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Bioinformatics: Volume 24, Number 23, 1 December 2008

This page summarizes the most current issue of Bioinformatics. Here is a summary of the original papers. Links are provided to the on-line HTML and PDF files for the research articles. You may have to have a subscription to read the on-line articles.

• Smarter clustering methods for SNP genotype calling
  [Abstract], [Full Text], [Print PDF]
  Get checked abstract Yan Lin, George C. Tseng, Soo Yeon Cheong, Lora J. H. Bean, Stephanie L. Sherman, and Eleanor Feingold
• Artemis and ACT: viewing, annotating and comparing sequences stored in a relational database
  [Abstract], [FREE Full Text], [Print PDF]
  Get checked abstract Tim Carver, Matthew Berriman, Adrian Tivey, Chinmay Patel, Ulrike Böhme, Barclay G. Barrell, Julian Parkhill, and Marie-Adèle Rajandream
• Specific alignment of structured RNA: stochastic grammars and sequence annealing
  [Abstract], [Full Text], [Print PDF]
  Get checked abstract Robert K. Bradley, Lior Pachter, and Ian Holmes
• Position-dependent motif characterization using non-negative matrix factorization
  [Abstract], [FREE Full Text], [Print PDF]
  Get checked abstract Lucie N. Hutchins, Sean M. Murphy, Priyam Singh, and Joel H. Graber
• Protease substrate site predictors derived from machine learning on multilevel substrate phage display data
  [Abstract], [Full Text], [Print PDF]
  Get checked abstract Ching-Tai Chen, Ei-Wen Yang, Hung-Ju Hsu, Yi-Kun Sun, Wen-Lian Hsu, and An-Suei Yang
• A novel method for comparing topological models of protein structures enhanced with ligand information
  [Abstract], [Full Text], [Print PDF]
  Get checked abstract Mallika Veeramalai and David Gilbert
• Improving 2D-DIGE protein expression analysis by two-stage linear mixed models: assessing experimental effects in a melanoma cell study
  [Abstract], [Full Text], [Print PDF]
  Get checked abstract Elmer A. Ferná;ndez, María R. Girotti, Juan A. López del Olmo, Andrea S. Llera, Osvaldo L. Podhajcer, Rodolfo J. C. Cantet, and Mónica Balzarini
• Inferring population history with DIY ABC: a user-friendly approach to approximate Bayesian computation
  [Abstract], [FREE Full Text], [Print PDF]
  Get checked abstract Jean-Marie Cornuet, Filipe Santos, Mark A. Beaumont, Christian P. Robert, Jean-Michel Marin, David J. Balding, Thomas Guillemaud, and Arnaud Estoup
• A better block partition and ligation strategy for individual haplotyping
  [Abstract], [Full Text], [Print PDF]
  Get checked abstract Yuzhong Zhao, Yun Xu, Zhihao Wang, Hong Zhang, and Guoliang Chen
• MeltDB: a software platform for the analysis and integration of metabolomics experiment data
  [Abstract], [Full Text], [Print PDF]
  Get checked abstract Heiko Neuweger, Stefan P. Albaum, Michael Dondrup, Marcus Persicke, Tony Watt, Karsten Niehaus, Jens Stoye, and Alexander Goesmann
• Optimal stepwise experimental design for pairwise functional interaction studies
  [Abstract], [Full Text], [Print PDF]
  Get checked abstract Fergal P. Casey, Gerard Cagney, Nevan J. Krogan, and Denis C. Shields
• Systems-level modeling of cellular glycosylation reaction networks: O-linked glycan formation on natural selectin ligands
  [Abstract], [Full Text], [Print PDF]
  Get checked abstract Gang Liu, Dhananjay D. Marathe, Khushi L. Matta, and Sriram Neelamegham
• Stochastic dynamics of genetic networks: modelling and parameter identification
  [Abstract], [Full Text], [Print PDF]
  Get checked abstract Eugenio Cinquemani, Andreas Milias-Argeitis, Sean Summers, and John Lygeros
• Impact of dimeric organization of enzyme on its function: the case of photosynthetic water splitting
  [Abstract], [Full Text], [Print PDF]
  Get checked abstract Jiri Jablonsky, Petr Susila, and Dusan Lazar
• A bioinformatics analysis of the cell line nomenclature
  [Abstract], [Full Text], [Print PDF]
  Get checked abstract Sirarat Sarntivijai, Alexander S. Ade, Brian D. Athey, and David J. States
• The Protein Feature Ontology: a tool for the unification of protein feature annotations
  [Abstract], [Full Text], [Print PDF]
  Get checked abstract Gabrielle A. Reeves, Karen Eilbeck, Michele Magrane, Claire O'Donovan, Luisa Montecchi-Palazzi, Midori A. Harris, Sandra Orchard, Rafael C. Jimenez, Andreas Prlic, Tim J. P. Hubbard, Henning Hermjakob, and Janet M. Thornton
• CNVDetector: locating copy number variations using array CGH data
  [Abstract], [Full Text], [Print PDF]
  Get checked abstract Peng-An Chen, Hsiao-Fei Liu, and Kun-Mao Chao
• Efficient mapping of Applied Biosystems SOLiD sequence data to a reference genome for functional genomic applications
  [Abstract], [FREE Full Text], [Print PDF]
  Get checked abstract Brian D. Ondov, Anjana Varadarajan, Karla D. Passalacqua, and Nicholas H. Bergman
• POPE—a tool to aid high-throughput phylogenetic analysis
  [Abstract], [FREE Full Text], [Print PDF]
  Get checked abstract Thorhildur Juliusdottir, Fredrik Pettersson, and Richard R. Copley
• Searching protein structure databases with DaliLite v.3
  [Abstract], [FREE Full Text], [Print PDF]
  Get checked abstract L. Holm, S. Kääriäinen, P. Rosenström, and A. Schenkel
• MSX-3D: a tool to validate 3D protein models using mass spectrometry
  [Abstract], [Full Text], [Print PDF]
  Get checked abstract Michaël Heymann, David Paramelle, Gilles Subra, Eric Forest, Jean Martinez, Christophe Geourjon, and Gilbert Deléage
• GSEA-SNP: applying gene set enrichment analysis to SNP data from genome-wide association studies
  [Abstract], [Full Text], [Print PDF]
  Get checked abstract Marit Holden, Shiwei Deng, Leszek Wojnowski, and Bettina Kulle
• A flexible forward simulator for populations subject to selection and demography
  [Abstract], [Full Text], [Print PDF]
  Get checked abstract Ryan D. Hernandez
• QGene 4.0, an extensible Java QTL-analysis platform
  [Abstract], [Full Text], [Print PDF]
  Get checked abstract Roby Joehanes and James C. Nelson
• FABSIM: a software for generating F_ST distributions with various ascertainment biases
  [Abstract], [Full Text], [Print PDF]
  Get checked abstract Anna Ramírez-Soriano and Francesc Calafell
• Identifying differentially expressed subnetworks with MMG
  [Abstract], [Full Text], [Print PDF]
  Get checked abstract Josselin Noirel, Guido Sanguinetti, and Phillip C. Wright
• WAVECLOCK: wavelet analysis of circadian oscillation
  [Abstract], [Full Text], [Print PDF]
  Get checked abstract Tom S. Price, Julie E. Baggs, Anne M. Curtis, Garret A. FitzGerald, and John B. Hogenesch
• mspire: mass spectrometry proteomics in Ruby
  [Abstract], [FREE Full Text], [Print PDF]
  Get checked abstract John T. Prince and Edward M. Marcotte
• GEOmetadb: powerful alternative search engine for the Gene Expression Omnibus
  [Abstract], [FREE Full Text], [Print PDF]
  Get checked abstract Yuelin Zhu, Sean Davis, Robert Stephens, Paul S. Meltzer, and Yidong Chen
• IPEP: an in silico tool to examine proteolytic peptides for mass spectrometry
  [Abstract], [Full Text], [Print PDF]
  Get checked abstract Dihui Lu, Richard Z. Liu, Victoria Izumi, David Fenstermacher, Eric B. Haura, John Koomen, and Steven A. Eschrich
• The Burkholderia Genome Database: facilitating flexible queries and comparative analyses
  [Abstract], [FREE Full Text], [Print PDF]
  Get checked abstract Geoffrey L. Winsor, Bhavjinder Khaira, Thea Van Rossum, Raymond Lo, Matthew D. Whiteside, and Fiona S. L. Brinkman
• Addendum. Cytoprophet: a Cytoscape plug-in for protein and domain interaction networks inference
  [Abstract], [Full Text], [Print PDF]
  Get checked abstract Faruck Morcos, Charles Lamanna, Marcin Sikora, and Jesús Izaguirre

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