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Briefings in Bioinformatics, Volume 14
Volume 14, Number 1, January 2013
- Emily J. Richardson, Mick Watson
:
The automatic annotation of bacterial genomes. 1-12 - Wei-Jiun Lin, James J. Chen:
Class-imbalanced classifiers for high-dimensional data. 13-26 - Leo Lahti
Cancer gene prioritization by integrative analysis of mRNA expression and DNA copy number data: a comparative review. 27-35 - Vernell S. Williamson, Albert Kim, Bin Xie, G. Omari McMichael, Yuan Gao, Vladimir I. Vladimirov:
Detecting miRNAs in deep-sequencing data: a software performance comparison and evaluation. 36-45 - Joseph A. Neuman
Analysis of insertion-deletion from deep-sequencing data: software evaluation for optimal detection. 46-55 - Xiao Yang, Sriram P. Chockalingam, Srinivas Aluru:
A survey of error-correction methods for next-generation sequencing. 56-66 - Kian Guan Lim, Chee Keong Kwoh, Li Yang Hsu
Review of tandem repeat search tools: a systematic approach to evaluating algorithmic performance. 67-81 - Zhong Wang, Xiaoming Pang, Yafei Lv, Fang Xu, Tao Zhou, Xin Li, Sisi Feng, Jiahan Li, Zhikang Li, Rongling Wu:
A dynamic framework for quantifying the genetic architecture of phenotypic plasticity. 82-95 - Xiaoxia Yang, Yafei Lv, Xiaoming Pang, Chunfa Tong
A unifying framework for bivalent multilocus linkage analysis of allotetraploids. 96-108 - Huajun Chen, Tong Yu, Jake Y. Chen
Semantic Web meets Integrative Biology: a survey. 109-125
- Artem Zykovich:
Bioinformatics for Biologists. Edited by Pavel Pevzner and Ron Shamir. 126-127
Volume 14, Number 2, March 2013
- Scott Markel, Richard Carter
Editorial. 129-130
- Jun Wang, Lei Kong, Ge Gao, Jingchu Luo:
A brief introduction to web-based genome browsers. 131-143 - Robert M. Kuhn, David Haussler, W. James Kent:
The UCSC genome browser and associated tools. 144-161 - Lincoln D. Stein:
Using GBrowse 2.0 to visualize and share next-generation sequence data. 162-171 - Oscar Westesson, Mitchell Skinner, Ian H. Holmes
Visualizing next-generation sequencing data with JBrowse. 172-177 - Helga Thorvaldsdóttir, James T. Robinson, Jill P. Mesirov:
Integrative Genomics Viewer (IGV): high-performance genomics data visualization and exploration. 178-192 - Iain Milne
Using Tablet for visual exploration of second-generation sequencing data. 193-202 - Tim Carver, Simon R. Harris
BamView: visualizing and interpretation of next-generation sequencing read alignments. 203-212 - Michael C. Schatz, Adam M. Phillippy
Hawkeye and AMOS: visualizing and assessing the quality of genome assemblies. 213-224 - Federico Zambelli
Motif discovery and transcription factor binding sites before and after the next-generation sequencing era. 225-237 - Vivekanand Sharma, Indra Neil Sarkar:
Bioinformatics opportunities for identification and study of medicinal plants. 238-250 - Rosanna Upstill-Goddard
Machine learning approaches for the discovery of gene-gene interactions in disease data. 251-260
Volume 14, Number 3, May 2013
- Jingchu Luo, Harm Nijveen
Obituary: In memory of Jack Leunissen. 261-262
- Ander Muniategui
Joint analysis of miRNA and mRNA expression data. 263-278 - Kemal Eren, Mehmet Deveci, Onur Küçüktunç, Ümit V. Çatalyürek
A comparative analysis of biclustering algorithms for gene expression data. 279-292 - Chaogang Shao, Ming Chen
A reversed framework for the identification of microRNA-target pairs in plants. 293-301 - Xiaoming Pang, Zhong Wang, John S. Yap, Jianxin Wang, Junjia Zhu, Wenhao Bo, Yafei Lv, Fang Xu, Tao Zhou, Shaofeng Peng, Dengfeng Shen, Rongling Wu:
A statistical procedure to map high-order epistasis for complex traits. 302-314 - Wouter G. Touw, Jumamurat R. Bayjanov, Lex Overmars, Lennart Backus, Jos Boekhorst
Data mining in the Life Sciences with Random Forest: a walk in the park or lost in the jungle? 315-326 - Yi Sun, Ruixin Zhu
Towards a bioinformatics analysis of anti-Alzheimer's herbal medicines from a target network perspective. 327-343 - Zexian Liu, Jian Ren, Jun Cao, Jiang He, Xuebiao Yao, Changjiang Jin, Yu Xue:
Systematic analysis of the Plk-mediated phosphoregulation in eukaryotes. 344-360 - David C. Dallas
Automated glycopeptide analysis - review of current state and future directions. 361-374 - Jürgen Hartler
Bioinformatics tools and challenges in structural analysis of lipidomics MS/MS data. 375-390
Volume 14, Number 4, July 2013
- Yunda Huang
Comparability and reproducibility of biomedical data. 391-401 - Kaye E. Basford
On the classification of microarray gene-expression data. 402-410 - Santo Motta
Mathematical modeling of biological systems. 411-422 - Roman Sloutsky
Accounting for noise when clustering biological data. 423-436 - Abu Z. Dayem Ullah, Nicholas R. Lemoine, Claude Chelala
A practical guide for the functional annotation of genetic variations using SNPnexus. 437-447 - Stefano Castellana
Congruency in the prediction of pathogenic missense mutations: state-of-the-art web-based tools. 448-459 - Yafei Lv, Xiaoxia Yang, Chunfa Tong
A multivalent three-point linkage analysis model of autotetraploids. 460-468 - Cosmin Lazar, Stijn Meganck, Jonatan Taminau, David Steenhoff, Alain Coletta, Colin Molter, David Y. Weiss Solís, Robin Duque, Hugues Bersini, Ann Nowé:
Batch effect removal methods for microarray gene expression data integration: a survey. 469-490 - Elaine L. Leung, Zhi-Wei Cao, Zhi-Hong Jiang
Network-based drug discovery by integrating systems biology and computational technologies. 491-505 - Qingguo Wang
Application of next generation sequencing to human gene fusion detection: computational tools, features and perspectives. 506-519 - Stanley J. F. Laulederkind, G. Thomas Hayman, Shur-Jen Wang, Jennifer R. Smith, Timothy Lowry, Rajni Nigam, Victoria Petri, Jeff de Pons, Melinda R. Dwinell, Mary Shimoyama, Diane H. Munzenmaier, Elizabeth A. Worthey, Howard J. Jacob:
The Rat Genome Database 2013 - data, tools and users. 520-526
Volume 14, Number 5, September 2013
- Maria Victoria Schneider, John R. Jungck:
Editorial: International, interdisciplinary, multi-level bioinformatics training and education. 527
- Allegra Via, Thomas Blicher, Erik Bongcam-Rudloff, Michelle D. Brazas
Best practices in bioinformatics training for life scientists. 528-537 - Benilton S. Carvalho
The challenges of delivering bioinformatics training in the analysis of high-throughput data. 538-547 - Jing-Woei Li
The NGS WikiBook: a dynamic collaborative online training effort with long-term sustainability. 548-555 - Michelle D. Brazas
Navigating the changing learning landscape: perspective from bioinformatics.ca. 556-562 - Nathan S. Watson-Haigh
Next-generation sequencing: a challenge to meet the increasing demand for training workshops in Australia. 563-574 - Jing Wang
Environmental bio-monitoring with high-throughput sequencing. 575-588 - Sanne Abeln
Bioinformatics and Systems Biology: bridging the gap between heterogeneous student backgrounds. 589-598 - John R. Jungck, Anton E. Weisstein:
Mathematics and evolutionary biology make bioinformatics education comprehensible. 599-609 - Ran Libeskind-Hadas, Eliot C. Bush:
A first course in computing with applications to biology. 610-617 - Tamás Korcsmáros
Teaching the bioinformatics of signaling networks: an integrated approach to facilitate multi-disciplinary learning. 618-632 - Dick de Ridder, Jeroen de Ridder
Pattern recognition in bioinformatics. 633-647 - Yossy Machluf
Integrating bioinformatics into senior high school: design principles and implications. 648-660 - Allan Orozco, Jessica Morera, Sergio Jiménez, Ricardo Boza:
A review of Bioinformatics training applied to research in Molecular Medicine, Agriculture and Biodiversity in Costa Rica and Central America. 661-670
Volume 14, Number 6, November 2013
- Marie-Agnès Dillies, Andrea Rau, Julie Aubert, Christelle Hennequet-Antier, Marine Jeanmougin
A comprehensive evaluation of normalization methods for Illumina high-throughput RNA sequencing data analysis. 671-683 - Stefano Castellana
A solid quality-control analysis of AB SOLiD short-read sequencing data. 684-695 - Robert Hoehndorf
Evaluation of research in biomedical ontologies. 696-712 - Sheng Zhu
A quantitative model of transcriptional differentiation driving host-pathogen interactions. 713-723 - Mehdi Maadooliat
Assessing protein conformational sampling methods based on bivariate lag-distributions of backbone angles. 724-736 - Monica Chagoyen
Tools for the functional interpretation of metabolomic experiments. 737-744 - Georgios A. Dalkas
State-of-the-art technology in modern computer-aided drug design. 745-752 - Stephen J. Goodswen
A guide to in silico vaccine discovery for eukaryotic pathogens. 753-774 - Heather M. Vincent, Christopher Page:
Developing an online programme in computational biology. 775-783
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