Works matching IS 14712105 AND DT 2024

Results: 388

OMD Curation Toolkit: a workflow for in-house curation of public omics datasets.

Published in:

BMC Bioinformatics, 2024, v. 25, n. 1, p. 1, doi. 10.1186/s12859-024-05803-9

By:

Piquer-Esteban, Samuel;
Arnau, Vicente;
Diaz, Wladimiro;
Moya, Andrés

Publication type:

Article

Biclustering analysis on tree-shaped time-series single cell gene expression data of Caenorhabditis elegans.

Published in:

BMC Bioinformatics, 2024, v. 25, n. 1, p. 1, doi. 10.1186/s12859-024-05800-y

By:

Guan, Qi;
Yan, Xianzhong;
Wu, Yida;
Zhou, Da;
Hu, Jie

Publication type:

Article

Prediction of anticancer drug sensitivity using an interpretable model guided by deep learning.

Published in:

BMC Bioinformatics, 2024, v. 25, n. 1, p. 1, doi. 10.1186/s12859-024-05669-x

By:

Pang, Weixiong;
Chen, Ming;
Qin, Yufang

Publication type:

Article

A comparison of RNA-Seq data preprocessing pipelines for transcriptomic predictions across independent studies.

Published in:

BMC Bioinformatics, 2024, v. 25, n. 1, p. 1, doi. 10.1186/s12859-024-05801-x

By:

Van, Richard;
Alvarez, Daniel;
Mize, Travis;
Gannavarapu, Sravani;
Chintham Reddy, Lohitha;
Nasoz, Fatma;
Han, Mira V.

Publication type:

Article

Integrated approach to generate artificial samples with low tumor fraction for somatic variant calling benchmarking.

Published in:

BMC Bioinformatics, 2024, v. 25, n. 1, p. 1, doi. 10.1186/s12859-024-05793-8

By:

Sergi, Aldo;
Beltrame, Luca;
Marchini, Sergio;
Masseroli, Marco

Publication type:

Article

Regulatory landscape enrichment analysis (RLEA): a computational toolkit for non-coding variant enrichment and cell type prioritization.

Published in:

BMC Bioinformatics, 2024, v. 25, n. 1, p. 1, doi. 10.1186/s12859-024-05794-7

By:

Rosean, Samuel;
Sosa, Eric A.;
O'Shea, Dónal;
Raj, Srilakshmi M.;
Seoighe, Cathal;
Greally, John M.

Publication type:

Article

Computer vision digitization of smartphone images of anesthesia paper health records from low-middle income countries.

Published in:

BMC Bioinformatics, 2024, v. 25, n. 1, p. 1, doi. 10.1186/s12859-024-05785-8

By:

Folks, Ryan D.;
Naik, Bhiken I.;
Brown, Donald E.;
Durieux, Marcel E.

Publication type:

Article

Freeprotmap: waiting-free prediction method for protein distance map.

Published in:

BMC Bioinformatics, 2024, v. 25, n. 1, p. 1, doi. 10.1186/s12859-024-05771-0

By:

Huang, Jiajian;
Li, Jinpeng;
Chen, Qinchang;
Wang, Xia;
Chen, Guangyong;
Tang, Jin

Publication type:

Article

ViroISDC: a method for calling integration sites of hepatitis B virus based on feature encoding.

Published in:

BMC Bioinformatics, 2024, v. 25, n. 1, p. 1, doi. 10.1186/s12859-024-05763-0

By:

Qiao, Lei;
Li, Chang;
Lin, Wei;
He, Xiaoqi;
Mi, Jia;
Tong, Yigang;
Gao, Jingyang

Publication type:

Article

A transformer model for cause-specific hazard prediction.

Published in:

BMC Bioinformatics, 2024, v. 25, n. 1, p. 1, doi. 10.1186/s12859-024-05799-2

By:

Oliver, Matthieu;
Allou, Nicolas;
Devineau, Marjolaine;
Allyn, Jèrôme;
Ferdynus, Cyril

Publication type:

Article

Protein function prediction through multi-view multi-label latent tensor reconstruction.

Published in:

BMC Bioinformatics, 2024, v. 25, n. 1, p. 1, doi. 10.1186/s12859-024-05789-4

By:

Armah-Sekum, Robert Ebo;
Szedmak, Sandor;
Rousu, Juho

Publication type:

Article

VCF2PCACluster: a simple, fast and memory-efficient tool for principal component analysis of tens of millions of SNPs.

Published in:

BMC Bioinformatics, 2024, v. 25, n. 1, p. 1, doi. 10.1186/s12859-024-05770-1

By:

He, Weiming;
Xu, Lian;
Wang, JingXian;
Yue, Zhen;
Jing, Yi;
Tai, Shuaishuai;
Yang, Jian;
Fang, Xiaodong

Publication type:

Article

Cold Spot SCANNER: Colab Notebook for predicting cold spots in protein–protein interfaces.

Published in:

BMC Bioinformatics, 2024, v. 25, n. 1, p. 1, doi. 10.1186/s12859-024-05796-5

By:

Gurusinghe, Sagara N. S.;
Shifman, Julia M.

Publication type:

Article

The effect of data transformation on low-dimensional integration of single-cell RNA-seq.

Published in:

BMC Bioinformatics, 2024, v. 25, n. 1, p. 1, doi. 10.1186/s12859-024-05788-5

By:

Park, Youngjun;
Hauschild, Anne-Christin

Publication type:

Article

Assessing the reliability of point mutation as data augmentation for deep learning with genomic data.

Published in:

BMC Bioinformatics, 2024, v. 25, n. 1, p. 1, doi. 10.1186/s12859-024-05787-6

By:

Lee, Hyunjung;
Ozbulak, Utku;
Park, Homin;
Depuydt, Stephen;
De Neve, Wesley;
Vankerschaver, Joris

Publication type:

Article

Cauchy hyper-graph Laplacian nonnegative matrix factorization for single-cell RNA-sequencing data analysis.

Published in:

BMC Bioinformatics, 2024, v. 25, n. 1, p. 1, doi. 10.1186/s12859-024-05797-4

By:

Wang, Gao-Fei;
Shen, Longying

Publication type:

Article

Optimizing spatio-temporal correlation structures for modeling food security in Africa: a simulation-based investigation.

Published in:

BMC Bioinformatics, 2024, v. 25, n. 1, p. 1, doi. 10.1186/s12859-024-05791-w

By:

Bofa, Adusei;
Zewotir, Temesgen

Publication type:

Article

Exploring combinations of dimensionality reduction, transfer learning, and regularization methods for predicting binary phenotypes with transcriptomic data.

Published in:

BMC Bioinformatics, 2024, v. 25, n. 1, p. 1, doi. 10.1186/s12859-024-05795-6

By:

Oshternian, S. R.;
Loipfinger, S.;
Bhattacharya, A.;
Fehrmann, R. S. N.

Publication type:

Article

OrthoRefine: automated enhancement of prior ortholog identification via synteny.

Published in:

BMC Bioinformatics, 2024, v. 25, n. 1, p. 1, doi. 10.1186/s12859-024-05786-7

By:

Ludwig, J.;
Mrázek, J.

Publication type:

Article

Biology System Description Language (BiSDL): a modeling language for the design of multicellular synthetic biological systems.

Published in:

BMC Bioinformatics, 2024, v. 25, n. 1, p. 1, doi. 10.1186/s12859-024-05782-x

By:

Giannantoni, Leonardo;
Bardini, Roberta;
Savino, Alessandro;
Di Carlo, Stefano

Publication type:

Article

Improvements in viral gene annotation using large language models and soft alignments.

Published in:

BMC Bioinformatics, 2024, v. 25, n. 1, p. 1, doi. 10.1186/s12859-024-05779-6

By:

Harrigan, William L.;
Ferrell, Barbra D.;
Wommack, K. Eric;
Polson, Shawn W.;
Schreiber, Zachary D.;
Belcaid, Mahdi

Publication type:

Article

Orthogonal multimodality integration and clustering in single-cell data.

Published in:

BMC Bioinformatics, 2024, v. 25, n. 1, p. 1, doi. 10.1186/s12859-024-05773-y

By:

Liu, Yufang;
Chen, Yongkai;
Lu, Haoran;
Zhong, Wenxuan;
Yuan, Guo-Cheng;
Ma, Ping

Publication type:

Article

OmicNavigator: open-source software for the exploration, visualization, and archival of omic studies.

Published in:

BMC Bioinformatics, 2024, v. 25, n. 1, p. 1, doi. 10.1186/s12859-024-05743-4

By:

Ernst, Terrence R.;
Blischak, John D.;
Nordlund, Paul;
Dalen, Joe;
Moore, Justin;
Bhamidipati, Akshay;
Dwivedi, Pankaj;
LoGrasso, Joe;
Curado, Marco Rocha;
Engelmann, Brett Warren

Publication type:

Article

Mora: abundance aware metagenomic read re-assignment for disentangling similar strains.

Published in:

BMC Bioinformatics, 2024, v. 25, n. 1, p. 1, doi. 10.1186/s12859-024-05768-9

By:

Zheng, Andrew;
Shaw, Jim;
Yu, Yun William

Publication type:

Article

SynGenes: a Python class for standardizing nomenclatures of mitochondrial and chloroplast genes and a web form for enhancing searches for evolutionary analyses.

Published in:

BMC Bioinformatics, 2024, p. 1, doi. 10.1186/s12859-024-05781-y

By:

Rabelo, Luan Pinto;
Sodré, Davidson;
de Sousa, Rodrigo Petry Corrêa;
Watanabe, Luciana;
Gomes, Grazielle;
Sampaio, Iracilda;
Vallinoto, Marcelo

Publication type:

Article

Drug-Online: an online platform for drug-target interaction, affinity, and binding sites identification using deep learning.

Published in:

BMC Bioinformatics, 2024, v. 25, n. 1, p. 1, doi. 10.1186/s12859-024-05783-w

By:

Zeng, Xin;
Su, Guang-Peng;
Li, Shu-Juan;
Lv, Shuang-Qing;
Wen, Meng-Liang;
Li, Yi

Publication type:

Article

TEC-miTarget: enhancing microRNA target prediction based on deep learning of ribonucleic acid sequences.

Published in:

BMC Bioinformatics, 2024, v. 25, n. 1, p. 1, doi. 10.1186/s12859-024-05780-z

By:

Yang, Tingpeng;
Wang, Yu;
He, Yonghong

Publication type:

Article

MMGAT: a graph attention network framework for ATAC-seq motifs finding.

Published in:

BMC Bioinformatics, 2024, v. 25, n. 1, p. 1, doi. 10.1186/s12859-024-05774-x

By:

Wu, Xiaotian;
Hou, Wenju;
Zhao, Ziqi;
Huang, Lan;
Sheng, Nan;
Yang, Qixing;
Zhang, Shuangquan;
Wang, Yan

Publication type:

Article

A protein network refinement method based on module discovery and biological information.

Published in:

BMC Bioinformatics, 2024, v. 25, n. 1, p. 1, doi. 10.1186/s12859-024-05772-z

By:

Pan, Li;
Wang, Haoyue;
Yang, Bo;
Li, Wenbin

Publication type:

Article

Noisecut: a python package for noise-tolerant classification of binary data using prior knowledge integration and max-cut solutions.

Published in:

BMC Bioinformatics, 2024, v. 25, n. 1, p. 1, doi. 10.1186/s12859-024-05769-8

By:

Samadi, Moein E.;
Mirzaieazar, Hedieh;
Mitsos, Alexander;
Schuppert, Andreas

Publication type:

Article

TrieDedup: a fast trie-based deduplication algorithm to handle ambiguous bases in high-throughput sequencing.

Published in:

BMC Bioinformatics, 2024, v. 25, n. 1, p. 1, doi. 10.1186/s12859-024-05775-w

By:

Hu, Jianqiao;
Luo, Sai;
Tian, Ming;
Ye, Adam Yongxin

Publication type:

Article

MetageNN: a memory-efcient neural network taxonomic classifer robust to sequencing errors and missing genomes.

Published in:

BMC Bioinformatics, 2024, v. 25, n. 1, p. 1, doi. 10.1186/s12859-024-05760-3

By:

Peres da Silva, Rafael;
Suphavilai, Chayaporn;
Nagarajan, Niranjan

Publication type:

Article

Biomedical semantic text summarizer.

Published in:

BMC Bioinformatics, 2024, v. 25, n. 1, p. 1, doi. 10.1186/s12859-024-05712-x

By:

Kirmani, Mahira;
Kour, Gagandeep;
Mohd, Mudasir;
Sheikh, Nasrullah;
Khan, Dawood Ashraf;
Maqbool, Zahid;
Wani, Mohsin Altaf;
Wani, Abid Hussain

Publication type:

Article

Inference of genomic landscapes using ordered Hidden Markov Models with emission densities (oHMMed).

Published in:

BMC Bioinformatics, 2024, v. 25, n. 1, p. 1, doi. 10.1186/s12859-024-05751-4

By:

Vogl, Claus;
Karapetiants, Mariia;
Yıldırım, Burçin;
Kjartansdóttir, Hrönn;
Kosiol, Carolin;
Bergman, Juraj;
Majka, Michal;
Mikula, Lynette Caitlin

Publication type:

Article

Designing and delivering bioinformatics project-based learning in East Africa.

Published in:

BMC Bioinformatics, 2024, v. 25, n. 1, p. 1, doi. 10.1186/s12859-024-05680-2

By:

Kibet, Caleb K.;
Entfellner, Jean-Baka Domelevo;
Jjingo, Daudi;
de Villiers, Etienne Pierre;
de Villiers, Santie;
Wambui, Karen;
Kinyanjui, Sam;
Masiga, Daniel

Publication type:

Article

Biomarker discovery with quantum neural networks: a case-study in CTLA4-activation pathways.

Published in:

BMC Bioinformatics, 2024, v. 25, n. 1, p. 1, doi. 10.1186/s12859-024-05755-0

By:

Nguyen, Phuong-Nam

Publication type:

Article

MultiToxPred 1.0: a novel comprehensive tool for predicting 27 classes of protein toxins using an ensemble machine learning approach.

Published in:

BMC Bioinformatics, 2024, v. 25, n. 1, p. 1, doi. 10.1186/s12859-024-05748-z

By:

Beltrán, Jorge F.;
Herrera-Belén, Lisandra;
Parraguez-Contreras, Fernanda;
Farías, Jorge G.;
Machuca-Sepúlveda, Jorge;
Short, Stefania

Publication type:

Article

KEGG orthology prediction of bacterial proteins using natural language processing.

Published in:

BMC Bioinformatics, 2024, v. 25, n. 1, p. 1, doi. 10.1186/s12859-024-05766-x

By:

Chen, Jing;
Wu, Haoyu;
Wang, Ning

Publication type:

Article

Control of false discoveries in grouped hypothesis testing for eQTL data.

Published in:

BMC Bioinformatics, 2024, v. 25, n. 1, p. 1, doi. 10.1186/s12859-024-05736-3

By:

Rudra, Pratyaydipta;
Zhou, Yi-Hui;
Nobel, Andrew;
Wright, Fred A.

Publication type:

Article

DPI_CDF: druggable protein identifier using cascade deep forest.

Published in:

BMC Bioinformatics, 2024, v. 25, n. 1, p. 1, doi. 10.1186/s12859-024-05744-3

By:

Arif, Muhammad;
Fang, Ge;
Ghulam, Ali;
Musleh, Saleh;
Alam, Tanvir

Publication type:

Article

Multiple phenotype association tests based on sliced inverse regression.

Published in:

BMC Bioinformatics, 2024, v. 25, n. 1, p. 1, doi. 10.1186/s12859-024-05731-8

By:

Sun, Wenyuan;
Jon, Kyongson;
Zhu, Wensheng

Publication type:

Article

Predicting condensate formation of protein and RNA under various environmental conditions.

Published in:

BMC Bioinformatics, 2024, v. 25, n. 1, p. 1, doi. 10.1186/s12859-024-05764-z

By:

Chin, Ka Yin;
Ishida, Shoichi;
Sasaki, Yukio;
Terayama, Kei

Publication type:

Article

CITEViz: interactively classify cell populations in CITE-Seq via a flow cytometry-like gating workflow using R-Shiny.

Published in:

BMC Bioinformatics, 2024, v. 25, n. 1, p. 1, doi. 10.1186/s12859-024-05762-1

By:

Kong, Garth L.;
Nguyen, Thai T.;
Rosales, Wesley K.;
Panikar, Anjali D.;
Cheney, John H. W.;
Lusardi, Theresa A.;
Yashar, William M.;
Curtiss, Brittany M.;
Carratt, Sarah A.;
Braun, Theodore P.;
Maxson, Julia E.

Publication type:

Article

CAT-DTI: cross-attention and Transformer network with domain adaptation for drug-target interaction prediction.

Published in:

BMC Bioinformatics, 2024, v. 25, n. 1, p. 1, doi. 10.1186/s12859-024-05753-2

By:

Zeng, Xiaoting;
Chen, Weilin;
Lei, Baiying

Publication type:

Article

MFSynDCP: multi-source feature collaborative interactive learning for drug combination synergy prediction.

Published in:

BMC Bioinformatics, 2024, v. 25, n. 1, p. 1, doi. 10.1186/s12859-024-05765-y

By:

Dong, Yunyun;
Chang, Yunqing;
Wang, Yuxiang;
Han, Qixuan;
Wen, Xiaoyuan;
Yang, Ziting;
Zhang, Yan;
Qiang, Yan;
Wu, Kun;
Fan, Xiaole;
Ren, Xiaoqiang

Publication type:

Article

Curare and GenExVis: a versatile toolkit for analyzing and visualizing RNA-Seq data.

Published in:

BMC Bioinformatics, 2024, v. 25, n. 1, p. 1, doi. 10.1186/s12859-024-05761-2

By:

Blumenkamp, Patrick;
Pfister, Max;
Diedrich, Sonja;
Brinkrolf, Karina;
Jaenicke, Sebastian;
Goesmann, Alexander

Publication type:

Article

Feature-specific quantile normalization and feature-specific mean–variance normalization deliver robust bi-directional classification and feature selection performance between microarray and RNAseq data.

Published in:

BMC Bioinformatics, 2024, v. 25, n. 1, p. 1, doi. 10.1186/s12859-024-05759-w

By:

Skubleny, Daniel;
Ghosh, Sunita;
Spratlin, Jennifer;
Schiller, Daniel E.;
Rayat, Gina R.

Publication type:

Article

DAE-CFR: detecting microRNA-disease associations using deep autoencoder and combined feature representation.

Published in:

BMC Bioinformatics, 2024, v. 25, n. 1, p. 1, doi. 10.1186/s12859-024-05757-y

By:

Liu, Yanling;
Zhang, Ruiyan;
Dong, Xiaojing;
Yang, Hong;
Li, Jing;
Cao, Hongyan;
Tian, Jing;
Zhang, Yanbo

Publication type:

Article

Towards a unified medical microbiome ecology of the OMU for metagenomes and the OTU for microbes.

Published in:

BMC Bioinformatics, 2024, v. 25, n. 1, p. 1, doi. 10.1186/s12859-023-05591-8

By:

Ma, Zhanshan

Publication type:

Article

GraphKM: machine and deep learning for K<sub>M</sub> prediction of wildtype and mutant enzymes.

Published in:

BMC Bioinformatics, 2024, v. 25, n. 1, p. 1, doi. 10.1186/s12859-024-05746-1

By:

He, Xiao;
Yan, Ming

Publication type:

Article