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ORCIDBioinformatics, Volume 33
Volume 33, Number 1, January 2017
Genome Analysis
- Wei Yang, Saurabh Sinha:
A novel method for predicting activity of cis-regulatory modules, based on a diverse training set. 1-7
- Rafael Rosales, Rodrigo D. Drummond, Renan Valieris, Emmanuel Dias-Neto, Israel T. da Silva:
signeR: an empirical Bayesian approach to mutational signature discovery. 8-16 - Sandra L. Taylor
, L. Renee Ruhaak, Robert H. Weiss, Karen Kelly, Kyoungmi Kim:
Multivariate two-part statistics for analysis of correlated mass spectrometry data from multiple biological specimens. 17-25
- Can Kockan, Faraz Hach, Iman Sarrafi, Robert H. Bell, Brian McConeghy, Kevin Beja, Anne Haegert, Alexander W. Wyatt, Stanislav Volik, Kim N. Chi, Colin C. Collins, Süleyman Cenk Sahinalp:
SiNVICT: ultra-sensitive detection of single nucleotide variants and indels in circulating tumour DNA. 26-34 - Bin Liu, Shanyi Wang, Ren Long, Kuo-Chen Chou:
iRSpot-EL: identify recombination spots with an ensemble learning approach. 35-41 - Akinori Awazu:
Prediction of nucleosome positioning by the incorporation of frequencies and distributions of three different nucleotide segment lengths into a general pseudo k-tuple nucleotide composition. 42-48 - Matei David, L. J. Dursi, Delia Yao, Paul C. Boutros, Jared T. Simpson:
Nanocall: an open source basecaller for Oxford Nanopore sequencing data. 49-55
- Lazaros Mavridis, Robert W. Janes:
PDB2CD: a web-based application for the generation of circular dichroism spectra from protein atomic coordinates. 56-63
- Il-Youp Kwak, Wei Pan:
Gene- and pathway-based association tests for multiple traits with GWAS summary statistics. 64-71 - Verena Heinrich, Tom Kamphans, Stefan Mundlos, Peter N. Robinson, Peter M. Krawitz:
A likelihood ratio-based method to predict exact pedigrees for complex families from next-generation sequencing data. 72-78 - Jie Zheng, Santiago Rodríguez, Charles Laurin, Denis Baird, Lea Trela-Larsen, Mesut A. Erzurumluoglu, Yi Zheng, Jon White, Claudia Giambartolomei, Delilah Zabaneh, Richard Morris, Meena Kumari, Juan P. Casas, Aroon D. Hingorani, David M. Evans, Tom R. Gaunt, Ian N. M. Day:
HAPRAP: a haplotype-based iterative method for statistical fine mapping using GWAS summary statistics. 79-86
- Minsuk Kim, Gwanggyu Sun, Dong-Yup Lee, Byung-Gee Kim:
BeReTa: a systematic method for identifying target transcriptional regulators to enhance microbial production of chemicals. 87-94 - Igor Marín de Mas, Eric Fanchon, Balázs Papp, Susana G. Kalko, Josep Roca, Marta Cascante:
Molecular mechanisms underlying COPD-muscle dysfunction unveiled through a systems medicine approach. 95-103 - Victor Jaravine, Silke Raffegerst, Dolores J. Schendel, Dmitrij Frishman:
Assessment of cancer and virus antigens for cross-reactivity in human tissues. 104-111
- Xiaowei Chen, Yajing Hao, Ya Cui, Zhen Fan, Shunmin He, Jianjun Luo, Runsheng Chen:
LncVar: a database of genetic variation associated with long non-coding genes. 112-118
Genome Analysis
- Anuj Gupta, I King Jordan, Lavanya Rishishwar:
stringMLST: a fast k-mer based tool for multilocus sequence typing. 119-121
- Yongchun Zuo, Yuan Li, Yingli Chen, Guangpeng Li, Zhenhe Yan, Lei Yang:
PseKRAAC: a flexible web server for generating pseudo K-tuple reduced amino acids composition. 122-124
- M. Stanley Fujimoto, Anton Suvorov, Nicholas O. Jensen, Mark J. Clement, Quinn Snell, Seth M. Bybee:
The OGCleaner: filtering false-positive homology clusters. 125-127 - Marta Nascimento, Adriano Sousa, Mário Ramirez, Alexandre P. Francisco, João A. Carriço, Cátia Vaz:
PHYLOViZ 2.0: providing scalable data integration and visualization for multiple phylogenetic inference methods. 128-129 - Michael R. McKain, Ryan H. Hartsock, Molly M. Wohl, Elizabeth A. Kellogg:
Verdant: automated annotation, alignment and phylogenetic analysis of whole chloroplast genomes. 130-132
- Sébastien Buchoux:
FATSLiM: a fast and robust software to analyze MD simulations of membranes. 133-134
- Samuel Wieczorek, Florence Combes, Cosmin Lazar, Quentin Giai Gianetto, Laurent Gatto, Alexia Dorffer, Anne-Marie Hesse, Yohann Couté, Myriam Ferro, Christophe Bruley, Thomas Burger:
DAPAR & ProStaR: software to perform statistical analyses in quantitative discovery proteomics. 135-136 - Ilias Georgakopoulos-Soares, Naman Jain, Jesse M. Gray, Martin Hemberg:
MPRAnator: a web-based tool for the design of massively parallel reporter assay experiments. 137-138 - Yi Zhong, Theofanis Karaletsos, Philipp Drewe, Vipin T. Sreedharan, David Kuo, Kamini Singh, Hans-Guido Wendel, Gunnar Rätsch:
RiboDiff: detecting changes of mRNA translation efficiency from ribosome footprints. 139-141
- Rudy Arthur, Ole Schulz-Trieglaff, Anthony J. Cox, Jared O'Connell:
AKT: ancestry and kinship toolkit. 142-144
- Takaya Saito, Marc Rehmsmeier:
Precrec: fast and accurate precision-recall and ROC curve calculations in R. 145-147
- Carlo Ravagli, Francois Pognan, Philippe Marc:
OntoBrowser: a collaborative tool for curation of ontologies by subject matter experts. 148-149
- Charlotte Siska, Russell Bowler, Katerina J. Kechris:
The discordant method: a novel approach for differential correlation. 150
Volume 33, Number 2, January 2017
Sequence Analysis
- Ahmed Arslan, Vera van Noort:
Evolutionary conservation of Ebola virus proteins predicts important functions at residue level. 151-154
Genome Analysis
- Niko Popitsch, WGS500 Consortium, Anna Schuh, Jenny C. Taylor:
ReliableGenome: annotation of genomic regions with high/low variant calling concordance. 155-160 - Xiao Wang, Jinghua Gu, Leena Hilakivi-Clarke, Robert Clarke, Jianhua Xuan:
DM-BLD: differential methylation detection using a hierarchical Bayesian model exploiting local dependency. 161-168 - Junwei Luo, Jianxin Wang, Zhen Zhang, Min Li, Fang-Xiang Wu:
BOSS: a novel scaffolding algorithm based on an optimized scaffold graph. 169-176 - Xi Chen, Xu Shi, Leena Hilakivi-Clarke, Ayesha N. Shajahan-Haq, Robert Clarke, Jianhua Xuan:
PSSV: a novel pattern-based probabilistic approach for somatic structural variation identification. 177-183
- Ying Liang, Kunlong Qiu, Bo Liao, Wen Zhu, Xuanlin Huang, Lin Li, Xiangtao Chen, Keqin Li:
Seeksv: an accurate tool for somatic structural variation and virus integration detection. 184-191 - Bo Liu, Yan Gao, Yadong Wang:
LAMSA: fast split read alignment with long approximate matches. 192-201 - Yuki Kato, Tomoya Mori, Kengo Sato, Shingo Maegawa, Hiroshi Hosokawa, Tatsuya Akutsu:
An accessibility-incorporated method for accurate prediction of RNA-RNA interactions from sequence data. 202-209 - Irene Rodríguez-Luján, Jeff Hasty, Ramón Huerta:
FBB: a fast Bayesian-bound tool to calibrate RNA-seq aligners. 210-218
- Michael Altenbuchinger, Thorsten Rehberg, H. U. Zacharias, Frank Stämmler, K. Dettmer, D. Weber, Andreas Hiergeist, A. Gessner, E. Holler, Peter J. Oefner, Rainer Spang:
Reference point insensitive molecular data analysis. 219-226 - Joseph Azofeifa, Robin D. Dowell:
A generative model for the behavior of RNA polymerase. 227-234 - Chunxuan Shao, Thomas Höfer:
Robust classification of single-cell transcriptome data by nonnegative matrix factorization. 235-242
- Wenyu Wang, Jingcan Hao, Shuyu Zheng, Qianrui Fan, Awen He, Yan Wen, Xiong Guo, Cuiyan Wu, Sen Wang, Tielin Yang, Hui Shen, Xiangding Chen, Qing Tian, Lijun Tan, Hong-Wen Deng, Feng Zhang:
Tissue-specific pathway association analysis using genome-wide association study summaries. 243-247 - Gleb Kichaev, Megan Roytman, Ruth Johnson, Eleazar Eskin, Sara Lindström, Peter Kraft, Bogdan Pasaniuc:
Improved methods for multi-trait fine mapping of pleiotropic risk loci. 248-255
- Yan Yan, Shangzhao Qiu, Zhuxuan Jin, Sihong Gong, Yun Bai, Jianwei Lu, Tianwei Yu:
Detecting subnetwork-level dynamic correlations. 256-265
- Muhammad Shoaib, Adnan Ahmad Ansari, Sung-Min Ahn:
cMapper: gene-centric connectivity mapper for EBI-RDF platform. 266-271 - Jie Zheng, Mesut A. Erzurumluoglu, Benjamin L. Elsworth, John P. Kemp, Laurence J. Howe, Philip C. Haycock, Gibran Hemani, Katherine Tansey, Charles Laurin, Early Genetics, Lifecourse Epidemiology (EAGLE) Eczema Consortium, Beate St. Pourcain, Nicole M. Warrington, Hilary K. Finucane, Alkes L. Price, Brendan K. Bulik-Sullivan, Verneri Anttila, Lavinia Paternoster, Tom R. Gaunt, David M. Evans, Benjamin M. Neale:
LD Hub: a centralized database and web interface to perform LD score regression that maximizes the potential of summary level GWAS data for SNP heritability and genetic correlation analysis. 272-279
Genome Analysis
- Sergii Ivakhno, Camilla Colombo, Stephen Tanner, Philip Tedder, Stefano Berri, Anthony J. Cox:
tHapMix: simulating tumour samples through haplotype mixtures. 280-282 - Val F. Lanza, Fernando Baquero, Fernando de la Cruz, Teresa M. Coque:
AcCNET (Accessory Genome Constellation Network): comparative genomics software for accessory genome analysis using bipartite networks. 283-285
- Jeongbin Park, Kayeong Lim, Jin-Soo Kim, Sangsu Bae:
Cas-analyzer: an online tool for assessing genome editing results using NGS data. 286-288 - Vladimir Perovic, Neven Sumonja, Branislava Gemovic, Eneda Toska, Stefan G. Roberts, Nevena Veljkovic:
TRI_tool: a web-tool for prediction of protein-protein interactions in human transcriptional regulation. 289-291 - Aaron M. Rosenfeld, Wenzhao Meng, Eline T. Luning Prak, Uri Hershberg:
ImmuneDB: a system for the analysis and exploration of high-throughput adaptive immune receptor sequencing data. 292-293
- Rasool Tahmasbi, Matthew C. Keller:
GeneEvolve: a fast and memory efficient forward-time simulator of realistic whole-genome sequence and SNP data. 294-296
- Hasan Baig, Jan Madsen:
D-VASim: an interactive virtual laboratory environment for the simulation and analysis of genetic circuits. 297-299
- Ruggero Ferrazza, Julian L. Griffin, Graziano Guella, Pietro Franceschi:
IsotopicLabelling: an R package for the analysis of MS isotopic patterns of labelled analytes. 300-302 - Max Klein, Rati Sharma, Christopher Herrick Bohrer, Cameron M. Avelis, Elijah Roberts:
Biospark: scalable analysis of large numerical datasets from biological simulations and experiments using Hadoop and Spark. 303-305
- Matthew Norris, Chun Kit Kwok, Jitender Cheema, Matthew Hartley, Richard J. Morris, Sharon Aviran, Yiliang Ding:
FoldAtlas: a repository for genome-wide RNA structure probing data. 306-308
Databases and Ontologies
- Andy L. Olivares, Miguel Ángel González Ballester, Jérôme Noailly:
Virtual exploration of early stage atherosclerosis. 309
Volume 33, Number 3, February 2017
Genome Analysis
- Alden King-Yung Leung, Tsz-Piu Kwok, Raymond Wan, Ming Xiao, Pui-Yan Kwok, Kevin Y. Yip, Ting-Fung Chan:
OMBlast: alignment tool for optical mapping using a seed-and-extend approach. 311-319 - Serge Moulin, Nicolas Seux, Stéphane Chrétien, Christophe Guyeux, Emmanuelle Lerat:
Simulation-based estimation of branching models for LTR retrotransposons. 320-326 - Sufang Wang, Michael Gribskov:
Comprehensive evaluation of de novo transcriptome assembly programs and their effects on differential gene expression analysis. 327-333
- Ilham A. Shahmuradov, Rozaimi Mohamad Razali, Salim Bougouffa, Aleksandar Radovanovic, Vladimir B. Bajic:
bTSSfinder: a novel tool for the prediction of promoters in cyanobacteria and Escherichia coli. 334-340 - Xiang Cheng, Shu-Guang Zhao, Xuan Xiao, Kuo-Chen Chou:
iATC-mISF: a multi-label classifier for predicting the classes of anatomical therapeutic chemicals. 341-346 - Castrense Savojardo, Pier Luigi Martelli, Piero Fariselli, Rita Casadio:
SChloro: directing Viridiplantae proteins to six chloroplastic sub-compartments. 347-353
- Iakov I. Davydov, Marc Robinson-Rechavi, Nicolas Salamin:
State aggregation for fast likelihood computations in molecular evolution. 354-362
- Shuaibing He, Manman Li, Xiaotong Ye, Hongyu Wang, Wenkang Yu, Wenjing He, Yun Wang, Yanjiang Qiao:
Site of metabolism prediction for oxidation reactions mediated by oxidoreductases based on chemical bond. 363-372 - Saulo Henrique Pires de Oliveira, Jiye Shi, Charlotte M. Deane:
Comparing co-evolution methods and their application to template-free protein structure prediction. 373-381 - Christopher L. Barrett, Fenix W. D. Huang, Christian M. Reidys:
Sequence-structure relations of biopolymers. 382-389 - Dmytro Guzenko, Sergei V. Strelkov:
Granular clustering of de novo protein models. 390-396
- Roman Hornung, David Causeur, Christoph Bernau, Anne-Laure Boulesteix:
Improving cross-study prediction through addon batch effect adjustment or addon normalization. 397-404
- Lili Liu, Zijun Zhang, Taotao Sheng, Ming Chen:
DEF: an automated dead-end filling approach based on quasi-endosymbiosis. 405-413 - Monther Alhamdoosh, Milica Ng, Nicholas J. Wilson, Julie M. Sheridan, Huy Huynh, Michael J. Wilson, Matthew E. Ritchie:
Combining multiple tools outperforms individual methods in gene set enrichment analyses. 414-424
Genome Analysis
- Stefan Canzar, Karlynn E. Neu, Qingming Tang, Patrick C. Wilson, Aly A. Khan:
BASIC: BCR assembly from single cells. 425-427 - Phuc-Loi Luu, Daniela Gerovska, Mikel Arrospide-Elgarresta, Sugoi Retegi-Carrión, Hans R. Schöler, Marcos J. Araúzo-Bravo:
P3BSseq: parallel processing pipeline software for automatic analysis of bisulfite sequencing data. 428-431 - Ekaterina A. Khramtsova, Barbara E. Stranger:
Assocplots: a Python package for static and interactive visualization of multiple-group GWAS results. 432-434
- Vojtech Bystrý, Tomas Reigl, Adam Krejci, Martin Demko, Barbora Hanakova, Andrea Grioni, Henrik Knecht, Max Schlitt, Peter Dreger, Leopold Sellner, Dietrich Herrmann, Marine Pingeon, Myriam Boudjoghra, Jos Rijntjes, Christiane Pott, Anton W. Langerak, Patricia J. T. A. Groenen, Frederic Davi, Monika Brüggemann, Nikos Darzentas, EuroClonality-NGS:
ARResT/Interrogate: an interactive immunoprofiler for IG/TR NGS data. 435-437
- Xingjian Xu, Zhaohua Ji, Zhang Zhang:
CloudPhylo: a fast and scalable tool for phylogeny reconstruction. 438-440
- Krishna Choudhary, Luyao Ruan, Fei Deng, Nathan P. Shih, Sharon Aviran:
SEQualyzer: interactive tool for quality control and exploratory analysis of high-throughput RNA structural profiling data. 441-443 - Giacomo Janson, Chengxin Zhang, Maria Giulia Prado, Alessandro Paiardini:
PyMod 2.0: improvements in protein sequence-structure analysis and homology modeling within PyMOL. 444-446
- Jonathan W. Nelson, Jiri Sklenar, Anthony P. Barnes, Jessica Minnier:
The START App: a web-based RNAseq analysis and visualization resource. 447-449 - Yu Zhang, Juan Xie, Jinyu Yang, Anne Fennell, Chi Zhang, Qin Ma:
QUBIC: a bioconductor package for qualitative biclustering analysis of gene co-expression data. 450-452 - Luca Bianco, Samantha Riccadonna, Enrico Lavezzo, Marco Falda, Elide Formentin, Duccio Cavalieri, Stefano Toppo, Paolo Fontana:
Pathway Inspector: a pathway based web application for RNAseq analysis of model and non-model organisms. 453-455 - Elisa Salviato, Vera Djordjilovic, Monica Chiogna, Chiara Romualdi:
simPATHy: a new method for simulating data from perturbed biological PATHways. 456-457
- Wei Lan, Min Li, Kaijie Zhao, Jin Liu, Fang-Xiang Wu, Yi Pan, Jianxin Wang:
LDAP: a web server for lncRNA-disease association prediction. 458-460
- Thomas Van Parys, Ine Melckenbeeck, Maarten Houbraken, Pieter Audenaert, Didier Colle, Mario Pickavet, Piet Demeester, Yves Van de Peer:
A Cytoscape app for motif enumeration with ISMAGS. 461-463 - Daniel P. Russo, Marlene T. Kim, Wenyi Wang, Daniel Pinolini, Sunil M. Shende, Judy Strickland, Thomas Hartung, Hao Zhu:
CIIPro: a new read-across portal to fill data gaps using public large-scale chemical and biological data. 464-466
- Zhi-Yong Liang, Hong-Yan Lai, Huan Yang, Chang-Jian Zhang, Hui Yang, Huan-Huan Wei, Xin-Xin Chen, Ya-Wei Zhao, Zhen-Dong Su, Wen-Chao Li, En-Ze Deng, Hua Tang, Wei Chen, Hao Lin:
Pro54DB: a database for experimentally verified sigma-54 promoters. 467-469
Databases and Ontologies
- Dalia Cohn-Alperovich, Alona Rabner, Ilona Kifer, Yael Mandel-Gutfreund, Zohar Yakhini:
Mutual enrichment in aggregated ranked lists with applications to gene expression regulation. 470
Volume 33, Number 4, February 2017
Genome Analysis
- João Fadista, Nikolay Oskolkov, Ola Hansson, Leif Groop:
LoFtool: a gene intolerance score based on loss-of-function variants in 60 706 individuals. 471-474 - Roye Rozov, Aya Brown Kav, David Bogumil, Naama Shterzer, Eran Halperin, Itzhak Mizrahi, Ron Shamir:
Recycler: an algorithm for detecting plasmids from de novo assembly graphs. 475-482 - Hai Yang, Qiang Wei, Xue Zhong, Hushan Yang, Bingshan Li:
Cancer driver gene discovery through an integrative genomics approach in a non-parametric Bayesian framework. 483-490 - Toby Dylan Hocking, Patricia Goerner-Potvin, Andreanne Morin, Xiaojian Shao, Tomi Pastinen, Guillaume Bourque:
Optimizing ChIP-seq peak detectors using visual labels and supervised machine learning. 491-499 - Wei Jiang, Weichuan Yu:
Controlling the joint local false discovery rate is more powerful than meta-analysis methods in joint analysis of summary statistics from multiple genome-wide association studies. 500-507
- Heydar Maboudi Afkham, Xuanbin Qiu, Matthew The, Lukas Käll:
Uncertainty estimation of predictions of peptides' chromatographic retention times in shotgun proteomics. 508-513 - Janne H. Korhonen, Kimmo Palin, Jussi Taipale, Esko Ukkonen:
Fast motif matching revisited: high-order PWMs, SNPs and indels. 514-521
- Weizhuang Zhou, Lichy Han, Russ B. Altman:
Imputing gene expression to maximize platform compatibility. 522-528
- Raphael Petegrosso, Sunho Park, TaeHyun Hwang, Rui Kuang:
Transfer learning across ontologies for phenome-genome association prediction. 529-536 - Ferhat Alkan, Cesim Erten:
RedNemo: topology-based PPI network reconstruction via repeated diffusion with neighborhood modifications. 537-544
Genome Analysis
- Fabian Grandke, Rod Snowdon, Birgit Samans:
gsrc: an R package for genome structure rearrangement calling. 545-546 - Emanuel Diego S. Penha, Egiebade Iriabho, Alex Dussaq, Diana Magalhaes de Oliveira, Jonas S. Almeida:
Isomorphic semantic mapping of variant call format (VCF2RDF). 547-548 - Diogo Almeida, Ida Skov, Artur Silva, Fabio Vandin, Qihua Tan, Richard Röttger, Jan Baumbach:
Efficient detection of differentially methylated regions using DiMmeR. 549-551 - Blake L. Joyce, Asher Haug-Baltzell, Sean Davey, Matthew Bomhoff, James C. Schnable, Eric Lyons:
FractBias: a graphical tool for assessing fractionation bias following polyploidy. 552-554 - Jin Zhang, Elaine R. Mardis, Christopher A. Maher:
INTEGRATE-neo: a pipeline for personalized gene fusion neoantigen discovery. 555-557 - Jean-Philippe Fortin, Timothy Triche, Kasper D. Hansen:
Preprocessing, normalization and integration of the Illumina HumanMethylationEPIC array with minfi. 558-560 - David C. Qian, Jonathan A. Busam, Xiangjun Xiao, Tracy A. O'Mara, Rosalind A. Eeles, Frederick R. Schumacher, Catherine M. Phelan, Christopher I. Amos:
seXY: a tool for sex inference from genotype arrays. 561-563
- Diego J. Zea, Diego Anfossi, Morten Nielsen, Cristina Marino Buslje:
MIToS.jl: mutual information tools for protein sequence analysis in the Julia language. 564-565 - Ankeeta Shah, Yingzhi Qian, Sebastien M. Weyn-Vanhentenryck, Chaolin Zhang:
CLIP Tool Kit (CTK): a flexible and robust pipeline to analyze CLIP sequencing data. 566-567 - Jaroslaw Surkont, Yoan Diekmann, José B. Pereira-Leal:
Rabifier2: an improved bioinformatic classifier of Rab GTPases. 568-570 - Ahmed Arslan, Vera van Noort:
yMap: an automated method to map yeast variants to protein modifications and functional regions. 571-573 - Daniel Mapleson, Gonzalo Garcia Accinelli, George Kettleborough, Jonathan Wright, Bernardo J. Clavijo:
KAT: a K-mer analysis toolkit to quality control NGS datasets and genome assemblies. 574-576 - Gabriel Renaud, Kristian Hanghøj, Eske Willerslev, Ludovic Orlando:
gargammel: a sequence simulator for ancient DNA. 577-579 - Ralf Eggeling, Ivo Grosse, Jan Grau:
InMoDe: tools for learning and visualizing intra-motif dependencies of DNA binding sites. 580-582