Works matching IS 13674803 AND DT 2021 AND VI 37 AND IP 20

Results: 56

DeepEBV: a deep learning model to predict Epstein–Barr virus (EBV) integration sites.

Published in:

Bioinformatics, 2021, v. 37, n. 20, p. 3405, doi. 10.1093/bioinformatics/btab388

By:

Liang, Jiuxing;
Cui, Zifeng;
Wu, Canbiao;
Yu, Yao;
Tian, Rui;
Xie, Hongxian;
Jin, Zhuang;
Fan, Weiwen;
Xie, Weiling;
Huang, Zhaoyue;
Xu, Wei;
Zhu, Jingjing;
You, Zeshan;
Guo, Xiaofang;
Qiu, Xiaofan;
Ye, Jiahao;
Lang, Bin;
Li, Mengyuan;
Tan, Songwei;
Hu, Zheng

Publication type:

Article

ExTraMapper: exon- and transcript-level mappings for orthologous gene pairs.

Published in:

Bioinformatics, 2021, v. 37, n. 20, p. 3412, doi. 10.1093/bioinformatics/btab393

By:

Chakraborty, Abhijit;
Ay, Ferhat;
Davuluri, Ramana V

Publication type:

Article

Family Rank: a graphical domain knowledge informed feature ranking algorithm.

Published in:

Bioinformatics, 2021, v. 37, n. 20, p. 3626, doi. 10.1093/bioinformatics/btab387

By:

Saul, Michelle;
Dinu, Valentin

Publication type:

Article

NICEpath: Finding metabolic pathways in large networks through atom-conserving substrate–product pairs.

Published in:

Bioinformatics, 2021, v. 37, n. 20, p. 3560, doi. 10.1093/bioinformatics/btab368

By:

Hafner, Jasmin;
Hatzimanikatis, Vassily

Publication type:

Article

Inferring the experimental design for accurate gene regulatory network inference.

Published in:

Bioinformatics, 2021, v. 37, n. 20, p. 3553, doi. 10.1093/bioinformatics/btab367

By:

Seçilmiş, Deniz;
Hillerton, Thomas;
Nelander, Sven;
Sonnhammer, Erik L L

Publication type:

Article

RNAcmap: a fully automatic pipeline for predicting contact maps of RNAs by evolutionary coupling analysis.

Published in:

Bioinformatics, 2021, v. 37, n. 20, p. 3494, doi. 10.1093/bioinformatics/btab391

By:

Zhang, Tongchuan;
Singh, Jaswinder;
Litfin, Thomas;
Zhan, Jian;
Paliwal, Kuldip;
Zhou, Yaoqi

Publication type:

Article

VeTra: a tool for trajectory inference based on RNA velocity.

Published in:

Bioinformatics, 2021, v. 37, n. 20, p. 3509, doi. 10.1093/bioinformatics/btab364

By:

Weng, Guangzheng;
Kim, Junil;
Won, Kyoung Jae

Publication type:

Article

Rapid T-cell receptor interaction grouping with ting.

Published in:

Bioinformatics, 2021, v. 37, n. 20, p. 3444, doi. 10.1093/bioinformatics/btab361

By:

Mölder, Felix;
Stervbo, Ulrik;
Loyal, Lucie;
Bacher, Petra;
Babel, Nina;
Rahmann, Sven

Publication type:

Article

Towards an automatic analysis of CHO-K1 suspension growth in microfluidic single-cell cultivation.

Published in:

Bioinformatics, 2021, v. 37, n. 20, p. 3632, doi. 10.1093/bioinformatics/btab386

By:

Stallmann, Dominik;
Göpfert, Jan P;
Schmitz, Julian;
Grünberger, Alexander;
Hammer, Barbara

Publication type:

Article

Autoencoder-based drug–target interaction prediction by preserving the consistency of chemical properties and functions of drugs.

Published in:

Bioinformatics, 2021, v. 37, n. 20, p. 3618, doi. 10.1093/bioinformatics/btab384

By:

Sun, Chang;
Cao, Yangkun;
Wei, Jin-Mao;
Liu, Jian

Publication type:

Article

combined recall and rank framework with online negative sampling for Chinese procedure terminology normalization.

Published in:

Bioinformatics, 2021, v. 37, n. 20, p. 3610, doi. 10.1093/bioinformatics/btab381

By:

Liang, Ming;
Xue, Kui;
Ye, Qi;
Ruan, Tong

Publication type:

Article

Comparison of structural variants detected by optical mapping with long-read next-generation sequencing.

Published in:

Bioinformatics, 2021, v. 37, n. 20, p. 3398, doi. 10.1093/bioinformatics/btab359

By:

Savara, Jakub;
Novosád, Tomáš;
Gajdoš, Petr;
Kriegová, Eva

Publication type:

Article

TimiRGeN: R/Bioconductor package for time series microRNA–mRNA integration and analysis.

Published in:

Bioinformatics, 2021, v. 37, n. 20, p. 3604, doi. 10.1093/bioinformatics/btab377

By:

Patel, K;
Chandrasegaran, S;
Clark, I M;
Proctor, C J;
Young, D A;
Shanley, D P

Publication type:

Article

eCOMPASS: evaluative comparison of multiple protein alignments by statistical score.

Published in:

Bioinformatics, 2021, v. 37, n. 20, p. 3456, doi. 10.1093/bioinformatics/btab374

By:

Neuwald, Andrew F;
Kolaczkowski, Bryan D;
Altschul, Stephen F

Publication type:

Article

ProteoMill: efficient network-based functional analysis portal for proteomics data.

Published in:

Bioinformatics, 2021, v. 37, n. 20, p. 3491, doi. 10.1093/bioinformatics/btab373

By:

Rydén, Martin;
Englund, Martin;
Ali, Neserin

Publication type:

Article

Clustering FunFams using sequence embeddings improves EC purity.

Published in:

Bioinformatics, 2021, v. 37, n. 20, p. 3449, doi. 10.1093/bioinformatics/btab371

By:

Littmann, Maria;
Bordin, Nicola;
Heinzinger, Michael;
Schütze, Konstantin;
Dallago, Christian;
Orengo, Christine;
Rost, Burkhard

Publication type:

Article

Target–Decoy MineR for determining the biological relevance of variables in noisy datasets.

Published in:

Bioinformatics, 2021, v. 37, n. 20, p. 3595, doi. 10.1093/bioinformatics/btab369

By:

Ovando-Vázquez, Cesaré;
Cázarez-García, Daniel;
Winkler, Robert

Publication type:

Article

Full-length de novo protein structure determination from cryo-EM maps using deep learning.

Published in:

Bioinformatics, 2021, v. 37, n. 20, p. 3480, doi. 10.1093/bioinformatics/btab357

By:

He, Jiahua;
Huang, Sheng-You

Publication type:

Article

In silico prediction of in vitro protein liquid–liquid phase separation experiments outcomes with multi-head neural attention.

Published in:

Bioinformatics, 2021, v. 37, n. 20, p. 3473, doi. 10.1093/bioinformatics/btab350

By:

Raimondi, Daniele;
Orlando, Gabriele;
Michiels, Emiel;
Pakravan, Donya;
Bratek-Skicki, Anna;
Bosch, Ludo Van Den;
Moreau, Yves;
Rousseau, Frederic;
Schymkowitz, Joost

Publication type:

Article

CrepHAN: cross-species prediction of enhancers by using hierarchical attention networks.

Published in:

Bioinformatics, 2021, v. 37, n. 20, p. 3436, doi. 10.1093/bioinformatics/btab349

By:

Hong, Jianwei;
Gao, Ruitian;
Yang, Yang

Publication type:

Article

Bayesian neural network with pretrained protein embedding enhances prediction accuracy of drug-protein interaction.

Published in:

Bioinformatics, 2021, v. 37, n. 20, p. 3428, doi. 10.1093/bioinformatics/btab346

By:

Kim, QHwan;
Ko, Joon-Hyuk;
Kim, Sunghoon;
Park, Nojun;
Jhe, Wonho

Publication type:

Article

TieBrush: an efficient method for aggregating and summarizing mapped reads across large datasets.

Published in:

Bioinformatics, 2021, v. 37, n. 20, p. 3650, doi. 10.1093/bioinformatics/btab342

By:

Varabyou, Ales;
Pertea, Geo;
Pockrandt, Christopher;
Pertea, Mihaela

Publication type:

Article

SKSV: ultrafast structural variation detection from circular consensus sequencing reads.

Published in:

Bioinformatics, 2021, v. 37, n. 20, p. 3647, doi. 10.1093/bioinformatics/btab341

By:

Liu, Yadong;
Jiang, Tao;
Su, Junhao;
Liu, Bo;
Zang, Tianyi;
Wang, Yadong

Publication type:

Article

Capturing dynamic relevance in Boolean networks using graph theoretical measures.

Published in:

Bioinformatics, 2021, v. 37, n. 20, p. 3530, doi. 10.1093/bioinformatics/btab277

By:

Weidner, Felix M;
Schwab, Julian D;
Werle, Silke D;
Ikonomi, Nensi;
Lausser, Ludwig;
Kestler, Hans A

Publication type:

Article

interacCircos: an R package based on JavaScript libraries for the generation of interactive circos plots.

Published in:

Bioinformatics, 2021, v. 37, n. 20, p. 3642, doi. 10.1093/bioinformatics/btab232

By:

Cui, Zhe;
Cui, Ya;
Zang, Tianyi;
Wang, Yadong

Publication type:

Article

IntAct App: a Cytoscape application for molecular interaction network visualization and analysis.

Published in:

Bioinformatics, 2021, v. 37, n. 20, p. 3684, doi. 10.1093/bioinformatics/btab319

By:

Ragueneau, Eliot;
Shrivastava, Anjali;
Morris, John H;
del-Toro, Noemi;
Hermjakob, Henning;
Porras, Pablo

Publication type:

Article

Assessment of significance of conditionally independent GWAS signals.

Published in:

Bioinformatics, 2021, v. 37, n. 20, p. 3521, doi. 10.1093/bioinformatics/btab332

By:

Ghasemi, Sahar;
Teumer, Alexander;
Wuttke, Matthias;
Becker, Tim

Publication type:

Article

mzRAPP: a tool for reliability assessment of data pre-processing in non-targeted metabolomics.

Published in:

Bioinformatics, 2021, v. 37, n. 20, p. 3678, doi. 10.1093/bioinformatics/btab231

By:

Abiead, Yasin El;
Milford, Maximilian;
Salek, Reza M;
Koellensperger, Gunda

Publication type:

Article

NeuroCirc: an integrative resource of circular RNA expression in the human brain.

Published in:

Bioinformatics, 2021, v. 37, n. 20, p. 3664, doi. 10.1093/bioinformatics/btab230

By:

Walsh, Kieran;
Gokool, Akira;
Alinejad-Rokny, Hamid;
Voineagu, Irina

Publication type:

Article

Multimodal regularized linear models with flux balance analysis for mechanistic integration of omics data.

Published in:

Bioinformatics, 2021, v. 37, n. 20, p. 3546, doi. 10.1093/bioinformatics/btab324

By:

Magazzù, Giuseppe;
Zampieri, Guido;
Angione, Claudio

Publication type:

Article

Evaluation of categorical matrix completion algorithms: toward improved active learning for drug discovery.

Published in:

Bioinformatics, 2021, v. 37, n. 20, p. 3538, doi. 10.1093/bioinformatics/btab322

By:

Sun, Huangqingbo;
Murphy, Robert F

Publication type:

Article

SeRenDIP-CE: sequence-based interface prediction for conformational epitopes.

Published in:

Bioinformatics, 2021, v. 37, n. 20, p. 3421, doi. 10.1093/bioinformatics/btab321

By:

Hou, Qingzhen;
Stringer, Bas;
Waury, Katharina;
Capel, Henriette;
Haydarlou, Reza;
Xue, Fuzhong;
Abeln, Sanne;
Heringa, Jaap;
Feenstra, K Anton

Publication type:

Article

GEInter: an R package for robust gene–environment interaction analysis.

Published in:

Bioinformatics, 2021, v. 37, n. 20, p. 3691, doi. 10.1093/bioinformatics/btab318

By:

Wu, Mengyun;
Qin, Xing;
Ma, Shuangge

Publication type:

Article

Omics community detection using multi-resolution clustering.

Published in:

Bioinformatics, 2021, v. 37, n. 20, p. 3588, doi. 10.1093/bioinformatics/btab317

By:

Rahnavard, Ali;
Chatterjee, Suvo;
Sayoldin, Bahar;
Crandall, Keith A;
Tekola-Ayele, Fasil;
Mallick, Himel

Publication type:

Article

SPOT-1D-Single: improving the single-sequence-based prediction of protein secondary structure, backbone angles, solvent accessibility and half-sphere exposures using a large training set and ensembled deep learning.

Published in:

Bioinformatics, 2021, v. 37, n. 20, p. 3464, doi. 10.1093/bioinformatics/btab316

By:

Singh, Jaspreet;
Litfin, Thomas;
Paliwal, Kuldip;
Singh, Jaswinder;
Hanumanthappa, Anil Kumar;
Zhou, Yaoqi

Publication type:

Article

MassExplorer: a computational tool for analyzing desorption electrospray ionization mass spectrometry data.

Published in:

Bioinformatics, 2021, v. 37, n. 20, p. 3688, doi. 10.1093/bioinformatics/btab282

By:

Shankar, Vishnu;
Tibshirani, Robert;
Zare, Richard N

Publication type:

Article

AMICI: high-performance sensitivity analysis for large ordinary differential equation models.

Published in:

Bioinformatics, 2021, v. 37, n. 20, p. 3676, doi. 10.1093/bioinformatics/btab227

By:

Fröhlich, Fabian;
Weindl, Daniel;
Schälte, Yannik;
Pathirana, Dilan;
Paszkowski, Łukasz;
Lines, Glenn Terje;
Stapor, Paul;
Hasenauer, Jan

Publication type:

Article

Customized de novo mutation detection for any variant calling pipeline: SynthDNM.

Published in:

Bioinformatics, 2021, v. 37, n. 20, p. 3640, doi. 10.1093/bioinformatics/btab225

By:

Lian, Aojie;
Guevara, James;
Xia, Kun;
Sebat, Jonathan

Publication type:

Article

GSpace: an exact coalescence simulator of recombining genomes under isolation by distance.

Published in:

Bioinformatics, 2021, v. 37, n. 20, p. 3673, doi. 10.1093/bioinformatics/btab261

By:

Virgoulay, Thimothée;
Rousset, François;
Noûs, Camille;
Leblois, Raphaël

Publication type:

Article

Determining optical mapping errors by simulations.

Published in:

Bioinformatics, 2021, v. 37, n. 20, p. 3391, doi. 10.1093/bioinformatics/btab259

By:

Vašinek, Michal;
Běhálek, Marek;
Gajdoš, Petr;
Fillerová, Regina;
Kriegová, Eva

Publication type:

Article

Quickomics: exploring omics data in an intuitive, interactive and informative manner.

Published in:

Bioinformatics, 2021, v. 37, n. 20, p. 3670, doi. 10.1093/bioinformatics/btab255

By:

Gao, Benbo;
Zhu, Jing;
Negi, Soumya;
Zhang, Xinmin;
Gyoneva, Stefka;
Casey, Fergal;
Wei, Ru;
Zhang, Baohong

Publication type:

Article

Evaluating disease similarity based on gene network reconstruction and representation.

Published in:

Bioinformatics, 2021, v. 37, n. 20, p. 3579, doi. 10.1093/bioinformatics/btab252

By:

Li, Yang;
Keqi, Wang;
Wang, Guohua

Publication type:

Article

VisuaLife: library for interactive visualization in rich web applications.

Published in:

Bioinformatics, 2021, v. 37, n. 20, p. 3662, doi. 10.1093/bioinformatics/btab251

By:

Kryś, Justyna D;
Gront, Dominik

Publication type:

Article

COBRAC: a fast implementation of convex biclustering with compression.

Published in:

Bioinformatics, 2021, v. 37, n. 20, p. 3667, doi. 10.1093/bioinformatics/btab248

By:

Yi, Haidong;
Huang, Le;
Mishne, Gal;
Chi, Eric C

Publication type:

Article

tSFM 1.0: tRNA Structure–Function Mapper.

Published in:

Bioinformatics, 2021, v. 37, n. 20, p. 3654, doi. 10.1093/bioinformatics/btab247

By:

Lawrence, Travis J;
Hadi-Nezhad, Fatemeh;
Grosse, Ivo;
Ardell, David H

Publication type:

Article

scConnect: a method for exploratory analysis of cell–cell communication based on single-cell RNA-sequencing data.

Published in:

Bioinformatics, 2021, v. 37, n. 20, p. 3501, doi. 10.1093/bioinformatics/btab245

By:

Jakobsson, Jon E T;
Spjuth, Ola;
Lagerström, Malin C

Publication type:

Article

TIMEx: tumor-immune microenvironment deconvolution web-portal for bulk transcriptomics using pan-cancer scRNA-seq signatures.

Published in:

Bioinformatics, 2021, v. 37, n. 20, p. 3681, doi. 10.1093/bioinformatics/btab244

By:

Xie, Mengyu;
Lee, Kyubum;
Lockhart, John H;
Cukras, Scott D;
Carvajal, Rodrigo;
Beg, Amer A;
Flores, Elsa R;
Teng, Mingxiang;
Chung, Christine H;
Tan, Aik Choon

Publication type:

Article

MANIEA: a microbial association network inference method based on improved Eclat association rule mining algorithm.

Published in:

Bioinformatics, 2021, v. 37, n. 20, p. 3569, doi. 10.1093/bioinformatics/btab241

By:

Liu, Maidi;
Ye, Yanqing;
Jiang, Jiang;
Yang, Kewei

Publication type:

Article

FPM app: an open-source MATLAB application for simple and intuitive Fourier ptychographic reconstruction.

Published in:

Bioinformatics, 2021, v. 37, n. 20, p. 3695, doi. 10.1093/bioinformatics/btab237

By:

Rogalski, Mikołaj;
Zdańkowski, Piotr;
Trusiak, Maciej

Publication type:

Article

SPDE: a multi-functional software for sequence processing and data extraction.

Published in:

Bioinformatics, 2021, v. 37, n. 20, p. 3686, doi. 10.1093/bioinformatics/btab235

By:

Xu, Dong;
Lu, Zhuchou;
Jin, Kangming;
Qiu, Wenmin;
Qiao, Guirong;
Han, Xiaojiao;
Zhuo, Renying

Publication type:

Article