Works matching IS 13674803 AND DT 2022 AND VI 38 AND IP 1

Results: 53

Learning sparse log-ratios for high-throughput sequencing data.

Published in:

Bioinformatics, 2022, v. 38, n. 1, p. 157, doi. 10.1093/bioinformatics/btab645

By:

Gordon-Rodriguez, Elliott;
Quinn, Thomas P;
Cunningham, John P

Publication type:

Article

Structure-aware protein–protein interaction site prediction using deep graph convolutional network.

Published in:

Bioinformatics, 2022, v. 38, n. 1, p. 125, doi. 10.1093/bioinformatics/btab643

By:

Yuan, Qianmu;
Chen, Jianwen;
Zhao, Huiying;
Zhou, Yaoqi;
Yang, Yuedong

Publication type:

Article

PsiNorm: a scalable normalization for single-cell RNA-seq data.

Published in:

Bioinformatics, 2022, v. 38, n. 1, p. 164, doi. 10.1093/bioinformatics/btab641

By:

Borella, Matteo;
Martello, Graziano;
Risso, Davide;
Romualdi, Chiara

Publication type:

Article

DisoLipPred: accurate prediction of disordered lipid-binding residues in protein sequences with deep recurrent networks and transfer learning.

Published in:

Bioinformatics, 2022, v. 38, n. 1, p. 115, doi. 10.1093/bioinformatics/btab640

By:

Katuwawala, Akila;
Zhao, Bi;
Kurgan, Lukasz

Publication type:

Article

Bayesian hierarchical model to estimate DNA methylation conservation in colorectal tumors.

Published in:

Bioinformatics, 2022, v. 38, n. 1, p. 22, doi. 10.1093/bioinformatics/btab637

By:

Murgas, Kevin A;
Ma, Yanlin;
Shahidi, Lidea K;
Mukherjee, Sayan;
Allen, Andrew S;
Shibata, Darryl;
Ryser, Marc D

Publication type:

Article

OPUS-X: an open-source toolkit for protein torsion angles, secondary structure, solvent accessibility, contact map predictions and 3D folding.

Published in:

Bioinformatics, 2022, v. 38, n. 1, p. 108, doi. 10.1093/bioinformatics/btab633

By:

Xu, Gang;
Wang, Qinghua;
Ma, Jianpeng

Publication type:

Article

Inferring causality in biological oscillators.

Published in:

Bioinformatics, 2022, v. 38, n. 1, p. 196, doi. 10.1093/bioinformatics/btab623

By:

Tyler, Jonathan;
Forger, Daniel;
Kim, Jae Kyoung

Publication type:

Article

de novo protein structure prediction by iterative partition sampling, topology adjustment and residue-level distance deviation optimization.

Published in:

Bioinformatics, 2022, v. 38, n. 1, p. 99, doi. 10.1093/bioinformatics/btab620

By:

Liu, Jun;
Zhao, Kai-Long;
He, Guang-Xing;
Wang, Liu-Jing;
Zhou, Xiao-Gen;
Zhang, Gui-Jun

Publication type:

Article

Hierarchical Bayesian models of transcriptional and translational regulation processes with delays.

Published in:

Bioinformatics, 2022, v. 38, n. 1, p. 187, doi. 10.1093/bioinformatics/btab618

By:

Cortez, Mark Jayson;
Hong, Hyukpyo;
Choi, Boseung;
Kim, Jae Kyoung;
Josić, Krešimir

Publication type:

Article

ProteinEvolverABC: coestimation of recombination and substitution rates in protein sequences by approximate Bayesian computation.

Published in:

Bioinformatics, 2022, v. 38, n. 1, p. 58, doi. 10.1093/bioinformatics/btab617

By:

Arenas, Miguel

Publication type:

Article

Precise estimation of residue relative solvent accessible area from Cα atom distance matrix using a deep learning method.

Published in:

Bioinformatics, 2022, v. 38, n. 1, p. 94, doi. 10.1093/bioinformatics/btab616

By:

Gao, Jianzhao;
Zheng, Shuangjia;
Yao, Mengting;
Wu, Peikun

Publication type:

Article

DeepAc4C: a convolutional neural network model with hybrid features composed of physicochemical patterns and distributed representation information for identification of N4-acetylcytidine in mRNA.

Published in:

Bioinformatics, 2022, v. 38, n. 1, p. 52, doi. 10.1093/bioinformatics/btab611

By:

Wang, Chao;
Ju, Ying;
Zou, Quan;
Lin, Chen

Publication type:

Article

Joint eQTL mapping and inference of gene regulatory network improves power of detecting both cis- and trans-eQTLs.

Published in:

Bioinformatics, 2022, v. 38, n. 1, p. 149, doi. 10.1093/bioinformatics/btab609

By:

Zhou, Xin;
Cai, Xiaodong

Publication type:

Article

Multi-omics data integration by generative adversarial network.

Published in:

Bioinformatics, 2022, v. 38, n. 1, p. 179, doi. 10.1093/bioinformatics/btab608

By:

Ahmed, Khandakar Tanvir;
Sun, Jiao;
Cheng, Sze;
Yong, Jeongsik;
Zhang, Wei

Publication type:

Article

compositional mediation model for a binary outcome: Application to microbiome studies.

Published in:

Bioinformatics, 2022, v. 38, n. 1, p. 16, doi. 10.1093/bioinformatics/btab605

By:

Sohn, Michael B;
Lu, Jiarui;
Li, Hongzhe

Publication type:

Article

qTeller: a tool for comparative multi-genomic gene expression analysis.

Published in:

Bioinformatics, 2022, v. 38, n. 1, p. 236, doi. 10.1093/bioinformatics/btab604

By:

Woodhouse, Margaret R;
Sen, Shatabdi;
Schott, David;
Portwood, John L;
Freeling, Michael;
Walley, Justin W;
Andorf, Carson M;
Schnable, James C

Publication type:

Article

Improved datasets and evaluation methods for the automatic prediction of DNA-binding proteins.

Published in:

Bioinformatics, 2022, v. 38, n. 1, p. 44, doi. 10.1093/bioinformatics/btab603

By:

Zaitzeff, Alexander;
Leiby, Nicholas;
Motta, Francis C;
Haase, Steven B;
Singer, Jedediah M

Publication type:

Article

role of CpG island methylator phenotype in the clinical course of hepatocellular carcinoma.

Published in:

Bioinformatics, 2022, v. 38, n. 1, p. 9, doi. 10.1093/bioinformatics/btab600

By:

Yan, Jun;
Man, Zhongsong;
Gao, Lu;
Cai, Lei;
Lu, Qian;
Dong, Jiahong

Publication type:

Article

De novo protein design by an energy function based on series expansion in distance and orientation dependence.

Published in:

Bioinformatics, 2022, v. 38, n. 1, p. 86, doi. 10.1093/bioinformatics/btab598

By:

Liang, Shide;
Li, Zhixiu;
Zhan, Jian;
Zhou, Yaoqi

Publication type:

Article

coronaSPAdes: from biosynthetic gene clusters to RNA viral assemblies.

Published in:

Bioinformatics, 2022, v. 38, n. 1, p. 1, doi. 10.1093/bioinformatics/btab597

By:

Meleshko, Dmitry;
Hajirasouliha, Iman;
Korobeynikov, Anton

Publication type:

Article

BitQT: a graph-based approach to the quality threshold clustering of molecular dynamics.

Published in:

Bioinformatics, 2022, v. 38, n. 1, p. 73, doi. 10.1093/bioinformatics/btab595

By:

González-Alemán, Roy;
Platero-Rochart, Daniel;
Hernández-Castillo, David;
Hernández-Rodríguez, Erix W;
Caballero, Julio;
Leclerc, Fabrice;
Montero-Cabrera, Luis

Publication type:

Article

Manifold alignment for heterogeneous single-cell multi-omics data integration using Pamona.

Published in:

Bioinformatics, 2022, v. 38, n. 1, p. 211, doi. 10.1093/bioinformatics/btab594

By:

Cao, Kai;
Hong, Yiguang;
Wan, Lin

Publication type:

Article

span-based joint model for extracting entities and relations of bacteria biotopes.

Published in:

Bioinformatics, 2022, v. 38, n. 1, p. 220, doi. 10.1093/bioinformatics/btab593

By:

Zuo, Mei;
Zhang, Yang

Publication type:

Article

Querying multiple sets of P-values through composed hypothesis testing.

Published in:

Bioinformatics, 2022, v. 38, n. 1, p. 141, doi. 10.1093/bioinformatics/btab592

By:

Mary-Huard, Tristan;
Das, Sarmistha;
Mukhopadhyay, Indranil;
Robin, Stéphane

Publication type:

Article

ezGeno: an automatic model selection package for genomic data analysis.

Published in:

Bioinformatics, 2022, v. 38, n. 1, p. 30, doi. 10.1093/bioinformatics/btab588

By:

Lin, Jun-Liang;
Hsieh, Tsung-Ting;
Tung, Yi-An;
Chen, Xuan-Jun;
Hsiao, Yu-Chun;
Yang, Chia-Lin;
Liu, Tyng-Luh;
Chen, Chien-Yu

Publication type:

Article

ramr: an R/Bioconductor package for detection of rare aberrantly methylated regions.

Published in:

Bioinformatics, 2022, v. 38, n. 1, p. 133, doi. 10.1093/bioinformatics/btab586

By:

Nikolaienko, Oleksii;
Lønning, Per Eystein;
Knappskog, Stian

Publication type:

Article

Deep learning-based classification of breast cancer cells using transmembrane receptor dynamics.

Published in:

Bioinformatics, 2022, v. 38, n. 1, p. 243, doi. 10.1093/bioinformatics/btab581

By:

Kim, Mirae;
Hong, Soonwoo;
Yankeelov, Thomas E;
Yeh, Hsin-Chih;
Liu, Yen-Liang

Publication type:

Article

cross-level information transmission network for hierarchical omics data integration and phenotype prediction from a new genotype.

Published in:

Bioinformatics, 2022, v. 38, n. 1, p. 204, doi. 10.1093/bioinformatics/btab580

By:

He, Di;
Xie, Lei

Publication type:

Article

Using high-throughput multi-omics data to investigate structural balance in elementary gene regulatory network motifs.

Published in:

Bioinformatics, 2022, v. 38, n. 1, p. 173, doi. 10.1093/bioinformatics/btab577

By:

Zenere, Alberto;
Rundquist, Olof;
Gustafsson, Mika;
Altafini, Claudio

Publication type:

Article

DAMA: a method for computing multiple alignments of protein structures using local structure descriptors.

Published in:

Bioinformatics, 2022, v. 38, n. 1, p. 80, doi. 10.1093/bioinformatics/btab571

By:

Daniluk, Paweł;
Oleniecki, Tymoteusz;
Lesyng, Bogdan

Publication type:

Article

Co-evolutionary distance predictions contain flexibility information.

Published in:

Bioinformatics, 2022, v. 38, n. 1, p. 65, doi. 10.1093/bioinformatics/btab562

By:

Schwarz, Dominik;
Georges, Guy;
Kelm, Sebastian;
Shi, Jiye;
Vangone, Anna;
Deane, Charlotte M

Publication type:

Article

DeepSec: a deep learning framework for secreted protein discovery in human body fluids.

Published in:

Bioinformatics, 2022, v. 38, n. 1, p. 228, doi. 10.1093/bioinformatics/btab545

By:

Shao, Dan;
Huang, Lan;
Wang, Yan;
He, Kai;
Cui, Xueteng;
Wang, Yao;
Ma, Qin;
Cui, Juan

Publication type:

Article

Alpha-XIC: a deep neural network for scoring the coelution of peak groups improves peptide identification by data-independent acquisition mass spectrometry.

Published in:

Bioinformatics, 2022, v. 38, n. 1, p. 38, doi. 10.1093/bioinformatics/btab544

By:

Song, Jian;
Yu, Changbin

Publication type:

Article

Ranked choice voting for representative transcripts with TRaCE.

Published in:

Bioinformatics, 2022, v. 38, n. 1, p. 261, doi. 10.1093/bioinformatics/btab542

By:

Olson, Andrew J;
Ware, Doreen

Publication type:

Article

SPOT: a web-tool enabling swift profiling of transcriptomes.

Published in:

Bioinformatics, 2022, v. 38, n. 1, p. 284, doi. 10.1093/bioinformatics/btab541

By:

Farr, Elias B;
Sattler, Julia M;
Frischknecht, Friedrich

Publication type:

Article

ModPhred: an integrative toolkit for the analysis and storage of nanopore sequencing DNA and RNA modification data.

Published in:

Bioinformatics, 2022, v. 38, n. 1, p. 257, doi. 10.1093/bioinformatics/btab539

By:

Pryszcz, Leszek P;
Novoa, Eva Maria

Publication type:

Article

MDContactCom: a tool to identify differences of protein molecular dynamics from two MD simulation trajectories in terms of interresidue contacts.

Published in:

Bioinformatics, 2022, v. 38, n. 1, p. 273, doi. 10.1093/bioinformatics/btab538

By:

Motono, Chie;
Yanagida, Shunsuke;
Sato, Miwa;
Hirokawa, Takatsugu

Publication type:

Article

Python interfaces for the Smoldyn simulator.

Published in:

Bioinformatics, 2022, v. 38, n. 1, p. 291, doi. 10.1093/bioinformatics/btab530

By:

Singh, Dilawar;
Andrews, Steven S

Publication type:

Article

Refget: standardized access to reference sequences.

Published in:

Bioinformatics, 2022, v. 38, n. 1, p. 299, doi. 10.1093/bioinformatics/btab524

By:

Yates, Andrew D;
Adams, Jeremy;
Chaturvedi, Somesh;
Davies, Robert M;
Laird, Matthew;
Leinonen, Rasko;
Nag, Rishi;
Sheffield, Nathan C;
Hofmann, Oliver;
Keane, Thomas M

Publication type:

Article

CoSMeD: a user-friendly web server to estimate 5-year survival probability of left-sided and right-sided colorectal cancer patients using molecular data.

Published in:

Bioinformatics, 2022, v. 38, n. 1, p. 278, doi. 10.1093/bioinformatics/btab523

By:

Xin, Junyi;
Wu, Yanling;
Ben, Shuai;
Li, Shuwei;
Chu, Haiyan;
Wang, Meilin;
Wang, Molin;
Song, Mingyang;
Du, Mulong;
Zhang, Zhengdong

Publication type:

Article

quincunx: an R package to query, download and wrangle PGS Catalog data.

Published in:

Bioinformatics, 2022, v. 38, n. 1, p. 294, doi. 10.1093/bioinformatics/btab522

By:

Magno, Ramiro;
Duarte, Isabel;
Maia, Ana-Teresa

Publication type:

Article

FlowGrid enables fast clustering of very large single-cell RNA-seq data.

Published in:

Bioinformatics, 2022, v. 38, n. 1, p. 282, doi. 10.1093/bioinformatics/btab521

By:

Fang, Xiunan;
Ho, Joshua W K

Publication type:

Article

Ontoclick: a web browser extension to facilitate biomedical knowledge curation.

Published in:

Bioinformatics, 2022, v. 38, n. 1, p. 301, doi. 10.1093/bioinformatics/btab520

By:

Xu, Anthony;
Venkateswaran, Aravind;
Zhou, Lianguizi;
Zankl, Andreas

Publication type:

Article

Optimal linkage disequilibrium splitting.

Published in:

Bioinformatics, 2022, v. 38, n. 1, p. 255, doi. 10.1093/bioinformatics/btab519

By:

Privé, Florian

Publication type:

Article

pKPDB: a protein data bank extension database of pKa and pI theoretical values.

Published in:

Bioinformatics, 2022, v. 38, n. 1, p. 297, doi. 10.1093/bioinformatics/btab518

By:

Reis, Pedro B P S;
Clevert, Djork-Arné;
Machuqueiro, Miguel

Publication type:

Article

CUT&RUNTools 2.0: a pipeline for single-cell and bulk-level CUT&RUN and CUT&Tag data analysis.

Published in:

Bioinformatics, 2022, v. 38, n. 1, p. 252, doi. 10.1093/bioinformatics/btab507

By:

Yu, Fulong;
Sankaran, Vijay G;
Yuan, Guo-Cheng

Publication type:

Article

BtToxin_Digger: a comprehensive and high-throughput pipeline for mining toxin protein genes from Bacillus thuringiensis.

Published in:

Bioinformatics, 2022, v. 38, n. 1, p. 250, doi. 10.1093/bioinformatics/btab506

By:

Liu, Hualin;
Zheng, Jinshui;
Bo, Dexin;
Yu, Yun;
Ye, Weixing;
Peng, Donghai;
Sun, Ming

Publication type:

Article

D-MANOVA: fast distance-based multivariate analysis of variance for large-scale microbiome association studies.

Published in:

Bioinformatics, 2022, v. 38, n. 1, p. 286, doi. 10.1093/bioinformatics/btab498

By:

Chen, Jun;
Zhang, Xianyang

Publication type:

Article

Swarm v3: towards tera-scale amplicon clustering.

Published in:

Bioinformatics, 2022, v. 38, n. 1, p. 267, doi. 10.1093/bioinformatics/btab493

By:

Mahé, Frédéric;
Czech, Lucas;
Stamatakis, Alexandros;
Quince, Christopher;
Vargas, Colomban de;
Dunthorn, Micah;
Rognes, Torbjørn

Publication type:

Article

BioVLAB-Cancer-Pharmacogenomics: tumor heterogeneity and pharmacogenomics analysis of multi-omics data from tumor on the cloud.

Published in:

Bioinformatics, 2022, v. 38, n. 1, p. 275, doi. 10.1093/bioinformatics/btab478

By:

Park, Sungjoon;
Lee, Dohoon;
Kim, Youngkuk;
Lim, Sangsoo;
Chae, Heejoon;
Kim, Sun

Publication type:

Article