Works matching IS 13674803 AND DT 2021 AND VI 37 AND IP 21

Results: 61

Sciviewer enables interactive visual interrogation of single-cell RNA-Seq data from the Python programming environment.

Published in:

Bioinformatics, 2021, v. 37, n. 21, p. 3961, doi. 10.1093/bioinformatics/btab689

By:

Kotliar, Dylan;
Colubri, Andrés

Publication type:

Article

ACES: Analysis of Conservation with an Extensive list of Species.

Published in:

Bioinformatics, 2021, v. 37, n. 21, p. 3920, doi. 10.1093/bioinformatics/btab684

By:

Padhi, Evin M;
Ng, Jeffrey K;
Mehinovic, Elvisa;
Sams, Eleanor I;
Turner, Tychele N

Publication type:

Article

IntelliPy: a GUI for analyzing IntelliCage data.

Published in:

Bioinformatics, 2021, v. 37, n. 21, p. 3972, doi. 10.1093/bioinformatics/btab682

By:

Ruffini, Nicolas;
Müller, Marianne B;
Schmitt, Ulrich;
Gerber, Susanne

Publication type:

Article

RLM: fast and simplified extraction of read-level methylation metrics from bisulfite sequencing data.

Published in:

Bioinformatics, 2021, v. 37, n. 21, p. 3934, doi. 10.1093/bioinformatics/btab663

By:

Hetzel, Sara;
Giesselmann, Pay;
Reinert, Knut;
Meissner, Alexander;
Kretzmer, Helene

Publication type:

Article

mspack: efficient lossless and lossy mass spectrometry data compression.

Published in:

Bioinformatics, 2021, v. 37, n. 21, p. 3923, doi. 10.1093/bioinformatics/btab636

By:

Hanau, Felix;
Röst, Hannes;
Ochoa, Idoia

Publication type:

Article

utr.annotation: a tool for annotating genomic variants that could influence post-transcriptional regulation.

Published in:

2021

By:

Liu, Yating;
Dougherty, Joseph D

Publication type:

Abstract

CellProfiler Analyst 3.0: accessible data exploration and machine learning for image analysis.

Published in:

Bioinformatics, 2021, v. 37, n. 21, p. 3992, doi. 10.1093/bioinformatics/btab634

By:

Stirling, David R;
Carpenter, Anne E;
Cimini, Beth A

Publication type:

Article

Improved estimation of model quality using predicted inter-residue distance.

Published in:

Bioinformatics, 2021, v. 37, n. 21, p. 3752, doi. 10.1093/bioinformatics/btab632

By:

Ye, Lisha;
Wu, Peikun;
Peng, Zhenling;
Gao, Jianzhao;
Liu, Jian;
Yang, Jianyi

Publication type:

Article

Prowler: a novel trimming algorithm for Oxford Nanopore sequence data.

Published in:

Bioinformatics, 2021, v. 37, n. 21, p. 3936, doi. 10.1093/bioinformatics/btab630

By:

Lee, Simon;
Nguyen, Loan T;
Hayes, Ben J;
Ross, Elizabeth M

Publication type:

Article

Differential transcript usage analysis of bulk and single-cell RNA-seq data with DTUrtle.

Published in:

Bioinformatics, 2021, v. 37, n. 21, p. 3781, doi. 10.1093/bioinformatics/btab629

By:

Tekath, Tobias;
Dugas, Martin

Publication type:

Article

FORUM: building a Knowledge Graph from public databases and scientific literature to extract associations between chemicals and diseases.

Published in:

Bioinformatics, 2021, v. 37, n. 21, p. 3896, doi. 10.1093/bioinformatics/btab627

By:

Delmas, Maxime;
Filangi, Olivier;
Paulhe, Nils;
Vinson, Florence;
Duperier, Christophe;
Garrier, William;
Saunier, Paul-Emeric;
Pitarch, Yoann;
Jourdan, Fabien;
Giacomoni, Franck;
Frainay, Clément

Publication type:

Article

pepsickle rapidly and accurately predicts proteasomal cleavage sites for improved neoantigen identification.

Published in:

Bioinformatics, 2021, v. 37, n. 21, p. 3723, doi. 10.1093/bioinformatics/btab628

By:

Weeder, Benjamin R;
Wood, Mary A;
Li, Ellysia;
Nellore, Abhinav;
Thompson, Reid F

Publication type:

Article

fobitools framework: the first steps towards food enrichment analysis.

Published in:

Bioinformatics, 2021, v. 37, n. 21, p. 3969, doi. 10.1093/bioinformatics/btab626

By:

Castellano-Escuder, Pol;
Andrés-Lacueva, Cristina;
Sánchez-Pla, Alex

Publication type:

Article

BleTIES: annotation of natural genome editing in ciliates using long read sequencing.

Published in:

Bioinformatics, 2021, v. 37, n. 21, p. 3929, doi. 10.1093/bioinformatics/btab613

By:

Seah, Brandon K B;
Swart, Estienne C

Publication type:

Article

DEMETER: efficient simultaneous curation of genome-scale reconstructions guided by experimental data and refined gene annotations.

Published in:

Bioinformatics, 2021, v. 37, n. 21, p. 3974, doi. 10.1093/bioinformatics/btab622

By:

Heinken, Almut;
Magnúsdóttir, Stefanía;
Fleming, Ronan M T;
Thiele, Ines

Publication type:

Article

FlexTaxD: flexible modification of taxonomy databases for improved sequence classification.

Published in:

Bioinformatics, 2021, v. 37, n. 21, p. 3932, doi. 10.1093/bioinformatics/btab621

By:

Sundell, David;
Öhrman, Caroline;
Svensson, Daniel;
Karlsson, Edvin;
Brindefalk, Björn;
Myrtennäs, Kerstin;
Ahlinder, Jon;
Antwerpen, Markus H;
Walter, Mathias C;
Forsman, Mats;
Stenberg, Per;
Sjödin, Andreas

Publication type:

Article

FRETraj: integrating single-molecule spectroscopy with molecular dynamics.

Published in:

Bioinformatics, 2021, v. 37, n. 21, p. 3953, doi. 10.1093/bioinformatics/btab615

By:

Steffen, Fabio D;
Sigel, Roland K O;
Börner, Richard

Publication type:

Article

Custom workflows to improve joint variant calling from multiple related tumour samples: FreeBayesSomatic and Strelka2Pass.

Published in:

Bioinformatics, 2021, v. 37, n. 21, p. 3916, doi. 10.1093/bioinformatics/btab606

By:

Hollizeck, S;
Wong, S Q;
Solomon, B;
Chandrananda, D;
Dawson, S-J

Publication type:

Article

Deep Subspace Mutual Learning for cancer subtypes prediction.

Published in:

Bioinformatics, 2021, v. 37, n. 21, p. 3715, doi. 10.1093/bioinformatics/btab625

By:

Yang, Bo;
Xin, Ting-Ting;
Pang, Shan-Min;
Wang, Meng;
Wang, Yi-Jie

Publication type:

Article

OpenPhi: an interface to access Philips iSyntax whole slide images for computational pathology.

Published in:

Bioinformatics, 2021, v. 37, n. 21, p. 3995, doi. 10.1093/bioinformatics/btab578

By:

Mulliqi, Nita;
Kartasalo, Kimmo;
Olsson, Henrik;
Ji, Xiaoyi;
Egevad, Lars;
Eklund, Martin;
Ruusuvuori, Pekka

Publication type:

Article

Predicting correlated outcomes from molecular data.

Published in:

Bioinformatics, 2021, v. 37, n. 21, p. 3889, doi. 10.1093/bioinformatics/btab576

By:

Rauschenberger, Armin;
Glaab, Enrico

Publication type:

Article

Maximization of non-idle enzymes improves the coverage of the estimated maximal in vivo enzyme catalytic rates in Escherichia coli.

Published in:

Bioinformatics, 2021, v. 37, n. 21, p. 3848, doi. 10.1093/bioinformatics/btab575

By:

Xu, Rudan;
Razaghi-Moghadam, Zahra;
Nikoloski, Zoran

Publication type:

Article

Detecting quantitative trait loci and exploring chromosomal pairing in autopolyploids using polyqtlR.

Published in:

Bioinformatics, 2021, v. 37, n. 21, p. 3822, doi. 10.1093/bioinformatics/btab574

By:

Bourke, Peter M;
Voorrips, Roeland E;
Hackett, Christine A;
Geest, Geert van;
Willemsen, Johan H;
Arens, Paul;
Smulders, Marinus J M;
Visser, Richard G F;
Maliepaard, Chris

Publication type:

Article

TCRpair: prediction of functional pairing between HLA-A*02:01-restricted T-cell receptor α and β chains.

Published in:

Bioinformatics, 2021, v. 37, n. 21, p. 3938, doi. 10.1093/bioinformatics/btab573

By:

Mösch, Anja;
Frishman, Dmitrij

Publication type:

Article

PZLAST: an ultra-fast amino acid sequence similarity search server against public metagenomes.

Published in:

Bioinformatics, 2021, v. 37, n. 21, p. 3944, doi. 10.1093/bioinformatics/btab492

By:

Mori, Hiroshi;
Ishikawa, Hitoshi;
Higashi, Koichi;
Kato, Yoshiaki;
Ebisuzaki, Toshikazu;
Kurokawa, Ken

Publication type:

Article

scAMACE: model-based approach to the joint analysis of single-cell data on chromatin accessibility, gene expression and methylation.

Published in:

Bioinformatics, 2021, v. 37, n. 21, p. 3874, doi. 10.1093/bioinformatics/btab426

By:

Wangwu, Jiaxuan;
Sun, Zexuan;
Lin, Zhixiang

Publication type:

Article

ClustENMD: efficient sampling of biomolecular conformational space at atomic resolution.

Published in:

Bioinformatics, 2021, v. 37, n. 21, p. 3956, doi. 10.1093/bioinformatics/btab496

By:

Kaynak, Burak T;
Zhang, She;
Bahar, Ivet;
Doruker, Pemra

Publication type:

Article

Sparse least trimmed squares regression with compositional covariates for high-dimensional data.

Published in:

Bioinformatics, 2021, v. 37, n. 21, p. 3805, doi. 10.1093/bioinformatics/btab572

By:

Monti, Gianna Serafina;
Filzmoser, Peter

Publication type:

Article

MHCVision: estimation of global and local false discovery rate for MHC class I peptide binding prediction.

Published in:

Bioinformatics, 2021, v. 37, n. 21, p. 3830, doi. 10.1093/bioinformatics/btab479

By:

Pearngam, Phorutai;
Sriswasdi, Sira;
Pisitkun, Trairak;
Jones, Andrew R

Publication type:

Article

Increasing the accuracy of single sequence prediction methods using a deep semi-supervised learning framework.

Published in:

Bioinformatics, 2021, v. 37, n. 21, p. 3744, doi. 10.1093/bioinformatics/btab491

By:

Moffat, Lewis;
Jones, David T

Publication type:

Article

NetControl4BioMed: a web-based platform for controllability analysis of protein–protein interaction networks.

Published in:

Bioinformatics, 2021, v. 37, n. 21, p. 3976, doi. 10.1093/bioinformatics/btab570

By:

Popescu, Victor-Bogdan;
Sánchez-Martín, José Ángel;
Schacherer, Daniela;
Safadoust, Sadra;
Majidi, Negin;
Andronescu, Andrei;
Nedea, Alexandru;
Ion, Diana;
Mititelu, Eduard;
Czeizler, Eugen;
Petre, Ion

Publication type:

Article

Assessing heterogeneity in spatial data using the HTA index with applications to spatial transcriptomics and imaging.

Published in:

Bioinformatics, 2021, v. 37, n. 21, p. 3796, doi. 10.1093/bioinformatics/btab569

By:

Levy-Jurgenson, Alona;
Tekpli, Xavier;
Yakhini, Zohar

Publication type:

Article

SAMPDI-3D: predicting the effects of protein and DNA mutations on protein–DNA interactions.

Published in:

Bioinformatics, 2021, v. 37, n. 21, p. 3760, doi. 10.1093/bioinformatics/btab567

By:

Li, Gen;
Panday, Shailesh Kumar;
Peng, Yunhui;
Alexov, Emil

Publication type:

Article

Mediation analysis for survival data with high-dimensional mediators.

Published in:

Bioinformatics, 2021, v. 37, n. 21, p. 3815, doi. 10.1093/bioinformatics/btab564

By:

Zhang, Haixiang;
Zheng, Yinan;
Hou, Lifang;
Zheng, Cheng;
Liu, Lei

Publication type:

Article

LipiDisease: associate lipids to diseases using literature mining.

Published in:

Bioinformatics, 2021, v. 37, n. 21, p. 3981, doi. 10.1093/bioinformatics/btab559

By:

More, Piyush;
Bindila, Laura;
Wild, Philipp;
Andrade-Navarro, Miguel;
Fontaine, Jean-Fred

Publication type:

Article

MERIDA: a novel Boolean logic-based integer linear program for personalized cancer therapy.

Published in:

Bioinformatics, 2021, v. 37, n. 21, p. 3881, doi. 10.1093/bioinformatics/btab546

By:

Lenhof, Kerstin;
Gerstner, Nico;
Kehl, Tim;
Eckhart, Lea;
Schneider, Lara;
Lenhof, Hans-Peter

Publication type:

Article

Medical concept normalization in clinical trials with drug and disease representation learning.

Published in:

Bioinformatics, 2021, v. 37, n. 21, p. 3856, doi. 10.1093/bioinformatics/btab474

By:

Miftahutdinov, Zulfat;
Kadurin, Artur;
Kudrin, Roman;
Tutubalina, Elena

Publication type:

Article

phyLoSTM: a novel deep learning model on disease prediction from longitudinal microbiome data.

Published in:

Bioinformatics, 2021, v. 37, n. 21, p. 3707, doi. 10.1093/bioinformatics/btab482

By:

Sharma, Divya;
Xu, Wei

Publication type:

Article

Tysserand—fast and accurate reconstruction of spatial networks from bioimages.

Published in:

Bioinformatics, 2021, v. 37, n. 21, p. 3989, doi. 10.1093/bioinformatics/btab490

By:

Coullomb, Alexis;
Pancaldi, Vera

Publication type:

Article

CStreet: a computed Cell State trajectory inference method for time-series single-cell RNA sequencing data.

Published in:

Bioinformatics, 2021, v. 37, n. 21, p. 3774, doi. 10.1093/bioinformatics/btab488

By:

Zhao, Chengchen;
Xiu, Wenchao;
Hua, Yuwei;
Zhang, Naiqian;
Zhang, Yong

Publication type:

Article

Non-parametric modelling of temporal and spatial counts data from RNA-seq experiments.

Published in:

Bioinformatics, 2021, v. 37, n. 21, p. 3788, doi. 10.1093/bioinformatics/btab486

By:

BinTayyash, Nuha;
Georgaka, Sokratia;
John, S T;
Ahmed, Sumon;
Boukouvalas, Alexis;
Hensman, James;
Rattray, Magnus

Publication type:

Article

Linear functional organization of the omic embedding space.

Published in:

Bioinformatics, 2021, v. 37, n. 21, p. 3839, doi. 10.1093/bioinformatics/btab487

By:

Xenos, A;
Malod-Dognin, N;
Milinković, S;
Pržulj, N

Publication type:

Article

MNHN-Tree-Tools: a toolbox for tree inference using multi-scale clustering of a set of sequences.

Published in:

Bioinformatics, 2021, v. 37, n. 21, p. 3947, doi. 10.1093/bioinformatics/btab430

By:

Haschka, Thomas;
Ponger, Loic;
Escudé, Christophe;
Mozziconacci, Julien

Publication type:

Article

wQFM: highly accurate genome-scale species tree estimation from weighted quartets.

Published in:

Bioinformatics, 2021, v. 37, n. 21, p. 3734, doi. 10.1093/bioinformatics/btab428

By:

Mahbub, Mahim;
Wahab, Zahin;
Reaz, Rezwana;
Rahman, M Saifur;
Bayzid, Md Shamsuzzoha

Publication type:

Article

TIGA: target illumination GWAS analytics.

Published in:

Bioinformatics, 2021, v. 37, n. 21, p. 3865, doi. 10.1093/bioinformatics/btab427

By:

Yang, Jeremy J;
Grissa, Dhouha;
Lambert, Christophe G;
Bologa, Cristian G;
Mathias, Stephen L;
Waller, Anna;
Wild, David J;
Jensen, Lars Juhl;
Oprea, Tudor I

Publication type:

Article

JBrowseR: an R interface to the JBrowse 2 genome browser.

Published in:

Bioinformatics, 2021, v. 37, n. 21, p. 3914, doi. 10.1093/bioinformatics/btab459

By:

Hershberg, Elliot A;
Stevens, Garrett;
Diesh, Colin;
Xie, Peter;
Martinez, Teresa De Jesus;
Buels, Robert;
Stein, Lincoln;
Holmes, Ian

Publication type:

Article

Structural discrimination analysis for constraint selection in protein modeling.

Published in:

Bioinformatics, 2021, v. 37, n. 21, p. 3766, doi. 10.1093/bioinformatics/btab425

By:

Bottino, Guilherme F;
Ferrari, Allan J R;
Gozzo, Fabio C;
Martínez, Leandro

Publication type:

Article

PDBe aggregated API: programmatic access to an integrative knowledge graph of molecular structure data.

Published in:

Bioinformatics, 2021, v. 37, n. 21, p. 3950, doi. 10.1093/bioinformatics/btab424

By:

Nair, Sreenath;
Váradi, Mihály;
Nadzirin, Nurul;
Pravda, Lukáš;
Anyango, Stephen;
Mir, Saqib;
Berrisford, John;
Armstrong, David;
Gutmanas, Aleksandras;
Velankar, Sameer

Publication type:

Article

SARS-CoV-2 sequence submission tool for the European Nucleotide Archive.

Published in:

Bioinformatics, 2021, v. 37, n. 21, p. 3983, doi. 10.1093/bioinformatics/btab421

By:

Roncoroni, Miguel;
Droesbeke, Bert;
Eguinoa, Ignacio;
Ruyck, Kim De;
D'Anna, Flora;
Yusuf, Dilmurat;
Grüning, Björn;
Backofen, Rolf;
Coppens, Frederik

Publication type:

Article

HGC: fast hierarchical clustering for large-scale single-cell data.

Published in:

Bioinformatics, 2021, v. 37, n. 21, p. 3964, doi. 10.1093/bioinformatics/btab420

By:

Zou, Ziheng;
Hua, Kui;
Zhang, Xuegong

Publication type:

Article