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BMC Bioinformatics, Volume 6 - Supplements
Volume 6, Number S-1, 2005
- 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
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
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
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
ProMiner: rule-based protein and gene entity recognition. - Katrin Fundel, Daniel Güttler, Ralf Zimmer
A simple approach for protein name identification: prospects and limits. - Christian Blaschke, Eduardo Andrés León
Evaluation of BioCreAtIvE assessment of task 2. - Evelyn Camon, Daniel Barrell
An evaluation of GO annotation retrieval for BioCreAtIvE and GOA. - Soumya Ray
Learning Statistical Models for Annotating Proteins with Function Information using Biomedical Text. - Martin Krallinger
A sentence sliding window approach to extract protein annotations from biomedical articles. - Karin Verspoor
Protein annotation as term categorization in the gene ontology using word proximity networks. - Francisco M. Couto
Finding genomic ontology terms in text using evidence content. - Simon B. Rice, Goran Nenadic
Mining protein function from text using term-based support vector machines. - Frédéric Ehrler, Antoine Geissbühler, Antonio Jimeno-Yepes
Data-poor categorization and passage retrieval for Gene Ontology Annotation in Swiss-Prot.
Volume 6, Number S-2, 2005
- Jonathan D. Wren
Proceedings of the Second Annual Conference of the MidSouth Computational Biology and Bioinformatics Society. - Jonathan D. Wren
Automating Genomic Data Mining via a Sequence-based Matrix Format and Associative Rule Set. - Andrey A. Ptitsyn
CLU: A new algorithm for EST clustering. - Qian Xie, Luke D. Ratnasinghe, Huixiao Hong
Decision Forest Analysis of 61 Single Nucleotide Polymorphisms in a Case-Control Study of Esophageal Cancer; a novel method. - Huixiao Hong
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
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
A microarray study of MPP+-treated PC12 Cells: Mechanisms of toxicity (MOT) analysis using bioinformatics tools. - Yong Tang, Yingfeng Chen, Cheryl F. Lichti
CLPM: A Cross-Linked Peptide Mapping Algorithm for Mass Spectrometric Analysis. - Nikhil R. Garge, Grier P. Page
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
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
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
- Euan A. Adie:
Speeding Disease Gene Discovery with SUSPECTS. - 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, Thomas B. L. 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 Petsalakis, Pantelis G. Bagos, Zoi I. Litou
N-terminal sequence-based prediction of subcellular location. - Syed Asad Rahman
Metabolic Network Analysis: Implication And Application. - Dov J. Stekel
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 D. 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
- Manuela Helmer-Citterich, Rita Casadio, Alessandro Guffanti, Giancarlo Mauri
Overview of BITS2005, the Second Annual Meeting of the Italian Bioinformatics Society. - Nicola Ancona
Regularized Least Squares Cancer Classifiers from DNA microarray data. - Giuliano Armano, Gianmaria Mancosu, Luciano Milanesi
A Hybrid Genetic-Neural System for Predicting Protein Secondary Structure. - Marcella Attimonelli, Matteo Accetturo, Monica Santamaria
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
MicroGen: a MIAME compliant web system for microarray experiment information and workflow management. - Federica Cavallo
An integrated approach of immunogenomics and bioinformatics to identify new Tumor Associated Antigens (TAA) for mammary cancer immunological prevention. - Maria Vittoria Cubellis
Secondary structure assignment that accurately reflects physical and evolutionary characteristics. - Nunzio D'Agostino
ParPEST: a pipeline for EST data analysis based on parallel computing. - Pasqualina D'Ursi, Erika Salvi
Modelling the interaction of steroid receptors with endocrine disrupting chemicals. - Barbara Di Camillo, Fátima Sánchez-Cabo, Gianna Toffolo, Sreekumaran K. Nair, Zlatko Trajanoski, Claudio Cobelli:
A quantization method based on threshold optimization for microarray short time series. - Piero Fariselli
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
Mining published lists of cancer related microarray experiments: Identification of a gene expression signature having a critical role in cell-cycle control. - Claudio Greco
-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
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
Inherited disorder phenotypes: controlled annotation and statistical analysis for knowledge mining from gene lists. - Ivan Merelli, Giulia Morra
High performance workflow implementation for protein surface characterization using grid technology. - Luciano Milanesi, Mauro Petrillo
Systematic analysis of human kinase genes: a large number of genes and alternative splicing events result in functional and structural diversity. - Maria Persico, Arnaud Céol
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
Improving interoperability between microbial information and sequence databases. - Paolo Romano
Web services and workflow management for biological resources.
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