Volume 6, Number S-1, 2005

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  Lynette Hirschman, Alexander S. Yeh, Christian Blaschke, Alfonso Valencia: Overview of BioCreAtIvE: critical assessment of information extraction for biology.
• 
  Alexander S. Yeh, Alexander A. Morgan, Marc E. Colosimo, Lynette Hirschman: BioCreAtIvE Task 1A: gene mention finding evaluation.
• 
  Lorraine K. Tanabe, Natalie Xie, Lynne H. Thom, Wayne Matten, W. John Wilbur: GENETAG: a tagged corpus for gene/protein named entity recognition.
• 
  Shuhei Kinoshita, K. Bretonnel Cohen, Philip V. Ogren, Lawrence Hunter: BioCreAtIvE Task1A: entity identification with a stochastic tagger.
• 
  Jenny Rose Finkel, Shipra Dingare, Christopher D. Manning, Malvina Nissim, Beatrice Alex, Claire Grover: Exploring the boundaries: gene and protein identification in biomedical text.
• 
  Ryan T. McDonald, Fernando Pereira: Identifying gene and protein mentions in text using conditional random fields.
• 
  Guodong Zhou, Dan Shen, Jie Zhang, Jian Su, Soon-Heng Tan: Recognition of protein/gene names from text using an ensemble of classifiers.
• 
  Tomohiro Mitsumori, Sevrani Fation, Masaki Murata, Kouichi Doi, Hirohumi Doi: Gene/protein name recognition based on support vector machine using dictionary as features.
• 
  Jörg Hakenberg, Steffen Bickel, Conrad Plake, Ulf Brefeld, Hagen Zahn, Lukas Faulstich, Ulf Leser, Tobias Scheffer: Systematic feature evaluation for gene name recognition.
• 
  Javier Tamames: Text Detective: a rule-based system for gene annotation in biomedical texts.
• 
  Lynette Hirschman, Marc E. Colosimo, Alexander A. Morgan, Alexander S. Yeh: Overview of BioCreAtIvE task 1B: normalized gene lists.
• 
  Marc E. Colosimo, Alexander A. Morgan, Alexander S. Yeh, Jeffrey B. Colombe, Lynette Hirschman: Data preparation and interannotator agreement: BioCreAtIvE Task 1B.
• 
  Jeremiah Crim, Ryan T. McDonald, Fernando Pereira: Automatically annotating documents with normalized gene lists.
• 
  Daniel Hanisch, Katrin Fundel, Heinz-Theodor Mevissen, Ralf Zimmer, Juliane Fluck: ProMiner: rule-based protein and gene entity recognition.
• 
  Katrin Fundel, Daniel Güttler, Ralf Zimmer, Joannis Apostolakis: A simple approach for protein name identification: prospects and limits.
• 
  Christian Blaschke, Eduardo Andrés León, Martin Krallinger, Alfonso Valencia: Evaluation of BioCreAtIvE assessment of task 2.
• 
  Evelyn Camon, Daniel Barrell, Emily Dimmer, Vivian Lee, Michele Magrane, John Maslen, David Binns, Rolf Apweiler: An evaluation of GO annotation retrieval for BioCreAtIvE and GOA.
• 
  Soumya Ray, Mark Craven: Learning Statistical Models for Annotating Proteins with Function Information using Biomedical Text.
• 
  Martin Krallinger, Maria Padron, Alfonso Valencia: A sentence sliding window approach to extract protein annotations from biomedical articles.
• 
  Karin Verspoor, Judith D. Cohn, Cliff Joslyn, Susan M. Mniszewski, Andreas Rechtsteiner, Luis Mateus Rocha, Tiago Simas: Protein annotation as term categorization in the gene ontology using word proximity networks.
• 
  Francisco M. Couto, Mário J. Silva, Pedro Coutinho: Finding genomic ontology terms in text using evidence content.
• 
  Simon B. Rice, Goran Nenadic, Benjamin J. Stapley: Mining protein function from text using term-based support vector machines.
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  Frédéric Ehrler, Antoine Geissbühler, Antonio Jimeno-Yepes, Patrick Ruch: Data-poor categorization and passage retrieval for Gene Ontology Annotation in Swiss-Prot.

Volume 6, Number S-2, 2005

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  Jonathan D. Wren, William Slikker Jr.: Proceedings of the Second Annual Conference of the MidSouth Computational Biology and Bioinformatics Society.
• 
  Jonathan D. Wren, David Johnson, Le Gruenwald: Automating Genomic Data Mining via a Sequence-based Matrix Format and Associative Rule Set.
• 
  Andrey A. Ptitsyn, Winston Hide: CLU: A new algorithm for EST clustering.
• 
  Qian Xie, Luke D. Ratnasinghe, Huixiao Hong, Roger Perkins, Ze-Zhong Tang, Nan Hu, Philip R. Taylor, Weida Tong: Decision Forest Analysis of 61 Single Nucleotide Polymorphisms in a Case-Control Study of Esophageal Cancer; a novel method.
• 
  Huixiao Hong, Yvonne P. Dragan, Joshua Epstein, Candee Teitel, Bangzheng Chen, Qian Xie, Hong Fang, Leming M. Shi, Roger Perkins, Weida Tong: Quality control and quality assessment of data from surface-enhanced laser desorption/ionization (SELDI) time-of flight (TOF) mass spectrometry (MS).
• 
  Hong Fang, Weida Tong, Roger Perkins, Leming M. Shi, Huixiao Hong, X. Cao, Qian Xie, S. H. Yim, J. M. Ward, Henry C. Pitot, Yvonne P. Dragan: Bioinformatics approaches for cross-species liver cancer analysis based on microarray gene expression profiling.
• 
  Ronald L. Frank, Fikret Erçal: Evaluation of Glycine max mRNA clusters.
• 
  Zengjun Xu, Tucker A. Patterson, Jonathan D. Wren, Tao Han, Leming M. Shi, Helen Duhart, Syed F. Ali, William Slikker Jr.: A microarray study of MPP⁺-treated PC12 Cells: Mechanisms of toxicity (MOT) analysis using bioinformatics tools.
• 
  Yong Tang, Yingfeng Chen, Cheryl F. Lichti, Roger A. Hall, Kevin D. Raney, Steven F. Jennings: CLPM: A Cross-Linked Peptide Mapping Algorithm for Mass Spectrometric Analysis.
• 
  Nikhil R. Garge, Grier P. Page, Alan P. Sprague, Bernard S. Gorman, David B. Allison: Reproducible Clusters from Microarray Research: Whither?
• 
  Leming M. Shi, Weida Tong, Zhenqiang Su, Tao Han, Jing Han, Raj K. Puri, Hong Fang, Felix W. Frueh, Federico M. Goodsaid, Lei Guo, William S. Branham, James J. Chen, Z. Alex Xu, Stephen C. Harris, Huixiao Hong, Qian Xie, Roger Perkins, James C. Fuscoe: Microarray scanner calibration curves: characteristics and implications.
• 
  Leming M. Shi, Weida Tong, Hong Fang, Uwe Scherf, Jing Han, Raj K. Puri, Felix W. Frueh, Federico M. Goodsaid, Lei Guo, Zhenqiang Su, Tao Han, James C. Fuscoe, Z. Alex Xu, Tucker A. Patterson, Huixiao Hong, Qian Xie, Roger Perkins, James J. Chen, Daniel A. Casciano: Cross-platform comparability of microarray technology: Intra-platform consistency and appropriate data analysis procedures are essential.
• 
  Robert R. Delongchamp, Cruz Velasco, Stacey Dial, Angela J. Harris: Genome-wide estimation of gender differences in the gene expression of human livers: Statistical design and analysis.

Volume 6, Number S-3, 2005

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  Euan A. Adie: Speeding Disease Gene Discovery with SUSPECTS.
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  Jeremy Austin: Sequence Analysis In Promoter Regions.
• 
  Subrata K. Bose, Hassan B. Kazemian, Kenneth White, Antony Browne: Use Of Neural Networks To Predict And Analyse Membrane Proteins In The Proteome.
• 
  Ross Buchan, Ian Stansfield: Codon pair bias in prokaryotic and eukaryotic genomes.
• 
  Colin Clarke, Michael Malecha, Selly Saini: NanoSNP: A computational platform for high throughput Quantum Dot encoded microsphere SNP genotyping.
• 
  Daniel R. Clutterbuck: Using Comparative Genomics & RNA Structure to Find RNA Editing Sites.
• 
  Pedro Coutinho: ZF-Human Disease Database: A Database for Zebrafish Models of Human Genetic Diseases.
• 
  Paul Craig, Jessie B. Kennedy, Andrew Cumming: Time-series Explorer: An Animated Information Visualisation for Microarray Time-course Data.
• 
  John Cumbers, J. Douglas Armstrong: Computational Analysis of Insulin in the Ageing Fruit Fly.
• 
  Stephen Edwards, Bonnie L. Webber, Carl Holt, Lindsay Sawyer: Text-mining, milk proteins and nutraceutical potential - the MilkER project.
• 
  Ana Sofia Figueiredo: Integration of open source software tools for the in silico design of metabolic pathways using flux balance analysis - an application to the production of recombinant human proteins.
• 
  Swanand P. Gore, David F. Burke, Tom L. Blundell: PROVAT - a versatile tool for Voronoi tessellation analysis of protein structures and complexes.
• 
  Graeme Grimes: GPX - An Integrative Environment for the Storage and Retrieval of Raw and Processed Microarray Data.
• 
  Richard J. Boys, Daniel Henderson, Thomas B. L. Kirkwood, Darren J. Wilkinson, W. Eryk Wolski: CaliBayes: Integration of GRID based simulation and data resources for Bayesian calibration of biological models.
• 
  Joanna Jakubowska, Ela Hunt, Matthew Chalmers, David Leader, Martin W. McBride, Anna F. Dominiczak: System level visualization of eQTLs and pQTLs.
• 
  Ajit Kumar Gopee: Gene Expression-Based Cross Species Tissue Mapping.
• 
  Andrew Lee: An analysis of allele sharing in a region of linkage with bipolar affective disorder.
• 
  Laurence Loewe: Evolution@home: Global computing quantifies evolution due to Muller's ratchet.
• 
  Sarah Luger, J. Stuart Aitken, Bonnie L. Webber: Automated Terminological and Structural Analysis of Human-Mouse Anatomical Ontology Mappings.
• 
  Sandy J. Macdonald, Colin W. Bayne, Malcolm Quirie, Frederick A. Lainson, Junli Liu, John C. Hodgson: Theoretical and quantitative aspects of iron acquisition by a bovine isolate of Pasteurella multocida A: 3.
• 
  Mark Mc Auley, Janette Jones, Darren J. Wilkinson, Tom Kirkwood: Modelling Lipid Metabolism to Improve Healthy Ageing.
• 
  Oscar Moya Mesa, Hermans Goar Contreras Díaz, Pedro Oromí Masoliver, Carlos Juan Clar: Bioinformatics in phylogeography: analitical methods and applications.
• 
  Douglas Roy, Peter Ghazal: Genomics and Pathway Biology - a new post-genomics M.Sc. programme from Edinburgh University.
• 
  Ajanthah Sangaralingam, Andrew J. Doig: Distinguishing between enzyme sequences & non-enzymes without using alignments.
• 
  Ole Schulz-Trieglaff: Stochastic Petri Nets in Systems Biology.
• 
  Gail Sinclair, Bonnie L. Webber, Duncan Davidson: Extracting Genetic Pathways From Text and Grounding at the Spatio-Temporal Level.
• 
  James Wasmuth, Ralf Schmid, Alasdair Anthony, John Parkinson, Mark L. Blaxter: Exploring Parasite Gene Space.
• 
  Andrew M. Waterhouse, James B. Procter, David M. A. Martin, Geoffrey J. Barton: Jalview: Visualization and Analysis of Molecular Sequences, Alignments, and Structures.
• 
  Le Yu, Stephen Marshall: A Method of Gene Expression Data Partitioning for the Construction of Context-Sensitive PBNs.
• 
  Nicholas M. Luscombe: Transcription regulation: a genomic network.
• 
  Andrew J. Millar: Biological clocks in theory and experiments.
• 
  José B. Pereira-Leal: The evolutionary origin of protein complexes.
• 
  J. Stuart Aitken, Thanyaluk Jirapech-Umpai, Rónán Daly: Inferring gene regulatory networks from classified microarray data: Initial results.
• 
  J. David Barrass, Jean D. Beggs: Investigation of mRNA Splicing in Saccharomyces cerevisiae using Microarrays.
• 
  Nicola D. Kerrison, Colin Selman, Steven J. Lingard, Janet M. Thornton, Linda Partridge, Dominic J. Withers: Living longer by dieting: analysis of transcriptional response after caloric restriction.
• 
  Raya Khanin, Veronica Vinciotti, Vassilis Mersinias, Colin P. Smith, Ernst Wit: Computational inference of regulator activity in a single input motif from gene expression data.
• 
  Judit Kumuthini: Extraction of Genetic Networks (GN) Using Static Bayesian Belief Networks From Genome-Wide Temporal Microarray Data.
• 
  Younes Mokrab, Kenji Mizuguchi: Amino-Acid Substitutions In Membrane Proteins: Applications To Homology Recognition And Comparative Modelling.
• 
  Jean-Christophe Nebel: Nestor3D: multiple alignment of protein structures based on ligand or prosthetic group position.
• 
  Evangelia I. Petsalakis, Pantelis G. Bagos, Zoi I. Litou, Stavros J. Hamodrakas: N-terminal sequence-based prediction of subcellular location.
• 
  Syed Asad Rahman, Pardha Saradhi Jonnalagadda, Jyothi Padiadpu, Kai Hartmann, Rainer Schrader, Dietmar Schomburg: Metabolic Network Analysis: Implication And Application.
• 
  Dov J. Stekel, Tim W. Overton, Jon L. Hobman, Charles W. Penn, Jeff A. Cole, Chrystala Constantinidou: Nonlinear Data Mining of Microarray Data Using Michaelis Menten Functions.
• 
  Frances S. Turner: Prioritisation of Disease Gene Candidates: A Systems Biology Approach.
• 
  Najl V. Valeyev, Andrei Skorinkin, Kristy Downing, Iain Campbell, Nikolai V. Kotov: The Important Role of Calcium in Regulation of Adhesion Disassembly and Cell Migration: Mathematical Modelling.

Volume 6, Number S-4, 2005

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  Manuela Helmer-Citterich, Rita Casadio, Alessandro Guffanti, Giancarlo Mauri, Luciano Milanesi, Graziano Pesole, Giorgio Valle, Cecilia Saccone: Overview of BITS2005, the Second Annual Meeting of the Italian Bioinformatics Society.
• 
  Nicola Ancona, Rosalia Maglietta, Annarita D'Addabbo, Sabino Liuni, Graziano Pesole: Regularized Least Squares Cancer Classifiers from DNA microarray data.
• 
  Giuliano Armano, Gianmaria Mancosu, Luciano Milanesi, Alessandro Orro, Massimiliano Saba, Eloisa Vargiu: A Hybrid Genetic-Neural System for Predicting Protein Secondary Structure.
• 
  Marcella Attimonelli, Matteo Accetturo, Monica Santamaria, Daniela Lascaro, Gaetano Scioscia, Graziano Pappadà, Luigi Russo, Luigi Zanchetta, Mila Tommaseo Ponzetta: HmtDB, a Human Mitochondrial Genomic Resource Based on Variability Studies Supporting Population Genetics and Biomedical Research.
• 
  Gabriele Ausiello, Allegra Via, Manuela Helmer-Citterich: Query3d: a new method for high-throughput analysis of functional residues in protein structures.
• 
  Sarah Burgarella, Dario Cattaneo, Francesco Pinciroli, Marco Masseroli: MicroGen: a MIAME compliant web system for microarray experiment information and workflow management.
• 
  Federica Cavallo, Annalisa Astolfi, Manuela Iezzi, Francesca Cordero, Pierluigi Lollini, Guido Forni, Raffaele Calogero: An integrated approach of immunogenomics and bioinformatics to identify new Tumor Associated Antigens (TAA) for mammary cancer immunological prevention.
• 
  Maria Vittoria Cubellis, Fabien Cailliez, Simon C. Lovell: Secondary structure assignment that accurately reflects physical and evolutionary characteristics.
• 
  Nunzio D'Agostino, Mario Aversano, Maria Luisa Chiusano: ParPEST: a pipeline for EST data analysis based on parallel computing.
• 
  Pasqualina D'Ursi, Erika Salvi, Paola Fossa, Luciano Milanesi, Ermanna Rovida: Modelling the interaction of steroid receptors with endocrine disrupting chemicals.
• 
  Barbara Di Camillo, Fatima Sanchez-Cabo, Gianna Toffolo, Sreekumaran K. Nair, Zlatko Trajanoski, Claudio Cobelli: A quantization method based on threshold optimization for microarray short time series.
• 
  Piero Fariselli, Pier Luigi Martelli, Rita Casadio: A new decoding algorithm for hidden Markov models improves the prediction of the topology of all-beta membrane proteins.
• 
  Enrico Ferraro, Allegra Via, Gabriele Ausiello, Manuela Helmer-Citterich: A neural strategy for the inference of SH3 domain-peptide interaction specificity.
• 
  Giacomo Finocchiaro, Francesco Mancuso, Heiko Müller: Mining published lists of cancer related microarray experiments: Identification of a gene expression signature having a critical role in cell-cycle control.
• 
  Claudio Greco, Piercarlo Fantucci, Luca De Gioia: -In silico functional characterization of a double histone fold domain from the Heliothis zea virus 1.
• 
  Barbara Lazzari, Andrea Caprera, Alberto Vecchietti, Alessandra Stella, Luciano Milanesi, Carlo Pozzi: ESTree db: a Tool for Peach Functional Genomics.
• 
  Gianmaria Mancosu, Massimiliano Cosso, Francesca Marras, Cesare Cappio Borlino, Giuseppe Ledda, Teresa Manias, Mauro Adamo, Donatella Serra, Paola M. Melis, Mario Pirastu: Browsing Isolated Population Data.
• 
  Marco Masseroli, Osvaldo Galati, Mauro Manzotti, Karina Gibert, Francesco Pinciroli: Inherited disorder phenotypes: controlled annotation and statistical analysis for knowledge mining from gene lists.
• 
  Ivan Merelli, Giulia Morra, Daniele D'Agostino, Andrea Clematis, Luciano Milanesi: High performance workflow implementation for protein surface characterization using grid technology.
• 
  Luciano Milanesi, Mauro Petrillo, Leandra Sepe, Angelo Boccia, Nunzio D'Agostino, Myriam Passamano, Salvatore Di Nardo, Gianluca Tasco, Rita Casadio, Giovanni Paolella: Systematic analysis of human kinase genes: a large number of genes and alternative splicing events result in functional and structural diversity.
• 
  Maria Persico, Arnaud Ceol, Caius Gavrila, Robert Hoffmann, Arnaldo Florio, Gianni Cesareni: HomoMINT: an inferred human network based on orthology mapping of protein interactions discovered in model organisms.
• 
  Davide Rambaldi, Alessandro Guffanti, Paolo Morandi, Giuseppe Cassata: NemaFootPrinter: a web based software for the identification of conserved non-coding genome sequence regions between C. elegans and C. briggsae.
• 
  Paolo Romano, Peter Dawyndt, Francesca Piersigilli, Jean Swings: Improving interoperability between microbial information and sequence databases.
• 
  Paolo Romano, Domenico Marra, Luciano Milanesi: Web services and workflow management for biological resources.

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