Works matching IS 13674803 AND DT 2024 AND VI 40 AND IP 12

Results: 47

Identification and annotation of centromeric hypomethylated regions with CDR-Finder.

Published in:

Bioinformatics, 2024, v. 40, n. 12, p. 1, doi. 10.1093/bioinformatics/btae733

By:

Mastrorosa, Francesco Kumara;
Oshima, Keisuke K;
Rozanski, Allison N;
Harvey, William T;
Eichler, Evan E;
Logsdon, Glennis A

Publication type:

Article

A BLAST from the past: revisiting blastp's E-value.

Published in:

Bioinformatics, 2024, v. 40, n. 12, p. 1, doi. 10.1093/bioinformatics/btae729

By:

Lu, Yang Young;
Keich, Uri

Publication type:

Article

HBFormer: a single-stream framework based on hybrid attention mechanism for identification of human-virus protein–protein interactions.

Published in:

Bioinformatics, 2024, v. 40, n. 12, p. 1, doi. 10.1093/bioinformatics/btae724

By:

Zhang, Liyuan;
Wang, Sicong;
Wang, Yadong;
Zhao, Tianyi

Publication type:

Article

VSS-Hi-C: variance-stabilized signals for chromatin contacts.

Published in:

Bioinformatics, 2024, v. 40, n. 12, p. 1, doi. 10.1093/bioinformatics/btae715

By:

Kenari, Neda Shokraneh;
Bayat, Faezeh;
Libbrecht, Maxwell W

Publication type:

Article

OpenVariant: a toolkit to parse and operate multiple input file formats.

Published in:

Bioinformatics, 2024, v. 40, n. 12, p. 1, doi. 10.1093/bioinformatics/btae714

By:

Martínez-Millán, David;
Brando, Federica;
Grau, Miguel L.;
Sánchez-Guixé, Mònica;
López-Elorduy, Carlos;
Reyes-Salazar, Iker;
Deu-Pons, Jordi;
López-Bigas, Núria;
González-Pérez, Abel

Publication type:

Article

GUEST: an R package for handling estimation of graphical structure and multiclassification for error-prone gene expression data.

Published in:

Bioinformatics, 2024, v. 40, n. 12, p. 1, doi. 10.1093/bioinformatics/btae731

By:

Chen, Li-Pang;
Tsao, Hui-Shan

Publication type:

Article

JARVIS3: an efficient encoder for genomic data.

Published in:

Bioinformatics, 2024, v. 40, n. 12, p. 1, doi. 10.1093/bioinformatics/btae725

By:

Sousa, Maria J P;
Pinho, Armando J;
Pratas, Diogo

Publication type:

Article

STRprofiler: efficient comparisons of short tandem repeat profiles for biomedical model authentication.

Published in:

Bioinformatics, 2024, v. 40, n. 12, p. 1, doi. 10.1093/bioinformatics/btae713

By:

Andrews, Jared M;
Lloyd, Michael W;
Neuhauser, Steven B;
Bundy, Margaret;
Jocoy, Emily L;
Airhart, Susan D;
Bult, Carol J;
Evrard, Yvonne A;
Chuang, Jeffrey H;
Baker, Suzanne

Publication type:

Article

spread.gl: visualizing pathogen dispersal in a high-performance browser application.

Published in:

Bioinformatics, 2024, v. 40, n. 12, p. 1, doi. 10.1093/bioinformatics/btae721

By:

Li, Yimin;
Bollen, Nena;
Hong, Samuel L;
Brusselmans, Marius;
Gambaro, Fabiana;
Klaps, Joon;
Suchard, Marc A;
Rambaut, Andrew;
Lemey, Philippe;
Dellicour, Simon;
Baele, Guy

Publication type:

Article

Panacus: fast and exact pangenome growth and core size estimation.

Published in:

Bioinformatics, 2024, v. 40, n. 12, p. 1, doi. 10.1093/bioinformatics/btae720

By:

Parmigiani, Luca;
Garrison, Erik;
Stoye, Jens;
Marschall, Tobias;
Doerr, Daniel

Publication type:

Article

Phasing nanopore genome assembly by integrating heterozygous variations and Hi-C data.

Published in:

Bioinformatics, 2024, v. 40, n. 12, p. 1, doi. 10.1093/bioinformatics/btae712

By:

Zhang, Jun;
Nie, Fan;
Luo, Feng;
Wang, Jianxin

Publication type:

Article

HAlign 4: a new strategy for rapidly aligning millions of sequences.

Published in:

Bioinformatics, 2024, v. 40, n. 12, p. 1, doi. 10.1093/bioinformatics/btae718

By:

Zhou, Tong;
Zhang, Pinglu;
Zou, Quan;
Han, Wu

Publication type:

Article

BWT construction and search at the terabase scale.

Published in:

Bioinformatics, 2024, v. 40, n. 12, p. 1, doi. 10.1093/bioinformatics/btae717

By:

Li, Heng

Publication type:

Article

easySCF: a tool for enhancing interoperability between R and Python for efficient single-cell data analysis.

Published in:

Bioinformatics, 2024, v. 40, n. 12, p. 1, doi. 10.1093/bioinformatics/btae710

By:

Zhang, Haoyun;
Zhang, Wentao;
Zhao, Shuai;
Xu, Guangyu;
Shen, Yi;
Jiang, Feng;
Qin, An;
Cui, Lei

Publication type:

Article

Virtual tissue expression analysis.

Published in:

Bioinformatics, 2024, v. 40, n. 12, p. 1, doi. 10.1093/bioinformatics/btae709

By:

Simeth, Jakob;
Hüttl, Paul;
Schön, Marian;
Nozari, Zahra;
Huttner, Michael;
Schmidt, Tobias;
Altenbuchinger, Michael;
Spang, Rainer

Publication type:

Article

lefser: implementation of metagenomic biomarker discovery tool, LEfSe, in R.

Published in:

Bioinformatics, 2024, v. 40, n. 12, p. 1, doi. 10.1093/bioinformatics/btae707

By:

Khleborodova, Asya;
Gamboa-Tuz, Samuel D;
Ramos, Marcel;
Segata, Nicola;
Waldron, Levi;
Oh, Sehyun

Publication type:

Article

Fast polypharmacy side effect prediction using tensor factorization.

Published in:

Bioinformatics, 2024, v. 40, n. 12, p. 1, doi. 10.1093/bioinformatics/btae706

By:

Lloyd, Oliver;
Liu, Yi;
Gaunt, Tom R

Publication type:

Article

ViraLM: empowering virus discovery through the genome foundation model.

Published in:

Bioinformatics, 2024, v. 40, n. 12, p. 1, doi. 10.1093/bioinformatics/btae704

By:

Peng, Cheng;
Shang, Jiayu;
Guan, Jiaojiao;
Wang, Donglin;
Sun, Yanni

Publication type:

Article

Sparse Neighbor Joining: rapid phylogenetic inference using a sparse distance matrix.

Published in:

Bioinformatics, 2024, v. 40, n. 12, p. 1, doi. 10.1093/bioinformatics/btae701

By:

Kurt, Semih;
Bouchard-Côté, Alexandre;
Lagergren, Jens

Publication type:

Article

OneSC: a computational platform for recapitulating cell state transitions.

Published in:

Bioinformatics, 2024, v. 40, n. 12, p. 1, doi. 10.1093/bioinformatics/btae703

By:

Peng, Da;
Cahan, Patrick

Publication type:

Article

Gene count estimation with pytximport enables reproducible analysis of bulk RNA sequencing data in Python.

Published in:

Bioinformatics, 2024, v. 40, n. 12, p. 1, doi. 10.1093/bioinformatics/btae700

By:

Kuehl, Malte;
Wong, Milagros N;
Wanner, Nicola;
Bonn, Stefan;
Puelles, Victor G

Publication type:

Article

FastTENET: an accelerated TENET algorithm based on manycore computing in Python.

Published in:

Bioinformatics, 2024, v. 40, n. 12, p. 1, doi. 10.1093/bioinformatics/btae699

By:

Sung, Rakbin;
Kim, Hyeonkyu;
Kim, Junil;
Lee, Daewon

Publication type:

Article

Polyphonia: detecting inter-sample contamination in viral genomic sequencing data.

Published in:

Bioinformatics, 2024, v. 40, n. 12, p. 1, doi. 10.1093/bioinformatics/btae698

By:

Krasilnikova, Lydia A;
Tomkins-Tinch, Christopher H;
Gayton, Alton C;
Schaffner, Stephen F;
Dobbins, Sabrina T;
Gladden-Young, Adrianne;
Siddle, Katherine J;
Park, Daniel J;
Sabeti, Pardis C

Publication type:

Article

PhosX: data-driven kinase activity inference from phosphoproteomics experiments.

Published in:

Bioinformatics, 2024, v. 40, n. 12, p. 1, doi. 10.1093/bioinformatics/btae697

By:

Lussana, Alessandro;
Müller-Dott, Sophia;
Saez-Rodriguez, Julio;
Petsalaki, Evangelia

Publication type:

Article

Mutual information for detecting multi-class biomarkers when integrating multiple bulk or single-cell transcriptomic studies.

Published in:

Bioinformatics, 2024, v. 40, n. 12, p. 1, doi. 10.1093/bioinformatics/btae696

By:

Zou, Jian;
Li, Zheqi;
Carleton, Neil;
Oesterreich, Steffi;
Lee, Adrian V;
Tseng, George C

Publication type:

Article

Damsel: analysis and visualisation of DamID sequencing in R.

Published in:

Bioinformatics, 2024, v. 40, n. 12, p. 1, doi. 10.1093/bioinformatics/btae695

By:

Page, Caitlin G;
Londsdale, Andrew;
Mitchell, Katrina A;
Schröder, Jan;
Harvey, Kieran F;
Oshlack, Alicia

Publication type:

Article

Accurate and transferable drug–target interaction prediction with DrugLAMP.

Published in:

Bioinformatics, 2024, v. 40, n. 12, p. 1, doi. 10.1093/bioinformatics/btae693

By:

Luo, Zhengchao;
Wu, Wei;
Sun, Qichen;
Wang, Jinzhuo

Publication type:

Article

DrugRepPT: a deep pretraining and fine-tuning framework for drug repositioning based on drug's expression perturbation and treatment effectiveness.

Published in:

Bioinformatics, 2024, v. 40, n. 12, p. 1, doi. 10.1093/bioinformatics/btae692

By:

Fan, Shuyue;
Yang, Kuo;
Lu, Kezhi;
Dong, Xin;
Li, Xianan;
Zhu, Qiang;
Li, Shao;
Zeng, Jianyang;
Zhou, Xuezhong

Publication type:

Article

Sensitivities in protein allocation models reveal distribution of metabolic capacity and flux control.

Published in:

Bioinformatics, 2024, v. 40, n. 12, p. 1, doi. 10.1093/bioinformatics/btae691

By:

van den Bogaard, Samira;
Saa, Pedro A;
Alter, Tobias B

Publication type:

Article

STRPsearch: fast detection of structured tandem repeat proteins.

Published in:

Bioinformatics, 2024, v. 40, n. 12, p. 1, doi. 10.1093/bioinformatics/btae690

By:

Mozaffari, Soroush;
Arrías, Paula Nazarena;
Clementel, Damiano;
Piovesan, Damiano;
Ferrari, Carlo;
Tosatto, Silvio C E;
Monzon, Alexander Miguel

Publication type:

Article

DeepDR: a deep learning library for drug response prediction.

Published in:

Bioinformatics, 2024, v. 40, n. 12, p. 1, doi. 10.1093/bioinformatics/btae688

By:

Jiang, Zhengxiang;
Li, Pengyong

Publication type:

Article

Tiberius: end-to-end deep learning with an HMM for gene prediction.

Published in:

Bioinformatics, 2024, v. 40, n. 12, p. 1, doi. 10.1093/bioinformatics/btae685

By:

Gabriel, Lars;
Becker, Felix;
Hoff, Katharina J;
Stanke, Mario

Publication type:

Article

Dynamic modelling of signalling pathways when ordinary differential equations are not feasible.

Published in:

Bioinformatics, 2024, v. 40, n. 12, p. 1, doi. 10.1093/bioinformatics/btae683

By:

Rachel, Timo;
Brombacher, Eva;
Wöhrle, Svenja;
Groß, Olaf;
Kreutz, Clemens

Publication type:

Article

Facilitating phenotyping from clinical texts: the medkit library.

Published in:

Bioinformatics, 2024, v. 40, n. 12, p. 1, doi. 10.1093/bioinformatics/btae681

By:

Neuraz, Antoine;
Vaillant, Ghislain;
Arias, Camila;
Birot, Olivier;
Huynh, Kim-Tam;
Fabacher, Thibaut;
Rogier, Alice;
Garcelon, Nicolas;
Lerner, Ivan;
Rance, Bastien;
Coulet, Adrien

Publication type:

Article

FAPM: functional annotation of proteins using multimodal models beyond structural modeling.

Published in:

Bioinformatics, 2024, v. 40, n. 12, p. 1, doi. 10.1093/bioinformatics/btae680

By:

Xiang, Wenkai;
Xiong, Zhaoping;
Chen, Huan;
Xiong, Jiacheng;
Zhang, Wei;
Fu, Zunyun;
Zheng, Mingyue;
Liu, Bing;
Shi, Qian

Publication type:

Article

LmRaC: a functionally extensible tool for LLM interrogation of user experimental results.

Published in:

Bioinformatics, 2024, v. 40, n. 12, p. 1, doi. 10.1093/bioinformatics/btae679

By:

Craig, Douglas B;
Drăghici, Sorin

Publication type:

Article

DeepRSMA: a cross-fusion-based deep learning method for RNA–small molecule binding affinity prediction.

Published in:

Bioinformatics, 2024, v. 40, n. 12, p. 1, doi. 10.1093/bioinformatics/btae678

By:

Huang, Zhijian;
Wang, Yucheng;
Chen, Song;
Tan, Yaw Sing;
Deng, Lei;
Wu, Min

Publication type:

Article

Predicting the subcellular location of prokaryotic proteins with DeepLocPro.

Published in:

Bioinformatics, 2024, v. 40, n. 12, p. 1, doi. 10.1093/bioinformatics/btae677

By:

Moreno, Jaime;
Nielsen, Henrik;
Winther, Ole;
Teufel, Felix

Publication type:

Article

CVR-BBI: an open-source VR platform for multi-user collaborative brain to brain interfaces.

Published in:

Bioinformatics, 2024, v. 40, n. 12, p. 1, doi. 10.1093/bioinformatics/btae676

By:

Liu, Di;
Wei, Yina

Publication type:

Article

Improved prediction of post-translational modification crosstalk within proteins using DeepPCT.

Published in:

Bioinformatics, 2024, v. 40, n. 12, p. 1, doi. 10.1093/bioinformatics/btae675

By:

Huang, Yu-Xiang;
Liu, Rong

Publication type:

Article

AltGosling: automatic generation of text descriptions for accessible genomics data visualization.

Published in:

Bioinformatics, 2024, v. 40, n. 12, p. 1, doi. 10.1093/bioinformatics/btae670

By:

Smits, Thomas C;
L'Yi, Sehi;
Mar, Andrew P;
Gehlenborg, Nils

Publication type:

Article

Micro-DeMix: a mixture beta-multinomial model for investigating the heterogeneity of the stool microbiome compositions.

Published in:

Bioinformatics, 2024, v. 40, n. 12, p. 1, doi. 10.1093/bioinformatics/btae667

By:

Liu, Ruoqian;
Wang, Yue;
Cheng, Dan

Publication type:

Article

Pod5Viewer: a GUI for inspecting raw nanopore sequencing data.

Published in:

Bioinformatics, 2024, v. 40, n. 12, p. 1, doi. 10.1093/bioinformatics/btae665

By:

Dietrich, Vincent;
Alagna, Nicolò;
Helm, Mark;
Gerber, Susanne;
Butto, Tamer

Publication type:

Article

FEHAT: efficient, large scale and automated heartbeat detection in Medaka fish embryos.

Published in:

Bioinformatics, 2024, v. 40, n. 12, p. 1, doi. 10.1093/bioinformatics/btae664

By:

Ferreira, Marcio Soares;
Stricker, Sebastian;
Fitzgerald, Tomas;
Monahan, Jack;
Defranoux, Fanny;
Watson, Philip;
Welz, Bettina;
Hammouda, Omar;
Wittbrodt, Joachim;
Birney, Ewan

Publication type:

Article

Afpdb: an efficient structure manipulation package for AI protein design.

Published in:

Bioinformatics, 2024, v. 40, n. 12, p. 1, doi. 10.1093/bioinformatics/btae654

By:

Zhou, Yingyao;
Cox, Jiayi;
Zhou, Bin;
Zhu, Steven;
Zhong, Yang;
Spraggon, Glen

Publication type:

Article

Ranking antibody binding epitopes and proteins across samples from whole proteome tiled linear peptides.

Published in:

Bioinformatics, 2024, v. 40, n. 12, p. 1, doi. 10.1093/bioinformatics/btae637

By:

McIlwain, Sean J;
Hoefges, Anna;
Erbe, Amy K;
Sondel, Paul M;
Ong, Irene M

Publication type:

Article

Knowledge mining of brain connectivity in massive literature based on transfer learning.

Published in:

Bioinformatics, 2024, v. 40, n. 12, p. 1, doi. 10.1093/bioinformatics/btae648

By:

Chai, Xiaokang;
An, Sile;
Chen, Simeng;
Li, Wenwei;
Feng, Zhao;
Li, Xiangning;
Gong, Hui;
Luo, Qingming;
Li, Anan

Publication type:

Article