Bioinformatics

ORIGINAL PAPER

Abstract ORIGINAL PAPER

Yan Lin, George Tseng, Soo Yeon Cheong, Lora J.H. Bean, Stephanie L. Sherman, and Eleanor Feingold
Smarter Clustering Methods for SNP Genotype Calling
Bioinformatics Advance Access published on September 29, 2008.
doi:10.1093/bioinformatics/btn509
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Abstract ORIGINAL PAPER

Aurélien Mazurie, Danail Bonchev, Benno Schwikowski, and Gregory A. Buck
Phylogenetic distances are encoded in networks of interacting pathways
Bioinformatics Advance Access published on September 26, 2008.
doi:10.1093/bioinformatics/btn503
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Abstract ORIGINAL PAPER

Christina Beargie, Tsunglin Liu, Mark Corriveau, Ha Youn Lee, Jonatha Gott, and Ralf Bundschuh
Genome annotation in the presence of insertional RNA editing
Bioinformatics Advance Access published on September 25, 2008.
doi:10.1093/bioinformatics/btn487
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Abstract ORIGINAL PAPER

Ryo Yoshida, Masao Nagasaki, Rui Yamaguchi, Seiya Imoto, Satoru Miyano, and Tomoyuki Higuchi
Bayesian learning of biological pathways on genomic data assimilation
Bioinformatics Advance Access published on September 25, 2008.
doi:10.1093/bioinformatics/btn483
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Abstract ORIGINAL PAPER

Elmer A. Fernández, María R. Girotti, del Olmo Juan A López, Andrea S. Llera, Osvaldo L. Podhajcer, Rodolfo J. C. Cantet, and Mónica Balzarini
Improving 2D-DIGE protein expression analysis by two-stage linear mixed models: Assessing experimental effects in a melanoma cell study.
Bioinformatics Advance Access published on September 25, 2008.
doi:10.1093/bioinformatics/btn508
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Abstract ORIGINAL PAPER

Melanie Osl, Stephan Dreiseitl, Bernhard Pfeifer, Klaus Weinberger, Helmut Klocker, Georg Bartsch, Georg Schäfer, Bernhard Tilg, Armin Graber, and Christian Baumgartner
A new rule-based algorithm for identifying metabolic markers in prostate cancer using tandem mass spectrometry
Bioinformatics Advance Access published on September 24, 2008.
doi:10.1093/bioinformatics/btn506
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Abstract ORIGINAL PAPER

Luis F. de Figueiredo, Stefan Schuster, Christoph Kaleta, and David A. Fell
Can sugars be produced from fatty acids? A test case for pathway analysis tools
Bioinformatics Advance Access published on September 19, 2008.
doi:10.1093/bioinformatics/btn500
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Abstract ORIGINAL PAPER

Fergal P. Casey, Gerard Cagney, Nevan J. Krogan, and Denis C. Shields
Optimal stepwise experimental design for pairwise functional interaction studies
Bioinformatics Advance Access published on September 18, 2008.
doi:10.1093/bioinformatics/btn472
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Abstract ORIGINAL PAPER

Robert K. Bradley, Lior Pachter, and Ian Holmes
Specific Alignment of Structured RNA: Stochastic Grammars and Sequence Annealing
Bioinformatics Advance Access published on September 16, 2008.
doi:10.1093/bioinformatics/btn495
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Abstract ORIGINAL PAPER Justin Klekota and Frederick P. Roth Chemical Substructures that Enrich for Biological Activity Bioinformatics Advance Access published on September 11, 2008. doi:10.1093/bioinformatics/btn479 [Abstract] [Accepted Manuscript] [Supplementary Data]     OPEN ACCESS ARTICLE

Abstract ORIGINAL PAPER

Assaf P. Oron, Zhen Jiang, and Robert Gentleman
Gene Set Enrichment Analysis using Linear Models and Diagnostics
Bioinformatics Advance Access published on September 11, 2008.
doi:10.1093/bioinformatics/btn465
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Abstract ORIGINAL PAPER

Seesandra V Rajagopala, Johannes Goll, ND Deve Gowda, Kumar C Sunil, Björn Titz, Arnab Mukherjee, Sharmilla S Mary, Naresh Raviswaran, Chetan S Poojari, Srinivas Ramachandra, Svetlana Shtivelband, Stephen M Blazie, Julia Hofmann, and Peter Uetz
MPI-LIT: A literature-curated dataset of microbial binary protein-protein interactions
Bioinformatics Advance Access published on September 11, 2008.
doi:10.1093/bioinformatics/btn481
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Abstract ORIGINAL PAPER

Antonio Reverter and Eva K.F. Chan
Combining partial correlation and an information theory approach to the reversed-engineering of gene co-expression networks
Bioinformatics Advance Access published on September 10, 2008.
doi:10.1093/bioinformatics/btn482
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Abstract ORIGINAL PAPER Zachary A. Szpiech, Mattias Jakobsson, and Noah A. Rosenberg ADZE: A rarefaction approach for counting alleles private to combinations of populations Bioinformatics Advance Access published on September 8, 2008. doi:10.1093/bioinformatics/btn478 [Abstract] [Accepted Manuscript]     OPEN ACCESS ARTICLE

Abstract ORIGINAL PAPER

Elissa J. Cosgrove, Yingchun Zhou, Timothy S. Gardner, and Eric D. Kolaczyk
Predicting Gene Targets of Perturbations via Network-Based Filtering of mRNA Expression Compendia
Bioinformatics Advance Access published on September 8, 2008.
doi:10.1093/bioinformatics/btn476
[Abstract] [Accepted Manuscript] [Supplementary Data] [Request Permissions]  

Abstract ORIGINAL PAPER Sriram Sankararaman and Kimmen Sjölander INTREPID – INformation-theoretic TREe traversal for Protein functional site IDentification Bioinformatics Advance Access published on September 6, 2008. doi:10.1093/bioinformatics/btn474 [Abstract] [Accepted Manuscript] [Supplementary Data]     OPEN ACCESS ARTICLE

Abstract ORIGINAL PAPER

Gautam Goel, I-Chun Chou, and Eberhard O. Voit
System Estimation from Metabolic Time Series Data
Bioinformatics Advance Access published on September 4, 2008.
doi:10.1093/bioinformatics/btn470
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Abstract ORIGINAL PAPER

Heiko Neuweger, Stefan P. Albaum, Michael Dondrup, Marcus Persicke, Tony Watt, Karsten Niehaus, Jens Stoye, and Alexander Goesmann
MeltDB: A software platform for the analysis and integration of metabolomics experiment data.
Bioinformatics Advance Access published on September 2, 2008.
doi:10.1093/bioinformatics/btn452
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Abstract ORIGINAL PAPER Mirabela Rusu, Stefan Birmanns, and Willy Wriggers Biomolecular Pleiomorphism Probed by Spatial Interpolation of Coarse Models Bioinformatics Advance Access published on August 30, 2008. doi:10.1093/bioinformatics/btn461 [Abstract] [Accepted Manuscript] [Supplementary Data]     OPEN ACCESS ARTICLE

Abstract ORIGINAL PAPER

Sol Katzman, Christian Barrett, Grant Thiltgen, Rachel Karchin, and Kevin Karplus
PREDICT-2ND: a tool for generalized protein local structure prediction
Bioinformatics Advance Access published on August 30, 2008.
doi:10.1093/bioinformatics/btn438
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Abstract ORIGINAL PAPER

Xi Chen, Lily Wang, Jonathan D. Smith, and Bing Zhang
Supervised Principal Component Analysis for Gene Set Enrichment of Microarray Data with Continuous or Survival Outcomes
Bioinformatics Advance Access published on August 27, 2008.
doi:10.1093/bioinformatics/btn458
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Abstract ORIGINAL PAPER

Alona Fyshe, Yifeng Liu, Duane Szafron, Russ Greiner, and Paul Lu
Improving Subcellular Localization Prediction using Text Classification and the Gene Ontology
Bioinformatics Advance Access published on August 26, 2008.
doi:10.1093/bioinformatics/btn463
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Abstract ORIGINAL PAPER

Osamu Gotoh
Direct Mapping and Alignment of Protein Sequences onto Genomic Sequence
Bioinformatics Advance Access published on August 26, 2008.
doi:10.1093/bioinformatics/btn460
[Abstract] [Accepted Manuscript] [Supplementary Data] [Request Permissions]  

Abstract ORIGINAL PAPER

B. Elliott, M. Kirac, A. Cakmak, G. Yavas, S. Mayes, E. Cheng, Y. Wang, C. Gupta, G. Ozsoyoglu, and Z.M. Ozsoyoglu
PathCase: Pathways Database System
Bioinformatics Advance Access published on August 26, 2008.
doi:10.1093/bioinformatics/btn459
[Abstract] [Accepted Manuscript] [Request Permissions]  

Abstract ORIGINAL PAPER

Chang-Tsun Li, Yinyin Yuan, and Roland Wilson
An Unsupervised Conditional Random Fields Approach for Clustering Gene Expression Time Series
Bioinformatics Advance Access published on August 20, 2008.
doi:10.1093/bioinformatics/btn375
[Abstract] [Accepted Manuscript] [Supplementary Data] [Request Permissions]  

Abstract ORIGINAL PAPER Hang Chang, Rosa Anna DeFilippis, Thea D. Tlsty, and Bahram Parvin Graphical Methods for Quantifying Macromolecules through Bright Field Imaging Bioinformatics Advance Access published on August 14, 2008. doi:10.1093/bioinformatics/btn426 [Abstract] [Accepted Manuscript]     OPEN ACCESS ARTICLE

Abstract ORIGINAL PAPER

Hao Lin, Zefeng Zhang, Michael Q. Zhang, Bin Ma, and Ming Li
ZOOM! Zillions Of Oligos Mapped
Bioinformatics Advance Access published on August 6, 2008.
doi:10.1093/bioinformatics/btn416
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Abstract ORIGINAL PAPER

James A. Koziol, Anne C. Feng, Zhenyu Jia, Yipeng Wang, Michael McClelland, and Dan Mercola
The Wisdom of the Commons: Ensemble Tree Classifiers for Prostate Cancer Prognosis
Bioinformatics Advance Access published on July 15, 2008.
doi:10.1093/bioinformatics/btn354
[Abstract] [Accepted Manuscript] [Request Permissions]  

Abstract ORIGINAL PAPER

Hiromi Arai, Satoru Watanabe, Takanori Kigawa, and Masayuki Yamamura
A new modeling method in feature construction for the HSQC spectra screening problem
Bioinformatics Advance Access published on July 4, 2008.
doi:10.1093/bioinformatics/btn345
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Abstract ORIGINAL PAPER

Hakim Tafer and Ivo L. Hofacker
RNAplex: a fast tool for RNA-RNA interaction search
Bioinformatics Advance Access published on April 23, 2008.
doi:10.1093/bioinformatics/btn193
[Abstract] [Accepted Manuscript] [Supplementary Data] [Request Permissions]  

Abstract ORIGINAL PAPER Holger Fröhlich, Mark Fellmann, Holger Sültmann, Annemarie Poustka, and Tim Beissbarth Estimating Large Scale Signaling Networks through Nested Effect Models with Intervention Effects from Microarray Data Bioinformatics Advance Access published on January 28, 2008. doi:10.1093/bioinformatics/btm634 [Abstract] [Accepted Manuscript]     OPEN ACCESS ARTICLE

APPLICATIONS NOTE

Abstract APPLICATIONS NOTE Michaël Heymann, David Paramelle, Gilles Subra, Eric Forest, Jean Martinez, Christophe Geourjon, and Gilbert Deléage MSX-3D : A tool to validate 3D protein models using mass spectrometry Bioinformatics Advance Access published on September 30, 2008. doi:10.1093/bioinformatics/btn510 [Abstract] [Accepted Manuscript]     OPEN ACCESS ARTICLE

Abstract APPLICATIONS NOTE

Josselin Noirel, Guido Sanguinetti, and Phillip C. Wright
Identifying differentially-expressed subnetworks with MMG
Bioinformatics Advance Access published on September 25, 2008.
doi:10.1093/bioinformatics/btn499
[Abstract] [Accepted Manuscript] [Request Permissions]  

Abstract APPLICATIONS NOTE L. Holm, S. Kääriäinen, P. Rosenström, and A. Schenkel Searching protein structure databases with DaliLite v.3 Bioinformatics Advance Access published on September 25, 2008. doi:10.1093/bioinformatics/btn507 [Abstract] [Accepted Manuscript]     OPEN ACCESS ARTICLE

Abstract APPLICATIONS NOTE

Jing Gao, Alex S. Ade, V. Glenn Tarcea, Terry E. Weymouth, Barbara R. Mirel, H.V. Jagadish, and David J. States
Integrating and Annotating the Interactome using the MiMI plugin for Cytoscape
Bioinformatics Advance Access published on September 23, 2008.
doi:10.1093/bioinformatics/btn501
[Abstract] [Accepted Manuscript] [Supplementary Data] [Request Permissions]  

Abstract APPLICATIONS NOTE

Shiyong Liu, Ying Gao, and Ilya A. Vakser
DOCKGROUND Protein-Protein Docking Decoy Set
Bioinformatics Advance Access published on September 23, 2008.
doi:10.1093/bioinformatics/btn497
[Abstract] [Accepted Manuscript] [Request Permissions]  

Abstract APPLICATIONS NOTE

Daehee Hwang, Ning Zhang, Hookeun Lee, Eugene Yi, Hui Zhang, Inyoul Y. Lee, Leroy Hood, and Ruedi Aebersold
MS-BID: a Java package for label-free LC-MS based comparative proteomic analysis
Bioinformatics Advance Access published on September 19, 2008.
doi:10.1093/bioinformatics/btn491
[Abstract] [Accepted Manuscript] [Request Permissions]  

Abstract APPLICATIONS NOTE

Khalid Belhajjame, Andrew R. Jones, and Norman W. Paton
A Toolkit for Capturing and Sharing FuGE Experiments
Bioinformatics Advance Access published on September 17, 2008.
doi:10.1093/bioinformatics/btn496
[Abstract] [Accepted Manuscript] [Request Permissions]  

Abstract APPLICATIONS NOTE

Edi Prifti, Jean-Daniel Zucker, Karine Clement, and Corneliu Henegar
FunNet: an integrative tool for exploring transcriptional interactions
Bioinformatics Advance Access published on September 17, 2008.
doi:10.1093/bioinformatics/btn492
[Abstract] [Accepted Manuscript] [Supplementary Data] [Request Permissions]  

Abstract APPLICATIONS NOTE

Ricardo Martinez, Nicolas Pasquier, and Claude Pasquier
GenMiner: Mining non-redundant association rules from integrated gene expression data and annotations
Bioinformatics Advance Access published on September 17, 2008.
doi:10.1093/bioinformatics/btn490
[Abstract] [Accepted Manuscript] [Request Permissions]  

Abstract APPLICATIONS NOTE

Liang Liu
BEST 2.0: A Bayesian coalescent approach for estimating species trees
Bioinformatics Advance Access published on September 17, 2008.
doi:10.1093/bioinformatics/btn484
[Abstract] [Accepted Manuscript] [Request Permissions]  

Abstract APPLICATIONS NOTE

Samone Khouangsathiene, Carlo Pearson, Summer Street, Betsy Ferguson, and Christopher Dubay
MonkeySNP: a web portal for non-human primate Single Nucleo-tide Polymorphisms (SNPs)
Bioinformatics Advance Access published on September 16, 2008.
doi:10.1093/bioinformatics/btn493
[Abstract] [Accepted Manuscript] [Supplementary Data] [Request Permissions]  

Abstract APPLICATIONS NOTE

Xin Zhou and Zhen Su
tCal: transcriptional probability calculator using thermodynamic model
Bioinformatics Advance Access published on September 16, 2008.
doi:10.1093/bioinformatics/btn494
[Abstract] [Accepted Manuscript] [Supplementary Data] [Request Permissions]  

Abstract APPLICATIONS NOTE

Francesco Sirocco and Silvio C.E. Tosatto
TESE: Generating specific protein structure test set ensembles
Bioinformatics Advance Access published on September 16, 2008.
doi:10.1093/bioinformatics/btn488
[Abstract] [Accepted Manuscript] [Request Permissions]  

Abstract APPLICATIONS NOTE

Craig E Jones, Julian Schwerdt, Tessa Arwen Bretag, Ute Baumann, and Alfred L Brown
GOSLING: a rule-based protein annotator using BLAST and GO
Bioinformatics Advance Access published on September 16, 2008.
doi:10.1093/bioinformatics/btn486
[Abstract] [Accepted Manuscript] [Request Permissions]  

Abstract APPLICATIONS NOTE Alan P. Boyle, Justin Guinney, Gregory E. Crawford, and Terrence S. Furey F-Seq: A Feature Density Estimator for High-Throughput Sequence Tags Bioinformatics Advance Access published on September 10, 2008. doi:10.1093/bioinformatics/btn480 [Abstract] [Accepted Manuscript]     OPEN ACCESS ARTICLE

Abstract APPLICATIONS NOTE Tian Xia and Julie A. Dickerson OmicsViz: Cytoscape plug-in for visualizing Omics data across species Bioinformatics Advance Access published on September 8, 2008. doi:10.1093/bioinformatics/btn473 [Abstract] [Accepted Manuscript]     OPEN ACCESS ARTICLE

Abstract APPLICATIONS NOTE

C. Nelson Hayes, Diego Diez, Nicolas Joannin, Wataru Honda, Minoru Kanehisa, Mats Wahlgren, Craig E. Wheelock, and Susumu Goto
varDB: a pathogen-specific sequence database of protein families involved in antigenic variation
Bioinformatics Advance Access published on September 6, 2008.
doi:10.1093/bioinformatics/btn477
[Abstract] [Accepted Manuscript] [Supplementary Data] [Request Permissions]  

Abstract APPLICATIONS NOTE Denis C. Bauer and Timothy L. Bailey STREAM: Static Thermodynamic REgulAtory Model of transcription Bioinformatics Advance Access published on September 6, 2008. doi:10.1093/bioinformatics/btn467 [Abstract] [Accepted Manuscript]     OPEN ACCESS ARTICLE

Abstract APPLICATIONS NOTE

Guillermo Rodrigo, Javier Carrera, Kristala Jones Prather, and Alfonso Jaramillo
DESHARKY: Automatic design of metabolic pathways for optimal cell growth
Bioinformatics Advance Access published on September 5, 2008.
doi:10.1093/bioinformatics/btn471
[Abstract] [Accepted Manuscript] [Supplementary Data] [Request Permissions]  

Abstract APPLICATIONS NOTE Yoshimasa Tsuruoka, Jun'ichi Tsujii, and Sophia Ananiadou FACTA: a text search engine for finding associated biomedical concepts Bioinformatics Advance Access published on September 4, 2008. doi:10.1093/bioinformatics/btn469 [Abstract] [Accepted Manuscript]     OPEN ACCESS ARTICLE

Abstract APPLICATIONS NOTE Dorothea Emig, Melissa S. Cline, Thomas Lengauer, and Mario Albrecht Integrating Expression Data with Domain Interaction Networks Bioinformatics Advance Access published on September 3, 2008. doi:10.1093/bioinformatics/btn437 [Abstract] [Accepted Manuscript]     OPEN ACCESS ARTICLE

Abstract APPLICATIONS NOTE

Salvador Ramírez-Flandes and Osvaldo Ulloa
Bosque: Integrated phylogenetic analysis software
Bioinformatics Advance Access published on September 1, 2008.
doi:10.1093/bioinformatics/btn466
[Abstract] [Accepted Manuscript] [Request Permissions]  

Abstract APPLICATIONS NOTE

Anthony D. Hill, Jonathan R. Tomshine, Emma M. B. Weeding, Vassilios Sotiropoulos, and Yiannis N. Kaznessis
SynBioSS: The Synthetic Biology Modeling Suite
Bioinformatics Advance Access published on August 30, 2008.
doi:10.1093/bioinformatics/btn468
[Abstract] [Accepted Manuscript] [Supplementary Data] [Request Permissions]  

Abstract APPLICATIONS NOTE

Mehdi Pirooznia, Tanwir Habib, Edward J Perkins, and Youping Deng
GOfetcher: A Database with Complex Searching Facility for Gene Ontology
Bioinformatics Advance Access published on August 26, 2008.
doi:10.1093/bioinformatics/btn441
[Abstract] [Accepted Manuscript] [Request Permissions]  

Abstract APPLICATIONS NOTE

Holger Fröhlich, Tim Beißbarth, Achim Tresch, Dennis Kostka, Juby Jacob, Rainer Spang, and F. Markowetz
Analyzing Gene Perturbation Screens With Nested Effects Models in R and Bioconductor
Bioinformatics Advance Access published on August 21, 2008.
doi:10.1093/bioinformatics/btn446
[Abstract] [Accepted Manuscript] [Request Permissions]  

Abstract APPLICATIONS NOTE Darren Kessner, Matt Chambers, Robert Burke, David Agus, and Parag Mallick ProteoWizard: Open Source Software for Rapid Proteomics Tools Development Bioinformatics Advance Access published on July 7, 2008. doi:10.1093/bioinformatics/btn323 [Abstract] [Accepted Manuscript] [Supplementary Data]     OPEN ACCESS ARTICLE

Abstract APPLICATIONS NOTE David J. States, Alex S. Ade, Zachary C. Wright, Aaron V. Bookvich, and Brian D. Athey MiSearch Adaptive PubMed Search Tool Bioinformatics Advance Access published on March 11, 2008. doi:10.1093/bioinformatics/btn033 [Abstract] [Accepted Manuscript]     OPEN ACCESS ARTICLE

DISCOVERY NOTE

Abstract DISCOVERY NOTE

Katrin Sameith, Philipp Antczak, Elliot Marston, Nil Turan, Dieter Maier, Tanja Stankovic, and Francesco Falciani
Functional Modules integrating essential cellular functions are predictive of the response of leukaemia cells to DNA damage
Bioinformatics Advance Access published on September 17, 2008.
doi:10.1093/bioinformatics/btn489
[Abstract] [Accepted Manuscript] [Supplementary Data] [Request Permissions]  

Abstract DISCOVERY NOTE Robson Francisco de Souza, Vivek Anantharaman, Sandro José de Souza, L. Aravind, and Frederico J. Gueiros-Filho AMIN domains have a predicted role in localization of diverse periplasmic protein complexes Bioinformatics Advance Access published on September 4, 2008. doi:10.1093/bioinformatics/btn449 [Abstract] [Accepted Manuscript]     OPEN ACCESS ARTICLE

Abstract DISCOVERY NOTE

Fanny Jadeau, Emmanuelle Bechet, Alain J. Cozzone, Gilbert Deléage, Christophe Grangeasse, and Christophe Combet
Identification of the idiosyncratic bacterial protein-tyrosine kinase (BY-kinase) family signature.
Bioinformatics Advance Access published on September 3, 2008.
doi:10.1093/bioinformatics/btn462
[Abstract] [Accepted Manuscript] [Request Permissions]  

LETTER TO THE EDITOR

LETTER TO THE EDITOR

Caiyan Li and Hongzhe Li
In Response to Comment on ‘Network-constrained regularization and variable selection for analysis of genomic data’
Bioinformatics Advance Access published on September 11, 2008.
doi:10.1093/bioinformatics/btn485
[Accepted Manuscript] [Supplementary Data] [Request Permissions]  

LETTER TO THE EDITOR

Harald Binder and Martin Schumacher
Comment on ‘Network-constrained regularization and variable selection for analysis of genomic data’
Bioinformatics Advance Access published on August 4, 2008.
doi:10.1093/bioinformatics/btn412
[Accepted Manuscript] [Supplementary Data] [Request Permissions]  

ARTICLE