Works matching IS 13674803 AND DT 2022 AND VI 38 AND IP 5

Results: 48

PHIST: fast and accurate prediction of prokaryotic hosts from metagenomic viral sequences.

Published in:

Bioinformatics, 2022, v. 38, n. 5, p. 1447, doi. 10.1093/bioinformatics/btab837

By:

Zielezinski, Andrzej;
Deorowicz, Sebastian;
Gudyś, Adam

Publication type:

Article

InDeep: 3D fully convolutional neural networks to assist in silico drug design on protein–protein interactions.

Published in:

Bioinformatics, 2022, v. 38, n. 5, p. 1261, doi. 10.1093/bioinformatics/btab849

By:

Mallet, Vincent;
Ruano, Luis Checa;
Franel, Alexandra Moine;
Nilges, Michael;
Druart, Karen;
Bouvier, Guillaume;
Sperandio, Olivier

Publication type:

Article

InterARTIC: an interactive web application for whole-genome nanopore sequencing analysis of SARS-CoV-2 and other viruses.

Published in:

Bioinformatics, 2022, v. 38, n. 5, p. 1443, doi. 10.1093/bioinformatics/btab846

By:

Ferguson, James M;
Gamaarachchi, Hasindu;
Nguyen, Thanh;
Gollon, Alyne;
Tong, Stephanie;
Aquilina-Reid, Chiara;
Bowen-James, Rachel;
Deveson, Ira W

Publication type:

Article

Virtifier: a deep learning-based identifier for viral sequences from metagenomes.

Published in:

Bioinformatics, 2022, v. 38, n. 5, p. 1216, doi. 10.1093/bioinformatics/btab845

By:

Miao, Yan;
Liu, Fu;
Hou, Tao;
Liu, Yun

Publication type:

Article

RNAglib: a python package for RNA 2.5 D graphs.

Published in:

Bioinformatics, 2022, v. 38, n. 5, p. 1458, doi. 10.1093/bioinformatics/btab844

By:

Mallet, Vincent;
Oliver, Carlos;
Broadbent, Jonathan;
Hamilton, William L;
Waldispühl, Jérôme

Publication type:

Article

convolutional neural network for segmentation of yeast cells without manual training annotations.

Published in:

Bioinformatics, 2022, v. 38, n. 5, p. 1427, doi. 10.1093/bioinformatics/btab835

By:

Kruitbosch, Herbert T;
Mzayek, Yasmin;
Omlor, Sara;
Guerra, Paolo;
Milias-Argeitis, Andreas

Publication type:

Article

swCAM: estimation of subtype-specific expressions in individual samples with unsupervised sample-wise deconvolution.

Published in:

Bioinformatics, 2022, v. 38, n. 5, p. 1403, doi. 10.1093/bioinformatics/btab839

By:

Chen, Lulu;
Wu, Chiung-Ting;
Lin, Chia-Hsiang;
Dai, Rujia;
Liu, Chunyu;
Clarke, Robert;
Yu, Guoqiang;
Eyk, Jennifer E Van;
Herrington, David M;
Wang, Yue

Publication type:

Article

Generation of ENSEMBL-based proteogenomics databases boosts the identification of non-canonical peptides.

Published in:

Bioinformatics, 2022, v. 38, n. 5, p. 1470, doi. 10.1093/bioinformatics/btab838

By:

Umer, Husen M;
Audain, Enrique;
Zhu, Yafeng;
Pfeuffer, Julianus;
Sachsenberg, Timo;
Lehtiö, Janne;
Branca, Rui M;
Perez-Riverol, Yasset

Publication type:

Article

EcoPLOT: dynamic analysis of biogeochemical data.

Published in:

Bioinformatics, 2022, v. 38, n. 5, p. 1480, doi. 10.1093/bioinformatics/btab842

By:

Sanchez, Christopher D;
Brown, J Benjamin;
Gal-Oz, Omree;
Singer, Esther

Publication type:

Article

On the relation between input and output distributions of scRNA-seq experiments.

Published in:

Bioinformatics, 2022, v. 38, n. 5, p. 1336, doi. 10.1093/bioinformatics/btab841

By:

Schwabe, Daniel;
Falcke, Martin

Publication type:

Article

CellMeSH: probabilistic cell-type identification using indexed literature.

Published in:

Bioinformatics, 2022, v. 38, n. 5, p. 1393, doi. 10.1093/bioinformatics/btab834

By:

Mao, Shunfu;
Zhang, Yue;
Seelig, Georg;
Kannan, Sreeram

Publication type:

Article

Structural feature-driven pattern analysis for multitarget modulator landscapes.

Published in:

Bioinformatics, 2022, v. 38, n. 5, p. 1385, doi. 10.1093/bioinformatics/btab832

By:

Namasivayam, Vigneshwaran;
Stefan, Katja;
Silbermann, Katja;
Pahnke, Jens;
Wiese, Michael;
Stefan, Sven Marcel

Publication type:

Article

scShaper: an ensemble method for fast and accurate linear trajectory inference from single-cell RNA-seq data.

Published in:

Bioinformatics, 2022, v. 38, n. 5, p. 1328, doi. 10.1093/bioinformatics/btab831

By:

Smolander, Johannes;
Junttila, Sini;
Venäläinen, Mikko S;
Elo, Laura L

Publication type:

Article

Unsupervised construction of computational graphs for gene expression data with explicit structural inductive biases.

Published in:

Bioinformatics, 2022, v. 38, n. 5, p. 1320, doi. 10.1093/bioinformatics/btab830

By:

Scherer, Paul;
Trębacz, Maja;
Simidjievski, Nikola;
Viñas, Ramon;
Shams, Zohreh;
Terre, Helena Andres;
Jamnik, Mateja;
Liò, Pietro

Publication type:

Article

EnGRaiN: a supervised ensemble learning method for recovery of large-scale gene regulatory networks.

Published in:

Bioinformatics, 2022, v. 38, n. 5, p. 1312, doi. 10.1093/bioinformatics/btab829

By:

Aluru, Maneesha;
Shrivastava, Harsh;
Chockalingam, Sriram P;
Shivakumar, Shruti;
Aluru, Srinivas

Publication type:

Article

CNApy: a CellNetAnalyzer GUI in Python for analyzing and designing metabolic networks.

Published in:

Bioinformatics, 2022, v. 38, n. 5, p. 1467, doi. 10.1093/bioinformatics/btab828

By:

Thiele, Sven;
Kamp, Axel von;
Bekiaris, Pavlos Stephanos;
Schneider, Philipp;
Klamt, Steffen

Publication type:

Article

No one tool to rule them all: prokaryotic gene prediction tool annotations are highly dependent on the organism of study.

Published in:

Bioinformatics, 2022, v. 38, n. 5, p. 1198, doi. 10.1093/bioinformatics/btab827

By:

Dimonaco, Nicholas J;
Aubrey, Wayne;
Kenobi, Kim;
Clare, Amanda;
Creevey, Christopher J

Publication type:

Article

network-based drug repurposing method via non-negative matrix factorization.

Published in:

Bioinformatics, 2022, v. 38, n. 5, p. 1369, doi. 10.1093/bioinformatics/btab826

By:

Sadeghi, Shaghayegh;
Lu, Jianguo;
Ngom, Alioune

Publication type:

Article

pystablemotifs: Python library for attractor identification and control in Boolean networks.

Published in:

Bioinformatics, 2022, v. 38, n. 5, p. 1465, doi. 10.1093/bioinformatics/btab825

By:

Rozum, Jordan C;
Deritei, Dávid;
Park, Kyu Hyong;
Zañudo, Jorge Gómez Tejeda;
Albert, Réka

Publication type:

Article

SCRIP: an accurate simulator for single-cell RNA sequencing data.

Published in:

Bioinformatics, 2022, v. 38, n. 5, p. 1304, doi. 10.1093/bioinformatics/btab824

By:

Qin, Fei;
Luo, Xizhi;
Xiao, Feifei;
Cai, Guoshuai

Publication type:

Article

miRe2e: a full end-to-end deep model based on transformers for prediction of pre-miRNAs.

Published in:

Bioinformatics, 2022, v. 38, n. 5, p. 1191, doi. 10.1093/bioinformatics/btab823

By:

Raad, Jonathan;
Bugnon, Leandro A;
Milone, Diego H;
Stegmayer, Georgina

Publication type:

Article

Automated classification of cytogenetic abnormalities in hematolymphoid neoplasms.

Published in:

Bioinformatics, 2022, v. 38, n. 5, p. 1420, doi. 10.1093/bioinformatics/btab822

By:

Cox, Andrew;
Park, Chanhee;
Koduru, Prasad;
Wilson, Kathleen;
Weinberg, Olga;
Chen, Weina;
García, Rolando;
Kim, Daehwan

Publication type:

Article

HDMC: a novel deep learning-based framework for removing batch effects in single-cell RNA-seq data.

Published in:

Bioinformatics, 2022, v. 38, n. 5, p. 1295, doi. 10.1093/bioinformatics/btab821

By:

Wang, Xiao;
Wang, Jia;
Zhang, Han;
Huang, Shenwei;
Yin, Yanbin

Publication type:

Article

springD2A: capturing uncertainty in disease–drug association prediction with model integration.

Published in:

Bioinformatics, 2022, v. 38, n. 5, p. 1353, doi. 10.1093/bioinformatics/btab820

By:

Wang, Weiwen;
Zhang, Xiwen;
Dai, Dao-Qing

Publication type:

Article

RCSB Protein Data Bank: improved annotation, search and visualization of membrane protein structures archived in the PDB.

Published in:

Bioinformatics, 2022, v. 38, n. 5, p. 1452, doi. 10.1093/bioinformatics/btab813

By:

Bittrich, Sebastian;
Rose, Yana;
Segura, Joan;
Lowe, Robert;
Westbrook, John D;
Duarte, Jose M;
Burley, Stephen K

Publication type:

Article

TreeAndLeaf: an R/Bioconductor package for graphs and trees with focus on the leaves.

Published in:

Bioinformatics, 2022, v. 38, n. 5, p. 1463, doi. 10.1093/bioinformatics/btab819

By:

Cardoso, Milena A;
Rizzardi, Luis E A;
Kume, Leonardo W;
Groeneveld, Clarice S;
Trefflich, Sheyla;
Morais, Diego A A;
Dalmolin, Rodrigo J S;
Ponder, Bruce A J;
Meyer, Kerstin B;
Castro, Mauro A A

Publication type:

Article

Back translation for molecule generation.

Published in:

Bioinformatics, 2022, v. 38, n. 5, p. 1244, doi. 10.1093/bioinformatics/btab817

By:

Fan, Yang;
Xia, Yingce;
Zhu, Jinhua;
Wu, Lijun;
Xie, Shufang;
Qin, Tao

Publication type:

Article

HolistIC: leveraging Hi–C and whole genome shotgun sequencing for double minute chromosome discovery.

Published in:

Bioinformatics, 2022, v. 38, n. 5, p. 1208, doi. 10.1093/bioinformatics/btab816

By:

Hayes, Matthew;
Nguyen, Angela;
Islam, Rahib;
Butler, Caryn;
Tran, Ethan;
Mullins, Derrick;
Hicks, Chindo

Publication type:

Article

Identification, semantic annotation and comparison of combinations of functional elements in multiple biological conditions.

Published in:

Bioinformatics, 2022, v. 38, n. 5, p. 1183, doi. 10.1093/bioinformatics/btab815

By:

Leone, Michele;
Galeota, Eugenia;
Masseroli, Marco;
Pelizzola, Mattia

Publication type:

Article

RCandy: an R package for visualizing homologous recombinations in bacterial genomes.

Published in:

Bioinformatics, 2022, v. 38, n. 5, p. 1450, doi. 10.1093/bioinformatics/btab814

By:

Chaguza, Chrispin;
Tonkin-Hill, Gerry;
Lo, Stephanie W;
Hadfield, James;
Croucher, Nicholas J;
Harris, Simon R;
Bentley, Stephen D

Publication type:

Article

3MCor: an integrative web server for metabolome–microbiome-metadata correlation analysis.

Published in:

Bioinformatics, 2022, v. 38, n. 5, p. 1378, doi. 10.1093/bioinformatics/btab818

By:

Sun, Tao;
Li, Mengci;
Yu, Xiangtian;
Liang, Dandan;
Xie, Guoxiang;
Sang, Chao;
Jia, Wei;
Chen, Tianlu

Publication type:

Article

Detecting spatially co-expressed gene clusters with functional coherence by graph-regularized convolutional neural network.

Published in:

Bioinformatics, 2022, v. 38, n. 5, p. 1344, doi. 10.1093/bioinformatics/btab812

By:

Song, Tianci;
Markham, Kathleen K;
Li, Zhuliu;
Muller, Kristen E;
Greenham, Kathleen;
Kuang, Rui

Publication type:

Article

Predicting the multi-label protein subcellular localization through multi-information fusion and MLSI dimensionality reduction based on MLFE classifier.

Published in:

Bioinformatics, 2022, v. 38, n. 5, p. 1223, doi. 10.1093/bioinformatics/btab811

By:

Liu, Yushuang;
Jin, Shuping;
Gao, Hongli;
Wang, Xue;
Wang, Congjing;
Zhou, Weifeng;
Yu, Bin

Publication type:

Article

DeepIDP-2L: protein intrinsically disordered region prediction by combining convolutional attention network and hierarchical attention network.

Published in:

Bioinformatics, 2022, v. 38, n. 5, p. 1252, doi. 10.1093/bioinformatics/btab810

By:

Tang, Yi-Jun;
Pang, Yi-He;
Liu, Bin

Publication type:

Article

ProteoDisco: a flexible R approach to generate customized protein databases for extended search space of novel and variant proteins in proteogenomic studies.

Published in:

Bioinformatics, 2022, v. 38, n. 5, p. 1437, doi. 10.1093/bioinformatics/btab809

By:

Geer, Wesley S van de;
Riet, Job van;
Werken, Harmen J G van de

Publication type:

Article

DeepCEL0 for 2D single-molecule localization in fluorescence microscopy.

Published in:

Bioinformatics, 2022, v. 38, n. 5, p. 1411, doi. 10.1093/bioinformatics/btab808

By:

Cascarano, Pasquale;
Comes, Maria Colomba;
Sebastiani, Andrea;
Mencattini, Arianna;
Piccolomini, Elena Loli;
Martinelli, Eugenio

Publication type:

Article

Isoform-level quantification for single-cell RNA sequencing.

Published in:

Bioinformatics, 2022, v. 38, n. 5, p. 1287, doi. 10.1093/bioinformatics/btab807

By:

Pan, Lu;
Dinh, Huy Q;
Pawitan, Yudi;
Vu, Trung Nghia

Publication type:

Article

Make Interactive Complex Heatmaps in R.

Published in:

Bioinformatics, 2022, v. 38, n. 5, p. 1460, doi. 10.1093/bioinformatics/btab806

By:

Gu, Zuguang;
Hübschmann, Daniel

Publication type:

Article

trfermikit: a tool to discover VNTR-associated deletions.

Published in:

Bioinformatics, 2022, v. 38, n. 5, p. 1231, doi. 10.1093/bioinformatics/btab805

By:

McHale, Peter;
Quinlan, Aaron R

Publication type:

Article

CellVGAE: an unsupervised scRNA-seq analysis workflow with graph attention networks.

Published in:

Bioinformatics, 2022, v. 38, n. 5, p. 1277, doi. 10.1093/bioinformatics/btab804

By:

Buterez, David;
Bica, Ioana;
Tariq, Ifrah;
Andrés-Terré, Helena;
Liò, Pietro

Publication type:

Article

SARS-CoV-2 Interactome 3D: A Web interface for 3D visualization and analysis of SARS-CoV-2–human mimicry and interactions.

Published in:

Bioinformatics, 2022, v. 38, n. 5, p. 1455, doi. 10.1093/bioinformatics/btab799

By:

Ovek, Damla;
Taweel, Ameer;
Abali, Zeynep;
Tezsezen, Ece;
Koroglu, Yunus Emre;
Tsai, Chung-Jung;
Nussinov, Ruth;
Keskin, Ozlem;
Gursoy, Attila

Publication type:

Article

SBGNview: towards data analysis, integration and visualization on all pathways.

Published in:

Bioinformatics, 2022, v. 38, n. 5, p. 1473, doi. 10.1093/bioinformatics/btab793

By:

Dong, Xiaoxi;
Vegesna, Kovidh;
Brouwer, Cory;
Luo, Weijun

Publication type:

Article

spiralize: an R package for visualizing data on spirals.

Published in:

Bioinformatics, 2022, v. 38, n. 5, p. 1434, doi. 10.1093/bioinformatics/btab778

By:

Gu, Zuguang;
Hübschmann, Daniel

Publication type:

Article

DeepKG: an end-to-end deep learning-based workflow for biomedical knowledge graph extraction, optimization and applications.

Published in:

Bioinformatics, 2022, v. 38, n. 5, p. 1477, doi. 10.1093/bioinformatics/btab767

By:

Li, Zongren;
Zhong, Qin;
Yang, Jing;
Duan, Yongjie;
Wang, Wenjun;
Wu, Chengkun;
He, Kunlun

Publication type:

Article

PhyloCSF++: a fast and user-friendly implementation of PhyloCSF with annotation tools.

Published in:

Bioinformatics, 2022, v. 38, n. 5, p. 1440, doi. 10.1093/bioinformatics/btab756

By:

Pockrandt, Christopher;
Steinegger, Martin;
Salzberg, Steven L

Publication type:

Article

SCANCell reveals diverse inter-cluster interaction patterns in systemic lupus erythematosus across the disease spectrum.

Published in:

Bioinformatics, 2022, v. 38, n. 5, p. 1361, doi. 10.1093/bioinformatics/btab713

By:

Zhang, Lulu;
Liu, Xiao;
Chen, Xiaoxiang;
Warden, Antony R;
Yu, Youyi;
Huang, Baozhen;
Ding, Xianting

Publication type:

Article

RoDiCE: robust differential protein co-expression analysis for cancer complexome.

Published in:

Bioinformatics, 2022, v. 38, n. 5, p. 1269, doi. 10.1093/bioinformatics/btab612

By:

Matsui, Yusuke;
Abe, Yuichi;
Uno, Kohei;
Miyano, Satoru

Publication type:

Article

DeepMP: a deep learning tool to detect DNA base modifications on Nanopore sequencing data.

Published in:

Bioinformatics, 2022, v. 38, n. 5, p. 1235, doi. 10.1093/bioinformatics/btab745

By:

Bonet, Jose;
Chen, Mandi;
Dabad, Marc;
Heath, Simon;
Gonzalez-Perez, Abel;
Lopez-Bigas, Nuria;
Lagergren, Jens

Publication type:

Article