Works by Orozco-Arias, Simon

Results: 24

Machine learning applications on intratumoral heterogeneity in glioblastoma using single-cell RNA sequencing data.

Published in:

Briefings in Functional Genomics, 2023, v. 22, n. 5, p. 428, doi. 10.1093/bfgp/elad002

By:

Arteaga-Arteaga, Harold Brayan;
Candamil-Cortés, Mariana S;
Breaux, Brian;
Guillen-Rondon, Pablo;
Orozco-Arias, Simon;
Tabares-Soto, Reinel

Publication type:

Article

Cov-caldas: A new COVID-19 chest X-Ray dataset from state of Caldas-Colombia.

Published in:

Scientific Data, 2022, p. 1, doi. 10.1038/s41597-022-01576-z

By:

Alzate-Grisales, Jesús Alejandro;
Mora-Rubio, Alejandro;
Arteaga-Arteaga, Harold Brayan;
Bravo-Ortiz, Mario Alejandro;
Arias-Garzón, Daniel;
López-Murillo, Luis Humberto;
Mercado-Ruiz, Esteban;
Villa-Pulgarin, Juan Pablo;
Cardona-Morales, Oscar;
Orozco-Arias, Simon;
Buitrago-Carmona, Felipe;
Palancares-Sosa, Maria Jose;
Martínez-Rodríguez, Fernanda;
Contreras-Ortiz, Sonia H.;
Saborit-Torres, Jose Manuel;
Montell Serrano, Joaquim Ángel;
Ramirez-Sánchez, María Mónica;
Sierra-Gaber, Mario Alfonso;
Jaramillo-Robledo, Oscar;
de la Iglesia-Vayá, Maria

Publication type:

Article

HERV-K (HML-2) insertion polymorphisms in the 8q24.13 region and their potential etiological associations with acute myeloid leukemia.

Published in:

Archives of Virology, 2023, v. 168, n. 4, p. 1, doi. 10.1007/s00705-023-05747-0

By:

Camargo-Forero, Nicolás;
Orozco-Arias, Simon;
Perez Agudelo, Juan M.;
Guyot, Romain

Publication type:

Article

InpactorDB: A Classified Lineage-Level Plant LTR Retrotransposon Reference Library for Free-Alignment Methods Based on Machine Learning.

Published in:

Genes, 2021, v. 12, n. 2, p. 190, doi. 10.3390/genes12020190

By:

Orozco-Arias, Simon;
Jaimes, Paula A.;
Candamil, Mariana S.;
Jiménez-Varón, Cristian Felipe;
Tabares-Soto, Reinel;
Isaza, Gustavo;
Guyot, Romain;
Grzebelus, Dariusz

Publication type:

Article

Retrotransposons in Plant Genomes: Structure, Identification, and Classification through Bioinformatics and Machine Learning.

Published in:

International Journal of Molecular Sciences, 2019, v. 20, n. 15, p. 3837, doi. 10.3390/ijms20153837

By:

Orozco-Arias, Simon;
Isaza, Gustavo;
Guyot, Romain

Publication type:

Article

Inpactor2: a software based on deep learning to identify and classify LTR-retrotransposons in plant genomes.

Published in:

Briefings in Bioinformatics, 2023, v. 24, n. 1, p. 1, doi. 10.1093/bib/bbac511

By:

Orozco-Arias, Simon;
Lopez-Murillo, Luis Humberto;
Candamil-Cortés, Mariana S;
Arias, Maradey;
Jaimes, Paula A;
Paschoal, Alexandre Rossi;
Tabares-Soto, Reinel;
Isaza, Gustavo;
Guyot, Romain

Publication type:

Article

Automatic curation of LTR retrotransposon libraries from plant genomes through machine learning.

Published in:

Journal of Integrative Bioinformatics, 2022, v. 19, n. 3, p. 1, doi. 10.1515/jib-2021-0036

By:

Orozco-Arias, Simon;
Candamil-Cortes, Mariana S.;
Jaimes, Paula A.;
Valencia-Castrillon, Estiven;
Tabares-Soto, Reinel;
Isaza, Gustavo;
Guyot, Romain

Publication type:

Article

Clasificación de cáncer cervical usando redes neuronales convolucionales, transferencia de aprendizaje y aumento de datos.

Published in:

Revista EIA, 2021, v. 18, n. 35, p. 1, doi. 10.24050/reia.v18i35.1462

By:

BRAVO ORTÍZ, MARIO ALEJANDRO;
ARTEAGA ARTEAGA, HAROLD BRAYAN;
SOTO, REINEL TABARES;
PADILLA BURITICÁ, JORGE IVÁN;
OROZCO-ARIAS, SIMÓN

Publication type:

Article

TIP_finder: An HPC Software to Detect Transposable Element Insertion Polymorphisms in Large Genomic Datasets.

Published in:

Biology (2079-7737), 2020, v. 9, n. 9, p. 281, doi. 10.3390/biology9090281

By:

Orozco-Arias, Simon;
Tobon-Orozco, Nicolas;
Piña, Johan S.;
Jiménez-Varón, Cristian Felipe;
Tabares-Soto, Reinel;
Guyot, Romain

Publication type:

Article

Inpactor, Integrated and Parallel Analyzer and Classifier of LTR Retrotransposons and Its Application for Pineapple LTR Retrotransposons Diversity and Dynamics.

Published in:

Biology (2079-7737), 2018, v. 7, n. 2, p. 32, doi. 10.3390/biology7020032

By:

Orozco-Arias, Simon;
Liu, Juan;
Tabares-Soto, Reinel;
Ceballos, Diego;
Silva Domingues, Douglas;
Garavito, Andréa;
Ming, Ray;
Guyot, Romain

Publication type:

Article

ALINEAMIENTO DE SECUENCIAS BIOINFORMÁTICAS EN UNA ARQUITECTURA gRID.

Published in:

Gerencia Tecnologica Informatica, 2017, v. 15, n. 43, p. 37

By:

OROZCO ARIAS, SIMON;
HERRERA GONZÁLEZ, MARCELO;
SOTO AGUDELO, LEONARDO;
ISAZA ECHEVERRY, GUSTAVO

Publication type:

Article

K-mer-based machine learning method to classify LTR-retrotransposons in plant genomes.

Published in:

PeerJ, 2021, p. 1, doi. 10.7717/peerj.11456

By:

Orozco-Arias, Simon;
Candamil-Cortés, Mariana S.;
Jaimes, Paula A.;
Piña, Johan S.;
Tabares-Soto, Reinel;
Guyot, Romain;
Isaza, Gustavo

Publication type:

Article

A systematic review of the application of machine learning in the detection and classification of transposable elements.

Published in:

PeerJ, 2019, p. 1, doi. 10.7717/peerj.8311

By:

Orozco-Arias, Simon;
Isaza, Gustavo;
Guyot, Romain;
Tabares-Soto, Reinel

Publication type:

Article

Worldwide co-occurrence analysis of 17 species of the genus Brachypodium using data mining.

Published in:

PeerJ, 2019, p. 1, doi. 10.7717/peerj.6193

By:

Orozco-Arias, Simon;
Núñez-Rincón, Ana María;
Tabares-Soto, Reinel;
López-Álvarez, Diana

Publication type:

Article

Genomic object detection: An improved approach for transposable elements detection and classification using convolutional neural networks.

Published in:

PLoS ONE, 2023, v. 18, n. 9, p. 1, doi. 10.1371/journal.pone.0291925

By:

Orozco-Arias, Simon;
Lopez-Murillo, Luis Humberto;
Piña, Johan S.;
Valencia-Castrillon, Estiven;
Tabares-Soto, Reinel;
Castillo-Ossa, Luis;
Isaza, Gustavo;
Guyot, Romain

Publication type:

Article

The absence of the caffeine synthase gene is involved in the naturally decaffeinated status of Coffea humblotiana, a wild species from Comoro archipelago.

Published in:

Scientific Reports, 2021, v. 11, n. 1, p. 1, doi. 10.1038/s41598-021-87419-0

By:

Raharimalala, Nathalie;
Rombauts, Stephane;
McCarthy, Andrew;
Garavito, Andréa;
Orozco-Arias, Simon;
Bellanger, Laurence;
Morales-Correa, Alexa Yadira;
Froger, Solène;
Michaux, Stéphane;
Berry, Victoria;
Metairon, Sylviane;
Fournier, Coralie;
Lepelley, Maud;
Mueller, Lukas;
Couturon, Emmanuel;
Hamon, Perla;
Rakotomalala, Jean-Jacques;
Descombes, Patrick;
Guyot, Romain;
Crouzillat, Dominique

Publication type:

Article

Measuring Performance Metrics of Machine Learning Algorithms for Detecting and Classifying Transposable Elements.

Published in:

Processes, 2020, v. 8, n. 6, p. 638, doi. 10.3390/pr8060638

By:

Orozco-Arias, Simon;
Piña, Johan S.;
Tabares-Soto, Reinel;
Castillo-Ossa, Luis F.;
Guyot, Romain;
Isaza, Gustavo

Publication type:

Article

A Machine Learning-based Pipeline for the Classification of CTX-M in Metagenomics Samples.

Published in:

Processes, 2019, v. 7, n. 4, p. 235, doi. 10.3390/pr7040235

By:

Ceballos, Diego;
López-Álvarez, Diana;
Isaza, Gustavo;
Tabares-Soto, Reinel;
Orozco-Arias, Simón;
Ferrin, Carlos D.

Publication type:

Article

Structure and Distribution of Centromeric Retrotransposons at Diploid and Allotetraploid Coffea Centromeric and Pericentromeric Regions.

Published in:

Frontiers in Plant Science, 2018, p. 1, doi. 10.3389/fpls.2018.00175

By:

de Castro Nunes, Renata;
Orozco-Arias, Simon;
Crouzillat, Dominique;
Mueller, Lukas A.;
Strickler, Suzy R.;
Descombes, Patrick;
Fournier, Coralie;
Moine, Deborah;
de Kochko, Alexandre;
Yuyama, Priscila M.;
Vanzela, André L. L.;
Guyot, Romain

Publication type:

Article

Optimized Convolutional Neural Network Models for Skin Lesion Classification.

Published in:

Computers, Materials & Continua, 2022, v. 70, n. 2, p. 2131, doi. 10.32604/cmc.2022.019529

By:

Villa-Pulgarin, Juan Pablo;
Ruales-Torres, Anderson Alberto;
Arias-Garzón, Daniel;
Bravo-Ortiz, Mario Alejandro;
Arteaga-Arteaga, Harold Brayan;
Mora-Rubio, Alejandro;
Alzate-Grisales, Jesus Alejandro;
Mercado-Ruiz, Esteban;
Hassaballah, M.;
Orozco-Arias, Simon;
Cardona-Morales, Oscar;
Tabares-Soto, Reinel

Publication type:

Article

G-SAIP: Graphical Sequence Alignment Through Parallel Programming in the Post-Genomic Era.

Published in:

Evolutionary Bioinformatics, 2023, p. 1, doi. 10.1177/11769343221150585

By:

Piña, Johan S.;
Orozco-Arias, Simon;
Tobón-Orozco, Nicolas;
Camargo-Forero, Leonardo;
Tabares-Soto, Reinel;
Guyot, Romain

Publication type:

Article

G-SAIP: Graphical Sequence Alignment Through Parallel Programming in the Post-Genomic Era.

Published in:

Evolutionary Bioinformatics, 2023, v. 19, p. 1, doi. 10.1177/11769343221150585

By:

Piña, Johan S.;
Orozco-Arias, Simon;
Tobón-Orozco, Nicolas;
Camargo-Forero, Leonardo;
Tabares-Soto, Reinel;
Guyot, Romain

Publication type:

Article

Composition and Diversity of LTR Retrotransposons in the Coffee Leaf Rust Genome (Hemileia vastatrix).

Published in:

Agronomy, 2022, v. 12, n. 7, p. 1665, doi. 10.3390/agronomy12071665

By:

Orozco-Arias, Simon;
Candamil, Mariana S.;
Jaimes, Paula A.;
Cristancho, Marco;
Tabares-Soto, Reinel;
Guyot, Romain

Publication type:

Article

High nucleotide similarity of three Copia lineage LTR retrotransposons among plant genomes.

Published in:

Genome, 2023, v. 66, n. 3, p. 51, doi. 10.1139/gen-2022-0026

By:

Orozco-Arias, Simon;
Dupeyron, Mathilde;
Gutiérrez-Duque, David;
Tabares-Soto, Reinel;
Guyot, Romain

Publication type:

Article