Works matching IS 13674803 AND DT 2024 AND VI 40 AND IP 5

Results: 59

Pathformer: a biological pathway informed transformer for disease diagnosis and prognosis using multi-omics data.

Published in:

Bioinformatics, 2024, v. 40, n. 5, p. 1, doi. 10.1093/bioinformatics/btae316

By:

Liu, Xiaofan;
Tao, Yuhuan;
Cai, Zilin;
Bao, Pengfei;
Ma, Hongli;
Li, Kexing;
Li, Mengtao;
Zhu, Yunping;
Lu, Zhi John

Publication type:

Article

Correction to: kb_DRAM: annotation and metabolic profiling of genomes with DRAM in KBase.

Published in:: 2024
Publication type:: Correction Notice

PQSDC: a parallel lossless compressor for quality scores data via sequences partition and run-length prediction mapping.

Published in:

Bioinformatics, 2024, v. 40, n. 5, p. 1, doi. 10.1093/bioinformatics/btae323

By:

Sun, Hui;
Zheng, Yingfeng;
Xie, Haonan;
Ma, Huidong;
Zhong, Cheng;
Yan, Meng;
Liu, Xiaoguang;
Wang, Gang

Publication type:

Article

GateMeClass: Gate Mining and Classification of cytometry data.

Published in:

Bioinformatics, 2024, v. 40, n. 5, p. 1, doi. 10.1093/bioinformatics/btae322

By:

Caligola, Simone;
Giacobazzi, Luca;
Canè, Stefania;
Vella, Antonio;
Adamo, Annalisa;
Ugel, Stefano;
Giugno, Rosalba;
Bronte, Vincenzo

Publication type:

Article

MUSE-XAE: MUtational Signature Extraction with eXplainable AutoEncoder enhances tumour types classification.

Published in:

Bioinformatics, 2024, v. 40, n. 5, p. 1, doi. 10.1093/bioinformatics/btae320

By:

Pancotti, Corrado;
Rollo, Cesare;
Codicè, Francesco;
Birolo, Giovanni;
Fariselli, Piero;
Sanavia, Tiziana

Publication type:

Article

Genotype sampling for deep-learning assisted experimental mapping of a combinatorially complete fitness landscape.

Published in:

Bioinformatics, 2024, v. 40, n. 5, p. 1, doi. 10.1093/bioinformatics/btae317

By:

Wagner, Andreas

Publication type:

Article

Automated segmentation and recognition of C. elegans whole-body cells.

Published in:

Bioinformatics, 2024, v. 40, n. 5, p. 1, doi. 10.1093/bioinformatics/btae324

By:

Li, Yuanyuan;
Lai, Chuxiao;
Wang, Meng;
Wu, Jun;
Li, Yongbin;
Peng, Hanchuan;
Qu, Lei

Publication type:

Article

MultiRNAflow: integrated analysis of temporal RNA-seq data with multiple biological conditions.

Published in:

Bioinformatics, 2024, v. 40, n. 5, p. 1, doi. 10.1093/bioinformatics/btae315

By:

Loubaton, Rodolphe;
Champagnat, Nicolas;
Vallois, Pierre;
Vallat, Laurent

Publication type:

Article

greenPipes: an integrated data analysis pipeline for greenCUT&RUN and CUT&RUN genome-localization datasets.

Published in:

Bioinformatics, 2024, v. 40, n. 5, p. 1, doi. 10.1093/bioinformatics/btae307

By:

Nizamuddin, Sheikh;
Timmers, H T Marc

Publication type:

Article

Bayesian modelling of time series data (BayModTS)—a FAIR workflow to process sparse and highly variable data.

Published in:

Bioinformatics, 2024, v. 40, n. 5, p. 1, doi. 10.1093/bioinformatics/btae312

By:

Höpfl, Sebastian;
Albadry, Mohamed;
Dahmen, Uta;
Herrmann, Karl-Heinz;
Kindler, Eva Marie;
König, Matthias;
Reichenbach, Jürgen Rainer;
Tautenhahn, Hans-Michael;
Wei, Weiwei;
Zhao, Wan-Ting;
Radde, Nicole Erika

Publication type:

Article

Parsnp 2.0: scalable core-genome alignment for massive microbial datasets.

Published in:

Bioinformatics, 2024, v. 40, n. 5, p. 1, doi. 10.1093/bioinformatics/btae311

By:

Kille, Bryce;
Nute, Michael G;
Huang, Victor;
Kim, Eddie;
Phillippy, Adam M;
Treangen, Todd J

Publication type:

Article

DeepPPAPredMut: deep ensemble method for predicting the binding affinity change in protein–protein complexes upon mutation.

Published in:

Bioinformatics, 2024, v. 40, n. 5, p. 1, doi. 10.1093/bioinformatics/btae309

By:

Nikam, Rahul;
Jemimah, Sherlyn;
Gromiha, M Michael

Publication type:

Article

BindingSiteDTI: differential-scale binding site modelling for drug–target interaction prediction.

Published in:

Bioinformatics, 2024, v. 40, n. 5, p. 1, doi. 10.1093/bioinformatics/btae308

By:

Pan, Feng;
Yin, Chong;
Liu, Si-Qi;
Huang, Tao;
Bian, Zhaoxiang;
Yuen, Pong Chi

Publication type:

Article

fastCCLasso: a fast and efficient algorithm for estimating correlation matrix from compositional data.

Published in:

Bioinformatics, 2024, v. 40, n. 5, p. 1, doi. 10.1093/bioinformatics/btae314

By:

Zhang, Shen;
Fang, Huaying;
Hu, Tao

Publication type:

Article

DiSMVC: a multi-view graph collaborative learning framework for measuring disease similarity.

Published in:

Bioinformatics, 2024, v. 40, n. 5, p. 1, doi. 10.1093/bioinformatics/btae306

By:

Wei, Hang;
Gao, Lin;
Wu, Shuai;
Jiang, Yina;
Liu, Bin

Publication type:

Article

DeepAVP-TPPred: identification of antiviral peptides using transformed image-based localized descriptors and binary tree growth algorithm.

Published in:

Bioinformatics, 2024, v. 40, n. 5, p. 1, doi. 10.1093/bioinformatics/btae305

By:

Ullah, Matee;
Akbar, Shahid;
Raza, Ali;
Zou, Quan

Publication type:

Article

Molecular property prediction based on graph structure learning.

Published in:

Bioinformatics, 2024, v. 40, n. 5, p. 1, doi. 10.1093/bioinformatics/btae304

By:

Zhao, Bangyi;
Xu, Weixia;
Guan, Jihong;
Zhou, Shuigeng

Publication type:

Article

Peptriever: a Bi-Encoder approach for large-scale protein–peptide binding search.

Published in:

Bioinformatics, 2024, v. 40, n. 5, p. 1, doi. 10.1093/bioinformatics/btae303

By:

Gurvich, Roni;
Markel, Gal;
Tanoli, Ziaurrehman;
Meirson, Tomer

Publication type:

Article

methscore: a comprehensive R function for DNA methylation-based health predictors.

Published in:

Bioinformatics, 2024, v. 40, n. 5, p. 1, doi. 10.1093/bioinformatics/btae302

By:

Xu, Zongli;
Niu, Liang;
Kresovich, Jacob K;
Taylor, Jack A

Publication type:

Article

Prioritizing genomic variants through neuro-symbolic, knowledge-enhanced learning.

Published in:

Bioinformatics, 2024, v. 40, n. 5, p. 1, doi. 10.1093/bioinformatics/btae301

By:

Althagafi, Azza;
Zhapa-Camacho, Fernando;
Hoehndorf, Robert

Publication type:

Article

Scalable integration of multiomic single-cell data using generative adversarial networks.

Published in:

Bioinformatics, 2024, v. 40, n. 5, p. 1, doi. 10.1093/bioinformatics/btae300

By:

Giansanti, Valentina;
Giannese, Francesca;
Botrugno, Oronza A;
Gandolfi, Giorgia;
Balestrieri, Chiara;
Antoniotti, Marco;
Tonon, Giovanni;
Cittaro, Davide

Publication type:

Article

PlasCAT: Plasmid Cloud Assembly Tool.

Published in:

Bioinformatics, 2024, v. 40, n. 5, p. 1, doi. 10.1093/bioinformatics/btae299

By:

Peccoud, Samuel;
Berezin, Casey-Tyler;
Hernandez, Sarah I;
Peccoud, Jean

Publication type:

Article

MPH: fast REML for large-scale genome partitioning of quantitative genetic variation.

Published in:

Bioinformatics, 2024, v. 40, n. 5, p. 1, doi. 10.1093/bioinformatics/btae298

By:

Jiang, Jicai

Publication type:

Article

Integrated convolution and self-attention for improving peptide toxicity prediction.

Published in:

Bioinformatics, 2024, v. 40, n. 5, p. 1, doi. 10.1093/bioinformatics/btae297

By:

Jiao, Shihu;
Ye, Xiucai;
Sakurai, Tetsuya;
Zou, Quan;
Liu, Ruijun

Publication type:

Article

Chainsaw: protein domain segmentation with fully convolutional neural networks.

Published in:

Bioinformatics, 2024, v. 40, n. 5, p. 1, doi. 10.1093/bioinformatics/btae296

By:

Wells, Jude;
Hawkins-Hooker, Alex;
Bordin, Nicola;
Sillitoe, Ian;
Paige, Brooks;
Orengo, Christine

Publication type:

Article

SharePro: an accurate and efficient genetic colocalization method accounting for multiple causal signals.

Published in:

Bioinformatics, 2024, v. 40, n. 5, p. 1, doi. 10.1093/bioinformatics/btae295

By:

Zhang, Wenmin;
Lu, Tianyuan;
Sladek, Robert;
Li, Yue;
Najafabadi, Hamed;
Dupuis, Josée

Publication type:

Article

metaGWASmanager: a toolbox for an automated workflow from phenotypes to meta-analysis in GWAS consortia.

Published in:

Bioinformatics, 2024, v. 40, n. 5, p. 1, doi. 10.1093/bioinformatics/btae294

By:

Rodriguez-Hernandez, Zulema;
Gorski, Mathias;
Tellez-Plaza, Maria;
Schlosser, Pascal;
Wuttke, Matthias

Publication type:

Article

scTPC: a novel semisupervised deep clustering model for scRNA-seq data.

Published in:

Bioinformatics, 2024, v. 40, n. 5, p. 1, doi. 10.1093/bioinformatics/btae293

By:

Qiu, Yushan;
Yang, Lingfei;
Jiang, Hao;
Zou, Quan

Publication type:

Article

RecGraph: recombination-aware alignment of sequences to variation graphs.

Published in:

Bioinformatics, 2024, v. 40, n. 5, p. 1, doi. 10.1093/bioinformatics/btae292

By:

Cartes, Jorge Avila;
Bonizzoni, Paola;
Ciccolella, Simone;
Vedova, Gianluca Della;
Denti, Luca;
Didelot, Xavier;
Monti, Davide Cesare;
Pirola, Yuri

Publication type:

Article

Inferring gene regulatory networks from single-cell transcriptomics based on graph embedding.

Published in:

Bioinformatics, 2024, v. 40, n. 5, p. 1, doi. 10.1093/bioinformatics/btae291

By:

Gan, Yanglan;
Yu, Jiacheng;
Xu, Guangwei;
Yan, Cairong;
Zou, Guobing

Publication type:

Article

LMCrot: an enhanced protein crotonylation site predictor by leveraging an interpretable window-level embedding from a transformer-based protein language model.

Published in:

Bioinformatics, 2024, v. 40, n. 5, p. 1, doi. 10.1093/bioinformatics/btae290

By:

Pratyush, Pawel;
Bahmani, Soufia;
Pokharel, Suresh;
Ismail, Hamid D;
KC, Dukka B

Publication type:

Article

CopyVAE: a variational autoencoder-based approach for copy number variation inference using single-cell transcriptomics.

Published in:

Bioinformatics, 2024, v. 40, n. 5, p. 1, doi. 10.1093/bioinformatics/btae284

By:

Kurt, Semih;
Chen, Mandi;
Toosi, Hosein;
Chen, Xinsong;
Engblom, Camilla;
Mold, Jeff;
Hartman, Johan;
Lagergren, Jens

Publication type:

Article

CASCC: a co-expression-assisted single-cell RNA-seq data clustering method.

Published in:

Bioinformatics, 2024, v. 40, n. 5, p. 1, doi. 10.1093/bioinformatics/btae283

By:

Cai, Lingyi;
Anastassiou, Dimitris

Publication type:

Article

DIMet: an open-source tool for differential analysis of targeted isotope-labeled metabolomics data.

Published in:

Bioinformatics, 2024, v. 40, n. 5, p. 1, doi. 10.1093/bioinformatics/btae282

By:

Galvis, Johanna;
Guyon, Joris;
Dartigues, Benjamin;
Hecht, Helge;
Grüning, Björn;
Specque, Florian;
Soueidan, Hayssam;
Karkar, Slim;
Daubon, Thomas;
Nikolski, Macha

Publication type:

Article

MammalMethylClock R package: software for DNA methylation-based epigenetic clocks in mammals.

Published in:

Bioinformatics, 2024, v. 40, n. 5, p. 1, doi. 10.1093/bioinformatics/btae280

By:

Zoller, Joseph;
Horvath, Steve

Publication type:

Article

CORDAX web server: an online platform for the prediction and 3D visualization of aggregation motifs in protein sequences.

Published in:

Bioinformatics, 2024, v. 40, n. 5, p. 1, doi. 10.1093/bioinformatics/btae279

By:

Louros, Nikolaos;
Rousseau, Frederic;
Schymkowitz, Joost

Publication type:

Article

For antibody sequence generative modeling, mixture models may be all you need.

Published in:

Bioinformatics, 2024, v. 40, n. 5, p. 1, doi. 10.1093/bioinformatics/btae278

By:

Parkinson, Jonathan;
Wang, Wei

Publication type:

Article

Large-scale structure-informed multiple sequence alignment of proteins with SIMSApiper.

Published in:

Bioinformatics, 2024, v. 40, n. 5, p. 1, doi. 10.1093/bioinformatics/btae276

By:

Crauwels, Charlotte;
Heidig, Sophie-Luise;
Díaz, Adrián;
Vranken, Wim F

Publication type:

Article

BTR: a bioinformatics tool recommendation system.

Published in:

Bioinformatics, 2024, v. 40, n. 5, p. 1, doi. 10.1093/bioinformatics/btae275

By:

Green, Ryan;
Qu, Xufeng;
Liu, Jinze;
Yu, Tingting

Publication type:

Article

GradHC: highly reliable gradual hash-based clustering for DNA storage systems.

Published in:

Bioinformatics, 2024, v. 40, n. 5, p. 1, doi. 10.1093/bioinformatics/btae274

By:

Shabat, Dvir Ben;
Hadad, Adar;
Boruchovsky, Avital;
Yaakobi, Eitan

Publication type:

Article

ITree: a user-driven tool for interactive decision-making with classification trees.

Published in:

Bioinformatics, 2024, v. 40, n. 5, p. 1, doi. 10.1093/bioinformatics/btae273

By:

Sokołowski, Hubert;
Czajkowski, Marcin;
Czajkowska, Anna;
Jurczuk, Krzysztof;
Kretowski, Marek

Publication type:

Article

wgd v2: a suite of tools to uncover and date ancient polyploidy and whole-genome duplication.

Published in:

Bioinformatics, 2024, v. 40, n. 5, p. 1, doi. 10.1093/bioinformatics/btae272

By:

Chen, Hengchi;
Zwaenepoel, Arthur;
Peer, Yves Van de

Publication type:

Article

Revisiting drug–protein interaction prediction: a novel global–local perspective.

Published in:

Bioinformatics, 2024, v. 40, n. 5, p. 1, doi. 10.1093/bioinformatics/btae271

By:

Zhou, Zhecheng;
Liao, Qingquan;
Wei, Jinhang;
Zhuo, Linlin;
Wu, Xiaonan;
Fu, Xiangzheng;
Zou, Quan

Publication type:

Article

Peptide set test: a peptide-centric strategy to infer differentially expressed proteins.

Published in:

Bioinformatics, 2024, v. 40, n. 5, p. 1, doi. 10.1093/bioinformatics/btae270

By:

Wang, Junmin;
Novick, Steven

Publication type:

Article

MEG-PPIS: a fast protein–protein interaction site prediction method based on multi-scale graph information and equivariant graph neural network.

Published in:

Bioinformatics, 2024, v. 40, n. 5, p. 1, doi. 10.1093/bioinformatics/btae269

By:

Ding, Hongzhen;
Li, Xue;
Han, Peifu;
Tian, Xu;
Jing, Fengrui;
Wang, Shuang;
Song, Tao;
Fu, Hanjiao;
Kang, Na

Publication type:

Article

AbLEF: antibody language ensemble fusion for thermodynamically empowered property predictions.

Published in:

Bioinformatics, 2024, v. 40, n. 5, p. 1, doi. 10.1093/bioinformatics/btae268

By:

Rollins, Zachary A;
Widatalla, Talal;
Waight, Andrew;
Cheng, Alan C;
Metwally, Essam

Publication type:

Article

Topological benchmarking of algorithms to infer gene regulatory networks from single-cell RNA-seq data.

Published in:

Bioinformatics, 2024, v. 40, n. 5, p. 1, doi. 10.1093/bioinformatics/btae267

By:

Stock, Marco;
Popp, Niclas;
Fiorentino, Jonathan;
Scialdone, Antonio

Publication type:

Article

BN-BacArena: Bayesian network extension of BacArena for the dynamic simulation of microbial communities.

Published in:

Bioinformatics, 2024, v. 40, n. 5, p. 1, doi. 10.1093/bioinformatics/btae266

By:

Blasco, Telmo;
Balzerani, Francesco;
Valcárcel, Luis V;
Larrañaga, Pedro;
Bielza, Concha;
Francino, María Pilar;
Rufián-Henares, José Ángel;
Planes, Francisco J;
Pérez-Burillo, Sergio

Publication type:

Article

scPRAM accurately predicts single-cell gene expression perturbation response based on attention mechanism.

Published in:

Bioinformatics, 2024, v. 40, n. 5, p. 1, doi. 10.1093/bioinformatics/btae265

By:

Jiang, Qun;
Chen, Shengquan;
Chen, Xiaoyang;
Jiang, Rui

Publication type:

Article

A data-adaptive methods in detecting exogenous methyltransferase accessible chromatin in human genome using nanopore sequencing.

Published in:

Bioinformatics, 2024, v. 40, n. 5, p. 1, doi. 10.1093/bioinformatics/btae206

By:

Tu, Kailing;
Li, Xuemei;
Zhang, Qilin;
Huang, Wei;
Xie, Dan

Publication type:

Article