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ORCIDBriefings 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, Concetto Spampinato:
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, François Belleau, Jacques Corbeil:
Building an HIV data mashup using Bio2RDF. 98-106 - Yijun Sun, Yunpeng Cai, Susan M. Huse, Rob Knight, William G. Farmerie, Xiaoyu Wang, Volker Mai:
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, Rudi Alberts, Danny Arends, Steffen Möller, Richard Mott, Pjotr Prins, K. Joeri van der Velde, Ritsert C. Jansen, Klaus Schughart:
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, Eugene V. Korotkov:
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, Scott A. Berceli, Rongling Wu:
How to cluster gene expression dynamics in response to environmental signals. 162-174 - Xia Li, Wei Jiang, Wei Li, Baofeng Lian, Shuyuan Wang, Mingzhi Liao, Xiaowen Chen, Yanqiu Wang, Yingli Lv, Shiyuan Wang, Lei Yang:
Dissection of human MiRNA regulatory influence to subpathway. 175-186 - Vladimir B. Teif, Karsten Rippe:
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, Tomasz Puton, Magdalena Rother, Ewa Wywial, Janusz M. Bujnicki:
A toolbox for developing bioinformatics software. 244-257 - Shin Kawano, Hiromasa Ono, Toshihisa Takagi, Hidemasa Bono:
Tutorial videos of bioinformatics resources: online distribution trial in Japan named TogoTV. 258-268
Volume 13, Number 3, May 2012
- Francesca Finotello, Enrico Lavezzo, Paolo Fontana, Denis Peruzzo, Alessandro Albiero, Luisa Barzon, Marco Falda, Barbara Di Camillo, Stefano Toppo:
Comparative analysis of algorithms for whole-genome assembly of pyrosequencing data. 269-280 - Jui-Hung Hung, Tun-Hsiang Yang, Zhenjun Hu, Zhiping Weng, Charles DeLisi:
Gene set enrichment analysis: performance evaluation and usage guidelines. 281-291 - Anne-Laure Boulesteix, Andreas Bender, Justo Lorenzo Bermejo, Carolin Strobl:
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, Xiaoming Pang, Zhong Wang, Yunqian Guo, Fang Du, Rongling Wu:
Functional mapping of ontogeny in flowering plants. 317-328 - Alfonso Benítez-Páez, Sonia Cárdenas-Brito, Andrés J. Gutiérrez:
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, Shanfeng Zhu:
Toward more accurate pan-specific MHC-peptide binding prediction: a review of current methods and tools. 350-364 - Rebekka Schlatter, Nicole Philippi, Gaby Wangorsch, Robert Pick, Oliver Sawodny, Christoph Borner, Jens Timmer, Michael Ederer, Thomas Dandekar:
Integration of Boolean models exemplified on hepatocyte signal transduction. 365-376 - Juan Wang, Zhi-xin Li, Chengxiang Qiu, Dong Wang, Qinghua Cui:
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, Kristian Rother, Aidan Budd, Allegra Via, Celia W. G. van Gelder, Joachim Jacob, Pedro L. Fernandes, Tommi H. Nyrönen, Javier De Las Rivas, Thomas Blicher, Rafael C. Jiménez, Jane E. Loveland, Jennifer McDowall, Philip Jones, Brendan W. Vaughan, Rodrigo Lopez, Teresa K. Attwood, Catherine Brooksbank:
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, Julie Bernauer, Seokmin Shin, Ruhong Zhou, Xuhui Huang:
Multiscale modeling of macromolecular biosystems. 395-405 - Jinlian Wang, Yuji Zhang, Catalin Marian, Habtom W. Ressom:
Identification of aberrant pathways and network activities from high-throughput data. 406-419 - James A. Foster, John Bunge, Jack A. Gilbert, Jason H. Moore:
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, Mingqing Xu, May D. Wang, Gil Alterovitz:
Reverse engineering biomolecular systems using -omic data: challenges, progress and opportunities. 430-445 - Gürkan Bebek, Mehmet Koyutürk, Nathan D. Price, Mark R. Chance:
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, Nathan L. Nehrt, Maricel G. Kann, Yana Bromberg:
Bioinformatics for personal genome interpretation. 495-512
Volume 13, Number 5, September 2012
- Tao Yu, Jialiang Li, Shuangge Ma:
Adjusting confounders in ranking biomarkers: a model-based ROC approach. 513-523 - Age K. Smilde, Marieke E. Timmerman, Margriet M. W. B. Hendriks, Jeroen J. Jansen, Huub C. J. Hoefsloot:
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, Luc Girard, John D. Minna, Yang Xie, Guanghua Xiao:
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, Concettina Guerra, Mario Cannataro:
Semantic similarity analysis of protein data: assessment with biological features and issues. 569-585 - Ting Huang, Jingjing Wang, Weichuan Yu, Zengyou He:
Protein inference: a review. 586-614 - Sarah A. Killcoyne, Jeremy Handcock, Thomas Robinson, Eric W. Deutsch, John Boyle:
Interfaces to PeptideAtlas: a case study of standard data access systems. 615-626 - Martin Krzywinski, Inanç Birol, Steven J. M. Jones, Marco A. Marra:
Hive plots - rational approach to visualizing networks. 627-644
Volume 13, Number 6, November 2012
- Gabriel Valiente, Graziano Pesole:
Editorial. 645
- Johannes Dröge, Alice Carolyn McHardy:
Taxonomic binning of metagenome samples generated by next-generation sequencing technologies. 646-655 - Weizhong Li, Limin Fu, Beifang Niu, Sitao Wu, John C. Wooley:
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, Bruno Fosso, Arianna Consiglio, Giorgio De Caro, Giorgio Grillo, Flavio Licciulli, Sabino Liuni, Marinella Marzano, Daniel Alonso-Alemany, Gabriel Valiente, Graziano Pesole:
Reference databases for taxonomic assignment in metagenomics. 682-695 - Carlotta De Filippo, Matteo Ramazzotti, Paolo Fontana, Duccio Cavalieri:
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, Alex L. Mitchell, Philip Jones, Craig McAnulla, Sebastien Pesseat, Maxim Scheremetjew, Sarah 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, Anil Wipat, Sirintra Nakjang, Philippe Sanseau, James R. Brown:
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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