Works matching IS 13674803 AND DT 2024 AND VI 40 AND IP 11

Results: 62

ViralPrimer: a web server to monitor viral nucleic acid amplification tests' primer efficiency during pandemics, with emphasis on SARS-CoV-2 and Mpox.

Published in:

Bioinformatics, 2024, v. 40, n. 11, p. 1, doi. 10.1093/bioinformatics/btae657

By:

Deutsch, Norbert;
Dosztányi, Zsuzsanna;
Csabai, István;
Medgyes-Horváth, Anna;
Pipek, Orsolya Anna;
Stéger, József;
Papp, Krisztián;
Visontai, Dávid;
Erdős, Gábor;
Mentes, Anikó

Publication type:

Article

quaqc: efficient and quick ATAC-seq quality control and filtering.

Published in:

Bioinformatics, 2024, v. 40, n. 11, p. 1, doi. 10.1093/bioinformatics/btae649

By:

Tremblay, Benjamin J M;
Qüesta, Julia I

Publication type:

Article

findGSEP: estimating genome size of polyploid species using k-mer frequencies.

Published in:

Bioinformatics, 2024, v. 40, n. 11, p. 1, doi. 10.1093/bioinformatics/btae647

By:

Fu, Laiyi;
Xie, Yanxin;
Ling, Shunkang;
Wang, Ying;
Wang, Binzhong;
Du, Hejun;
Peng, Qinke;
Sun, Hequan

Publication type:

Article

M<sup>2</sup>ara: unraveling metabolomic drug responses in whole-cell MALDI mass spectrometry bioassays.

Published in:

Bioinformatics, 2024, v. 40, n. 11, p. 1, doi. 10.1093/bioinformatics/btae694

By:

Enzlein, Thomas;
Geisel, Alexander;
Hopf, Carsten;
Schmidt, Stefan

Publication type:

Article

APAtizer: a tool for alternative polyadenylation analysis of RNA-Seq data.

Published in:

Bioinformatics, 2024, v. 40, n. 11, p. 1, doi. 10.1093/bioinformatics/btae689

By:

Sousa, Bruno;
Bessa, Maria;
Mendonça, Filipa L de;
Ferreira, Pedro G;
Moreira, Alexandra;
Pereira-Castro, Isabel

Publication type:

Article

Detecting transposable elements in long-read genomes using sTELLeR.

Published in:

Bioinformatics, 2024, v. 40, n. 11, p. 1, doi. 10.1093/bioinformatics/btae686

By:

Saether, Kristine Bilgrav;
Eisfeldt, Jesper

Publication type:

Article

Protein structure alignment by Reseek improves sensitivity to remote homologs.

Published in:

Bioinformatics, 2024, v. 40, n. 11, p. 1, doi. 10.1093/bioinformatics/btae687

By:

Edgar, Robert C

Publication type:

Article

R3DMCS: a web server for visualizing structural variation in RNA motifs across experimental 3D structures from the same organism or across species.

Published in:

Bioinformatics, 2024, v. 40, n. 11, p. 1, doi. 10.1093/bioinformatics/btae682

By:

Appasamy, Sri Devan;
Zirbel, Craig L

Publication type:

Article

Optimizing multi-omics data imputation with NMF and GAN synergy.

Published in:

Bioinformatics, 2024, v. 40, n. 11, p. 1, doi. 10.1093/bioinformatics/btae674

By:

Ansari, Md Istiaq;
Ahmed, Khandakar Tanvir;
Zhang, Wei

Publication type:

Article

PRONA: an R-package for Patient Reported Outcomes Network Analysis.

Published in:

Bioinformatics, 2024, v. 40, n. 11, p. 1, doi. 10.1093/bioinformatics/btae671

By:

Bergsneider, Brandon H;
Celiku, Orieta

Publication type:

Article

Pf-HaploAtlas: an interactive web app for spatiotemporal analysis of Plasmodium falciparum genes.

Published in:

Bioinformatics, 2024, v. 40, n. 11, p. 1, doi. 10.1093/bioinformatics/btae673

By:

Lee, Chiyun;
Ünlü, Eyyüb S;
White, Nina F D;
Almagro-Garcia, Jacob;
Ariani, Cristina;
Pearson, Richard D

Publication type:

Article

PubMed Computed Authors in 2024: an open resource of disambiguated author names in biomedical literature.

Published in:

Bioinformatics, 2024, v. 40, n. 11, p. 1, doi. 10.1093/bioinformatics/btae672

By:

Tian, Shubo;
Chen, Qingyu;
Comeau, Donald C;
Wilbur, W John;
Lu, Zhiyong

Publication type:

Article

RUCova: Removal of Unwanted Covariance in mass cytometry data.

Published in:

Bioinformatics, 2024, v. 40, n. 11, p. 1, doi. 10.1093/bioinformatics/btae669

By:

Astaburuaga-García, Rosario;
Sell, Thomas;
Mutlu, Samet;
Sieber, Anja;
Lauber, Kirsten;
Blüthgen, Nils

Publication type:

Article

BindCompare: a novel integrated protein–nucleic acid binding analysis platform.

Published in:

Bioinformatics, 2024, v. 40, n. 11, p. 1, doi. 10.1093/bioinformatics/btae668

By:

Mahableshwarkar, Pranav;
Shum, Jasmine;
Ray, Mukulika;
Larschan, Erica

Publication type:

Article

Improving ncRNA family prediction using multi-modal contrastive learning of sequence and structure.

Published in:

Bioinformatics, 2024, v. 40, n. 11, p. 1, doi. 10.1093/bioinformatics/btae640

By:

Xu, Ruiting;
Li, Dan;
Yang, Wen;
Wang, Guohua;
Li, Yang

Publication type:

Article

MR Corge: sensitivity analysis of Mendelian randomization based on the core gene hypothesis for polygenic exposures.

Published in:

Bioinformatics, 2024, v. 40, n. 11, p. 1, doi. 10.1093/bioinformatics/btae666

By:

Zhang, Wenmin;
Su, Chen-Yang;
Yoshiji, Satoshi;
Lu, Tianyuan

Publication type:

Article

A signal-diffusion-based unsupervised contrastive representation learning for spatial transcriptomics analysis.

Published in:

Bioinformatics, 2024, v. 40, n. 11, p. 1, doi. 10.1093/bioinformatics/btae663

By:

Chen, Nan;
Yu, Xiao;
Li, Weimin;
Liu, Fangfang;
Luo, Yin;
Zuo, Zhongkun

Publication type:

Article

Memprot.GPCR-ModSim: modelling and simulation of membrane proteins in a nutshell.

Published in:

Bioinformatics, 2024, v. 40, n. 11, p. 1, doi. 10.1093/bioinformatics/btae662

By:

Broek, Remco L van den;
Bello, Xabier;
Küpper, Rebecca V;
Westen, Gerard J P van;
Jespers, Willem;
Gutiérrez-de-Terán, Hugo

Publication type:

Article

ADAPT: Analysis of Microbiome Differential Abundance by Pooling Tobit Models.

Published in:

Bioinformatics, 2024, v. 40, n. 11, p. 1, doi. 10.1093/bioinformatics/btae661

By:

Wang, Mukai;
Fontaine, Simon;
Jiang, Hui;
Li, Gen

Publication type:

Article

p-IgGen: a paired antibody generative language model.

Published in:

Bioinformatics, 2024, v. 40, n. 11, p. 1, doi. 10.1093/bioinformatics/btae659

By:

Turnbull, Oliver M;
Oglic, Dino;
Croasdale-Wood, Rebecca;
Deane, Charlotte M

Publication type:

Article

ADTGP: correcting single-cell antibody sequencing data using Gaussian process regression.

Published in:

Bioinformatics, 2024, v. 40, n. 11, p. 1, doi. 10.1093/bioinformatics/btae660

By:

Liu, Alex C H;
Chan, Steven M

Publication type:

Article

Differential expression and co-expression reveal cell types relevant to genetic disorder phenotypes.

Published in:

Bioinformatics, 2024, v. 40, n. 11, p. 1, doi. 10.1093/bioinformatics/btae646

By:

Alías-Segura, Sergio;
Pazos, Florencio;
Chagoyen, Monica

Publication type:

Article

Causal relationships between diseases mined from the literature improve the use of polygenic risk scores.

Published in:

Bioinformatics, 2024, v. 40, n. 11, p. 1, doi. 10.1093/bioinformatics/btae639

By:

Toonsi, Sumyyah;
Gauran, Iris Ivy;
Ombao, Hernando;
Schofield, Paul N;
Hoehndorf, Robert

Publication type:

Article

BS-clock, advancing epigenetic age prediction with high-resolution DNA methylation bisulfite sequencing data.

Published in:

Bioinformatics, 2024, v. 40, n. 11, p. 1, doi. 10.1093/bioinformatics/btae656

By:

Hu, Congcong;
Li, Yunxiao;
Li, Longhui;
Zhang, Naiqian;
Zheng, Xiaoqi

Publication type:

Article

InterLabelGO+: unraveling label correlations in protein function prediction.

Published in:

Bioinformatics, 2024, v. 40, n. 11, p. 1, doi. 10.1093/bioinformatics/btae655

By:

Liu, Quancheng;
Zhang, Chengxin;
Freddolino, Lydia

Publication type:

Article

A deep learning method to integrate extracelluar miRNA with mRNA for cancer studies.

Published in:

Bioinformatics, 2024, v. 40, n. 11, p. 1, doi. 10.1093/bioinformatics/btae653

By:

Athaya, Tasbiraha;
Li, Xiaoman;
Hu, Haiyan

Publication type:

Article

ENKIE: a package for predicting enzyme kinetic parameter values and their uncertainties.

Published in:

Bioinformatics, 2024, v. 40, n. 11, p. 1, doi. 10.1093/bioinformatics/btae652

By:

Gollub, Mattia G;
Backes, Thierry;
Kaltenbach, Hans-Michael;
Stelling, Jörg

Publication type:

Article

Quantifying defective and wild-type viruses from high-throughput RNA sequencing.

Published in:

Bioinformatics, 2024, v. 40, n. 11, p. 1, doi. 10.1093/bioinformatics/btae651

By:

Muñoz-Sánchez, Juan C;
Olmo-Uceda, María J;
Oteo, José-Ángel;
Elena, Santiago F

Publication type:

Article

Graphlet-based hyperbolic embeddings capture evolutionary dynamics in genetic networks.

Published in:

Bioinformatics, 2024, v. 40, n. 11, p. 1, doi. 10.1093/bioinformatics/btae650

By:

Windels, Sam F L;
Velasco, Daniel Tello;
Rotkevich, Mikhail;
Malod-Dognin, Noël;
Pržulj, Nataša

Publication type:

Article

Collapsible tree: interactive web app to present collapsible hierarchies.

Published in:

Bioinformatics, 2024, v. 40, n. 11, p. 1, doi. 10.1093/bioinformatics/btae645

By:

Gao, Yuan;
Patro, Rob;
Jiang, Peng

Publication type:

Article

Detection and quantification of introgression using Bayesian inference based on conjugate priors.

Published in:

Bioinformatics, 2024, v. 40, n. 11, p. 1, doi. 10.1093/bioinformatics/btae642

By:

Pfeifer, Bastian;
Kapan, Durrell D;
Herzog, Sereina A

Publication type:

Article

iSeq: an integrated tool to fetch public sequencing data.

Published in:

Bioinformatics, 2024, v. 40, n. 11, p. 1, doi. 10.1093/bioinformatics/btae641

By:

Chao, Haoyu;
Li, Zhuojin;
Chen, Dijun;
Chen, Ming

Publication type:

Article

Prediction of human O-linked glycosylation sites using stacked generalization and embeddings from pre-trained protein language model.

Published in:

Bioinformatics, 2024, v. 40, n. 11, p. 1, doi. 10.1093/bioinformatics/btae643

By:

Pakhrin, Subash Chandra;
Chauhan, Neha;
Khan, Salman;
Upadhyaya, Jamie;
Beck, Moriah Rene;
Blanco, Eduardo

Publication type:

Article

CompariPSSM: a PSSM–PSSM comparison tool for motif-binding determinant analysis.

Published in:

Bioinformatics, 2024, v. 40, n. 11, p. 1, doi. 10.1093/bioinformatics/btae644

By:

Tsitsa, Ifigenia;
Krystkowiak, Izabella;
Davey, Norman E

Publication type:

Article

GEEES: inferring cell-specific gene–enhancer interactions from multi-modal single-cell data.

Published in:

Bioinformatics, 2024, v. 40, n. 11, p. 1, doi. 10.1093/bioinformatics/btae638

By:

Chen, Shuyang;
Keleş, Sündüz

Publication type:

Article

EuDockScore: Euclidean graph neural networks for scoring protein–protein interfaces.

Published in:

Bioinformatics, 2024, v. 40, n. 11, p. 1, doi. 10.1093/bioinformatics/btae636

By:

McFee, Matthew;
Kim, Jisun;
Kim, Philip M

Publication type:

Article

PONYTA: prioritization of phenotype-related genes from mouse KO events using PU learning on a biological network.

Published in:

Bioinformatics, 2024, v. 40, n. 11, p. 1, doi. 10.1093/bioinformatics/btae634

By:

Kim, Jun Hyeong;
Koo, Bonil;
Kim, Sun

Publication type:

Article

GCI: a continuity inspector for complete genome assembly.

Published in:

Bioinformatics, 2024, v. 40, n. 11, p. 1, doi. 10.1093/bioinformatics/btae633

By:

Chen, Quanyu;
Yang, Chentao;
Zhang, Guojie;
Wu, Dongya

Publication type:

Article

Improving bioinformatics software quality through teamwork.

Published in:

Bioinformatics, 2024, v. 40, n. 11, p. 1, doi. 10.1093/bioinformatics/btae632

By:

Ferenc, Katalin;
Rauluseviciute, Ieva;
Hovan, Ladislav;
Kumar, Vipin;
Kuijjer, Marieke L;
Mathelier, Anthony

Publication type:

Article

BIMSA: accelerating long sequence alignment using processing-in-memory.

Published in:

Bioinformatics, 2024, v. 40, n. 11, p. 1, doi. 10.1093/bioinformatics/btae631

By:

Alonso-Marín, Alejandro;
Fernandez, Ivan;
Aguado-Puig, Quim;
Gómez-Luna, Juan;
Marco-Sola, Santiago;
Mutlu, Onur;
Moreto, Miquel

Publication type:

Article

Target controllability: a feed-forward greedy algorithm in complex networks, meeting Kalman's rank condition.

Published in:

Bioinformatics, 2024, v. 40, n. 11, p. 1, doi. 10.1093/bioinformatics/btae630

By:

Khezri, Seyedeh Fatemeh;
Ebrahimi, Ali;
Eslahchi, Changiz

Publication type:

Article

Weighted families of contact maps to characterize conformational ensembles of (highly-)flexible proteins.

Published in:

Bioinformatics, 2024, v. 40, n. 11, p. 1, doi. 10.1093/bioinformatics/btae627

By:

González-Delgado, Javier;
Bernadó, Pau;
Neuvial, Pierre;
Cortés, Juan

Publication type:

Article

k-nonical space: sketching with reverse complements.

Published in:

Bioinformatics, 2024, v. 40, n. 11, p. 1, doi. 10.1093/bioinformatics/btae629

By:

Marçais, Guillaume;
Elder, C S;
Kingsford, Carl

Publication type:

Article

FungiFun3: systemic gene set enrichment analysis for fungal species.

Published in:

Bioinformatics, 2024, v. 40, n. 11, p. 1, doi. 10.1093/bioinformatics/btae620

By:

Lopez, Albert Garcia;
Albrecht-Eckardt, Daniela;
Panagiotou, Gianni;
Schäuble, Sascha

Publication type:

Article

q2-metnet: QIIME2 package to analyse 16S rRNA data via high-quality metabolic reconstructions of the human gut microbiota.

Published in:

Bioinformatics, 2024, v. 40, n. 11, p. 1, doi. 10.1093/bioinformatics/btae455

By:

Balzerani, Francesco;
Blasco, Telmo;
Pérez-Burillo, Sergio;
Francino, M Pilar;
Rufián-Henares, José Á;
Valcarcel, Luis V;
Planes, Francisco J

Publication type:

Article

Lifestyle factors in the biomedical literature: an ontology and comprehensive resources for named entity recognition.

Published in:

Bioinformatics, 2024, v. 40, n. 11, p. 1, doi. 10.1093/bioinformatics/btae613

By:

Nourani, Esmaeil;
Koutrouli, Mikaela;
Xie, Yijia;
Vagiaki, Danai;
Pyysalo, Sampo;
Nastou, Katerina;
Brunak, Søren;
Jensen, Lars Juhl

Publication type:

Article

OpenDock: a pytorch-based open-source framework for protein–ligand docking and modelling.

Published in:

Bioinformatics, 2024, v. 40, n. 11, p. 1, doi. 10.1093/bioinformatics/btae628

By:

Hu, Qiuyue;
Wang, Zechen;
Meng, Jintao;
Li, Weifeng;
Guo, Jingjing;
Mu, Yuguang;
Wang, Sheng;
Zheng, Liangzhen;
Wei, Yanjie

Publication type:

Article

Addressing the antibody germline bias and its effect on language models for improved antibody design.

Published in:

Bioinformatics, 2024, v. 40, n. 11, p. 1, doi. 10.1093/bioinformatics/btae618

By:

Olsen, Tobias H;
Moal, Iain H;
Deane, Charlotte M

Publication type:

Article

Deep learning-based enhancement of fluorescence labeling for accurate cell lineage tracing during embryogenesis.

Published in:

Bioinformatics, 2024, v. 40, n. 11, p. 1, doi. 10.1093/bioinformatics/btae626

By:

Li, Zelin;
Xie, Dongying;
Ma, Yiming;
Zhao, Cunmin;
You, Sicheng;
Yan, Hong;
Zhao, Zhongying

Publication type:

Article

DPNN-ac4C: a dual-path neural network with self-attention mechanism for identification of N4-acetylcytidine (ac4C) in mRNA.

Published in:

Bioinformatics, 2024, v. 40, n. 11, p. 1, doi. 10.1093/bioinformatics/btae625

By:

Yuan, Jiahao;
Wang, Ziyi;
Pan, Zhuoyu;
Li, Aohan;
Zhang, Zilong;
Cui, Feifei

Publication type:

Article