Jorge Alexander Duitama Castellanos

Grupo:: Research Group:

TICSw-Tecnologías de Información y Construcción de Software

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Oficina: Office: ML 622

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Extensión: Extension: 1686

Ingeniería de sistemas y computación, Universidad de los Andes, Colombia
Magíster en ingeniería de sistemas y computación. Universidad de los Andes, Colombia
Ph.D. en ciencias de computación e ingeniería, University of Connecticut, Estados Unidos

Intereses y líneas de Investigación:

Bioinformática

Grupo:: Research Group:

TICSw-Tecnologías de Información y Construcción de Software

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Accurate, Efficient and User-Friendly Mutation Calling and Sample Identification for TILLING Experiments Artículo

2021

Gil J, Andrade J, Duitama J. (2021) Accurate, Efficient and User-Friendly Mutation Calling and Sample Identification for TILLING Experiments. Frontiers in Genetics (ISSN 1664-8021) 12 (N/A), pp. 54-54. - 2021
Comprehensive genomic resources related to domestication and crop improvement traits in Lima bean Artículo

2021

Garcia T, Duitama J, Zullo S, Gil J, Zullo S, Dohle S, Palkovic A, Skeen P, Bermudez C, Debouck D, Martinez J, Gepts P, Chacón-Sanchez M. (2021) Comprehensive genomic resources related to domestication and crop improvement traits in Lima bean. Nature Communications (ISSN 2041-1723) 12 (N/A), pp. 702-702. - 2021
Discovery of new potential CDK2/VEGFR2 type II inhibitors by fragmentation and virtual screening of natural products Artículo

2021

Vasquez A, Reyes A, Duitama J, Gonzalez A. (2021) Discovery of new potential CDK2/VEGFR2 type II inhibitors by fragmentation and virtual screening of natural products. Journal of Biomolecular Structure and Dynamics (ISSN 0739-1102) 39 (9), pp. 3285-3299. - 2021
Gene Flow in Phaseolus Beans and Its Role as a Plausible Driver of Ecological Fitness and Expansion of Cultigens Artículo

2021

Chacón-Sanchez M, Martinez J, Duitama J, Debouck D. (2021) Gene Flow in Phaseolus Beans and Its Role as a Plausible Driver of Ecological Fitness and Expansion of Cultigens. Frontiers in Ecology and Evolution (ISSN 2296-701X) 9 (N/A), pp. 618709-618709. - 2021
New algorithms for accurate and efficient de-novo genome assembly from long DNA sequencing reads Evento

2021

Gonzalez L, Duitama J.(2021). New algorithms for accurate and efficient de-novo genome assembly from long DNA sequencing reads. - 2021
Non-extensive fragmentation of natural products and pharmacophore-based virtual screening as a practical approach to identify novel promising chemical scaffolds Artículo

2021

Vasquez A, Reyes A, Duitama J, Gonzalez A. (2021) Non-extensive fragmentation of natural products and pharmacophore-based virtual screening as a practical approach to identify novel promising chemical scaffolds. FRONTIERS IN CHEMISTRY (ISSN 2296-2646) 9 (N/A), pp. 700802-1-700802-13. - 2021
Peptidomic analysis of whey protein hydrolysates and prediction of their antioxidant peptides Artículo

2021

Morales J, Duitama J, Gonzalez A. (2021) Peptidomic analysis of whey protein hydrolysates and prediction of their antioxidant peptides. Food Science and Human Wellness (ISSN 2213-4530) 11 (2), pp. 349-355. - 2021
Robust and efficient software for reference-free genomic diversity analysis of genotyping-by-sequencing data on diploid and polyploid species Artículo

2021

Parra A, Gomez J, Lozano-Arce D, Reyes-Herrera P, Duitama J. (2021) Robust and efficient software for reference-free genomic diversity analysis of genotyping-by-sequencing data on diploid and polyploid species. Molecular Ecology Resources (ISSN 1755-0998) 1 (N/A), pp. 1-1. - 2021
Unraveling the Genome of a High Yielding Colombian Sugarcane Hybrid Artículo

2021

Trujillo-Montenegro J, Rodriguez M, Loaiza C, Quintero M, Espitia H, Salazar F, Viveros C, Gonzalez A, De Vega J, Duitama J, Riascos JJ. (2021) Unraveling the Genome of a High Yielding Colombian Sugarcane Hybrid . Frontiers in Plant Science (ISSN 1664-462X) 12 (n/a), pp. 694859-694859. - 2021
Using RNA-seq to characterize pollen-stigma interactions for pollination studies Artículo

2021

Lobaton J, Andrew R, Duitama J, Kirkland L, Macfadyen S, Rader R. (2021) Using RNA-seq to characterize pollen-stigma interactions for pollination studies. SCIENTIFIC REPORTS (ISSN 2045-2322) 11 (1), pp. 6635-6635. - 2021
Whole-Genome Transformation Promotes tRNA Anticodon Suppressor Mutations under Stress Artículo

2021

Deparis Q, Duitama J, Foulquié-moreno M, Thevelein J. (2021) Whole-Genome Transformation Promotes tRNA Anticodon Suppressor Mutations under Stress. mBio (ISSN 2150-7511) 12 (2), pp. e03649-20-e03649-20. - 2021
Análisis automático de geles de poliacrilamida Tesis

2020

Tejon R .(2020). Análisis automático de geles de poliacrilamida. Trabajo Dirigido por: Duitama J - 2020
Análisis de Herramientas y Métodos: Predicción de Estructura Proteica Terciaria Tesis

2020

Rengifo D .(2020). Análisis de Herramientas y Métodos: Predicción de Estructura Proteica Terciaria. Trabajo Dirigido por: Duitama J - 2020
Desarrollo de una herramienta computacionalactualizada para la identificación de TandemRepeats en secuencias de ADN OTHER

2020

Duitama J. Desarrollo de una herramienta computacionalactualizada para la identificación de TandemRepeats en secuencias de ADN. (2020) - 2020
Development of a variant interpretation framework for the SIGEN genomic diagnostic service Tesis

2020

Mahecha D .(2020). Development of a variant interpretation framework for the SIGEN genomic diagnostic service. Trabajo Dirigido por: Duitama J - 2020
Gene clustering for ortholog group discovery Tesis

2020

Gomez J .(2020). Gene clustering for ortholog group discovery. Trabajo Dirigido por: Duitama J - 2020
Genetic mapping for agronomic traits in a MAGIC population of common bean (Phaseolus vulgaris L.) under drought conditions Artículo

2020

Diaz S, Ariza-suarez D, Izquierdo P, Lobaton J, Acevedo F, Duitama J, Guerrero A, Cajiao C, Mayor V, Beebe S, Raatz B. (2020) Genetic mapping for agronomic traits in a MAGIC population of common bean (Phaseolus vulgaris L.) under drought conditions. BMC Genomics (ISSN 1471-2164) 21 (1), pp. 799-799. - 2020
Genomic Variability of Phytophthora palmivora Isolates from Different Oil Palm Cultivation Regions in Colombia Artículo

2020

Gil J, Herrera M, Duitama J, Sarria G, Restrepo S, Romero H. (2020) Genomic Variability of Phytophthora palmivora Isolates from Different Oil Palm Cultivation Regions in Colombia. Phytopathology (ISSN 0031-949X) 110 (9), pp. 1553-1564. - 2020
Grafo Métrico Y No Dirigido Para El Ensamblaje De Novo De Genomas Completos Tesis

2020

Bojaca J .(2020). Grafo Métrico Y No Dirigido Para El Ensamblaje De Novo De Genomas Completos. Trabajo Dirigido por: Duitama J - 2020
Modern Visualizations for Gene and Protein Multiple Sequence Alignments Tesis

2020

Ramirez D .(2020). Modern Visualizations for Gene and Protein Multiple Sequence Alignments. Trabajo Dirigido por: Duitama J - 2020
Programming language comparison in bioinformatics Tesis

2020

Arenas J .(2020). Programming language comparison in bioinformatics. Trabajo Dirigido por: Duitama J - 2020
Robust and efficient software platform for de-novo genomic diversity analysis Tesis

2020

Parra A .(2020). Robust and efficient software platform for de-novo genomic diversity analysis. Trabajo Dirigido por: Duitama J - 2020
The Hamiltonian path problem applied to genomes assembly Tesis

2020

Trujillo M .(2020). The Hamiltonian path problem applied to genomes assembly. Trabajo Dirigido por: Duitama J - 2020
Time series transcriptome analysis reveals adaptable activation of defense related genes in tree tomato infected with late blight Evento

2020

Bautista D, Guayazan N, Botero D, Duitama J, Bernal A, Restrepo S. Time series transcriptome analysis reveals adaptable activation of defense related genes in tree tomato infected with late blight. (2020) - 2020
Alineador de secuencias en NGSEP Tesis

2019

Andrade G .(2019). Alineador de secuencias en NGSEP. Trabajo Dirigido por: Duitama J - 2019
ENSAMBLAJE EFICIENTE DE GENOMAS DE NOVO USANDO GRAFOS NO DIRIGIDOS Tesis

2019

Guevara F .(2019). ENSAMBLAJE EFICIENTE DE GENOMAS DE NOVO USANDO GRAFOS NO DIRIGIDOS. Trabajo Dirigido por: Duitama J - 2019
Enzymatic Hydrolysis Modeling of Whey Proteins for Obtaining Antioxidant Peptide."V Congreso Colombiano de Biología y Computacional y Bioinformatica Ibague Colombia Noviembre 6-9 2019" Evento

2019

Morales J, Duitama J, Gonzalez A.(2019). Enzymatic Hydrolysis Modeling of Whey Proteins for Obtaining Antioxidant Peptide."V Congreso Colombiano de Biología y Computacional y Bioinformatica Ibague Colombia Noviembre 6-9 2019". - 2019
Haplotipado Molecular de Individuos Tesis

2019

Chavarro C .(2019). Haplotipado Molecular de Individuos. Trabajo Dirigido por: Duitama J - 2019
Molecular dynamics and metadynamics study on back pocket-binders of CDK2 and VEGFR2 as potential small-molecule dual inhibitors."V Congreso Colombiano de Biología y Computacional y Bioinformatica Ibague Colombia Octubre 6-9 2019" Evento

2019

Vasquez A, Duitama J, Gonzalez A.(2019). Molecular dynamics and metadynamics study on back pocket-binders of CDK2 and VEGFR2 as potential small-molecule dual inhibitors."V Congreso Colombiano de Biología y Computacional y Bioinformatica Ibague Colombia Octubre 6-9 2019". - 2019
NGSEP3: accurate variant calling across species and sequencing protocols Artículo

2019

Tello D, Gil J, Loaiza C, Riascos JJ, N. Cardozo, Duitama J. (2019) NGSEP3: accurate variant calling across species and sequencing protocols. Bioinformatics (ISSN 1367-4803) 35 (-), pp. 4716-4723. - 2019
Prediction of Transposable Elements Tesis

2019

Jimenez S .(2019). Prediction of Transposable Elements. Trabajo Dirigido por: Duitama J - 2019
Prototipo de interfaz para NGSEP Tesis

2019

Reyes F .(2019). Prototipo de interfaz para NGSEP. Trabajo Dirigido por: Duitama J - 2019
Revisión de algoritmos para la detección de CNVs Tesis

2019

Castro L .(2019). Revisión de algoritmos para la detección de CNVs. Trabajo Dirigido por: Duitama J - 2019
Structural variants in 3000 rice genomes Artículo

2019

Fuentes R, Chebotarov D, Duitama J, Smith S, de la Hoz JF, Mohiyuddin M, Wing R, Mcnally K, Tatarinova T, Grigoriev A, Mauleon R, Alexandrov N. (2019) Structural variants in 3000 rice genomes. Genome Research (ISSN 1088-9051) 29 (5), pp. 870-880. - 2019
Translocation of a parthenogenesis gene candidate to an alternate carrier chromosome in apomictic Brachiaria humidicola Artículo

2019

Worthington M, Ebina M, Yamanaka N, Heffelfinger C, Quintero C, Zapata Y, Perez J, Selvaraj M, Ishitani M, Duitama J, de la Hoz JF, Rao I, Dellaporta S, Tohme J, Arango J. (2019) Translocation of a parthenogenesis gene candidate to an alternate carrier chromosome in apomictic Brachiaria humidicola. BMC Genomics (ISSN 1471-2164) 20 (NA), pp. 41-41. - 2019
Visualizaciones de alineamientos de genomas Tesis

2019

Garcia R .(2019). Visualizaciones de alineamientos de genomas. Trabajo Dirigido por: Duitama J - 2019
Development of a software solution for genome alignment Tesis

2018

Tello D .(2018). Development of a software solution for genome alignment. Trabajo Dirigido por: Duitama J - 2018
Genomic Analysis of Colombian Leishmania panamensis strains with different level of virulence Artículo

2018

Urrea D, Duitama J, Imamura H, Alzate J, Gil J, Triana O. (2018) Genomic Analysis of Colombian Leishmania panamensis strains with different level of virulence. SCIENTIFIC REPORTS (ISSN 2045-2322) 8 (N/A), pp. 17336-17336. - 2018
Resequencing of common bean identifies regions of inter–gene pool introgression and provides comprehensive resources for molecular breeding Artículo

2018

Lobaton JD, Miller T, Gil J, Ariza D, de la Hoz JF, Soler A, Beebe S, Duitama J, Gepts P, Raatz B. (2018) Resequencing of common bean identifies regions of inter–gene pool introgression and provides comprehensive resources for molecular breeding. The Plant Genome () 11 (-), pp. 170068-170068. - 2018
A fosmid pool-based next generation sequencing approach to haplotype-resolve whole genomes Capítulo de libro

2017

Duitama J. (2017) A fosmid pool-based next generation sequencing approach to haplotype-resolve whole genomes. Methods in Molecular Biology (ISBN 978-1-4939-6748-3) pp. ---. Springer Nature - 2017
Deep Assessment of Genomic Diversity in Cassava for Herbicide Tolerance and Starch Biosynthesis. Artículo

2017

Duitama J, Kafuri L, Tello D, Leiva A, Hofinger B, Datta S, Lentini Z, Aranzales E, Till B, Ceballos H. (2017) Deep Assessment of Genomic Diversity in Cassava for Herbicide Tolerance and Starch Biosynthesis.. Computational and Structural Biotechnology Journal (ISSN 2001-0370) 15 (1), pp. 185-194. - 2017
The sole introduction of two single-point mutations establishes glycerol utilization in Saccharomyces cerevisiae CEN. PK derivatives Artículo

2017

Ho P, Swinnen Steve, Duitama J, Nevoigt E. (2017) The sole introduction of two single-point mutations establishes glycerol utilization in Saccharomyces cerevisiae CEN. PK derivatives. Biotechnology for Biofuels (ISSN 1754-6834) 10 (1), pp. --10. - 2017
Bioinformatic analysis of genotype by sequencing (GBS) data with NGSEP Artículo

2016

Duitama J. (2016) Bioinformatic analysis of genotype by sequencing (GBS) data with NGSEP. BMC Genomics () 17 (S5), pp. 498-498. - 2016
Combining image analysis, genome wide association studies and different field trials to reveal stable genetic regions related to panicle architecture and the number of spikelets per panicle in rice Artículo

2016

Duitama J. (2016) Combining image analysis, genome wide association studies and different field trials to reveal stable genetic regions related to panicle architecture and the number of spikelets per panicle in rice. Frontiers in Plant Science () 7 (-), pp. ---. - 2016
Genomic Variants Detection and Genotyping Capítulo de libro

2016

Duitama J. (2016) Genomic Variants Detection and Genotyping. Computational Methods for Next Generation Sequencing Data Analysis (ISBN 9781118169483) pp. 133-147. John Wiley & Sons - 2016
Genomic saturation mutagenesis and polygenic analysis identify novel yeast genes affecting ethyl acetate production, a non-selectable polygenic trait Artículo

2016

Duitama J. (2016) Genomic saturation mutagenesis and polygenic analysis identify novel yeast genes affecting ethyl acetate production, a non-selectable polygenic trait. Microbial Cell () 3 (4), pp. -175. - 2016
Whole genome sequencing of elite rice cultivars as a comprehensive information resource for marker assisted selection Artículo

2015

Duitama J. (2015) Whole genome sequencing of elite rice cultivars as a comprehensive information resource for marker assisted selection. PLoS ONE (ISSN 1932-6203) 10 (4), pp. e0124617- e0124617. - 2015
An integrated framework for discovery and genotyping of genomic variants from high-throughput sequencing experiments Artículo

2014

Duitama J. (2014) An integrated framework for discovery and genotyping of genomic variants from high-throughput sequencing experiments. Nucleic Acids Research (ISSN 0305-1048) 42 (6), pp. e44-e44. - 2014
Genomic and bioinformatic profiling of mutational neoepitopes reveals new rules to predict anticancer immunogenicity Artículo

2014

Duitama J. (2014) Genomic and bioinformatic profiling of mutational neoepitopes reveals new rules to predict anticancer immunogenicity. Journal of Experimental Medicine (ISSN 0022-1007) 211 (11), pp. 2231-2248. - 2014
Rice Breeding in Latin America Capítulo de libro

2014

Duitama J. (2014) Rice Breeding in Latin America. Plant Breeding Reviews (ISBN 9781118916834) pp. 187-278. Wiley Blackwell - 2014
Comparative Polygenic Analysis of Maximal Ethanol Accumulation Capacity and Tolerance to High Ethanol Levels of Cell Proliferation in Yeast Artículo

2013

Duitama J. (2013) Comparative Polygenic Analysis of Maximal Ethanol Accumulation Capacity and Tolerance to High Ethanol Levels of Cell Proliferation in Yeast. PLoS Genetics (ISSN 1553-7390) 9 (6), pp. e1003548--. - 2013
Identification of cassava microRNAs under abiotic stress Artículo

2013

Duitama J. (2013) Identification of cassava microRNAs under abiotic stress. International Journal of Genomics (ISSN 2314-436X) 2013 (-), pp. 857986-857986. - 2013
Identification of multiple interacting alleles conferring low glycerol and high ethanol yield in Saccharomyces cerevisiae ethanolic fermentation Artículo

2013

Duitama J. (2013) Identification of multiple interacting alleles conferring low glycerol and high ethanol yield in Saccharomyces cerevisiae ethanolic fermentation. Biotechnology for Biofuels (ISSN 1754-6834) 6 (1), pp. 87--. - 2013
Quantitative trait analysis of yeast biodiversity yields novel gene tools for metabolic engineering Artículo

2013

Duitama J. (2013) Quantitative trait analysis of yeast biodiversity yields novel gene tools for metabolic engineering. Metabolic Engineering (ISSN 1096-7176) 17 (-), pp. 68-81. - 2013
Fosmid-based whole genome haplotyping of a HapMap trio child: Evaluation of Single Individual Haplotyping techniques Artículo

2012

Duitama J. (2012) Fosmid-based whole genome haplotyping of a HapMap trio child: Evaluation of Single Individual Haplotyping techniques. Nucleic Acids Research (ISSN 0305-1048) 40 (5), pp. 2041-2053. - 2012
Functional divergence of gene duplicates through ectopic recombination Artículo

2012

Duitama J. (2012) Functional divergence of gene duplicates through ectopic recombination. EMBO Reports () 13 (12), pp. 1145-1151. - 2012
Towards accurate detection and genotyping of expressed variants from whole transcriptome sequencing data Artículo

2012

Duitama J. (2012) Towards accurate detection and genotyping of expressed variants from whole transcriptome sequencing data. BMC Genomics (ISSN 1471-2164) 13 (Suppl 2), pp. S6--. - 2012
A comprehensively molecular haplotype-resolved genome of a European individual Artículo

2011

Duitama J. (2011) A comprehensively molecular haplotype-resolved genome of a European individual. Genome Research (ISSN 1088-9051) 21 (10), pp. 1672-1685. - 2011
Linkage disequilibrium based genotype calling from low-coverage shotgun sequencing reads Artículo

2011

Duitama J. (2011) Linkage disequilibrium based genotype calling from low-coverage shotgun sequencing reads. BMC Bioinformatics (ISSN 1471-2105) 12 (SUPPL. 1), pp. ---. - 2011
ReFHap: A reliable and fast algorithm for single individual haplotyping Artículo

2010

Duitama J. (2010) ReFHap: A reliable and fast algorithm for single individual haplotyping. 2010 ACM International Conference on Bioinformatics and Computational Biology, ACM-BCB 2010 () - (-), pp. 160-169. - 2010
PrimerHunter: A primer design tool for PCR-based virus subtype identification Artículo

2009

Duitama J. (2009) PrimerHunter: A primer design tool for PCR-based virus subtype identification. Nucleic Acids Research (ISSN 0305-1048) 37 (8), pp. 2483-2492. - 2009

2016-20

ALGORIT.BIOLOGIA COMPUTACIONAL

ALGORITMICA Y PROGR. OBJ. I

2017-10

ESTADISTICA BIOLOGIA COMPUTAC.

ALGORITMICA Y PROGR. OBJ. I

FUNDAM.PROG. CIENCIAS BIOLOGIC

2017-19

DISEÑO Y ANALISIS DE ALGORI.

2017-20

ALGORIT.BIOLOGIA COMPUTACIONAL

DISEÑO Y ANALISIS DE ALGORI.

2018-10

FUNDAM.PROG. CIENCIAS BIOLOGIC

DISEÑO Y ANALISIS DE ALGORI.

MATEMÁTICA ESTRUCTURAL Y LÓGIC

2018-20

ANALISIS DATOS GENOMICA POBLAC

ALGORIT.BIOLOGIA COMPUTACIONAL

DISEÑO Y ANALISIS DE ALGORI.

2019-10

FUNDAM.PROG. CIENCIAS BIOLOGIC

DISEÑO Y ANALISIS DE ALGORI.

ALGORITMICA Y PROGR. OBJ. I

2019-20

ALGORIT.BIOLOGIA COMPUTACIONAL

ALGORITMICA Y PROGR. OBJ. I

DISEÑO Y ANALISIS DE ALGORI.

2020-10

DISEÑO Y ANÁLISIS DE ALGORI.

INTRODUCCIÓN A LA PROGRAMACIÓN

FUNDAM.PROG. CIENCIAS BIOLOGIC

2020-20

DISEÑO Y ANÁLISIS DE ALGORI.

ALGORIT.BIOLOGIA COMPUTACIONAL

INTRODUCCIÓN A LA PROGRAMACIÓN

POYECTO DE PROFUNDIZACIÓN

2021-10

ESTADISTICA BIOLOGIA COMPUTAC.

DISEÑO Y ANÁLISIS DE ALGORI.

POYECTO DE PROFUNDIZACIÓN

2021-20

POYECTO DE PROFUNDIZACIÓN

DISEÑO Y ANÁLISIS DE ALGORI.

ALGORIT.BIOLOGIA COMPUTACIONAL

2022-10

DISEÑO Y ANÁLISIS DE ALGORI.

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ESTADISTICA BIOLOGIA COMPUTAC.

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