Works matching IS 13674803 AND DT 2023 AND VI 39 AND IP 10

Results: 53

Struct2GO: protein function prediction based on graph pooling algorithm and AlphaFold2 structure information.

Published in:

Bioinformatics, 2023, v. 39, n. 10, p. 1, doi. 10.1093/bioinformatics/btad637

By:

Jiao, Peishun;
Wang, Beibei;
Wang, Xuan;
Liu, Bo;
Wang, Yadong;
Li, Junyi

Publication type:

Article

Evaluation of haplotype-aware long-read error correction with hifieval.

Published in:

Bioinformatics, 2023, v. 39, n. 10, p. 1, doi. 10.1093/bioinformatics/btad631

By:

Guo, Yujie;
Feng, Xiaowen;
Li, Heng

Publication type:

Article

stVAE deconvolves cell-type composition in large-scale cellular resolution spatial transcriptomics.

Published in:

Bioinformatics, 2023, v. 39, n. 10, p. 1, doi. 10.1093/bioinformatics/btad642

By:

Li, Chen;
Chan, Ting-Fung;
Yang, Can;
Lin, Zhixiang

Publication type:

Article

Privacy-preserving federated genome-wide association studies via dynamic sampling.

Published in:

Bioinformatics, 2023, v. 39, n. 10, p. 1, doi. 10.1093/bioinformatics/btad639

By:

Wang, Xinyue;
Dervishi, Leonard;
Li, Wentao;
Ayday, Erman;
Jiang, Xiaoqian;
Vaidya, Jaideep

Publication type:

Article

Semla: a versatile toolkit for spatially resolved transcriptomics analysis and visualization.

Published in:

Bioinformatics, 2023, v. 39, n. 10, p. 1, doi. 10.1093/bioinformatics/btad626

By:

Larsson, Ludvig;
Franzén, Lovisa;
Ståhl, Patrik L;
Lundeberg, Joakim

Publication type:

Article

SBILib: a handle for protein modeling and engineering.

Published in:

Bioinformatics, 2023, v. 39, n. 10, p. 1, doi. 10.1093/bioinformatics/btad613

By:

Gohl, Patrick;
Bonet, Jaume;
Fornes, Oriol;
Planas-Iglesias, Joan;
Fernandez-Fuentes, Narcís;
Oliva, Baldo

Publication type:

Article

scHiCDiff: detecting differential chromatin interactions in single-cell Hi-C data.

Published in:

Bioinformatics, 2023, v. 39, n. 10, p. 1, doi. 10.1093/bioinformatics/btad625

By:

Liu, Huiling;
Ma, Wenxiu

Publication type:

Article

CAAStools: a toolbox to identify and test Convergent Amino Acid Substitutions.

Published in:

Bioinformatics, 2023, v. 39, n. 10, p. 1, doi. 10.1093/bioinformatics/btad623

By:

Barteri, Fabio;
Valenzuela, Alejandro;
Farré, Xavier;
Juan, David de;
Muntané, Gerard;
Esteve-Altava, Borja;
Navarro, Arcadi

Publication type:

Article

ggkegg: analysis and visualization of KEGG data utilizing the grammar of graphics.

Published in:

Bioinformatics, 2023, v. 39, n. 10, p. 1, doi. 10.1093/bioinformatics/btad622

By:

Sato, Noriaki;
Uematsu, Miho;
Fujimoto, Kosuke;
Uematsu, Satoshi;
Imoto, Seiya

Publication type:

Article

PanKmer: k-mer-based and reference-free pangenome analysis.

Published in:

Bioinformatics, 2023, v. 39, n. 10, p. 1, doi. 10.1093/bioinformatics/btad621

By:

Aylward, Anthony J;
Petrus, Semar;
Mamerto, Allen;
Hartwick, Nolan T;
Michael, Todd P

Publication type:

Article

Predicting enzymatic function of protein sequences with attention.

Published in:

Bioinformatics, 2023, v. 39, n. 10, p. 1, doi. 10.1093/bioinformatics/btad620

By:

Buton, Nicolas;
Coste, François;
Cunff, Yann Le

Publication type:

Article

Constructing maps between distinct cell fates and parametric conditions by systematic perturbations.

Published in:

Bioinformatics, 2023, v. 39, n. 10, p. 1, doi. 10.1093/bioinformatics/btad624

By:

Tang, Ruoyu;
He, Xinyu;
Wang, Ruiqi

Publication type:

Article

MsQuality: an interoperable open-source package for the calculation of standardized quality metrics of mass spectrometry data.

Published in:

Bioinformatics, 2023, v. 39, n. 10, p. 1, doi. 10.1093/bioinformatics/btad618

By:

Naake, Thomas;
Rainer, Johannes;
Huber, Wolfgang

Publication type:

Article

Investigation of the BERT model on nucleotide sequences with non-standard pre-training and evaluation of different k-mer embeddings.

Published in:

Bioinformatics, 2023, v. 39, n. 10, p. 1, doi. 10.1093/bioinformatics/btad617

By:

Zhang, Yao-zhong;
Bai, Zeheng;
Imoto, Seiya

Publication type:

Article

DeepPeptide predicts cleaved peptides in proteins using conditional random fields.

Published in:

Bioinformatics, 2023, v. 39, n. 10, p. 1, doi. 10.1093/bioinformatics/btad616

By:

Teufel, Felix;
Refsgaard, Jan Christian;
Madsen, Christian Toft;
Stahlhut, Carsten;
Grønborg, Mads;
Winther, Ole;
Madsen, Dennis

Publication type:

Article

simpleaf: a simple, flexible, and scalable framework for single-cell data processing using alevin-fry.

Published in:

Bioinformatics, 2023, v. 39, n. 10, p. 1, doi. 10.1093/bioinformatics/btad614

By:

He, Dongze;
Patro, Rob

Publication type:

Article

iLSGRN: inference of large-scale gene regulatory networks based on multi-model fusion.

Published in:

Bioinformatics, 2023, v. 39, n. 10, p. 1, doi. 10.1093/bioinformatics/btad619

By:

Wu, Yiming;
Qian, Bing;
Wang, Anqi;
Dong, Heng;
Zhu, Enqiang;
Ma, Baoshan

Publication type:

Article

SHIP: identifying antimicrobial resistance gene transfer between plasmids.

Published in:

Bioinformatics, 2023, v. 39, n. 10, p. 1, doi. 10.1093/bioinformatics/btad612

By:

Teixeira, Marco;
Pillay, Stephanie;
Urhan, Aysun;
Abeel, Thomas

Publication type:

Article

optima: an open-source R package for the Tapestri platform for integrative single cell multiomics data analysis.

Published in:

Bioinformatics, 2023, v. 39, n. 10, p. 1, doi. 10.1093/bioinformatics/btad611

By:

Pei, Dong;
Griffard, Rachel;
Yellapu, Nanda Kumar;
Nissen, Emily;
Koestler, Devin C

Publication type:

Article

Scalable inference of cell differentiation networks in gene therapy clonal tracking studies of haematopoiesis.

Published in:

Bioinformatics, 2023, v. 39, n. 10, p. 1, doi. 10.1093/bioinformatics/btad605

By:

Core, Luca Del;
Pellin, Danilo;
Wit, Ernst C;
Grzegorczyk, Marco A

Publication type:

Article

UDock2: interactive real-time multi-body protein–protein docking software.

Published in:

Bioinformatics, 2023, v. 39, n. 10, p. 1, doi. 10.1093/bioinformatics/btad609

By:

Plateau-Holleville, Cyprien;
Guionnière, Simon;
Boyer, Benjamin;
Jiménez-Garcia, Brian;
Levieux, Guillaume;
Mérillou, Stéphane;
Maria, Maxime;
Montes, Matthieu

Publication type:

Article

Surfaces: a software to quantify and visualize interactions within and between proteins and ligands.

Published in:

Bioinformatics, 2023, v. 39, n. 10, p. 1, doi. 10.1093/bioinformatics/btad608

By:

Teruel, Natália;
Borges, Vinicius Magalhães;
Najmanovich, Rafael

Publication type:

Article

Predicting synergistic anticancer drug combination based on low-rank global attention mechanism and bilinear predictor.

Published in:

Bioinformatics, 2023, v. 39, n. 10, p. 1, doi. 10.1093/bioinformatics/btad607

By:

Gan, Yanglan;
Huang, Xingyu;
Guo, Wenjing;
Yan, Cairong;
Zou, Guobing

Publication type:

Article

Aliro: an automated machine learning tool leveraging large language models.

Published in:

Bioinformatics, 2023, v. 39, n. 10, p. 1, doi. 10.1093/bioinformatics/btad606

By:

Choi, Hyunjun;
Moran, Jay;
Matsumoto, Nicholas;
Hernandez, Miguel E;
Moore, Jason H

Publication type:

Article

Adjustment of spurious correlations in co-expression measurements from RNA-Sequencing data.

Published in:

Bioinformatics, 2023, v. 39, n. 10, p. 1, doi. 10.1093/bioinformatics/btad610

By:

Hsieh, Ping-Han;
Lopes-Ramos, Camila Miranda;
Zucknick, Manuela;
Sandve, Geir Kjetil;
Glass, Kimberly;
Kuijjer, Marieke Lydia

Publication type:

Article

Evidential meta-model for molecular property prediction.

Published in:

Bioinformatics, 2023, v. 39, n. 10, p. 1, doi. 10.1093/bioinformatics/btad604

By:

Ham, Kyung Pyo;
Sael, Lee

Publication type:

Article

An improved rhythmicity analysis method using Gaussian Processes detects cell-density dependent circadian oscillations in stem cells.

Published in:

Bioinformatics, 2023, v. 39, n. 10, p. 1, doi. 10.1093/bioinformatics/btad602

By:

Sahay, Shabnam;
Adhikari, Shishir;
Hormoz, Sahand;
Chakrabarti, Shaon

Publication type:

Article

Design of optimal labeling patterns for optical genome mapping via information theory.

Published in:

Bioinformatics, 2023, v. 39, n. 10, p. 1, doi. 10.1093/bioinformatics/btad601

By:

Nogin, Yevgeni;
Bar-Lev, Daniella;
Hanania, Dganit;
Zur, Tahir Detinis;
Ebenstein, Yuval;
Yaakobi, Eitan;
Weinberger, Nir;
Shechtman, Yoav

Publication type:

Article

Balancing biomass reaction stoichiometry and measured fluxes in flux balance analysis.

Published in:

Bioinformatics, 2023, v. 39, n. 10, p. 1, doi. 10.1093/bioinformatics/btad600

By:

Kamp, Axel von;
Klamt, Steffen

Publication type:

Article

GNorm2: an improved gene name recognition and normalization system.

Published in:

Bioinformatics, 2023, v. 39, n. 10, p. 1, doi. 10.1093/bioinformatics/btad599

By:

Wei, Chih-Hsuan;
Luo, Ling;
Islamaj, Rezarta;
Lai, Po-Ting;
Lu, Zhiyong

Publication type:

Article

Extending protein interaction networks using proteoforms and small molecules.

Published in:

Bioinformatics, 2023, v. 39, n. 10, p. 1, doi. 10.1093/bioinformatics/btad598

By:

Sánchez, Luis Francisco Hernández;
Burger, Bram;
Campos, Rodrigo Alexander Castro;
Johansson, Stefan;
Njølstad, Pål Rasmus;
Barsnes, Harald;
Vaudel, Marc

Publication type:

Article

Correction to: BIODICA: a computational environment for Independent Component Analysis of omics data.

Published in:: 2023
Publication type:: Correction Notice

DeepCCI: a deep learning framework for identifying cell–cell interactions from single-cell RNA sequencing data.

Published in:

Bioinformatics, 2023, v. 39, n. 10, p. 1, doi. 10.1093/bioinformatics/btad596

By:

Yang, Wenyi;
Wang, Pingping;
Luo, Meng;
Cai, Yideng;
Xu, Chang;
Xue, Guangfu;
Jin, Xiyun;
Cheng, Rui;
Que, Jinhao;
Pang, Fenglan;
Yang, Yuexin;
Nie, Huan;
Jiang, Qinghua;
Liu, Zhigang;
Xu, Zhaochun

Publication type:

Article

compleasm: a faster and more accurate reimplementation of BUSCO.

Published in:

Bioinformatics, 2023, v. 39, n. 10, p. 1, doi. 10.1093/bioinformatics/btad595

By:

Huang, Neng;
Li, Heng

Publication type:

Article

ScribbleDom: using scribble-annotated histology images to identify domains in spatial transcriptomics data.

Published in:

Bioinformatics, 2023, v. 39, n. 10, p. 1, doi. 10.1093/bioinformatics/btad594

By:

Rahman, Mohammad Nuwaisir;
Noman, Abdullah Al;
Turza, Abir Mohammad;
Abrar, Mohammed Abid;
Samee, Md Abul Hassan;
Rahman, M Saifur

Publication type:

Article

SPA-STOCSY: an automated tool for identifying annotated and non-annotated metabolites in high-throughput NMR spectra.

Published in:

Bioinformatics, 2023, v. 39, n. 10, p. 1, doi. 10.1093/bioinformatics/btad593

By:

Han, Xu;
Wang, Wanli;
Ma, Li-Hua;
AI-Ramahi, Ismael;
Botas, Juan;
MacKenzie, Kevin;
Allen, Genevera I;
Young, Damian W;
Liu, Zhandong;
Maletic-Savatic, Mirjana

Publication type:

Article

MuDCoD: multi-subject community detection in personalized dynamic gene networks from single-cell RNA sequencing.

Published in:

Bioinformatics, 2023, v. 39, n. 10, p. 1, doi. 10.1093/bioinformatics/btad592

By:

Şapcı, Ali Osman Berk;
Lu, Shan;
Yan, Shuchen;
Ay, Ferhat;
Tastan, Oznur;
Keleş, Sündüz

Publication type:

Article

DeepUMQA3: a web server for accurate assessment of interface residue accuracy in protein complexes.

Published in:

Bioinformatics, 2023, v. 39, n. 10, p. 1, doi. 10.1093/bioinformatics/btad591

By:

Liu, Jun;
Liu, Dong;
Zhang, Gui-Jun

Publication type:

Article

Using a novel structure/function approach to select diverse swine major histocompatibility complex 1 alleles to predict epitopes for vaccine development.

Published in:

Bioinformatics, 2023, v. 39, n. 10, p. 1, doi. 10.1093/bioinformatics/btad590

By:

Khatooni, Zahed;
Teymourian, Navid;
Wilson, Heather L

Publication type:

Article

Unbiased curriculum learning enhanced global-local graph neural network for protein thermodynamic stability prediction.

Published in:

Bioinformatics, 2023, v. 39, n. 10, p. 1, doi. 10.1093/bioinformatics/btad589

By:

Gong, Haifan;
Zhang, Yumeng;
Dong, Chenhe;
Wang, Yue;
Chen, Guanqi;
LiangBilin;
Li, Haofeng;
Liu, Lanxuan;
Xu, Jie;
Li, Guanbin

Publication type:

Article

cudaMMC: GPU-enhanced multiscale Monte Carlo chromatin 3D modelling.

Published in:

Bioinformatics, 2023, v. 39, n. 10, p. 1, doi. 10.1093/bioinformatics/btad588

By:

Wlasnowolski, Michal;
Grabowski, Pawel;
Roszczyk, Damian;
Kaczmarski, Krzysztof;
Plewczynski, Dariusz

Publication type:

Article

Simulating structurally variable nuclear pore complexes for microscopy.

Published in:

Bioinformatics, 2023, v. 39, n. 10, p. 1, doi. 10.1093/bioinformatics/btad587

By:

Theiss, Maria;
Hériché, Jean-Karim;
Russell, Craig;
Helekal, David;
Soppitt, Alisdair;
Ries, Jonas;
Ellenberg, Jan;
Brazma, Alvis;
Uhlmann, Virginie

Publication type:

Article

Phables: from fragmented assemblies to high-quality bacteriophage genomes.

Published in:

Bioinformatics, 2023, v. 39, n. 10, p. 1, doi. 10.1093/bioinformatics/btad586

By:

Mallawaarachchi, Vijini;
Roach, Michael J;
Decewicz, Przemyslaw;
Papudeshi, Bhavya;
Giles, Sarah K;
Grigson, Susanna R;
Bouras, George;
Hesse, Ryan D;
Inglis, Laura K;
Hutton, Abbey L K;
Dinsdale, Elizabeth A;
Edwards, Robert A

Publication type:

Article

A cell-level discriminative neural network model for diagnosis of blood cancers.

Published in:

Bioinformatics, 2023, v. 39, n. 10, p. 1, doi. 10.1093/bioinformatics/btad585

By:

Robles, Edgar E;
Jin, Ye;
Smyth, Padhraic;
Scheuermann, Richard H;
Bui, Jack D;
Wang, Huan-You;
Oak, Jean;
Qian, Yu

Publication type:

Article

phippery: a software suite for PhIP-Seq data analysis.

Published in:

2023

By:

Galloway, Jared G;
Sung, Kevin;
Minot, Samuel S;
Garrett, Meghan E;
Stoddard, Caitlin I;
Willcox, Alexandra C;
Yaffe, Zak A;
Yucha, Ryan;
Overbaugh, Julie;
Matsen, Frederick A

Publication type:

Abstract

GOAT: Gene-level biomarker discovery from multi-Omics data using graph ATtention neural network for eosinophilic asthma subtype.

Published in:

Bioinformatics, 2023, v. 39, n. 10, p. 1, doi. 10.1093/bioinformatics/btad582

By:

Jeong, Dabin;
Koo, Bonil;
Oh, Minsik;
Kim, Tae-Bum;
Kim, Sun

Publication type:

Article

HQAlign: aligning nanopore reads for SV detection using current-level modeling.

Published in:

Bioinformatics, 2023, v. 39, n. 10, p. 1, doi. 10.1093/bioinformatics/btad580

By:

Joshi, Dhaivat;
Diggavi, Suhas;
Chaisson, Mark J P;
Kannan, Sreeram

Publication type:

Article

pLM-BLAST: distant homology detection based on direct comparison of sequence representations from protein language models.

Published in:

Bioinformatics, 2023, v. 39, n. 10, p. 1, doi. 10.1093/bioinformatics/btad579

By:

Kaminski, Kamil;
Ludwiczak, Jan;
Pawlicki, Kamil;
Alva, Vikram;
Dunin-Horkawicz, Stanislaw

Publication type:

Article

Automated detection of apoptotic bodies and cells in label-free time-lapse high-throughput video microscopy using deep convolutional neural networks.

Published in:

Bioinformatics, 2023, v. 39, n. 10, p. 1, doi. 10.1093/bioinformatics/btad584

By:

Wu, Kwan-Ling;
Martinez-Paniagua, Melisa;
Reichel, Kate;
Menon, Prashant S;
Deo, Shravani;
Roysam, Badrinath;
Varadarajan, Navin

Publication type:

Article

BondGraphs.jl: composable energy-based modelling in systems biology.

Published in:

Bioinformatics, 2023, v. 39, n. 10, p. 1, doi. 10.1093/bioinformatics/btad578

By:

Forrest, Joshua;
Rajagopal, Vijay;
Stumpf, Michael P H;
Pan, Michael

Publication type:

Article