Works matching IS 13674803 AND DT 2024 AND VI 40 AND IP 3

Results: 55

EpiVar Browser: advanced exploration of epigenomics data under controlled access.

Published in:

Bioinformatics, 2024, v. 40, n. 3, p. 1, doi. 10.1093/bioinformatics/btae136

By:

Lougheed, David R;
Liu, Hanshi;
Aracena, Katherine A;
Grégoire, Romain;
Pacis, Alain;
Pastinen, Tomi;
Barreiro, Luis B;
Joly, Yann;
Bujold, David;
Bourque, Guillaume

Publication type:

Article

Tutorial on survival modeling with applications to omics data.

Published in:

Bioinformatics, 2024, v. 40, n. 3, p. 1, doi. 10.1093/bioinformatics/btae132

By:

Zhao, Zhi;
Zobolas, John;
Zucknick, Manuela;
Aittokallio, Tero

Publication type:

Article

Digger: directed annotation of immunoglobulin and T cell receptor V, D, and J gene sequences and assemblies.

Published in:

Bioinformatics, 2024, v. 40, n. 3, p. 1, doi. 10.1093/bioinformatics/btae144

By:

Lees, William D;
Saha, Swati;
Yaari, Gur;
Watson, Corey T

Publication type:

Article

Incorporating temporal information during feature engineering bolsters emulation of spatio-temporal emergence.

Published in:

Bioinformatics, 2024, v. 40, n. 3, p. 1, doi. 10.1093/bioinformatics/btae131

By:

Cain, Jason Y;
Evarts, Jacob I;
Yu, Jessica S;
Bagheri, Neda

Publication type:

Article

Rapid generation of high-quality structure figures for publication with PyMOL-PUB.

Published in:

Bioinformatics, 2024, v. 40, n. 3, p. 1, doi. 10.1093/bioinformatics/btae139

By:

Chen, Yuting;
Zhang, Haoling;
Wang, Wen;
Shen, Yue;
Ping, Zhi

Publication type:

Article

Shu: visualization of high-dimensional biological pathways.

Published in:

Bioinformatics, 2024, v. 40, n. 3, p. 1, doi. 10.1093/bioinformatics/btae140

By:

Muriel, Jorge Carrasco;
Cowie, Nicholas;
Parkins, Shannara Taylor;
Mansouvar, Marjan;
Groves, Teddy;
Nielsen, Lars Keld

Publication type:

Article

AACFlow: an end-to-end model based on attention augmented convolutional neural network and flow-attention mechanism for identification of anticancer peptides.

Published in:

Bioinformatics, 2024, v. 40, n. 3, p. 1, doi. 10.1093/bioinformatics/btae142

By:

Zhang, Shengli;
Zhao, Ya;
Liang, Yunyun

Publication type:

Article

NPSV-deep: a deep learning method for genotyping structural variants in short read genome sequencing data.

Published in:

Bioinformatics, 2024, v. 40, n. 3, p. 1, doi. 10.1093/bioinformatics/btae129

By:

Linderman, Michael D;
Wallace, Jacob;
van der Heyde, Alderik;
Wieman, Eliza;
Brey, Daniel;
Shi, Yiran;
Hansen, Peter;
Shamsi, Zahra;
Liu, Jeremiah;
Gelb, Bruce D;
Bashir, Ali

Publication type:

Article

Uncertainty-aware single-cell annotation with a hierarchical reject option.

Published in:

Bioinformatics, 2024, v. 40, n. 3, p. 1, doi. 10.1093/bioinformatics/btae128

By:

Theunissen, Lauren;
Mortier, Thomas;
Saeys, Yvan;
Waegeman, Willem

Publication type:

Article

Identifying TAD-like domains on single-cell Hi-C data by graph embedding and changepoint detection.

Published in:

Bioinformatics, 2024, v. 40, n. 3, p. 1, doi. 10.1093/bioinformatics/btae138

By:

Liu, Erhu;
Lyu, Hongqiang;
Liu, Yuan;
Fu, Laiyi;
Cheng, Xiaoliang;
Yin, Xiaoran

Publication type:

Article

iNGNN-DTI: prediction of drug–target interaction with interpretable nested graph neural network and pretrained molecule models.

Published in:

Bioinformatics, 2024, v. 40, n. 3, p. 1, doi. 10.1093/bioinformatics/btae135

By:

Sun, Yan;
Li, Yan Yi;
Leung, Carson K;
Hu, Pingzhao

Publication type:

Article

pyM<sup>2</sup>aia: Python interface for mass spectrometry imaging with focus on deep learning.

Published in:

Bioinformatics, 2024, v. 40, n. 3, p. 1, doi. 10.1093/bioinformatics/btae133

By:

Cordes, Jonas;
Enzlein, Thomas;
Hopf, Carsten;
Wolf, Ivo

Publication type:

Article

MetaCerberus: distributed highly parallelized HMM-based processing for robust functional annotation across the tree of life.

Published in:

Bioinformatics, 2024, v. 40, n. 3, p. 1, doi. 10.1093/bioinformatics/btae119

By:

III, Jose L Figueroa;
Dhungel, Eliza;
Bellanger, Madeline;
Brouwer, Cory R;
III, Richard Allen White

Publication type:

Article

SpatialView: an interactive web application for visualization of multiple samples in spatial transcriptomics experiments.

Published in:

Bioinformatics, 2024, v. 40, n. 3, p. 1, doi. 10.1093/bioinformatics/btae117

By:

Mohanty, Chitrasen;
Prasad, Aman;
Cheng, Lingxin;
Arkin, Lisa M;
Shields, Bridget E;
Drolet, Beth;
Kendziorski, Christina

Publication type:

Article

BERMAD: batch effect removal for single-cell RNA-seq data using a multi-layer adaptation autoencoder with dual-channel framework.

Published in:

Bioinformatics, 2024, v. 40, n. 3, p. 1, doi. 10.1093/bioinformatics/btae127

By:

Zhan, Xiangxin;
Yin, Yanbin;
Zhang, Han

Publication type:

Article

Uncovering genetic associations in the human diseasome using an endophenotype-augmented disease network.

Published in:

Bioinformatics, 2024, v. 40, n. 3, p. 1, doi. 10.1093/bioinformatics/btae126

By:

Woerner, Jakob;
Sriram, Vivek;
Nam, Yonghyun;
Verma, Anurag;
Kim, Dokyoon

Publication type:

Article

Ribotin: automated assembly and phasing of rDNA morphs.

Published in:

Bioinformatics, 2024, v. 40, n. 3, p. 1, doi. 10.1093/bioinformatics/btae124

By:

Rautiainen, Mikko

Publication type:

Article

GPro: generative AI-empowered toolkit for promoter design.

Published in:

Bioinformatics, 2024, v. 40, n. 3, p. 1, doi. 10.1093/bioinformatics/btae123

By:

Wang, Haochen;
Du, Qixiu;
Wang, Ye;
Xu, Hanwen;
Wei, Zheng;
Wang, Xiaowo

Publication type:

Article

Information-incorporated gene network construction with FDR control.

Published in:

Bioinformatics, 2024, v. 40, n. 3, p. 1, doi. 10.1093/bioinformatics/btae125

By:

Wang, Hao;
Qiu, Yumou;
Guo, Hongqing;
Yin, Yanhai;
Liu, Peng

Publication type:

Article

MARS: a motif-based autoregressive model for retrosynthesis prediction.

Published in:

Bioinformatics, 2024, v. 40, n. 3, p. 1, doi. 10.1093/bioinformatics/btae115

By:

Liu, Jiahan;
Yan, Chaochao;
Yu, Yang;
Lu, Chan;
Huang, Junzhou;
Ou-Yang, Le;
Zhao, Peilin

Publication type:

Article

PySNV for complex intra-host variation detection.

Published in:

Bioinformatics, 2024, v. 40, n. 3, p. 1, doi. 10.1093/bioinformatics/btae116

By:

Li, Liandong;
Fu, Haoyi;
Ma, Wentai;
Li, Mingkun

Publication type:

Article

AutoGVP: a dockerized workflow integrating ClinVar and InterVar germline sequence variant classification.

Published in:

Bioinformatics, 2024, v. 40, n. 3, p. 1, doi. 10.1093/bioinformatics/btae114

By:

Kim, Jung;
Naqvi, Ammar S;
Corbett, Ryan J;
Kaufman, Rebecca S;
Vaksman, Zalman;
Brown, Miguel A;
Miller, Daniel P;
Phul, Saksham;
Geng, Zhuangzhuang;
Storm, Phillip B;
Resnick, Adam C;
Stewart, Douglas R;
Rokita, Jo Lynne;
Diskin, Sharon J

Publication type:

Article

AbFlex: designing antibody complementarity determining regions with flexible CDR definition.

Published in:

Bioinformatics, 2024, v. 40, n. 3, p. 1, doi. 10.1093/bioinformatics/btae122

By:

Jeon, Woosung;
Kim, Dongsup

Publication type:

Article

A dual-rule encoding DNA storage system using chaotic mapping to control GC content.

Published in:

Bioinformatics, 2024, v. 40, n. 3, p. 1, doi. 10.1093/bioinformatics/btae113

By:

Zhang, Xuncai;
Qi, Baonan;
Niu, Ying

Publication type:

Article

Graph-theoretical prediction of biological modules in quaternary structures of large protein complexes.

Published in:

Bioinformatics, 2024, v. 40, n. 3, p. 1, doi. 10.1093/bioinformatics/btae112

By:

Gisdon, Florian J;
Zunker, Mariella;
Wolf, Jan Niclas;
Prüfer, Kai;
Ackermann, Jörg;
Welsch, Christoph;
Koch, Ina

Publication type:

Article

Correction to: OncoThreads: visualization of large-scale longitudinal cancer molecular data.

Published in:: 2024
Publication type:: Correction Notice

ElemeNT 2023: an enhanced tool for detection and curation of core promoter elements.

Published in:

Bioinformatics, 2024, v. 40, n. 3, p. 1, doi. 10.1093/bioinformatics/btae110

By:

Adato, Orit;
Sloutskin, Anna;
Komemi, Hodaya;
Brabb, Ian;
Duttke, Sascha;
Bucher, Philipp;
Unger, Ron;
Juven-Gershon, Tamar

Publication type:

Article

CryoTransformer: a transformer model for picking protein particles from cryo-EM micrographs.

Published in:

Bioinformatics, 2024, v. 40, n. 3, p. 1, doi. 10.1093/bioinformatics/btae109

By:

Dhakal, Ashwin;
Gyawali, Rajan;
Wang, Liguo;
Cheng, Jianlin

Publication type:

Article

Nanometa Live: a user-friendly application for real-time metagenomic data analysis and pathogen identification.

Published in:

Bioinformatics, 2024, v. 40, n. 3, p. 1, doi. 10.1093/bioinformatics/btae108

By:

Sandås, Kristofer;
Lewerentz, Jacob;
Karlsson, Edvin;
Karlsson, Linda;
Sundell, David;
Simonyté-Sjödin, Kotryna;
Sjödin, Andreas

Publication type:

Article

CAM3.0: determining cell type composition and expression from bulk tissues with fully unsupervised deconvolution.

Published in:

Bioinformatics, 2024, v. 40, n. 3, p. 1, doi. 10.1093/bioinformatics/btae107

By:

Wu, Chiung-Ting;
Du, Dongping;
Chen, Lulu;
Dai, Rujia;
Liu, Chunyu;
Yu, Guoqiang;
Bhardwaj, Saurabh;
Parker, Sarah J;
Zhang, Zhen;
Clarke, Robert;
Herrington, David M;
Wang, Yue

Publication type:

Article

Lambda3: homology search for protein, nucleotide, and bisulfite-converted sequences.

Published in:

Bioinformatics, 2024, v. 40, n. 3, p. 1, doi. 10.1093/bioinformatics/btae097

By:

Hauswedell, Hannes;
Hetzel, Sara;
Gottlieb, Simon G;
Kretzmer, Helene;
Meissner, Alexander;
Reinert, Knut

Publication type:

Article

Selection among site-dependent structurally constrained substitution models of protein evolution by approximate Bayesian computation.

Published in:

Bioinformatics, 2024, v. 40, n. 3, p. 1, doi. 10.1093/bioinformatics/btae096

By:

Ferreiro, David;
Branco, Catarina;
Arenas, Miguel

Publication type:

Article

Structured Prompt Interrogation and Recursive Extraction of Semantics (SPIRES): a method for populating knowledge bases using zero-shot learning.

Published in:

Bioinformatics, 2024, v. 40, n. 3, p. 1, doi. 10.1093/bioinformatics/btae104

By:

Caufield, J Harry;
Hegde, Harshad;
Emonet, Vincent;
Harris, Nomi L;
Joachimiak, Marcin P;
Matentzoglu, Nicolas;
Kim, HyeongSik;
Moxon, Sierra;
Reese, Justin T;
Haendel, Melissa A;
Robinson, Peter N;
Mungall, Christopher J

Publication type:

Article

Optimizing representations for integrative structural modeling using Bayesian model selection.

Published in:

Bioinformatics, 2024, v. 40, n. 3, p. 1, doi. 10.1093/bioinformatics/btae106

By:

Arvindekar, Shreyas;
Pathak, Aditi S;
Majila, Kartik;
Viswanath, Shruthi

Publication type:

Article

SENSAAS-Flex: a joint optimization approach for aligning 3D shapes and exploring the molecular conformation space.

Published in:

Bioinformatics, 2024, v. 40, n. 3, p. 1, doi. 10.1093/bioinformatics/btae105

By:

Biyuzan, Hamza;
Masrour, Mohamed-Akram;
Grandmougin, Lucas;
Payan, Frédéric;
Douguet, Dominique

Publication type:

Article

HIResist: a database of HIV-1 resistance to broadly neutralizing antibodies.

Published in:

Bioinformatics, 2024, v. 40, n. 3, p. 1, doi. 10.1093/bioinformatics/btae103

By:

Misra, Milind;
Jeffy, Jeffy;
Liao, Charis;
Pickthorn, Stephanie;
Wagh, Kshitij;
Herschhorn, Alon

Publication type:

Article

Flexiplex: a versatile demultiplexer and search tool for omics data.

Published in:

Bioinformatics, 2024, v. 40, n. 3, p. 1, doi. 10.1093/bioinformatics/btae102

By:

Cheng, Oliver;
Ling, Min Hao;
Wang, Changqing;
Wu, Shuyi;
Ritchie, Matthew E;
Göke, Jonathan;
Amin, Noorul;
Davidson, Nadia M

Publication type:

Article

LAVASET: Latent Variable Stochastic Ensemble of Trees. An ensemble method for correlated datasets with spatial, spectral, and temporal dependencies.

Published in:

Bioinformatics, 2024, v. 40, n. 3, p. 1, doi. 10.1093/bioinformatics/btae101

By:

Kasapi, Melpomeni;
Xu, Kexin;
Ebbels, Timothy M D;
O'Regan, Declan P;
Ware, James S;
Posma, Joram M

Publication type:

Article

A compressive seeding algorithm in conjunction with reordering-based compression.

Published in:

Bioinformatics, 2024, v. 40, n. 3, p. 1, doi. 10.1093/bioinformatics/btae100

By:

Ji, Fahu;
Zhou, Qian;
Ruan, Jue;
Zhu, Zexuan;
Liu, Xianming

Publication type:

Article

imputomics: web server and R package for missing values imputation in metabolomics data.

Published in:

Bioinformatics, 2024, v. 40, n. 3, p. 1, doi. 10.1093/bioinformatics/btae098

By:

Chilimoniuk, Jarosław;
Grzesiak, Krystyna;
Kała, Jakub;
Nowakowski, Dominik;
Krętowski, Adam;
Kolenda, Rafał;
Ciborowski, Michał;
Burdukiewicz, Michał

Publication type:

Article

vizAPA: visualizing dynamics of alternative polyadenylation from bulk and single-cell data.

Published in:

Bioinformatics, 2024, v. 40, n. 3, p. 1, doi. 10.1093/bioinformatics/btae099

By:

Bi, Xingyu;
Ye, Wenbin;
Cheng, Xin;
Yang, Ning;
Wu, Xiaohui

Publication type:

Article

Fast and scalable querying of eukaryotic linear motifs with gget elm.

Published in:

Bioinformatics, 2024, v. 40, n. 3, p. 1, doi. 10.1093/bioinformatics/btae095

By:

Luebbert, Laura;
Hoang, Chi;
Kumar, Manjeet;
Pachter, Lior

Publication type:

Article

ViTAL: Vision TrAnsformer based Low coverage SARS-CoV-2 lineage assignment.

Published in:

Bioinformatics, 2024, v. 40, n. 3, p. 1, doi. 10.1093/bioinformatics/btae093

By:

Jahshan, Zuher;
Yavits, Leonid

Publication type:

Article

EvoAug-TF: extending evolution-inspired data augmentations for genomic deep learning to TensorFlow.

Published in:

Bioinformatics, 2024, v. 40, n. 3, p. 1, doi. 10.1093/bioinformatics/btae092

By:

Yu, Yiyang;
Muthukumar, Shivani;
Koo, Peter K

Publication type:

Article

KaMRaT: a C++ toolkit for k-mer count matrix dimension reduction.

Published in:

Bioinformatics, 2024, v. 40, n. 3, p. 1, doi. 10.1093/bioinformatics/btae090

By:

Xue, Haoliang;
Gallopin, Mélina;
Marchet, Camille;
Nguyen, Ha N;
Wang, Yunfeng;
Lainé, Antoine;
Bessiere, Chloé;
Gautheret, Daniel

Publication type:

Article

ICELLNET v2: a versatile method for cell–cell communication analysis from human transcriptomic data.

Published in:

Bioinformatics, 2024, v. 40, n. 3, p. 1, doi. 10.1093/bioinformatics/btae089

By:

Massenet-Regad, Lucile;
Soumelis, Vassili

Publication type:

Article

ARGprofiler—a pipeline for large-scale analysis of antimicrobial resistance genes and their flanking regions in metagenomic datasets.

Published in:

Bioinformatics, 2024, v. 40, n. 3, p. 1, doi. 10.1093/bioinformatics/btae086

By:

Martiny, Hannah-Marie;
Pyrounakis, Nikiforos;
Petersen, Thomas N;
Lukjančenko, Oksana;
Aarestrup, Frank M;
Clausen, Philip T L C;
Munk, Patrick

Publication type:

Article

preon: Fast and accurate entity normalization for drug names and cancer types in precision oncology.

Published in:

Bioinformatics, 2024, v. 40, n. 3, p. 1, doi. 10.1093/bioinformatics/btae085

By:

Ermshaus, Arik;
Piechotta, Michael;
Rüter, Gina;
Keilholz, Ulrich;
Leser, Ulf;
Benary, Manuela

Publication type:

Article

RT-Transformer: retention time prediction for metabolite annotation to assist in metabolite identification.

Published in:

Bioinformatics, 2024, v. 40, n. 3, p. 1, doi. 10.1093/bioinformatics/btae084

By:

Xue, Jun;
Wang, Bingyi;
Ji, Hongchao;
Li, WeiHua

Publication type:

Article

SST-editing: in silico spatial transcriptomic editing at single-cell resolution.

Published in:

Bioinformatics, 2024, v. 40, n. 3, p. 1, doi. 10.1093/bioinformatics/btae077

By:

Wu, Jiqing;
Koelzer, Viktor H

Publication type:

Article