Works matching IS 13674803 AND DT 2022 AND VI 38

Results: 1005

Neuron tracing from light microscopy images: automation, deep learning and bench testing.

Published in:

Bioinformatics, 2022, v. 38, n. 24, p. 5329, doi. 10.1093/bioinformatics/btac712

By:

Liu, Yufeng;
Wang, Gaoyu;
Ascoli, Giorgio A;
Zhou, Jiangning;
Liu, Lijuan

Publication type:

Article

Integrating transformer and imbalanced multi-label learning to identify antimicrobial peptides and their functional activities.

Published in:

Bioinformatics, 2022, v. 38, n. 24, p. 5368, doi. 10.1093/bioinformatics/btac711

By:

Pang, Yuxuan;
Yao, Lantian;
Xu, Jingyi;
Wang, Zhuo;
Lee, Tzong-Yi

Publication type:

Article

EvAM-Tools: tools for evolutionary accumulation and cancer progression models.

Published in:

Bioinformatics, 2022, v. 38, n. 24, p. 5457, doi. 10.1093/bioinformatics/btac710

By:

Diaz-Uriarte, Ramon;
Herrera-Nieto, Pablo

Publication type:

Article

ConsensuSV—from the whole-genome sequencing data to the complete variant list.

Published in:

Bioinformatics, 2022, v. 38, n. 24, p. 5440, doi. 10.1093/bioinformatics/btac709

By:

Chiliński, Mateusz;
Plewczynski, Dariusz

Publication type:

Article

HaploDMF: viral haplotype reconstruction from long reads via deep matrix factorization.

Published in:

Bioinformatics, 2022, v. 38, n. 24, p. 5360, doi. 10.1093/bioinformatics/btac708

By:

Cai, Dehan;
Shang, Jiayu;
Sun, Yanni

Publication type:

Article

Identifying the critical state of complex biological systems by the directed-network rank score method.

Published in:

Bioinformatics, 2022, v. 38, n. 24, p. 5398, doi. 10.1093/bioinformatics/btac707

By:

Zhong, Jiayuan;
Han, Chongyin;
Wang, Yangkai;
Chen, Pei;
Liu, Rui

Publication type:

Article

ADViSELipidomics: a workflow for analyzing lipidomics data.

Published in:

Bioinformatics, 2022, v. 38, n. 24, p. 5460, doi. 10.1093/bioinformatics/btac706

By:

Prete, Eugenio Del;
Campos, Ana Margarida;
Rocca, Fabio Della;
Gallo, Carmela;
Fontana, Angelo;
Nuzzo, Genoveffa;
Angelini, Claudia

Publication type:

Article

3DPolyS-LE: an accessible simulation framework to model the interplay between chromatin and loop extrusion.

Published in:

Bioinformatics, 2022, v. 38, n. 24, p. 5454, doi. 10.1093/bioinformatics/btac705

By:

Gitchev, Todor;
Zala, Gabriel;
Meister, Peter;
Jost, Daniel

Publication type:

Article

GlycoEnzOnto: a GlycoEnzyme pathway and molecular function ontology.

Published in:

Bioinformatics, 2022, v. 38, n. 24, p. 5413, doi. 10.1093/bioinformatics/btac704

By:

Groth, Theodore;
Diehl, Alexander D;
Gunawan, Rudiyanto;
Neelamegham, Sriram

Publication type:

Article

EcoTransLearn: an R-package to easily use transfer learning for ecological studies—a plankton case study.

Published in:

Bioinformatics, 2022, v. 38, n. 24, p. 5469, doi. 10.1093/bioinformatics/btac703

By:

Wacquet, Guillaume;
Lefebvre, Alain

Publication type:

Article

HAT: haplotype assembly tool using short and error-prone long reads.

Published in:

Bioinformatics, 2022, v. 38, n. 24, p. 5352, doi. 10.1093/bioinformatics/btac702

By:

Zade, Ramin Shirali Hossein;
Urhan, Aysun;
Souza, Alvaro Assis de;
Singh, Akash;
Abeel, Thomas

Publication type:

Article

AHoJ: rapid, tailored search and retrieval of apo and holo protein structures for user-defined ligands.

Published in:

Bioinformatics, 2022, v. 38, n. 24, p. 5452, doi. 10.1093/bioinformatics/btac701

By:

Feidakis, Christos P;
Krivak, Radoslav;
Hoksza, David;
Novotny, Marian

Publication type:

Article

Convex hull as diagnostic tool in single-molecule localization microscopy.

Published in:

Bioinformatics, 2022, v. 38, n. 24, p. 5421, doi. 10.1093/bioinformatics/btac700

By:

Ebert, Vincent;
Eiring, Patrick;
Helmerich, Dominic A;
Seifert, Rick;
Sauer, Markus;
Doose, Sören

Publication type:

Article

DeepPerVar: a multi-modal deep learning framework for functional interpretation of genetic variants in personal genome.

Published in:

Bioinformatics, 2022, v. 38, n. 24, p. 5340, doi. 10.1093/bioinformatics/btac696

By:

Wang, Ye;
Chen, Li

Publication type:

Article

Biomedical evidence engineering for data-driven discovery.

Published in:

Bioinformatics, 2022, v. 38, n. 23, p. 5270, doi. 10.1093/bioinformatics/btac675

By:

Zhao, Sendong;
Wang, Aobo;
Qin, Bing;
Wang, Fei

Publication type:

Article

CAMML with the Integration of Marker Proteins (ChIMP).

Published in:

Bioinformatics, 2022, v. 38, n. 23, p. 5206, doi. 10.1093/bioinformatics/btac674

By:

Schiebout, Courtney;
Frost, H Robert

Publication type:

Article

SATINN: an automated neural network-based classification of testicular sections allows for high-throughput histopathology of mouse mutants.

Published in:

Bioinformatics, 2022, v. 38, n. 23, p. 5288, doi. 10.1093/bioinformatics/btac673

By:

Yang, Ran;
Stendahl, Alexandra M;
Vigh-Conrad, Katinka A;
Held, Madison;
Lima, Ana C;
Conrad, Donald F

Publication type:

Article

LCD-Composer webserver: high-specificity identification and functional analysis of low-complexity domains in proteins.

Published in:

Bioinformatics, 2022, v. 38, n. 24, p. 5446, doi. 10.1093/bioinformatics/btac699

By:

Cascarina, Sean M;
Ross, Eric D

Publication type:

Article

GTDB-Tk v2: memory friendly classification with the genome taxonomy database.

Published in:

Bioinformatics, 2022, v. 38, n. 23, p. 5315, doi. 10.1093/bioinformatics/btac672

By:

Chaumeil, Pierre-Alain;
Mussig, Aaron J;
Hugenholtz, Philip;
Parks, Donovan H

Publication type:

Article

OmicsEV: a tool for comprehensive quality evaluation of omics data tables.

Published in:

Bioinformatics, 2022, v. 38, n. 24, p. 5463, doi. 10.1093/bioinformatics/btac698

By:

Wen, Bo;
Jaehnig, Eric J;
Zhang, Bing

Publication type:

Article

CRISPRon/off: CRISPR/Cas9 on- and off-target gRNA design.

Published in:

Bioinformatics, 2022, v. 38, n. 24, p. 5437, doi. 10.1093/bioinformatics/btac697

By:

Anthon, Christian;
Corsi, Giulia Ilaria;
Gorodkin, Jan

Publication type:

Article

MAGScoT: a fast, lightweight and accurate bin-refinement tool.

Published in:

Bioinformatics, 2022, v. 38, n. 24, p. 5430, doi. 10.1093/bioinformatics/btac694

By:

Rühlemann, Malte Christoph;
Wacker, Eike Matthias;
Ellinghaus, David;
Franke, Andre

Publication type:

Article

SYNPHONI: scale-free and phylogeny-aware reconstruction of synteny conservation and transformation across animal genomes.

Published in:

Bioinformatics, 2022, v. 38, n. 24, p. 5434, doi. 10.1093/bioinformatics/btac695

By:

Robert, Nicolas Serge Matthieu;
Sarigol, Fatih;
Zieger, Elisabeth;
Simakov, Oleg

Publication type:

Article

Defining the extent of gene function using ROC curvature.

Published in:

Bioinformatics, 2022, v. 38, n. 24, p. 5390, doi. 10.1093/bioinformatics/btac692

By:

Fischer, Stephan;
Gillis, Jesse

Publication type:

Article

BraneMF: integration of biological networks for functional analysis of proteins.

Published in:

Bioinformatics, 2022, v. 38, n. 24, p. 5383, doi. 10.1093/bioinformatics/btac691

By:

Jagtap, Surabhi;
Çelikkanat, Abdulkadir;
Pirayre, Aurélie;
Bidard, Frédérique;
Duval, Laurent;
Malliaros, Fragkiskos D

Publication type:

Article

kmdiff, large-scale and user-friendly differential k-mer analyses.

Published in:

Bioinformatics, 2022, v. 38, n. 24, p. 5443, doi. 10.1093/bioinformatics/btac689

By:

Lemane, Téo;
Chikhi, Rayan;
Peterlongo, Pierre

Publication type:

Article

in silico genome-wide screen for circadian clock strength in human samples.

Published in:

Bioinformatics, 2022, v. 38, n. 24, p. 5375, doi. 10.1093/bioinformatics/btac686

By:

Wu, Gang;
Ruben, Marc D;
Francey, Lauren J;
Lee, Yin Yeng;
Anafi, Ron C;
Hogenesch, John B

Publication type:

Article

LaGAT: link-aware graph attention network for drug–drug interaction prediction.

Published in:

Bioinformatics, 2022, v. 38, n. 24, p. 5406, doi. 10.1093/bioinformatics/btac682

By:

Hong, Yue;
Luo, Pengyu;
Jin, Shuting;
Liu, Xiangrong

Publication type:

Article

DREAMM: a web-based server for drugging protein-membrane interfaces as a novel workflow for targeted drug design.

Published in:

Bioinformatics, 2022, v. 38, n. 24, p. 5449, doi. 10.1093/bioinformatics/btac680

By:

Chatzigoulas, Alexios;
Cournia, Zoe

Publication type:

Article

Common data model for COVID-19 datasets.

Published in:

Bioinformatics, 2022, v. 38, n. 24, p. 5466, doi. 10.1093/bioinformatics/btac651

By:

Wegner, Philipp;
Jose, Geena Mariya;
Lage-Rupprecht, Vanessa;
Khatami, Sepehr Golriz;
Zhang, Bide;
Springstubbe, Stephan;
Jacobs, Marc;
Linden, Thomas;
Ku, Cindy;
Schultz, Bruce;
Hofmann-Apitius, Martin;
Kodamullil, Alpha Tom;
Consortium, for the COPERIMOplus

Publication type:

Article

Powerful and interpretable control of false discoveries in two-group differential expression studies.

Published in:

Bioinformatics, 2022, v. 38, n. 23, p. 5214, doi. 10.1093/bioinformatics/btac693

By:

Enjalbert-Courrech, Nicolas;
Neuvial, Pierre

Publication type:

Article

Improving and evaluating deep learning models of cellular organization.

Published in:

Bioinformatics, 2022, v. 38, n. 23, p. 5299, doi. 10.1093/bioinformatics/btac688

By:

Sun, Huangqingbo;
Fu, Xuecong;
Abraham, Serena;
Jin, Shen;
Murphy, Robert F

Publication type:

Article

CoxMKF: a knockoff filter for high-dimensional mediation analysis with a survival outcome in epigenetic studies.

Published in:

Bioinformatics, 2022, v. 38, n. 23, p. 5229, doi. 10.1093/bioinformatics/btac687

By:

Tian, Peixin;
Yao, Minhao;
Huang, Tao;
Liu, Zhonghua

Publication type:

Article

ATLIGATOR: editing protein interactions with an atlas-based approach.

Published in:

Bioinformatics, 2022, v. 38, n. 23, p. 5199, doi. 10.1093/bioinformatics/btac685

By:

Kynast, Josef Paul;
Schwägerl, Felix;
Höcker, Birte

Publication type:

Article

scGNN 2.0: a graph neural network tool for imputation and clustering of single-cell RNA-Seq data.

Published in:

Bioinformatics, 2022, v. 38, n. 23, p. 5322, doi. 10.1093/bioinformatics/btac684

By:

Gu, Haocheng;
Cheng, Hao;
Ma, Anjun;
Li, Yang;
Wang, Juexin;
Xu, Dong;
Ma, Qin

Publication type:

Article

AIscEA: unsupervised integration of single-cell gene expression and chromatin accessibility via their biological consistency.

Published in:

Bioinformatics, 2022, v. 38, n. 23, p. 5236, doi. 10.1093/bioinformatics/btac683

By:

Jafari, Elham;
Johnson, Travis;
Wang, Yue;
Liu, Yunlong;
Huang, Kun;
Wang, Yijie

Publication type:

Article

Evaluation of efficiency prediction algorithms and development of ensemble model for CRISPR/Cas9 gRNA selection.

Published in:

Bioinformatics, 2022, v. 38, n. 23, p. 5175, doi. 10.1093/bioinformatics/btac681

By:

Chen, Yuhao;
Wang, Xiaowei

Publication type:

Article

Estimation of speciation times under the multispecies coalescent.

Published in:

Bioinformatics, 2022, v. 38, n. 23, p. 5182, doi. 10.1093/bioinformatics/btac679

By:

Peng, Jing;
Swofford, David L;
Kubatko, Laura

Publication type:

Article

E-SNPs&GO: embedding of protein sequence and function improves the annotation of human pathogenic variants.

Published in:

Bioinformatics, 2022, v. 38, n. 23, p. 5168, doi. 10.1093/bioinformatics/btac678

By:

Manfredi, Matteo;
Savojardo, Castrense;
Martelli, Pier Luigi;
Casadio, Rita

Publication type:

Article

novel pipeline for computerized mouse spermatogenesis staging.

Published in:

Bioinformatics, 2022, v. 38, n. 23, p. 5307, doi. 10.1093/bioinformatics/btac677

By:

Lu, Haoda;
Zang, Min;
Marini, Gabriel Pik Liang;
Wang, Xiangxue;
Jiao, Yiping;
Ao, Nianfei;
Ong, Kokhaur;
Huo, Xinmi;
Li, Longjie;
Xu, Eugene Yujun;
Goh, Wilson Wen Bin;
Yu, Weimiao;
Xu, Jun

Publication type:

Article

Prediction of drug-likeness using graph convolutional attention network.

Published in:

Bioinformatics, 2022, v. 38, n. 23, p. 5262, doi. 10.1093/bioinformatics/btac676

By:

Sun, Jinyu;
Wen, Ming;
Wang, Huabei;
Ruan, Yuezhe;
Yang, Qiong;
Kang, Xiao;
Zhang, Hailiang;
Zhang, Zhimin;
Lu, Hongmei

Publication type:

Article

MSNet-4mC: learning effective multi-scale representations for identifying DNA N4-methylcytosine sites.

Published in:

Bioinformatics, 2022, v. 38, n. 23, p. 5160, doi. 10.1093/bioinformatics/btac671

By:

Liu, Chunting;
Song, Jiangning;
Ogata, Hiroyuki;
Akutsu, Tatsuya

Publication type:

Article

scHiCPTR: unsupervised pseudotime inference through dual graph refinement for single-cell Hi-C data.

Published in:

Bioinformatics, 2022, v. 38, n. 23, p. 5151, doi. 10.1093/bioinformatics/btac670

By:

Lyu, Hongqiang;
Liu, Erhu;
Wu, Zhifang;
Li, Yao;
Liu, Yuan;
Yin, Xiaoran

Publication type:

Article

Tree2GD: a phylogenomic method to detect large-scale gene duplication events.

Published in:

Bioinformatics, 2022, v. 38, n. 23, p. 5317, doi. 10.1093/bioinformatics/btac669

By:

Chen, Duoyuan;
Zhang, Taikui;
Chen, Yamao;
Ma, Hong;
Qi, Ji

Publication type:

Article

MDSCAN: RMSD-based HDBSCAN clustering of long molecular dynamics.

Published in:

Bioinformatics, 2022, v. 38, n. 23, p. 5191, doi. 10.1093/bioinformatics/btac666

By:

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

Publication type:

Article

CEDA: integrating gene expression data with CRISPR-pooled screen data identifies essential genes with higher expression.

Published in:

Bioinformatics, 2022, v. 38, n. 23, p. 5245, doi. 10.1093/bioinformatics/btac668

By:

Zhao, Yue;
Yu, Lianbo;
Wu, Xue;
Li, Haoran;
Coombes, Kevin R;
Au, Kin Fai;
Cheng, Lijun;
Li, Lang

Publication type:

Article

Correction to: plotsr: visualizing structural similarities and rearrangements between multiple genomes.

Published in:: 2022
Publication type:: Correction Notice

Learning temporal difference embeddings for biomedical hypothesis generation.

Published in:

Bioinformatics, 2022, v. 38, n. 23, p. 5253, doi. 10.1093/bioinformatics/btac660

By:

Zhou, Huiwei;
Jiang, Haibin;
Yao, Weihong;
Du, Xun

Publication type:

Article

penalized linear mixed model with generalized method of moments estimators for complex phenotype prediction.

Published in:

Bioinformatics, 2022, v. 38, n. 23, p. 5222, doi. 10.1093/bioinformatics/btac659

By:

Wang, Xiaqiong;
Wen, Yalu

Publication type:

Article

METAbolomics data Balancing with Over-sampling Algorithms (META-BOA): an online resource for addressing class imbalance.

Published in:

Bioinformatics, 2022, v. 38, n. 23, p. 5326, doi. 10.1093/bioinformatics/btac649

By:

Hashimoto-Roth, Emily;
Surendra, Anuradha;
Lavallée-Adam, Mathieu;
Bennett, Steffany A L;
Čuperlović-Culf, Miroslava

Publication type:

Article