Briefings in Bioinformatics, Volume 12

Volume 12, Number 1, January 2011

Papers

• 
  Carol Wong, Yuran Li, Chih Lee, Chun-Hsi Huang:
  Ensemble learning algorithms for classification of mtDNA into haplogroups. 1-9
• 
  Mark A. van de Wiel, Franck Picard, Wessel N. van Wieringen, Bauke Ylstra:
  Preprocessing and downstream analysis of microarray DNA copy number profiles. 10-21
• 
  Léon-Charles Tranchevent, Francisco Bonachela Capdevila, Daniela Nitsch, Bart De Moor, Patrick De Causmaecker, Yves Moreau:
  A guide to web tools to prioritize candidate genes. 22-32
• 
  Shuangge Ma, Xiao Song:
  Ranking prognosis markers in cancer genomic studies. 33-40
• 
  Melissa J. Hubisz, Katherine S. Pollard, Adam C. Siepel:
  PHAST and RPHAST: phylogenetic analysis with space/time models. 41-51
• 
  Emanuela Gadaleta, Nicholas R. Lemoine, Claude Chelala:
  Online resources of cancer data: barriers, benefits and lessons. 52-63
• 
  Francisco Azuaje:
  Computational discrete models of tissue growth and regeneration. 64-77

Book Reviews

• 
  Medha Bhagwat, Lynn Young:
  Bioinformatics.Charlie Hodgman, Andrew French and David Westhead Instant. 78-79
• 
  Xiang Zhang:
  Proteome Bioinformatics. Edited by Simon J. Hubbard and Andrew R. Jones, . 80-81
• 
  Seonho Kim:
  Knowledge-Based Bioinformatics - From analysis to interpretation.Edited by Gil Alterovitz and Marco Ramoni. 82-85

Letter to the Editor

• 
  Malu Luz Calle, Víctor Urrea:
  Letter to the Editor: Stability of Random Forest importance measures. 86-89

Volume 12, Number 2, March 2011

• 
  Anália Lourenço, Sónia Carneiro, Miguel Rocha, Eugénio C. Ferreira, Isabel Rocha:
  Challenges in integrating Escherichia coli molecular biology data. 91-103
• 
  Danny Barash, Alexander Churkin:
  Mutational analysis in RNAs: comparing programs for RNA deleterious mutation prediction. 104-114
• 
  Xinbin Dai, Zhaohong Zhuang, Patrick Xuechun Zhao:
  Computational analysis of miRNA targets in plants: current status and challenges. 115-121
• 
  Georg Fuellen:
  Evolution of gene regulation - on the road towards computational inferences. 122-131
• 
  Yanping Xi, Yi-Ping Phoebe Chen, Chen Qian, Fei Wang:
  Comparative study of computational methods to detect the correlated reaction sets in biochemical networks. 132-150
• 
  Andrés Pinzón, Luis Miguel Rodriguez-Rojas, Andrés González, Adriana Bernal, Silvia Restrepo:
  Targeted metabolic reconstruction: a novel approach for the characterization of plant-pathogen interactions. 151-162
• 
  Singaravelu Kalaimathy, Ramanathan Sowdhamini, Karuppiah Kanagarajadurai:
  Critical assessment of structure-based sequence alignment methods at distant relationships. 163-175
• 
  Pascal Roy, Caroline Truntzer, Delphine Maucort-Boulch, Thomas Jouve, Nicolas Molinari:
  Protein mass spectra data analysis for clinical biomarker discovery: a global review. 176-186

Volume 12, Number 3, May 2011

Editorial

• 
  Anne-Laure Boulesteix:
  Editorial. 187-188

Special Issue Papers

• 
  Peter J. Castaldi, Issa J. Dahabreh, John P. A. Ioannidis:
  An empirical assessment of validation practices for molecular classifiers. 189-202
• 
  Richard M. Simon, Jyothi Subramanian, Ming-Chung Li, Supriya Menezes:
  Using cross-validation to evaluate predictive accuracy of survival risk classifiers based on high-dimensional data. 203-214
• 
  Anne-Laure Boulesteix, Willi Sauerbrei:
  Added predictive value of high-throughput molecular data to clinical data and its validation. 215-229
• 
  Ulrich Mansmann, Vindi Jurinovic:
  Biological feature validation of estimated gene interaction networks from microarray data: a case study on MYC in lymphomas. 230-244
• 
  Edward R. Dougherty:
  Validation of gene regulatory networks: scientific and inferential. 245-252
• 
  Inke R. König:
  Validation in Genetic Association Studies. 253-258
• 
  John R. Thompson, John Attia, Cosetta Minelli:
  The meta-analysis of genome-wide association studies. 259-269
• 
  Alexandros Stamatakis, Fernando Izquierdo-Carrasco:
  Result verification, code verification and computation of support values in phylogenetics. 270-279
• 
  Zhide Fang, Xiangqin Cui:
  Design and validation issues in RNA-seq experiments. 280-287
• 
  Torsten Hothorn, Friedrich Leisch:
  Case studies in reproducibility. 288-300

Volume 12, Number 4, July 2011

• 
  Philippe Sanseau, Jacob Koehler:
  Editorial: Computational methods for drug repurposing. 301-302
• 
  Joel Dudley, Tarangini Deshpande, Atul J. Butte:
  Exploiting drug-disease relationships for computational drug repositioning. 303-311
• 
  V. Joachim Haupt, Michael Schroeder:
  Old friends in new guise: repositioning of known drugs with structural bioinformatics. 312-326
• 
  Sanjay Joshua Swamidass:
  Mining small-molecule screens to repurpose drugs. 327-335
• 
  Fabrice Moriaud, Stéphane B. Richard, Stewart A. Adcock, Laetitia Chanas-Martin, Jean-Sébastien Surgand, Marouane Ben Jelloul, François Delfaud:
  Identify drug repurposing candidates by mining the Protein Data Bank. 336-340
• 
  Kui Xu, Timothy R. Coté:
  Database identifies FDA-approved drugs with potential to be repurposed for treatment of orphan diseases. 341-345
• 
  Divya Sardana, Cheng Zhu, Minlu Zhang, Ranga Chandra Gudivada, Lun Yang, Anil G. Jegga:
  Drug repositioning for orphan diseases. 346-356
• 
  Christos Andronis, Anuj Sharma, Vassilis Virvilis, Spyros Deftereos, Aris Persidis:
  Literature mining, ontologies and information visualization for drug repurposing. 357-368
• 
  Kristin K. Nicodemus:
  Letter to the Editor: On the stability and ranking of predictors from random forest variable importance measures. 369-373

Volume 12, Number 5, September 2011

Editorial

• 
  Christophe Dessimoz:
  Editorial: Orthology and applications. 375-376

Obituary

• 
  Eugene V. Koonin:
  Obituary: Walter Fitch and the orthology paradigm. 377-378

Special Issue Papers

• 
  David M. Kristensen, Yuri I. Wolf, Arcady R. Mushegian, Eugene V. Koonin:
  Computational methods for Gene Orthology inference. 379-391
• 
  Jean-Philippe Doyon, Vincent Ranwez, Vincent Daubin, Vincent Berry:
  Models, algorithms and programs for phylogeny reconciliation. 392-400
• 
  Colin N. Dewey:
  Positional orthology: putting genomic evolutionary relationships into context. 401-412
• 
  Kimmen Sjölander, Ruchira S. Datta, Yaoqing Shen, Grant M. Shoffner:
  Ortholog identification in the presence of domain architecture rearrangement. 413-422
• 
  Brigitte Boeckmann, Marc Robinson-Rechavi, Ioannis Xenarios, Christophe Dessimoz:
  Conceptual framework and pilot study to benchmark phylogenomic databases based on reference gene trees. 423-435
• 
  Walid H. Gharib, Marc Robinson-Rechavi:
  When orthologs diverge between human and mouse. 436-441
• 
  Jaime Huerta-Cepas, Joaquín Dopazo, Martijn A. Huynen, Toni Gabaldón:
  Evidence for short-time divergence and long-time conservation of tissue-specific expression after gene duplication. 442-448
• 
  Pascale Gaudet, Michael S. Livstone, Suzanna E. Lewis, Paul D. Thomas:
  Phylogenetic-based propagation of functional annotations within the Gene Ontology consortium. 449-462
• 
  Kristoffer Forslund, Fabian Schreiber, Nattaphon Thanintorn, Erik L. L. Sonnhammer:
  OrthoDisease: tracking disease gene orthologs across 100 species. 463-473
• 
  Christophe Dessimoz, Stefan Zoller, Tereza Manousaki, Huan Qiu, Axel Meyer, Shigehiro Kuraku:
  Comparative genomics approach to detecting split-coding regions in a low-coverage genome: lessons from the chimaera Callorhinchus milii (Holocephali, Chondrichthyes). 474-484

Letter to the Editor

• 
  Thomas Schmitt, David N. Messina, Fabian Schreiber, Erik L. L. Sonnhammer:
  Letter to the Editor: SeqXML and OrthoXML: standards for sequence and orthology information. 485-488

Non Special Issue Papers

• 
  Christian Ledergerber, Christophe Dessimoz:
  Base-calling for next-generation sequencing platforms. 489-497
• 
  Alan Wee-Chung Liew, Ngai-Fong Law, Hong Yan:
  Missing value imputation for gene expression data: computational techniques to recover missing data from available information. 498-513
• 
  Nicolas von Ahsen, Carl T. Wittwer, Ekkehard Schütz:
  Monovalent and divalent salt correction algorithms for T_m prediction - recommendations for Primer3 usage. 514-517
• 
  Rob Jelier, Jelle J. Goeman, Kristina M. Hettne, Martijn J. Schuemie, Johan T. den Dunnen, Peter A. C. 't Hoen:
  Literature-aided interpretation of gene expression data with the weighted global test. 518-529
• 
  Yves Sucaet, Taru Deva:
  Evolution and applications of plant pathway resources and databases. 530-544

Letter to the Editor

• 
  Adam Wittek, Karol Miller:
  Letter to the Editor: Current progress in patient-specific modeling by Neal and Kerckhoffs (2010). 545-546

Volume 12, Number 6, November 2011

Editorial

• 
  Paolo Romano, Rosalba Giugno, Alfredo Pulvirenti:
  Editorial. 547-548

Special Issue Papers

• 
  Paolo Romano, Rosalba Giugno, Alfredo Pulvirenti:
  Tools and collaborative environments for bioinformatics research. 549-561
• 
  Andrea Splendiani, Michaela Gündel, Jonathan M. Austyn, Duccio Cavalieri, Ciro Scognamiglio, Marco Brandizi:
  Knowledge sharing and collaboration in translational research, and the DC-THERA Directory. 562-575
• 
  Ismael Navas Delgado, Alejandro Real-Chicharro, Miguel Angel Medina, Francisca Sánchez-Jiménez, José Francisco Aldana Montes:
  Social pathway annotation: extensions of the systems biology metabolic modelling assistant. 576-587
• 
  Dario Corrada, Federica Viti, Ivan Merelli, Cristina Battaglia, Luciano Milanesi:
  myMIR: a genome-wide microRNA targets identification and annotation tool. 588-600
• 
  Magdalena Rother, Kristian Rother, Tomasz Puton, Janusz M. Bujnicki:
  RNA tertiary structure prediction with ModeRNA. 601-613
• 
  Paolo Ribeca, Gabriel Valiente:
  Computational challenges of sequence classification in microbiomic data. 614-625

Non Special Issue Papers

• 
  Adam M. Szalkowski, Christoph D. Schmid:
  Rapid innovation in ChIP-seq peak-calling algorithms is outdistancing benchmarking efforts. 626-633
• 
  Helen E. Lockstone:
  Exon array data analysis using Affymetrix power tools and R statistical software. 634-644
• 
  Yijun Meng, Chaogang Shao, Ming Chen:
  Toward microRNA-mediated gene regulatory networks in plants. 645-659
• 
  Shannon L. N. Mayne, Hugh-George Patterton:
  Bioinformatics tools for the structural elucidation of multi-subunit protein complexes by mass spectrometric analysis of protein-protein cross-links. 660-671
• 
  Hua Zhang, Tuo Zhang, Ke Chen, Kanaka Durga Kedarisetti, Marcin J. Mizianty, Qingbo Bao, Wojciech Stach, Lukasz A. Kurgan:
  Critical assessment of high-throughput standalone methods for secondary structure prediction. 672-688
• 
  Matthieu Chavent, Bruno Lévy, Michael Krone, Katrin Bidmon, Jean-Philippe Nomine, Thomas Ertl, Marc Baaden:
  GPU-powered tools boost molecular visualization. 689-701
• 
  Tomas Klingström, Dariusz Plewczynski:
  Protein-protein interaction and pathway databases, a graphical review. 702-713
• 
  Shuangge Ma, Ying Dai:
  Principal component analysis based methods in bioinformatics studies. 714-722
• 
  Louis du Plessis, Nives Skunca, Christophe Dessimoz:
  The what, where, how and why of gene ontology - a primer for bioinformaticians. 723-735