


default search action
Briefings in Bioinformatics, Volume 12
Volume 12, Number 1, January 2011
- 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
- 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
- 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 Velasco, 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
- Anne-Laure Boulesteix
:
Editorial. 187-188
- 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 R. 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
- Christophe Dessimoz
:
Editorial: Orthology and applications. 375-376
- Eugene V. Koonin:
Obituary: Walter Fitch and the orthology paradigm. 377-378
- 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
- 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
- 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 Tm 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
- 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
- Paolo Romano
, Rosalba Giugno
, Alfredo Pulvirenti
:
Editorial. 547-548
- 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
- 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

manage site settings
To protect your privacy, all features that rely on external API calls from your browser are turned off by default. You need to opt-in for them to become active. All settings here will be stored as cookies with your web browser. For more information see our F.A.Q.