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Bioinformatics, 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