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Bioinformatics, Volume 35
Volume 35, Number 1, January 2019
Genome Analysis
- Nilotpal Sanyal
, Min-Tzu Lo, Karolina Kauppi
, Srdjan Djurovic
, Ole A. Andreassen, Valen E. Johnson, Chi-Hua Chen:
GWASinlps: non-local prior based iterative SNP selection tool for genome-wide association studies. 1-11
- Nelson Gil
, András Fiser
:
The choice of sequence homologs included in multiple sequence alignments has a dramatic impact on evolutionary conservation analysis. 12-19 - Ehsan Haghshenas, Süleyman Cenk Sahinalp, Faraz Hach
:
lordFAST: sensitive and Fast Alignment Search Tool for LOng noisy Read sequencing Data. 20-27
- Kieran R. Campbell
, Christopher Yau
:
A descriptive marker gene approach to single-cell pseudotime inference. 28-35 - Eleonora Lusito
, Barbara Felice, Giovanni D'Ario, Alessandro Ogier, Francesca Montani
, Pier Paolo Di Fiore, Fabrizio Bianchi
:
Unraveling the role of low-frequency mutated genes in breast cancer. 36-46 - Sumon Ahmed
, Magnus Rattray
, Alexis Boukouvalas:
GrandPrix: scaling up the Bayesian GPLVM for single-cell data. 47-54 - Marjan Farahbod, Paul Pavlidis:
Differential coexpression in human tissues and the confounding effect of mean expression levels. 55-61 - Andrea Rau, Michael Flister, Hallgeir Rui, Paul L. Auer:
Exploring drivers of gene expression in the Cancer Genome Atlas. 62-68
- Christian X. Weichenberger
, Johannes Rainer
, Cristian Pattaro
, Peter P. Pramstaller
, Francisco S. Domingues:
Comparative assessment of different familial aggregation methods in the context of large and unstructured pedigrees. 69-76
- Lei Han, Lei Li
, Feng Wen, Lei Zhong, Tong Zhang, Xiu-Feng Wan:
Graph-guided multi-task sparse learning model: a method for identifying antigenic variants of influenza A(H3N2) virus. 77-87 - Barnali Das
, Abhijeet Rajendra Patil, Pralay Mitra
:
A network-based zoning for parallel whole-cell simulation. 88-94 - Mohammad Sajjad Ghaemi, Daniel B. DiGiulio, Kévin Contrepois, Benjamin J. Callahan
, Thuy T. M. Ngo, Brittany Lee-McMullen, Benoit Lehallier, Anna Robaczewska, David Mcilwain, Yael Rosenberg-Hasson, Ronald J. Wong, Cecele Quaintance, Anthony Culos, Natalie Stanley, Athena Tanada, Amy Tsai
, Dyani Gaudilliere
, Edward Ganio, Xiaoyuan Han, Kazuo Ando
, Leslie McNeil, Martha Tingle, Paul H. Wise, Ivana Maric, Marina Sirota, Tony Wyss-Coray
, Virginia D. Winn
, Maurice L. Druzin
, Ronald Gibbs, Gary L. Darmstadt
, David B. Lewis, Vahid Partovi Nia
, Bruno Agard
, Robert Tibshirani, Garry P. Nolan, Michael P. Snyder
, David A. Relman, Stephen R. Quake, Gary M. Shaw
, David K. Stevenson, Martin S. Angst, Brice Gaudilliere, Nima Aghaeepour:
Multiomics modeling of the immunome, transcriptome, microbiome, proteome and metabolome adaptations during human pregnancy. 95-103 - Fangping Wan
, Lixiang Hong, An Xiao, Tao Jiang
, Jianyang Zeng:
NeoDTI: neural integration of neighbor information from a heterogeneous network for discovering new drug-target interactions. 104-111
- Jianwen Fang:
Tightly integrated genomic and epigenomic data mining using tensor decomposition. 112-118
Genome Analysis
- Jerome Kelleher
, Mike Lin, Carl H. Albach, Ewan Birney
, Robert Davies, Marina Gourtovaia, David Glazer, Cristina Y. González
, David K. Jackson
, Aaron Kemp, John Marshall
, Andrew Nowak, Alexander Senf
, Jaime M. Tovar-Corona, Alexander Vikhorev, Thomas M. Keane
, GA4GH Streaming Task Team:
htsget: a protocol for securely streaming genomic data. 119-121 - Velimir Gayevskiy
, Tony Roscioli, Marcel E. Dinger
, Mark J. Cowley
:
Seave: a comprehensive web platform for storing and interrogating human genomic variation. 122-125 - Zhaohui Gu
, Charles Mullighan:
ShinyCNV: a Shiny/R application to view and annotate DNA copy number variations. 126-129 - André Gohr
, Manuel Irimia
:
Matt: Unix tools for alternative splicing analysis. 130-132 - Sebastian Deorowicz
, Adam Gudys
, Maciej Dlugosz
, Marek Kokot, Agnieszka Danek
:
Kmer-db: instant evolutionary distance estimation. 133-136 - Patrick K. Kimes
, Alejandro Reyes
:
Reproducible and replicable comparisons using SummarizedBenchmark. 137-139 - Marc Chakiachvili
, Sylvain Milanesi, Anne-Muriel Arigon Chifolleau, Vincent Lefort
:
WAVES: a web application for versatile enhanced bioinformatic services. 140-142
- Levent Albayrak, Kamil Khanipov
, George Golovko
, Yuriy Fofanov:
Broom: application for non-redundant storage of high throughput sequencing data. 143-145 - Seyed Morteza Hosseini
, Diogo Pratas
, Armando J. Pinho
:
Cryfa: a secure encryption tool for genomic data. 146-148
- Salvatore Cosentino
, Wataru Iwasaki
:
SonicParanoid: fast, accurate and easy orthology inference. 149-151
- Maciej Antczak
, Marcin Zablocki, Tomasz Zok
, Agnieszka Rybarczyk, Jacek Blazewicz
, Marta Szachniuk
:
RNAvista: a webserver to assess RNA secondary structures with non-canonical base pairs. 152-155
- Jamil Najafov, Ayaz Najafov
:
GECO: gene expression correlation analysis after genetic algorithm-driven deconvolution. 156-159
- Shijia Zhu, Tongqi Qian, Yujin Hoshida, Yuan Shen, Jing Yu, Ke Hao:
GIGSEA: genotype imputed gene set enrichment analysis using GWAS summary level data. 160-163 - Corbin Quick
, Christian Fuchsberger
, Daniel Taliun
, Gonçalo R. Abecasis, Michael Boehnke, Hyun Min Kang:
emeraLD: rapid linkage disequilibrium estimation with massive datasets. 164-166
- Pierre Salvy
, Georgios Fengos, Meriç Ataman
, Thomas Pathier, Keng C. Soh, Vassily Hatzimanikatis:
pyTFA and matTFA: a Python package and a Matlab toolbox for Thermodynamics-based Flux Analysis. 167-169
- Jean-Michel Claverie
, Thi Ngan Ta
:
ACDtool: a web-server for the generic analysis of large data sets of counts. 170-171
- Chuan Jiao
, Pengpeng Yan, Cuihua Xia
, Zhaoming Shen, Zexi Tan, Yanyan Tan, Kangli Wang, Yi Jiang, Lingling Huang, Rujia Dai
, Yu Wei, Yan Xia, Qingtuan Meng, Yanmei Ouyang, Liu Yi, Fangyuan Duan, Jiacheng Dai, Shunan Zhao, Chunyu Liu, Chao Chen
:
BrainEXP: a database featuring with spatiotemporal expression variations and co-expression organizations in human brains. 172-174 - Zeyu Wen, Jiahua He
, Huanyu Tao, Sheng-You Huang:
PepBDB: a comprehensive structural database of biological peptide-protein interactions. 175-177
- Paolo Inglese
, Gonçalo D. S. Correia, Zoltan Takats, Jeremy K. Nicholson
, Robert C. Glen:
SPUTNIK: an R package for filtering of spatially related peaks in mass spectrometry imaging data. 178-180
Volume 35, Number 2, January 2019
Genome Analysis
- Joeri J. Meijsen
, Alexandros Rammos
, Archie Campbell, Caroline Hayward, David J. Porteous, Ian J. Deary
, Riccardo E. Marioni
, Kristin K. Nicodemus:
Using tree-based methods for detection of gene-gene interactions in the presence of a polygenic signal: simulation study with application to educational attainment in the Generation Scotland Cohort Study. 181-188 - Malene Juul
, Tobias Madsen, Qianyun Guo, Johanna Bertl
, Asger Hobolth
, Manolis Kellis, Jakob Skou Pedersen
:
ncdDetect2: improved models of the site-specific mutation rate in cancer and driver detection with robust significance evaluation. 189-199 - Bianca Dumitrascu
, Gregory Darnell
, Julien Ayroles, Barbara E. Engelhardt
:
Statistical tests for detecting variance effects in quantitative trait studies. 200-210 - Chris-André Leimeister, Thomas Dencker, Burkhard Morgenstern:
Accurate multiple alignment of distantly related genome sequences using filtered spaced word matches as anchor points. 211-218 - Yunan Luo
, Yun William Yu, Jianyang Zeng, Bonnie Berger, Jian Peng:
Metagenomic binning through low-density hashing. 219-226
- Sebastian Deorowicz
, Joanna Walczyszyn, Agnieszka Debudaj-Grabysz:
CoMSA: compression of protein multiple sequence alignment files. 227-234
- Yu-Chen Lo, Tianyun Liu, Kari M. Morrissey, Satoko Kakiuchi-Kiyota, Adam R. Johnson, Fabio Broccatelli, Yu Zhong, Amita Joshi, Russ B. Altman
:
Computational analysis of kinase inhibitor selectivity using structural knowledge. 235-242 - Miha Skalic
, Alejandro Varela-Rial
, José Jiménez
, Gerard Martínez-Rosell, Gianni De Fabritiis:
LigVoxel: inpainting binding pockets using 3D-convolutional neural networks. 243-250
- Jiaan Dai, Wei Jiang
, Fengchao Yu
, Weichuan Yu:
Xolik: finding cross-linked peptides with maximum paired scores in linear time. 251-257 - Emmanuel Curis
, Cindie Courtin, Pierre Alexis Geoffroy
, Jean-Louis Laplanche
, Bruno Saubaméa, Cynthia Marie-Claire
:
Determination of sets of covariating gene expression using graph analysis on pairwise expression ratios. 258-265
- Matthias P. Gerstl, Stefan Müller
, Georg Regensburger
, Jürgen Zanghellini
:
Flux tope analysis: studying the coordination of reaction directions in metabolic networks. 266-273 - Clément Frainay
, Sandrine Aros
, Maxime Chazalviel, Thomas Garcia, Florence Vinson, Nicolas Weiss
, Benoit Colsch
, Frédéric Sedel, Dominique Thabut, Christophe Junot, Fabien Jourdan
:
MetaboRank: network-based recommendation system to interpret and enrich metabolomics results. 274-283 - Olivia Eriksson, Alexandra Jauhiainen, Sara Maad Sasane, Andrei Kramer
, Anu G. Nair
, Carolina Sartorius, Jeanette Hellgren Kotaleski
:
Uncertainty quantification, propagation and characterization by Bayesian analysis combined with global sensitivity analysis applied to dynamical intracellular pathway models. 284-292
- Piotr Klukowski
, Mario Schubert
:
Chemical shift-based identification of monosaccharide spin-systems with NMR spectroscopy to complement untargeted glycomics. 293-300 - Etienne Becht
, Yannick Simoni
, Elaine Coustan-Smith, Maximilien Evrard
, Yang Cheng, Lai Guan Ng, Dario Campana, Evan W. Newell
:
Reverse-engineering flow-cytometry gating strategies for phenotypic labelling and high-performance cell sorting. 301-308 - Masashi Tsubaki, Kentaro Tomii
, Jun Sese:
Compound-protein interaction prediction with end-to-end learning of neural networks for graphs and sequences. 309-318
- Renmin Han
, Xiaohua Wan, Lun Li
, Albert F. Lawrence, Peng Yang, Yu Li
, Sheng Wang
, Fei Sun, Zhiyong Liu, Xin Gao, Fa Zhang:
AuTom-dualx: a toolkit for fully automatic fiducial marker-based alignment of dual-axis tilt series with simultaneous reconstruction. 319-328
Genome Analysis
- Pierre Simon Garcia
, Frédéric Jauffrit, Christophe Grangeasse
, Céline Brochier-Armanet
:
GeneSpy, a user-friendly and flexible genomic context visualizer. 329-331
- David Jakubec
, Jirí Vondrásek, Robert D. Finn
:
3DPatch: fast 3D structure visualization with residue conservation. 332-334 - Sebastian Uhrig
, Holger Klein
:
PingPongPro: a tool for the detection of piRNA-mediated transposon-silencing in small RNA-Seq data. 335-336 - James K. Bonfield
, Shane A. McCarthy
, Richard Durbin
:
Crumble: reference free lossy compression of sequence quality values. 337-339
- Dana Wyman
, Ali Mortazavi:
TranscriptClean: variant-aware correction of indels, mismatches and splice junctions in long-read transcripts. 340-342 - Sara B. Linker, Jonathan Y. Hsu, Adela Pfaff, Debha Amatya, Shu-Meng Ko, Sarah Voter, Quinn Wong, Fred H. Gage:
BrainImageR: spatiotemporal gene set analysis referencing the human brain. 343-345
- Soumita Ghosh, Abhik Datta, Kaisen Tan
, Hyungwon Choi
:
SLIDE - a web-based tool for interactive visualization of large-scale - omics data. 346-348
- David R. Damerell, Claire Strain-Damerell
, Sefa Garsot, Stephen P. Joyce, Paul Barrett, Brian D. Marsden:
SATurn: a modular bioinformatics framework for the design of robust maintainable web-based and standalone applications. 349-351
Databases and Ontologies
- Hojjat Naderi-Meshkin
, Xin Lai
, Raheleh Amirkhah
, Julio Vera
, John E. J. Rasko, Ulf Schmitz
:
Exosomal lncRNAs and cancer: connecting the missing links. 352-360
Volume 35, Number 3, February 2019
Systems Biology
- Hua Yu
, Lu Lu, Bingke Jiao, Chengzhi Liang:
Systematic discovery of novel and valuable plant gene modules by large-scale RNA-seq samples. 361-364
Genome Analysis
- Nora von Thenen, Erman Ayday, A. Ercüment Çiçek
:
Re-identification of individuals in genomic data-sharing beacons via allele inference. 365-371
- Luca Parca
, Bruno Ariano
, Andrea Cabibbo, Marco Paoletti, Annalaura Tamburrini, Antonio Palmeri
, Gabriele Ausiello, Manuela Helmer-Citterich
:
Kinome-wide identification of phosphorylation networks in eukaryotic proteomes. 372-379 - Wei Zheng, Qi Mao, Robert J. Genco, Jean Wactawski-Wende
, Michael Buck, Yunpeng Cai
, Yijun Sun:
A parallel computational framework for ultra-large-scale sequence clustering analysis. 380-388 - Xinguo Lu, Xin Qian
, Xing Li, Qiumai Miao, Shaoliang Peng
:
DMCM: a Data-adaptive Mutation Clustering Method to identify cancer-related mutation clusters. 389-397 - Xiang Cheng, Wei-Zhong Lin, Xuan Xiao, Kuo-Chen Chou:
pLoc_bal-mAnimal: predict subcellular localization of animal proteins by balancing training dataset and PseAAC. 398-406 - Harun Mustafa
, Ingo Schilken, Mikhail Karasikov
, Carsten Eickhoff, Gunnar Rätsch
, André Kahles
:
Dynamic compression schemes for graph coloring. 407-414 - Chen Sun
, Paul Medvedev:
Toward fast and accurate SNP genotyping from whole genome sequencing data for bedside diagnostics. 415-420 - Ben Langmead
, Christopher Wilks, Valentin Antonescu, Rone Charles:
Scaling read aligners to hundreds of threads on general-purpose processors. 421-432 - Avdesh Mishra, Pujan Pokhrel, Md. Tamjidul Hoque
:
StackDPPred: a stacking based prediction of DNA-binding protein from sequence. 433-441 - Jeffrey M. Yunes
, Patricia C. Babbitt
:
Effusion: prediction of protein function from sequence similarity networks. 442-451
- Marcin Kowiel, Dariusz Brzezinski
, Przemyslaw J. Porebski, Ivan G. Shabalin
, Mariusz Jaskolski
, Wladek Minor:
Automatic recognition of ligands in electron density by machine learning. 452-461 - Justina Jankauskaite, Brian Jiménez-García
, Justas Dapkunas
, Juan Fernández-Recio
, Iain H. Moal
:
SKEMPI 2.0: an updated benchmark of changes in protein-protein binding energy, kinetics and thermodynamics upon mutation. 462-469 - Rubén Sánchez García, Carlos Oscar Sánchez Sorzano
, José María Carazo, Joan Segura
:
BIPSPI: a method for the prediction of partner-specific protein-protein interfaces. 470-477
- Rasmus Henningsson, Magnus Fontes:
SMSSVD: SubMatrix Selection Singular Value Decomposition. 478-486 - Shiquan Sun
, Jiaqiang Zhu
, Sahar Mozaffari
, Carole Ober
, Mengjie Chen, Xiang Zhou:
Heritability estimation and differential analysis of count data with generalized linear mixed models in genomic sequencing studies. 487-496
- Alberto Valdeolivas
, Laurent Tichit, Claire Navarro, Sophie Perrin
, Gaëlle Odelin
, Nicolas Levy, Pierre Cau, Elisabeth Remy, Anaïs Baudot:
Random walk with restart on multiplex and heterogeneous biological networks. 497-505
- Bruce A. Corliss
, H. Clifton Ray, James T. Patrie, Jennifer Mansour
, Sam Kesting, Janice H. Park, Gustavo K. Rohde, Paul A. Yates, Kevin A. Janes, Shayn M. Peirce
:
CIRCOAST: a statistical hypothesis test for cellular colocalization with network structures. 506-514
Genome Analysis
- Caralyn Reisle, Karen L. Mungall, Caleb Choo, Daniel Paulino, Dustin W. Bleile, Amir Muhammadzadeh, Andrew J. Mungall
, Richard A. Moore, Inna Shlafman, Robin Coope, Stephen Pleasance, Yussanne Ma, Steven J. M. Jones
:
MAVIS: merging, annotation, validation, and illustration of structural variants. 515-517 - Haiming Tang, Robert D. Finn
, Paul D. Thomas
:
TreeGrafter: phylogenetic tree-based annotation of proteins with Gene Ontology terms and other annotations. 518-520
- Hadrien Gourlé
, Oskar Karlsson-Lindsjö
, Juliette Hayer
, Erik Bongcam-Rudloff:
Simulating Illumina metagenomic data with InSilicoSeq. 521-522 - Robert Lanfear
, Miriam Schalamun
, David Kainer
, Weiwen Wang
, Benjamin Schwessinger
:
MinIONQC: fast and simple quality control for MinION sequencing data. 523-525
- Emmanuel Paradis, Klaus Schliep
:
ape 5.0: an environment for modern phylogenetics and evolutionary analyses in R. 526-528
- Zongxiao He, Lu Wang, Andrew Thomas DeWan, Suzanne M. Leal
:
MendelProb: probability and sample size calculations for Mendelian studies of exome and whole genome sequence data. 529-531
- Kieu Trinh Do, David J. N. P. Rasp
, Gabi Kastenmüller
, Karsten Suhre
, Jan Krumsiek:
MoDentify: phenotype-driven module identification in metabolomics networks at different resolutions. 532-534 - Iñigo Apaolaza
, Luis Vitores Valcarcel
, Francisco J. Planes:
gMCS: fast computation of genetic minimal cut sets in large networks. 535-537
- Zainab Noor
, Jemma X. Wu, Dana Pascovici
, Abidali Mohamedali
, Mark P. Molloy
, Mark S. Baker
, Shoba Ranganathan
:
iSwathX: an interactive web-based application for extension of DIA peptide reference libraries. 538-539
Data and Text Mining
- Peter M. Bourke, Geert van Geest, Roeland E. Voorrips, Johannes Jansen, Twan Kranenburg, Arwa Shahin, Richard G. F. Visser, Paul Arens, Marinus J. M. Smulders, Chris Maliepaard:
polymapR - linkage analysis and genetic map construction from F1 populations of outcrossing polyploids. 540
Volume 35, Number 4, February 2019
Sequence Analysis
- Reuben J. Pengelly
, Andrew Collins
:
Linkage disequilibrium maps to guide contig ordering for genome assembly. 541-545
Genome Analysis
- Justin Miller, Brandon D. Pickett
, Perry G. Ridge:
JustOrthologs: a fast, accurate and user-friendly ortholog identification algorithm. 546-552 - Zi Yang, George Michailidis:
Quantifying heterogeneity of expression data based on principal components. 553-559 - Timothy J. Peters, Hugh J. French
, Stephen T. Bradford
, Ruth Pidsley
, Clare Stirzaker, Hilal Varinli, Shalima Nair, Wenjia Qu, Jenny Song, Katherine A. Giles
, Aaron L. Statham, Helen Speirs, Terence P. Speed, Susan J. Clark
:
Evaluation of cross-platform and interlaboratory concordance via consensus modelling of genomic measurements. 560-570 - Jack M. Fu
, Elizabeth J. Leslie, Alan F. Scott, Jeffrey C. Murray, Mary L. Marazita, Terri H. Beaty, Robert B. Scharpf, Ingo Ruczinski:
Detection of de novo copy number deletions from targeted sequencing of trios. 571-578 - Markus Fricke, Ruman Gerst, Bashar Ibrahim
, Michael Niepmann, Manja Marz
:
Global importance of RNA secondary structures in protein-coding sequences. 579-583
- Bansho Masutani, Shinichi Morishita
:
A framework and an algorithm to detect low-abundance DNA by a handy sequencer and a palm-sized computer. 584-592 - Wenying He
, Cangzhi Jia, Quan Zou:
4mCPred: machine learning methods for DNA N4-methylcytosine sites prediction. 593-601
- Jiazhou Chen, Hong Peng, Guoqiang Han, Hongmin Cai
, Jiulun Cai:
HOGMMNC: a higher order graph matching with multiple network constraints model for gene-drug regulatory modules identification. 602-610 - Magdalena E. Strauß
, John E. Reid
, Lorenz Wernisch:
GPseudoRank: a permutation sampler for single cell orderings. 611-618 - Sungwon Jung:
KEDDY: a knowledge-based statistical gene set test method to detect differential functional protein-protein interactions. 619-627
- Miao-Xin Li
, Lin Jiang, Timothy Shin Heng Mak
, Johnny S. H. Kwan, Chao Xue
, Peikai Chen
, Henry Chi-Ming Leung, Liqian Cui, Tao Li
, Pak Chung Sham:
A powerful conditional gene-based association approach implicated functionally important genes for schizophrenia. 628-635
- Beibei Ru, Yin Tong, Jiangwen Zhang:
MR4Cancer: a web server prioritizing master regulators for cancer. 636-642 - Eunji Kim, Ivan Ivanov, Edward R. Dougherty:
Quantifying the notions of canalizing and master genes in a gene regulatory network - a Boolean network modeling perspective. 643-649
- Tatiana Radchenko
, Fabien Fontaine, Luca Morettoni, Ismael Zamora:
WebMetabase: cleavage sites analysis tool for natural and unnatural substrates from diverse data source. 650-655
- Magnus Palmblad
, Anna-Lena Lamprecht
, Jon C. Ison
, Veit Schwämmle
:
Automated workflow composition in mass spectrometry-based proteomics. 656-664 - Richard Wilton
, Sarah J. Wheelan, Alexander S. Szalay
, Steven L. Salzberg:
The Terabase Search Engine: a large-scale relational database of short-read sequences. 665-670
Genome Analysis
- Xiaofei Zhao
:
BinDash, software for fast genome distance estimation on a typical personal laptop. 671-673