Works matching IS 13674803 AND DT 2024 AND VI 40 AND IP 10

Results: 52

Analysis of metadynamics simulations by metadynminer.py.

Published in:

Bioinformatics, 2024, v. 40, n. 10, p. 1, doi. 10.1093/bioinformatics/btae614

By:

Beránek, Jan;
Křenek, Aleš;
Spiwok, Vojtěch

Publication type:

Article

SurvBal: compositional microbiome balances for survival outcomes.

Published in:

Bioinformatics, 2024, v. 40, n. 10, p. 1, doi. 10.1093/bioinformatics/btae612

By:

Li, Ying;
Lee, Teresa;
Marin, Kai;
Hua, Xing;
Srinivasan, Sujatha;
Fredricks, David N;
Lee, John R;
Ling, Wodan

Publication type:

Article

DAVID Ortholog: an integrative tool to enhance functional analysis through orthologs.

Published in:

Bioinformatics, 2024, v. 40, n. 10, p. 1, doi. 10.1093/bioinformatics/btae615

By:

Sherman, Brad T;
Panzade, Ganesh;
Imamichi, Tomozumi;
Chang, Weizhong

Publication type:

Article

MOIRE: a software package for the estimation of allele frequencies and effective multiplicity of infection from polyallelic data.

Published in:

Bioinformatics, 2024, v. 40, n. 10, p. 1, doi. 10.1093/bioinformatics/btae619

By:

Murphy, Maxwell;
Greenhouse, Bryan

Publication type:

Article

Correction to: Teaching bioinformatics through the analysis of SARS-CoV-2: project-based training for computer science students.

Published in:: 2024
Publication type:: Correction Notice

A multi-modality and multi-granularity collaborative learning framework for identifying spatial domains and spatially variable genes.

Published in:

Bioinformatics, 2024, v. 40, n. 10, p. 1, doi. 10.1093/bioinformatics/btae607

By:

Liang, Xiao;
Liu, Pei;
Xue, Li;
Chen, Baiyun;
Liu, Wei;
Shi, Wanwan;
Wang, Yongwang;
Chen, Xiangtao;
Luo, Jiawei

Publication type:

Article

Statistical batch-aware embedded integration, dimension reduction, and alignment for spatial transcriptomics.

Published in:

Bioinformatics, 2024, v. 40, n. 10, p. 1, doi. 10.1093/bioinformatics/btae611

By:

Li, Yanfang;
Zhang, Shihua

Publication type:

Article

Biologically weighted LASSO: enhancing functional interpretability in gene expression data analysis.

Published in:

Bioinformatics, 2024, v. 40, n. 10, p. 1, doi. 10.1093/bioinformatics/btae605

By:

Mongardi, Sofia;
Cascianelli, Silvia;
Masseroli, Marco

Publication type:

Article

Dual-view jointly learning improves personalized drug synergy prediction.

Published in:

Bioinformatics, 2024, v. 40, n. 10, p. 1, doi. 10.1093/bioinformatics/btae604

By:

Li, Xueliang;
Shen, Bihan;
Feng, Fangyoumin;
Li, Kunshi;
Tang, Zhixuan;
Ma, Liangxiao;
Li, Hong

Publication type:

Article

Anti-symmetric framework for balanced learning of protein–protein interactions.

Published in:

Bioinformatics, 2024, v. 40, n. 10, p. 1, doi. 10.1093/bioinformatics/btae603

By:

Tang, Tao;
Li, Tianyang;
Li, Weizhuo;
Cao, Xiaofeng;
Liu, Yuansheng;
Zeng, Xiangxiang

Publication type:

Article

MNBC: a multithreaded Minimizer-based Naïve Bayes Classifier for improved metagenomic sequence classification.

Published in:

Bioinformatics, 2024, v. 40, n. 10, p. 1, doi. 10.1093/bioinformatics/btae601

By:

Lu, Ruipeng;
Dumonceaux, Tim;
Anzar, Muhammad;
Zovoilis, Athanasios;
Antonation, Kym;
Barker, Dillon;
Corbett, Cindi;
Nadon, Celine;
Robertson, James;
Eagle, Shannon H C;
Lung, Oliver;
Rudar, Josip;
Surujballi, Om;
Laing, Chad

Publication type:

Article

Correction to: AgIn: measuring the landscape of CpG methylation of individual repetitive elements.

Published in:: 2024
Publication type:: Correction Notice

scDRMAE: integrating masked autoencoder with residual attention networks to leverage omics feature dependencies for accurate cell clustering.

Published in:

Bioinformatics, 2024, v. 40, n. 10, p. 1, doi. 10.1093/bioinformatics/btae599

By:

Zhang, Tianjiao;
Zhang, Hongfei;
Ren, Jixiang;
Wu, Zhenao;
Zhao, Zhongqian;
Wang, Guohua

Publication type:

Article

TarKG: a comprehensive biomedical knowledge graph for target discovery.

Published in:

Bioinformatics, 2024, v. 40, n. 10, p. 1, doi. 10.1093/bioinformatics/btae598

By:

Zhou, Cong;
Cai, Chui-Pu;
Huang, Xiao-Tian;
Wu, Song;
Yu, Jun-Lin;
Wu, Jing-Wei;
Fang, Jian-Song;
Li, Guo-Bo

Publication type:

Article

RTF: an R package for modelling time course data.

Published in:

Bioinformatics, 2024, v. 40, n. 10, p. 1, doi. 10.1093/bioinformatics/btae597

By:

Brombacher, Eva;
Kreutz, Clemens

Publication type:

Article

MSDAFL: molecular substructure-based dual attention feature learning framework for predicting drug–drug interactions.

Published in:

Bioinformatics, 2024, v. 40, n. 10, p. 1, doi. 10.1093/bioinformatics/btae596

By:

Hou, Chao;
Duan, Guihua;
Yan, Cheng

Publication type:

Article

CyCadas: accelerating interactive annotation and analysis of clustered cytometry data.

Published in:

Bioinformatics, 2024, v. 40, n. 10, p. 1, doi. 10.1093/bioinformatics/btae595

By:

Hunewald, Oliver;
Demczuk, Agnieszka;
Longworth, Joseph;
Ollert, Markus

Publication type:

Article

PocketDTA: an advanced multimodal architecture for enhanced prediction of drug−target affinity from 3D structural data of target binding pockets.

Published in:

Bioinformatics, 2024, v. 40, n. 10, p. 1, doi. 10.1093/bioinformatics/btae594

By:

Zhao, Long;
Wang, Hongmei;
Shi, Shaoping

Publication type:

Article

PCBS: an R package for fast and accurate analysis of bisulfite sequencing data.

Published in:

Bioinformatics, 2024, v. 40, n. 10, p. 1, doi. 10.1093/bioinformatics/btae593

By:

Lande, Kathryn;
Williams, April E

Publication type:

Article

BioPred: an R package for biomarkers analysis in precision medicine.

Published in:

Bioinformatics, 2024, v. 40, n. 10, p. 1, doi. 10.1093/bioinformatics/btae592

By:

Liu, Zihuan;
Sun, Yan;
Huang, Xin

Publication type:

Article

Castanet: a pipeline for rapid analysis of targeted multi-pathogen genomic data.

Published in:

Bioinformatics, 2024, v. 40, n. 10, p. 1, doi. 10.1093/bioinformatics/btae591

By:

Mayne, Richard;
Secret, Shannah;
Geoghegan, Cyndi;
Trebes, Amy;
Kean, Kai;
Reid, Kaitlin;
Lin, Gu-Lung;
Ansari, M Azim;
Cesare, Mariateresa de;
Bonsall, David;
Elliott, Ivo;
Piazza, Paolo;
Brown, Anthony;
Bray, James;
Knight, Julian C;
Harvala, Heli;
Breuer, Judith;
Simmonds, Peter;
Bowden, Rory J;
Golubchik, Tanya

Publication type:

Article

BEATRICE: Bayesian fine-mapping from summary data using deep variational inference.

Published in:

Bioinformatics, 2024, v. 40, n. 10, p. 1, doi. 10.1093/bioinformatics/btae590

By:

Ghosal, Sayan;
Schatz, Michael C;
Venkataraman, Archana

Publication type:

Article

Learning to explain is a good biomedical few-shot learner.

Published in:

Bioinformatics, 2024, v. 40, n. 10, p. 1, doi. 10.1093/bioinformatics/btae589

By:

Chen, Peng;
Wang, Jian;
Luo, Ling;
Lin, Hongfei;
Yang, Zhihao

Publication type:

Article

Combined LC-MS/MS feature grouping, statistical prioritization, and interactive networking in msFeaST.

Published in:

Bioinformatics, 2024, v. 40, n. 10, p. 1, doi. 10.1093/bioinformatics/btae584

By:

Mildau, Kevin;
Büschl, Christoph;
Zanghellini, Jürgen;
Hooft, Justin J J van der

Publication type:

Article

Identifying nucleotide-binding leucine-rich repeat receptor and pathogen effector pairing using transfer-learning and bilinear attention network.

Published in:

Bioinformatics, 2024, v. 40, n. 10, p. 1, doi. 10.1093/bioinformatics/btae581

By:

Qiao, Baixue;
Wang, Shuda;
Hou, Mingjun;
Chen, Haodi;
Zhou, Zhengwenyang;
Xie, Xueying;
Pang, Shaozi;
Yang, Chunxue;
Yang, Fenglong;
Zou, Quan;
Sun, Shanwen

Publication type:

Article

Pair-EGRET: enhancing the prediction of protein–protein interaction sites through graph attention networks and protein language models.

Published in:

Bioinformatics, 2024, v. 40, n. 10, p. 1, doi. 10.1093/bioinformatics/btae588

By:

Alam, Ramisa;
Mahbub, Sazan;
Bayzid, Md Shamsuzzoha

Publication type:

Article

MPRAVarDB: an online database and web server for exploring regulatory effects of genetic variants.

Published in:

Bioinformatics, 2024, v. 40, n. 10, p. 1, doi. 10.1093/bioinformatics/btae578

By:

Jin, Weijia;
Xia, Yi;
Nizomov, Javlon;
Liu, Yunlong;
Li, Zhigang;
Lu, Qing;
Chen, Li

Publication type:

Article

NeoDesign: a computational tool for optimal selection of polyvalent neoantigen combinations.

Published in:

Bioinformatics, 2024, v. 40, n. 10, p. 1, doi. 10.1093/bioinformatics/btae585

By:

Yu, Wenqian;
Yu, Hongwu;
Zhao, Jingjing;
Zhang, Hena;
Ke, Kalam;
Hu, Zhixiang;
Huang, Shenglin

Publication type:

Article

OligoFormer: an accurate and robust prediction method for siRNA design.

Published in:

Bioinformatics, 2024, v. 40, n. 10, p. 1, doi. 10.1093/bioinformatics/btae577

By:

Bai, Yilan;
Zhong, Haochen;
Wang, Taiwei;
Lu, Zhi John

Publication type:

Article

BatchFLEX: feature-level equalization of X-batch.

Published in:

Bioinformatics, 2024, v. 40, n. 10, p. 1, doi. 10.1093/bioinformatics/btae587

By:

Davis, Joshua T;
Obermayer, Alyssa N;
Soupir, Alex C;
Hesterberg, Rebecca S;
Duong, Thac;
Yang, Ching-Yao;
Dao, Ken Phong;
Manley, Brandon J;
Grass, G Daniel;
Avram, Dorina;
Rodriguez, Paulo C;
Fridley, Brooke L;
Yu, Xiaoqing;
Teng, Mingxiang;
Wang, Xuefeng;
Shaw, Timothy I

Publication type:

Article

DockQ v2: improved automatic quality measure for protein multimers, nucleic acids, and small molecules.

Published in:

Bioinformatics, 2024, v. 40, n. 10, p. 1, doi. 10.1093/bioinformatics/btae586

By:

Mirabello, Claudio;
Wallner, Björn

Publication type:

Article

Towards the accurate modelling of antibody−antigen complexes from sequence using machine learning and information-driven docking.

Published in:

Bioinformatics, 2024, v. 40, n. 10, p. 1, doi. 10.1093/bioinformatics/btae583

By:

Giulini, Marco;
Schneider, Constantin;
Cutting, Daniel;
Desai, Nikita;
Deane, Charlotte M;
Bonvin, Alexandre M J J

Publication type:

Article

ABodyBuilder3: improved and scalable antibody structure predictions.

Published in:

Bioinformatics, 2024, v. 40, n. 10, p. 1, doi. 10.1093/bioinformatics/btae576

By:

Kenlay, Henry;
Dreyer, Frédéric A;
Cutting, Daniel;
Nissley, Daniel;
Deane, Charlotte M

Publication type:

Article

Causal enhanced drug–target interaction prediction based on graph generation and multi-source information fusion.

Published in:

Bioinformatics, 2024, v. 40, n. 10, p. 1, doi. 10.1093/bioinformatics/btae570

By:

Qiao, Guanyu;
Wang, Guohua;
Li, Yang

Publication type:

Article

VirTAXA: enhancing RNA virus taxonomic classification with remote homology search and tree-based validation.

Published in:

Bioinformatics, 2024, v. 40, n. 10, p. 1, doi. 10.1093/bioinformatics/btae575

By:

Zhu, Yilin;
Chen, Guowei;
Sun, Yanni

Publication type:

Article

Second-order group knockoffs with applications to genome-wide association studies.

Published in:

Bioinformatics, 2024, v. 40, n. 10, p. 1, doi. 10.1093/bioinformatics/btae580

By:

Chu, Benjamin B;
Gu, Jiaqi;
Chen, Zhaomeng;
Morrison, Tim;
Candès, Emmanuel;
He, Zihuai;
Sabatti, Chiara

Publication type:

Article

GNN4DM: a graph neural network-based method to identify overlapping functional disease modules.

Published in:

Bioinformatics, 2024, v. 40, n. 10, p. 1, doi. 10.1093/bioinformatics/btae573

By:

Gézsi, András;
Antal, Péter

Publication type:

Article

MGRN: toward robust drug recommendation via multi-view gating retrieval network.

Published in:

Bioinformatics, 2024, v. 40, n. 10, p. 1, doi. 10.1093/bioinformatics/btae572

By:

Meng, Fanjun;
Li, Xiaobo;
Hou, Xiaodi;
Lu, Mingyu;
Zhang, Yijia

Publication type:

Article

TAWFN: a deep learning framework for protein function prediction.

Published in:

Bioinformatics, 2024, v. 40, n. 10, p. 1, doi. 10.1093/bioinformatics/btae571

By:

Meng, Lu;
Wang, Xiaoran

Publication type:

Article

Structure-inclusive similarity based directed GNN: a method that can control information flow to predict drug–target binding affinity.

Published in:

Bioinformatics, 2024, v. 40, n. 10, p. 1, doi. 10.1093/bioinformatics/btae563

By:

Huang, Jipeng;
Sun, Chang;
Li, Minglei;
Tang, Rong;
Xie, Bin;
Wang, Shuqin;
Wei, Jin-Mao

Publication type:

Article

Chain-aware graph neural networks for molecular property prediction.

Published in:

Bioinformatics, 2024, v. 40, n. 10, p. 1, doi. 10.1093/bioinformatics/btae574

By:

Wang, Honghao;
Zhang, Acong;
Zhong, Yuan;
Tang, Junlei;
Zhang, Kai;
Li, Ping

Publication type:

Article

Accurate segmentation of intracellular organelle networks using low-level features and topological self-similarity.

Published in:

Bioinformatics, 2024, v. 40, n. 10, p. 1, doi. 10.1093/bioinformatics/btae559

By:

Huang, Jiaxing;
Luo, Yaoru;
Guo, Yuanhao;
Li, Wenjing;
Wang, Zichen;
Liu, Guole;
Yang, Ge

Publication type:

Article

Chemical reaction enhanced graph learning for molecule representation.

Published in:

Bioinformatics, 2024, v. 40, n. 10, p. 1, doi. 10.1093/bioinformatics/btae558

By:

Li, Anchen;
Casiraghi, Elena;
Rousu, Juho

Publication type:

Article

GENEVIC: GENetic data Exploration and Visualization via Intelligent interactive Console.

Published in:

Bioinformatics, 2024, v. 40, n. 10, p. 1, doi. 10.1093/bioinformatics/btae500

By:

Nath, Anindita;
Mwesigwa, Savannah;
Dai, Yulin;
Jiang, Xiaoqian;
Zhao, Zhongming

Publication type:

Article

A self-training interpretable cell type annotation framework using specific marker gene.

Published in:

Bioinformatics, 2024, v. 40, n. 10, p. 1, doi. 10.1093/bioinformatics/btae569

By:

Chen, Hegang;
Lu, Yuyin;
Rao, Yanghui

Publication type:

Article

vSPACE: exploring virtual spatial representation of articular chondrocytes at the single-cell level.

Published in:

Bioinformatics, 2024, v. 40, n. 10, p. 1, doi. 10.1093/bioinformatics/btae568

By:

Zhang, Chenyu;
Wang, Honglin;
Chung, Yeonsoo;
Hong, Seung-Hyun;
Olmer, Merissa;
Swahn, Hannah;
Lotz, Martin;
Maye, Peter;
Rowe, David;
Shin, Dong-Guk

Publication type:

Article

Kssdtree: an interactive Python package for phylogenetic analysis based on sketching technique.

Published in:

Bioinformatics, 2024, v. 40, n. 10, p. 1, doi. 10.1093/bioinformatics/btae566

By:

Yang, Hang;
Lu, Xiaoxin;
Chang, Jiaxing;
Chang, Qing;
Zheng, Wen;
Chen, Zehua;
Yi, Huiguang

Publication type:

Article

HunFlair2 in a cross-corpus evaluation of biomedical named entity recognition and normalization tools.

Published in:

Bioinformatics, 2024, v. 40, n. 10, p. 1, doi. 10.1093/bioinformatics/btae564

By:

Sänger, Mario;
Garda, Samuele;
Wang, Xing David;
Weber-Genzel, Leon;
Droop, Pia;
Fuchs, Benedikt;
Akbik, Alan;
Leser, Ulf

Publication type:

Article

Computational prediction of multiple antigen epitopes.

Published in:

Bioinformatics, 2024, v. 40, n. 10, p. 1, doi. 10.1093/bioinformatics/btae556

By:

Viswanathan, Rajalakshmi;
Carroll, Moshe;
Roffe, Alexandra;
Fajardo, Jorge E;
Fiser, Andras

Publication type:

Article

The GenoPred pipeline: a comprehensive and scalable pipeline for polygenic scoring.

Published in:

Bioinformatics, 2024, v. 40, n. 10, p. 1, doi. 10.1093/bioinformatics/btae551

By:

Pain, Oliver;
Al-Chalabi, Ammar;
Lewis, Cathryn M

Publication type:

Article