Summary
I'm a Colombian computational biologist who builds methods and software that turn single-cell and multi-omics data into biological and therapeutic insight. My work spans gene regulatory network inference (scTenifoldNet, SCORPION), in-silico perturbation (scTenifoldKnk), and drug discovery, spanning disease-specific drug response signatures (retriever) and drug combination prediction for cancer. I'm a Senior Scientific Consultant at QIAGEN Digital Insights, working with pharma and biotech teams.
Core Skills
- Methods
- Gene regulatory network inference · Virtual knockout and perturbation modeling · Transfer learning · Single-cell RNA-seq analysis · Multi-modal data integration · Applied statistics · Genome-scale metabolic modeling
- Applications
- Drug response and combination prediction · Cancer genomics · Single-cell data quality control · Population-level network comparison
- Software
- R (6 active CRAN packages, 9 released) · Python (pySCORPION) · C++ · Reproducible, documented scientific software
- Industry
- Client-facing scientific consulting for pharma and biotech (QIAGEN Digital Insights) · Research computing (Boston Children's Hospital)
Experience
Research Computing Data Scientist III
Research Computing Group at Boston Children's
Hospital 2022-2023
Harvard Medical School, Boston, MA, USA.
Postdoctoral Fellow
Song (Stephen) Yi's Lab of Bioinformatics and Developmental Therapeutics2021-2022
Livestrong Cancer Institutes, University of Texas at Austin, Austin, TX, USA.
Marie Skłodowska-Curie Postdoctoral Scientia II Fellow
Marieke Kuijjer's Lab of Computational Biology and
Systems Medicine2021
Norwegian Centre for Molecular Medicine (NCMM), University of Oslo, Oslo, Norway.
Graduate Research/Teaching Assistant
James J. Cai's Lab of Computational Systems
Biology2017-2021
Department of Veterinary Integrative Biosciences, Texas A&M University, College Station, TX, USA.
Software Developer – Metabolic Reconstructions Team
Janneth González's
Lab of Computational and Structural Biochemistry2016
Department of Biochemistry, Pontificia Universidad Javeriana, Bogotá, Colombia.
Adjunct Professor
Taught Computer Programming (C++) 2015-2016
Department of Systems and Industrial Engineering, Universidad Nacional de Colombia, Bogotá, Colombia.
Undergraduate Student Assistant
Maintained webpages and databases 2011-2013
Natural History Museum, School of Biology, Universidad Industrial de Santander, Bucaramanga, Colombia.
Selected Publications
eLife First author Corresponding
Nature Computational Science First author Corresponding
Patterns First author
Bioinformatics First author Corresponding
Software Packages
Brings SCORPION's sample-level gene regulatory network reconstruction to Python workflows.
Builds comparable, sample-level gene regulatory networks from single-cell data for population-scale comparisons.
Distills LINCS-L1000 drug responses into disease-specific signatures, independent of cell line, dose and time.
Downloads and merges cell-type-labeled single-cell RNA-seq data from PanglaoDB.
Runs virtual gene knockouts on wild-type single-cell data to predict gene function.
Builds and compares single-cell gene regulatory networks across conditions to pinpoint rewired genes.
Turns gene expression into flux balance analysis bounds using each reaction's gene-protein-reaction rules.
Finds and fills gaps in metabolic reconstructions using weighted reactions from a reference network.
Validates stoichiometric reactions: flags orphan metabolites and checks mass and charge balance.
Education
Ph.D., Biomedical Sciences (Biomedical Genomics
and Bioinformatics)
Texas A&M University, College Station, TX, USA. 2017-2021
Dissertation: Single-cell gene expression variability: Functional assessment and applications in functional genomics.
Advisor: Dr. James J. Cai
Applied Statistics Certificate
Texas A&M University, College Station, TX, USA.
2017-2020
M.Sc., Bioinformatics
Universidad Nacional de Colombia, Bogotá, Colombia.2015-2017
Thesis: Identifying proteins and metabolic pathways associated with the neuroprotective response mediated by tibolone in astrocytes under an induced inflammatory model.
Advisors: Dr. Janneth González and Dr. Andrés Pinzón
B.Sc., Biology
Universidad Industrial de Santander, Bucaramanga, Colombia.2008-2014
Research Project: Analysis of potential membrane disruption and stability of antimicrobial cationic peptides by molecular dynamics simulations.
Advisors: Dr. Rodrigo Torres and Dr. Paola Rondón-Villareal
Awards, Grants and Fellowships
Familien Blix fond til fremme av medisinsk forskning (Blix Family Fund for Medical Research)
Proposal: Quinolinate Phosphoribosyltransferase (QPRT) as a target gene for the reduction of
resistance development in ER-positive breast cancer2021
Amount: NOK 50,000
Norwegian Centre for Molecular Medicine (NCMM)
University of Oslo, Oslo, Norway.
Marie Skłodowska-Curie Postdoctoral Scientia II
Fellowship
Norwegian Centre for Molecular Medicine (NCMM)2021
University of Oslo, Oslo, Norway.
CVM Graduate Student Research Trainee Grant
Proposal: A single-cell multi-omic approach for understanding regulatory interactions between
human host cells and Epstein-Barr virus2020
Amount: USD 5,000
College of Veterinary Medicine and Biomedical Sciences
Texas A&M University, College Station, TX, USA.
Meritorious Master's Thesis
College of Engineering 2017
Universidad Nacional de Colombia, Bogotá, Colombia.
Best GPA Scholarship
Department of Systems and Industrial Engineering 2015
Universidad Nacional de Colombia, Bogotá, Colombia.
Adjunct Professor Scholarship
Department of Systems and Industrial Engineering 2015-2016
Universidad Nacional de Colombia, Bogotá, Colombia.
Laureate Undergraduate Research Project
Academic Board 2014
Universidad Industrial de Santander, Bucaramanga, Colombia.
Publications
(2) Preprints (31) Research Articles (3) Review (2) Conference Papers (2) Commentaries (19) First Author (10) Corresponding Author
Show all 40 publications
2026
Research article. Longitudinal zone- and cell type-specific pattern-triggered immune responses in Arabidopsis roots
Developmental Cell 2026
DOI: 10.1016/j.devcel.2026.07.002
Authors: Xu, L., Ortiz-Morea, F.A., Kim, S., Ferrari, C., Yan, Y., Liu, D., Osorio, D., Cai, J.J., Vandepoele, K., Shan, L., He, P.
Research article. Digit regeneration in mice is stimulated by sequential treatment with FGF2 and BMP2
Nature Communications 2026
DOI: 10.1038/s41467-026-72066-8
Authors: Yu, L., Yan, M., Scaturro, K.Z., Qureshi, O., Lin, Y.L., Bartelle, B.B., Smith, C.A., Osorio, D., Cai, J.J., Dawson, L.A., Brunauer, R., Suva, L.J., Han, M., Dolan, C.P., Muneoka, K.
Commentary. The evolution of gene regulatory networks
Nature Computational Science 2026
DOI: 10.1038/s43588-026-00981-3
Authors: Belova, T., Osorio, D., Kuijjer, M.L.
2025
Preprint. Pan-cancer analysis of patient-specific gene
regulatory landscapes identifies
recurrent PD-1 pathway dysregulation linked to outcome
bioRxiv (preprint) 2025
DOI: 10.1101/2025.10.03.680219
Authors: Belova, T., Hsieh, P., Hovan, L., Osorio, D., Kuijjer, M.L.
Review. scTenifoldNet and scTenifoldKnk: a package suite for
single-cell gene regulatory network construction, comparison, and perturbation analysis
Statistical Theory and Related Fields 2025
DOI: 10.1080/24754269.2025.2557719
Authors: Zhong, Y., Osorio, D., Li, G., Xu, Q., Yongjian, Y., Huang, J.Z. and Cai, J.J.
Research article. Renal Single-Cell RNA Sequencing and Digital Cytometry in
Dogs with X-Linked Hereditary Nephropathy
Animals 2025
DOI: 10.3390/ani15142061
Authors: Chu, C.P., Osorio, D., Nabity, M.B.
First author. Corresponding author. Research article. Drug combination prediction for cancer treatment using disease-specific
drug response profiles and single-cell transcriptional signatures
eLife 2025
DOI: 10.7554/eLife.102442
Authors: Osorio, D., Shahrouzi, P., Tekpli, X., Kristensen, V.N., Kuijjer, M.L.
2024
Research article. Targeting IRE1α reprograms the tumor
microenvironment and enhances anti-tumor immunity in prostate cancer
Nature Communications 2024
DOI: 10.1038/s41467-024-53039-1
Authors: Unal, B., Kuzu, O.F., Jin, Y., Osorio, D., Kildal, W., Pradhan M., Kung S.H.Y., Oo H.Z., Daugaard M., Vendelbo M., Patterson J., Kristian M., Thomsen M.K., Kuijjer M.L., Saatcioglu F.
Research article. Lymphoid origin of intrinsically activated plasmacytoid
dendritic cells in mice
eLife 2024
DOI: 10.7554/eLife.96394.3
Authors: Araujo, A. M., Dekker, J. D., Garrison, K., Su, Z., Rhee, C., Hu, Z., Lee, B., Osorio, D., Lee, J., Iyer, V., Ehrlich, L., Georgiou, G., Ippolito, G., Yi, S., Tucker, H.
Research article. Deciphering the impact of genomic variation on function
Nature 2024
DOI: 10.1038/s41586-024-07510-0
Authors: IGVF Consortium (Osorio, D. as member of the Yi Lab)
First author. Commentary. Enabling comparative gene regulatory network analysis on single-cell data with SCORPION
Nature Computational Science 2024
DOI: 10.1038/s43588-024-00615-6
Authors: Osorio, D., Kuijjer, M.L.
First author. Corresponding author. Research article. Population-level comparisons of gene regulatory networks modeled on
high-throughput single-cell transcriptomics data
Nature Computational Science 2024
DOI: 10.1038/s43588-024-00597-5
Authors: Osorio, D., Capasso, A., Eckhardt, S.G., Giri, U., Somma, A., Pitts, T.M., Lieu, C.H., Messersmith, W.A., Bagby, S.M., Singh, H., Das, J., Sahni, N., Yi, S.S., Kuijjer, M.L.
2023
Research article. Mapping oto-pharyngeal development in a human inner ear
organoid model
Development 2023
DOI: 10.1242/dev.201871
Authors: Steinhart, M. R., van der Valk, W. H., Osorio, D., Serdy, S. A., Zhang, J., Nist-Lund, C., Kim, J., Moncada-Reid, C., Sun, L., Lee, J., Koehler, K. R.
Research article. A single-cell level comparison of human inner ear
organoids with the human cochlea and vestibular organs
Cell Reports 2023
DOI: 10.1016/j.celrep.2023.112623
Authors: van der Valk, W.H., van Beelen, E.S.A., Steinhart, M.R., Nist-Lund, C., Osorio, D., de Groot, J.C.M.J., Sun, L., van Benthem, P.P.G., Koehler, K.R., Locher, H.
2022
First author. Corresponding author. Preprint. Drug combination prioritization for cancer treatment using single-cell
RNA-seq based transfer learning
bioRxiv (preprint) 2022
DOI: 10.1101/2022.04.06.487357
Authors: Osorio, D., McGrail, D.J., Sahni, N., Yi, S.S.
Research article. Ablation of long noncoding RNA MALAT1 activates
antioxidant pathway and alleviates sepsis in mice
Redox Biology 2022
DOI: 10.1016/j.redox.2022.102377
Authors: Chen, J., Tang, S., Ke, S., Cai, J.J., Osorio, D., Golovko, A., Morpurgo, B., Guo, S., Sun, Y., Winkle, M., Calin, G.A., Tian, Y.
Research article. Gag-like proteins: Novel mediators of prenatal alcohol
exposure in neural development
Alcoholism: Clinical and Experimental Research 2022
DOI: 10.1111/acer.14796
Authors: Pinson, M.R., Chung, D.D., Mahnke, A.H., Salem, N.A., Osorio, D., Nair, V., Payne, E.A., del Real, J.J., Cai, J.J. and Miranda, R.C
Research article. scInTime: A Computational Method Leveraging Single-Cell
Trajectory and Gene Regulatory Networks to Identify Master Regulators of Cellular Differentiation
Genes 2022
DOI: 10.3390/genes13020371
Authors: Xu, Q., Li, G., Osorio, D., Zhong, Y., Yang, Y., Lin, Y.-T., Zhang, X., and Cai, J.J.
First author. Research article. scTenifoldKnk: An efficient
virtual knockout tool for gene function predictions via single-cell gene regulatory network perturbation
Patterns 2022
DOI: 10.1016/j.patter.2022.100434
Authors: Osorio, D., Zhong, Y., Li, G., Xu, Q., Yongjian, Y., Tian, Y., Chapkin, R.S., Huang, J.Z. and Cai, J.J.
First author. Corresponding author. Review. Interpretable multi-modal data integration
Nature Computational Science 2022
DOI: 10.1038/s43588-021-00186-w
Authors: Osorio, D.
Research article. Hyaline cartilage differentiation of fibroblasts in
regeneration and regenerative medicine
Development 2022
DOI: 10.1242/dev.200249
Authors: Yu, L., Lin, Y.L., Yan, M., Li, T., Wu, E.Y., Zimmel, K., Qureshi, A.F., Sherman, K.M., Huggings, S.S., Osorio, D., Suva, L., Gaddy, D., Cai, J.J., Brunauer, R., Dawson, L.A., Muneoka, K.
Research article. Single-cell RNA sequencing reveals how the aryl
hydrocarbon receptor shapes cellular differentiation potency in the mouse colon
Cancer Prevention Research 2022
DOI: 10.1158/1940-6207.CAPR-21-0378
Authors: Yang, Y., Osorio, D., Davidson, L.A., Han, H., Mullens, D.A., Jayaraman, A., Safe, S., Ivanov, I., Cai, J.J. and Chapkin, R.S.
First author. Corresponding author. Research article.
rPanglaoDB: an R package to download and merge labeled single-cell RNA-seq data from the PanglaoDB
database
Bioinformatics 2022
DOI: 10.1093/bioinformatics/btab549
Authors: Osorio, D., Kuijjer, M.L. and Cai, J.J.
2021
Research article. Regulatory network of PD1 signaling is associated with
prognosis in glioblastoma multiforme
Cancer Research 2021
DOI: 10.1158/0008-5472.CAN-21-0730
Authors: Lopes-Ramos, C.M., Belova, T., Brunner, T.H., Ben Guebila, M., Osorio, D., Quackenbush, J., and Kuijjer, M.L.
First author. Corresponding author. Research article.
G2F as a Novel Tool to Find and Fill Gaps in Metabolic Networks
The R Journal 2021
DOI: 10.32614/RJ-2021-064
Authors: Osorio, D., Botero, K., Pinzón-Velasco, A., Mendoza-Mejía, N., Rojas-Rodríguez, F., and González, J.
First author. Corresponding author. Research article.
Systematic determination of the mitochondrial proportion in human and mice tissues for single-cell RNA
sequencing data quality control
Bioinformatics 2021
DOI: 10.1093/bioinformatics/btaa751
Authors: Osorio, D. and Cai, J.J.
Conference paper. Single-cell gene regulatory network analysis reveals
potential mechanisms of action of antimalarials against SARS-CoV-2
Lecture Notes in Computer Science 2021
DOI: 10.1007/978-3-030-79290-9_8
Authors: Cai, J.J. and Osorio, D.
2020
First author. Research article. scTenifoldNet: a machine
learning workflow for constructing and comparing transcriptome-wide gene regulatory networks from
single-cell data
Patterns 2020
DOI: 10.1016/j.patter.2020.100139
Authors: Osorio, D., Zhong, Y., Li, G., Huang, J.Z. and Cai, J.J.
Research article. Site-specific and substrate-specific control of accurate mRNA
editing by a helicase complex in trypanosomes
RNA 2020
DOI: 10.1261/rna.076513.120
Authors: Kumar, V., Ivens, A., Goodall, Z., Meehan, J., Doharey, P.K., Hillhouse, A., Osorio, D., Cai, J.J., Zhang, X., Schnaufer, A. and Cruz-Reyes, J.
Research article. Modelling of 3D-structures of the rare
Melanocortin-1-receptor mutations associated to melanism in the bananaquit
Acta Biológica Colombiana 2020
DOI: 10.15446/abc.v26n1.81432
Authors: Sedano-Cruz, R. and Osorio, D.
First author. Research article. Antecedent presentation of
neurological phenotypes in the Collaborative Cross reveals four classes with complex sex-dependencies
Scientific Reports 2020
DOI: 10.1038/s41598-020-64862-z
Authors: Eldridge, R., Osorio, D., Amstalden, K., Edwards, C., Young, C.R., Cai, J.J., Konganti, K., Hillhouse, A., Threadgill, D.W., Welsh, C.J. and Brinkmeyer-Langford, C.
First author. Research article. Overdispersed gene expression
in schizophrenia
npj Schizophrenia 2020
DOI: 10.1038/s41537-020-0097-5
Authors: Huang, G., Osorio, D., Guan, J., Ji, G. and Cai, J.J.
First author. Corresponding author. Research article.
Multiple pathways involved in palmitic acid-induced toxicity: A system biology approach
Frontiers in Neuroscience 2020
DOI: 10.3389/fnins.2019.01410
Authors: Osorio, D., Pinzón, A., Martín-Jiménez, C., Barreto, G.E. and González, J.
First author. Research article. Single-Cell Expression
Variability Implies Cell Function
Cells 2020
DOI: 10.3390/cells9010014
Authors: Osorio, D., Yu, X., Zhong, Y., Li, G., Serpedin, E., Huang, J.Z. and Cai, J.J.
2019
First author. Research article. Single-cell RNA sequencing of a
European and an African lymphoblastoid cell line
Scientific Data 2019
DOI: 10.1038/s41597-019-0116-4
Authors: Osorio, D., Yu, X., Yu, P., Serpedin, E. and Cai, J.J.
2017
First author. Review. L-type calcium channels
modulation by estradiol
Molecular Neurobiology 2017
DOI: 10.1007/s12035-016-0045-6
Authors: Vega-Vela, N.E., Osorio, D., Avila-Rodriguez, M., Gonzalez, J., García-Segura, L.M., Echeverria, V. and Barreto, G.E.
First author. Corresponding author. Research article.
minval: An R package for MINimal VALidation of Stoichiometric Reactions
The R Journal 2017
DOI: 10.32614/RJ-2017-031
Authors: Osorio, D., González, J. and Pinzón, A
Research article. Genome sequencing of three bacteria associated to black band
disease from a Colombian reef-building coral
Genomics Data 2017
DOI: 10.1016/j.gdata.2016.12.008
Authors: Henao, J., Pérez, H., Abril, D., Ospina, K., Piza A., Botero, K., Rincón, C., Donato, J., Hurtado, A., García E., Otero, V., del-Risco, A., Guerra, B., Cifuentes, Y., Ordoñez, A., Rojas, D., Suarez, K., Osorio, D. and Pinzón, A.
2015
First author. Corresponding author. Research article.
Peptides: a package for data mining of antimicrobial peptides
The R Journal 2015
DOI: 10.32614/RJ-2015-001
Authors: Osorio, D., Rondón-Villarreal, P. and Torres, R.
2014
First author. Conference paper. Stability Analysis of
Antimicrobial Peptides in Solvation Conditions by Molecular Dynamics
Advances in Intelligent Systems and Computing 2014
DOI: 10.1007/978-3-319-01568-2_19
Authors: Osorio, D., Rondón-Villarreal, P. and Torres, R.