Journal: Briefings in Bioinformatics

Volume 16, Issue 6

905 -- 911Libo Jiang, Jingyuan Liu, Xuli Zhu, Meixia Ye, Lidan Sun, Xavier Lacaze, Rongling Wu. 2HiGWAS: a unifying high-dimensional platform to infer the global genetic architecture of trait development
912 -- 921Xia Jiang, Richard E. Neapolitan. Evaluation of a two-stage framework for prediction using big genomic data
922 -- 931Wenhua Lv, Jiajia Zheng, Meiwei Luan, Miao Shi, Hongjie Zhu, Mingming Zhang, Hongchao Lv, Zhenwei Shang, Lian Duan, Ruijie Zhang, Yongshuai Jiang. Comparing the evolutionary conservation between human essential genes, human orthologs of mouse essential genes and human housekeeping genes
932 -- 940Jürgen Jänes, Fengyuan Hu, Alex Lewin, Ernest Turro. A comparative study of RNA-seq analysis strategies
941 -- 949Frida Danielsson, Tojo James, David Gomez-Cabrero, Mikael Huss. Assessing the consistency of public human tissue RNA-seq data sets
950 -- 963Shirley Tam, Ming-Sound Tsao, John D. McPherson. Optimization of miRNA-seq data preprocessing
964 -- 973Andrei Lihu, Stefan Holban. de novo motif discovery in ChIP-Seq data
974 -- 986Iurie Caraus, Abdulaziz A. Alsuwailem, Robert Nadon, Vladimir Makarenkov. Detecting and overcoming systematic bias in high-throughput screening technologies: a comprehensive review of practical issues and methodological solutions
987 -- 999Ming Fan, Hiroyuki Kuwahara, Xiaolei Wang, Suojin Wang, Xin Gao. Parameter estimation methods for gene circuit modeling from time-series mRNA data: a comparative study
1000 -- 1007Angelika Modelska, Alessandro Quattrone, Angela Re. Molecular portraits: the evolution of the concept of transcriptome-based cancer signatures
1008 -- 1024Li-Ling Lin, Hsuan-Cheng Huang, Hsueh-Fen Juan. Circadian systems biology in Metazoa
1025 -- 1034Surabhi Maheshwari, Michal Brylinski. Predicting protein interface residues using easily accessible on-line resources
1035 -- 1044Bernhard Knapp, Samuel Demharter, Reyhaneh Esmaielbeiki, Charlotte M. Deane. Current status and future challenges in T-cell receptor/peptide/MHC molecular dynamics simulations
1045 -- 1056Robert Rentzsch, Bernhard Y. Renard. Docking small peptides remains a great challenge: an assessment using AutoDock Vina
1057 -- 1068Aarthi Ravikrishnan, Karthik Raman. Critical assessment of genome-scale metabolic networks: the need for a unified standard
1069 -- 1080Robert Hoehndorf, Paul N. Schofield, Georgios V. Gkoutos. The role of ontologies in biological and biomedical research: a functional perspective

Volume 16, Issue 5

735 -- 744Xingjie Shi, Huangdi Yi, Shuangge Ma. Measures for the degree of overlap of gene signatures and applications to TCGA
745 -- 758Marie Lisandra Zepeda Mendoza, Thomas Sicheritz-Pontén, M. Thomas P. Gilbert. Environmental genes and genomes: understanding the differences and challenges in the approaches and software for their analyses
759 -- 768Meng Wang, Shili Lin. Detecting associations of rare variants with common diseases: collapsing or haplotyping?
769 -- 779Sabine C. Mueller, Christina Backes, Jan Haas, Hugo A. Katus, Benjamin Meder, Eckart Meese, Andreas Keller. Pathogenicity prediction of non-synonymous single nucleotide variants in dilated cardiomyopathy
780 -- 794Xiao Fan, Lukasz A. Kurgan. Comprehensive overview and assessment of computational prediction of microRNA targets in animals
795 -- 805Patricia Thébault, Romain Bourqui, William Benchimol, Christine Gaspin, Pascal Sirand-Pugnet, Raluca Uricaru, Isabelle Dutour. Advantages of mixing bioinformatics and visualization approaches for analyzing sRNA-mediated regulatory bacterial networks
806 -- 812Jianwei Li, Wei Ma, Pan Zeng, Junyi Wang, Bin Geng, Jichun Yang, Qinghua Cui. LncTar: a tool for predicting the RNA targets of long noncoding RNAs
813 -- 819Elise Billoir, Vincent Navratil, Benjamin J. Blaise. Sample size calculation in metabolic phenotyping studies
820 -- 829Brett Trost, Scott Napper, Anthony J. Kusalik. Case study: using sequence homology to identify putative phosphorylation sites in an evolutionarily distant species (honeybee)
830 -- 851Sanghamitra Bandyopadhyay, Sumanta Ray, Anirban Mukhopadhyay 0001, Ujjwal Maulik. in silico approaches for analysis and prediction of HIV-1-human protein-protein interactions
852 -- 864Ke Lin, Sandra Smit, Guusje Bonnema, Gabino Sanchez-Perez, Dick de Ridder. Making the difference: integrating structural variation detection tools
865 -- 872Zachary Chiang, Åke Västermark, Marco Punta, Penelope Coggill, Jaina Mistry, Robert D. Finn, Milton H. Saier Jr.. The complexity, challenges and benefits of comparing two transporter classification systems in TCDB and Pfam
873 -- 883Cen Wu, Shuangge Ma. A selective review of robust variable selection with applications in bioinformatics
884 -- 900Xiaoqing Liu, Jun Wu, Feiyang Gu, Jie Wang, Zengyou He. Discriminative pattern mining and its applications in bioinformatics
901 -- 903Daniel G. Hurley, David M. Budden, Edmund J. Crampin. Virtual Reference Environments: a simple way to make research reproducible

Volume 16, Issue 4

549 -- 562Qian Liu, Elizabeth T. Cirulli, Yujun Han, Song Yao, Song Liu, Qianqian Zhu. Systematic assessment of imputation performance using the 1000 Genomes reference panels
563 -- 575Andrea Ganna, Donghwan Lee, Erik Ingelsson, Yudi Pawitan. Rediscovery rate estimation for assessing the validation of significant findings in high-throughput studies
576 -- 587Luis Quintales, Enrique Vázquez, Francisco Antequera. Comparative analysis of methods for genome-wide nucleosome cartography
588 -- 599Michael Molnar, Lucian Ilie. Correcting Illumina data
600 -- 615Morgane Pierre-Jean, Guillem Rigaill, Pierre Neuvial. Performance evaluation of DNA copy number segmentation methods
616 -- 628David M. Budden, Daniel G. Hurley, Edmund J. Crampin. Predictive modelling of gene expression from transcriptional regulatory elements
629 -- 639Leng Han, Kasey C. Vickers, David C. Samuels, Yan Guo. Alternative applications for distinct RNA sequencing strategies
640 -- 657Zhen Chen, Yuan Zhou, Ziding Zhang, Jiangning Song. Towards more accurate prediction of ubiquitination sites: a comprehensive review of current methods, tools and features
658 -- 674Ben-teng, Can Zhao, Xiaoqing Liu, Zengyou He. Network inference from AP-MS data: computational challenges and solutions
675 -- 699Shazia Nafis, Ponnusamy Kalaiarasan, R. K. Brojen Singh, Mohammad Husain, Rameshwar N. K. Bamezai. Apoptosis regulatory protein-protein interaction demonstrates hierarchical scale-free fractal network
700 -- 709David Roy Smith. Buying in to bioinformatics: an introduction to commercial sequence analysis software
710 -- 731Shipra Gupta, Sonali Chavan, Dileep N. Deobagkar, Deepti D. Deobagkar. Bio/chemoinformatics in India: an outlook
732 -- 734Dawei Lin. Next Generation Microarray Bioinformatics: Methods and Protocols. Edited by Junbai Wang, Aik Choon Tan and Tianhai Tian

Volume 16, Issue 3

369 -- 379Swarnaseetha Adusumalli, Mohd Feroz Mohd Omar, Richie Soong, Touati Benoukraf. Methodological aspects of whole-genome bisulfite sequencing analysis
380 -- 392Latha Kadalayil, Sajjad Rafiq, Matthew J. J. Rose-Zerilli, Reuben J. Pengelly, Helen Parker, David Oscier, Jonathan C. Strefford, William J. Tapper, Jane Gibson, Sarah Ennis, Andrew Collins. Exome sequence read depth methods for identifying copy number changes
393 -- 412Mulin Jun Li, Bin Yan, Pak Chung Sham, Junwen Wang. Exploring the function of genetic variants in the non-coding genomic regions: approaches for identifying human regulatory variants affecting gene expression
413 -- 428Jiajia Chen, Maomin Sun, Bairong Shen. Deciphering oncogenic drivers: from single genes to integrated pathways
429 -- 448Siobhan Connolly, Elizabeth A. Heron. Review of statistical methodologies for the detection of parent-of-origin effects in family trio genome-wide association data with binary disease traits
449 -- 460Lidan Sun, Xuli Zhu, Wenhao Bo, Fang Xu, Tangren Cheng, Qixiang Zhang, Rongling Wu. An open-pollinated design for mapping imprinting genes in natural populations
461 -- 474Atefeh Taherian-Fard, Sriganesh Srihari, Mark A. Ragan. Breast cancer classification: linking molecular mechanisms to disease prognosis
475 -- 496Thuc Duy Le, Lin Liu 0001, Junpeng Zhang, Bing Liu 0002, Jiuyong Li. From miRNA regulation to miRNA-TF co-regulation: computational approaches and challenges
497 -- 525Ngoc Tam L. Tran, Sominder Mohan, Zhuoqing Xu, Chun-Hsi Huang. Current innovations and future challenges of network motif detection
526 -- 535Meixia Ye, Libo Jiang, Ke Mao, Yaqun Wang, Zhong Wang, Rongling Wu. Functional mapping of seasonal transition in perennial plants
536 -- 548Anup Som. Causes, consequences and solutions of phylogenetic incongruence

Volume 16, Issue 2

183 -- 192Xuefeng Wang, Eric P. Xing, Daniel J. Schaid. Kernel methods for large-scale genomic data analysis
193 -- 204Minh Duc Cao, Sureshkumar Balasubramanian, Mikael Bodén. Sequencing technologies and tools for short tandem repeat variation detection
205 -- 215Meixia Ye, Zhong Wang, Yaqun Wang, Rongling Wu. A multi-Poisson dynamic mixture model to cluster developmental patterns of gene expression by RNA-seq
216 -- 231Stefan Naulaerts, Pieter Meysman, Wout Bittremieux, Trung-Nghia Vu, Wim Vanden Berghe, Bart Goethals, Kris Laukens. A primer to frequent itemset mining for bioinformatics
232 -- 241Vinod Kumar Yadav, Subhajyoti De. An assessment of computational methods for estimating purity and clonality using genomic data derived from heterogeneous tumor tissue samples
242 -- 254Amjad Alkodsi, Riku Louhimo, Sampsa Hautaniemi. Comparative analysis of methods for identifying somatic copy number alterations from deep sequencing data
255 -- 264Michael Yourshaw, S. Paige Taylor, Aliz R. Rao, Martín G. Martín, Stanley F. Nelson. Rich annotation of DNA sequencing variants by leveraging the Ensembl Variant Effect Predictor with plugins
265 -- 279Alberto Rezola, Jon Pey, Luis Tobalina, Ángel Rubio, John E. Beasley, Francisco J. Planes. Advances in network-based metabolic pathway analysis and gene expression data integration
280 -- 290Vincent Canuel, Bastien Rance, Paul Avillach, Patrice Degoulet, Anita Burgun. Translational research platforms integrating clinical and omics data: a review of publicly available solutions
291 -- 303Qing Zhao, Xingjie Shi, Yang Xie, Jian Huang, Ben-Chang Shia, Shuangge Ma. Combining multidimensional genomic measurements for predicting cancer prognosis: observations from TCGA
304 -- 313Guoli Ji, Jinting Guan, Yong Zeng, Qingshun Quinn Li, Xiaohui Wu. Genome-wide identification and predictive modeling of polyadenylation sites in eukaryotes
314 -- 324Catherine Ching Han Chang, Beng Ti Tey, Jiangning Song, Ramakrishnan Nagasundara Ramanan. Towards more accurate prediction of protein folding rates: a review of the existing web-based bioinformatics approaches
325 -- 337Tapio Pahikkala, Antti Airola, Sami Pietilä, Sushil Shakyawar, Agnieszka Szwajda, Jing Tang, Tero Aittokallio. Toward more realistic drug-target interaction predictions
338 -- 345Anne-Laure Boulesteix, Silke Janitza, Alexander Hapfelmeier, Kristel Van Steen, Carolin Strobl. Letter to the Editor: On the term 'interaction' and related phrases in the literature on Random Forests
346 -- 354Philip Machanick, Özlem Tastan Bishop. How to establish a bioinformatics postgraduate degree programme - a case study from South Africa
355 -- 364Özlem Tastan Bishop, Ezekiel F. Adebiyi, Ahmed M. Alzohairy, Dean Everett, Kais Ghedira, Amel Ghouila, Judit Kumuthini, Nicola J. Mulder, Sumir Panji, Hugh-G. Patterton. Bioinformatics Education - Perspectives and Challenges out of Africa
365 -- 366Anne-Laure Boulesteix. Letter to the Editor: On Reviews and Papers on New Methods

Volume 16, Issue 1

1 -- 15Zexuan Zhu, Yongpeng Zhang, Zhen Ji, Shan He 0001, Xiao Yang. High-throughput DNA sequence data compression
16 -- 23Andrew Collins. The genomic and functional characteristics of disease genes
24 -- 31Tao Zhou, Yafei Lyu, Fang Xu, Wenhao Bo, Yi Zhai, Jian Zhang, Xiaoming Pang, Bingsong Zheng, Rongling Wu. A QTL model to map the common genetic basis for correlative phenotypic plasticity
32 -- 38Fang Xu, Chunfa Tong, Yafei Lyu, Wenhao Bo, Xiaoming Pang, Rongling Wu. Allotetraploid and autotetraploid models of linkage analysis
39 -- 44Toomas Haller, Mart Kals, Tõnu Esko, Reedik Mägi, Krista Fischer. RegScan: a GWAS tool for quick estimation of allele effects on continuous traits and their combinations
45 -- 58Hong-mei Zhang, Shuzhen Kuang, Xushen Xiong, Tianliuyun Gao, Chenglin Liu, An-Yuan Guo. Transcription factor and microRNA co-regulatory loops: important regulatory motifs in biological processes and diseases
59 -- 70Fatemeh Seyednasrollah, Asta Laiho, Laura L. Elo. Comparison of software packages for detecting differential expression in RNA-seq studies
71 -- 88Abhijit Chakraborty, Saikat Chakrabarti. A survey on prediction of specificity-determining sites in proteins
89 -- 103Catia M. Machado, Dietrich Rebholz-Schuhmann, Ana T. Freitas, Francisco M. Couto. The semantic web in translational medicine: current applications and future directions
104 -- 117Robert Smith, Dan Ventura, John T. Prince. LC-MS alignment in theory and practice: a comprehensive algorithmic review
118 -- 136Simona Panni, Simona E. Rombo. Searching for repetitions in biological networks: methods, resources and tools
137 -- 152Himanshu Kaul, Yiannis Ventikos. Investigating biocomplexity through the agent-based paradigm
153 -- 168Matthias Schmid, Hans A. Kestler, Sergej Potapov. On the validity of time-dependent AUC estimators
169 -- 182Nadine Castelhano Santos, Maria Olívia Pereira, Anália Lourenço. Pathogenicity phenomena in three model systems: from network mining to emerging system-level properties