Simon Orozco-Arias

Loop profile Scopus Author ID ORCID

Publication Activity (10 Years)

Years Active: 2018-2024
Publications (10 Years): 29

Top Venues

Nature genetics

PeerJ. Computer science

PeerJ

Genome

Universidad Autónoma de Manizales

Universidad de Caldas (PHD)

This page only lists publications with an associated author ORCID identifier.

Affiliation History

Universidad Autónoma de Manizales Jan 28 2018

Colombia

Professor :: Department of Electronics and Automatization

Bioinformatics and Computational Biology Center BIOS Mar 01 2016 - Feb 01 2018

Colombia

HPC engineer :: Scientific Computing

Education History

Universidad de Caldas Aug 01 2018

Colombia

PHD :: Systems and Computing

Publications

Jarkko Salojärvi, Aditi Rambani, Zhe Yu, Romain Guyot, Susan Strickler, Maud Lepelley, Cui Wang, Sitaram Rajaraman, Pasi Rastas, Chunfang Zheng, Daniella Santos Muñoz, João Meidanis, Alexandre Rossi Paschoal, Yves Bawin, Trevor J Krabbenhoft, Zhen Qin Wang, Steven J Fleck, Rudy Aussel, Laurence Bellanger, Aline Charpagne, Coralie Fournier, Mohamed Kassam, Gregory Lefebvre, Sylviane Métairon, Déborah Moine, Michel Rigoreau, Jens Stolte, Perla Hamon, Emmanuel Couturon, Christine Tranchant-Dubreuil, Minakshi Mukherjee, Tianying Lan, Jan Engelhardt, Peter F Stadler, Samara Mireza Correia De Lemos, Suzana Ivamoto Suzuki, Ucu Sumirat, Ching Man Jennifer Wai, Nicolas Dauchot, Simon Orozco-Arias, Andréa Garavito, Catherine Kiwuka, Pascal Musoli, Anne Nalukenge, Erwan Guichoux, Havinga Reinout, Martin Smit, Lorenzo Carretero-Paulet, Oliveiro Guerreiro Filho, Masako Toma Braghini, Lilian Padilha, Gustavo Hiroshi Sera, Tom Ruttink, Robert Henry, Pierre Marraccini, Yves Van de Peer, Alan Andrade, Douglas Silva Domingues, Giovanni Giuliano, Lukas Mueller, Luiz Filipe Pereira, Stéphane Plaisance, Valerie Poncet, Stéphane Rombauts, David Sankoff, Victor A Albert, Dominique Crouzillat, Alexandre de Kochko, Patrick Descombes
The genome and population genomics of allopolyploid Coffea arabica reveal the diversification history of modern coffee cultivars. Nature genetics 56 (4) (2024)
Jarkko Salojärvi, Aditi Rambani, Zhe Yu, Romain Guyot, Susan Strickler, Maud Lepelley, Cui Wang, Sitaram Rajaraman, Pasi Rastas, Chunfang Zheng, Daniella Santos Muñoz, João Meidanis, Alexandre Rossi Paschoal, Yves Bawin, Trevor J Krabbenhoft, Zhen Qin Wang, Steven J Fleck, Rudy Aussel, Laurence Bellanger, Aline Charpagne, Coralie Fournier, Mohamed Kassam, Gregory Lefebvre, Sylviane Métairon, Déborah Moine, Michel Rigoreau, Jens Stolte, Perla Hamon, Emmanuel Couturon, Christine Tranchant-Dubreuil, Minakshi Mukherjee, Tianying Lan, Jan Engelhardt, Peter F Stadler, Samara Mireza Correia De Lemos, Suzana Ivamoto Suzuki, Ucu Sumirat, Ching Man Jennifer Wai, Nicolas Dauchot, Simon Orozco-Arias, Andréa Garavito, Catherine Kiwuka, Pascal Musoli, Anne Nalukenge, Erwan Guichoux, Havinga Reinout, Martin Smit, Lorenzo Carretero-Paulet, Oliveiro Guerreiro Filho, Masako Toma Braghini, Lilian Padilha, Gustavo Hiroshi Sera, Tom Ruttink, Robert Henry, Pierre Marraccini, Yves Van de Peer, Alan Andrade, Douglas Silva Domingues, Giovanni Giuliano, Lukas Mueller, Luiz Filipe Pereira, Stéphane Plaisance, Valerie Poncet, Stéphane Rombauts, David Sankoff, Victor A Albert, Dominique Crouzillat, Alexandre de Kochko, Patrick Descombes
The genome and population genomics of allopolyploid Coffea arabica reveal the diversification history of modern coffee cultivars. Nature genetics 56 (4) (2024)
Jarkko Salojärvi, Aditi Rambani, Zhe Yu, Romain Guyot, Susan Strickler, Maud Lepelley, Cui Wang, Sitaram Rajaraman, Pasi Rastas, Chunfang Zheng, Daniella Santos Muñoz, João Meidanis, Alexandre Rossi Paschoal, Yves Bawin, Trevor J Krabbenhoft, Zhen Qin Wang, Steven J Fleck, Rudy Aussel, Laurence Bellanger, Aline Charpagne, Coralie Fournier, Mohamed Kassam, Gregory Lefebvre, Sylviane Métairon, Déborah Moine, Michel Rigoreau, Jens Stolte, Perla Hamon, Emmanuel Couturon, Christine Tranchant-Dubreuil, Minakshi Mukherjee, Tianying Lan, Jan Engelhardt, Peter F Stadler, Samara Mireza Correia De Lemos, Suzana Ivamoto Suzuki, Ucu Sumirat, Ching Man Jennifer Wai, Nicolas Dauchot, Simon Orozco-Arias, Andréa Garavito, Catherine Kiwuka, Pascal Musoli, Anne Nalukenge, Erwan Guichoux, Havinga Reinout, Martin Smit, Lorenzo Carretero-Paulet, Oliveiro Guerreiro Filho, Masako Toma Braghini, Lilian Padilha, Gustavo Hiroshi Sera, Tom Ruttink, Robert Henry, Pierre Marraccini, Yves Van de Peer, Alan Andrade, Douglas Silva Domingues, Giovanni Giuliano, Lukas Mueller, Luiz Filipe Pereira, Stéphane Plaisance, Valerie Poncet, Stéphane Rombauts, David Sankoff, Victor A Albert, Dominique Crouzillat, Alexandre de Kochko, Patrick Descombes
The genome and population genomics of allopolyploid Coffea arabica reveal the diversification history of modern coffee cultivars. Nature genetics 56 (4) (2024)
Jarkko Salojärvi, Aditi Rambani, Zhe Yu, Romain Guyot, Susan Strickler, Maud Lepelley, Cui Wang, Sitaram Rajaraman, Pasi Rastas, Chunfang Zheng, Daniella Santos Muñoz, João Meidanis, Alexandre Rossi Paschoal, Yves Bawin, Trevor J Krabbenhoft, Zhen Qin Wang, Steven J Fleck, Rudy Aussel, Laurence Bellanger, Aline Charpagne, Coralie Fournier, Mohamed Kassam, Gregory Lefebvre, Sylviane Métairon, Déborah Moine, Michel Rigoreau, Jens Stolte, Perla Hamon, Emmanuel Couturon, Christine Tranchant-Dubreuil, Minakshi Mukherjee, Tianying Lan, Jan Engelhardt, Peter F Stadler, Samara Mireza Correia De Lemos, Suzana Ivamoto Suzuki, Ucu Sumirat, Ching Man Jennifer Wai, Nicolas Dauchot, Simon Orozco-Arias, Andréa Garavito, Catherine Kiwuka, Pascal Musoli, Anne Nalukenge, Erwan Guichoux, Havinga Reinout, Martin Smit, Lorenzo Carretero-Paulet, Oliveiro Guerreiro Filho, Masako Toma Braghini, Lilian Padilha, Gustavo Hiroshi Sera, Tom Ruttink, Robert Henry, Pierre Marraccini, Yves Van de Peer, Alan Andrade, Douglas Silva Domingues, Giovanni Giuliano, Lukas Mueller, Luiz Filipe Pereira, Stéphane Plaisance, Valerie Poncet, Stéphane Rombauts, David Sankoff, Victor A Albert, Dominique Crouzillat, Alexandre de Kochko, Patrick Descombes
The genome and population genomics of allopolyploid Coffea arabica reveal the diversification history of modern coffee cultivars. Nature genetics 56 (4) (2024)
Jarkko Salojärvi, Aditi Rambani, Zhe Yu, Romain Guyot, Susan Strickler, Maud Lepelley, Cui Wang, Sitaram Rajaraman, Pasi Rastas, Chunfang Zheng, Daniella Santos Muñoz, João Meidanis, Alexandre Rossi Paschoal, Yves Bawin, Trevor J Krabbenhoft, Zhen Qin Wang, Steven J Fleck, Rudy Aussel, Laurence Bellanger, Aline Charpagne, Coralie Fournier, Mohamed Kassam, Gregory Lefebvre, Sylviane Métairon, Déborah Moine, Michel Rigoreau, Jens Stolte, Perla Hamon, Emmanuel Couturon, Christine Tranchant-Dubreuil, Minakshi Mukherjee, Tianying Lan, Jan Engelhardt, Peter F Stadler, Samara Mireza Correia De Lemos, Suzana Ivamoto Suzuki, Ucu Sumirat, Ching Man Jennifer Wai, Nicolas Dauchot, Simon Orozco-Arias, Andréa Garavito, Catherine Kiwuka, Pascal Musoli, Anne Nalukenge, Erwan Guichoux, Havinga Reinout, Martin Smit, Lorenzo Carretero-Paulet, Oliveiro Guerreiro Filho, Masako Toma Braghini, Lilian Padilha, Gustavo Hiroshi Sera, Tom Ruttink, Robert Henry, Pierre Marraccini, Yves Van de Peer, Alan Andrade, Douglas Silva Domingues, Giovanni Giuliano, Lukas Mueller, Luiz Filipe Pereira, Stéphane Plaisance, Valerie Poncet, Stéphane Rombauts, David Sankoff, Victor A Albert, Dominique Crouzillat, Alexandre de Kochko, Patrick Descombes
The genome and population genomics of allopolyploid Coffea arabica reveal the diversification history of modern coffee cultivars. Nature genetics 56 (4) (2024)
Jarkko Salojärvi, Aditi Rambani, Zhe Yu, Romain Guyot, Susan Strickler, Maud Lepelley, Cui Wang, Sitaram Rajaraman, Pasi Rastas, Chunfang Zheng, Daniella Santos Muñoz, João Meidanis, Alexandre Rossi Paschoal, Yves Bawin, Trevor J Krabbenhoft, Zhen Qin Wang, Steven J Fleck, Rudy Aussel, Laurence Bellanger, Aline Charpagne, Coralie Fournier, Mohamed Kassam, Gregory Lefebvre, Sylviane Métairon, Déborah Moine, Michel Rigoreau, Jens Stolte, Perla Hamon, Emmanuel Couturon, Christine Tranchant-Dubreuil, Minakshi Mukherjee, Tianying Lan, Jan Engelhardt, Peter F Stadler, Samara Mireza Correia De Lemos, Suzana Ivamoto Suzuki, Ucu Sumirat, Ching Man Jennifer Wai, Nicolas Dauchot, Simon Orozco-Arias, Andréa Garavito, Catherine Kiwuka, Pascal Musoli, Anne Nalukenge, Erwan Guichoux, Havinga Reinout, Martin Smit, Lorenzo Carretero-Paulet, Oliveiro Guerreiro Filho, Masako Toma Braghini, Lilian Padilha, Gustavo Hiroshi Sera, Tom Ruttink, Robert Henry, Pierre Marraccini, Yves Van de Peer, Alan Andrade, Douglas Silva Domingues, Giovanni Giuliano, Lukas Mueller, Luiz Filipe Pereira, Stéphane Plaisance, Valerie Poncet, Stéphane Rombauts, David Sankoff, Victor A Albert, Dominique Crouzillat, Alexandre de Kochko, Patrick Descombes
The genome and population genomics of allopolyploid Coffea arabica reveal the diversification history of modern coffee cultivars. Nature genetics 56 (4) (2024)
Jarkko Salojärvi, Aditi Rambani, Zhe Yu, Romain Guyot, Susan Strickler, Maud Lepelley, Cui Wang, Sitaram Rajaraman, Pasi Rastas, Chunfang Zheng, Daniella Santos Muñoz, João Meidanis, Alexandre Rossi Paschoal, Yves Bawin, Trevor J Krabbenhoft, Zhen Qin Wang, Steven J Fleck, Rudy Aussel, Laurence Bellanger, Aline Charpagne, Coralie Fournier, Mohamed Kassam, Gregory Lefebvre, Sylviane Métairon, Déborah Moine, Michel Rigoreau, Jens Stolte, Perla Hamon, Emmanuel Couturon, Christine Tranchant-Dubreuil, Minakshi Mukherjee, Tianying Lan, Jan Engelhardt, Peter F Stadler, Samara Mireza Correia De Lemos, Suzana Ivamoto Suzuki, Ucu Sumirat, Ching Man Jennifer Wai, Nicolas Dauchot, Simon Orozco-Arias, Andréa Garavito, Catherine Kiwuka, Pascal Musoli, Anne Nalukenge, Erwan Guichoux, Havinga Reinout, Martin Smit, Lorenzo Carretero-Paulet, Oliveiro Guerreiro Filho, Masako Toma Braghini, Lilian Padilha, Gustavo Hiroshi Sera, Tom Ruttink, Robert Henry, Pierre Marraccini, Yves Van de Peer, Alan Andrade, Douglas Silva Domingues, Giovanni Giuliano, Lukas Mueller, Luiz Filipe Pereira, Stéphane Plaisance, Valerie Poncet, Stéphane Rombauts, David Sankoff, Victor A Albert, Dominique Crouzillat, Alexandre de Kochko, Patrick Descombes
The genome and population genomics of allopolyploid Coffea arabica reveal the diversification history of modern coffee cultivars. Nature genetics 56 (4) (2024)
Jarkko Salojärvi, Aditi Rambani, Zhe Yu, Romain Guyot, Susan Strickler, Maud Lepelley, Cui Wang, Sitaram Rajaraman, Pasi Rastas, Chunfang Zheng, Daniella Santos Muñoz, João Meidanis, Alexandre Rossi Paschoal, Yves Bawin, Trevor J Krabbenhoft, Zhen Qin Wang, Steven J Fleck, Rudy Aussel, Laurence Bellanger, Aline Charpagne, Coralie Fournier, Mohamed Kassam, Gregory Lefebvre, Sylviane Métairon, Déborah Moine, Michel Rigoreau, Jens Stolte, Perla Hamon, Emmanuel Couturon, Christine Tranchant-Dubreuil, Minakshi Mukherjee, Tianying Lan, Jan Engelhardt, Peter F Stadler, Samara Mireza Correia De Lemos, Suzana Ivamoto Suzuki, Ucu Sumirat, Ching Man Jennifer Wai, Nicolas Dauchot, Simon Orozco-Arias, Andréa Garavito, Catherine Kiwuka, Pascal Musoli, Anne Nalukenge, Erwan Guichoux, Havinga Reinout, Martin Smit, Lorenzo Carretero-Paulet, Oliveiro Guerreiro Filho, Masako Toma Braghini, Lilian Padilha, Gustavo Hiroshi Sera, Tom Ruttink, Robert Henry, Pierre Marraccini, Yves Van de Peer, Alan Andrade, Douglas Silva Domingues, Giovanni Giuliano, Lukas Mueller, Luiz Filipe Pereira, Stéphane Plaisance, Valerie Poncet, Stéphane Rombauts, David Sankoff, Victor A Albert, Dominique Crouzillat, Alexandre de Kochko, Patrick Descombes
The genome and population genomics of allopolyploid Coffea arabica reveal the diversification history of modern coffee cultivars. Nature genetics 56 (4) (2024)
Jarkko Salojärvi, Aditi Rambani, Zhe Yu, Romain Guyot, Susan Strickler, Maud Lepelley, Cui Wang, Sitaram Rajaraman, Pasi Rastas, Chunfang Zheng, Daniella Santos Muñoz, João Meidanis, Alexandre Rossi Paschoal, Yves Bawin, Trevor J Krabbenhoft, Zhen Qin Wang, Steven J Fleck, Rudy Aussel, Laurence Bellanger, Aline Charpagne, Coralie Fournier, Mohamed Kassam, Gregory Lefebvre, Sylviane Métairon, Déborah Moine, Michel Rigoreau, Jens Stolte, Perla Hamon, Emmanuel Couturon, Christine Tranchant-Dubreuil, Minakshi Mukherjee, Tianying Lan, Jan Engelhardt, Peter F Stadler, Samara Mireza Correia De Lemos, Suzana Ivamoto Suzuki, Ucu Sumirat, Ching Man Jennifer Wai, Nicolas Dauchot, Simon Orozco-Arias, Andréa Garavito, Catherine Kiwuka, Pascal Musoli, Anne Nalukenge, Erwan Guichoux, Havinga Reinout, Martin Smit, Lorenzo Carretero-Paulet, Oliveiro Guerreiro Filho, Masako Toma Braghini, Lilian Padilha, Gustavo Hiroshi Sera, Tom Ruttink, Robert Henry, Pierre Marraccini, Yves Van de Peer, Alan Andrade, Douglas Silva Domingues, Giovanni Giuliano, Lukas Mueller, Luiz Filipe Pereira, Stéphane Plaisance, Valerie Poncet, Stéphane Rombauts, David Sankoff, Victor A Albert, Dominique Crouzillat, Alexandre de Kochko, Patrick Descombes
The genome and population genomics of allopolyploid Coffea arabica reveal the diversification history of modern coffee cultivars. Nature genetics 56 (4) (2024)
Nicolás Camargo-Forero, Simon Orozco-Arias, Juan M Perez Agudelo, Romain Guyot
HERV-K (HML-2) insertion polymorphisms in the 8q24.13 region and their potential etiological associations with acute myeloid leukemia. Archives of virology 168 (4) (2023)
Simon Orozco-Arias, Luis Humberto Lopez-Murillo, Johan S Piña, Estiven Valencia-Castrillon, Reinel Tabares-Soto, Luis Castillo-Ossa, Gustavo Isaza, Romain Guyot
Genomic object detection: An improved approach for transposable elements detection and classification using convolutional neural networks. PloS one 18 (9) (2023)
Harold Brayan Arteaga-Arteaga, Mariana S Candamil-Cortés, Brian Breaux, Pablo Guillen-Rondon, Simon Orozco-Arias, Reinel Tabares-Soto
Machine learning applications on intratumoral heterogeneity in glioblastoma using single-cell RNA sequencing data. Briefings in functional genomics (2023)
Simon Orozco-Arias, Mathilde Dupeyron, David Gutiérrez-Duque, Reinel Tabares-Soto, Romain Guyot
High nucleotide similarity of three Copia lineage LTR retrotransposons among plant genomes. Genome (2023)
Nicolás Camargo-Forero, Simon Orozco-Arias, Juan M Perez Agudelo, Romain Guyot
HERV-K (HML-2) insertion polymorphisms in the 8q24.13 region and their potential etiological associations with acute myeloid leukemia. Archives of virology 168 (4) (2023)
Nicolás Camargo-Forero, Simon Orozco-Arias, Juan M Perez Agudelo, Romain Guyot
HERV-K (HML-2) insertion polymorphisms in the 8q24.13 region and their potential etiological associations with acute myeloid leukemia. Archives of virology 168 (4) (2023)
Simon Orozco-Arias, Mathilde Dupeyron, David Gutiérrez-Duque, Reinel Tabares-Soto, Romain Guyot
High nucleotide similarity of three Copia lineage LTR retrotransposons among plant genomes. Genome 66 (3) (2023)
Simon Orozco-Arias, Mathilde Dupeyron, David Gutiérrez-Duque, Reinel Tabares-Soto, Romain Guyot
High nucleotide similarity of three Copia lineage LTR retrotransposons among plant genomes. Genome 66 (3) (2023)
Simon Orozco-Arias, Mariana S Candamil-Cortes, Paula A Jaimes, Estiven Valencia-Castrillon, Reinel Tabares-Soto, Gustavo Isaza, Romain Guyot
Automatic curation of LTR retrotransposon libraries from plant genomes through machine learning. Journal of integrative bioinformatics 19 (3) (2022)
Reinel Tabares-Soto, Harold Brayan Arteaga-Arteaga, Alejandro Mora-Rubio, Mario Alejandro Bravo-Ortíz, Daniel Arias-Garzón, Jesús Alejandro Alzate-Grisales, Simon Orozco-Arias, Gustavo Isaza, Raúl Ramos-Pollán
Sensitivity of deep learning applied to spatial image steganalysis. PeerJ. Computer science 7 (2021)
Harold Brayan Arteaga-Arteaga, Alejandro Mora-Rubio, Frank Florez, Nicolas Murcia-Orjuela, Cristhian Eduardo Diaz-Ortega, Simon Orozco-Arias, Melissa delaPava, Mario Alejandro Bravo-Ortíz, Melvin Robinson, Pablo Guillen-Rondon, Reinel Tabares-Soto
Machine learning applications to predict two-phase flow patterns. PeerJ. Computer science 7 (2021)
Simon Orozco-Arias, Mariana S Candamil-Cortés, Paula A Jaimes, Johan S Piña, Reinel Tabares-Soto, Romain Guyot, Gustavo Isaza
K-mer-based machine learning method to classify LTR-retrotransposons in plant genomes. PeerJ 9 (2021)
Simon Orozco-Arias, Paula A Jaimes, Mariana S Candamil, Cristian Felipe Jiménez-Varón, Reinel Tabares-Soto, Gustavo Isaza, Romain Guyot
InpactorDB: A Classified Lineage-Level Plant LTR Retrotransposon Reference Library for Free-Alignment Methods Based on Machine Learning. Genes 12 (2) (2021)
Reinel Tabares-Soto, Harold Brayan Arteaga-Arteaga, Alejandro Mora-Rubio, Mario Alejandro Bravo-Ortíz, Daniel Arias-Garzón, Jesús Alejandro Alzate Grisales, Alejandro Burbano Jacome, Simon Orozco-Arias, Gustavo Isaza, Raul Ramos Pollan
Strategy to improve the accuracy of convolutional neural network architectures applied to digital image steganalysis in the spatial domain. PeerJ. Computer science 7 (2021)
Reinel Tabares-Soto, Simon Orozco-Arias, Victor Romero-Cano, Vanesa Segovia Bucheli, José Luis Rodríguez-Sotelo, Cristian Felipe Jiménez-Varón
A comparative study of machine learning and deep learning algorithms to classify cancer types based on microarray gene expression data. PeerJ. Computer science 6 (2020)
Simon Orozco-Arias, Nicolas Tobon-Orozco, Johan S Piña, Cristian Felipe Jiménez-Varón, Reinel Tabares-Soto, Romain Guyot
TIP_finder: An HPC Software to Detect Transposable Element Insertion Polymorphisms in Large Genomic Datasets. Biology 9 (9) (2020)
Simon Orozco-Arias, Gustavo Isaza, Romain Guyot, Reinel Tabares-Soto
A systematic review of the application of machine learning in the detection and classification of transposable elements. PeerJ 7 (2019)
Simon Orozco-Arias, Ana María Núñez-Rincón, Reinel Tabares-Soto, Diana López-Álvarez
Worldwide co-occurrence analysis of 17 species of the genus Brachypodium using data mining. PeerJ 6 (2019)
Simon Orozco-Arias, Gustavo Isaza, Romain Guyot
Retrotransposons in Plant Genomes: Structure, Identification, and Classification through Bioinformatics and Machine Learning. International journal of molecular sciences 20 (15) (2019)
Simon Orozco-Arias, Juan Liu, Reinel Tabares-Soto, Diego Ceballos, Douglas Silva Domingues, Andréa Garavito, Ray Ming, Romain Guyot
Inpactor, Integrated and Parallel Analyzer and Classifier of LTR Retrotransposons and Its Application for Pineapple LTR Retrotransposons Diversity and Dynamics. Biology 7 (2) (2018)

Simon Orozco-Arias.css-eqlu8i{font-size:small;padding-left:4px;}

Publication Activity (10 Years)

Top Topics

Top Venues

Simon Orozco-Arias