Works matching IS 13674803 AND DT 2022 AND VI 38 AND IP 4

Results: 52

Uncovering complementary sets of variants for predicting quantitative phenotypes.

Published in:

Bioinformatics, 2022, v. 38, n. 4, p. 908, doi. 10.1093/bioinformatics/btab803

By:

Yilmaz, Serhan;
Fakhouri, Mohamad;
Koyutürk, Mehmet;
Çiçek, A Ercüment;
Tastan, Oznur

Publication type:

Article

GPA-Tree: statistical approach for functional-annotation-tree-guided prioritization of GWAS results.

Published in:

Bioinformatics, 2022, v. 38, n. 4, p. 1067, doi. 10.1093/bioinformatics/btab802

By:

Khatiwada, Aastha;
Wolf, Bethany J;
Yilmaz, Ayse Selen;
Ramos, Paula S;
Pietrzak, Maciej;
Lawson, Andrew;
Hunt, Kelly J;
Kim, Hang J;
Chung, Dongjun

Publication type:

Article

NetSolP: predicting protein solubility in Escherichia coli using language models.

Published in:

Bioinformatics, 2022, v. 38, n. 4, p. 941, doi. 10.1093/bioinformatics/btab801

By:

Thumuluri, Vineet;
Martiny, Hannah-Marie;
Armenteros, Jose J Almagro;
Salomon, Jesper;
Nielsen, Henrik;
Johansen, Alexander Rosenberg

Publication type:

Article

Computational modeling of mRNA degradation dynamics using deep neural networks.

Published in:

Bioinformatics, 2022, v. 38, n. 4, p. 1087, doi. 10.1093/bioinformatics/btab800

By:

Yaish, Ofir;
Orenstein, Yaron

Publication type:

Article

Guide tree optimization with genetic algorithm to improve multiple protein 3D-structure alignment.

Published in:

Bioinformatics, 2022, v. 38, n. 4, p. 985, doi. 10.1093/bioinformatics/btab798

By:

Shegay, Maksim V;
Švedas, Vytas K;
Voevodin, Vladimir V;
Suplatov, Dmitry A;
Popova, Nina N

Publication type:

Article

KCOSS: an ultra-fast k-mer counter for assembled genome analysis.

Published in:

Bioinformatics, 2022, v. 38, n. 4, p. 933, doi. 10.1093/bioinformatics/btab797

By:

Tang, Deyou;
Li, Yucheng;
Tan, Daqiang;
Fu, Juan;
Tang, Yelei;
Lin, Jiabin;
Zhao, Rong;
Du, Hongli;
Zhao, Zhongming

Publication type:

Article

Hubness reduction improves clustering and trajectory inference in single-cell transcriptomic data.

Published in:

Bioinformatics, 2022, v. 38, n. 4, p. 1045, doi. 10.1093/bioinformatics/btab795

By:

Amblard, Elise;
Bac, Jonathan;
Chervov, Alexander;
Soumelis, Vassili;
Zinovyev, Andrei

Publication type:

Article

Cryo-shift: reducing domain shift in cryo-electron subtomograms with unsupervised domain adaptation and randomization.

Published in:

Bioinformatics, 2022, v. 38, n. 4, p. 977, doi. 10.1093/bioinformatics/btab794

By:

Bandyopadhyay, Hmrishav;
Deng, Zihao;
Ding, Leiting;
Liu, Sinuo;
Uddin, Mostofa Rafid;
Zeng, Xiangrui;
Behpour, Sima;
Xu, Min

Publication type:

Article

Graph2MDA: a multi-modal variational graph embedding model for predicting microbe–drug associations.

Published in:

Bioinformatics, 2022, v. 38, n. 4, p. 1118, doi. 10.1093/bioinformatics/btab792

By:

Deng, Lei;
Huang, Yibiao;
Liu, Xuejun;
Liu, Hui

Publication type:

Article

GLYCO: a tool to quantify glycan shielding of glycosylated proteins.

Published in:

Bioinformatics, 2022, v. 38, n. 4, p. 1152, doi. 10.1093/bioinformatics/btab791

By:

Lee, Myungjin;
Reveiz, Mateo;
Rawi, Reda;
Kwong, Peter D;
Chuang, Gwo-Yu

Publication type:

Article

metaSNV v2: detection of SNVs and subspecies in prokaryotic metagenomes.

Published in:

Bioinformatics, 2022, v. 38, n. 4, p. 1162, doi. 10.1093/bioinformatics/btab789

By:

Rossum, Thea Van;
Costea, Paul I;
Paoli, Lucas;
Alves, Renato;
Thielemann, Roman;
Sunagawa, Shinichi;
Bork, Peer

Publication type:

Article

MAGUS+eHMMs: improved multiple sequence alignment accuracy for fragmentary sequences.

Published in:

Bioinformatics, 2022, v. 38, n. 4, p. 918, doi. 10.1093/bioinformatics/btab788

By:

Shen, Chengze;
Zaharias, Paul;
Warnow, Tandy

Publication type:

Article

GNN-based embedding for clustering scRNA-seq data.

Published in:

Bioinformatics, 2022, v. 38, n. 4, p. 1037, doi. 10.1093/bioinformatics/btab787

By:

Ciortan, Madalina;
Defrance, Matthieu

Publication type:

Article

PIntMF: Penalized Integrative Matrix Factorization method for multi-omics data.

Published in:

Bioinformatics, 2022, v. 38, n. 4, p. 900, doi. 10.1093/bioinformatics/btab786

By:

Pierre-Jean, Morgane;
Mauger, Florence;
Deleuze, Jean-François;
Floch, Edith Le

Publication type:

Article

Biobox: a toolbox for biomolecular modelling.

Published in:

Bioinformatics, 2022, v. 38, n. 4, p. 1149, doi. 10.1093/bioinformatics/btab785

By:

Rudden, Lucas S P;
Musson, Samuel C;
Benesch, Justin L P;
Degiacomi, Matteo T

Publication type:

Article

TDFragMapper: a visualization tool for evaluating experimental parameters in top-down proteomics.

Published in:

Bioinformatics, 2022, v. 38, n. 4, p. 1136, doi. 10.1093/bioinformatics/btab784

By:

Dhenin, Jonathan;
Lima, Diogo Borges;
Dupré, Mathieu;
Chamot-Rooke, Julia

Publication type:

Article

Idéfix: identifying accidental sample mix-ups in biobanks using polygenic scores.

Published in:

Bioinformatics, 2022, v. 38, n. 4, p. 1059, doi. 10.1093/bioinformatics/btab783

By:

Warmerdam, Robert;
Lanting, Pauline;
Study, Lifelines Cohort;
Deelen, Patrick;
Franke, Lude

Publication type:

Article

COBREXA.jl: constraint-based reconstruction and exascale analysis.

Published in:

Bioinformatics, 2022, v. 38, n. 4, p. 1171, doi. 10.1093/bioinformatics/btab782

By:

Kratochvíl, Miroslav;
Heirendt, Laurent;
Wilken, St Elmo;
Pusa, Taneli;
Arreckx, Sylvain;
Noronha, Alberto;
Aalst, Marvin van;
Satagopam, Venkata P;
Ebenhöh, Oliver;
Schneider, Reinhard;
Trefois, Christophe;
Gu, Wei

Publication type:

Article

Toward the assessment of predicted inter-residue distance.

Published in:

Bioinformatics, 2022, v. 38, n. 4, p. 962, doi. 10.1093/bioinformatics/btab781

By:

Du, Zongyang;
Peng, Zhenling;
Yang, Jianyi

Publication type:

Article

minoTour, real-time monitoring and analysis for nanopore sequencers.

Published in:

Bioinformatics, 2022, v. 38, n. 4, p. 1133, doi. 10.1093/bioinformatics/btab780

By:

Munro, Rory;
Santos, Roberto;
Payne, Alexander;
Forey, Teri;
Osei, Solomon;
Holmes, Nadine;
Loose, Matthew

Publication type:

Article

tcplfit2: an R-language general purpose concentration–response modeling package.

Published in:

Bioinformatics, 2022, v. 38, n. 4, p. 1157, doi. 10.1093/bioinformatics/btab779

By:

Sheffield, Thomas;
Brown, Jason;
Davidson, Sarah;
Friedman, Katie Paul;
Judson, Richard

Publication type:

Article

Seq-SetNet: directly exploiting multiple sequence alignment for protein secondary structure prediction.

Published in:

Bioinformatics, 2022, v. 38, n. 4, p. 990, doi. 10.1093/bioinformatics/btab777

By:

Ju, Fusong;
Zhu, Jianwei;
Zhang, Qi;
Wei, Guozheng;
Sun, Shiwei;
Zheng, Wei-Mou;
Bu, Dongbo

Publication type:

Article

Variant Library Annotation Tool (VaLiAnT): an oligonucleotide library design and annotation tool for saturation genome editing and other deep mutational scanning experiments.

Published in:

Bioinformatics, 2022, v. 38, n. 4, p. 892, doi. 10.1093/bioinformatics/btab776

By:

Barbon, Luca;
Offord, Victoria;
Radford, Elizabeth J;
Butler, Adam P;
Gerety, Sebastian S;
Adams, David J;
Tan, Hong Kee;
Waters, Andrew J

Publication type:

Article

BioCCP.jl: collecting coupons in combinatorial biotechnology.

Published in:

Bioinformatics, 2022, v. 38, n. 4, p. 1144, doi. 10.1093/bioinformatics/btab775

By:

Huffel, Kirsten Van;
Stock, Michiel;
Baets, Bernard De

Publication type:

Article

Modeling dependency structures in 450k DNA methylation data.

Published in:

Bioinformatics, 2022, v. 38, n. 4, p. 885, doi. 10.1093/bioinformatics/btab774

By:

Nustad, Haakon E;
Steinsland, Ingelin;
Ollikainen, Miina;
Cazaly, Emma;
Kaprio, Jaakko;
Benjamini, Yuval;
Gervin, Kristina;
Lyle, Robert

Publication type:

Article

A2Sign: Agnostic Algorithms for Signatures—a universal method for identifying molecular signatures from transcriptomic datasets prior to cell-type deconvolution.

Published in:

Bioinformatics, 2022, v. 38, n. 4, p. 1015, doi. 10.1093/bioinformatics/btab773

By:

Boldina, Galina;
Fogel, Paul;
Rocher, Corinne;
Bettembourg, Charles;
Luta, George;
Augé, Franck

Publication type:

Article

Deep graph representations embed network information for robust disease marker identification.

Published in:

Bioinformatics, 2022, v. 38, n. 4, p. 1075, doi. 10.1093/bioinformatics/btab772

By:

Maddouri, Omar;
Qian, Xiaoning;
Yoon, Byung-Jun

Publication type:

Article

DD-GUI: a graphical user interface for deep learning-accelerated virtual screening of large chemical libraries (Deep Docking).

Published in:

Bioinformatics, 2022, v. 38, n. 4, p. 1146, doi. 10.1093/bioinformatics/btab771

By:

Yaacoub, Jean Charle;
Gleave, James;
Gentile, Francesco;
Stern, Abraham;
Cherkasov, Artem

Publication type:

Article

T2-DAG: a powerful test for differentially expressed gene pathways via graph-informed structural equation modeling.

Published in:

Bioinformatics, 2022, v. 38, n. 4, p. 1005, doi. 10.1093/bioinformatics/btab770

By:

Jin, Jin;
Wang, Yue

Publication type:

Article

Explainable multimodal machine learning model for classifying pregnancy drug safety.

Published in:

Bioinformatics, 2022, v. 38, n. 4, p. 1102, doi. 10.1093/bioinformatics/btab769

By:

Shtar, Guy;
Rokach, Lior;
Shapira, Bracha;
Kohn, Elkana;
Berkovitch, Matitiahu;
Berlin, Maya

Publication type:

Article

Vernal: a tool for mining fuzzy network motifs in RNA.

Published in:

Bioinformatics, 2022, v. 38, n. 4, p. 970, doi. 10.1093/bioinformatics/btab768

By:

Oliver, Carlos;
Mallet, Vincent;
Philippopoulos, Pericles;
Hamilton, William L;
Waldispühl, Jérôme

Publication type:

Article

GADGETS: a genetic algorithm for detecting epistasis using nuclear families.

Published in:

Bioinformatics, 2022, v. 38, n. 4, p. 1052, doi. 10.1093/bioinformatics/btab766

By:

Nodzenski, Michael;
Shi, Min;
Krahn, Juno M;
Wise, Alison S;
Li, Yuanyuan;
Li, Leping;
Umbach, David M;
Weinberg, Clarice R

Publication type:

Article

Scalable inference of transcriptional kinetic parameters from MS2 time series data.

Published in:

Bioinformatics, 2022, v. 38, n. 4, p. 1030, doi. 10.1093/bioinformatics/btab765

By:

Bowles, Jonathan R;
Hoppe, Caroline;
Ashe, Hilary L;
Rattray, Magnus

Publication type:

Article

ProSeqViewer: an interactive, responsive and efficient TypeScript library for visualization of sequences and alignments in web applications.

Published in:

Bioinformatics, 2022, v. 38, n. 4, p. 1129, doi. 10.1093/bioinformatics/btab764

By:

Bevilacqua, Martina;
Paladin, Lisanna;
Tosatto, Silvio C E;
Piovesan, Damiano

Publication type:

Article

comparison of rule-based and centroid single-sample multiclass predictors for transcriptomic classification.

Published in:

Bioinformatics, 2022, v. 38, n. 4, p. 1022, doi. 10.1093/bioinformatics/btab763

By:

Eriksson, Pontus;
Marzouka, Nour-al-dain;
Sjödahl, Gottfrid;
Bernardo, Carina;
Liedberg, Fredrik;
Höglund, Mattias

Publication type:

Article

CSM-AB: graph-based antibody–antigen binding affinity prediction and docking scoring function.

Published in:

Bioinformatics, 2022, v. 38, n. 4, p. 1141, doi. 10.1093/bioinformatics/btab762

By:

Myung, Yoochan;
Pires, Douglas E V;
Ascher, David B

Publication type:

Article

Deep graph learning of inter-protein contacts.

Published in:

Bioinformatics, 2022, v. 38, n. 4, p. 947, doi. 10.1093/bioinformatics/btab761

By:

Xie, Ziwei;
Xu, Jinbo

Publication type:

Article

Limits and potential of combined folding and docking.

Published in:

Bioinformatics, 2022, v. 38, n. 4, p. 954, doi. 10.1093/bioinformatics/btab760

By:

Pozzati, Gabriele;
Zhu, Wensi;
Bassot, Claudio;
Lamb, John;
Kundrotas, Petras;
Elofsson, Arne

Publication type:

Article

nextNEOpi: a comprehensive pipeline for computational neoantigen prediction.

Published in:

Bioinformatics, 2022, v. 38, n. 4, p. 1131, doi. 10.1093/bioinformatics/btab759

By:

Rieder, Dietmar;
Fotakis, Georgios;
Ausserhofer, Markus;
René, Geyeregger;
Paster, Wolfgang;
Trajanoski, Zlatko;
Finotello, Francesca

Publication type:

Article

bollito: a flexible pipeline for comprehensive single-cell RNA-seq analyses.

Published in:

Bioinformatics, 2022, v. 38, n. 4, p. 1155, doi. 10.1093/bioinformatics/btab758

By:

García-Jimeno, Luis;
Fustero-Torre, Coral;
Jiménez-Santos, María José;
Gómez-López, Gonzalo;
Domenico, Tomás Di;
Al-Shahrour, Fátima

Publication type:

Article

Peakhood: individual site context extraction for CLIP-seq peak regions.

Published in:

Bioinformatics, 2022, v. 38, n. 4, p. 1139, doi. 10.1093/bioinformatics/btab755

By:

Uhl, Michael;
Rabsch, Dominik;
Eggenhofer, Florian;
Backofen, Rolf

Publication type:

Article

Mian: interactive web-based microbiome data table visualization and machine learning platform.

Published in:

Bioinformatics, 2022, v. 38, n. 4, p. 1176, doi. 10.1093/bioinformatics/btab754

By:

Jin, Boyang Tom;
Xu, Feng;
Ng, Raymond T;
Hogg, James C

Publication type:

Article

AOP-helpFinder webserver: a tool for comprehensive analysis of the literature to support adverse outcome pathways development.

Published in:

Bioinformatics, 2022, v. 38, n. 4, p. 1173, doi. 10.1093/bioinformatics/btab750

By:

Jornod, Florence;
Jaylet, Thomas;
Blaha, Ludek;
Sarigiannis, Denis;
Tamisier, Luc;
Audouze, Karine

Publication type:

Article

MatrixQCvis: shiny-based interactive data quality exploration for omics data.

Published in:

Bioinformatics, 2022, v. 38, n. 4, p. 1181, doi. 10.1093/bioinformatics/btab748

By:

Naake, Thomas;
Huber, Wolfgang

Publication type:

Article

power of word-frequency-based alignment-free functions: a comprehensive large-scale experimental analysis.

Published in:

Bioinformatics, 2022, v. 38, n. 4, p. 925, doi. 10.1093/bioinformatics/btab747

By:

Cattaneo, Giuseppe;
Petrillo, Umberto Ferraro;
Giancarlo, Raffaele;
Palini, Francesco;
Romualdi, Chiara

Publication type:

Article

SigTools: exploratory visualization for genomic signals.

Published in:

Bioinformatics, 2022, v. 38, n. 4, p. 1126, doi. 10.1093/bioinformatics/btab742

By:

Masoumi, Shohre;
Libbrecht, Maxwell W;
Wiese, Kay C

Publication type:

Article

maplet: an extensible R toolbox for modular and reproducible metabolomics pipelines.

Published in:

Bioinformatics, 2022, v. 38, n. 4, p. 1168, doi. 10.1093/bioinformatics/btab741

By:

Chetnik, Kelsey;
Benedetti, Elisa;
Gomari, Daniel P;
Schweickart, Annalise;
Batra, Richa;
Buyukozkan, Mustafa;
Wang, Zeyu;
Arnold, Matthias;
Zierer, Jonas;
Suhre, Karsten;
Krumsiek, Jan

Publication type:

Article

PheneBank: a literature-based database of phenotypes.

Published in:

Bioinformatics, 2022, v. 38, n. 4, p. 1179, doi. 10.1093/bioinformatics/btab740

By:

Pilehvar, Mohammad Taher;
Bernard, Adam;
Smedley, Damian;
Collier, Nigel

Publication type:

Article

LocalNgsRelate: a software tool for inferring IBD sharing along the genome between pairs of individuals from low-depth NGS data.

Published in:

Bioinformatics, 2022, v. 38, n. 4, p. 1159, doi. 10.1093/bioinformatics/btab732

By:

Severson, Alissa L;
Korneliussen, Thorfinn Sand;
Moltke, Ida

Publication type:

Article

Plasma protein binding prediction focusing on residue-level features and circularity of cyclic peptides by deep learning.

Published in:

Bioinformatics, 2022, v. 38, n. 4, p. 1110, doi. 10.1093/bioinformatics/btab726

By:

Li, Jianan;
Yanagisawa, Keisuke;
Yoshikawa, Yasushi;
Ohue, Masahito;
Akiyama, Yutaka

Publication type:

Article