Works matching IS 13674803 AND DT 2021 AND VI 37 AND IP 24

Results: 49

Erratum to: BAli-Phy version 3: model-based co-estimation of alignment and phylogeny.

Published in:

2021

By:

Redelings, Benjamin D

Publication type:

Correction Notice

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

Published in:

Bioinformatics, 2021, v. 37, n. 24, p. 4903, doi. 10.1093/bioinformatics/btab707

By:

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

Publication type:

Article

Learning embedding features based on multisense-scaled attention architecture to improve the predictive performance of anticancer peptides.

Published in:

Bioinformatics, 2021, v. 37, n. 24, p. 4684, doi. 10.1093/bioinformatics/btab560

By:

He, Wenjia;
Wang, Yu;
Cui, Lizhen;
Su, Ran;
Wei, Leyi

Publication type:

Article

Deconvolution of expression for nascent RNA-sequencing data (DENR) highlights pre-RNA isoform diversity in human cells.

Published in:

Bioinformatics, 2021, v. 37, n. 24, p. 4727, doi. 10.1093/bioinformatics/btab582

By:

Zhao, Yixin;
Dukler, Noah;
Barshad, Gilad;
Toneyan, Shushan;
Danko, Charles G;
Siepel, Adam

Publication type:

Article

Multi-project and Multi-profile joint Non-negative Matrix Factorization for cancer omic datasets.

Published in:

Bioinformatics, 2021, v. 37, n. 24, p. 4801, doi. 10.1093/bioinformatics/btab579

By:

Salazar, D A;
Pržulj, N;
Valencia, C F

Publication type:

Article

BioERP: biomedical heterogeneous network-based self-supervised representation learning approach for entity relationship predictions.

Published in:

Bioinformatics, 2021, v. 37, n. 24, p. 4793, doi. 10.1093/bioinformatics/btab565

By:

Wang, Xiaoqi;
Yang, Yaning;
Li, Kenli;
Li, Wentao;
Li, Fei;
Peng, Shaoliang

Publication type:

Article

Improved identification and quantification of peptides in mass spectrometry data via chemical and random additive noise elimination (CRANE).

Published in:

Bioinformatics, 2021, v. 37, n. 24, p. 4719, doi. 10.1093/bioinformatics/btab563

By:

Seneviratne, Akila J;
Peters, Sean;
Clarke, David;
Dausmann, Michael;
Hecker, Michael;
Tully, Brett;
Hains, Peter G;
Zhong, Qing

Publication type:

Article

iDNA-ABT: advanced deep learning model for detecting DNA methylation with adaptive features and transductive information maximization.

Published in:

Bioinformatics, 2021, v. 37, n. 24, p. 4603, doi. 10.1093/bioinformatics/btab677

By:

Yu, Yingying;
He, Wenjia;
Jin, Junru;
Xiao, Guobao;
Cui, Lizhen;
Zeng, Rao;
Wei, Leyi

Publication type:

Article

astonishing wealth of new proteasome homologs.

Published in:

Bioinformatics, 2021, v. 37, n. 24, p. 4694, doi. 10.1093/bioinformatics/btab558

By:

Fuchs, Adrian C D;
Alva, Vikram;
Lupas, Andrei N

Publication type:

Article

spheresDT/Mpacts-PiCS: cell tracking and shape retrieval in membrane-labeled embryos.

Published in:

Bioinformatics, 2021, v. 37, n. 24, p. 4851, doi. 10.1093/bioinformatics/btab557

By:

Thiels, Wim;
Smeets, Bart;
Cuvelier, Maxim;
Caroti, Francesca;
Jelier, Rob

Publication type:

Article

Automatic improvement of deep learning-based cell segmentation in time-lapse microscopy by neural architecture search.

Published in:

Bioinformatics, 2021, v. 37, n. 24, p. 4844, doi. 10.1093/bioinformatics/btab556

By:

Zhu, Yanming;
Meijering, Erik

Publication type:

Article

Accurate large-scale phylogeny-aware alignment using BAli-Phy.

Published in:

Bioinformatics, 2021, v. 37, n. 24, p. 4677, doi. 10.1093/bioinformatics/btab555

By:

Gupta, Maya;
Zaharias, Paul;
Warnow, Tandy

Publication type:

Article

CHIT: an allele-specific method for testing the association between molecular quantitative traits and phenotype–genotype interaction.

Published in:

Bioinformatics, 2021, v. 37, n. 24, p. 4764, doi. 10.1093/bioinformatics/btab554

By:

Yan, Qi;
Forno, Erick;
Celedón, Juan C;
Chen, Wei;
Weeks, Daniel E

Publication type:

Article

PhosIDN: an integrated deep neural network for improving protein phosphorylation site prediction by combining sequence and protein–protein interaction information.

Published in:

Bioinformatics, 2021, v. 37, n. 24, p. 4668, doi. 10.1093/bioinformatics/btab551

By:

Yang, Hangyuan;
Wang, Minghui;
Liu, Xia;
Zhao, Xing-Ming;
Li, Ao

Publication type:

Article

DTI-Voodoo: machine learning over interaction networks and ontology-based background knowledge predicts drug–target interactions.

Published in:

Bioinformatics, 2021, v. 37, n. 24, p. 4835, doi. 10.1093/bioinformatics/btab548

By:

Hinnerichs, Tilman;
Hoehndorf, Robert

Publication type:

Article

Transformation and differential abundance analysis of microbiome data incorporating phylogeny.

Published in:

Bioinformatics, 2021, v. 37, n. 24, p. 4652, doi. 10.1093/bioinformatics/btab543

By:

Zhou, Chao;
Zhao, Hongyu;
Wang, Tao

Publication type:

Article

Accurate spliced alignment of long RNA sequencing reads.

Published in:

Bioinformatics, 2021, v. 37, n. 24, p. 4643, doi. 10.1093/bioinformatics/btab540

By:

Sahlin, Kristoffer;
Mäkinen, Veli

Publication type:

Article

GdClean: removal of Gadolinium contamination in mass cytometry data.

Published in:

Bioinformatics, 2021, v. 37, n. 24, p. 4787, doi. 10.1093/bioinformatics/btab537

By:

Liu, Junwei;
Liu, Lulu;
Qu, Saisi;
Zhang, Tongtong;
Wang, Danyang;
Ji, Qinghua;
Wang, Tian;
Shi, Hongyu;
Song, Kaichen;
Fang, Weijia;
Chen, Wei;
Yin, Weiwei

Publication type:

Article

Organism-specific training improves performance of linear B-cell epitope prediction.

Published in:

Bioinformatics, 2021, v. 37, n. 24, p. 4826, doi. 10.1093/bioinformatics/btab536

By:

Ashford, Jodie;
Reis-Cunha, João;
Lobo, Igor;
Lobo, Francisco;
Campelo, Felipe

Publication type:

Article

Cancer subtype identification by consensus guided graph autoencoders.

Published in:

Bioinformatics, 2021, v. 37, n. 24, p. 4779, doi. 10.1093/bioinformatics/btab535

By:

Liang, Cheng;
Shang, Mingchao;
Luo, Jiawei

Publication type:

Article

CCIP: predicting CTCF-mediated chromatin loops with transitivity.

Published in:

Bioinformatics, 2021, v. 37, n. 24, p. 4635, doi. 10.1093/bioinformatics/btab534

By:

Wang, Weibing;
Gao, Lin;
Ye, Yusen;
Gao, Yong

Publication type:

Article

Transfer learning via multi-scale convolutional neural layers for human–virus protein–protein interaction prediction.

Published in:

Bioinformatics, 2021, v. 37, n. 24, p. 4771, doi. 10.1093/bioinformatics/btab533

By:

Yang, Xiaodi;
Yang, Shiping;
Lian, Xianyi;
Wuchty, Stefan;
Zhang, Ziding

Publication type:

Article

DMIL-IsoFun: predicting isoform function using deep multi-instance learning.

Published in:

Bioinformatics, 2021, v. 37, n. 24, p. 4818, doi. 10.1093/bioinformatics/btab532

By:

Yu, Guoxian;
Zhou, Guangjie;
Zhang, Xiangliang;
Domeniconi, Carlotta;
Guo, Maozu

Publication type:

Article

LINADMIX: evaluating the effect of ancient admixture events on modern populations.

Published in:

Bioinformatics, 2021, v. 37, n. 24, p. 4744, doi. 10.1093/bioinformatics/btab531

By:

Agranat-Tamir, Lily;
Waldman, Shamam;
Rosen, Naomi;
Yakir, Benjamin;
Carmi, Shai;
Carmel, Liran

Publication type:

Article

3Cnet: pathogenicity prediction of human variants using multitask learning with evolutionary constraints.

Published in:

Bioinformatics, 2021, v. 37, n. 24, p. 4626, doi. 10.1093/bioinformatics/btab529

By:

Won, Dhong-Gun;
Kim, Dong-Wook;
Woo, Junwoo;
Lee, Kyoungyeul

Publication type:

Article

Nanopore base calling on the edge.

Published in:

Bioinformatics, 2021, v. 37, n. 24, p. 4661, doi. 10.1093/bioinformatics/btab528

By:

Perešíni, Peter;
Boža, Vladimír;
Brejová, Broňa;
Vinař, Tomáš

Publication type:

Article

Nanopanel2 calls phased low-frequency variants in Nanopore panel sequencing data.

Published in:

Bioinformatics, 2021, v. 37, n. 24, p. 4620, doi. 10.1093/bioinformatics/btab526

By:

Popitsch, Niko;
Preuner, Sandra;
Lion, Thomas

Publication type:

Article

Phosphate binding sites prediction in phosphorylation-dependent protein–protein interactions.

Published in:

Bioinformatics, 2021, v. 37, n. 24, p. 4712, doi. 10.1093/bioinformatics/btab525

By:

Lu, Zheng-Chang;
Jiang, Fan;
Wu, Yun-Dong

Publication type:

Article

Founder reconstruction enables scalable and seamless pangenomic analysis.

Published in:

Bioinformatics, 2021, v. 37, n. 24, p. 4611, doi. 10.1093/bioinformatics/btab516

By:

Norri, Tuukka;
Cazaux, Bastien;
Dönges, Saska;
Valenzuela, Daniel;
Mäkinen, Veli

Publication type:

Article

Openness weighted association studies: leveraging personal genome information to prioritize non-coding variants.

Published in:

Bioinformatics, 2021, v. 37, n. 24, p. 4737, doi. 10.1093/bioinformatics/btab514

By:

Song, Shuang;
Shan, Nayang;
Wang, Geng;
Yan, Xiting;
Liu, Jun S;
Hou, Lin

Publication type:

Article

Tumor heterogeneity assessed by sequencing and fluorescence in situ hybridization (FISH) data.

Published in:

Bioinformatics, 2021, v. 37, n. 24, p. 4704, doi. 10.1093/bioinformatics/btab504

By:

Lei, Haoyun;
Gertz, E Michael;
Schäffer, Alejandro A;
Fu, Xuecong;
Tao, Yifeng;
Heselmeyer-Haddad, Kerstin;
Torres, Irianna;
Li, Guibo;
Xu, Liqin;
Hou, Yong;
Wu, Kui;
Shi, Xulian;
Dean, Michael;
Ried, Thomas;
Schwartz, Russell

Publication type:

Article

Stable Iterative Variable Selection.

Published in:

Bioinformatics, 2021, v. 37, n. 24, p. 4810, doi. 10.1093/bioinformatics/btab501

By:

Mahmoudian, Mehrad;
Venäläinen, Mikko S;
Klén, Riku;
Elo, Laura L

Publication type:

Article

fast data-driven method for genotype imputation, phasing and local ancestry inference: MendelImpute.jl.

Published in:

Bioinformatics, 2021, v. 37, n. 24, p. 4756, doi. 10.1093/bioinformatics/btab489

By:

Chu, Benjamin B;
Sobel, Eric M;
Wasiolek, Rory;
Ko, Seyoon;
Sinsheimer, Janet S;
Zhou, Hua;
Lange, Kenneth

Publication type:

Article

fastsimcoal2: demographic inference under complex evolutionary scenarios.

Published in:

Bioinformatics, 2021, v. 37, n. 24, p. 4882, doi. 10.1093/bioinformatics/btab468

By:

Excoffier, Laurent;
Marchi, Nina;
Marques, David Alexander;
Matthey-Doret, Remi;
Gouy, Alexandre;
Sousa, Vitor C

Publication type:

Article

3Dscript.server: true server-side 3D animation of microscopy images using a natural language-based syntax.

Published in:

Bioinformatics, 2021, v. 37, n. 24, p. 4901, doi. 10.1093/bioinformatics/btab462

By:

Schmid, Benjamin;
Tripal, Philipp;
Winter, Zoltán;
Palmisano, Ralph

Publication type:

Article

DUI: the drug use insights web server.

Published in:

Bioinformatics, 2021, v. 37, n. 24, p. 4895, doi. 10.1093/bioinformatics/btab461

By:

Prince, Zachary;
Jha, Deeptanshu;
Singh, Rahul

Publication type:

Article

DNA methylation haplotype (mHap) format and mHapTools.

Published in:

Bioinformatics, 2021, v. 37, n. 24, p. 4892, doi. 10.1093/bioinformatics/btab458

By:

Zhang, Zhiqiang;
Dan, Yuhao;
Xu, Yaochen;
Zhang, Jiarui;
Zheng, Xiaoqi;
Shi, Jiantao

Publication type:

Article

Unfazed: parent-of-origin detection for large and small de novo variants.

Published in:

Bioinformatics, 2021, v. 37, n. 24, p. 4860, doi. 10.1093/bioinformatics/btab454

By:

Belyeu, Jonathan R;
Sasani, Thomas A;
Pedersen, Brent S;
Quinlan, Aaron R

Publication type:

Article

Cheetah-MS: a web server to model protein complexes using tandem cross-linking mass spectrometry data.

Published in:

Bioinformatics, 2021, v. 37, n. 24, p. 4871, doi. 10.1093/bioinformatics/btab449

By:

Khakzad, Hamed;
Happonen, Lotta;
Malmström, Johan;
Malmström, Lars

Publication type:

Article

VoroContacts: a tool for the analysis of interatomic contacts in macromolecular structures.

Published in:

Bioinformatics, 2021, v. 37, n. 24, p. 4873, doi. 10.1093/bioinformatics/btab448

By:

Olechnovič, Kliment;
Venclovas, Česlovas

Publication type:

Article

ClusTCR: a python interface for rapid clustering of large sets of CDR3 sequences with unknown antigen specificity.

Published in:

Bioinformatics, 2021, v. 37, n. 24, p. 4865, doi. 10.1093/bioinformatics/btab446

By:

Valkiers, Sebastiaan;
Houcke, Max Van;
Laukens, Kris;
Meysman, Pieter

Publication type:

Article

Methylscaper: an R/Shiny app for joint visualization of DNA methylation and nucleosome occupancy in single-molecule and single-cell data.

Published in:

Bioinformatics, 2021, v. 37, n. 24, p. 4857, doi. 10.1093/bioinformatics/btab438

By:

Knight, Parker;
Gauthier, Marie-Pierre L;
Pardo, Carolina E;
Darst, Russell P;
Kapadia, Kevin;
Browder, Hadley;
Morton, Eliza;
Riva, Alberto;
Kladde, Michael P;
Bacher, Rhonda

Publication type:

Article

libOmexMeta: enabling semantic annotation of models to support FAIR principles.

Published in:

Bioinformatics, 2021, v. 37, n. 24, p. 4898, doi. 10.1093/bioinformatics/btab445

By:

Welsh, Ciaran;
Nickerson, David P;
Rampadarath, Anand;
Neal, Maxwell L;
Sauro, Herbert M;
Gennari, John H

Publication type:

Article

SANS serif: alignment-free, whole-genome-based phylogenetic reconstruction.

Published in:

Bioinformatics, 2021, v. 37, n. 24, p. 4868, doi. 10.1093/bioinformatics/btab444

By:

Rempel, Andreas;
Wittler, Roland

Publication type:

Article

PAX2GRAPHML: a python library for large-scale regulation network analysis using BioPAX.

Published in:

Bioinformatics, 2021, v. 37, n. 24, p. 4889, doi. 10.1093/bioinformatics/btab441

By:

Moreews, François;
Simon, Hugo;
Siegel, Anne;
Gondret, Florence;
Becker, Emmanuelle

Publication type:

Article

RENANO: a REference-based compressor for NANOpore FASTQ files.

Published in:

Bioinformatics, 2021, v. 37, n. 24, p. 4862, doi. 10.1093/bioinformatics/btab437

By:

Álvarez, Guillermo Dufort y;
Seroussi, Gadiel;
Smircich, Pablo;
Sotelo-Silveira, José;
Ochoa, Idoia;
Martín, Álvaro

Publication type:

Article

NaViA: a program for the visual analysis of complex mass spectra.

Published in:

Bioinformatics, 2021, v. 37, n. 24, p. 4876, doi. 10.1093/bioinformatics/btab436

By:

Quetschlich, Daniel;
Esser, Tim K;
Newport, Thomas D;
Fiorentino, Francesco;
Shutin, Denis;
Chen, Siyun;
Davis, Rachel;
Lovera, Silvia;
Liko, Idlir;
Stansfeld, Phillip J;
Robinson, Carol V

Publication type:

Article

AQUARIUM: accurate quantification of circular isoforms using model-based strategy.

Published in:

Bioinformatics, 2021, v. 37, n. 24, p. 4879, doi. 10.1093/bioinformatics/btab435

By:

Wen, Guoxia;
Li, Musheng;
Li, Fuyu;
Yang, Zengyan;
Zhou, Tong;
Gu, Wanjun

Publication type:

Article

peakPantheR, an R package for large-scale targeted extraction and integration of annotated metabolic features in LC–MS profiling datasets.

Published in:

Bioinformatics, 2021, v. 37, n. 24, p. 4886, doi. 10.1093/bioinformatics/btab433

By:

Wolfer, Arnaud M;
Correia, Gonçalo D S;
Sands, Caroline J;
Camuzeaux, Stephane;
Yuen, Ada H Y;
Chekmeneva, Elena;
Takáts, Zoltán;
Pearce, Jake T M;
Lewis, Matthew R

Publication type:

Article