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Daniel Osorio, Ph.D.
Senior Scientific Consultant
Single-Cell Transcriptomics
Gene Expression Regulation
Data mining
Metabolic Modeling
Bioactive Peptides
About me
I'm a Colombian computational biologist and Senior Scientific Consultant at QIAGEN Digital Insights. I earned my PhD in Biomedical Sciences, specializing in Biomedical Genomics and Bioinformatics, from Texas A&M University. My postdoctoral training took me to the Norwegian Centre for Molecular Medicine (NCMM) at the University of Oslo and the Livestrong Cancer Institutes at UT Austin, where I focused on network analysis and cancer genomics. My research explores a diverse range of topics, from developing software for high-throughput single-cell RNA-seq data analysis to studying gene regulatory networks, data mining, metabolic modeling, and bioactive peptides.
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
Experience
Research Computing Data Scientist III
Research Computing Group at Boston Childrens
Hospital 2022-2023
Harvard Medical School, Boston, MA, USA.
Postdoctoral Fellow
Song (Stephen) Yi's Lab of Bioinformatics and
Developmental Therapeutics 2021-2022
Livestrong Cancer Institutes, University of Texas at Austin, Austin, TX, USA.
Marie Skłodowska-Curie Postdoctoral Scientia Fellow
Marieke Kuijjer's Lab of Computational Biology and
Systems Medicine2021-2021
Norwegian Center 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 Biochemistry2016-2016
Department of Biochemistry, Pontificia Universidad Javeriana, Bogotá, Colombia.
Adjunct Professor
Computer Programming (C++) 2015-2016
Department of Systems and Industrial Engineering, Universidad Nacional de Colombia, Bogotá, Colombia.
Undergraduate Student Assistant
Webpages and Databases Maintainer 2011-2013
Natural History Museum, School of Biology, Universidad Industrial de Santander, Bucaramanga, Colombia.
Awards, Grants and Fellowships
Familien Blix Fond Til Fremme Av Medisinsk Forskning
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 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.
Software Packages
A Python package to reconstruct comparable, fully-connected, weighted, and directed transcriptome-wide gene regulatory networks suitable for use in population-level studies.
An R package to reconstruct comparable, fully-connected, weighted, and directed transcriptome-wide gene regulatory networks suitable for use in population-level studies.
An R package to generate disease-specific response signatures from the LINCS-L1000 data.
An R package to download and merge labeled single-cell RNA-seq data from the PanglaoDB database.
An R package to perform in-silico knockout experiments using single-cell RNA sequencing data from wild-type control samples as input.
An R package to construct and compare single-cell gene regulatory networks using single-cell RNA-seq data from different conditions.
exp2flux
Code | 2016
An R package to convert gene expression values to the FBA boundaries for each reaction based in the boolean rules described in its associated GPR.
An R package to find the gaps in metabolic reconstruction and fill them from the reactions of a reference using a weighting function.
An R package to identify orphan metabolites and evaluate the mass and charge balance of stoichiometric reactions.
Publications
(3) Preprints | (29) Research Articles | (3) Review | (2) Conference Papers | (18) First Author | (10) Corresponding AuthorPan-cancer analysis of patient-specific gene
regulatory landscapes identifies
recurrent PD-1 pathway dysregulation linked to outcome
DOI:
10.1101/2025.10.03.680219 2025
Authors: Belova, T., Hsieh, P., Hovan, L., Osorio, D. , Kuijjer, M.L.
Digit regeneration in mice is stimulated by
sequential treatment with FGF2 and BMP2
DOI:
10.21203/rs.3.rs-6762312/v1 2025
Authors: Yu, L., Yan, M., Scaturro, K., Qureshi, O., Osorio, D. , Cai, J.J., Dawson, L., Brunauer, R., Suva, L., Dolan, C., Han, M., Lin, Y.L., Muneoka, K.
scTenifoldNet and scTenifoldKnk: a package suite for
single-cell gene regulatory network construction, comparison, and perturbation analysis
DOI:
10.1080/24754269.2025.2557719 2025
Authors: Zhong, Y., Osorio, D. , Li, G., Xu, Q., Yongjian, Y., Huang, J.Z. and Cai, J.J.
Renal Single-Cell RNA Sequencing and Digital Cytometry in
Dogs with X-Linked Hereditary Nephropathy
DOI:
10.3390/ani15142061 2025
Authors: Chu, C.P., Osorio, D. , Nabity, M.B.
Drug combination prediction for cancer treatment using disease-specific
drug response profiles and single-cell transcriptional signatures
DOI:
10.7554/eLife.102442 2025
Authors: Osorio, D. , Tekpli, X., Kristensen, V.N., Kuijjer, M.L.
Targeting IRE1α reprograms the tumor
microenvironment and enhances anti-tumor immunity in prostate cancer
DOI:
10.1038/s41467-024-53039-1 2024
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.
Lymphoid origin of intrinsically activated plasmacytoid
dendritic cells in mice
DOI:
10.7554/eLife.96394.3 2024
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.
Deciphering the impact of genomic variation on function
DOI:
10.1038/s41586-024-07510-0 2024
Authors: IGVF Consortium (Osorio, D. as member of the Yi Lab)
Population-level comparisons of gene regulatory networks modeled on
high-throughput single-cell transcriptomics data
DOI:
10.1038/s43588-024-00597-5 2024
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.
Mapping oto-pharyngeal development in a human inner ear
organoid model
DOI:
10.1242/dev.201871 2023
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.
A single-cell level comparison of human inner ear
organoids with the human cochlea and vestibular organs
DOI:
10.1016/j.celrep.2023.112623 2023
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.
Drug combination prioritization for cancer treatment using single-cell
RNA-seq based transfer learning
DOI:
10.1101/2022.04.06.487357 2022
Authors: Osorio, D. , McGrail, D.J., Sahni, N., Yi, S.S.
Ablation of long noncoding RNA MALAT1 activates
antioxidant pathway and alleviates sepsis in mice
DOI:
10.1016/j.redox.2022.102377 2022
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.
Gag-like proteins: Novel mediators of prenatal alcohol
exposure in neural development
DOI: 10.1111/acer.14796
2022
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
scInTime: A Computational Method Leveraging Single-Cell
Trajectory and Gene Regulatory Networks to Identify Master Regulators of Cellular Differentiation
DOI: 10.3390/genes13020371
2022
Authors: Xu, Q., Li, G., Osorio, D., Zhong, Y., Yang, Y., Lin, Y.-T., Zhang, X., and Cai, J.J.
scTenifoldKnk: An efficient
virtual knockout tool for gene function predictions via single-cell gene regulatory network perturbation
DOI:
10.1016/j.patter.2022.100434 2022
Authors: Osorio, D. , Zhong, Y., Li, G., Xu, Q., Yongjian, Y., Tian, Y., Chapkin, R.S., Huang, J.Z. and Cai, J.J.
Hyaline cartilage differentiation of fibroblasts in
regeneration and regenerative medicine
DOI: 10.1242/dev.200249
2022
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.
Single-cell RNA sequencing reveals how the aryl
hydrocarbon receptor shapes cellular differentiation potency in the mouse colon
DOI:
10.1158/1940-6207.CAPR-21-0378 2022
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.
rPanglaoDB: an R package to download and merge labeled single-cell RNA-seq data from the PanglaoDB
database
DOI: 10.1093/bioinformatics/btab549 2022
Authors: Osorio, D. , Kuijjer, M.L. and Cai, J.J.
Regulatory network of PD1 signaling is associated with
prognosis in glioblastoma multiforme
DOI:
10.1158/0008-5472.CAN-21-0730 2021
Authors: Lopes-Ramos, C.M., Belova, T., Brunner,T.H., Ben Guebila, M., Osorio, D. , Quackenbush, J., and Kuijjer, M.L.
G2F as a Novel Tool to Find and Fill Gaps in Metabolic Networks
DOI:
10.32614/RJ-2021-064 2021
Authors: Osorio, D. , Botero, K., Pinzón-Velasco, A., Mendoza-Mejía, N., Rojas-Rodríguez, F., and González J.
Systematic determination of the mitochondrial proportion in human and mice tissues for single-cell RNA
sequencing data quality control
DOI:
10.1093/bioinformatics/btaa751 2021
Authors: Osorio, D. and Cai, J.J.
Single-cell gene regulatory network analysis reveals
potential mechanisms of action of antimalarials against SARS-CoV-2
DOI:
10.1007/978-3-030-79290-9_8 2021
Authors: Cai, J.J. and Osorio, D.
scTenifoldNet: a machine
learning workflow for constructing and comparing transcriptome-wide gene regulatory networks from
single-cell data
DOI:
10.1016/j.patter.2020.100139 2020
Authors: Osorio, D. , Zhong, Y., Li, G., Huang, J.Z. and Cai, J.J.
Site-specific and mRNA-specific control of accurate mRNA
editing by a helicase complex in trypanosomes
DOI: 10.1261/rna.076513.120
2020
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.
Modelling of 3D-structures of the rare
Melanocortin-1-receptor mutations associated to melanism in the bananaquit
DOI:
10.15446/abc.v26n1.81432 2020
Authors: Sedano-Cruz, R. and Osorio, D.
Antecedent presentation of
neurological phenotypes in the Collaborative Cross reveals four classes with complex sex-dependencies
DOI:
10.1038/s41598-020-64862-z 2020
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.
Overdispersed gene expression
in schizophrenia
DOI:
10.1038/s41537-020-0097-5 2020
Authors: Huang, G., Osorio, D. , Guan, J., Ji, G. and Cai, J.J.
Multiple pathways involved in palmitic acid-induced toxicity: A system biology approach
DOI:
10.1038/10.3389/fnins.2019.01410 2020
Authors: Osorio, D. , Pinzón, A., Martín-Jiménez, C., Barreto, G.E. and González, J.
Single-Cell Expression
Variability Implies Cell Function
DOI: 10.3390/cells9010014
2020
Authors: Osorio, D. , Yu, X., Zhong, Y., Li, G., Serpedin, E., Huang, J.Z. and Cai, J.J.
Single-cell RNA sequencing of a
European and an African lymphoblastoid cell line
DOI:
10.1038/s41597-019-0116-4 2019
Authors: Osorio, D. , Yu, X., Yu, P., Serpedin, E. and Cai, J.J.
L-type calcium channels
modulation by estradiol
DOI:
10.1007/s12035-016-0045-6 2017
Authors: Vega-Vela, N.E., Osorio, D. , Avila-Rodriguez, M., Gonzalez, J., García-Segura, L.M., Echeverria, V. and Barreto, G.E.
minval: An R package for MINimal VALidation of Stoichiometric Reactions.
DOI: 10.32614/RJ-2017-031
2017
Authors: Osorio, D. , González, J. and Pinzón, A
Genome sequencing of three bacteria associated to black band
disease from a Colombian reef-building coral
DOI:
10.1016/j.gdata.2016.12.008 2017
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.
Peptides: a package for data mining of antimicrobial peptides.
DOI: 10.32614/RJ-2015-001
2015
Authors: Osorio, D. , Rondón-Villarreal, P. and Torres, R.
Stability Analysis of
Antimicrobial Peptides in Solvation Conditions by Molecular Dynamics.
DOI:
10.1007/978-3-319-01568-2_19 2014
Authors: Osorio, D. , Rondón-Villarreal, P. and Torres, R.