whole genome microbial surface protein prediction and classification.2819-2820
• 
  Mario A. Fares,David McNally:
  CAPS: coevolution analysis using protein sequences.2821-2822

Phylogenetics

• 
  Luke Sheneman,Jason Evans,James A. Foster:
  Clearcut: a fast implementation of relaxed neighbor joining.2823-2824

Gene Expression

• 
  Fangxin 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.2825-2827

Genetics and Population Analysis

• 
  Torsten Hothorn,Peter Bühlmann:
  Model-based boosting in high dimensions.2828-2829

Data and Text Mining

• 
  Brendan MacLean,Jimmy K. Eng,Ronald C. Beavis,Martin McIntosh:
  General framework for developing and evaluating database scoring algorithms using the TANDEM search engine.2830-2832
• 
  Lei Zhang,Daiwen Yang:
  SCAssign: a sparky extension for the NMR resonance assignment of aliphatic side-chains of uniformly¹³C,¹⁵N-labeled large proteins.2833-2834

Databases and Ontologies

• 
  Eric J. Vallender,Justin E. Paschall,Christine M. Malcom,Bruce T. Lahn,Gerald J. Wyckoff:
  SPEED: a molecular-evolution-based database of mammalian orthologous groups.2835-2837
• 
  Kris Laukens,Rune Matthiesen,Filip Lemière,Eddy Esmans,Harry Van Onckelen,Ole Nørregaard Jensen,Erwin Witters:
  Integration of gel-based proteome data with pProRep.2838-2840

Volume 22, Number 23, December 2006

Discovery Note - Sequence Analysis

• 
  Zoë Birtle,Chris P. Ponting:
  Meisetz and the birth of the KRAB motif.2841-2845

Structural Bioinformatics

• 
  Melissa Da Silva,Ling Shen,Vasily Tcherepanov,Cristalle Watson,Chris Upton:
  Predicted function of the vaccinia virus G5R protein.2846-2850

Original Papers - Sequence Analysis

• 
  Torben Friedrich,Birgit Pils,Thomas Dandekar,Jörg Schultz,Tobias Müller:
  Modelling interaction sites in protein domains with interaction profile hidden Markov models.2851-2857
• 
  Nora Pierstorff,Casey M. Bergman,Thomas Wiehe:
  Identifyingcis-regulatory modules by combining comparative and compositional analysis of DNA.2858-2864
• 
  László Kaján,Attila Kertész-Farkas,Dino Franklin,Neli Ivanova,András Kocsor,Sándor Pongor:
  Application of a simple likelihood ratio approximant to protein sequence classification.2865-2869
• 
  Nak-Kyeong Kim,Kannan Tharakaraman,John L. Spouge:
  Adding sequence context to a Markov background model improves the identification of regulatory elements.2870-2875

Structural Bioinformatics

• 
  Qifang Xu,Adrian A. Canutescu,Zoran Obradovic,Roland L. Dunbrack Jr.:
  ProtBuD: a database of biological unit structures of protein families and superfamilies.2876-2882

Gene Expression

• 
  Dong 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.2883-2889
• 
  Curtis Huttenhower,Matthew A. Hibbs,Chad L. Myers,Olga G. Troyanskaya:
  A scalable method for integration and functional analysis of multiple microarray datasets.2890-2897
• 
  Sukjoon Yoon,Young Yang,Jiwon Choi,Jeeweon Seong:
  Large scale data mining approach for gene-specific standardization of microarray gene expression data.2898-2904
• 
  Alexander Begun:
  Robust method for detecting differential gene expression in twin studies.2905-2909
• 
  Antti Lehmussola,Pekka Ruusuvuori,Olli Yli-Harja:
  Evaluating the performance of microarray segmentation algorithms.2910-2917

Systems Biology

• 
  Christopher Sanford,Matthew L. K. Yip,Carl White,John Parkinson:
  Cell++ - simulating biochemical pathways.2918-2925

Data and Text Mining

• 
  Jeffrey T. Chang,Joseph Nevins:
  GATHER: a systems approach to interpreting genomic signatures.2926-2933

Databases and Ontologies

• 
  Sorin Draghici,Sivakumar Sellamuthu,Purvesh Khatri:
  Babel's tower revisited: a universal resource for cross-referencing across annotation databases.2934-2939
• 
  Shipra Agrawal,Chetan Kumar,M. R. S. Rao:
  CREMOFAC - a database of chromatin remodeling factors.2940-2944

Applications Note - Genome Analysis

• 
  Yan V. Sun,Douglas M. Jacobsen,Sharon L. R. Kardia:
  ChromoScan: a scan statistic application for identifying chromosomal regions in genomic studies.2945-2947

Structural Bioinformatics

• 
  Oxana V. Galzitskaya,Sergiy O. Garbuzynskiy,Michail Yu. Lobanov:
  FoldUnfold: web server for the prediction of disordered regions in protein chain.2948-2949

Gene Expression

• 
  James W. MacDonald,Debashis Ghosh:
  COPA - cancer outlier profile analysis.2950-2951
• 
  Xiaohui Chen,Ming Chen,Kaida Ning:
  BNArray: an R package for constructing gene regulatory networks from microarray data by using Bayesian network.2952-2954
• 
  Xiangfeng Wang,Hang He,Lei Li,Runsheng Chen,Xing Wang Deng,Songgang Li:
  NMPP: a user-customized NimbleGen microarray data processing pipeline.2955-2957
• 
  Nicolas Goffard,Georg Weiller:
  Extending MapMan: application to legume genome arrays.2958-2959

Genetics and Population Analysis

• 
  Dale R. Nyholt:
  ssSNPer: identifying statistically similar SNPs to aid interpretation of genetic association studies.2960-2961

Systems Biology

• 
  Boyke 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.2962-2965
• 
  Anastasia Deckard,Frank T. Bergmann,Herbert M. Sauro:
  Supporting the SBML layout extension.2966-2967
• 
  Kevin 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.2968-2970

Databases and Ontologies

• 
  S. Blair Hedges,Joel Dudley,Sudhir Kumar:
  TimeTree: a public knowledge-base of divergence times among organisms.2971-2972

Volume 22, Number 24, December 2006

Editorials

• 
  Trey Ideker,Alfonso Valencia:
  Bioinformatics in the human interactome project.2973-2974

Discovery Note - Sequence Analysis

• 
  Koen Deforche,Tomi Silander,Ricardo Camacho,Zehava Grossman,M. A. Soares,Kristel Van Laethem,Rami Kantor,Yves Moreau,Anne-Mieke Vandamme:
  Analysis of HIV-1pol sequences using Bayesian Networks: implications for drug resistance.2975-2979

Original Papers - Sequence Analysis

• 
  Xuehui Li,Tamer Kahveci:
  A Novel algorithm for identifying low-complexity regions in a protein sequence.2980-2987
• 
  Stinus Lindgreen,Paul P. Gardner,Anders Krogh:
  Measuring covariation in RNA alignments: physical realism improves information measures.2988-2995
• 
  Nuno 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.2996-3002
• 
  Mireia Vilardell,Alex Sánchez-Pla:
  Hypothesis testing approaches to the exon prediction problem.3003-3008

Structural Bioinformatics

• 
  Olav Zimmermann,Ulrich H. E. Hansmann:
  Support vector machines for prediction of dihedral angle regions.3009-3015

Gene Expression

• 
  Jiang 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.3016-3024
• 
  Yudi Pawitan,Stefano Calza,Alexander Ploner:
  Estimation of false discovery proportion under general dependence.3025-3031
• 
  Cathal Seoighe,Victoria Nembaware,Konrad Scheffler:
  Maximum likelihood inference of imprinting and allele-specific expression from EST data.3032-3039
• 
  Mark P. Brynildsen,Linh M. Tran,James C. Liao:
  A Gibbs sampler for the identification of gene expression and network connectivity consistency.3040-3046
• 
  János Z. Kelemen,Attila Kertész-Farkas,András Kocsor,László G. Puskás:
  Kalman filtering for disease-state estimation from microarray data.3047-3053
• 
  Daniel S. Yuan,Rafael A. Irizarry:
  High-resolution spatial normalization for microarrays containing embedded technical replicates.3054-3060

Genetics and Populations Analysis

• 
  Paul Fearnhead:
  SequenceLDhot: detecting recombination hotspots.3061-3066

Systems Biology

• 
  Stefan Hoops,Sven Sahle,Ralph Gauges,Christine Lee,Jürgen Pahle,Natalia Simus,Mudita Singhal,Liang Xu,Pedro Mendes,Ursula Kummer:
  COPASI - a COmplex PAthway SImulator.3067-3074
• 
  Claudio Eccher,Corrado Priami:
  Design and implementation of a tool for translating SBML into the biochemical stochastic pi-calculus.3075-3081
• 
  Fangping Mu,Pat J. Unkefer,Clifford J. Unkefer,William S. Hlavacek:
  Prediction of oxidoreductase-catalyzed reactions based on atomic properties of metabolites.3082-3088

Data and Text Mining

• 
  Naoaki Okazaki,Sophia Ananiadou:
  Building an abbreviation dictionary using a term recognition approach.3089-3095

Applications Note - Sequence Analysis

• 
  Sergei L. Kosakovsky Pond,David Posada,Michael B. Gravenor,Christopher H. Woelk,Simon D. W. Frost:
  GARD: a genetic algorithm for recombination detection.3096-3098
• 
  Jan Mrázek,Shaohua Xie:
  Pattern locator: a new tool for finding local sequence patterns in genomic DNA sequences.3099-3100

Structural Bioinformatics

• 
  G. Andrew Woolley,En-shiun Lee,Fuzhong Zhang:
  sGAL: a computational method for finding surface exposed sites in proteins suitable for Cys-mediated cross-linking.3101-3102

Genetics and Population Analysis

• 
  Thomas Hoffmann,Christoph Lange:
  P²BAT: a massive parallel implementation of PBAT for genome-wide association studies in R.3103-3105

Systems Biology

• 
  Jeongah Yoon,Anselm Blumer,Kyongbum Lee:
  An algorithm for modularity analysis of directed and weighted biological networks based on edge-betweenness centrality.3106-3108