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Bioinformatics, Volume 34
Volume 34, Number 1, January 2018
Genome Analysis
- Karolina Elzbieta Kaczor-Urbanowicz
, Yong Kim, Feng Li
, Timur Galeev, Robert R. Kitchen, Mark Gerstein, Kikuye Koyano, Sung-Hee Jeong, Xiaoyan Wang, David Elashoff, So Young Kang, Su Mi Kim, Kyoung Kim, Sung Kim, David Chia, Xinshu Xiao
, Joel S. Rozowsky, David T. W. Wong:
Novel approaches for bioinformatic analysis of salivary RNA sequencing data for development. 1-8 - Sha Joe Zhu
, Jacob Almagro-Garcia, Gil McVean:
Deconvolution of multiple infections in Plasmodium falciparum from high throughput sequencing data. 9-15 - Brian J. Mendoza, Cong T. Trinh
:
Enhanced guide-RNA design and targeting analysis for precise CRISPR genome editing of single and consortia of industrially relevant and non-model organisms. 16-23
- Ergude Bao, Chang-Jin Song, Lingxiao Lan:
ReMILO: reference assisted misassembly detection algorithm using short and long reads. 24-32 - Bin Liu, Fan Yang, De-Shuang Huang, Kuo-Chen Chou:
iPromoter-2L: a two-layer predictor for identifying promoters and their types by multi-window-based PseKNC. 33-40
- Konrad Krawczyk
, Samuel Demharter
, Bernhard Knapp, Charlotte M. Deane
, Peter Minary:
In silico structural modeling of multiple epigenetic marks on DNA. 41-48 - Brian Jiménez-García
, Jorge Roel-Touris, Miguel Romero-Durana
, Miquel Vidal
, Daniel Jiménez-González
, Juan Fernández-Recio:
LightDock: a new multi-scale approach to protein-protein docking. 49-55
- Xu Shi
, Xiao Wang, Tian-Li Wang, Leena Hilakivi-Clarke, Robert Clarke
, Jianhua Xuan
:
SparseIso: a novel Bayesian approach to identify alternatively spliced isoforms from RNA-seq data. 56-63
- Andrew Elliott
, Elizabeth Leicht, Alan Whitmore, Gesine Reinert
, Felix Reed-Tsochas:
A nonparametric significance test for sampled networks. 64-71
- Lewis H. Mervin
, Krishna C. Bulusu
, Leen Kalash, Avid M. Afzal, Fredrik Svensson, Mike A. Firth, Ian P. Barrett, Ola Engkvist
, Andreas Bender:
Orthologue chemical space and its influence on target prediction. 72-79 - Chih-Hsuan Wei
, Lon Phan, Juliana Feltz, Rama Maiti, Tim Hefferon, Zhiyong Lu:
tmVar 2.0: integrating genomic variant information from literature with dbSNP and ClinVar for precision medicine. 80-87
- Elco Bakker, Peter S. Swain
, Matthew M. Crane
:
Morphologically constrained and data informed cell segmentation of budding yeast. 88-96 - Carlo Biffi
, Antonio de Marvao
, Mark I Attard, Timothy J. W. Dawes, Nicola Whiffin, Wenjia Bai, Wenzhe Shi, Catherine Francis
, Hannah Meyer
, Rachel J. Buchan
, Stuart A. Cook, Daniel Rueckert, Declan P. O'Regan
:
Three-dimensional cardiovascular imaging-genetics: a mass univariate framework. 97-103
Genome Analysis
- Laura Seaman
, Indika Rajapakse:
4D nucleome Analysis Toolbox: analysis of Hi-C data with abnormal karyotype and time series capabilities. 104-106 - Jochen Singer, Hans-Joachim Ruscheweyh, Ariane L. Hofmann, Thomas Thurnherr, Franziska Singer
, Nora C. Toussaint
, Charlotte K. Y. Ng
, Salvatore Piscuoglio
, Christian Beisel
, Gerhard Christofori, Reinhard Dummer, Michael N. Hall
, Wilhelm Krek, Mitchell P. Levesque, Markus G. Manz
, Holger Moch, Andreas Papassotiropoulos
, Daniel J. Stekhoven
, Peter Wild, Thomas Wüst, Bernd Rinn, Niko Beerenwinkel:
NGS-pipe: a flexible, easily extendable and highly configurable framework for NGS analysis. 107-108 - Kun-Tze Chen, Chia-Liang Liu, Shang-Hao Huang, Hsin-Ting Shen, Yi-Kung Shieh, Hsien-Tai Chiu, Chin Lung Lu:
CSAR: a contig scaffolding tool using algebraic rearrangements. 109-111 - Nils Ternès, Federico Rotolo
, Stefan Michiels
:
biospear: an R package for biomarker selection in penalized Cox regression. 112-113
- Christopher Wilks, Phani Gaddipati
, Abhinav Nellore
, Ben Langmead
:
Snaptron: querying splicing patterns across tens of thousands of RNA-seq samples. 114-116 - Houxiang Zhu, Emily Richmond, Chun Liang:
CRISPR-RT: a web application for designing CRISPR-C2c2 crRNA with improved target specificity. 117-119
- Yuri Binev, Daniela Peixoto
, Florbela Pereira
, Ian Rodrigues, Sofia Cavaco
, Ana M. Lobo
, João Aires-de-Sousa
:
NavMol 3.0: enabling the representation of metabolic reactions by blind users. 120-121 - Damiano Piovesan
, Silvio C. E. Tosatto
:
Mobi 2.0: an improved method to define intrinsic disorder, mobility and linear binding regions in protein structures. 122-123
- Carl D. Christensen, Jan-Hendrik S. Hofmeyr, Johann M. Rohwer
:
PySCeSToolbox: a collection of metabolic pathway analysis tools. 124-125 - Sara Brin Rosenthal
, Julia Len, Mikayla Webster, Aaron Gary, Amanda Birmingham, Kathleen M. Fisch
:
Interactive network visualization in Jupyter notebooks: visJS2jupyter. 126-128
- Oded Rimon
, Dana Reichmann
:
Kfits: a software framework for fitting and cleaning outliers in kinetic measurements. 129-130
- Oriol López-Massaguer
, Ferran Sanz
, Manuel Pastor
:
An automated tool for obtaining QSAR-ready series of compounds using semantic web technologies. 131-133
- Rani Arielly
, Yuval Ebenstein:
Irys Extract. 134-136 - Kristoffer Bernhem, Hjalmar Brismar
:
SMLocalizer, a GPU accelerated ImageJ plugin for single molecule localization microscopy. 137-138
Gene expression
- Zhe Sun, Ting Wang
, Ke Deng, Xiao-Feng Wang, Robert Lafyatis, Ying Ding, Ming Hu, Wei Chen:
DIMM-SC: a Dirichlet mixture model for clustering droplet-based single cell transcriptomic data. 139-146
- Roye Rozov, Gil Goldshlager, Eran Halperin, Ron Shamir:
Faucet: streaming de novo assembly graph construction. 147-154
- Vikas Bansal:
An accurate algorithm for the detection of DNA fragments from dilution pool sequencing experiments. 155-162 - Pavel Skums, Alex Zelikovsky
, Rahul Singh, Walker Gussler, Zoya Dimitrova, Sergey Knyazev
, Igor Mandric, Sumathi Ramachandran, David S. Campo
, Deeptanshu Jha, Leonid Bunimovich, Elizabeth Costenbader, Connie Sexton, Siobhán O'Connor, Guo-liang Xia, Yury Khudyakov:
QUENTIN: reconstruction of disease transmissions from viral quasispecies genomic data. 163-170 - Xinan Liu, Ye Yu
, Jinpeng Liu, Corrine F. Elliott
, Chen Qian, Jinze Liu:
A novel data structure to support ultra-fast taxonomic classification of metagenomic sequences with k-mer signatures. 171-178
Sequence Analysis
- Greg Malysa, Mikel Hernaez
, Idoia Ochoa, Milind Rao, Karthik Ganesan
, Tsachy Weissman:
QVZ: lossy compression of quality values. 179
Sequence Analysis
- Zhi-Kai Yang
, Feng Gao:
The systematic analysis of ultraconserved genomic regions in the budding yeast. 180
Volume 34, Number 2, January 2018
Genome Analysis
- Gulce Kale, Erman Ayday, Oznur Tastan
:
A utility maximizing and privacy preserving approach for protecting kinship in genomic databases. 181-189
- Hsin-Nan Lin
, Wen-Lian Hsu:
DART: a fast and accurate RNA-seq mapper with a partitioning strategy. 190-197 - Jun Ding
, Xiaoman Li, Haiyan Hu:
CCmiR: a computational approach for competitive and cooperative microRNA binding prediction. 198-206
- Matteo Tiberti, Alessandro Pandini
, Franca Fraternali
, Arianna Fornili:
In silico identification of rescue sites by double force scanning. 207-214 - Dmytro Guzenko, Sergei V. Strelkov:
CCFold: rapid and accurate prediction of coiled-coil structures and application to modelling intermediate filaments. 215-222 - Thomas C. Northey, Anja Baresic, Andrew C. R. Martin
:
IntPred: a structure-based predictor of protein-protein interaction sites. 223-229 - Jing Yang, Hong-Bin Shen:
MemBrain-contact 2.0: a new two-stage machine learning model for the prediction enhancement of transmembrane protein residue contacts in the full chain. 230-238
- Qiu Xiao
, Jiawei Luo, Cheng Liang, Jie Cai, Pingjian Ding:
A graph regularized non-negative matrix factorization method for identifying microRNA-disease associations. 239-248 - Yiming Kang
, Hien-Haw Liow, Ezekiel J. Maier
, Michael R. Brent
:
NetProphet 2.0: mapping transcription factor networks by exploiting scalable data resources. 249-257 - Nan Papili Gao, S. M. Minhaz Ud-Dean, Olivier Gandrillon, Rudiyanto Gunawan
:
SINCERITIES: inferring gene regulatory networks from time-stamped single cell transcriptional expression profiles. 258-266
- Yingli Zhong, Ping Xuan
, Xiao Wang, Tiangang Zhang, Jianzhong Li, Yong Liu, Weixiong Zhang
:
A non-negative matrix factorization based method for predicting disease-associated miRNAs in miRNA-disease bilayer network. 267-277
- Lei Du, Kefei Liu, Tuo Zhang, Xiaohui Yao, Jingwen Yan, Shannon L. Risacher
, Junwei Han, Lei Guo, Andrew J. Saykin, Li Shen
:
A novel SCCA approach via truncated ℓ1-norm and truncated group lasso for brain imaging genetics. 278-285
Genome Analysis
- Chris Chatzinakos, Donghyung Lee, Bradley Todd Webb
, Vladimir I. Vladimirov, Kenneth S. Kendler, Silviu-Alin Bacanu
:
JEPEGMIX2: improved gene-level joint analysis of eQTLs in cosmopolitan cohorts. 286-288 - Roberto Vera Alvarez
, Shan Li, David Landsman, Ivan Ovcharenko:
SNPDelScore: combining multiple methods to score deleterious effects of noncoding mutations in the human genome. 289-291
- James Hadfield, Nicholas J. Croucher
, Richard J. Goater, Khalil AbuDahab, David M. Aanensen, Simon R. Harris:
Phandango: an interactive viewer for bacterial population genomics. 292-293
- Guillaume Brysbaert
, Kevin Lorgouilloux, Wim F. Vranken
, Marc F. Lensink
:
RINspector: a Cytoscape app for centrality analyses and DynaMine flexibility prediction. 294-296 - Anastasia A. Anashkina
, Yuri Kravatsky
, Eugene N. Kuznetsov
, Alexander A. Makarov, Alexei A. Adzhubei
:
Meta-server for automatic analysis, scoring and ranking of docking models. 297-299
- Christopher J. Green, Matthew R. Gazzara
, Yoseph Barash
:
MAJIQ-SPEL: web-tool to interrogate classical and complex splicing variations from RNA-Seq data. 300-302
- Daniel Boloc
, Natalia Rodríguez
, Patricia Gassó
, Josep F. Abril, Miquel Bernardo
, Amalia Lafuente, Sergi Mas
:
SiNoPsis: Single Nucleotide Polymorphisms selection and promoter profiling. 303-305 - Lisa A. Ouellette
, Robert W. Reid
, Steven G. Blanchard, Cory R. Brouwer:
LinkageMapView - rendering high-resolution linkage and QTL maps. 306-307
- Michael Seifert, Andreas Beyer
:
regNet: an R package for network-based propagation of gene expression alterations. 308-311 - Maxime Chazalviel
, Clément Frainay
, Nathalie Poupin
, Florence Vinson, Benjamin Merlet, Yoann Gloaguen
, Ludovic Cottret
, Fabien Jourdan
:
MetExploreViz: web component for interactive metabolic network visualization. 312-313 - Huey-Eng Chua, Sourav S. Bhowmick
, Jie Zheng:
TROVE: a user-friendly tool for visualizing and analyzing cancer hallmarks in signaling networks. 314-316
- Joe Wandy
, Yunfeng Zhu, Justin J. J. van der Hooft
, Rónán Daly, Michael P. Barrett, Simon Rogers:
Ms2lda.org: web-based topic modelling for substructure discovery in mass spectrometry. 317-318
- Kun-Hsing Yu
, Michael R. Fitzpatrick, Luke Pappas, Warren Chan, Jessica Kung, Michael Snyder:
Omics AnalySIs System for PRecision Oncology (OASISPRO): a web-based omics analysis tool for clinical phenotype prediction. 319-320 - Jonathan Lo, Deric Zhang, Emily Speranza
, Jose A. Negron, John H. Connor
:
HoTResDB: host transcriptional response database for viral hemorrhagic fevers. 321-322
Genome Analysis
- Kristoffer Forslund
, Cécile Pereira, Salvador Capella-Gutiérrez
, Alan W. Sousa da Silva
, Adrian M. Altenhoff
, Jaime Huerta-Cepas
, Matthieu Muffato
, Mateus Patricio
, Klaas Vandepoele
, Ingo Ebersberger, Judith A. Blake, Jesualdo Tomás Fernández-Breis
, The Quest for Orthologs Consortium, Brigitte Boeckmann, Toni Gabaldón, Erik L. L. Sonnhammer, Christophe Dessimoz
, Suzanna Lewis:
Gearing up to handle the mosaic nature of life in the quest for orthologs. 323-329
Genome Analysis
- Xiaoqing Huang, Damian Wójtowicz
, Teresa M. Przytycka
:
Detecting presence of mutational signatures in cancer with confidence. 330-337 - Abhijit Chakraborty, Ferhat Ay
:
Identification of copy number variations and translocations in cancer cells from Hi-C data. 338-345
- Layla Oesper, Simone Dantas, Benjamin J. Raphael
:
Identifying simultaneous rearrangements in cancer genomes. 346-352 - Rebecca Elyanow
, Hsin-Ta Wu, Benjamin J. Raphael
:
Identifying structural variants using linked-read sequencing data. 353-360
Volume 34, Number 3, February 2018
Genome Analysis
- Zhi-Kai Yang, Feng Gao
:
The systematic analysis of ultraconserved genomic regions in the budding yeast. 361-366
- Zeljko Tomljanovic
, Mitesh Patel
, William Shin, Andrea Califano
, Andrew F. Teich
:
ZCCHC17 is a master regulator of synaptic gene expression in Alzheimer's disease. 367-371
Genome Analysis
- Tarmo Äijö
, Christian L. Müller, Richard Bonneau:
Temporal probabilistic modeling of bacterial compositions derived from 16S rRNA sequencing. 372-380 - Weilong Guo
, Ping Zhu
, Matteo Pellegrini
, Michael Q. Zhang, Xiangfeng Wang
, Zhongfu Ni:
CGmapTools improves the precision of heterozygous SNV calls and supports allele-specific methylation detection and visualization in bisulfite-sequencing data. 381-387 - Sun-Ah Kim, Chang-Sung Cho, Suh-Ryung Kim, Shelley B. Bull, Yun Joo Yoo:
A new haplotype block detection method for dense genome sequencing data based on interval graph modeling of clusters of highly correlated SNPs. 388-397 - Wei Tang, Shixiang Wan, Zhen Yang, Andrew E. Teschendorff, Quan Zou
:
Tumor origin detection with tissue-specific miRNA and DNA methylation markers. 398-406
- Paul D. Blischak
, Laura Salter Kubatko, Andrea D. Wolfe:
SNP genotyping and parameter estimation in polyploids using low-coverage sequencing data. 407-415 - Haoyu Cheng
, Ming Wu, Yun Xu:
FMtree: a fast locating algorithm of FM-indexes for genomic data. 416-424 - Tom Paridaens
, Glenn Van Wallendael
, Wesley De Neve, Peter Lambert:
AQUa: an adaptive framework for compression of sequencing quality scores with random access functionality. 425-433 - Evgenii I Olekhnovich
, Artem T. Vasilyev
, Vladimir Ulyantsev
, Elena S. Kostryukova, Alexander V. Tyakht:
MetaCherchant: analyzing genomic context of antibiotic resistance genes in gut microbiota. 434-444
- Marco Necci
, Damiano Piovesan
, Zsuzsanna Dosztányi, Peter Tompa, Silvio C. E. Tosatto
:
A comprehensive assessment of long intrinsic protein disorder from the DisProt database. 445-452 - Yumeng Yan, Sheng-You Huang:
RRDB: a comprehensive and non-redundant benchmark for RNA-RNA docking and scoring. 453-458 - Francesca Nadalin
, Alessandra Carbone
:
Protein-protein interaction specificity is captured by contact preferences and interface composition. 459-468 - Hyun-Ho Kyeong, Yoonjoo Choi
, Hak-Sung Kim:
GradDock: rapid simulation and tailored ranking functions for peptide-MHC Class I docking. 469-476 - Ghazaleh Taherzadeh, Yaoqi Zhou
, Alan Wee-Chung Liew
, Yuedong Yang
:
Structure-based prediction of protein- peptide binding regions using Random Forest. 477-484
- Ghislain Durif
, Laurent Modolo, Jakob Michaelsson, Jeff E. Mold, Sophie Lambert-Lacroix, Franck Picard
:
High dimensional classification with combined adaptive sparse PLS and logistic regression. 485-493
- Claudio Angione
:
Integrating splice-isoform expression into genome-scale models characterizes breast cancer metabolism. 494-501 - Zhengwei Xie
, Tianyu Zhang, Qi Ouyang:
Genome-scale fluxes predicted under the guidance of enzyme abundance using a novel hyper-cube shrink algorithm. 502-510
Genome Analysis
- Mark F. Rogers, Hashem A. Shihab, Matthew E. Mort, David N. Cooper, Tom R. Gaunt
, Colin Campbell:
FATHMM-XF: accurate prediction of pathogenic point mutations via extended features. 511-513 - Fabiano B. Menegidio
, Daniela L. Jabes
, Regina Costa de Oliveira
, Luiz R. Nunes
:
Dugong: a Docker image, based on Ubuntu Linux, focused on reproducibility and replicability for bioinformatics analyses. 514-515 - Sergii Ivakhno, Eric Roller, Camilla Colombo, Philip Tedder, Anthony J. Cox:
Canvas SPW: calling de novo copy number variants in pedigrees. 516-518 - Ho Jang, Hyunju Lee
:
Identification of cancer driver genes in focal genomic aberrations from whole-exome sequencing data. 519-521 - Javier Palarea-Albaladejo
, Kevin McLean, Frank Wright, David G. E. Smith:
MALDIrppa: quality control and robust analysis for mass spectrometry data. 522-523
- María José Nueda
, Jordi Martorell-Marugan
, Cristina Martí
, Sonia Tarazona, Ana Conesa
:
Identification and visualization of differential isoform expression in RNA-seq time series. 524-526
- Anna Okula Basile
, Marta Byrska-Bishop, John R. Wallace, Alex Thomas Frase, Marylyn D. Ritchie:
Novel features and enhancements in BioBin, a tool for the biologically inspired binning and association analysis of rare variants. 527-529
- Mahito Sugiyama
, M. Elisabetta Ghisu, Felipe Llinares-López, Karsten M. Borgwardt
:
graphkernels: R and Python packages for graph comparison. 530-532
- Sergio Picart-Armada
, Wesley K. Thompson, Alfonso Buil, Alexandre Perera-Lluna
:
diffuStats: an R package to compute diffusion-based scores on biological networks. 533-534
- Éva Schád, Erzsébet Fichó
, Rita Pancsa, István Simon
, Zsuzsanna Dosztányi, Bálint Mészáros
:
DIBS: a repository of disordered binding sites mediating interactions with ordered proteins. 535-537
- Virginie Uhlmann
, Carsten Haubold, Fred A. Hamprecht, Michael Unser
:
DiversePathsJ: diverse shortest paths for bioimage analysis. 538-540
Volume 34, Number 4, February 2018
Genome Analysis
- Cristian A. Yones
, Georgina Stegmayer
, Diego H. Milone
:
Genome-wide pre-miRNA discovery from few labeled examples. 541-549 - Hequan Sun, Jia Ding, Mathieu Piednoël, Korbinian Schneeberger:
findGSE: estimating genome size variation within human and Arabidopsis using k-mer frequencies. 550-557 - Shubham Chandak
, Kedar Tatwawadi, Tsachy Weissman:
Compression of genomic sequencing reads via hash-based reordering: algorithm and analysis. 558-567
- Prashant Pandey, Michael A. Bender, Rob Johnson, Rob Patro:
Squeakr: an exact and approximate k-mer counting system. 568-575 - Taikai Takeda, Michiaki Hamada
:
Beyond similarity assessment: selecting the optimal model for sequence alignment via the Factorized Asymptotic Bayesian algorithm. 576-584 - Pierre Pericard
, Yoann Dufresne
, Loïc Couderc, Samuel Blanquart, Hélène Touzet
:
MATAM: reconstruction of phylogenetic marker genes from short sequencing reads in metagenomes. 585-591
- Manuel Alejandro Marín-López
, Joan Planas-Iglesias
, Joaquim Aguirre-Plans
, Jaume Bonet
, Javier García-García, Narcis Fernandez-Fuentes
, Baldo Oliva:
On the mechanisms of protein interactions: predicting their affinity from unbound tertiary structures. 592-598 - Stanislav A. Bondarev, Olga V. Bondareva, Galina A. Zhouravleva, Andrey V. Kajava
:
BetaSerpentine: a bioinformatics tool for reconstruction of amyloid structures. 599-608 - Jasmin Cevost, Cédric Vaillant, Sam Meyer
:
ThreaDNA: predicting DNA mechanics' contribution to sequence selectivity of proteins along whole genomes. 609-616
- Y. X. Rachel Wang
, Ke Liu, Elizabeth Theusch
, Jerome I Rotter, Marisa W. Medina, Michael S. Waterman, Haiyan Huang:
Generalized correlation measure using count statistics for gene expression data with ordered samples. 617-624 - Angela Serra
, Pietro Coretto, Michele Fratello, Roberto Tagliaferri
:
Robust and sparse correlation matrix estimation for the analysis of high-dimensional genomics data. 625-634
- Xiayuan Huang
, Robert C. Elston, Guilherme J. Rosa, John Mayer, Zhan Ye, Terrie E. Kitchner, Murray H. Brilliant, David Page, Scott J. Hebbring
:
Applying family analyses to electronic health records to facilitate genetic research. 635-642 - Jun Chen, Emily King
, Rebecca Deek
, Zhi Wei
, Yue Yu, Diane E. Grill, Karla V. Ballman:
An omnibus test for differential distribution analysis of microbiome sequencing data. 643-651