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ORCIDBriefings in Bioinformatics, Volume 16
Volume 16, Number 1, January 2015
- Zexuan Zhu, Yongpeng Zhang, Zhen Ji, Shan He, Xiao Yang:
High-throughput DNA sequence data compression. 1-15 - Andrew Collins
:
The genomic and functional characteristics of disease genes. 16-23 - Tao 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. 24-31 - Fang Xu, Chunfa Tong, Yafei Lyu, Wenhao Bo, Xiaoming Pang, Rongling Wu:
Allotetraploid and autotetraploid models of linkage analysis. 32-38 - Toomas 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. 39-44 - Hong-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. 45-58 - Fatemeh Seyednasrollah, Asta Laiho, Laura L. Elo:
Comparison of software packages for detecting differential expression in RNA-seq studies. 59-70 - Abhijit Chakraborty, Saikat Chakrabarti:
A survey on prediction of specificity-determining sites in proteins. 71-88 - Catia M. Machado, Dietrich Rebholz-Schuhmann, Ana T. Freitas, Francisco M. Couto:
The semantic web in translational medicine: current applications and future directions. 89-103 - Robert Smith, Dan Ventura, John T. Prince:
LC-MS alignment in theory and practice: a comprehensive algorithmic review. 104-117 - Simona Panni, Simona E. Rombo:
Searching for repetitions in biological networks: methods, resources and tools. 118-136 - Himanshu Kaul, Yiannis Ventikos:
Investigating biocomplexity through the agent-based paradigm. 137-152 - Matthias Schmid, Hans A. Kestler, Sergej Potapov:
On the validity of time-dependent AUC estimators. 153-168 - Nadine Castelhano Santos, Maria Olívia Pereira, Anália Lourenço:
Pathogenicity phenomena in three model systems: from network mining to emerging system-level properties. 169-182
Volume 16, Number 2, March 2015
- Xuefeng Wang, Eric P. Xing, Daniel J. Schaid:
Kernel methods for large-scale genomic data analysis. 183-192 - Minh Duc Cao, Sureshkumar Balasubramanian, Mikael Bodén:
Sequencing technologies and tools for short tandem repeat variation detection. 193-204 - Meixia Ye, Zhong Wang, Yaqun Wang, Rongling Wu:
A multi-Poisson dynamic mixture model to cluster developmental patterns of gene expression by RNA-seq. 205-215 - Stefan Naulaerts, Pieter Meysman, Wout Bittremieux, Trung-Nghia Vu, Wim Vanden Berghe, Bart Goethals, Kris Laukens:
A primer to frequent itemset mining for bioinformatics. 216-231 - Vinod Kumar Yadav, Subhajyoti De:
An assessment of computational methods for estimating purity and clonality using genomic data derived from heterogeneous tumor tissue samples. 232-241 - Amjad Alkodsi, Riku Louhimo, Sampsa Hautaniemi:
Comparative analysis of methods for identifying somatic copy number alterations from deep sequencing data. 242-254 - Michael 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. 255-264 - Alberto 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. 265-279 - Vincent Canuel, Bastien Rance, Paul Avillach, Patrice Degoulet, Anita Burgun:
Translational research platforms integrating clinical and omics data: a review of publicly available solutions. 280-290 - Qing Zhao, Xingjie Shi, Yang Xie, Jian Huang, Ben-Chang Shia, Shuangge Ma:
Combining multidimensional genomic measurements for predicting cancer prognosis: observations from TCGA. 291-303 - Guoli Ji, Jinting Guan, Yong Zeng, Qingshun Quinn Li, Xiaohui Wu:
Genome-wide identification and predictive modeling of polyadenylation sites in eukaryotes. 304-313 - Catherine 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. 314-324 - Tapio Pahikkala, Antti Airola, Sami Pietilä, Sushil Kumar Shakyawar, Agnieszka Szwajda, Jing Tang, Tero Aittokallio:
Toward more realistic drug-target interaction predictions. 325-337 - Anne-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. 338-345 - Philip Machanick, Özlem Tastan Bishop:
How to establish a bioinformatics postgraduate degree programme - a case study from South Africa. 346-354 - Özlem Tastan Bishop, Ezekiel F. Adebiyi, Ahmed M. Alzohairy, Dean Everett, Kais Ghedira, Amel Ghouila, Judit Kumuthini, Nicola J. Mulder, Sumir Panji, Hugh-George Patterton:
Bioinformatics Education - Perspectives and Challenges out of Africa. 355-364 - Anne-Laure Boulesteix:
Letter to the Editor: On Reviews and Papers on New Methods. 365-366
Volume 16, Number 3, May 2015
- Swarnaseetha Adusumalli, Mohd Feroz Mohd Omar, Richie Soong, Touati Benoukraf:
Methodological aspects of whole-genome bisulfite sequencing analysis. 369-379 - Latha 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. 380-392 - Mulin 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. 393-412 - Jiajia Chen, Maomin Sun, Bairong Shen:
Deciphering oncogenic drivers: from single genes to integrated pathways. 413-428 - Siobhan 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. 429-448 - Lidan Sun, Xuli Zhu, Wenhao Bo, Fang Xu, Tangren Cheng, Qixiang Zhang, Rongling Wu:
An open-pollinated design for mapping imprinting genes in natural populations. 449-460 - Atefeh Taherian Fard, Sriganesh Srihari, Mark A. Ragan:
Breast cancer classification: linking molecular mechanisms to disease prognosis. 461-474 - Thuc Duy Le, Lin Liu, Junpeng Zhang, Bing Liu, Jiuyong Li:
From miRNA regulation to miRNA-TF co-regulation: computational approaches and challenges. 475-496 - Ngoc Tam L. Tran, Sominder Mohan, Zhuoqing Xu, Chun-Hsi Huang:
Current innovations and future challenges of network motif detection. 497-525 - Meixia Ye, Libo Jiang, Ke Mao, Yaqun Wang, Zhong Wang, Rongling Wu:
Functional mapping of seasonal transition in perennial plants. 526-535 - Anup Som:
Causes, consequences and solutions of phylogenetic incongruence. 536-548
Volume 16, Number 4, July 2015
- Qian Liu, Elizabeth T. Cirulli, Yujun Han, Song Yao, Song Liu, Qianqian Zhu:
Systematic assessment of imputation performance using the 1000 Genomes reference panels. 549-562 - Andrea Ganna, Donghwan Lee, Erik Ingelsson, Yudi Pawitan:
Rediscovery rate estimation for assessing the validation of significant findings in high-throughput studies. 563-575 - Luis Quintales, Enrique Vázquez, Francisco Antequera:
Comparative analysis of methods for genome-wide nucleosome cartography. 576-587 - Michael Molnar, Lucian Ilie:
Correcting Illumina data. 588-599 - Morgane Pierre-Jean, Guillem Rigaill, Pierre Neuvial:
Performance evaluation of DNA copy number segmentation methods. 600-615 - David M. Budden, Daniel G. Hurley, Edmund J. Crampin:
Predictive modelling of gene expression from transcriptional regulatory elements. 616-628 - Leng Han, Kasey C. Vickers, David C. Samuels, Yan Guo:
Alternative applications for distinct RNA sequencing strategies. 629-639 - Zhen Chen, Yuan Zhou, Ziding Zhang, Jiangning Song:
Towards more accurate prediction of ubiquitination sites: a comprehensive review of current methods, tools and features. 640-657 - Ben Teng, Can Zhao, Xiaoqing Liu, Zengyou He:
Network inference from AP-MS data: computational challenges and solutions. 658-674 - Shazia Nafis, Ponnusamy Kalaiarasan, R. K. Brojen Singh, Mohammad Husain, Rameshwar N. K. Bamezai:
Apoptosis regulatory protein-protein interaction demonstrates hierarchical scale-free fractal network. 675-699 - David Roy Smith:
Buying in to bioinformatics: an introduction to commercial sequence analysis software. 700-709 - Shipra Gupta, Sonali Chavan, Dileep N. Deobagkar, Deepti D. Deobagkar:
Bio/chemoinformatics in India: an outlook. 710-731
- Dawei Lin:
Next Generation Microarray Bioinformatics: Methods and Protocols. Edited by Junbai Wang, Aik Choon Tan and Tianhai Tian. 732-734
Volume 16, Number 5, September 2015
- Xingjie Shi, Huangdi Yi, Shuangge Ma:
Measures for the degree of overlap of gene signatures and applications to TCGA. 735-744 - Marie 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. 745-758 - Meng Wang, Shili Lin:
Detecting associations of rare variants with common diseases: collapsing or haplotyping? 759-768 - Sabine 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. 769-779 - Xiao Fan, Lukasz A. Kurgan:
Comprehensive overview and assessment of computational prediction of microRNA targets in animals. 780-794 - Patricia 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. 795-805 - Jianwei 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. 806-812
- Elise Billoir, Vincent Navratil, Benjamin J. Blaise:
Sample size calculation in metabolic phenotyping studies. 813-819
- Brett Trost, Scott Napper, Anthony J. Kusalik:
Case study: using sequence homology to identify putative phosphorylation sites in an evolutionarily distant species (honeybee). 820-829 - Sanghamitra Bandyopadhyay, Sumanta Ray, Anirban Mukhopadhyay, Ujjwal Maulik:
A review of in silico approaches for analysis and prediction of HIV-1-human protein-protein interactions. 830-851 - Ke Lin, Sandra Smit, Guusje Bonnema, Gabino Sanchez-Perez, Dick de Ridder:
Making the difference: integrating structural variation detection tools. 852-864 - Zachary 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. 865-872 - Cen Wu, Shuangge Ma:
A selective review of robust variable selection with applications in bioinformatics. 873-883 - Xiaoqing Liu, Jun Wu, Feiyang Gu, Jie Wang, Zengyou He:
Discriminative pattern mining and its applications in bioinformatics. 884-900
- Daniel G. Hurley, David M. Budden, Edmund J. Crampin:
Virtual Reference Environments: a simple way to make research reproducible. 901-903
Volume 16, Number 6, November 2015
- Libo 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. 905-911 - Xia Jiang, Richard E. Neapolitan:
Evaluation of a two-stage framework for prediction using big genomic data. 912-921 - Wenhua 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. 922-931 - Jürgen Jänes, Fengyuan Hu, Alex Lewin, Ernest Turro:
A comparative study of RNA-seq analysis strategies. 932-940 - Frida Danielsson, Tojo James, David Gomez-Cabrero, Mikael Huss:
Assessing the consistency of public human tissue RNA-seq data sets. 941-949 - Shirley Tam, Ming-Sound Tsao, John D. McPherson:
Optimization of miRNA-seq data preprocessing. 950-963 - Andrei Lihu, Stefan Holban:
A review of ensemble methods for de novo motif discovery in ChIP-Seq data. 964-973 - Iurie 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. 974-986 - Ming Fan, Hiroyuki Kuwahara, Xiaolei Wang, Suojin Wang, Xin Gao:
Parameter estimation methods for gene circuit modeling from time-series mRNA data: a comparative study. 987-999 - Angelika Modelska, Alessandro Quattrone, Angela Re:
Molecular portraits: the evolution of the concept of transcriptome-based cancer signatures. 1000-1007 - Li-Ling Lin, Hsuan-Cheng Huang, Hsueh-Fen Juan:
Circadian systems biology in Metazoa. 1008-1024
- Surabhi Maheshwari, Michal Brylinski:
Predicting protein interface residues using easily accessible on-line resources. 1025-1034
- Bernhard Knapp, Samuel Demharter, Reyhaneh Esmaielbeiki, Charlotte M. Deane:
Current status and future challenges in T-cell receptor/peptide/MHC molecular dynamics simulations. 1035-1044 - Robert Rentzsch, Bernhard Y. Renard:
Docking small peptides remains a great challenge: an assessment using AutoDock Vina. 1045-1056 - Aarthi Ravikrishnan, Karthik Raman:
Critical assessment of genome-scale metabolic networks: the need for a unified standard. 1057-1068 - Robert Hoehndorf, Paul N. Schofield, Georgios V. Gkoutos:
The role of ontologies in biological and biomedical research: a functional perspective. 1069-1080
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