Volume 9, Number 1, January 2008
- Wentian Li:
Three lectures on case-control genetic association analysis.
1-13
- Martin Yuille, Gert-Jan B. van Ommen, Christian Bréchot, Anne Cambon-Thomsen, Georges Dagher, Ulf Landegren, Jan-Eric Litton, Markus Pasterk, Leena Peltonen, Mike Taussig, H.-Erich Wichmann, Kurt Zatloukal:
Biobanking for Europe.
14-24
- Jose M. Arteaga-Salas, Harry Zuzan, William B. Langdon, Graham J. G. Upton, Andrew P. Harrison:
An overview of image-processing methods for Affymetrix GeneChips.
25-33
- Matteo Brilli, Renato Fani, Pietro Liò:
Current trends in the bioinformatic sequence analysis of metabolic pathways in prokaryotes.
34-45
- David Stephen Horner, Walter Pirovano, Graziano Pesole:
Correlated substitution analysis and the prediction of amino acid structural contacts.
46-56
- Paolo Romano:
Automation of in-silico data analysis processes through workflow management systems.
57-68
- Sean D. Mooney, Peter H. Baenziger:
Extensible open source content management systems and frameworks: a solution for many needs of a bioinformatics group.
69-74
- Daniel L. Rubin, Nigam Shah, Natalya Fridman Noy:
Biomedical ontologies: a functional perspective.
75-90
Book reviews
- Jihoon Yang:
Bioinformatics - From Genomes to Therapies: Edited by Thomas Lengauer.
91-93
- Ann E. Loraine:
Bioinformatics, Genomics, and Proteomics: Getting the Big Picture (Biotechnology in the 21st Century): Ann Finney Batiza.
94-95
Volume 9, Number 2, March 2008
Special Issue:
Computational Proteomics
- Mario Cannataro:
Computational proteomics: management and analysis of proteomics data.
97-101
Papers
- Melanie Hilario, Alexandros Kalousis:
Approaches to dimensionality reduction in proteomic biomarker studies.
102-118
- Annalisa Barla, Giuseppe Jurman, Samantha Riccadonna, Stefano Merler, Marco Chierici, Cesare Furlanello:
Machine learning methods for predictive proteomics.
119-128
- Thomas Villmann, Frank-Michael Schleif, Markus Kostrzewa, Axel Walch, Barbara Hammer:
Classification of mass-spectrometric data in clinical proteomics using learning vector quantization methods.
129-143
- Pierangelo Veltri:
Algorithms and tools for analysis and management of mass spectrometry data.
144-155
- Jason W. H. Wong, Matthew J. Sullivan, Gerard Cagney:
Computational methods for the comparative quantification of proteins in label-free LCn-MS experiments.
156-165
- Sandra E. Orchard, Henning Hermjakob:
The HUPO proteomics standards initiative - easing communication and minimizing data loss in a changing world.
166-173
Software Review
Volume 9, Number 3, May 2008
- Dougu Nam, Seon-Young Kim:
Gene-set approach for expression pattern analysis.
189-197
- Paolo Sonego, András Kocsor, Sándor Pongor:
ROC analysis: applications to the classification of biological sequences and 3D structures.
198-209
- Stephen John Sammut, Robert D. Finn, Alex Bateman:
Pfam 10 years on: 10 000 families and still growing.
210-219
- Interoperability with Moby 1.0 - It's better than sharing your toothbrush!
220-231
- Ina Koch, Georg Fuellen:
A review of bioinformatics education in Germany.
232-242
- Alexander Sczyrba, Susanne Konermann, Robert Giegerich:
Two interactive Bioinformatics courses at the Bielefeld University Bioinformatics Server.
243-249
- Robert Giegerich, Alvis Brazma, Inge Jonassen, Esko Ukkonen, Martin Vingron:
The BREW workshop series: a stimulating experience in PhD education.
250-253
Book Reviews
- Narayanan Perumal:
Cardiac Gene Expression: Methods and Protocols.: Edited by Jun Zhang and Gregg Rokosh.
254-255
- Zhen Lin:
Bioinformatics Basics: Applications in Biological Science and Medicine.: Edited by Lukas K. Buehler and Hooman H. Rashidi.
256-257
- Zhaohui S. Qin:
Data Analysis and Graphics Using R: An Example-Based Approach, Second Edition.: John Maindonald and John Braun.
258-259
Volume 9, Number 4, July 2008
Special Issue:
Critical Technologies for Bioinformatics
- Vladimir Brusic, Shoba Ranganathan:
Critical technologies for bioinformatics.
261-262
- Marie-Paule Lefranc, Véronique Giudicelli, Laetitia Regnier, Patrice Duroux:
IMGT, a system and an ontology that bridge biological and computational spheres in bioinformatics.
263-275
- Daron M. Standley, Akira R. Kinjo, Kengo Kinoshita, Haruki Nakamura:
Protein structure databases with new web services for structural biology and biomedical research.
276-285
- Kazutaka Katoh, Hiroyuki Toh:
Recent developments in the MAFFT multiple sequence alignment program.
286-298
- Sudhir Kumar, Masatoshi Nei, Joel Dudley, Koichiro Tamura:
MEGA: A biologist-centric software for evolutionary analysis of DNA and protein sequences.
299-306
- Gary B. Fogel:
Computational intelligence approaches for pattern discovery in biological systems.
307-316
- Zhenjun Hu, Evan S. Snitkin, Charles DeLisi:
VisANT: an integrative framework for networks in systems biology.
317-325
- Edgar Wingender:
The TRANSFAC project as an example of framework technology that supports the analysis of genomic regulation.
326-332
- Peter J. Hunter, Edmund J. Crampin, Poul M. F. Nielsen:
Bioinformatics, multiscale modeling and the IUPS Physiome Project.
333-343
Volume 9, Number 5, September 2008
- Roderic D. M. Page:
Biodiversity informatics: the challenge of linking data and the role of shared identifiers.
345-354
- Angelika Merkel, Neil Gemmell:
Detecting short tandem repeats from genome data: opening the software black box.
355-366
- Rutger W. W. Brouwer, Oscar P. Kuipers, Sacha A. F. T. van Hijum:
The relative value of operon predictions.
367-375
- Natalia V. Sernova, Mikhail S. Gelfand:
Identification of replication origins in prokaryotic genomes.
376-391
- Shuangge Ma, Jian Huang:
Penalized feature selection and classification in bioinformatics.
392-403
- Rainer Breitling, David Gilbert, Monika Heiner, Richard J. Orton:
A structured approach for the engineering of biochemical network models, illustrated for signalling pathways.
404-421
- Francisco J. Planes, John E. Beasley:
A critical examination of stoichiometric and path-finding approaches to metabolic pathways.
422-436
- Lorenzo Dematté, Corrado Priami, Alessandro Romanel:
The Beta Workbench: a computational tool to study the dynamics of biological systems.
437-449
Erratum
Volume 9, Number 6, November 2008
Editorial
Papers
- Jung-jae Kim, Dietrich Rebholz-Schuhmann:
Categorization of services for seeking information in biomedical literature: a typology for improvement of practice.
452-465
- Rainer Winnenburg, Thomas Wächter, Conrad Plake, Andreas Doms, Michael Schroeder:
Facts from text: can text mining help to scale-up high-quality manual curation of gene products with ontologies?
466-478
- Pankaj Agarwal, David B. Searls:
Literature mining in support of drug discovery.
479-492
- Heinz Stockinger, Teresa K. Attwood, Shahid Nadeem Chohan, Richard G. Côté, Philippe Cudré-Mauroux, Laurent Falquet, Pedro Fernandes, Robert D. Finn, Taavi Hupponen, Eija Korpelainen, Alberto Labarga, Aurélie Laugraud, Tania Lima, Evangelos Pafilis, Marco Pagni, Steve Pettifer, Isabelle Phan, Nazim Rahman:
Experience using web services for biological sequence analysis.
493-505
- Carole A. Goble, Robert Stevens, Duncan Hull, Katy Wolstencroft, Rodrigo Lopez:
Data curation + process curation=data integration + science.
506-517
- Holger Michael, Jennifer Hogan, Alexander E. Kel, Olga V. Kel-Margoulis, Frank Schacherer, Nico Voss, Edgar Wingender:
Building a knowledge base for systems pathology.
518-531
- Damian Smedley, Morris A. Swertz, Katy Wolstencroft, Glenn Proctor, Michael Zouberakis, Jonathan B. L. Bard, John M. Hancock, Paul N. Schofield:
Solutions for data integration in functional genomics: a critical assessment and case study.
532-544
Book Reviews
- Jean-Jacques Daudin:
Methods in Microarray Normalization, Edited by Phillip Stafford.
545-546
- Jim Whitfield:
Mathematics of Evolution and Phylogeny, Edited by Olivier Gascuel.
547-549
- Mihaela Pertea:
Problems and Solutions in Biological Sequence Analysis, Mark Borodovsky, Svetlana Ekisheva.
550-551
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