Works matching IS 13674803 AND DT 2021 AND VI 37 AND IP 16

Results: 48

Subtype-GAN: a deep learning approach for integrative cancer subtyping of multi-omics data.

Published in:

Bioinformatics, 2021, v. 37, n. 16, p. 2231, doi. 10.1093/bioinformatics/btab109

By:

Yang, Hai;
Chen, Rui;
Li, Dongdong;
Wang, Zhe

Publication type:

Article

ESCO: single cell expression simulation incorporating gene co-expression.

Published in:

Bioinformatics, 2021, v. 37, n. 16, p. 2374, doi. 10.1093/bioinformatics/btab116

By:

Tian, Jinjin;
Wang, Jiebiao;
Roeder, Kathryn

Publication type:

Article

Inferring perturbation profiles of cancer samples.

Published in:

Bioinformatics, 2021, v. 37, n. 16, p. 2441, doi. 10.1093/bioinformatics/btab113

By:

Pirkl, Martin;
Beerenwinkel, Niko

Publication type:

Article

A variable selection approach for highly correlated predictors in high-dimensional genomic data.

Published in:

Bioinformatics, 2021, v. 37, n. 16, p. 2238, doi. 10.1093/bioinformatics/btab114

By:

Zhu, Wencan;
Lévy-Leduc, Céline;
Ternès, Nils

Publication type:

Article

Erratum to: An information-theoretic approach for measuring the distance of organ tissue samples using their transcriptomic signatures.

Published in:

Bioinformatics, 2021, v. 37, n. 16, p. 2512, doi. 10.1093/bioinformatics/btab483

By:

Manatakis, Dimitris V;
VanDevender, Aaron;
Manolakos, Elias S

Publication type:

Article

ELIXIR: providing a sustainable infrastructure for life science data at European scale.

Published in:

Bioinformatics, 2021, v. 37, n. 16, p. 2506, doi. 10.1093/bioinformatics/btab481

By:

Harrow, Jennifer;
Drysdale, Rachel;
Smith, Andrew;
Repo, Susanna;
Lanfear, Jerry;
Blomberg, Niklas

Publication type:

Article

lncLocator 2.0: a cell-line-specific subcellular localization predictor for long non-coding RNAs with interpretable deep learning.

Published in:

Bioinformatics, 2021, v. 37, n. 16, p. 2308, doi. 10.1093/bioinformatics/btab127

By:

Lin, Yang;
Pan, Xiaoyong;
Shen, Hong-Bin

Publication type:

Article

Accurate deep learning off-target prediction with novel sgRNA-DNA sequence encoding in CRISPR-Cas9 gene editing.

Published in:

Bioinformatics, 2021, v. 37, n. 16, p. 2299, doi. 10.1093/bioinformatics/btab112

By:

Charlier, Jeremy;
Nadon, Robert;
Makarenkov, Vladimir

Publication type:

Article

Granger-causal testing for irregularly sampled time series with application to nitrogen signalling in Arabidopsis.

Published in:

Bioinformatics, 2021, v. 37, n. 16, p. 2450, doi. 10.1093/bioinformatics/btab126

By:

Heerah, Sachin;
Molinari, Roberto;
Guerrier, Stéphane;
Marshall-Colon, Amy

Publication type:

Article

Gene-set integrative analysis of multi-omics data using tensor-based association test.

Published in:

Bioinformatics, 2021, v. 37, n. 16, p. 2259, doi. 10.1093/bioinformatics/btab125

By:

Chang, Sheng-Mao;
Yang, Meng;
Lu, Wenbin;
Huang, Yu-Jyun;
Huang, Yueyang;
Hung, Hung;
Miecznikowski, Jeffrey C;
Lu, Tzu-Pin;
Tzeng, Jung-Ying

Publication type:

Article

Tandem repeat interval pattern identifies animal taxa.

Published in:

Bioinformatics, 2021, v. 37, n. 16, p. 2250, doi. 10.1093/bioinformatics/btab124

By:

Bhattacharyya, Balaram;
Mitra, Uddalak;
Bhattacharyya, Ramkishore

Publication type:

Article

Active learning to classify macromolecular structures in situ for less supervision in cryo-electron tomography.

Published in:

Bioinformatics, 2021, v. 37, n. 16, p. 2340, doi. 10.1093/bioinformatics/btab123

By:

Du, Xuefeng;
Wang, Haohan;
Zhu, Zhenxi;
Zeng, Xiangrui;
Chang, Yi-Wei;
Zhang, Jing;
Xing, Eric;
Xu, Min

Publication type:

Article

BloodGen3Module: blood transcriptional module repertoire analysis and visualization using R.

Published in:

Bioinformatics, 2021, v. 37, n. 16, p. 2382, doi. 10.1093/bioinformatics/btab121

By:

Rinchai, Darawan;
Roelands, Jessica;
Toufiq, Mohammed;
Hendrickx, Wouter;
Altman, Matthew C;
Bedognetti, Davide;
Chaussabel, Damien

Publication type:

Article

VoroCNN: deep convolutional neural network built on 3D Voronoi tessellation of protein structures.

Published in:

Bioinformatics, 2021, v. 37, n. 16, p. 2332, doi. 10.1093/bioinformatics/btab118

By:

Igashov, Ilia;
Olechnovič, Kliment;
Kadukova, Maria;
Venclovas, Česlovas;
Grudinin, Sergei

Publication type:

Article

d-PBWT: dynamic positional Burrows–Wheeler transform.

Published in:

Bioinformatics, 2021, v. 37, n. 16, p. 2390, doi. 10.1093/bioinformatics/btab117

By:

Sanaullah, Ahsan;
Zhi, Degui;
Zhang, Shaojie

Publication type:

Article

Graph contextualized attention network for predicting synthetic lethality in human cancers.

Published in:

Bioinformatics, 2021, v. 37, n. 16, p. 2432, doi. 10.1093/bioinformatics/btab110

By:

Long, Yahui;
Wu, Min;
Liu, Yong;
Zheng, Jie;
Kwoh, Chee Keong;
Luo, Jiawei;
Li, Xiaoli

Publication type:

Article

E-MAGMA: an eQTL-informed method to identify risk genes using genome-wide association study summary statistics.

Published in:

Bioinformatics, 2021, v. 37, n. 16, p. 2245, doi. 10.1093/bioinformatics/btab115

By:

Gerring, Zachary F;
Mina-Vargas, Angela;
Gamazon, Eric R;
Derks, Eske M

Publication type:

Article

CuBlock: a cross-platform normalization method for gene-expression microarrays.

Published in:

Bioinformatics, 2021, v. 37, n. 16, p. 2365, doi. 10.1093/bioinformatics/btab105

By:

Junet, Valentin;
Farrés, Judith;
Mas, José M;
Daura, Xavier

Publication type:

Article

Genozip: a universal extensible genomic data compressor.

Published in:

Bioinformatics, 2021, v. 37, n. 16, p. 2225, doi. 10.1093/bioinformatics/btab102

By:

Lan, Divon;
Tobler, Ray;
Souilmi, Yassine;
Llamas, Bastien

Publication type:

Article

PPIT: an R package for inferring microbial taxonomy from nifH sequences.

Published in:

Bioinformatics, 2021, v. 37, n. 16, p. 2289, doi. 10.1093/bioinformatics/btab100

By:

Kapili, Bennett J;
Dekas, Anne E

Publication type:

Article

Inference of gene regulatory networks using pseudo-time series data.

Published in:

Bioinformatics, 2021, v. 37, n. 16, p. 2423, doi. 10.1093/bioinformatics/btab099

By:

Zhang, Yuelei;
Chang, Xiao;
Liu, Xiaoping

Publication type:

Article

NetQuilt: deep multispecies network-based protein function prediction using homology-informed network similarity.

Published in:

Bioinformatics, 2021, v. 37, n. 16, p. 2414, doi. 10.1093/bioinformatics/btab098

By:

Barot, Meet;
Gligorijević, Vladimir;
Cho, Kyunghyun;
Bonneau, Richard

Publication type:

Article

PhyKIT: a broadly applicable UNIX shell toolkit for processing and analyzing phylogenomic data.

Published in:

Bioinformatics, 2021, v. 37, n. 16, p. 2325, doi. 10.1093/bioinformatics/btab096

By:

Steenwyk, Jacob L;
Buida, Thomas J;
Labella, Abigail L;
Li, Yuanning;
Shen, Xing-Xing;
Rokas, Antonis

Publication type:

Article

Differentially conserved amino acid positions may reflect differences in SARS-CoV-2 and SARS-CoV behaviour.

Published in:

Bioinformatics, 2021, v. 37, n. 16, p. 2282, doi. 10.1093/bioinformatics/btab094

By:

Bojkova, Denisa;
McGreig, Jake E;
McLaughlin, Katie-May;
Masterson, Stuart G;
Antczak, Magdalena;
Widera, Marek;
Krähling, Verena;
Ciesek, Sandra;
Wass, Mark N;
Michaelis, Martin;
Cinatl, Jindrich

Publication type:

Article

FASTRAL: improving scalability of phylogenomic analysis.

Published in:

Bioinformatics, 2021, v. 37, n. 16, p. 2317, doi. 10.1093/bioinformatics/btab093

By:

Dibaeinia, Payam;
Tabe-Bordbar, Shayan;
Warnow, Tandy

Publication type:

Article

A novel method for data fusion over entity-relation graphs and its application to protein–protein interaction prediction.

Published in:

Bioinformatics, 2021, v. 37, n. 16, p. 2275, doi. 10.1093/bioinformatics/btab092

By:

Raimondi, Daniele;
Simm, Jaak;
Arany, Adam;
Moreau, Yves

Publication type:

Article

Per-sample standardization and asymmetric winsorization lead to accurate clustering of RNA-seq expression profiles.

Published in:

Bioinformatics, 2021, v. 37, n. 16, p. 2356, doi. 10.1093/bioinformatics/btab091

By:

Risso, Davide;
Pagnotta, Stefano Maria

Publication type:

Article

An OMICs-based meta-analysis to support infection state stratification.

Published in:

Bioinformatics, 2021, v. 37, n. 16, p. 2347, doi. 10.1093/bioinformatics/btab089

By:

Myall, Ashleigh C;
Perkins, Simon;
Rushton, David;
David, Jonathan;
Spencer, Phillippa;
Jones, Andrew R;
Antczak, Philipp

Publication type:

Article

Multi-layered network-based pathway activity inference using directed random walks: application to predicting clinical outcomes in urologic cancer.

Published in:

Bioinformatics, 2021, v. 37, n. 16, p. 2405, doi. 10.1093/bioinformatics/btab086

By:

Kim, So Yeon;
Choe, Eun Kyung;
Shivakumar, Manu;
Kim, Dokyoon;
Sohn, Kyung-Ah

Publication type:

Article

Detecting high-scoring local alignments in pangenome graphs.

Published in:

Bioinformatics, 2021, v. 37, n. 16, p. 2266, doi. 10.1093/bioinformatics/btab077

By:

Schulz, Tizian;
Wittler, Roland;
Rahmann, Sven;
Hach, Faraz;
Stoye, Jens

Publication type:

Article

MEWpy: a computational strain optimization workbench in Python.

Published in:

Bioinformatics, 2021, v. 37, n. 16, p. 2494, doi. 10.1093/bioinformatics/btab013

By:

Pereira, Vítor;
Cruz, Fernando;
Rocha, Miguel

Publication type:

Article

SubtypeDrug: a software package for prioritization of candidate cancer subtype-specific drugs.

Published in:

Bioinformatics, 2021, v. 37, n. 16, p. 2491, doi. 10.1093/bioinformatics/btab011

By:

Han, Xudong;
Kong, Qingfei;
Liu, Chonghui;
Cheng, Liang;
Han, Junwei

Publication type:

Article

ProDerAl: reference position dependent alignment.

Published in:

Bioinformatics, 2021, v. 37, n. 16, p. 2479, doi. 10.1093/bioinformatics/btab008

By:

Crysup, Benjamin;
Budowle, Bruce;
Woerner, August E

Publication type:

Article

clinker & clustermap.js: automatic generation of gene cluster comparison figures.

Published in:

Bioinformatics, 2021, v. 37, n. 16, p. 2473, doi. 10.1093/bioinformatics/btab007

By:

Gilchrist, Cameron L M;
Chooi, Yit-Heng

Publication type:

Article

SWITCHES: Searchable Web Interface for Topologies of CHEmical Switches.

Published in:

Bioinformatics, 2021, v. 37, n. 16, p. 2504, doi. 10.1093/bioinformatics/btab006

By:

HarshaRani, G V;
Moza, S;
Ramakrishnan, N;
Bhalla, U S

Publication type:

Article

MBG: Minimizer-based sparse de Bruijn Graph construction.

Published in:

Bioinformatics, 2021, v. 37, n. 16, p. 2476, doi. 10.1093/bioinformatics/btab004

By:

Rautiainen, Mikko;
Marschall, Tobias

Publication type:

Article

Nebulosa recovers single-cell gene expression signals by kernel density estimation.

Published in:

Bioinformatics, 2021, v. 37, n. 16, p. 2485, doi. 10.1093/bioinformatics/btab003

By:

Alquicira-Hernandez, Jose;
Powell, Joseph E

Publication type:

Article

Bios2cor: an R package integrating dynamic and evolutionary correlations to identify functionally important residues in proteins.

Published in:

Bioinformatics, 2021, v. 37, n. 16, p. 2483, doi. 10.1093/bioinformatics/btab002

By:

Taddese, Bruck;
Garnier, Antoine;
Deniaud, Madeline;
Henrion, Daniel;
Chabbert, Marie

Publication type:

Article

FinaleDB: a browser and database of cell-free DNA fragmentation patterns.

Published in:

Bioinformatics, 2021, v. 37, n. 16, p. 2502, doi. 10.1093/bioinformatics/btaa999

By:

Zheng, Haizi;
Zhu, Michelle S;
Liu, Yaping

Publication type:

Article

movAPA: modeling and visualization of dynamics of alternative polyadenylation across biological samples.

Published in:

Bioinformatics, 2021, v. 37, n. 16, p. 2470, doi. 10.1093/bioinformatics/btaa997

By:

Ye, Wenbin;
Liu, Tao;
Fu, Hongjuan;
Ye, Congting;
Ji, Guoli;
Wu, Xiaohui

Publication type:

Article

LexExp: a system for automatically expanding concept lexicons for noisy biomedical texts.

Published in:

Bioinformatics, 2021, v. 37, n. 16, p. 2499, doi. 10.1093/bioinformatics/btaa995

By:

Sarker, Abeed

Publication type:

Article

AVIA 3.0: interactive portal for genomic variant and sample level analysis.

Published in:

Bioinformatics, 2021, v. 37, n. 16, p. 2467, doi. 10.1093/bioinformatics/btaa994

By:

Reardon, Hue V;
Che, Anney;
Luke, Brian T;
Ravichandran, Sarangan;
Collins, Jack R;
Mudunuri, Uma S

Publication type:

Article

i2d: an R package for simulating data from images and the implications in biomedical research.

Published in:

Bioinformatics, 2021, v. 37, n. 16, p. 2497, doi. 10.1093/bioinformatics/btaa991

By:

Liang, Xiaoyu;
Hu, Ying;
Yan, Chunhua;
Xu, Ke

Publication type:

Article

miqoGraph: fitting admixture graphs using mixed-integer quadratic optimization.

Published in:

Bioinformatics, 2021, v. 37, n. 16, p. 2488, doi. 10.1093/bioinformatics/btaa988

By:

Yan, Julia;
Patterson, Nick;
Narasimhan, Vagheesh M

Publication type:

Article

pdm_utils: a SEA-PHAGES MySQL phage database management toolkit.

Published in:

Bioinformatics, 2021, v. 37, n. 16, p. 2464, doi. 10.1093/bioinformatics/btaa983

By:

Mavrich, Travis N;
Gauthier, Christian;
Abad, Lawrence;
Bowman, Charles A;
Cresawn, Steven G;
Hatfull, Graham F

Publication type:

Article

Quantification of aneuploidy in targeted sequencing data using ASCETS.

Published in:

Bioinformatics, 2021, v. 37, n. 16, p. 2461, doi. 10.1093/bioinformatics/btaa980

By:

Spurr, Liam F;
Touat, Mehdi;
Taylor, Alison M;
Dubuc, Adrian M;
Shih, Juliann;
Meredith, David M;
Pisano, William V;
Meyerson, Matthew L;
Ligon, Keith L;
Cherniack, Andrew D;
Li, Yvonne Y;
Beroukhim, Rameen

Publication type:

Article

eMPRess: a systematic cophylogeny reconciliation tool.

Published in:

Bioinformatics, 2021, v. 37, n. 16, p. 2481, doi. 10.1093/bioinformatics/btaa978

By:

Santichaivekin, Santi;
Yang, Qing;
Liu, Jingyi;
Mawhorter, Ross;
Jiang, Justin;
Wesley, Trenton;
Wu, Yi-Chieh;
Libeskind-Hadas, Ran

Publication type:

Article

BiCoN: network-constrained biclustering of patients and omics data.

Published in:

Bioinformatics, 2021, v. 37, n. 16, p. 2398, doi. 10.1093/bioinformatics/btaa1076

By:

Lazareva, Olga;
Canzar, Stefan;
Yuan, Kevin;
Baumbach, Jan;
Blumenthal, David B;
Tieri, Paolo;
Kacprowski, Tim;
List, Markus

Publication type:

Article