Daniel Restrepo-Montoya

Works (15)

Updated: April 24th, 2025 09:18

2022 article

Genome-Wide Association Study of Listeria monocytogenes Isolates Causing Three Different Clinical Outcomes

Cardenas-Alvarez, M. X., Restrepo-Montoya, D., & Bergholz, T. M. (2022, September 29). Microorganisms.

By: M. Cardenas-Alvarez *, D. Restrepo-Montoya*  & T. Bergholz *

topics (OpenAlex): Listeria monocytogenes in Food Safety; Salmonella and Campylobacter epidemiology; Microbial Inactivation Methods
TL;DR: The orthologous results indicated that genes of phage phiX174, transfer RNAs, and type I restriction-modification system genes along with SNPs in loci involved in environmental adaptation were associated with one or more clinical outcomes. (via Semantic Scholar)
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UN Sustainable Development Goal Categories
14. Life Below Water (OpenAlex)
Source: ORCID
Added: January 29, 2024

2022 article

Leveraging National Germplasm Collections to Determine Significantly Associated Categorical Traits in Crops: Upland and Pima Cotton as a Case Study

Restrepo-Montoya, D., Hulse-Kemp, A. M., Scheffler, J. A., Haigler, C. H., Hinze, L. L., Love, J., … Frelichowski, J. (2022, April 26). Frontiers in Plant Science, Vol. 4.

By: D. Restrepo-Montoya n , A. Hulse-Kemp n , J. Scheffler *, C. Haigler n , L. Hinze *, J. Love*, R. Percy*, D. Jones *, J. Frelichowski *

author keywords: trait association; categorical data; cotton; crop germplasm; breeding
topics (OpenAlex): Research in Cotton Cultivation; Plant and Fungal Interactions Research; Plant Virus Research Studies
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UN Sustainable Development Goal Categories
2. Zero Hunger (Web of Science)
13. Climate Action (Web of Science)
Sources: Web Of Science, ORCID, NC State University Libraries
Added: May 31, 2022

2021 article

Orthology and synteny analysis of receptor-like kinases “RLK” and receptor-like proteins “RLP” in legumes

Restrepo-Montoya, D., McClean, P. E., & Osorno, J. M. (2021, February 10). BMC Genomics.

By: D. Restrepo-Montoya* , P. McClean * & J. Osorno *

author keywords: Dicots; Plasma membrane receptors; Target synteny blocks; Legumes; non-legumes
MeSH headings : Arabidopsis; Phosphotransferases; Phylogeny; Soybeans; Synteny
topics (OpenAlex): Legume Nitrogen Fixing Symbiosis; Genetic and Environmental Crop Studies; Agricultural pest management studies
TL;DR: The identification of RLK and RLP genes among the synteny blocks in legumes revealed multiple highly conserved syntenic blocks on multiple chromosomes and suggests that P. vulgaris is an appropriate anchor species for comparative genomics among legumes. (via Semantic Scholar)
Source: ORCID
Added: June 29, 2022

2020 article

Computational identification of receptor-like kinases “RLK” and receptor-like proteins “RLP” in legumes

Restrepo-Montoya, D., Brueggeman, R., McClean, P. E., & Osorno, J. M. (2020, July 3). BMC Genomics, Vol. 21.

By: D. Restrepo-Montoya* , R. Brueggeman *, P. McClean * & J. Osorno *

author keywords: Dicots; Model plants; Resistance genes; proteins; Legumes; Plasma membrane receptors
MeSH headings : Computational Biology; Enzymes / chemistry; Fabaceae / chemistry; Fabaceae / enzymology; Plant Proteins / chemistry; Plant Proteins / classification; Protein Domains; Receptors, Cell Surface / chemistry; Receptors, Cell Surface / classification
topics (OpenAlex): Legume Nitrogen Fixing Symbiosis; Genetic and Environmental Crop Studies; Agricultural pest management studies
TL;DR: A computational approach to identify and classify RLK and RLP proteins is presented and suggests that about 2% of the proteins of each genome belong to the RLK family and less than 1% belong to RLP family. (via Semantic Scholar)
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UN Sustainable Development Goal Categories
15. Life on Land (OpenAlex)
Source: ORCID
Added: June 29, 2022

2019 article

Comparative genomics identifies potential virulence factors inClostridium tertiumandC. paraputrificum

Muñoz, M., Restrepo-Montoya, D., Kumar, N., Iraola, G., Herrera, G., Ríos-Chaparro, D. I., … Ramírez, J. D. (2019, January 1). Virulence.

By: M. Muñoz *, D. Restrepo-Montoya* , N. Kumar *, G. Iraola *, G. Herrera *, D. Ríos-Chaparro *, D. Díaz-Arévalo *, M. Patarroyo *, T. Lawley *, J. Ramírez *

author keywords: Clostridium tertium; Clostridium paraputrificum; Clostridial species; genetic diversity; virulence factors
MeSH headings : Bacterial Proteins / genetics; Clostridioides difficile / genetics; Clostridium Infections / microbiology; Clostridium tertium / genetics; Colombia; Genetic Variation; Genome, Bacterial; Genomics; Humans; Virulence Factors / genetics
topics (OpenAlex): Clostridium difficile and Clostridium perfringens research; Bacterial Identification and Susceptibility Testing; Streptococcal Infections and Treatments; Gut microbiota and health
TL;DR: Complete genome description of two clostridiales species revealing high levels of intra-taxa diversity, accessory genomes containing virulence-factors encoding genes (especially in C. paraputrificum), suggest the need to advance in the study of those species with potential importance at public health level. (via Semantic Scholar)
Source: ORCID
Added: June 29, 2022

2019 article

Integrated genomic epidemiology and phenotypic profiling of Clostridium difficile across intra-hospital and community populations in Colombia

Muñoz, M., Restrepo-Montoya, D., Kumar, N., Iraola, G., Camargo, M., Díaz-Arévalo, D., … Ramírez, J. D. (2019, August 5). Scientific Reports.

By: M. Muñoz *, D. Restrepo-Montoya* , N. Kumar *, G. Iraola *, M. Camargo *, D. Díaz-Arévalo *, N. Roa-Molina *, M. Tellez* ...

MeSH headings : Anti-Infective Agents / therapeutic use; Clostridioides difficile / genetics; Clostridium Infections / epidemiology; Clostridium Infections / genetics; Clostridium Infections / microbiology; Colombia / epidemiology; Diarrhea / epidemiology; Diarrhea / genetics; Diarrhea / microbiology; Drug Resistance, Bacterial / genetics; Enterotoxins / genetics; Fluoroquinolones / adverse effects; Fluoroquinolones / therapeutic use; Genome, Bacterial; Genomics; Hospitals; Humans; Microbial Sensitivity Tests; Molecular Epidemiology; Phenotype
topics (OpenAlex): Clostridium difficile and Clostridium perfringens research; Antimicrobial Resistance in Staphylococcus; Helicobacter pylori-related gastroenterology studies
TL;DR: A robust genomic and phenotypic profiling of clinical isolates established from diarrheal samples from either intrahospital (IH) or community (CO) populations in central Colombia highlights the regional differences that C. difficile isolates display. (via Semantic Scholar)
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UN Sustainable Development Goal Categories
3. Good Health and Well-being (OpenAlex)
Source: ORCID
Added: June 29, 2022

2017 article

Genetic Architecture of Flooding Tolerance in the Dry Bean Middle-American Diversity Panel

Soltani, A., MafiMoghaddam, S., Walter, K., Restrepo-Montoya, D., Mamidi, S., Schroder, S., … Osorno, J. M. (2017, July 5). Frontiers in Plant Science.

By: A. Soltani *, S. MafiMoghaddam*, K. Walter*, D. Restrepo-Montoya* , S. Mamidi *, S. Schroder *, R. Lee*, P. McClean *, J. Osorno *

author keywords: common bean; flooding; abiotic stress; anoxia; waterlogging; GWAS
topics (OpenAlex): Plant responses to water stress; Plant pathogens and resistance mechanisms; Soybean genetics and cultivation
TL;DR: A genome-wide association study using ~150 K SNPs was performed to discover genomic regions associated with multiple physiological responses in soybean that contribute to flooding tolerance, suggesting a conserved evolutionary pathway involved in flooding tolerance for these related legumes. (via Semantic Scholar)
Source: ORCID
Added: June 29, 2022

2015 article

Changes in Macrophage Gene Expression Associated with Leishmania (Viannia) braziliensis Infection

Ovalle-Bracho, C., Franco-Muñoz, C., Londoño-Barbosa, D., Restrepo-Montoya, D., & Clavijo-Ramírez, C. (2015, June 8). PLoS ONE.

By: C. Ovalle-Bracho *, C. Franco-Muñoz *, D. Londoño-Barbosa*, D. Restrepo-Montoya*  & C. Clavijo-Ramírez *

MeSH headings : Cholesterol / biosynthesis; Gene Expression Profiling; Gene Expression Regulation; Humans; Leishmania braziliensis / physiology; Leishmaniasis, Cutaneous / genetics; Leishmaniasis, Cutaneous / parasitology; Macrophages / metabolism; Macrophages / parasitology; Oligonucleotide Array Sequence Analysis; Real-Time Polymerase Chain Reaction; Reproducibility of Results; U937 Cells
topics (OpenAlex): Research on Leishmaniasis Studies; Insect Pest Control Strategies; Trypanosoma species research and implications
TL;DR: Differential transcriptional results suggest a negative regulation of the genetic regulatory network involved in cholesterol biosynthesis, which contrasts with those from studies involving other Leishmania species at earlier infection stages, where gene up-regulation for this metabolic pathway has been reported. (via Semantic Scholar)
Source: ORCID
Added: June 29, 2022

2013 article

A Multi-objective Optimization Energy Approach to Predict the Ligand Conformation in a Docking Process

Sandoval-Perez, A., Becerra, D., Vanegas, D., Restrepo-Montoya, D., & Nino, F. (2013, January 1). Lecture Notes in Computer Science.

By: A. Sandoval-Perez *, D. Becerra *, D. Vanegas *, D. Restrepo-Montoya*  & F. Nino *

topics (OpenAlex): Computational Drug Discovery Methods; Free Radicals and Antioxidants; Chemistry and Chemical Engineering
TL;DR: The proposed approach is an improvement over others in the field, where the principle insight is that a Pareto front helps to understand the tradeoffs in the actual problem. (via Semantic Scholar)
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UN Sustainable Development Goal Categories
7. Affordable and Clean Energy (OpenAlex)
Source: ORCID
Added: June 29, 2022

2012 article

The Autoimmune Tautology: An In Silico Approach

Cifuentes, R. A., Restrepo-Montoya, D., & Anaya, J.-M. (2012, January 1). Autoimmune Diseases.

By: R. Cifuentes *, D. Restrepo-Montoya*  & J. Anaya *

topics (OpenAlex): Biomedical Text Mining and Ontologies; Bioinformatics and Genomic Networks; Machine Learning in Bioinformatics
TL;DR: The results support the common origin of AIDs and the role of genes involved in apoptosis such as CTLA4, FASLG, and IL10 and find three clusters in which the genes with the highest contribution encoded proteins that showed strong and specific interactions. (via Semantic Scholar)
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UN Sustainable Development Goal Categories
3. Good Health and Well-being (OpenAlex)
Source: ORCID
Added: June 29, 2022

2011 article

Identification of Plasmodium vivax Proteins with Potential Role in Invasion Using Sequence Redundancy Reduction and Profile Hidden Markov Models

Restrepo-Montoya, D., Becerra, D., Carvajal-Patiño, J. G., Mongui, A., Niño, L. F., Patarroyo, M. E., & Patarroyo, M. A. (2011, October 3). PLoS ONE.

By: D. Restrepo-Montoya* , D. Becerra *, J. Carvajal-Patiño *, A. Mongui *, L. Niño*, M. Patarroyo *, M. Patarroyo *

MeSH headings : Computational Biology; Databases, Protein; Markov Chains; Models, Biological; Plasmodium vivax / metabolism; Protozoan Proteins / analysis; Protozoan Proteins / chemistry; Sequence Analysis, Protein / methods
topics (OpenAlex): Malaria Research and Control; vaccines and immunoinformatics approaches; Machine Learning in Bioinformatics
TL;DR: The results support the idea that probabilistic techniques like profile HMMs improve similarity searches and lead to targeting 32 proteins for further testing regarding their ability to induce protective immune responses against P. vivax malaria. (via Semantic Scholar)
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UN Sustainable Development Goal Categories
3. Good Health and Well-being (OpenAlex)
Source: ORCID
Added: June 29, 2022

2011 article

NClassG+: A classifier for non-classically secreted Gram-positive bacterial proteins

Restrepo-Montoya, D., Pino, C., Nino, L. F., Patarroyo, M. E., & Patarroyo, M. A. (2011, January 14). BMC Bioinformatics.

By: D. Restrepo-Montoya* , C. Pino*, L. Nino*, M. Patarroyo * & M. Patarroyo *

MeSH headings : Artificial Intelligence; Bacterial Proteins / classification; Bacterial Proteins / metabolism; Computational Biology / methods; Databases, Protein; Gram-Positive Bacteria / metabolism; Models, Theoretical; Software
topics (OpenAlex): Machine Learning in Bioinformatics; Genomics and Phylogenetic Studies; RNA and protein synthesis mechanisms
TL;DR: The implementation of a sequence-based classifier, denoted as NClassG+, for identifying non-classically secreted Gram-positive bacterial proteins, obtaining better predictive performance compared to SecretomeP V 2.0 and SecretPV2.0. (via Semantic Scholar)
Source: ORCID
Added: June 29, 2022

2010 article

A parallel multi-objective ab initio approach for protein structure prediction

Becerra, D., Sandoval, A., Restrepo-Montoya, D., & Luis, F. N. (2010, December 1). 2010 IEEE International Conference on Bioinformatics and Biomedicine (BIBM).

By: D. Becerra *, A. Sandoval *, D. Restrepo-Montoya*  & F. Luis*

topics (OpenAlex): Protein Structure and Dynamics; Microbial Metabolic Engineering and Bioproduction; Enzyme Structure and Function
TL;DR: This work proposes a novel and suitable methodology to model protein structure prediction with atomic-level detail by using a parallel multi-objective ab initio approach and was validated on a set of benchmark proteins obtaining very promising results. (via Semantic Scholar)
Source: ORCID
Added: June 29, 2022

2010 article

Computational Prediction and Experimental Assessment of Secreted/Surface Proteins from Mycobacterium tuberculosis H37Rv

Vizcaíno, C., Restrepo-Montoya, D., Rodríguez, D., Niño, L. F., Ocampo, M., Vanegas, M., … Patarroyo, M. A. (2010, June 24). PLoS Computational Biology.

By: C. Vizcaíno*, D. Restrepo-Montoya* , D. Rodríguez*, L. Niño*, M. Ocampo *, M. Vanegas *, M. Reguero*, N. Martínez*, M. Patarroyo *, M. Patarroyo *

MeSH headings : Animals; Antibodies, Bacterial / chemistry; Antibodies, Bacterial / metabolism; Artificial Intelligence; Bacterial Outer Membrane Proteins / chemistry; Bacterial Outer Membrane Proteins / metabolism; Cell Fractionation; Computational Biology / methods; Electrophoresis, Polyacrylamide Gel; Epitopes, B-Lymphocyte / immunology; Epitopes, B-Lymphocyte / metabolism; Escherichia coli / metabolism; Immunoblotting; Microscopy, Immunoelectron; Models, Statistical; Mycobacterium smegmatis / metabolism; Mycobacterium tuberculosis / chemistry; Mycobacterium tuberculosis / metabolism; Peptides / immunology; Peptides / metabolism; Rabbits; Sonication; Subcellular Fractions / metabolism
topics (OpenAlex): vaccines and immunoinformatics approaches; RNA and protein synthesis mechanisms; Tuberculosis Research and Epidemiology
TL;DR: The genome of Mycobacterium tuberculosis H37Rv was screened using Machine Learning tools that included feature-based predictors, general localizers and transmembrane topology predictors to identify proteins that are potentially secreted to the surface of M. tuberculosis or to the extracellular milieu through different secretory pathways. (via Semantic Scholar)
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UN Sustainable Development Goal Categories
3. Good Health and Well-being (OpenAlex)
Source: ORCID
Added: June 29, 2022

2009 article

Validating subcellular localization prediction tools with mycobacterial proteins

Restrepo-Montoya, D., Vizcaíno, C., Niño, L. F., Ocampo, M., Patarroyo, M. E., & Patarroyo, M. A. (2009, May 7). BMC Bioinformatics.

By: D. Restrepo-Montoya* , C. Vizcaíno*, L. Niño*, M. Ocampo *, M. Patarroyo * & M. Patarroyo *

MeSH headings : Algorithms; Bacterial Proteins / analysis; Bacterial Proteins / chemistry; Computational Biology / methods; Databases, Protein; Mycobacterium / chemistry; Mycobacterium / metabolism; Software
topics (OpenAlex): Machine Learning in Bioinformatics; RNA and protein synthesis mechanisms; Genomics and Phylogenetic Studies
TL;DR: Both subcellular localization approaches had high predictive specificity and high recognition of true negatives for the tested data set, and SignalP 2.0 was the best tool among the ones using a feature-based approach. (via Semantic Scholar)
UN Sustainable Development Goals Color Wheel
UN Sustainable Development Goal Categories
3. Good Health and Well-being (OpenAlex)
Source: ORCID
Added: June 29, 2022

Employment

Updated: January 24th, 2022 15:30

2022 - present

Universidad Nacional de Colombia Bogotá, CO
Principal Investigator - Max Planck Tandem Group Leader Facultad de Ingeniería

2018 - 2021

NC State University North Carolina Agricultural Research Service Raleigh, NC, US

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