Works matching IS 13674803 AND DT 2021 AND VI 37 AND IP 23

Results: 50

PATO: Pangenome Analysis Toolkit.

Published in:

Bioinformatics, 2021, v. 37, n. 23, p. 4564, doi. 10.1093/bioinformatics/btab697

By:

Fernández-de-Bobadilla, Miguel D;
Talavera-Rodríguez, Alba;
Chacón, Lucía;
Baquero, Fernando;
Coque, Teresa M;
Lanza, Val F

Publication type:

Article

iNucs: inter-nucleosome interactions.

Published in:

Bioinformatics, 2021, v. 37, n. 23, p. 4562, doi. 10.1093/bioinformatics/btab698

By:

Oveisi, Mehrdad;
Shukla, Manu;
Seymen, Nogayhan;
Ohno, Masae;
Taniguchi, Yuichi;
Nahata, Sunil;
Loos, Remco;
Mufti, Ghulam J;
Allshire, Robin C;
Dimitrov, Stefan;
Karimi, Mohammad M

Publication type:

Article

Coral: a web-based visual analysis tool for creating and characterizing cohorts.

Published in:

Bioinformatics, 2021, v. 37, n. 23, p. 4559, doi. 10.1093/bioinformatics/btab695

By:

Adelberger, Patrick;
Eckelt, Klaus;
Bauer, Markus J;
Streit, Marc;
Haslinger, Christian;
Zichner, Thomas

Publication type:

Article

COVID-19 Knowledge Graph from semantic integration of biomedical literature and databases.

Published in:

Bioinformatics, 2021, v. 37, n. 23, p. 4597, doi. 10.1093/bioinformatics/btab694

By:

Chen, Chuming;
Ross, Karen E;
Gavali, Sachin;
Cowart, Julie E;
Wu, Cathy H

Publication type:

Article

spatialTIME and iTIME: R package and Shiny application for visualization and analysis of immunofluorescence data.

Published in:

Bioinformatics, 2021, v. 37, n. 23, p. 4584, doi. 10.1093/bioinformatics/btab757

By:

Creed, Jordan H;
Wilson, Christopher M;
Soupir, Alex C;
Colin-Leitzinger, Christelle M;
Kimmel, Gregory J;
Ospina, Oscar E;
Chakiryan, Nicholas H;
Markowitz, Joseph;
Peres, Lauren C;
Coghill, Anna;
Fridley, Brooke L

Publication type:

Article

Normalized coefficient of variation (nCV): a method to evaluate circadian clock robustness in population scale data.

Published in:

Bioinformatics, 2021, v. 37, n. 23, p. 4581, doi. 10.1093/bioinformatics/btab731

By:

Wu, Gang;
Francey, Lauren J;
Ruben, Marc D;
Hogenesch, John B

Publication type:

Article

New strategies to improve minimap2 alignment accuracy.

Published in:

Bioinformatics, 2021, v. 37, n. 23, p. 4572, doi. 10.1093/bioinformatics/btab705

By:

Li, Heng

Publication type:

Article

Panache: a web browser-based viewer for linearized pangenomes.

Published in:

Bioinformatics, 2021, v. 37, n. 23, p. 4556, doi. 10.1093/bioinformatics/btab688

By:

Durant, Éloi;
Sabot, François;
Conte, Matthieu;
Rouard, Mathieu

Publication type:

Article

CNN-PepPred: an open-source tool to create convolutional NN models for the discovery of patterns in peptide sets—application to peptide–MHC class II binding prediction.

Published in:

Bioinformatics, 2021, v. 37, n. 23, p. 4567, doi. 10.1093/bioinformatics/btab687

By:

Junet, Valentin;
Daura, Xavier

Publication type:

Article

RCytoGPS: an R package for reading and visualizing cytogenetics data.

Published in:

Bioinformatics, 2021, v. 37, n. 23, p. 4589, doi. 10.1093/bioinformatics/btab683

By:

Abrams, Zachary B;
Tally, Dwayne G;
Abruzzo, Lynne V;
Coombes, Kevin R

Publication type:

Article

MungeSumstats: a Bioconductor package for the standardization and quality control of many GWAS summary statistics.

Published in:

Bioinformatics, 2021, v. 37, n. 23, p. 4593, doi. 10.1093/bioinformatics/btab665

By:

Murphy, Alan E;
Schilder, Brian M;
Skene, Nathan G

Publication type:

Article

LipidQuant 1.0: automated data processing in lipid class separation–mass spectrometry quantitative workflows.

Published in:

Bioinformatics, 2021, v. 37, n. 23, p. 4591, doi. 10.1093/bioinformatics/btab644

By:

Wolrab, Denise;
Cífková, Eva;
Čáň, Pavel;
Lísa, Miroslav;
Peterka, Ondřej;
Chocholoušková, Michaela;
Jirásko, Robert;
Holčapek, Michal

Publication type:

Article

VOLTA: adVanced mOLecular neTwork Analysis.

Published in:

Bioinformatics, 2021, v. 37, n. 23, p. 4587, doi. 10.1093/bioinformatics/btab642

By:

Pavel, Alisa;
Federico, Antonio;
Giudice, Giusy del;
Serra, Angela;
Greco, Dario

Publication type:

Article

Socket2: a program for locating, visualizing and analyzing coiled-coil interfaces in protein structures.

Published in:

Bioinformatics, 2021, v. 37, n. 23, p. 4575, doi. 10.1093/bioinformatics/btab631

By:

Kumar, Prasun;
Woolfson, Derek N

Publication type:

Article

tsRNAsearch: a pipeline for the identification of tRNA and ncRNA fragments from small RNA-sequencing data.

Published in:

Bioinformatics, 2021, v. 37, n. 23, p. 4424, doi. 10.1093/bioinformatics/btab515

By:

Donovan, Paul D;
McHale, Natalie M;
Venø, Morten T;
Prehn, Jochen H M

Publication type:

Article

TempoMAGE: a deep learning framework that exploits the causal dependency between time-series data to predict histone marks in open chromatin regions at time-points with missing ChIP-seq datasets.

Published in:

Bioinformatics, 2021, v. 37, n. 23, p. 4336, doi. 10.1093/bioinformatics/btab513

By:

Hallal, Mohammad;
Awad, Mariette;
Khoueiry, Pierre

Publication type:

Article

Efficient gradient-based parameter estimation for dynamic models using qualitative data.

Published in:

Bioinformatics, 2021, v. 37, n. 23, p. 4493, doi. 10.1093/bioinformatics/btab512

By:

Schmiester, Leonard;
Weindl, Daniel;
Hasenauer, Jan

Publication type:

Article

Comparative evaluation of shape retrieval methods on macromolecular surfaces: an application of computer vision methods in structural bioinformatics.

Published in:

Bioinformatics, 2021, v. 37, n. 23, p. 4375, doi. 10.1093/bioinformatics/btab511

By:

Machat, Mohamed;
Langenfeld, Florent;
Craciun, Daniela;
Sirugue, Léa;
Labib, Taoufik;
Lagarde, Nathalie;
Maria, Maxime;
Montes, Matthieu

Publication type:

Article

XRRpred: accurate predictor of crystal structure quality from protein sequence.

Published in:

Bioinformatics, 2021, v. 37, n. 23, p. 4366, doi. 10.1093/bioinformatics/btab509

By:

Ghadermarzi, Sina;
Krawczyk, Bartosz;
Song, Jiangning;
Kurgan, Lukasz

Publication type:

Article

Probabilistic identification of bacterial essential genes via insertion density using TraDIS data with Tn5 libraries.

Published in:

Bioinformatics, 2021, v. 37, n. 23, p. 4343, doi. 10.1093/bioinformatics/btab508

By:

Nlebedim, Valentine U;
Chaudhuri, Roy R;
Walters, Kevin

Publication type:

Article

2DProts: database of family-wide protein secondary structure diagrams.

Published in:

Bioinformatics, 2021, v. 37, n. 23, p. 4599, doi. 10.1093/bioinformatics/btab505

By:

Vařeková, Ivana Hutařová;
Hutař, Jan;
Midlik, Adam;
Horský, Vladimír;
Hladká, Eva;
Svobodová, Radka;
Berka, Karel

Publication type:

Article

UCSC Cell Browser: visualize your single-cell data.

Published in:

Bioinformatics, 2021, v. 37, n. 23, p. 4578, doi. 10.1093/bioinformatics/btab503

By:

Speir, Matthew L;
Bhaduri, Aparna;
Markov, Nikolay S;
Moreno, Pablo;
Nowakowski, Tomasz J;
Papatheodorou, Irene;
Pollen, Alex A;
Raney, Brian J;
Seninge, Lucas;
Kent, W James;
Haeussler, Maximilian

Publication type:

Article

Differential network analysis by simultaneously considering changes in gene interactions and gene expression.

Published in:

Bioinformatics, 2021, v. 37, n. 23, p. 4414, doi. 10.1093/bioinformatics/btab502

By:

Tu, Jia-Juan;
Ou-Yang, Le;
Zhu, Yuan;
Yan, Hong;
Qin, Hong;
Zhang, Xiao-Fei

Publication type:

Article

sequential niche multimodal conformational sampling algorithm for protein structure prediction.

Published in:

Bioinformatics, 2021, v. 37, n. 23, p. 4357, doi. 10.1093/bioinformatics/btab500

By:

Xia, Yu-Hao;
Peng, Chun-Xiang;
Zhou, Xiao-Gen;
Zhang, Gui-Jun

Publication type:

Article

HieRFIT: a hierarchical cell type classification tool for projections from complex single-cell atlas datasets.

Published in:

Bioinformatics, 2021, v. 37, n. 23, p. 4431, doi. 10.1093/bioinformatics/btab499

By:

Kaymaz, Yasin;
Ganglberger, Florian;
Tang, Ming;
Haslinger, Christian;
Fernandez-Albert, Francesc;
Lawless, Nathan;
Sackton, Timothy B

Publication type:

Article

Fully unsupervised deep mode of action learning for phenotyping high-content cellular images.

Published in:

Bioinformatics, 2021, v. 37, n. 23, p. 4548, doi. 10.1093/bioinformatics/btab497

By:

Janssens, Rens;
Zhang, Xian;
Kauffmann, Audrey;
Weck, Antoine de;
Durand, Eric Y

Publication type:

Article

On the stability of log-rank test under labeling errors.

Published in:

Bioinformatics, 2021, v. 37, n. 23, p. 4451, doi. 10.1093/bioinformatics/btab495

By:

Galili, Ben;
Samohi, Anat;
Yakhini, Zohar

Publication type:

Article

Ryūtō: improved multi-sample transcript assembly for differential transcript expression analysis and more.

Published in:

Bioinformatics, 2021, v. 37, n. 23, p. 4307, doi. 10.1093/bioinformatics/btab494

By:

Gatter, Thomas;
Stadler, Peter F

Publication type:

Article

Toward comprehensive functional analysis of gene lists weighted by gene essentiality scores.

Published in:

Bioinformatics, 2021, v. 37, n. 23, p. 4399, doi. 10.1093/bioinformatics/btab475

By:

Fan, Rui;
Cui, Qinghua

Publication type:

Article

HEMDAG: a family of modular and scalable hierarchical ensemble methods to improve Gene Ontology term prediction.

Published in:

Bioinformatics, 2021, v. 37, n. 23, p. 4526, doi. 10.1093/bioinformatics/btab485

By:

Notaro, Marco;
Frasca, Marco;
Petrini, Alessandro;
Gliozzo, Jessica;
Casiraghi, Elena;
Robinson, Peter N;
Valentini, Giorgio

Publication type:

Article

PolarProtPred: predicting apical and basolateral localization of transmembrane proteins using putative short linear motifs and deep learning.

Published in:

Bioinformatics, 2021, v. 37, n. 23, p. 4328, doi. 10.1093/bioinformatics/btab480

By:

Dobson, Laszlo;
Zeke, András;
Tusnády, Gábor E

Publication type:

Article

Identifying driver genes for individual patients through inductive matrix completion.

Published in:

Bioinformatics, 2021, v. 37, n. 23, p. 4477, doi. 10.1093/bioinformatics/btab477

By:

Zhang, Tong;
Zhang, Shao-Wu;
Li, Yan

Publication type:

Article

HFBD: a biomarker knowledge database for heart failure heterogeneity and personalized applications.

Published in:

Bioinformatics, 2021, v. 37, n. 23, p. 4534, doi. 10.1093/bioinformatics/btab470

By:

He, Hongxin;
Shi, Manhong;
Lin, Yuxin;
Zhan, Chaoying;
Wu, Rongrong;
Bi, Cheng;
Liu, Xingyun;
Ren, Shumin;
Shen, Bairong

Publication type:

Article

MultiDTI: drug–target interaction prediction based on multi-modal representation learning to bridge the gap between new chemical entities and known heterogeneous network.

Published in:

Bioinformatics, 2021, v. 37, n. 23, p. 4485, doi. 10.1093/bioinformatics/btab473

By:

Zhou, Deshan;
Xu, Zhijian;
Li, WenTao;
Xie, Xiaolan;
Peng, Shaoliang

Publication type:

Article

MMpred: a distance-assisted multimodal conformation sampling for de novo protein structure prediction.

Published in:

Bioinformatics, 2021, v. 37, n. 23, p. 4350, doi. 10.1093/bioinformatics/btab484

By:

Zhao, Kai-Long;
Liu, Jun;
Zhou, Xiao-Gen;
Su, Jian-Zhong;
Zhang, Yang;
Zhang, Gui-Jun

Publication type:

Article

S2L-PSIBLAST: a supervised two-layer search framework based on PSI-BLAST for protein remote homology detection.

Published in:

Bioinformatics, 2021, v. 37, n. 23, p. 4321, doi. 10.1093/bioinformatics/btab472

By:

Jin, Xiaopeng;
Liao, Qing;
Liu, Bin

Publication type:

Article

SOMDE: a scalable method for identifying spatially variable genes with self-organizing map.

Published in:

Bioinformatics, 2021, v. 37, n. 23, p. 4392, doi. 10.1093/bioinformatics/btab471

By:

Hao, Minsheng;
Hua, Kui;
Zhang, Xuegong

Publication type:

Article

TimeCycle: topology inspired method for the detection of cycling transcripts in circadian time-series data.

Published in:

Bioinformatics, 2021, v. 37, n. 23, p. 4405, doi. 10.1093/bioinformatics/btab476

By:

Ness-Cohn, Elan;
Braun, Rosemary

Publication type:

Article

EpitopeVec: linear epitope prediction using deep protein sequence embeddings.

Published in:

Bioinformatics, 2021, v. 37, n. 23, p. 4517, doi. 10.1093/bioinformatics/btab467

By:

Bahai, Akash;
Asgari, Ehsaneddin;
Mofrad, Mohammad R K;
Kloetgen, Andreas;
McHardy, Alice C

Publication type:

Article

Predicting anti-cancer drug response by finding optimal subset of drugs.

Published in:

Bioinformatics, 2021, v. 37, n. 23, p. 4509, doi. 10.1093/bioinformatics/btab466

By:

Meybodi, Fatemeh Yassaee;
Eslahchi, Changiz

Publication type:

Article

Node similarity-based graph convolution for link prediction in biological networks.

Published in:

Bioinformatics, 2021, v. 37, n. 23, p. 4501, doi. 10.1093/bioinformatics/btab464

By:

Coşkun, Mustafa;
Koyutürk, Mehmet

Publication type:

Article

EPSOL: sequence-based protein solubility prediction using multidimensional embedding.

Published in:

Bioinformatics, 2021, v. 37, n. 23, p. 4314, doi. 10.1093/bioinformatics/btab463

By:

Wu, Xiang;
Yu, Liang

Publication type:

Article

AdaTiSS: a novel data-Adaptive robust method for identifying Tissue Specificity Scores.

Published in:

Bioinformatics, 2021, v. 37, n. 23, p. 4469, doi. 10.1093/bioinformatics/btab460

By:

Wang, Meng;
Jiang, Lihua;
Snyder, Michael P

Publication type:

Article

VSS: variance-stabilized signals for sequencing-based genomic signals.

Published in:

Bioinformatics, 2021, v. 37, n. 23, p. 4383, doi. 10.1093/bioinformatics/btab457

By:

Bayat, Faezeh;
Libbrecht, Maxwell

Publication type:

Article

RápidoPGS: a rapid polygenic score calculator for summary GWAS data without a test dataset.

Published in:

Bioinformatics, 2021, v. 37, n. 23, p. 4444, doi. 10.1093/bioinformatics/btab456

By:

Reales, Guillermo;
Vigorito, Elena;
Kelemen, Martin;
Wallace, Chris

Publication type:

Article

Embeddings of genomic region sets capture rich biological associations in lower dimensions.

Published in:

Bioinformatics, 2021, v. 37, n. 23, p. 4299, doi. 10.1093/bioinformatics/btab439

By:

Gharavi, Erfaneh;
Gu, Aaron;
Zheng, Guangtao;
Smith, Jason P;
Cho, Hyun Jae;
Zhang, Aidong;
Brown, Donald E;
Sheffield, Nathan C

Publication type:

Article

Assessing consistency across functional screening datasets in cancer cells.

Published in:

Bioinformatics, 2021, v. 37, n. 23, p. 4540, doi. 10.1093/bioinformatics/btab423

By:

Cai, Ling;
Liu, Hongyu;
Minna, John D;
DeBerardinis, Ralph J;
Xiao, Guanghua;
Xie, Yang

Publication type:

Article

Visual exploration of large metabolic models.

Published in:

Bioinformatics, 2021, v. 37, n. 23, p. 4460, doi. 10.1093/bioinformatics/btab335

By:

Aichem, Michael;
Czauderna, Tobias;
Zhu, Yan;
Zhao, Jinxin;
Klapperstück, Matthias;
Klein, Karsten;
Li, Jian;
Schreiber, Falk

Publication type:

Article

Survival analysis on rare events using group-regularized multi-response Cox regression.

Published in:

Bioinformatics, 2021, v. 37, n. 23, p. 4437, doi. 10.1093/bioinformatics/btab095

By:

Li, Ruilin;
Tanigawa, Yosuke;
Justesen, Johanne M;
Taylor, Jonathan;
Hastie, Trevor;
Tibshirani, Robert;
Rivas, Manuel A

Publication type:

Article

Cellsnp-lite: an efficient tool for genotyping single cells.

Published in:

Bioinformatics, 2021, v. 37, n. 23, p. 4569, doi. 10.1093/bioinformatics/btab358

By:

Huang, Xianjie;
Huang, Yuanhua

Publication type:

Article