Works matching IS 13674803 AND DT 2020 AND VI 36 AND IP 12

Results: 63

Sequoya: multiobjective multiple sequence alignment in Python.

Published in:

Bioinformatics, 2020, v. 36, n. 12, p. 3892, doi. 10.1093/bioinformatics/btaa257

By:

Benítez-Hidalgo, Antonio;
Nebro, Antonio J;
Aldana-Montes, José F

Publication type:

Article

HotSpot3D web server: an integrated resource for mutation analysis in protein 3D structures.

Published in:

Bioinformatics, 2020, v. 36, n. 12, p. 3944, doi. 10.1093/bioinformatics/btaa258

By:

Chen, Shanyu;
He, Xiaoyu;
Li, Ruilin;
Duan, Xiaohong;
Niu, Beifang

Publication type:

Article

alona: a web server for single-cell RNA-seq analysis.

Published in:

Bioinformatics, 2020, v. 36, n. 12, p. 3910, doi. 10.1093/bioinformatics/btaa269

By:

Franzén, Oscar;
Björkegren, Johan L M

Publication type:

Article

GREMA: modelling of emulated gene regulatory networks with confidence levels based on evolutionary intelligence to cope with the underdetermined problem.

Published in:

Bioinformatics, 2020, v. 36, n. 12, p. 3833, doi. 10.1093/bioinformatics/btaa267

By:

Tsai, Ming-Ju;
Wang, Jyun-Rong;
Ho, Shinn-Jang;
Shu, Li-Sun;
Huang, Wen-Lin;
Ho, Shinn-Ying

Publication type:

Article

ShallowHRD: detection of homologous recombination deficiency from shallow whole genome sequencing.

Published in:

Bioinformatics, 2020, v. 36, n. 12, p. 3888, doi. 10.1093/bioinformatics/btaa261

By:

Eeckhoutte, Alexandre;
Houy, Alexandre;
Manié, Elodie;
Reverdy, Manon;
Bièche, Ivan;
Marangoni, Elisabetta;
Goundiam, Oumou;
Vincent-Salomon, Anne;
Stoppa-Lyonnet, Dominique;
Bidard, François-Clément;
Stern, Marc-Henri;
Popova, Tatiana

Publication type:

Article

APAlyzer: a bioinformatics package for analysis of alternative polyadenylation isoforms.

Published in:

Bioinformatics, 2020, v. 36, n. 12, p. 3907, doi. 10.1093/bioinformatics/btaa266

By:

Wang, Ruijia;
Tian, Bin

Publication type:

Article

Vargas: heuristic-free alignment for assessing linear and graph read aligners.

Published in:

Bioinformatics, 2020, v. 36, n. 12, p. 3712, doi. 10.1093/bioinformatics/btaa265

By:

Darby, Charlotte A;
Gaddipati, Ravi;
Schatz, Michael C;
Langmead, Ben

Publication type:

Article

scHLAcount: allele-specific HLA expression from single-cell gene expression data.

Published in:

Bioinformatics, 2020, v. 36, n. 12, p. 3905, doi. 10.1093/bioinformatics/btaa264

By:

Darby, Charlotte A;
Stubbington, Michael J T;
Marks, Patrick J;
Barrio, Álvaro Martínez;
Fiddes, Ian T

Publication type:

Article

yacrd and fpa: upstream tools for long-read genome assembly.

Published in:

Bioinformatics, 2020, v. 36, n. 12, p. 3894, doi. 10.1093/bioinformatics/btaa262

By:

Marijon, Pierre;
Chikhi, Rayan;
Varré, Jean-Stéphane

Publication type:

Article

Advancing PICO element detection in biomedical text via deep neural networks.

Published in:

Bioinformatics, 2020, v. 36, n. 12, p. 3856, doi. 10.1093/bioinformatics/btaa256

By:

Jin, Di;
Szolovits, Peter

Publication type:

Article

TranspoScope: interactive visualization of retrotransposon insertions.

Published in:

Bioinformatics, 2020, v. 36, n. 12, p. 3877, doi. 10.1093/bioinformatics/btaa244

By:

Grivainis, Mark;
Tang, Zuojian;
Fenyö, David

Publication type:

Article

ntJoin: Fast and lightweight assembly-guided scaffolding using minimizer graphs.

Published in:

Bioinformatics, 2020, v. 36, n. 12, p. 3885, doi. 10.1093/bioinformatics/btaa253

By:

Coombe, Lauren;
Nikolić, Vladimir;
Chu, Justin;
Birol, Inanc;
Warren, René L

Publication type:

Article

Phigaro: high-throughput prophage sequence annotation.

Published in:

Bioinformatics, 2020, v. 36, n. 12, p. 3882, doi. 10.1093/bioinformatics/btaa250

By:

Starikova, Elizaveta V;
Tikhonova, Polina O;
Prianichnikov, Nikita A;
Rands, Chris M;
Zdobnov, Evgeny M;
Ilina, Elena N;
Govorun, Vadim M

Publication type:

Article

Serpentine: a flexible 2D binning method for differential Hi-C analysis.

Published in:

Bioinformatics, 2020, v. 36, n. 12, p. 3645, doi. 10.1093/bioinformatics/btaa249

By:

Baudry, Lyam;
Millot, Gaël A;
Thierry, Agnes;
Koszul, Romain;
Scolari, Vittore F

Publication type:

Article

SparkINFERNO: a scalable high-throughput pipeline for inferring molecular mechanisms of non-coding genetic variants.

Published in:

Bioinformatics, 2020, v. 36, n. 12, p. 3879, doi. 10.1093/bioinformatics/btaa246

By:

Kuksa, Pavel P;
Lee, Chien-Yueh;
Amlie-Wolf, Alexandre;
Gangadharan, Prabhakaran;
Mlynarski, Elizabeth E;
Chou, Yi-Fan;
Lin, Han-Jen;
Issen, Heather;
Greenfest-Allen, Emily;
Valladares, Otto;
Leung, Yuk Yee;
Wang, Li-San

Publication type:

Article

Pooled variable scaling for cluster analysis.

Published in:

Bioinformatics, 2020, v. 36, n. 12, p. 3849, doi. 10.1093/bioinformatics/btaa243

By:

Raymaekers, Jakob;
Zamar, Ruben H

Publication type:

Article

MIAMI––a tool for non-targeted detection of metabolic flux changes for mode of action identification.

Published in:

Bioinformatics, 2020, v. 36, n. 12, p. 3925, doi. 10.1093/bioinformatics/btaa251

By:

Dudek, Christian-Alexander;
Reuse, Carsten;
Fuchs, Regine;
Hendriks, Janneke;
Starck, Veronique;
Hiller, Karsten

Publication type:

Article

CScape-somatic: distinguishing driver and passenger point mutations in the cancer genome.

Published in:

Bioinformatics, 2020, v. 36, n. 12, p. 3637, doi. 10.1093/bioinformatics/btaa242

By:

Rogers, Mark F;
Gaunt, Tom R;
Campbell, Colin

Publication type:

Article

CRNT4SBML: a Python package for the detection of bistability in biochemical reaction networks.

Published in:

Bioinformatics, 2020, v. 36, n. 12, p. 3922, doi. 10.1093/bioinformatics/btaa241

By:

Reyes, Brandon C;
Otero-Muras, Irene;
Shuen, Michael T;
Tartakovsky, Alexandre M;
Petyuk, Vladislav A

Publication type:

Article

EnrichrBot: Twitter bot tracking tweets about human genes.

Published in:

Bioinformatics, 2020, v. 36, n. 12, p. 3932, doi. 10.1093/bioinformatics/btaa240

By:

Bartal, Alon;
Lachmann, Alexander;
Clarke, Daniel J B;
Seiden, Allison H;
Jagodnik, Kathleen M;
Ma'ayan, Avi

Publication type:

Article

Blood-based multi-tissue gene expression inference with Bayesian ridge regression.

Published in:

Bioinformatics, 2020, v. 36, n. 12, p. 3788, doi. 10.1093/bioinformatics/btaa239

By:

Xu, Wenjian;
Liu, Xuanshi;
Leng, Fei;
Li, Wei

Publication type:

Article

GlyGen data model and processing workflow.

Published in:

Bioinformatics, 2020, v. 36, n. 12, p. 3941, doi. 10.1093/bioinformatics/btaa238

By:

Kahsay, Robel;
Vora, Jeet;
Navelkar, Rahi;
Mousavi, Reza;
Fochtman, Brian C;
Holmes, Xavier;
Pattabiraman, Nagarajan;
Ranzinger, Rene;
Mahadik, Rupali;
Williamson, Tatiana;
Kulkarni, Sujeet;
Agarwal, Gaurav;
Martin, Maria;
Vasudev, Preethi;
Garcia, Leyla;
Edwards, Nathan;
Zhang, Wenjin;
Natale, Darren A;
Ross, Karen;
Aoki-Kinoshita, Kiyoko F

Publication type:

Article

MONET: a toolbox integrating top-performing methods for network modularization.

Published in:

Bioinformatics, 2020, v. 36, n. 12, p. 3920, doi. 10.1093/bioinformatics/btaa236

By:

Tomasoni, Mattia;
Gómez, Sergio;
Crawford, Jake;
Zhang, Weijia;
Choobdar, Sarvenaz;
Marbach, Daniel;
Bergmann, Sven

Publication type:

Article

MODifieR: an Ensemble R Package for Inference of Disease Modules from Transcriptomics Networks.

Published in:

Bioinformatics, 2020, v. 36, n. 12, p. 3918, doi. 10.1093/bioinformatics/btaa235

By:

Weerd, Hendrik A de;
Badam, Tejaswi V S;
Martínez-Enguita, David;
Åkesson, Julia;
Muthas, Daniel;
Gustafsson, Mika;
Lubovac-Pilav, Zelmina

Publication type:

Article

FASPR: an open-source tool for fast and accurate protein side-chain packing.

Published in:

Bioinformatics, 2020, v. 36, n. 12, p. 3758, doi. 10.1093/bioinformatics/btaa234

By:

Huang, Xiaoqiang;
Pearce, Robin;
Zhang, Yang

Publication type:

Article

gplas: a comprehensive tool for plasmid analysis using short-read graphs.

Published in:

Bioinformatics, 2020, v. 36, n. 12, p. 3874, doi. 10.1093/bioinformatics/btaa233

By:

Arredondo-Alonso, Sergio;
Bootsma, Martin;
Hein, Yaïr;
Rogers, Malbert R C;
Corander, Jukka;
Willems, Rob J L;
Schürch, Anita C

Publication type:

Article

CircMiner: accurate and rapid detection of circular RNA through splice-aware pseudo-alignment scheme.

Published in:

Bioinformatics, 2020, v. 36, n. 12, p. 3703, doi. 10.1093/bioinformatics/btaa232

By:

Asghari, Hossein;
Lin, Yen-Yi;
Xu, Yang;
Haghshenas, Ehsan;
Collins, Colin C;
Hach, Faraz

Publication type:

Article

Joint learning dimension reduction and clustering of single-cell RNA-sequencing data.

Published in:

Bioinformatics, 2020, v. 36, n. 12, p. 3825, doi. 10.1093/bioinformatics/btaa231

By:

Wu, Wenming;
Ma, Xiaoke

Publication type:

Article

Learning transferable deep convolutional neural networks for the classification of bacterial virulence factors.

Published in:

Bioinformatics, 2020, v. 36, n. 12, p. 3693, doi. 10.1093/bioinformatics/btaa230

By:

Zheng, Dandan;
Pang, Guansong;
Liu, Bo;
Chen, Lihong;
Yang, Jian

Publication type:

Article

Prioritizing genetic variants in GWAS with lasso using permutation-assisted tuning.

Published in:

Bioinformatics, 2020, v. 36, n. 12, p. 3811, doi. 10.1093/bioinformatics/btaa229

By:

Yang, Songshan;
Wen, Jiawei;
Eckert, Scott T;
Wang, Yaqun;
Liu, Dajiang J;
Wu, Rongling;
Li, Runze;
Zhan, Xiang

Publication type:

Article

MaveQuest: a web resource for planning experimental tests of human variant effects.

Published in:

Bioinformatics, 2020, v. 36, n. 12, p. 3938, doi. 10.1093/bioinformatics/btaa228

By:

Kuang, Da;
Weile, Jochen;
Li, Roujia;
Ouellette, Tom W;
Barber, Jarry A;
Roth, Frederick P

Publication type:

Article

annonex2embl: automatic preparation of annotated DNA sequences for bulk submissions to ENA.

Published in:

Bioinformatics, 2020, v. 36, n. 12, p. 3841, doi. 10.1093/bioinformatics/btaa209

By:

Gruenstaeudl, Michael

Publication type:

Article

GenMap: ultra-fast computation of genome mappability.

Published in:

Bioinformatics, 2020, v. 36, n. 12, p. 3687, doi. 10.1093/bioinformatics/btaa222

By:

Pockrandt, Christopher;
Alzamel, Mai;
Iliopoulos, Costas S;
Reinert, Knut

Publication type:

Article

T-Gene: improved target gene prediction.

Published in:

Bioinformatics, 2020, v. 36, n. 12, p. 3902, doi. 10.1093/bioinformatics/btaa227

By:

O'Connor, Timothy;
Grant, Charles E;
Bodén, Mikael;
Bailey, Timothy L

Publication type:

Article

ADFinder: accurate detection of programmed DNA elimination using NGS high-throughput sequencing data.

Published in:

Bioinformatics, 2020, v. 36, n. 12, p. 3632, doi. 10.1093/bioinformatics/btaa226

By:

Zheng, Weibo;
Chen, Jing;
Doak, Thomas G;
Song, Weibo;
Yan, Ying

Publication type:

Article

corto: a lightweight R package for gene network inference and master regulator analysis.

Published in:

Bioinformatics, 2020, v. 36, n. 12, p. 3916, doi. 10.1093/bioinformatics/btaa223

By:

Mercatelli, Daniele;
Lopez-Garcia, Gonzalo;
Giorgi, Federico M

Publication type:

Article

QuartataWeb: Integrated Chemical–Protein-Pathway Mapping for Polypharmacology and Chemogenomics.

Published in:

Bioinformatics, 2020, v. 36, n. 12, p. 3935, doi. 10.1093/bioinformatics/btaa210

By:

Li, Hongchun;
Pei, Fen;
Taylor, D Lansing;
Bahar, Ivet

Publication type:

Article

EVICAN—a balanced dataset for algorithm development in cell and nucleus segmentation.

Published in:

Bioinformatics, 2020, v. 36, n. 12, p. 3863, doi. 10.1093/bioinformatics/btaa225

By:

Schwendy, Mischa;
Unger, Ronald E;
Parekh, Sapun H

Publication type:

Article

A parallelized strategy for epistasis analysis based on Empirical Bayesian Elastic Net models.

Published in:

Bioinformatics, 2020, v. 36, n. 12, p. 3803, doi. 10.1093/bioinformatics/btaa216

By:

Wen, Jia;
Ford, Colby T;
Janies, Daniel;
Shi, Xinghua

Publication type:

Article

Annotation of tandem mass spectrometry data using stochastic neural networks in shotgun proteomics.

Published in:

Bioinformatics, 2020, v. 36, n. 12, p. 3781, doi. 10.1093/bioinformatics/btaa206

By:

Sulimov, Pavel;
Voronkova, Anastasia;
Kertész-Farkas, Attila

Publication type:

Article

TwisTranscripT: stochastic simulation of the transcription-supercoiling coupling.

Published in:

Bioinformatics, 2020, v. 36, n. 12, p. 3899, doi. 10.1093/bioinformatics/btaa221

By:

Houdaigui, Bilal El;
Meyer, Sam

Publication type:

Article

Plant 3D (P3D): a plant phenotyping toolkit for 3D point clouds.

Published in:

Bioinformatics, 2020, v. 36, n. 12, p. 3949, doi. 10.1093/bioinformatics/btaa220

By:

Ziamtsov, Illia;
Navlakha, Saket

Publication type:

Article

ScaffoldGraph: an open-source library for the generation and analysis of molecular scaffold networks and scaffold trees.

Published in:

Bioinformatics, 2020, v. 36, n. 12, p. 3930, doi. 10.1093/bioinformatics/btaa219

By:

Scott, Oliver B;
Chan, A W Edith

Publication type:

Article

PolishEM: image enhancement in FIB–SEM.

Published in:

Bioinformatics, 2020, v. 36, n. 12, p. 3947, doi. 10.1093/bioinformatics/btaa218

By:

Fernandez, Jose-Jesus;
Torres, Teobaldo E;
Martin-Solana, Eva;
Goya, Gerardo F;
Fernandez-Fernandez, Maria-Rosario

Publication type:

Article

FUpred: detecting protein domains through deep-learning-based contact map prediction.

Published in:

Bioinformatics, 2020, v. 36, n. 12, p. 3749, doi. 10.1093/bioinformatics/btaa217

By:

Zheng, Wei;
Zhou, Xiaogen;
Wuyun, Qiqige;
Pearce, Robin;
Li, Yang;
Zhang, Yang

Publication type:

Article

CNV-BAC: Copy number Variation Detection in Bacterial Circular Genome.

Published in:

Bioinformatics, 2020, v. 36, n. 12, p. 3890, doi. 10.1093/bioinformatics/btaa208

By:

Wu, Linjie;
Wang, Han;
Xia, Yuchao;
Xi, Ruibin

Publication type:

Article

A knowledge-based scoring function to assess quaternary associations of proteins.

Published in:

Bioinformatics, 2020, v. 36, n. 12, p. 3739, doi. 10.1093/bioinformatics/btaa207

By:

Dhawanjewar, Abhilesh S;
Roy, Ankit A;
Madhusudhan, Mallur S

Publication type:

Article

Gcluster: a simple-to-use tool for visualizing and comparing genome contexts for numerous genomes.

Published in:

Bioinformatics, 2020, v. 36, n. 12, p. 3871, doi. 10.1093/bioinformatics/btaa212

By:

Li, Xiangyang;
Chen, Fang;
Chen, Yunpeng

Publication type:

Article

debCAM: a bioconductor R package for fully unsupervised deconvolution of complex tissues.

Published in:

Bioinformatics, 2020, v. 36, n. 12, p. 3927, doi. 10.1093/bioinformatics/btaa205

By:

Chen, Lulu;
Wu, Chiung-Ting;
Wang, Niya;
Herrington, David M;
Clarke, Robert;
Wang, Yue

Publication type:

Article

Cancer subtype classification and modeling by pathway attention and propagation.

Published in:

Bioinformatics, 2020, v. 36, n. 12, p. 3818, doi. 10.1093/bioinformatics/btaa203

By:

Lee, Sangseon;
Lim, Sangsoo;
Lee, Taeheon;
Sung, Inyoung;
Kim, Sun

Publication type:

Article