Works matching IS 13674803 AND DT 2021 AND VI 37 AND IP 18

Results: 59

OMAmer: tree-driven and alignment-free protein assignment to subfamilies outperforms closest sequence approaches.

Published in:

Bioinformatics, 2021, v. 37, n. 18, p. 2866, doi. 10.1093/bioinformatics/btab219

By:

Rossier, Victor;
Vesztrocy, Alex Warwick;
Robinson-Rechavi, Marc;
Dessimoz, Christophe

Publication type:

Article

BLight: efficient exact associative structure for k-mers.

Published in:

Bioinformatics, 2021, v. 37, n. 18, p. 2858, doi. 10.1093/bioinformatics/btab217

By:

Marchet, Camille;
Kerbiriou, Mael;
Limasset, Antoine

Publication type:

Article

A critical assessment of gene catalogs for metagenomic analysis.

Published in:

Bioinformatics, 2021, v. 37, n. 18, p. 2848, doi. 10.1093/bioinformatics/btab216

By:

Commichaux, Seth;
Shah, Nidhi;
Ghurye, Jay;
Stoppel, Alexander;
Goodheart, Jessica A;
Luque, Guillermo G;
Cummings, Michael P;
Pop, Mihai

Publication type:

Article

CoCoNet: an efficient deep learning tool for viral metagenome binning.

Published in:

Bioinformatics, 2021, v. 37, n. 18, p. 2803, doi. 10.1093/bioinformatics/btab213

By:

Arisdakessian, Cédric G;
Nigro, Olivia D;
Steward, Grieg F;
Poisson, Guylaine;
Belcaid, Mahdi

Publication type:

Article

HiG2Vec: hierarchical representations of Gene Ontology and genes in the Poincaré ball.

Published in:

Bioinformatics, 2021, v. 37, n. 18, p. 2971, doi. 10.1093/bioinformatics/btab193

By:

Kim, Jaesik;
Kim, Dokyoon;
Sohn, Kyung-Ah

Publication type:

Article

Improving deconvolution methods in biology through open innovation competitions: an application to the connectivity map.

Published in:

Bioinformatics, 2021, v. 37, n. 18, p. 2889, doi. 10.1093/bioinformatics/btab192

By:

Blasco, Andrea;
Natoli, Ted;
Endres, Michael G;
Sergeev, Rinat A;
Randazzo, Steven;
Paik, Jin H;
Macaluso, N J Maximilian;
Narayan, Rajiv;
Lu, Xiaodong;
Peck, David;
Lakhani, Karim R;
Subramanian, Aravind

Publication type:

Article

Drug repurposing against breast cancer by integrating drug-exposure expression profiles and drug–drug links based on graph neural network.

Published in:

Bioinformatics, 2021, v. 37, n. 18, p. 2930, doi. 10.1093/bioinformatics/btab191

By:

Cui, Chen;
Ding, Xiaoyu;
Wang, Dingyan;
Chen, Lifan;
Xiao, Fu;
Xu, Tingyang;
Zheng, Mingyue;
Luo, Xiaomin;
Jiang, Hualiang;
Chen, Kaixian

Publication type:

Article

DCI: learning causal differences between gene regulatory networks.

Published in:

Bioinformatics, 2021, v. 37, n. 18, p. 3067, doi. 10.1093/bioinformatics/btab167

By:

Belyaeva, Anastasiya;
Squires, Chandler;
Uhler, Caroline

Publication type:

Article

Omixer: multivariate and reproducible sample randomization to proactively counter batch effects in omics studies.

Published in:

Bioinformatics, 2021, v. 37, n. 18, p. 3051, doi. 10.1093/bioinformatics/btab159

By:

Sinke, Lucy;
Cats, Davy;
Heijmans, Bastiaan T

Publication type:

Article

L<sub>2,1</sub>-norm regularized multivariate regression model with applications to genomic prediction.

Published in:

Bioinformatics, 2021, v. 37, n. 18, p. 2896, doi. 10.1093/bioinformatics/btab212

By:

Mbebi, Alain J;
Tong, Hao;
Nikoloski, Zoran

Publication type:

Article

SumGNN: multi-typed drug interaction prediction via efficient knowledge graph summarization.

Published in:

Bioinformatics, 2021, v. 37, n. 18, p. 2988, doi. 10.1093/bioinformatics/btab207

By:

Yu, Yue;
Huang, Kexin;
Zhang, Chao;
Glass, Lucas M;
Sun, Jimeng;
Xiao, Cao

Publication type:

Article

ZEAL: protein structure alignment based on shape similarity.

Published in:

Bioinformatics, 2021, v. 37, n. 18, p. 2874, doi. 10.1093/bioinformatics/btab205

By:

Ljung, Filip;
André, Ingemar

Publication type:

Article

A convolutional neural network and graph convolutional network-based method for predicting the classification of anatomical therapeutic chemicals.

Published in:

Bioinformatics, 2021, v. 37, n. 18, p. 2841, doi. 10.1093/bioinformatics/btab204

By:

Zhao, Haochen;
Li, Yaohang;
Wang, Jianxin

Publication type:

Article

STREME: accurate and versatile sequence motif discovery.

Published in:

Bioinformatics, 2021, v. 37, n. 18, p. 2834, doi. 10.1093/bioinformatics/btab203

By:

Bailey, Timothy L

Publication type:

Article

Quantification of cell behaviors and computational modeling show that cell directional behaviors drive zebrafish pectoral fin morphogenesis.

Published in:

Bioinformatics, 2021, v. 37, n. 18, p. 2946, doi. 10.1093/bioinformatics/btab201

By:

Dokmegang, Joel;
Nguyen, Hanh;
Kardash, Elena;
Savy, Thierry;
Cavaliere, Matteo;
Peyriéras, Nadine;
Doursat, René

Publication type:

Article

TALE: Transformer-based protein function Annotation with joint sequence–Label Embedding.

Published in:

Bioinformatics, 2021, v. 37, n. 18, p. 2825, doi. 10.1093/bioinformatics/btab198

By:

Cao, Yue;
Shen, Yang

Publication type:

Article

FraGAT: a fragment-oriented multi-scale graph attention model for molecular property prediction.

Published in:

Bioinformatics, 2021, v. 37, n. 18, p. 2981, doi. 10.1093/bioinformatics/btab195

By:

Zhang, Ziqiao;
Guan, Jihong;
Zhou, Shuigeng

Publication type:

Article

Probabilistic thermodynamic analysis of metabolic networks.

Published in:

Bioinformatics, 2021, v. 37, n. 18, p. 2938, doi. 10.1093/bioinformatics/btab194

By:

Gollub, Mattia G;
Kaltenbach, Hans-Michael;
Stelling, Jörg

Publication type:

Article

Fast and sensitive taxonomic assignment to metagenomic contigs.

Published in:

Bioinformatics, 2021, v. 37, n. 18, p. 3029, doi. 10.1093/bioinformatics/btab184

By:

Mirdita, M;
Steinegger, M;
Breitwieser, F;
Söding, J;
Karin, E Levy

Publication type:

Article

LSTrAP-Kingdom: an automated pipeline to generate annotated gene expression atlases for kingdoms of life.

Published in:

Bioinformatics, 2021, v. 37, n. 18, p. 3053, doi. 10.1093/bioinformatics/btab168

By:

Goh, William;
Mutwil, Marek

Publication type:

Article

LocusZoom.js: interactive and embeddable visualization of genetic association study results.

Published in:

Bioinformatics, 2021, v. 37, n. 18, p. 3017, doi. 10.1093/bioinformatics/btab186

By:

Boughton, Andrew P;
Welch, Ryan P;
Flickinger, Matthew;
VandeHaar, Peter;
Taliun, Daniel;
Abecasis, Gonçalo R;
Boehnke, Michael

Publication type:

Article

Integrative transcription start site identification with iTiSS.

Published in:

Bioinformatics, 2021, v. 37, n. 18, p. 3056, doi. 10.1093/bioinformatics/btab170

By:

Jürges, Christopher S;
Dölken, Lars;
Erhard, Florian

Publication type:

Article

GPDBN: deep bilinear network integrating both genomic data and pathological images for breast cancer prognosis prediction.

Published in:

Bioinformatics, 2021, v. 37, n. 18, p. 2963, doi. 10.1093/bioinformatics/btab185

By:

Wang, Zhiqin;
Li, Ruiqing;
Wang, Minghui;
Li, Ao

Publication type:

Article

FRC-QE: a robust and comparable 3D microscopy image quality metric for cleared organoids.

Published in:

Bioinformatics, 2021, v. 37, n. 18, p. 3088, doi. 10.1093/bioinformatics/btab160

By:

Preusser, Friedrich;
Santos, Natália dos;
Contzen, Jörg;
Stachelscheid, Harald;
Costa, Érico Tosoni;
Mergenthaler, Philipp;
Preibisch, Stephan

Publication type:

Article

HCMMCNVs: hierarchical clustering mixture model of copy number variants detection using whole exome sequencing technology.

Published in:

Bioinformatics, 2021, v. 37, n. 18, p. 3026, doi. 10.1093/bioinformatics/btab183

By:

Song, Chi;
Su, Shih-Chi;
Huo, Zhiguang;
Vural, Suleyman;
Galvin, James E;
Chang, Lun-Ching

Publication type:

Article

Multiscale part mutual information for quantifying nonlinear direct associations in networks.

Published in:

Bioinformatics, 2021, v. 37, n. 18, p. 2920, doi. 10.1093/bioinformatics/btab182

By:

Shang, Junliang;
Wang, Jing;
Sun, Yan;
Li, Feng;
Liu, Jin-Xing;
Zhang, Honghai

Publication type:

Article

Detecting m<sup>6</sup>A methylation regions from Methylated RNA Immunoprecipitation Sequencing.

Published in:

Bioinformatics, 2021, v. 37, n. 18, p. 2818, doi. 10.1093/bioinformatics/btab181

By:

Guo, Zhenxing;
Shafik, Andrew M;
Jin, Peng;
Wu, Zhijin;
Wu, Hao

Publication type:

Article

POKY: a software suite for multidimensional NMR and 3D structure calculation of biomolecules.

Published in:

Bioinformatics, 2021, v. 37, n. 18, p. 3041, doi. 10.1093/bioinformatics/btab180

By:

Lee, Woonghee;
Rahimi, Mehdi;
Lee, Yeongjoon;
Chiu, Abigail

Publication type:

Article

ExperimentSubset: an R package to manage subsets of Bioconductor Experiment objects.

Published in:

Bioinformatics, 2021, v. 37, n. 18, p. 3058, doi. 10.1093/bioinformatics/btab179

By:

Sarfraz, Irzam;
Asif, Muhammad;
Campbell, Joshua D

Publication type:

Article

PRISM: recovering cell-type-specific expression profiles from individual composite RNA-seq samples.

Published in:

Bioinformatics, 2021, v. 37, n. 18, p. 2882, doi. 10.1093/bioinformatics/btab178

By:

Häkkinen, Antti;
Zhang, Kaiyang;
Alkodsi, Amjad;
Andersson, Noora;
Erkan, Erdogan Pekcan;
Dai, Jun;
Kaipio, Katja;
Lamminen, Tarja;
Mansuri, Naziha;
Huhtinen, Kaisa;
Vähärautio, Anna;
Carpén, Olli;
Hynninen, Johanna;
Hietanen, Sakari;
Lehtonen, Rainer;
Hautaniemi, Sampsa

Publication type:

Article

Queueing theory model of Krebs cycle.

Published in:

Bioinformatics, 2021, v. 37, n. 18, p. 2912, doi. 10.1093/bioinformatics/btab177

By:

Kloska, Sylwester;
Pałczyński, Krzysztof;
Marciniak, Tomasz;
Talaśka, Tomasz;
Nitz, Marissa;
Wysocki, Beata J;
Davis, Paul;
Wysocki, Tadeusz A

Publication type:

Article

FrustratometeR: an R-package to compute local frustration in protein structures, point mutants and MD simulations.

Published in:

Bioinformatics, 2021, v. 37, n. 18, p. 3038, doi. 10.1093/bioinformatics/btab176

By:

Rausch, Atilio O;
Freiberger, Maria I;
Leonetti, Cesar O;
Luna, Diego M;
Radusky, Leandro G;
Wolynes, Peter G;
Ferreiro, Diego U;
Parra, R Gonzalo

Publication type:

Article

Modeling multifunctionality of genes with secondary gene co-expression networks in human brain provides novel disease insights.

Published in:

Bioinformatics, 2021, v. 37, n. 18, p. 2905, doi. 10.1093/bioinformatics/btab175

By:

Sánchez, Juan A;
Gil-Martinez, Ana L;
Cisterna, Alejandro;
García-Ruíz, Sonia;
Gómez-Pascual, Alicia;
Reynolds, Regina H;
Nalls, Mike;
Hardy, John;
Ryten, Mina;
Botía, Juan A

Publication type:

Article

Polypharmacy side-effect prediction with enhanced interpretability based on graph feature attention network.

Published in:

Bioinformatics, 2021, v. 37, n. 18, p. 2955, doi. 10.1093/bioinformatics/btab174

By:

Bang, Sunjoo;
Jhee, Jong Ho;
Shin, Hyunjung

Publication type:

Article

BART3D: inferring transcriptional regulators associated with differential chromatin interactions from Hi-C data.

Published in:

Bioinformatics, 2021, v. 37, n. 18, p. 3075, doi. 10.1093/bioinformatics/btab173

By:

Wang, Zhenjia;
Zhang, Yifan;
Zang, Chongzhi

Publication type:

Article

Tumor IsomiR Encyclopedia (TIE): a pan-cancer database of miRNA isoforms.

Published in:

Bioinformatics, 2021, v. 37, n. 18, p. 3023, doi. 10.1093/bioinformatics/btab172

By:

Ros, Xavier Bofill-De;
Luke, Brian;
Guthridge, Robert;
Mudunuri, Uma;
Loss, Michael;
Gu, Shuo

Publication type:

Article

Megadepth: efficient coverage quantification for BigWigs and BAMs.

Published in:

Bioinformatics, 2021, v. 37, n. 18, p. 3014, doi. 10.1093/bioinformatics/btab152

By:

Wilks, Christopher;
Ahmed, Omar;
Baker, Daniel N;
Zhang, David;
Collado-Torres, Leonardo;
Langmead, Ben

Publication type:

Article

multiTFA: a Python package for multi-variate thermodynamics-based flux analysis.

Published in:

Bioinformatics, 2021, v. 37, n. 18, p. 3064, doi. 10.1093/bioinformatics/btab151

By:

Mahamkali, Vishnuvardhan;
McCubbin, Tim;
Beber, Moritz Emanuel;
Noor, Elad;
Marcellin, Esteban;
Nielsen, Lars Keld

Publication type:

Article

pgainsim: an R-package to assess the mode of inheritance for quantitative trait loci in GWAS.

Published in:

Bioinformatics, 2021, v. 37, n. 18, p. 3061, doi. 10.1093/bioinformatics/btab150

By:

Scherer, Nora;
Sekula, Peggy;
Pfaffelhuber, Peter;
Schlosser, Pascal

Publication type:

Article

RNA-SeQC 2: efficient RNA-seq quality control and quantification for large cohorts.

Published in:

Bioinformatics, 2021, v. 37, n. 18, p. 3048, doi. 10.1093/bioinformatics/btab135

By:

Graubert, Aaron;
Aguet, François;
Ravi, Arvind;
Ardlie, Kristin G;
Getz, Gad

Publication type:

Article

Characterizing protein conformers by cross-linking mass spectrometry and pattern recognition.

Published in:

Bioinformatics, 2021, v. 37, n. 18, p. 3035, doi. 10.1093/bioinformatics/btab149

By:

Kurt, Louise U;
Clasen, Milan A;
Santos, Marlon D M;
Lyra, Eduardo S B;
Santos, Luana O;
Ramos, Carlos H I;
Lima, Diogo B;
Gozzo, Fabio C;
Carvalho, Paulo C

Publication type:

Article

orfipy: a fast and flexible tool for extracting ORFs.

Published in:

Bioinformatics, 2021, v. 37, n. 18, p. 3019, doi. 10.1093/bioinformatics/btab090

By:

Singh, Urminder;
Wurtele, Eve Syrkin

Publication type:

Article

DeepS: a web server for image optical sectioning and super resolution microscopy based on a deep learning framework.

Published in:

Bioinformatics, 2021, v. 37, n. 18, p. 3086, doi. 10.1093/bioinformatics/btab144

By:

Zhu, Qingjie;
Shao, Yi;
Wang, Zhicheng;
Chen, Xingjun;
Li, Chunqiong;
Liang, Zihan;
Jia, Mingyue;
Guo, Qingchun;
Zhao, Hu;
Kong, Lei;
Zhang, Li

Publication type:

Article

S3V2-IDEAS: a package for normalizing, denoising and integrating epigenomic datasets across different cell types.

Published in:

Bioinformatics, 2021, v. 37, n. 18, p. 3011, doi. 10.1093/bioinformatics/btab148

By:

Xiang, Guanjue;
Giardine, Belinda M;
Mahony, Shaun;
Zhang, Yu;
Hardison, Ross C

Publication type:

Article

ASimulatoR: splice-aware RNA-Seq data simulation.

Published in:

Bioinformatics, 2021, v. 37, n. 18, p. 3008, doi. 10.1093/bioinformatics/btab142

By:

Manz, Quirin;
Tsoy, Olga;
Fenn, Amit;
Baumbach, Jan;
Völker, Uwe;
List, Markus;
Kacprowski, Tim

Publication type:

Article

multiclassPairs: an R package to train multiclass pair-based classifier.

Published in:

Bioinformatics, 2021, v. 37, n. 18, p. 3043, doi. 10.1093/bioinformatics/btab088

By:

Marzouka, Nour-Al-Dain;
Eriksson, Pontus

Publication type:

Article

HeteroGGM: an R package for Gaussian graphical model-based heterogeneity analysis.

Published in:

Bioinformatics, 2021, v. 37, n. 18, p. 3073, doi. 10.1093/bioinformatics/btab134

By:

Ren, Mingyang;
Zhang, Sanguo;
Zhang, Qingzhao;
Ma, Shuangge

Publication type:

Article

Bali-Phy version 3: model-based co-estimation of alignment and phylogeny.

Published in:

Bioinformatics, 2021, v. 37, n. 18, p. 3032, doi. 10.1093/bioinformatics/btab129

By:

Redelings, Benjamin D

Publication type:

Article

PICS2: next-generation fine mapping via probabilistic identification of causal SNPs.

Published in:

Bioinformatics, 2021, v. 37, n. 18, p. 3004, doi. 10.1093/bioinformatics/btab122

By:

Taylor, Kimberly E;
Ansel, K Mark;
Marson, Alexander;
Criswell, Lindsey A;
Farh, Kyle Kai-How

Publication type:

Article

An enhanced loss function simplifies the deep learning model for characterizing the 3D organoid models.

Published in:

Bioinformatics, 2021, v. 37, n. 18, p. 3084, doi. 10.1093/bioinformatics/btab120

By:

Winkelmaier, Garrett;
Parvin, Bahram

Publication type:

Article