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Briefings in Bioinformatics, Volume 13
Volume 13, Number 1, January 2012
- Kristel Van Steen
:
Travelling the world of gene-gene interactions. 1-19 - Raphaël Mourad, Christine Sinoquet, Philippe Leray
Probabilistic graphical models for genetic association studies. 20-33 - Chenguang Wang, Zhong Wang, Daniel R. Prows, Rongling Wu:
A computational framework for the inheritance pattern of genomic imprinting for complex traits. 34-45 - André Koschmieder, Karin Zimmermann, Silke Trißl, Thomas Stoltmann, Ulf Leser:
Tools for managing and analyzing microarray data. 46-60 - Alberto Faro, Daniela Giordano
Combining literature text mining with microarray data: advances for system biology modeling. 61-82 - Daniel P. Berrar, Peter A. Flach
Caveats and pitfalls of ROC analysis in clinical microarray research (and how to avoid them). 83-97 - Marc-Alexandre Nolin, Michel Dumontier
Building an HIV data mashup using Bio2RDF. 98-106 - Yijun Sun, Yunpeng Cai, Susan M. Huse, Rob Knight
A large-scale benchmark study of existing algorithms for taxonomy-independent microbial community analysis. 107-121 - Ahmed Ragab Nabhan, Indra Neil Sarkar:
The impact of taxon sampling on phylogenetic inference: a review of two decades of controversy. 122-134
Volume 13, Number 2, March 2012
- Caroline Durrant, Morris A. Swertz
Bioinformatics tools and database resources for systems genetics analysis in mice - a short review and an evaluation of future needs. 135-142 - Andrew A. Shelenkov
LEPSCAN - a web server for searching latent periodicity in DNA sequences. 143-149 - Ming Wu, Christina Chan:
Learning transcriptional regulation on a genome scale: a theoretical analysis based on gene expression data. 150-161 - Yakun Wang, Meng Xu, Zhong Wang, Ming Tao, Junjia Zhu, Li Wang, Runze Li
How to cluster gene expression dynamics in response to environmental signals. 162-174 - Xia Li, Wei Jiang
Dissection of human MiRNA regulatory influence to subpathway. 175-186 - Vladimir B. Teif
Calculating transcription factor binding maps for chromatin. 187-201 - Elisabeth Wong, Brittany A. Baur, Saad Quader, Chun-Hsi Huang:
Biological network motif detection: principles and practice. 202-215 - Jing Wang, Xianxiao Zhou, Jing Zhu, Yunyan Gu, Wenyuan Zhao, Jinfeng Zou, Zheng Guo:
GO-function: deriving biologically relevant functions from statistically significant functions. 216-227 - Julien Dutheil
Detecting coevolving positions in a molecule: why and how to account for phylogeny. 228-243 - Kristian Rother, Wojciech Potrzebowski
A toolbox for developing bioinformatics software. 244-257 - Shin Kawano
Tutorial videos of bioinformatics resources: online distribution trial in Japan named TogoTV. 258-268
Volume 13, Number 3, May 2012
- Francesca Finotello
Comparative analysis of algorithms for whole-genome assembly of pyrosequencing data. 269-280 - Jui-Hung Hung
Gene set enrichment analysis: performance evaluation and usage guidelines. 281-291 - Anne-Laure Boulesteix
Random forest Gini importance favours SNPs with large minor allele frequency: impact, sources and recommendations. 292-304 - Norman Huang, Parantu K. Shah, Cheng Li:
Lessons from a decade of integrating cancer copy number alterations with gene expression profiles. 305-316 - Xiyang Zhao, Chunfa Tong
Functional mapping of ontogeny in flowering plants. 317-328 - Alfonso Benítez-Páez
A practical guide for the computational selection of residues to be experimentally characterized in protein families. 329-336 - David duVerle, Hiroshi Mamitsuka
A review of statistical methods for prediction of proteolytic cleavage. 337-349 - Lianming Zhang, Keiko Udaka, Hiroshi Mamitsuka
Toward more accurate pan-specific MHC-peptide binding prediction: a review of current methods and tools. 350-364 - Rebekka Schlatter, Nicole Philippi, Gaby Wangorsch
Integration of Boolean models exemplified on hepatocyte signal transduction. 365-376 - Juan Wang, Zhi-xin Li, Chengxiang Qiu
The relationship between rational drug design and drug side effects. 377-382 - Maria Victoria Schneider, Peter Walter, Marie-Claude Blatter, James Watson, Michelle D. Brazas
Bioinformatics Training Network (BTN): a community resource for bioinformatics trainers. 383-389
- Li Shen:
Principles of Computational Modeling in NeuroscienceDavid Sterratt, Bruce Graham, Andrew Gillies and David Willshaw. 390-392
Volume 13, Number 4, July 2012
- Russ B. Altman:
Editorial: Current progress in Bioinformatics 2012. 393-394
- Samuel Flores
Multiscale modeling of macromolecular biosystems. 395-405 - Jinlian Wang, Yuji Zhang
Identification of aberrant pathways and network activities from high-throughput data. 406-419 - James A. Foster
Measuring the microbiome: perspectives on advances in DNA-based techniques for exploring microbial life. 420-429 - Chang F. Quo, Chanchala Kaddi, John H. Phan, Amin Zollanvari
Reverse engineering biomolecular systems using -omic data: challenges, progress and opportunities. 430-445 - Gürkan Bebek, Mehmet Koyutürk
Network biology methods integrating biological data for translational science. 446-459 - Udo Hahn, Kevin Bretonnel Cohen, Yael Garten, Nigam H. Shah:
Mining the pharmacogenomics literature - a survey of the state of the art. 460-494 - Emidio Capriotti
Bioinformatics for personal genome interpretation. 495-512
Volume 13, Number 5, September 2012
- Tao Yu, Jialiang Li
Adjusting confounders in ranking biomarkers: a model-based ROC approach. 513-523 - Age K. Smilde
Generic framework for high-dimensional fixed-effects ANOVA. 524-535 - Matthew N. McCall, Anthony Almudevar:
Affymetrix GeneChip microarray preprocessing for multivariate analyses. 536-546 - Jeffrey D. Allen, Siling Wang, Min Chen
Probe mapping across multiple microarray platforms. 547-554 - Runqing Yang, Xin Wang, Yuehua Cui:
Bayesian inference for genomic imprinting underlying developmental characteristics. 555-568 - Pietro Hiram Guzzi, Marco Mina
Semantic similarity analysis of protein data: assessment with biological features and issues. 569-585 - Ting Huang, Jingjing Wang, Weichuan Yu
Protein inference: a review. 586-614 - Sarah A. Killcoyne
Interfaces to PeptideAtlas: a case study of standard data access systems. 615-626 - Martin Krzywinski, Inanç Birol
Hive plots - rational approach to visualizing networks. 627-644
Volume 13, Number 6, November 2012
- Gabriel Valiente
Editorial. 645
- Johannes Dröge
Taxonomic binning of metagenome samples generated by next-generation sequencing technologies. 646-655 - Weizhong Li
Ultrafast clustering algorithms for metagenomic sequence analysis. 656-668 - Sharmila S. Mande, Monzoorul Haque Mohammed, Tarini Shankar Ghosh:
Classification of metagenomic sequences: methods and challenges. 669-681 - Monica Santamaria
Reference databases for taxonomic assignment in metagenomics. 682-695 - Carlotta De Filippo
Bioinformatic approaches for functional annotation and pathway inference in metagenomics data. 696-710 - Tulika Prakash, Todd D. Taylor:
Functional assignment of metagenomic data: challenges and applications. 711-727 - Hanno Teeling, Frank Oliver Glöckner:
Current opportunities and challenges in microbial metagenome analysis - a bioinformatic perspective. 728-742 - Chris I. Hunter
Metagenomic analysis: the challenge of the data bonanza. 743-746 - Catherine Ngom-Bru, Caroline Barretto
Gut microbiota: methodological aspects to describe taxonomy and functionality. 747-750 - Matthew Collison, Robert P. Hirt
Data mining the human gut microbiota for therapeutic targets. 751-768 - Elhanan Borenstein:
Computational systems biology and in silico modeling of the human microbiome. 769-780
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