Works matching IS 13674803 AND DT 2024 AND VI 40 AND IP 4

Results: 60

Correction to: Rapid generation of high-quality structure figures for publication with PyMOL-PUB.

Published in:: 2024
Publication type:: Correction Notice

Hi-GeoMVP: a hierarchical geometry-enhanced deep learning model for drug response prediction.

Published in:

Bioinformatics, 2024, v. 40, n. 4, p. 1, doi. 10.1093/bioinformatics/btae204

By:

Chen, Yurui;
Zhang, Louxin

Publication type:

Article

GAUSS: a summary-statistics-based R package for accurate estimation of linkage disequilibrium for variants, Gaussian imputation, and TWAS analysis of cosmopolitan cohorts.

Published in:

Bioinformatics, 2024, v. 40, n. 4, p. 1, doi. 10.1093/bioinformatics/btae203

By:

Lee, Donghyung;
Bacanu, Silviu-Alin

Publication type:

Article

VirusPredictor: XGBoost-based software to predict virus-related sequences in human data.

Published in:

Bioinformatics, 2024, v. 40, n. 4, p. 1, doi. 10.1093/bioinformatics/btae192

By:

Liu, Guangchen;
Chen, Xun;
Luan, Yihui;
Li, Dawei

Publication type:

Article

scDAC: deep adaptive clustering of single-cell transcriptomic data with coupled autoencoder and Dirichlet process mixture model.

Published in:

Bioinformatics, 2024, v. 40, n. 4, p. 1, doi. 10.1093/bioinformatics/btae198

By:

An, Sijing;
Shi, Jinhui;
Liu, Runyan;
Chen, Yaowen;
Wang, Jing;
Hu, Shuofeng;
Xia, Xinyu;
Dong, Guohua;
Bo, Xiaochen;
He, Zhen;
Ying, Xiaomin

Publication type:

Article

DrivR-Base: a feature extraction toolkit for variant effect prediction model construction.

Published in:

Bioinformatics, 2024, v. 40, n. 4, p. 1, doi. 10.1093/bioinformatics/btae197

By:

Francis, Amy;
Campbell, Colin;
Gaunt, Tom R

Publication type:

Article

Coding genomes with gapped pattern graph convolutional network.

Published in:

Bioinformatics, 2024, v. 40, n. 4, p. 1, doi. 10.1093/bioinformatics/btae188

By:

Wang, Ruo Han;
Ng, Yen Kaow;
Zhang, Xianglilan;
Wang, Jianping;
Li, Shuai Cheng

Publication type:

Article

rnaCrosslinkOO: an object-oriented R package for the analysis of RNA structural data generated by RNA crosslinking experiments.

Published in:

Bioinformatics, 2024, v. 40, n. 4, p. 1, doi. 10.1093/bioinformatics/btae193

By:

Price, Jonathan L;
Ziv, Omer;
Pinckert, Malte L;
Lim, Andrew;
Miska, Eric A

Publication type:

Article

pyaging: a Python-based compendium of GPU-optimized aging clocks.

Published in:

Bioinformatics, 2024, v. 40, n. 4, p. 1, doi. 10.1093/bioinformatics/btae200

By:

Camillo, Lucas Paulo de Lima

Publication type:

Article

EpiCarousel: memory- and time-efficient identification of metacells for atlas-level single-cell chromatin accessibility data.

Published in:

Bioinformatics, 2024, v. 40, n. 4, p. 1, doi. 10.1093/bioinformatics/btae191

By:

Li, Sijie;
Li, Yuxi;
Sun, Yu;
Li, Yaru;
Chen, Xiaoyang;
Tang, Songming;
Chen, Shengquan

Publication type:

Article

Improving the performance of supervised deep learning for regulatory genomics using phylogenetic augmentation.

Published in:

Bioinformatics, 2024, v. 40, n. 4, p. 1, doi. 10.1093/bioinformatics/btae190

By:

Duncan, Andrew G;
Mitchell, Jennifer A;
Moses, Alan M

Publication type:

Article

Effect of tokenization on transformers for biological sequences.

Published in:

Bioinformatics, 2024, v. 40, n. 4, p. 1, doi. 10.1093/bioinformatics/btae196

By:

Dotan, Edo;
Jaschek, Gal;
Pupko, Tal;
Belinkov, Yonatan

Publication type:

Article

Designing efficient randstrobes for sequence similarity analyses.

Published in:

Bioinformatics, 2024, v. 40, n. 4, p. 1, doi. 10.1093/bioinformatics/btae187

By:

Karami, Moein;
Mohammadi, Aryan Soltani;
Martin, Marcel;
Ekim, Barış;
Shen, Wei;
Guo, Lidong;
Xu, Mengyang;
Pibiri, Giulio Ermanno;
Patro, Rob;
Sahlin, Kristoffer

Publication type:

Article

Regional analysis to delineate intrasample heterogeneity with RegionalST.

Published in:

Bioinformatics, 2024, v. 40, n. 4, p. 1, doi. 10.1093/bioinformatics/btae186

By:

Lyu, Yue;
Wu, Chong;
Sun, Wei;
Li, Ziyi

Publication type:

Article

Literature mining discerns latent disease–gene relationships.

Published in:

Bioinformatics, 2024, v. 40, n. 4, p. 1, doi. 10.1093/bioinformatics/btae185

By:

Rai, Priyadarshini;
Jain, Atishay;
Kumar, Shivani;
Sharma, Divya;
Jha, Neha;
Chawla, Smriti;
Raj, Abhijit;
Gupta, Apoorva;
Poonia, Sarita;
Majumdar, Angshul;
Chakraborty, Tanmoy;
Ahuja, Gaurav;
Sengupta, Debarka

Publication type:

Article

Prioritization of oligogenic variant combinations in whole exomes.

Published in:

Bioinformatics, 2024, v. 40, n. 4, p. 1, doi. 10.1093/bioinformatics/btae184

By:

Gravel, Barbara;
Renaux, Alexandre;
Papadimitriou, Sofia;
Smits, Guillaume;
Nowé, Ann;
Lenaerts, Tom

Publication type:

Article

VarChat: the generative AI assistant for the interpretation of human genomic variations.

Published in:

Bioinformatics, 2024, v. 40, n. 4, p. 1, doi. 10.1093/bioinformatics/btae183

By:

Paoli, Federica De;
Berardelli, Silvia;
Limongelli, Ivan;
Rizzo, Ettore;
Zucca, Susanna

Publication type:

Article

Pacybara: accurate long-read sequencing for barcoded mutagenized allelic libraries.

Published in:

Bioinformatics, 2024, v. 40, n. 4, p. 1, doi. 10.1093/bioinformatics/btae182

By:

Weile, Jochen;
Ferra, Gabrielle;
Boyle, Gabriel;
Pendyala, Sriram;
Amorosi, Clara;
Yeh, Chiann-Ling;
Cote, Atina G;
Kishore, Nishka;
Tabet, Daniel;
Loggerenberg, Warren van;
Rayhan, Ashyad;
Fowler, Douglas M;
Dunham, Maitreya J;
Roth, Frederick P

Publication type:

Article

Integrative annotation scores of variants for impact on RNA binding protein activities.

Published in:

Bioinformatics, 2024, v. 40, n. 4, p. 1, doi. 10.1093/bioinformatics/btae181

By:

Duan, Jingqi;
Gasch, Audrey P;
Keleş, Sündüz

Publication type:

Article

Causal-ARG: a causality-guided framework for annotating properties of antibiotic resistance genes.

Published in:

Bioinformatics, 2024, v. 40, n. 4, p. 1, doi. 10.1093/bioinformatics/btae180

By:

Zhao, Weizhong;
Wu, Junze;
Jiang, Xingpeng;
He, Tingting;
Hu, Xiaohua

Publication type:

Article

Efficient cytometry analysis with FlowSOM in Python boosts interoperability with other single-cell tools.

Published in:

Bioinformatics, 2024, v. 40, n. 4, p. 1, doi. 10.1093/bioinformatics/btae179

By:

Couckuyt, Artuur;
Rombaut, Benjamin;
Saeys, Yvan;
Gassen, Sofie Van

Publication type:

Article

EpiSegMix: a flexible distribution hidden Markov model with duration modeling for chromatin state discovery.

Published in:

Bioinformatics, 2024, v. 40, n. 4, p. 1, doi. 10.1093/bioinformatics/btae178

By:

Schmitz, Johanna Elena;
Aggarwal, Nihit;
Laufer, Lukas;
Walter, Jörn;
Salhab, Abdulrahman;
Rahmann, Sven

Publication type:

Article

ViNe-Seg: deep-learning-assisted segmentation of visible neurons and subsequent analysis embedded in a graphical user interface.

Published in:

Bioinformatics, 2024, v. 40, n. 4, p. 1, doi. 10.1093/bioinformatics/btae177

By:

Ruffini, Nicolas;
Altahini, Saleh;
Weißbach, Stephan;
Weber, Nico;
Milkovits, Jonas;
Wierczeiko, Anna;
Backhaus, Hendrik;
Stroh, Albrecht

Publication type:

Article

GraphPath: a graph attention model for molecular stratification with interpretability based on the pathway–pathway interaction network.

Published in:

Bioinformatics, 2024, v. 40, n. 4, p. 1, doi. 10.1093/bioinformatics/btae165

By:

Ma, Teng;
Wang, Jianxin

Publication type:

Article

MoleMCL: a multi-level contrastive learning framework for molecular pre-training.

Published in:

Bioinformatics, 2024, v. 40, n. 4, p. 1, doi. 10.1093/bioinformatics/btae164

By:

Zhang, Xinyi;
Xu, Yanni;
Jiang, Changzhi;
Shen, Lian;
Liu, Xiangrong

Publication type:

Article

A machine-readable specification for genomics assays.

Published in:

Bioinformatics, 2024, v. 40, n. 4, p. 1, doi. 10.1093/bioinformatics/btae168

By:

Booeshaghi, Ali Sina;
Chen, Xi;
Pachter, Lior

Publication type:

Article

The IDSM mass spectrometry extension: searching mass spectra using SPARQL.

Published in:

Bioinformatics, 2024, v. 40, n. 4, p. 1, doi. 10.1093/bioinformatics/btae174

By:

Galgonek, Jakub;
Vondrášek, Jiří

Publication type:

Article

shinyExprPortal: a configurable 'shiny' portal for sharing analysis of molecular expression data.

Published in:

Bioinformatics, 2024, v. 40, n. 4, p. 1, doi. 10.1093/bioinformatics/btae172

By:

Henkin, Rafael;
Goldmann, Katriona;
Lewis, Myles;
Barnes, Michael R

Publication type:

Article

DrugMGR: a deep bioactive molecule binding method to identify compounds targeting proteins.

Published in:

Bioinformatics, 2024, v. 40, n. 4, p. 1, doi. 10.1093/bioinformatics/btae176

By:

Li, Xiaokun;
Yang, Qiang;
Xu, Long;
Dong, Weihe;
Luo, Gongning;
Wang, Wei;
Dong, Suyu;
Wang, Kuanquan;
Xuan, Ping;
Zhang, Xianyu;
Gao, Xin

Publication type:

Article

POCP-nf: an automatic Nextflow pipeline for calculating the percentage of conserved proteins in bacterial taxonomy.

Published in:

Bioinformatics, 2024, v. 40, n. 4, p. 1, doi. 10.1093/bioinformatics/btae175

By:

Hölzer, Martin

Publication type:

Article

3Dmapper: a command line tool for BioBank-scale mapping of variants to protein structures.

Published in:

Bioinformatics, 2024, v. 40, n. 4, p. 1, doi. 10.1093/bioinformatics/btae171

By:

Ruiz-Serra, Victoria;
Valentini, Samuel;
Madroñero, Sergi;
Valencia, Alfonso;
Porta-Pardo, Eduard

Publication type:

Article

FPLS-DC: functional partial least squares through distance covariance for imaging genetics.

Published in:

Bioinformatics, 2024, v. 40, n. 4, p. 1, doi. 10.1093/bioinformatics/btae173

By:

Pan, Wenliang;
Shan, Yue;
Li, Chuang;
Huang, Shuai;
Li, Tengfei;
Li, Yun;
Zhu, Hongtu

Publication type:

Article

ICARUS v3, a massively scalable web server for single-cell RNA-seq analysis of millions of cells.

Published in:

Bioinformatics, 2024, v. 40, n. 4, p. 1, doi. 10.1093/bioinformatics/btae167

By:

Jiang, Andrew;
Snell, Russell G;
Lehnert, Klaus

Publication type:

Article

PyCoM: a python library for large-scale analysis of residue–residue coevolution data.

Published in:

Bioinformatics, 2024, v. 40, n. 4, p. 1, doi. 10.1093/bioinformatics/btae166

By:

Bibik, Philipp;
Alibai, Sabriyeh;
Pandini, Alessandro;
Dantu, Sarath Chandra

Publication type:

Article

MotGen: a closed-loop bacterial motility control framework using generative adversarial networks.

Published in:

Bioinformatics, 2024, v. 40, n. 4, p. 1, doi. 10.1093/bioinformatics/btae170

By:

Seo, BoGeum;
Lee, DoHee;
Jeon, Heungjin;
Ha, Junhyoung;
Suh, SeungBeum

Publication type:

Article

Clustering single-cell multi-omics data via graph regularized multi-view ensemble learning.

Published in:

Bioinformatics, 2024, v. 40, n. 4, p. 1, doi. 10.1093/bioinformatics/btae169

By:

Chen, Fuqun;
Zou, Guanhua;
Wu, Yongxian;
Ou-Yang, Le

Publication type:

Article

Advancing entity recognition in biomedicine via instruction tuning of large language models.

Published in:

Bioinformatics, 2024, v. 40, n. 4, p. 1, doi. 10.1093/bioinformatics/btae163

By:

Keloth, Vipina K;
Hu, Yan;
Xie, Qianqian;
Peng, Xueqing;
Wang, Yan;
Zheng, Andrew;
Selek, Melih;
Raja, Kalpana;
Wei, Chih Hsuan;
Jin, Qiao;
Lu, Zhiyong;
Chen, Qingyu;
Xu, Hua

Publication type:

Article

AleRax: a tool for gene and species tree co-estimation and reconciliation under a probabilistic model of gene duplication, transfer, and loss.

Published in:

Bioinformatics, 2024, v. 40, n. 4, p. 1, doi. 10.1093/bioinformatics/btae162

By:

Morel, Benoit;
Williams, Tom A;
Stamatakis, Alexandros;
Szöllősi, Gergely J

Publication type:

Article

phylaGAN: data augmentation through conditional GANs and autoencoders for improving disease prediction accuracy using microbiome data.

Published in:

Bioinformatics, 2024, v. 40, n. 4, p. 1, doi. 10.1093/bioinformatics/btae161

By:

Sharma, Divya;
Lou, Wendy;
Xu, Wei

Publication type:

Article

Integrating physics in deep learning algorithms: a force field as a PyTorch module.

Published in:

Bioinformatics, 2024, v. 40, n. 4, p. 1, doi. 10.1093/bioinformatics/btae160

By:

Orlando, Gabriele;
Serrano, Luis;
Schymkowitz, Joost;
Rousseau, Frederic

Publication type:

Article

HyperTMO: a trusted multi-omics integration framework based on hypergraph convolutional network for patient classification.

Published in:

Bioinformatics, 2024, v. 40, n. 4, p. 1, doi. 10.1093/bioinformatics/btae159

By:

Wang, Haohua;
Lin, Kai;
Zhang, Qiang;
Shi, Jinlong;
Song, Xinyu;
Wu, Jue;
Zhao, Chenghui;
He, Kunlun

Publication type:

Article

TemStaPro: protein thermostability prediction using sequence representations from protein language models.

Published in:

Bioinformatics, 2024, v. 40, n. 4, p. 1, doi. 10.1093/bioinformatics/btae157

By:

Pudžiuvelytė, Ieva;
Olechnovič, Kliment;
Godliauskaite, Egle;
Sermokas, Kristupas;
Urbaitis, Tomas;
Gasiunas, Giedrius;
Kazlauskas, Darius

Publication type:

Article

Rapid multiple protein sequence search by parallel and heterogeneous computation.

Published in:

Bioinformatics, 2024, v. 40, n. 4, p. 1, doi. 10.1093/bioinformatics/btae151

By:

Li, Jiefu;
Wang, Ziyuan;
Fan, Xuwei;
Yao, Ruijie;
Zhang, Guoqing;
Fan, Rui;
Wang, Zefeng

Publication type:

Article

scPathoQuant: a tool for efficient alignment and quantification of pathogen sequence reads from 10× single cell sequencing datasets.

Published in:

Bioinformatics, 2024, v. 40, n. 4, p. 1, doi. 10.1093/bioinformatics/btae145

By:

Whitmore, Leanne S;
Tisoncik-Go, Jennifer;
Gale, Michael

Publication type:

Article

Icarust, a real-time simulator for Oxford Nanopore adaptive sampling.

Published in:

Bioinformatics, 2024, v. 40, n. 4, p. 1, doi. 10.1093/bioinformatics/btae141

By:

Munro, Rory;
Wibowo, Satrio;
Payne, Alexander;
Loose, Matthew

Publication type:

Article

NIEND: neuronal image enhancement through noise disentanglement.

Published in:

Bioinformatics, 2024, v. 40, n. 4, p. 1, doi. 10.1093/bioinformatics/btae158

By:

Zhao, Zuo-Han;
Liu, Lijuan;
Liu, Yufeng

Publication type:

Article

CONSULT-II: accurate taxonomic identification and profiling using locality-sensitive hashing.

Published in:

Bioinformatics, 2024, v. 40, n. 4, p. 1, doi. 10.1093/bioinformatics/btae150

By:

Şapcı, Ali Osman Berk;
Rachtman, Eleonora;
Mirarab, Siavash

Publication type:

Article

Contrastive pre-training and 3D convolution neural network for RNA and small molecule binding affinity prediction.

Published in:

Bioinformatics, 2024, v. 40, n. 4, p. 1, doi. 10.1093/bioinformatics/btae155

By:

Sun, Saisai;
Gao, Lin

Publication type:

Article

A model-based hierarchical Bayesian approach to Sholl analysis.

Published in:

Bioinformatics, 2024, v. 40, n. 4, p. 1, doi. 10.1093/bioinformatics/btae156

By:

VonKaenel, Erik;
Feidler, Alexis;
Lowery, Rebecca;
Andersh, Katherine;
Love, Tanzy;
Majewska, Ania;
McCall, Matthew N

Publication type:

Article

MIKE: an ultrafast, assembly-, and alignment-free approach for phylogenetic tree construction.

Published in:

Bioinformatics, 2024, v. 40, n. 4, p. 1, doi. 10.1093/bioinformatics/btae154

By:

Wang, Fang;
Wang, Yibin;
Zeng, Xiaofei;
Zhang, Shengcheng;
Yu, Jiaxin;
Li, Dongxi;
Zhang, Xingtan

Publication type:

Article