Works matching IS 13674803 AND DT 2022 AND VI 38 AND IP 3

Results: 47

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

Published in:

2022

By:

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

Publication type:

Correction Notice

ORT: a workflow linking genome-scale metabolic models with reactive transport codes.

Published in:

Bioinformatics, 2022, v. 38, n. 3, p. 778, doi. 10.1093/bioinformatics/btab753

By:

Rubinstein, Rebecca L;
Borton, Mikayla A;
Zhou, Haiyan;
Shaffer, Michael;
Hoyt, David W;
Stegen, James;
Henry, Christopher S;
Wrighton, Kelly C;
Versteeg, Roelof

Publication type:

Article

Density-based binning of gene clusters to infer function or evolutionary history using GeneGrouper.

Published in:

Bioinformatics, 2022, v. 38, n. 3, p. 612, doi. 10.1093/bioinformatics/btab752

By:

McFarland, Alexander G;
Kennedy, Nolan W;
Mills, Carolyn E;
Tullman-Ercek, Danielle;
Huttenhower, Curtis;
Hartmann, Erica M

Publication type:

Article

Importance-Penalized Joint Graphical Lasso (IPJGL): differential network inference via GGMs.

Published in:

Bioinformatics, 2022, v. 38, n. 3, p. 770, doi. 10.1093/bioinformatics/btab751

By:

Leng, Jiacheng;
Wu, Ling-Yun

Publication type:

Article

Population-scale detection of non-reference sequence variants using colored de Bruijn graphs.

Published in:

Bioinformatics, 2022, v. 38, n. 3, p. 604, doi. 10.1093/bioinformatics/btab749

By:

Krannich, Thomas;
White, W Timothy J;
Niehus, Sebastian;
Holley, Guillaume;
Halldórsson, Bjarni V;
Kehr, Birte

Publication type:

Article

CpG Transformer for imputation of single-cell methylomes.

Published in:

Bioinformatics, 2022, v. 38, n. 3, p. 597, doi. 10.1093/bioinformatics/btab746

By:

Waele, Gaetan De;
Clauwaert, Jim;
Menschaert, Gerben;
Waegeman, Willem

Publication type:

Article

CoCoPRED: coiled-coil protein structural feature prediction from amino acid sequence using deep neural networks.

Published in:

Bioinformatics, 2022, v. 38, n. 3, p. 720, doi. 10.1093/bioinformatics/btab744

By:

Feng, Shi-Hao;
Xia, Chun-Qiu;
Shen, Hong-Bin

Publication type:

Article

preciseTAD: a transfer learning framework for 3D domain boundary prediction at base-pair resolution.

Published in:

Bioinformatics, 2022, v. 38, n. 3, p. 621, doi. 10.1093/bioinformatics/btab743

By:

Stilianoudakis, Spiro C;
Marshall, Maggie A;
Dozmorov, Mikhail G

Publication type:

Article

EDCNN: identification of genome-wide RNA-binding proteins using evolutionary deep convolutional neural network.

Published in:

Bioinformatics, 2022, v. 38, n. 3, p. 678, doi. 10.1093/bioinformatics/btab739

By:

Wang, Yawei;
Yang, Yuning;
Ma, Zhiqiang;
Wong, Ka-Chun;
Li, Xiangtao

Publication type:

Article

ConsAlifold: considering RNA structural alignments improves prediction accuracy of RNA consensus secondary structures.

Published in:

Bioinformatics, 2022, v. 38, n. 3, p. 710, doi. 10.1093/bioinformatics/btab738

By:

Tagashira, Masaki;
Asai, Kiyoshi

Publication type:

Article

DeepTrio: a ternary prediction system for protein–protein interaction using mask multiple parallel convolutional neural networks.

Published in:

Bioinformatics, 2022, v. 38, n. 3, p. 694, doi. 10.1093/bioinformatics/btab737

By:

Hu, Xiaotian;
Feng, Cong;
Zhou, Yincong;
Harrison, Andrew;
Chen, Ming

Publication type:

Article

computational methodology to diagnose sequence-variant dynamic perturbations by comparing atomic protein structures.

Published in:

Bioinformatics, 2022, v. 38, n. 3, p. 703, doi. 10.1093/bioinformatics/btab736

By:

Pacini, Lorenza;
Lesieur, Claire

Publication type:

Article

Phylotranscriptomic patterns of network stochasticity and pathway dynamics during embryogenesis.

Published in:

Bioinformatics, 2022, v. 38, n. 3, p. 763, doi. 10.1093/bioinformatics/btab735

By:

Ko, Kuei-Yueh;
Chen, Cho-Yi;
Juan, Hsueh-Fen;
Huang, Hsuan-Cheng

Publication type:

Article

TargetNet: functional microRNA target prediction with deep neural networks.

Published in:

Bioinformatics, 2022, v. 38, n. 3, p. 671, doi. 10.1093/bioinformatics/btab733

By:

Min, Seonwoo;
Lee, Byunghan;
Yoon, Sungroh

Publication type:

Article

DULoc: quantitatively unmixing protein subcellular location patterns in immunofluorescence images based on deep learning features.

Published in:

Bioinformatics, 2022, v. 38, n. 3, p. 827, doi. 10.1093/bioinformatics/btab730

By:

Xue, Min-Qi;
Zhu, Xi-Liang;
Wang, Ge;
Xu, Ying-Ying

Publication type:

Article

HPODNets: deep graph convolutional networks for predicting human protein–phenotype associations.

Published in:

Bioinformatics, 2022, v. 38, n. 3, p. 799, doi. 10.1093/bioinformatics/btab729

By:

Liu, Lizhi;
Mamitsuka, Hiroshi;
Zhu, Shanfeng

Publication type:

Article

GPSmatch: an R package for comparing Genomic-binding Profile Similarity among transcriptional regulators using customizable databases.

Published in:

Bioinformatics, 2022, v. 38, n. 3, p. 853, doi. 10.1093/bioinformatics/btab728

By:

Dong, Amy;
Bao, Xiaomin

Publication type:

Article

PMLB v1.0: an open-source dataset collection for benchmarking machine learning methods.

Published in:

Bioinformatics, 2022, v. 38, n. 3, p. 878, doi. 10.1093/bioinformatics/btab727

By:

Romano, Joseph D;
Le, Trang T;
Cava, William La;
Gregg, John T;
Goldberg, Daniel J;
Chakraborty, Praneel;
Ray, Natasha L;
Himmelstein, Daniel;
Fu, Weixuan;
Moore, Jason H

Publication type:

Article

Optimizing viral genome subsampling by genetic diversity and temporal distribution (TARDiS) for phylogenetics.

Published in:

Bioinformatics, 2022, v. 38, n. 3, p. 856, doi. 10.1093/bioinformatics/btab725

By:

Marini, Simone;
Mavian, Carla;
Riva, Alberto;
Prosperi, Mattia;
Salemi, Marco;
Magalis, Brittany Rife

Publication type:

Article

dsRBPBind: modeling the effect of RNA secondary structure on double-stranded RNA–protein binding.

Published in:

Bioinformatics, 2022, v. 38, n. 3, p. 687, doi. 10.1093/bioinformatics/btab724

By:

Shatoff, Elan;
Bundschuh, Ralf

Publication type:

Article

AncestralClust: clustering of divergent nucleotide sequences by ancestral sequence reconstruction using phylogenetic trees.

Published in:

Bioinformatics, 2022, v. 38, n. 3, p. 663, doi. 10.1093/bioinformatics/btab723

By:

Pipes, Lenore;
Nielsen, Rasmus

Publication type:

Article

Multimodal medical image fusion using adaptive co-occurrence filter-based decomposition optimization model.

Published in:

Bioinformatics, 2022, v. 38, n. 3, p. 818, doi. 10.1093/bioinformatics/btab721

By:

Zhu, Rui;
Li, Xiongfei;
Huang, Sa;
Zhang, Xiaoli

Publication type:

Article

BalLeRMix+: mixture model approaches for robust joint identification of both positive selection and long-term balancing selection.

Published in:

Bioinformatics, 2022, v. 38, n. 3, p. 861, doi. 10.1093/bioinformatics/btab720

By:

Cheng, Xiaoheng;
DeGiorgio, Michael

Publication type:

Article

WGA-LP: a pipeline for whole genome assembly of contaminated reads.

Published in:

Bioinformatics, 2022, v. 38, n. 3, p. 846, doi. 10.1093/bioinformatics/btab719

By:

Rossi, N;
Colautti, A;
Iacumin, L;
Piazza, C

Publication type:

Article

Accurate inference of gene regulatory interactions from spatial gene expression with deep contrastive learning.

Published in:

Bioinformatics, 2022, v. 38, n. 3, p. 746, doi. 10.1093/bioinformatics/btab718

By:

Zheng, Lujing;
Liu, Zhenhuan;
Yang, Yang;
Shen, Hong-Bin

Publication type:

Article

PMCE: efficient inference of expressive models of cancer evolution with high prognostic power.

Published in:

Bioinformatics, 2022, v. 38, n. 3, p. 754, doi. 10.1093/bioinformatics/btab717

By:

Angaroni, Fabrizio;
Chen, Kevin;
Damiani, Chiara;
Caravagna, Giulio;
Graudenzi, Alex;
Ramazzotti, Daniele

Publication type:

Article

Neuron segmentation using 3D wavelet integrated encoder–decoder network.

Published in:

Bioinformatics, 2022, v. 38, n. 3, p. 809, doi. 10.1093/bioinformatics/btab716

By:

Li, Qiufu;
Shen, Linlin

Publication type:

Article

HyperAttentionDTI: improving drug–protein interaction prediction by sequence-based deep learning with attention mechanism.

Published in:

Bioinformatics, 2022, v. 38, n. 3, p. 655, doi. 10.1093/bioinformatics/btab715

By:

Zhao, Qichang;
Zhao, Haochen;
Zheng, Kai;
Wang, Jianxin

Publication type:

Article

scMRA: a robust deep learning method to annotate scRNA-seq data with multiple reference datasets.

Published in:

Bioinformatics, 2022, v. 38, n. 3, p. 738, doi. 10.1093/bioinformatics/btab700

By:

Yuan, Musu;
Chen, Liang;
Deng, Minghua

Publication type:

Article

WikiNetworks: translating manually created biological pathways for topological analysis.

Published in:

Bioinformatics, 2022, v. 38, n. 3, p. 869, doi. 10.1093/bioinformatics/btab699

By:

Palshikar, Mukta G;
Hilchey, Shannon P;
Zand, Martin S;
Thakar, Juilee

Publication type:

Article

Multi-instance learning of graph neural networks for aqueous pKa prediction.

Published in:

Bioinformatics, 2022, v. 38, n. 3, p. 792, doi. 10.1093/bioinformatics/btab714

By:

Xiong, Jiacheng;
Li, Zhaojun;
Wang, Guangchao;
Fu, Zunyun;
Zhong, Feisheng;
Xu, Tingyang;
Liu, Xiaomeng;
Huang, Ziming;
Liu, Xiaohong;
Chen, Kaixian;
Jiang, Hualiang;
Zheng, Mingyue

Publication type:

Article

BERT-Kcr: prediction of lysine crotonylation sites by a transfer learning method with pre-trained BERT models.

Published in:

Bioinformatics, 2022, v. 38, n. 3, p. 648, doi. 10.1093/bioinformatics/btab712

By:

Qiao, Yanhua;
Zhu, Xiaolei;
Gong, Haipeng

Publication type:

Article

ImmuCellAI-mouse: a tool for comprehensive prediction of mouse immune cell abundance and immune microenvironment depiction.

Published in:

Bioinformatics, 2022, v. 38, n. 3, p. 785, doi. 10.1093/bioinformatics/btab711

By:

Miao, Ya-Ru;
Xia, Mengxuan;
Luo, Mei;
Luo, Tao;
Yang, Mei;
Guo, An-Yuan

Publication type:

Article

vcf2gwas: Python API for comprehensive GWAS analysis using GEMMA.

Published in:

Bioinformatics, 2022, v. 38, n. 3, p. 839, doi. 10.1093/bioinformatics/btab710

By:

Vogt, Frank;
Shirsekar, Gautam;
Weigel, Detlef

Publication type:

Article

Rediscover: an R package to identify mutually exclusive mutations.

Published in:

Bioinformatics, 2022, v. 38, n. 3, p. 844, doi. 10.1093/bioinformatics/btab709

By:

Ferrer-Bonsoms, Juan A;
Jareno, Laura;
Rubio, Angel

Publication type:

Article

FindNonCoding: rapid and simple detection of non-coding RNAs in genomes.

Published in:

Bioinformatics, 2022, v. 38, n. 3, p. 841, doi. 10.1093/bioinformatics/btab708

By:

Wright, Erik S

Publication type:

Article

MS2AI: automated repurposing of public peptide LC-MS data for machine learning applications.

Published in:

Bioinformatics, 2022, v. 38, n. 3, p. 875, doi. 10.1093/bioinformatics/btab701

By:

Rehfeldt, Tobias Greisager;
Krawczyk, Konrad;
Bøgebjerg, Mathias;
Schwämmle, Veit;
Röttger, Richard

Publication type:

Article

MCRL: using a reference library to compress a metagenome into a non-redundant list of sequences, considering viruses as a case study.

Published in:

Bioinformatics, 2022, v. 38, n. 3, p. 631, doi. 10.1093/bioinformatics/btab703

By:

Tadmor, Arbel D;
Phillips, Rob

Publication type:

Article

BioVAE: a pre-trained latent variable language model for biomedical text mining.

Published in:

Bioinformatics, 2022, v. 38, n. 3, p. 872, doi. 10.1093/bioinformatics/btab702

By:

Trieu, Hai-Long;
Miwa, Makoto;
Ananiadou, Sophia

Publication type:

Article

Multiomix: a cloud-based platform to infer cancer genomic and epigenomic events associated with gene expression modulation.

Published in:

Bioinformatics, 2022, v. 38, n. 3, p. 866, doi. 10.1093/bioinformatics/btab678

By:

Camele, Genaro;
Menazzi, Sebastian;
Chanfreau, Hernán;
Marraco, Agustin;
Hasperué, Waldo;
Butti, Matias D;
Abba, Martin C

Publication type:

Article

ShinyArchR.UiO: user-friendly,integrative and open-source tool for visualization of single-cell ATAC-seq data using ArchR.

Published in:

Bioinformatics, 2022, v. 38, n. 3, p. 834, doi. 10.1093/bioinformatics/btab680

By:

Sharma, Ankush;
Akshay, Akshay;
Rogne, Marie;
Eskeland, Ragnhild

Publication type:

Article

MuWU: Mutant-seq library analysis and annotation.

Published in:

Bioinformatics, 2022, v. 38, n. 3, p. 837, doi. 10.1093/bioinformatics/btab679

By:

Stöcker, Tyll;
Altrogge, Lena;
Marcon, Caroline;
Win, Yan Naing;
Hochholdinger, Frank;
Schoof, Heiko

Publication type:

Article

AlphaMap: an open-source Python package for the visual annotation of proteomics data with sequence-specific knowledge.

Published in:

Bioinformatics, 2022, v. 38, n. 3, p. 849, doi. 10.1093/bioinformatics/btab674

By:

Voytik, Eugenia;
Bludau, Isabell;
Willems, Sander;
Hansen, Fynn M;
Brunner, Andreas-David;
Strauss, Maximilian T;
Mann, Matthias

Publication type:

Article

systems biology simulation core library.

Published in:

Bioinformatics, 2022, v. 38, n. 3, p. 864, doi. 10.1093/bioinformatics/btab669

By:

Panchiwala, Hemil;
Shah, Shalin;
Planatscher, Hannes;
Zakharchuk, Mykola;
König, Matthias;
Dräger, Andreas

Publication type:

Article

Corrigendum to: Decombinator V4: an improved AIRR-C compliant software package for T-cell receptor sequence annotation.

Published in:

2022

By:

Peacock, Thomas;
Heather, James M;
Ronel, Tahel;
Chain, Benny

Publication type:

Correction Notice

DiscoRhythm: an easy-to-use web application and R package for discovering rhythmicity.

Published in:

Bioinformatics, 2022, v. 38, n. 3, p. 882, doi. 10.1093/bioinformatics/btab517

By:

Carlucci, Matthew;
Kriščiūnas, Algimantas;
Li, Haohan;
Gibas, Povilas;
Koncevičius, Karolis;
Petronis, Art;
Oh, Gabriel

Publication type:

Article

Adversarial generation of gene expression data.

Published in:

Bioinformatics, 2022, v. 38, n. 3, p. 730, doi. 10.1093/bioinformatics/btab035

By:

Viñas, Ramon;
Andrés-Terré, Helena;
Liò, Pietro;
Bryson, Kevin

Publication type:

Article