Works matching IS 13674803 AND DT 2024 AND VI 40 AND IP 7

Results: 67

Compound-SNE: comparative alignment of t-SNEs for multiple single-cell omics data visualization.

Published in:

Bioinformatics, 2024, v. 40, n. 7, p. 1, doi. 10.1093/bioinformatics/btae471

By:

Cess, Colin G;
Haghverdi, Laleh

Publication type:

Article

MetaHD: a multivariate meta-analysis model for metabolomics data.

Published in:

Bioinformatics, 2024, v. 40, n. 7, p. 1, doi. 10.1093/bioinformatics/btae470

By:

Liyanage, Jayamini C;
Prendergast, Luke;
Staudte, Robert;
Livera, Alysha M De

Publication type:

Article

Melodia: a Python library for protein structure analysis.

Published in:

Bioinformatics, 2024, v. 40, n. 7, p. 1, doi. 10.1093/bioinformatics/btae468

By:

Montalvão, Rinaldo W;
Pitt, William R;
Pinheiro, Vitor B;
Blundell, Tom L

Publication type:

Article

Single-cell and spatial multiomic inference of gene regulatory networks using SCRIPro.

Published in:

Bioinformatics, 2024, v. 40, n. 7, p. 1, doi. 10.1093/bioinformatics/btae466

By:

Chang, Zhanhe;
Xu, Yunfan;
Dong, Xin;
Gao, Yawei;
Wang, Chenfei

Publication type:

Article

Correction to: The 2024 ISCB Innovator Award—Dr Su-In Lee.

Published in:: Bioinformatics, 2024, v. 40, n. 7, p. 1, doi. 10.1093/bioinformatics/btae460
Publication type:: Article

MetaboLink: a web application for streamlined processing and analysis of large-scale untargeted metabolomics data.

Published in:

Bioinformatics, 2024, v. 40, n. 7, p. 1, doi. 10.1093/bioinformatics/btae459

By:

Mendes, Ana;
Havelund, Jesper Foged;
Lemvig, Jonas;
Schwämmle, Veit;
Færgeman, Nils J

Publication type:

Article

Controlled noise: evidence of epigenetic regulation of single-cell expression variability.

Published in:

Bioinformatics, 2024, v. 40, n. 7, p. 1, doi. 10.1093/bioinformatics/btae457

By:

Zhong, Yan;
Cui, Siwei;
Yang, Yongjian;
Cai, James J

Publication type:

Article

Exploring gene content with pangene graphs.

Published in:

Bioinformatics, 2024, v. 40, n. 7, p. 1, doi. 10.1093/bioinformatics/btae456

By:

Li, Heng;
Marin, Maximillian;
Farhat, Maha R

Publication type:

Article

isolateR: an R package for generating microbial libraries from Sanger sequencing data.

Published in:

Bioinformatics, 2024, v. 40, n. 7, p. 1, doi. 10.1093/bioinformatics/btae448

By:

Daisley, Brendan;
Vancuren, Sarah J;
Brettingham, Dylan J L;
Wilde, Jacob;
Renwick, Simone;
Macpherson, Christine V;
Good, David A;
Botschner, Alexander J;
Yen, Sandi;
Hill, Janet E;
Sorbara, Matthew T;
Allen-Vercoe, Emma

Publication type:

Article

Enhancing predictions of protein stability changes induced by single mutations using MSA-based language models.

Published in:

Bioinformatics, 2024, v. 40, n. 7, p. 1, doi. 10.1093/bioinformatics/btae447

By:

Cuturello, Francesca;
Celoria, Marco;
Ansuini, Alessio;
Cazzaniga, Alberto

Publication type:

Article

Adaptive space search-based molecular evolution optimization algorithm.

Published in:

Bioinformatics, 2024, v. 40, n. 7, p. 1, doi. 10.1093/bioinformatics/btae446

By:

Wang, Fei;
Cheng, Xianglong;
Xia, Xin;
Zheng, Chunhou;
Su, Yansen

Publication type:

Article

SCCNAInfer: a robust and accurate tool to infer the absolute copy number on scDNA-seq data.

Published in:

Bioinformatics, 2024, v. 40, n. 7, p. 1, doi. 10.1093/bioinformatics/btae454

By:

Zhang, Liting;
Zhou, Xin Maizie;
Mallory, Xian

Publication type:

Article

ALLSTAR: inference of reliAble causaL ruLes between Somatic muTAtions and canceR phenotypes.

Published in:

Bioinformatics, 2024, v. 40, n. 7, p. 1, doi. 10.1093/bioinformatics/btae449

By:

Simionato, Dario;
Collesei, Antonio;
Miglietta, Federica;
Vandin, Fabio

Publication type:

Article

HyperGen: compact and efficient genome sketching using hyperdimensional vectors.

Published in:

Bioinformatics, 2024, v. 40, n. 7, p. 1, doi. 10.1093/bioinformatics/btae452

By:

Xu, Weihong;
Hsu, Po-Kai;
Moshiri, Niema;
Yu, Shimeng;
Rosing, Tajana

Publication type:

Article

scMaSigPro: differential expression analysis along single-cell trajectories.

Published in:

Bioinformatics, 2024, v. 40, n. 7, p. 1, doi. 10.1093/bioinformatics/btae443

By:

Srivastava, Priyansh;
Coll, Marta Benegas;
Götz, Stefan;
Nueda, María José;
Conesa, Ana

Publication type:

Article

Unraveling spatial domain characterization in spatially resolved transcriptomics with robust graph contrastive clustering.

Published in:

Bioinformatics, 2024, v. 40, n. 7, p. 1, doi. 10.1093/bioinformatics/btae451

By:

Zhang, Yingxi;
Yu, Zhuohan;
Wong, Ka-Chun;
Li, Xiangtao

Publication type:

Article

Drawing mitochondrial genomes with circularMT.

Published in:

Bioinformatics, 2024, v. 40, n. 7, p. 1, doi. 10.1093/bioinformatics/btae450

By:

Goodman, Simon J;
Carr, Ian M

Publication type:

Article

Automated, image-based quantification of peroxisome characteristics with perox-per-cell.

Published in:

Bioinformatics, 2024, v. 40, n. 7, p. 1, doi. 10.1093/bioinformatics/btae442

By:

Neal, Maxwell L;
Shukla, Nandini;
Mast, Fred D;
Farré, Jean-Claude;
Pacio, Therese M;
Raney-Plourde, Katelyn E;
Prasad, Sumedh;
Subramani, Suresh;
Aitchison, John D

Publication type:

Article

DeepGSEA: explainable deep gene set enrichment analysis for single-cell transcriptomic data.

Published in:

Bioinformatics, 2024, v. 40, n. 7, p. 1, doi. 10.1093/bioinformatics/btae434

By:

Xiong, Guangzhi;
LeRoy, Nathan J;
Bekiranov, Stefan;
Sheffield, Nathan C;
Zhang, Aidong

Publication type:

Article

SFINN: inferring gene regulatory network from single-cell and spatial transcriptomic data with shared factor neighborhood and integrated neural network.

Published in:

Bioinformatics, 2024, v. 40, n. 7, p. 1, doi. 10.1093/bioinformatics/btae433

By:

Wang, Yongjie;
Zhou, Fengfan;
Guan, Jinting

Publication type:

Article

A curated rotamer library for common post-translational modifications of proteins.

Published in:

Bioinformatics, 2024, v. 40, n. 7, p. 1, doi. 10.1093/bioinformatics/btae444

By:

Zhang, Oufan;
Naik, Shubhankar A;
Liu, Zi Hao;
Forman-Kay, Julie;
Head-Gordon, Teresa

Publication type:

Article

Unravelling reference bias in ancient DNA datasets.

Published in:

Bioinformatics, 2024, v. 40, n. 7, p. 1, doi. 10.1093/bioinformatics/btae436

By:

Dolenz, Stephanie;
van der Valk, Tom;
Jin, Chenyu;
Oppenheimer, Jonas;
Sharif, Muhammad Bilal;
Orlando, Ludovic;
Shapiro, Beth;
Dalén, Love;
Heintzman, Peter D

Publication type:

Article

DualNetGO: a dual network model for protein function prediction via effective feature selection.

Published in:

Bioinformatics, 2024, v. 40, n. 7, p. 1, doi. 10.1093/bioinformatics/btae437

By:

Chen, Zhuoyang;
Luo, Qiong

Publication type:

Article

Reverse network diffusion to remove indirect noise for better inference of gene regulatory networks.

Published in:

Bioinformatics, 2024, v. 40, n. 7, p. 1, doi. 10.1093/bioinformatics/btae435

By:

Yu, Jiating;
Leng, Jiacheng;
Yuan, Fan;
Sun, Duanchen;
Wu, Ling-Yun

Publication type:

Article

LarvaTagger: manual and automatic tagging of Drosophila larval behaviour.

Published in:

Bioinformatics, 2024, v. 40, n. 7, p. 1, doi. 10.1093/bioinformatics/btae441

By:

Laurent, François;
Blanc, Alexandre;
May, Lilly;
Gándara, Lautaro;
Cocanougher, Benjamin T;
Jones, Benjamin M W;
Hague, Peter;
Barré, Chloé;
Vestergaard, Christian L;
Crocker, Justin;
Zlatic, Marta;
Jovanic, Tihana;
Masson, Jean-Baptiste

Publication type:

Article

InstaPrism: an R package for fast implementation of BayesPrism.

Published in:

Bioinformatics, 2024, v. 40, n. 7, p. 1, doi. 10.1093/bioinformatics/btae440

By:

Hu, Mengying;
Chikina, Maria

Publication type:

Article

GALEON: a comprehensive bioinformatic tool to analyse and visualize gene clusters in complete genomes.

Published in:

Bioinformatics, 2024, v. 40, n. 7, p. 1, doi. 10.1093/bioinformatics/btae439

By:

Pisarenco, Vadim A;
Vizueta, Joel;
Rozas, Julio

Publication type:

Article

GraphADT: empowering interpretable predictions of acute dermal toxicity with multi-view graph pooling and structure remapping.

Published in:

Bioinformatics, 2024, v. 40, n. 7, p. 1, doi. 10.1093/bioinformatics/btae438

By:

Ma, Xinqian;
Fu, Xiangzheng;
Wang, Tao;
Zhuo, Linlin;
Zou, Quan

Publication type:

Article

msproteomics sitereport: reporting DIA-MS phosphoproteomics experiments at site level with ease.

Published in:

Bioinformatics, 2024, v. 40, n. 7, p. 1, doi. 10.1093/bioinformatics/btae432

By:

Pham, Thang V;
Henneman, Alex A;
Truong, Nam X;
Jimenez, Connie R

Publication type:

Article

A Spatial Omnibus Test (SPOT) for Spatial Proteomic Data.

Published in:

Bioinformatics, 2024, v. 40, n. 7, p. 1, doi. 10.1093/bioinformatics/btae425

By:

Samorodnitsky, Sarah;
Campbell, Katie;
Ribas, Antoni;
Wu, Michael C

Publication type:

Article

Detecting gene–environment interactions from multiple continuous traits.

Published in:

Bioinformatics, 2024, v. 40, n. 7, p. 1, doi. 10.1093/bioinformatics/btae419

By:

Lin, Wan-Yu

Publication type:

Article

FastHPOCR: pragmatic, fast, and accurate concept recognition using the human phenotype ontology.

Published in:

Bioinformatics, 2024, v. 40, n. 7, p. 1, doi. 10.1093/bioinformatics/btae406

By:

Groza, Tudor;
Gration, Dylan;
Baynam, Gareth;
Robinson, Peter N

Publication type:

Article

hopsy — a methods marketplace for convex polytope sampling in Python.

Published in:

Bioinformatics, 2024, v. 40, n. 7, p. 1, doi. 10.1093/bioinformatics/btae430

By:

Paul, Richard D;
Jadebeck, Johann F;
Stratmann, Anton;
Wiechert, Wolfgang;
Nöh, Katharina

Publication type:

Article

A multi-bin rarefying method for evaluating alpha diversities in TCR sequencing data.

Published in:

Bioinformatics, 2024, v. 40, n. 7, p. 1, doi. 10.1093/bioinformatics/btae431

By:

Li, Mo;
Hua, Xing;
Li, Shuai;
Wu, Michael C;
Zhao, Ni

Publication type:

Article

MiPRIME: an integrated and intelligent platform for mining primer and probe sequences of microbial species.

Published in:

Bioinformatics, 2024, v. 40, n. 7, p. 1, doi. 10.1093/bioinformatics/btae429

By:

Zhang, Zhiming;
Ren, Jing;
Ren, Lili;
Zhang, Lanying;
Ai, Qubo;
Long, Haixin;
Ren, Yi;
Yang, Kun;
Feng, Huiying;
Li, Sabrina;
Li, Xu

Publication type:

Article

Efficient protein structure archiving using ProteStAr.

Published in:

Bioinformatics, 2024, v. 40, n. 7, p. 1, doi. 10.1093/bioinformatics/btae428

By:

Deorowicz, Sebastian;
Gudyś, Adam

Publication type:

Article

DODGE: automated point source bacterial outbreak detection using cumulative long term genomic surveillance.

Published in:

Bioinformatics, 2024, v. 40, n. 7, p. 1, doi. 10.1093/bioinformatics/btae427

By:

Payne, Michael;
Hu, Dalong;
Wang, Qinning;
Sullivan, Geraldine;
Graham, Rikki M;
Rathnayake, Irani U;
Jennison, Amy V;
Sintchenko, Vitali;
Lan, Ruiting

Publication type:

Article

ScType enables fast and accurate cell type identification from spatial transcriptomics data.

Published in:

Bioinformatics, 2024, v. 40, n. 7, p. 1, doi. 10.1093/bioinformatics/btae426

By:

Nader, Kristen;
Tasci, Misra;
Ianevski, Aleksandr;
Erickson, Andrew;
Verschuren, Emmy W;
Aittokallio, Tero;
Miihkinen, Mitro

Publication type:

Article

PredGCN: a Pruning-enabled Gene-Cell Net for automatic cell annotation of single cell transcriptome data.

Published in:

Bioinformatics, 2024, v. 40, n. 7, p. 1, doi. 10.1093/bioinformatics/btae421

By:

Qi, Qi;
Wang, Yunhe;
Huang, Yujian;
Fan, Yi;
Li, Xiangtao

Publication type:

Article

Efficient construction and utilization of k-ordered FM-indexes with kISS for ultra-fast read mapping in large genomes.

Published in:

Bioinformatics, 2024, v. 40, n. 7, p. 1, doi. 10.1093/bioinformatics/btae409

By:

Yang, Zheng-Dao;
Kuo, Hsuan-Yu;
Hsieh, Po-Wei;
Hung, Jui-Hung

Publication type:

Article

Assessing citation integrity in biomedical publications: corpus annotation and NLP models.

Published in:

Bioinformatics, 2024, v. 40, n. 7, p. 1, doi. 10.1093/bioinformatics/btae420

By:

Sarol, Maria Janina;
Ming, Shufan;
Radhakrishna, Shruthan;
Schneider, Jodi;
Kilicoglu, Halil

Publication type:

Article

deTELpy: Python package for high-throughput detection of amino acid substitutions in mass spectrometry datasets.

Published in:

Bioinformatics, 2024, v. 40, n. 7, p. 1, doi. 10.1093/bioinformatics/btae424

By:

Landerer, Cedric;
Scheremetjew, Maxim;
Moon, HongKee;
Hersemann, Lena;
Toth-Petroczy, Agnes

Publication type:

Article

mLiftOver: harmonizing data across Infinium DNA methylation platforms.

Published in:

Bioinformatics, 2024, v. 40, n. 7, p. 1, doi. 10.1093/bioinformatics/btae423

By:

Chen, Brian H;
Zhou, Wanding

Publication type:

Article

Document-level biomedical relation extraction via hierarchical tree graph and relation segmentation module.

Published in:

Bioinformatics, 2024, v. 40, n. 7, p. 1, doi. 10.1093/bioinformatics/btae418

By:

Yuan, Jianyuan;
Zhang, Fengyu;
Qiu, Yimeng;
Lin, Hongfei;
Zhang, Yijia

Publication type:

Article

hictk: blazing fast toolkit to work with.hic and.cool files.

Published in:

Bioinformatics, 2024, v. 40, n. 7, p. 1, doi. 10.1093/bioinformatics/btae408

By:

Rossini, Roberto;
Paulsen, Jonas

Publication type:

Article

Geometric epitope and paratope prediction.

Published in:

Bioinformatics, 2024, v. 40, n. 7, p. 1, doi. 10.1093/bioinformatics/btae405

By:

Pegoraro, Marco;
Dominé, Clémentine;
Rodolà, Emanuele;
Veličković, Petar;
Deac, Andreea

Publication type:

Article

Calib-RT: an open source python package for peptide retention time calibration in DIA mass spectrometry data.

Published in:

Bioinformatics, 2024, v. 40, n. 7, p. 1, doi. 10.1093/bioinformatics/btae417

By:

Zhang, Yichi;
Hu, Chenghui;
Wu, Xiaohui;
Song, Jian

Publication type:

Article

ADMET-AI: a machine learning ADMET platform for evaluation of large-scale chemical libraries.

Published in:

Bioinformatics, 2024, v. 40, n. 7, p. 1, doi. 10.1093/bioinformatics/btae416

By:

Swanson, Kyle;
Walther, Parker;
Leitz, Jeremy;
Mukherjee, Souhrid;
Wu, Joseph C;
Shivnaraine, Rabindra V;
Zou, James

Publication type:

Article

Optimizing data integration improves gene regulatory network inference in Arabidopsis thaliana.

Published in:

Bioinformatics, 2024, v. 40, n. 7, p. 1, doi. 10.1093/bioinformatics/btae415

By:

Cassan, Océane;
Lecellier, Charles-Henri;
Martin, Antoine;
Bréhélin, Laurent;
Lèbre, Sophie

Publication type:

Article

Surface-based multimodal protein–ligand binding affinity prediction.

Published in:

Bioinformatics, 2024, v. 40, n. 7, p. 1, doi. 10.1093/bioinformatics/btae413

By:

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

Publication type:

Article