Works matching IS 13674803 AND DT 2024 AND VI 40 AND IP 1

Results: 47

Sensommatic: an efficient pipeline to mine and predict sensory receptor genes in the era of reference-quality genomes.

Published in:

Bioinformatics, 2024, v. 40, n. 1, p. 1, doi. 10.1093/bioinformatics/btae040

By:

Ryan, Louise;
Lawless, Colleen;
Hughes, Graham M

Publication type:

Article

QATS: an ImageJ plugin for the quantification of toroidal nuclei in biological images.

Published in:

Bioinformatics, 2024, v. 40, n. 1, p. 1, doi. 10.1093/bioinformatics/btae026

By:

Pons, Carles;
Mauvezin, Caroline

Publication type:

Article

MetaNorm: incorporating meta-analytic priors into normalization of NanoString nCounter data.

Published in:

Bioinformatics, 2024, v. 40, n. 1, p. 1, doi. 10.1093/bioinformatics/btae024

By:

Barth, Jackson;
Yang, Yuqiu;
Xiao, Guanghua;
Wang, Xinlei

Publication type:

Article

Assembling spatial clustering framework for heterogeneous spatial transcriptomics data with GRAPHDeep.

Published in:

Bioinformatics, 2024, v. 40, n. 1, p. 1, doi. 10.1093/bioinformatics/btae023

By:

Liu, Teng;
Fang, Zhaoyu;
Li, Xin;
Zhang, Lining;
Cao, Dong-Sheng;
Li, Min;
Yin, Mingzhu

Publication type:

Article

Text mining for contexts and relationships in cancer genomics literature.

Published in:

Bioinformatics, 2024, v. 40, n. 1, p. 1, doi. 10.1093/bioinformatics/btae021

By:

Collins, Charlotte;
Baker, Simon;
Brown, Jason;
Zheng, Huiyuan;
Chan, Adelyne;
Stenius, Ulla;
Narita, Masashi;
Korhonen, Anna

Publication type:

Article

scMAE: a masked autoencoder for single-cell RNA-seq clustering.

Published in:

Bioinformatics, 2024, v. 40, n. 1, p. 1, doi. 10.1093/bioinformatics/btae020

By:

Fang, Zhaoyu;
Zheng, Ruiqing;
Li, Min

Publication type:

Article

nf-core/nanostring: a pipeline for reproducible NanoString nCounter analysis.

Published in:

Bioinformatics, 2024, v. 40, n. 1, p. 1, doi. 10.1093/bioinformatics/btae019

By:

Peltzer, Alexander;
Mohr, Christopher;
Stadermann, Kai B;
Zwick, Matthias;
Schmid, Ramona

Publication type:

Article

ViralWasm: a client-side user-friendly web application suite for viral genomics.

Published in:

Bioinformatics, 2024, v. 40, n. 1, p. 1, doi. 10.1093/bioinformatics/btae018

By:

Ji, Daniel;
Aboukhalil, Robert;
Moshiri, Niema

Publication type:

Article

Fragmentstein—facilitating data reuse for cell-free DNA fragment analysis.

Published in:

Bioinformatics, 2024, v. 40, n. 1, p. 1, doi. 10.1093/bioinformatics/btae017

By:

Balázs, Zsolt;
Gitchev, Todor;
Ivanković, Ivna;
Krauthammer, Michael

Publication type:

Article

ReMASTER: improved phylodynamic simulation for BEAST 2.7.

Published in:

2024

By:

Vaughan, Timothy G

Publication type:

Letter to the Editor

FMAlign2: a novel fast multiple nucleotide sequence alignment method for ultralong datasets.

Published in:

Bioinformatics, 2024, v. 40, n. 1, p. 1, doi. 10.1093/bioinformatics/btae014

By:

Zhang, Pinglu;
Liu, Huan;
Wei, Yanming;
Zhai, Yixiao;
Tian, Qinzhong;
Zou, Quan

Publication type:

Article

Multiomics-integrated deep language model enables in silico genome-wide detection of transcription factor binding site in unexplored biosamples.

Published in:

Bioinformatics, 2024, v. 40, n. 1, p. 1, doi. 10.1093/bioinformatics/btae013

By:

Yang, Zikun;
Li, Xin;
Sheng, Lele;
Zhu, Ming;
Lan, Xun;
Gu, Fei

Publication type:

Article

SeedMatchR: identify off-target effects mediated by siRNA seed regions in RNA-seq experiments.

Published in:

Bioinformatics, 2024, v. 40, n. 1, p. 1, doi. 10.1093/bioinformatics/btae011

By:

Cazares, Tareian;
Higgs, Richard E;
Wang, Jibo;
Ozer, Hatice Gulcin

Publication type:

Article

SimService: a lightweight library for building simulation services in Python.

Published in:

Bioinformatics, 2024, v. 40, n. 1, p. 1, doi. 10.1093/bioinformatics/btae009

By:

Sego, T J

Publication type:

Article

GatekeepR: an R Shiny application for the identification of nodes with high dynamic impact in Boolean networks.

Published in:

Bioinformatics, 2024, v. 40, n. 1, p. 1, doi. 10.1093/bioinformatics/btae007

By:

Weidner, Felix M;
Ikonomi, Nensi;
Werle, Silke D;
Schwab, Julian D;
Kestler, Hans A

Publication type:

Article

selscan 2.0: scanning for sweeps in unphased data.

Published in:

Bioinformatics, 2024, v. 40, n. 1, p. 1, doi. 10.1093/bioinformatics/btae006

By:

Szpiech, Zachary A

Publication type:

Article

RPEMHC: improved prediction of MHC–peptide binding affinity by a deep learning approach based on residue–residue pair encoding.

Published in:

Bioinformatics, 2024, v. 40, n. 1, p. 1, doi. 10.1093/bioinformatics/btad785

By:

Wang, Xuejiao;
Wu, Tingfang;
Jiang, Yelu;
Chen, Taoning;
Pan, Deng;
Jin, Zhi;
Xie, Jingxin;
Quan, Lijun;
Lyu, Qiang

Publication type:

Article

Mosaic-PICASSO: accurate crosstalk removal for multiplex fluorescence imaging.

Published in:

Bioinformatics, 2024, v. 40, n. 1, p. 1, doi. 10.1093/bioinformatics/btad784

By:

Cang, Hu;
Liu, Yang;
Xing, Jianhua

Publication type:

Article

ESQmodel: biologically informed evaluation of 2-D cell segmentation quality in multiplexed tissue images.

Published in:

Bioinformatics, 2024, v. 40, n. 1, p. 1, doi. 10.1093/bioinformatics/btad783

By:

Lee, Eric;
Lee, Dongkyu;
Fan, Wayne;
Lytle, Andrew;
Fu, Yuxiang;
Consortium, IMAXT;
Scott, David W;
Steidl, Christian;
Aparicio, Samuel;
Roth, Andrew

Publication type:

Article

FLAMS: Find Lysine Acylations and other Modification Sites.

Published in:

Bioinformatics, 2024, v. 40, n. 1, p. 1, doi. 10.1093/bioinformatics/btae005

By:

Longin, Hannelore;
Broeckaert, Nand;
Langen, Maarten;
Hari, Roshan;
Kramarska, Anna;
Oikarinen, Kasper;
Hendrix, Hanne;
Lavigne, Rob;
Noort, Vera van

Publication type:

Article

methyLImp2: faster missing value estimation for DNA methylation data.

Published in:

Bioinformatics, 2024, v. 40, n. 1, p. 1, doi. 10.1093/bioinformatics/btae001

By:

Plaksienko, Anna;
Lena, Pietro Di;
Nardini, Christine;
Angelini, Claudia

Publication type:

Article

Embedding-based alignment: combining protein language models with dynamic programming alignment to detect structural similarities in the twilight-zone.

Published in:

Bioinformatics, 2024, v. 40, n. 1, p. 1, doi. 10.1093/bioinformatics/btad786

By:

Pantolini, Lorenzo;
Studer, Gabriel;
Pereira, Joana;
Durairaj, Janani;
Tauriello, Gerardo;
Schwede, Torsten

Publication type:

Article

CircSI-SSL: circRNA-binding site identification based on self-supervised learning.

Published in:

Bioinformatics, 2024, v. 40, n. 1, p. 1, doi. 10.1093/bioinformatics/btae004

By:

Cao, Chao;
Wang, Chunyu;
Yang, Shuhong;
Zou, Quan

Publication type:

Article

Microbial interactions from a new perspective: reinforcement learning reveals new insights into microbiome evolution.

Published in:

Bioinformatics, 2024, v. 40, n. 1, p. 1, doi. 10.1093/bioinformatics/btae003

By:

Ghadermazi, Parsa;
Chan, Siu Hung Joshua

Publication type:

Article

Guiding discovery of protein sequence-structure-function modeling.

Published in:

Bioinformatics, 2024, v. 40, n. 1, p. 1, doi. 10.1093/bioinformatics/btae002

By:

Hussain, Azam;
III, Charles L Brooks

Publication type:

Article

M-Ionic: prediction of metal-ion-binding sites from sequence using residue embeddings.

Published in:

Bioinformatics, 2024, v. 40, n. 1, p. 1, doi. 10.1093/bioinformatics/btad782

By:

Shenoy, Aditi;
Kalakoti, Yogesh;
Sundar, Durai;
Elofsson, Arne

Publication type:

Article

MHCSeqNet2—improved peptide-class I MHC binding prediction for alleles with low data.

Published in:

Bioinformatics, 2024, v. 40, n. 1, p. 1, doi. 10.1093/bioinformatics/btad780

By:

Wongklaew, Patiphan;
Sriswasdi, Sira;
Chuangsuwanich, Ekapol

Publication type:

Article

ExEmPLAR (Extracting, Exploring, and Embedding Pathways Leading to Actionable Research): a user-friendly interface for knowledge graph mining.

Published in:

2024

By:

Beasley, Jon-Michael T;
Korn, Daniel R;
Tucker, Nyssa N;
Alves, Erick T M;
Muratov, Eugene N;
Bizon, Chris;
Tropsha, Alexander

Publication type:

Case Study

TEFDTA: a transformer encoder and fingerprint representation combined prediction method for bonded and non-bonded drug–target affinities.

Published in:

Bioinformatics, 2024, v. 40, n. 1, p. 1, doi. 10.1093/bioinformatics/btad778

By:

Li, Zongquan;
Ren, Pengxuan;
Yang, Hao;
Zheng, Jie;
Bai, Fang

Publication type:

Article

Subset scanning for multi-trait analysis using GWAS summary statistics.

Published in:

Bioinformatics, 2024, v. 40, n. 1, p. 1, doi. 10.1093/bioinformatics/btad777

By:

Cao, Rui;
Olawsky, Evan;
McFowland, Edward;
Marcotte, Erin;
Spector, Logan;
Yang, Tianzhong

Publication type:

Article

Pathway analysis through mutual information.

Published in:

Bioinformatics, 2024, v. 40, n. 1, p. 1, doi. 10.1093/bioinformatics/btad776

By:

Jeuken, Gustavo S;
Käll, Lukas

Publication type:

Article

HAT: de novo variant calling for highly accurate short-read and long-read sequencing data.

Published in:

Bioinformatics, 2024, v. 40, n. 1, p. 1, doi. 10.1093/bioinformatics/btad775

By:

Ng, Jeffrey K;
Turner, Tychele N

Publication type:

Article

GeNNius: an ultrafast drug–target interaction inference method based on graph neural networks.

Published in:

Bioinformatics, 2024, v. 40, n. 1, p. 1, doi. 10.1093/bioinformatics/btad774

By:

Veleiro, Uxía;
Fuente, Jesús de la;
Serrano, Guillermo;
Pizurica, Marija;
Casals, Mikel;
Pineda-Lucena, Antonio;
Vicent, Silve;
Ochoa, Idoia;
Gevaert, Olivier;
Hernaez, Mikel

Publication type:

Article

CellularPotts.jl: simulating multiscale cellular models in Julia.

Published in:

Bioinformatics, 2024, v. 40, n. 1, p. 1, doi. 10.1093/bioinformatics/btad773

By:

Gregg, Robert W;
Benos, Panayiotis V

Publication type:

Article

scDMV: a zero–one inflated beta mixture model for DNA methylation variability with scBS-seq data.

Published in:

Bioinformatics, 2024, v. 40, n. 1, p. 1, doi. 10.1093/bioinformatics/btad772

By:

Zhou, Yan;
Zhang, Ying;
Peng, Minjiao;
Zhang, Yaru;
Li, Chenghao;
Shu, Lianjie;
Hu, Yaohua;
Su, Jianzhong;
Xu, Jinfeng

Publication type:

Article

Mining literature and pathway data to explore the relations of ketamine with neurotransmitters and gut microbiota using a knowledge-graph.

Published in:

Bioinformatics, 2024, v. 40, n. 1, p. 1, doi. 10.1093/bioinformatics/btad771

By:

Liu, Ting;
Feenstra, K Anton;
Huang, Zhisheng;
Heringa, Jaap

Publication type:

Article

A fast machine learning dataloader for epigenetic tracks from BigWig files.

Published in:

Bioinformatics, 2024, v. 40, n. 1, p. 1, doi. 10.1093/bioinformatics/btad767

By:

Retel, Joren Sebastian;
Poehlmann, Andreas;
Chiou, Josh;
Steffen, Andreas;
Clevert, Djork-Arné

Publication type:

Article

SOHPIE: statistical approach via pseudo-value information and estimation for differential network analysis of microbiome data.

Published in:

Bioinformatics, 2024, v. 40, n. 1, p. 1, doi. 10.1093/bioinformatics/btad766

By:

Ahn, Seungjun;
Datta, Somnath

Publication type:

Article

ELISL: early–late integrated synthetic lethality prediction in cancer.

Published in:

Bioinformatics, 2024, v. 40, n. 1, p. 1, doi. 10.1093/bioinformatics/btad764

By:

Tepeli, Yasin I;
Seale, Colm;
Gonçalves, Joana P

Publication type:

Article

pyCapsid: identifying dominant dynamics and quasi-rigid mechanical units in protein shells.

Published in:

Bioinformatics, 2024, v. 40, n. 1, p. 1, doi. 10.1093/bioinformatics/btad761

By:

Brown, Colin;
Agarwal, Anuradha;
Luque, Antoni

Publication type:

Article

MK-BMC: a Multi-Kernel framework with Boosted distance metrics for Microbiome data for Classification.

Published in:

Bioinformatics, 2024, v. 40, n. 1, p. 1, doi. 10.1093/bioinformatics/btad757

By:

Xu, Huang;
Wang, Tian;
Miao, Yuqi;
Qian, Min;
Yang, Yaning;
Wang, Shuang

Publication type:

Article

SciDataFlow: a tool for improving the flow of data through science.

Published in:

Bioinformatics, 2024, v. 40, n. 1, p. 1, doi. 10.1093/bioinformatics/btad754

By:

Buffalo, Vince

Publication type:

Article

Coracle—a machine learning framework to identify bacteria associated with continuous variables.

Published in:

Bioinformatics, 2024, v. 40, n. 1, p. 1, doi. 10.1093/bioinformatics/btad749

By:

Staab, Sebastian;
Cardénas, Anny;
Peixoto, Raquel S;
Schreiber, Falk;
Voolstra, Christian R

Publication type:

Article

Artificial intelligence-assisted quantification and assessment of whole slide images for pediatric kidney disease diagnosis.

Published in:

Bioinformatics, 2024, v. 40, n. 1, p. 1, doi. 10.1093/bioinformatics/btad740

By:

Feng, Chunyue;
Ong, Kokhaur;
Young, David M;
Chen, Bingxian;
Li, Longjie;
Huo, Xinmi;
Lu, Haoda;
Gu, Weizhong;
Liu, Fei;
Tang, Hongfeng;
Zhao, Manli;
Yang, Min;
Zhu, Kun;
Huang, Limin;
Wang, Qiang;
Marini, Gabriel Pik Liang;
Gui, Kun;
Han, Hao;
Sanders, Stephan J;
Li, Lin

Publication type:

Article

Clumppling: cluster matching and permutation program with integer linear programming.

Published in:

Bioinformatics, 2024, v. 40, n. 1, p. 1, doi. 10.1093/bioinformatics/btad751

By:

Liu, Xiran;
Kopelman, Naama M;
Rosenberg, Noah A

Publication type:

Article

Drug repositioning with adaptive graph convolutional networks.

Published in:

Bioinformatics, 2024, v. 40, n. 1, p. 1, doi. 10.1093/bioinformatics/btad748

By:

Sun, Xinliang;
Jia, Xiao;
Lu, Zhangli;
Tang, Jing;
Li, Min

Publication type:

Article

Seq-InSite: sequence supersedes structure for protein interaction site prediction.

Published in:

Bioinformatics, 2024, v. 40, n. 1, p. 1, doi. 10.1093/bioinformatics/btad738

By:

Hosseini, SeyedMohsen;
Golding, G Brian;
Ilie, Lucian

Publication type:

Article