CVRRICVLVM VITAE

Yes, I've been a nerd since I was little.

Concise PDF version

See my academic CV (PDF).

What follows below is a much more comprehensive version of my CV.

Contact information

Email me using the "envelope" link above.

Personal information

• Name. Note that the maternal family name is used only in Mexican documents, and not in American ones. Please see Spanish naming customs.
  • Given Name: Alejandro
  • Paternal Family Name: Ochoa
  • Maternal Family Name: García
• Date of Birth: 1984-06-09
• Place of Birth: El Paso, Texas, United States of America
• Raised in: Ciudad Juarez, Chihuahua, Mexico
• Citizenship: United States of America

Education

• 2006-09 to 2013-06. Doctor of Philosophy. Incidental Masters. Department of Molecular Biology, Princeton University, Princeton, NJ. Grade Point Average: 3.925/4.000. Doctoral dissertation: Protein domain prediction using context statistics, the false discovery rate, and comparative genomics, with application to Plasmodium falciparum
• 2002-09 to 2006-06. Bachelor of Science in Biology, and Bachelor of Science in Theoretical Mathematics. Massachusetts Institute of Technology, Cambridge, MA. Grade Point Average: 4.7/5.0. Humanities concentration in French
• 1999-09 to 2002-05. High school. Monterrey Institute of Technology and Higher Education, Ciudad Juarez, CHIH, Mexico. Grade Point Average: 93/100.

Awards

• 2020-01-13. Whitehead Scholar, Whitehead Charitable Foundation. For Duke junior faculty with exceptional potential for research and research training in the biomedical sciences.
• 2008-04-11. Ford Foundation Diversity Fellowship 2008 Predoctoral Competition. Administered by the National Research Council of the National Academies. Awarded, but I had to decline this fellowship in favor of the NSF fellowship below. My name therefore appears in the 2008 honorable mention list
• 2008-04-01. NSF Graduate Research Fellowship 2008. Provides three years of support for graduate study leading to research-based master’s or doctoral degrees and is intended for students who are in the early stages of their graduate study. Field of Study: Life Sciences - Computational Biology. Annual stipend rate is $30,000. Browse the NSF awardee list
• 2006-05-17. MIT Department of Biology Merck Prize 2005-2006. Awarded to a graduating senior for outstanding research and academic performance in biophysical or bioinformatics sciences. Diploma and $1,500 prize!
• 2001-12-01. Mexican Math Olympiad Gold Medal. Awarded to top 15 competitors at the national level. Diploma

Employment

• 2018-07-02 to present. Assistant professor. Duke Center for Statistical Genetics and Genomics, Department of Biostatistics and Bioinformatics, Duke University, Durham, NC. Ochoa Lab.
• 2013-07-01 to 2018-06-31 Postdoctoral research associate. Lewis-Sigler Institute for Integrative Genomics and Center for Statistics and Machine Learning, Princeton University, Princeton, NJ. Storey Lab.

Publications

• Alejandro Ochoa, John D Storey. New kinship and F_ST estimates reveal higher levels of differentiation in the global human population. bioRxiv 2019-05-30.
• Alejandro Ochoa, John D Storey. F_ST and kinship for arbitrary population structures I: Generalized definitions. bioRxiv 2016-10-27.
• 2023-10-06. Rachel Kate Cason, Eileen T Chambers, Tiffany Tu, Megan Chryst-Stangl, Kinsie Huggins, Brandon M Lane, Alejandro Ochoa, Annette M Jackson, Rasheed Gbadegesin. Genetic risk variants for childhood nephrotic syndrome and corticosteroid response. Frontiers in Pediatrics. 11:1248733. PubMed. PubMed Central. Article.
• 2023-05-04. Yiqi Yao, Alejandro Ochoa. Limitations of principal components in quantitative genetic association models for human studies. eLife. 79238. PubMed. PubMed Central. Article. bioRxiv 2022-03-27. bioRxiv 2019-11-29.
• 2023-02-27. Zhuoran Hou, Alejandro Ochoa. Genetic association models are robust to common population kinship estimation biases. Genetics. iyad030. PubMed. PubMed Central. Article. bioRxiv 2022-11-08.
• 2021-12-07. Brandon M Lane, Megan Chryst-Stangl, Guanghong Wu, Mohamed Shalaby, Sherif El Desoky, Claire Middleton, Kinsie Huggins, Amika Sood, Alejandro Ochoa, Andrew F Malone, Ricardo Vancini, Sara Miller, Gentzon Hall, So Young Kim, David Howell, Jameela A Kari, Rasheed Gbadegesin. CLVS1, a candidate gene for steroid sensitive nephrotic syndrome, regulates podocyte oxidative stress and endocytosis. JCI Insight. 7(2) e152102. PubMed. PubMed Central. Article.
• 2021-08-26. Brian I Shaw, Alejandro Ochoa, Cliburn Chan, Chloe Nobuhara, Rasheed Gbadegesin, Annette M Jackson, Eileen T Chambers. HLA Loci and Recurrence of Focal Segmental Glomerulosclerosis In Pediatric Kidney Transplantation. Transplant Direct. 7(10) e748. PubMed. PubMed Central. Article.
• 2021-05-01. Young-Sook Kim, Graham D Johnson, Jungkyun Seo, Alejandro Barrera, Thomas N. Cowart, William H Majoros, Alejandro Ochoa, Andrew S Allen, Timothy E Reddy. Correcting signal biases and detecting regulatory elements in STARR-seq data. Genome Res. 31(5) 877-889. PubMed. PubMed Central. Article. bioRxiv 2020-08-07.
• 2021-01-19. Alejandro Ochoa, John D Storey. Estimating F_ST and kinship for arbitrary population structures. PLoS Genet. 17(1) e1009241. PubMed. PubMed Central. Article. bioRxiv 2016-10-27.
• 2017-04-12. Alejandro Ochoa, Mona Singh. Domain prediction with probabilistic directional context. Bioinf. 33(16) 2471-8. PubMed. PubMed Central. Article. bioRxiv 2016-12-14.
• 2016-01-27. Simon A Cobbold, Joana M Santos, Alejandro Ochoa, David H Perlman, Manuel Llinás. Proteome-wide analysis reveals widespread lysine acetylation of major protein complexes in the malaria parasite. Sci Rep. 2016;6:19722. PubMed. PubMed Central. Article.
• 2015-11-17. Alejandro Ochoa, John D Storey, Manuel Llinás, Mona Singh. Beyond the E-value: stratified statistics for protein domain prediction. PLoS Comput Biol. 11 e1004509. PubMed. PubMed Central. Article. arXiv 2014-09-23.
• 2013-11-13. Moriah L Szpara, Derek Gatherer, Alejandro Ochoa, Benjamin Greenbaum, Aidan Dolan, Rory J Bowden, Lynn W Enquist, Matthieu Legendre, Andrew J Davison. Evolution and diversity in human herpes simplex virus genomes. J Virol. 88:1209-27. PubMed. PubMed Central. Article.
• 2011-03-31. Alejandro Ochoa, Manuel Llinás, Mona Singh. Using context to improve protein domain identification. BMC Bioinformatics. 12:90. PubMed. PubMed Central. Article.
• 2007-11-01. Gevorg Grigoryan, Alejandro Ochoa, Amy E Keating. Computing van der Waals energies in the context of the rotamer approximation. Proteins. 68(4) 863-78. PubMed. Article.

Distributed software

Major packages

• 2021-07-30 - 2024-01-25. simfam. Simulate and Model Family Pedigrees With Structured Founders. R, C++. CRAN. GitHub.
• 2019-03-15 - 2024-02-27. genio. Genetics Input/Output Functions. R, C++. CRAN. GitHub.
• 2019-02-13 - 2023-04-10. simtrait. Simulate Complex Traits from Genotypes. R. CRAN. GitHub.
• 2017-09-11 - 2023-01-06. popkin. Estimate Kinship and FST under Arbitrary Population Structure. R, C++. CRAN. GitHub.
• 2017-09-11 - 2023-07-21. bnpsd. Model and Simulate Admixed Populations. R. CRAN. GitHub.
• 2014-09-18 - 2020-07-15. dPUC2. Domain Prediction Using Context, Version 2. Perl, C. GitHub.
• 2014-06-23 - 2020-07-15. DomStratStats. Domain Stratified Statistics (q-values and local FDRs). Perl. GitHub.
• 2014-09-12 - 2019-09-12. RandProt. High-order Markov random models for protein sequences. Perl. GitHub.
• 2011-02-06 - 2011-02-06. dPUC. Domain Prediction Using Context. Perl, C. princeton.edu. viiia.org.

Minor packages

• 2021-08-27 - 2023-02-01. simgenphen. Simulate Genotypes and Phenotypes. R. GitHub.
• 2021-08-14 - 2023-05-11. genbin. R wrappers for binaries in genetics. R. GitHub.
• 2020-06-26 - 2023-01-04. ligera. LIght GEnetic Robust Association. R, C++. GitHub.
• 2019-05-22 - 2022-05-11. popkinsuppl. Supplement to "popkin" package. R. GitHub.

Paper repositories

• 2021-08-23 - 2023-02-19. bias-assoc-paper. Kinship bias association project. R, bash, LaTeX, markdown. GitHub.
• 2019-08-29 - 2023-04-24. pca-assoc-paper. PCA association project. R, bash, LaTeX, markdown. GitHub.
• 2019-09-04 - 2023-05-26. data. Instructions for real data processing shared across projects. R, bash, Perl, markdown. GitHub.
• 2019-04-25 - 2019-10-17. human-differentiation-manuscript. Human differentiation analysis. R, bash, markdown. GitHub.

Presentations/Talks

• 2024-04-28. Tiffany Tu, Alejandro Ochoa. The presence of cryptic relatedness creates inflation in meta-analyses of genome-wide association studies. The 12th RECOMB Satellite Workshop on Computational Methods in Genetics. Stata Center, Massachusetts Institute of Technology, Cambridge, MA. Presented by Tiffany Tu.
• 2024-04-22. Alejandro Ochoa. Models for diverse human genetic data. Princeton QCB seminar. Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ.
• 2023-11-18. Alejandro Ochoa. Genetic association and heritability estimation in structured populations. Duke Computational Biology and Bioinformatics (CBB) retreat. Holston Presbytery Camp and Retreat Center, Banner Elk, NC.
• 2023-10-11. Alejandro Ochoa. Outreach activities: Duke Genomic Scholars Program. NIH Centers for Excellence in Genomics Science (CEGS) Annual Meeting. Kimmel Center, New York University, New York, NY.
• 2023-10-09. Alejandro Ochoa. Genetic Association Studies and Population Structure in Nephrotic Syndrome. Duke Genomic Scholars Program. Medical Science Research Building III (MSRB3), Duke University, Durham, NC.
• 2023-06-16. Rasheed Gbadegesin, Annette M Jackson, Alejandro Ochoa, Cliburn Chan, Eileen T Chambers. Defining the Landscape of HLA Risk Alleles in Primary Nephrotic Syndrome and Post Kidney Transplant Recurrence. HLA and KIR region genomics in immune-mediated diseases consortium (virtual). National Institute of Allergy and Infectious Diseases (NIAID), National Institutes of Health (NIH), Bethesda, MD.
• 2023-06-21. Alejandro Ochoa. Admixture and genetic association models for complex populations with cryptic relatedness. HCHS/SOL (Hispanic Community Health Study / Study of Latinos) Genetics Special Interest Group (Virtual). Department of Biostatistics, Harvard University, Cambridge, MA.
• 2023-04-20. Alejandro Ochoa, Yuncheng Duan, Revathy Venukuttan, Shannon Clarke, Timothy E Reddy. Development of Genomic Resource Modules for a Diverse Workforce. NIH Centers for Excellence in Genomics Science (CEGS) Virtual Outreach Meeting. The Jackson Laboratory, Bar Harbor, ME.
• 2023-03-19. Alejandro Ochoa, Amika Sood. Inference of admixture model parameters from genetic covariance. American Mathematical Society (AMS) 2023 Spring Southeastern Sectional Meeting. Georgia Institute of Technology, Atlanta, GA.
• 2022-11-03. Rachel Kate Cason, Megan Chryst-Stangl, Kinsie Huggins, Brandon M Lane, Tiffany Tu, Alejandro Ochoa, Rasheed Gbadegesin. HLA Antigens And Recurrence Of Focal Segmental Glomerulosclerosis In Pediatric Kidney Transplantation. American Society of Nephrology Kidney Week. Orlando, FL. Presented by Rachel Kate Cason.
• 2022-08-26. Alejandro Ochoa. Genetic association models for related samples and population structure. BERD Core Seminar. Department of Biostatistics and Bioinformatics, Duke University, Durham, NC.
• 2022-07-08. Alejandro Ochoa. Statistical Genetics Research: Kinship, Bias, Admixture. Latinx in the Mathematical Sciences Conference 2022 (LatMath2022). Institute for Pure and Applied Mathematics, University of California, Los Angeles, Los Angeles, CA.
• 2022-06-11. Alejandro Ochoa. Statistical Genetics Research: Kinship, Bias, Admixture. Duke University Program in Genetics and Genomics (UPGG) retreat. Suite 4, Durham, NC.
• 2022-04-28. Rasheed Gbadegesin, Annette M Jackson, Alejandro Ochoa, Cliburn Chan, Eileen T Chambers. Defining the Landscape of HLA Risk Alleles in Primary Nephrotic Syndrome and Post Kidney Transplant Recurrence. HLA and KIR region genomics in immune-mediated diseases consortium (virtual). National Institute of Allergy and Infectious Diseases (NIAID), National Institutes of Health (NIH), Bethesda, MD.
• 2021-08-19. Alejandro Ochoa. Statistical Genetics Research: Kinship, Bias, Admixture. Orientation for MB and PhD students. Department of Biostatistics and Bioinformatics, Duke University, Durham, NC.
• 2021-06-05. Brian I Shaw, Alejandro Ochoa, Cliburn Chan, Rasheed Gbadegesin, Annette M Jackson, Eileen T Chambers. HLA Antigens And Recurrence Of Focal Segmental Glomerulosclerosis In Pediatric Kidney Transplantation.. American Transplant Congress. Virtual. Presented by Brian I Shaw.
• 2021-04-06. Rasheed Gbadegesin, Annette M Jackson, Alejandro Ochoa, Cliburn Chan, Eileen T Chambers. Defining the Landscape of HLA Risk Alleles in Primary Nephrotic Syndrome and Post Kidney Transplant Recurrence. HLA and KIR region genomics in immune-mediated diseases consortium (virtual). National Institute of Allergy and Infectious Diseases (NIAID), National Institutes of Health (NIH), Bethesda, MD.
• 2021-03-10. Alejandro Ochoa. Statistical models and methods for human genetic data. Statistics seminar. Department of Mathematics and Statistics, Washington State University, Pullman, WA.
• 2021-02-19. Alejandro Ochoa. Master's Student Research in the Ochoa Lab. Master of Biostatistics Virtual Visit Day. Department of Biostatistics and Bioinformatics, Duke University, Durham, NC.
• 2020-10-27. Amika Sood, Alejandro Ochoa. Estimating ancestry from a population kinship matrix under arbitrary ancestral subpopulation structure. American Society of Human Genetics (ASHG) Annual Meeting. Virtual. Presented by Amika Sood.
• 2020-02-18. Alejandro Ochoa. Population Kinship and Differentiation in Human Studies. University Program in Genetics and Genomics (UPGG) seminar. Room 147, Nanaline Duke building, Duke University, Durham, NC.
• 2019-09-28. Alejandro Ochoa. Modeling Relatedness in Genetic Association Studies. Duke Computational Biology and Bioinformatics (CBB) retreat. Holiday Inn Resort, Wrightsville Beach, NC.
• 2019-08-21. Alejandro Ochoa, John D Storey. Genetic Analyses under General Relatedness. Computational Biology and Bioinformatics (CBB) orientation. The Fitzpatrick Center for Interdisciplinary Engineering, Medicine and Applied Sciences (FCIEMAS), Duke University, Durham, NC.
• 2019-02-04. Alejandro Ochoa, John D Storey. Relatedness and differentiation in arbitrary population structures. Computational Biology and Bioinformatics (CBB) seminar. French Family Science Center, Duke University, Durham, NC.
• 2019-01-11. Alejandro Ochoa, John D Storey. Relatedness and differentiation in arbitrary population structures (lightning talk). 4th Mexico Population Genomics Meeting. Amoxcalli Complex, Faculty of Sciences, University City, National Autonomous University of Mexico, Mexico City, DF, Mexico.
• 2018-09-27. Alejandro Ochoa, John D Storey. Relatedness and differentiation in arbitrary population structures. Population Biology seminar, Department of Biology, Duke University, Durham, NC.
• 2018-02-21. Alejandro Ochoa, John D Storey. Relatedness and differentiation in arbitrary population structures. Department of Biostatistics and Bioinformatics, Duke University, Durham, NC.
• 2018-01-22. Alejandro Ochoa, John D Storey. Relatedness and differentiation in arbitrary population structures. Department of Biostatistics, Johns Hopkins University, Baltimore, MD.
• 2017-11-10. Alejandro Ochoa, John D Storey. Relatedness and differentiation in arbitrary population structures. Department of Biology, University of Richmond, Richmond, VA.
• 2017-11-03. Alejandro Ochoa, John D Storey. Relatedness and differentiation in arbitrary population structures. Genomics Retreat. Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ.
• 2017-06-14. Alejandro Ochoa, John D Storey. Measuring relatedness in human populations from DNA. Summer Undergraduate Research Program. Princeton University, Princeton, NJ.
• 2017-05-11. Alejandro Ochoa, John D Storey. Measuring relatedness in human populations from DNA. Princeton Research Day. Princeton University, Princeton, NJ.
• 2017-02-13. Alejandro Ochoa, John D Storey. F_ST and kinship for arbitrary population structures. Department of Genetics, University of North Carolina, Chapel Hill, NC.
• 2016-06-09. Alejandro Ochoa, John D Storey. F_ST generalized for arbitrary population structures. Summer Undergraduate Research Program. Princeton University, Princeton, NJ.
• 2016-05-06. Andrew J Bass, Alejandro Ochoa, Emily Nelson, John D Storey. Storey Lab lightning talk. Genomics Retreat. Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ.
• 2016-03-02. Alejandro Ochoa, John D Storey. F_ST generalized for arbitrary population structures. ICAhN Think and Drink. Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ.
• 2016-01-21. Alejandro Ochoa, John D Storey. F_ST generalized for arbitrary population structures. New York Area Population Genomics Workshop 2016. Princeton University, Princeton, NJ.
• 2015-10-15. Alejandro Ochoa, John D Storey, Manuel Llinás, Mona Singh. Beyond the E-value: stratified statistics for protein domain prediction. Probabilistic Modeling in Genomics (ProbGen) conference. Cold Spring Harbor Laboratory, Cold Spring Harbor, NY.
• 2013-06-27. Alejandro Ochoa. Protein domain prediction using context statistics, the false discovery rate, and comparative genomics, with application to Plasmodium falciparum. PhD defense. Department of Molecular Biology, Princeton University, Princeton, NJ.
• 2013-04-17. Alejandro Ochoa, John D Storey, Manuel Llinás, Mona Singh. Forget the E-value: family-based q-values for protein domain prediction, and empirical error detection. Telepresentation for Yun Song's group. UC Berkeley, Berkeley, CA.
• 2013-03-25. Alejandro Ochoa, John D Storey, Manuel Llinás, Mona Singh. Forget the E-value: q-values for domains (poster blitz). Biological sequence analysis and probabilistic models (ProbGen) conference. HHMI Janelia Farm, Ashburn, VA.
• 2013-02-25. Alejandro Ochoa, John D Storey, Manuel Llinás, Mona Singh. Forget the E-value: family-based q-values for protein domain prediction, and empirical error detection. National Center for Biotechnology Information (NCBI), National Institutes of Health (NIH), Bethesda, MD.
• 2012-03-01. Alejandro Ochoa, Manuel Llinás, Mona Singh. Domain Prediction Using Context in Plasmodium falciparum. Recruiting conference. Department of Computer Science, Princeton University, Princeton, NJ.
• 2010-10-09. Alejandro Ochoa, Manuel Llinás, Mona Singh. Improving domain prediction in Plasmodium falciparum. Retreat. Department of Molecular Biology, Princeton University, Princeton, NJ.
• 2010-03-04. Alejandro Ochoa, Manuel Llinás, Mona Singh. Domain Prediction Using Context (dPUC): a framework for enhancing protein domain predictions across diverse organisms. Graduate Colloquium. Department of Molecular Biology, Princeton University, Princeton, NJ.
• 2009-02-05. Alejandro Ochoa, Manuel Llinás, Mona Singh. Using domain context for protein domain prediction in Plasmodium falciparum. Graduate Colloquium. Department of Molecular Biology, Princeton University, Princeton, NJ.
• 2007-10-25. Alejandro Ochoa, Mona Singh. Distant homology, networks, and Plasmodium falciparum. Graduate Colloquium. Department of Molecular Biology, Princeton University, Princeton, NJ.
• 2004-08-26. Alejandro Ochoa. La Biología Molecular. Rotary Club Paso del Norte, Ciudad Juarez, CHIH, Mexico. Recognition.

Posters

• 2024-04-28. Tiffany Tu, Alejandro Ochoa. The presence of cryptic relatedness creates inflation in meta-analyses of genome-wide association studies. The 12th RECOMB Satellite Workshop on Computational Methods in Genetics, and 28th Annual International Conference on Research in Computational Molecular Biology (RECOMB). Stata Center, Massachusetts Institute of Technology, Cambridge, MA. Presented by Tiffany Tu.
• 2023-11-04. Tiffany Tu, Rasheed Gbadegesin, Adebowale Adeyemo, Alejandro Ochoa. A test of genotyping platform bias for multiethnic case/control association studies merging external controls. American Society of Human Genetics (ASHG) Annual Meeting. Walter E. Washington Convention Center, DC. Presented by Tiffany Tu.
• 2023-11-03. Ratchanon Pornmongkolsuk, Alejandro Ochoa. Single-locus imputation of ancient African DNA using novel regression-based approach. American Society of Human Genetics (ASHG) Annual Meeting. Walter E. Washington Convention Center, DC. Presented by Ratchanon Pornmongkolsuk.
• 2023-10-11. Shannon Clarke, Makenzie Beaman, Yuncheng Duan, Apoorva Iyengar, Revathy Venukuttan, Eden Harris, Allison Ashley-Koch, Rasheed Gbadegesin, Opeyemi Olabisi, William H Majoros, Timothy E Reddy, Alejandro Ochoa. Duke Genomic Scholars Program: Providing Accessible Genomic Training for a Diverse Workforce. NIH Centers for Excellence in Genomics Science (CEGS) Annual Meeting. Kimmel Center, New York University, New York, NY. Presented by Shannon Clarke.
• 2022-10-27. Zhuoran Hou, Alejandro Ochoa. Genetic association models are robust to common population kinship estimation biases. American Society of Human Genetics (ASHG) Annual Meeting. Convention Center, Downtown, Los Angeles, CA. Presented by Zhuoran Hou.
• 2022-10-19. Alejandro Ochoa, Yuncheng Duan, Revathy Venukuttan, Shannon Clarke, Timothy E Reddy. Development of Genomic Resource Modules for a Diverse Workforce. NIH Centers for Excellence in Genomics Science (CEGS) Annual Meeting. The Mary Duke Biddle Trent Semans Center for Health Education, Duke University, Durham, NC.
• 2021-04-14. Alejandro Ochoa, Amika Sood. Joint inference of admixture and population history from the genetic covariance structure. Probabilistic Modeling in Genomics (ProbGen) conference. Virtual.
• 2020-10-27. Alejandro Ochoa, John D Storey. New kinship and F_ST estimates applied to the global human population. American Society of Human Genetics (ASHG) Annual Meeting. Virtual.
• 2019-01-11. Alejandro Ochoa, John D Storey. Relatedness and Differentiation in Arbitrary Population Structures. 4th Mexico Population Genomics Meeting. Amoxcalli Complex, Faculty of Sciences, University City, National Autonomous University of Mexico, Mexico City, DF, Mexico.
• 2018-11-05. Alejandro Ochoa, John D Storey. Relatedness and Differentiation in Arbitrary Population Structures. Probabilistic Modeling in Genomics (ProbGen) conference. Cold Spring Harbor Laboratory, Cold Spring Harbor, NY.
• 2018-05-15. Alejandro Ochoa, John D Storey. Relatedness and Differentiation in Arbitrary Population Structures. Population, Evolutionary and Quantitative Genetics Conference. Madison Concourse Hotel, Madison, WI.
• 2016-11-03. Alejandro Ochoa, John D Storey, Srikanth Gottipati, Shashank Rohatagi, Andrew Forbes, Deborah Profit, Raymond Sanchez, Margaretta Nyilas, William Carson. Mixed Effects Modeling of Placebo Response Across 8 Placebo-controlled Aripiprazole Trials Spanning 20 Years in Acutely Relapsed Schizophrenia Patients. Neuroscience Education Institute Psychopharmacology Congress. Broadmoor Convention Center, Colorado Springs, CO.
• 2016-11-03. Srikanth Gottipati, Alejandro Ochoa, Shashank Rohatagi, Andrew Forbes, Deborah Profit, Raymond Sanchez, Margaretta Nyilas, William Carson. Canonical Loadings of PANSS Subscales Show Differential Placebo and Aripiprazole Drug Responses in Schizophrenia Patients. Neuroscience Education Institute Psychopharmacology Congress. Broadmoor Convention Center, Colorado Springs, CO. Presented by Srikanth Gottipati.
• 2015-09-18. Alejandro Ochoa, John D Storey. F_ST generalized for arbitrary population structures. John W. Tukey 100th Birthday Celebration conference. Center for Statistics and Machine Learning, Princeton University, Princeton, NJ.
• 2013-03-25. Alejandro Ochoa, John D Storey, Manuel Llinás, Mona Singh. Forget the E-value: family-based q-values for protein domain prediction, and empirical error detection. Biological sequence analysis and probabilistic models (ProbGen) conference. HHMI Janelia Farm, Ashburn, VA.
• 2010-11-09. Alejandro Ochoa, Manuel Llinás, Mona Singh. Using context to predict protein domains across diverse organisms. Research in Computational Molecular Biology (RECOMB) 3rd Joint Conference on Systems Biology, Regulatory Genomics, and DREAM Challenges. Columbia University, New York, NY.
• 2010-04-17. Alejandro Ochoa, Manuel Llinás, Mona Singh. Using context to predict protein domains across diverse organisms. Center for Quantitative Biology Symposium. Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ.
• 2008-01-19. Alejandro Ochoa, Mona Singh. Sequence and systems approaches to uncovering protein function in Plasmodium falciparum. Center for Quantitative Biology Symposium. Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ.
• 2007-09-10. Alejandro Ochoa, Mona Singh. Using domain information and functional networks to predict protein interactions. Princeton University Molecular Biology Annual Retreat. Fernwood Hotel and Resort, Bushkill, PA.

Research experience

• 2013-07 to 2018-06. Postdoctoral Research. Princeton University. Storey Lab. Developed new definitions and tools to study arbitrary population structures. Also applied mathematical modeling to drug trial timeseries.
• 2007-05 to 2013-06. Graduate Research Thesis. Princeton University. Singh Lab and Llinás Lab. Programmed in Perl and C, to improve sequence-based domain predictions in general, but with extensive analysis on the Plasmodium falciparum proteome. Also used experimental biology (cloning, protein purification and protein-binding microarray analysis) to determine if novel AP2 domains bind DNA.
• 2007-03 to 2007-05. Graduate Rotation. Princeton University. Tavazoie Lab. Experimental biology, cloned an RNA aptamer for use in a phage display assay.
• 2006-12 to 2007-02. Graduate Rotation. Princeton University. Singh Lab. Analyzed protein interactions predicted from the presence of interacting domain pairs.
• 2006-09 to 2006-11. Graduate Rotation. Princeton University. Troyanskaya Lab. Built and analyzed a potential "gold standard" of Gene Ontology terms integrated from predictions of multiple sources, in Saccharomyces cerevisiae and Homo sapiens.
• 2005-01 to 2006-08. Undergraduate Research Assistant. MIT. Keating Lab. Tested and analyzed computational protein designs using modified van der Waals potentials using full-atom physical potentials.

Mentoring

Current trainees, primary adviser

• 2020-now. Tiffany Tu. PhD. Graduate rotation, Dissertation adviser. Ochoa Laboratory. Computational Biology and Bioinformatics Program, Duke University.
• 2022-now. Ratchanon "RP" Pornmongkolsuk. PhD. Graduate rotation, Dissertation adviser. Ochoa Laboratory. University Program in Genetics and Genomics, Duke University.
• 2022-now. Zhuoran Hou. PhD. Graduate rotation, Dissertation adviser. Ochoa Laboratory. Department of Biostatistics and Bioinformatics, Duke University.

Current trainees, secondary adviser

• 2021-now. Cymfenee Dean-Phifer. PhD. Graduate rotation, Dissertation committee. Goldberg Laboratory. Computational Biology and Bioinformatics Program, Duke University.
• 2022-now. Changxin Wan. PhD. Dissertation committee. Ji Laboratory. Computational Biology and Bioinformatics Program, Duke University.
• 2023-now. Bide "Peter" Chen. PhD. Dissertation committee. Goldberg Laboratory. University Program in Genetics and Genomics, Duke University.
• 2023-now. Gabriel Kennedy. PhD. Dissertation committee. Goldberg Laboratory. University Program in Genetics and Genomics, Duke University.
• 2023-now. Anvita Kulshrestha. PhD. Dissertation committee. Ashley-Koch Laboratory. University Program in Genetics and Genomics, Duke University.
• 2024-now. Jennifer Drucker Varner. Fellow. Scholarship Oversight Committee. Gbadegesin Laboratory. Department of Pediatrics, Duke University.

Past trainees, primary adviser

• 2019-2020. Yiqi Yao. Master's. BCTIP internship, Master's project adviser. Ochoa Laboratory. Department of Biostatistics and Bioinformatics, Duke University. Now Senior Business Analyst at BenHealth.
• 2019-2022. Amika Sood. Postdoctoral. Postdoctoral adviser. Ochoa Laboratory. Department of Biostatistics and Bioinformatics, Duke University. Now Staff Scientist at Complex Carbohydrate Research Center (CCRC), The University of Georgia.
• 2020-2021. Zhuoran Hou. Master's. BCTIP internship. Ochoa Laboratory. Department of Biostatistics and Bioinformatics, Duke University. Now PhD Student at Duke University, BB.
• 2020-2022. Jiajie Shen. Master's. Research, Master's project adviser. Ochoa Laboratory. Department of Biostatistics and Bioinformatics, Duke University.
• 2021-2022. Emmanuel Mokel. Undergraduate. Research Independent Study. Ochoa Laboratory. Department of Statistical Science, Duke University.
• 2023-2023. Danielle Mensah. Undergraduate. Research Independent Study. Ochoa Laboratory. Department of Computer Science, Duke University.

Past trainees, secondary adviser

• 2009. Neo Christopher Chung. PhD. Graduate rotation. Llinás Laboratory. Quantitative Computational Biology Program, Princeton University. Now Adjunct Faculty at University of Warsaw.
• 2010. Jeremy Bigness. PhD. Graduate rotation. Singh Laboratory. Quantitative Computational Biology Program, Princeton University. Now PhD Student at Brown University.
• 2011. Sebastian Nasamu. Undergraduate. Summer project. Llinás Laboratory. Department of Molecular Biology, Princeton University. Now Post-doctoral Research Fellow at Johns Hopkins Bloomberg School of Public Health.
• 2019. Yuncheng Duan. PhD. Graduate rotation. Ochoa Laboratory. Department of Biology, Duke University. Now PhD Student at Duke University, Allen Lab.
• 2019-2020. Shengyu Li. Master's. Master's project committee. Allen Laboratory. Department of Biostatistics and Bioinformatics, Duke University. Now PhD Student at Duke University, CBB.
• 2019-2024. Xue "Scarlett" Zou. PhD. Dissertation committee. Allen Laboratory. Computational Biology and Bioinformatics Program, Duke University.
• 2020-2022. Iman Hamid. PhD. Dissertation committee. Goldberg Laboratory. University Program in Genetics and Genomics, Duke University. Now Scientist at Variant Bio.
• 2020-2021. Bobby Boone IV. Master's. Master's project committee. Landstrom Laboratory. Department of Biostatistics and Bioinformatics, Duke University. Now Biostatistician II at University of Utah Health.
• 2020-2023. Brandon M. Lê. PhD. Dissertation committee. Ashley-Koch Laboratory. University Program in Genetics and Genomics, Duke University.
• 2020-2023. Rachel Cason. Resident physician. Scholarship Oversight Committee, Master's project committee. Gbadegesin Laboratory. Department of Pediatrics, Duke University.
• 2021-2022. Valerie Gartner. PhD. Dissertation committee. Wray Laboratory. University Program in Genetics and Genomics, Duke University.
• 2021-2022. Hongyu Du. Master's. Master's project committee. Allen Laboratory. Department of Biostatistics and Bioinformatics, Duke University.
• 2021-2022. Krista Pipho. PhD. Dissertation committee. Goldberg Laboratory. University Program in Genetics and Genomics, Duke University.
• 2021-2022. Weiliang "Frank" Tian. Master's. Master's project committee. Soderling Laboratory. Department of Biostatistics and Bioinformatics, Duke University.
• 2023-2023. Grace E. Rhodes. PhD. Graduate rotation. Ochoa Laboratory. Department of Biostatistics and Bioinformatics, Duke University.
• 2023-2024. Jinting Justin Liu. Master's. Master's project committee. Majoros Laboratory. Department of Biostatistics and Bioinformatics, Duke University.

Teaching experience

• 2017-09-13 to 2018-01-16. Co-Lecturer to Introduction to Genomics and Computational Molecular Biology (QCB/MOL/COS 455). Lecturers Mona Singh, Michael S. Levine, Alejandro Ochoa, and Joshua Akey. Princeton University. Quantitative and Computational Biology, Molecular Biology, and Computer Science.
• 2017-06-14 to 2017-08-11. Discussion leader. Summer undergraduate research program. Princeton University
• 2016-09-09. Statistical treatment of data workshop. For first year graduate students in Molecular Biology (MOL) and Quantitative and Computational Biology (QCB). Princeton University
• 2016-06-09 to 2016-08-04. Discussion leader. Summer undergraduate research program. Princeton University
• 2015-09-15. Statistical treatment of data workshop. For first year graduate students in Molecular Biology (MOL) and Quantitative and Computational Biology (QCB). Princeton University
• 2014-09-11. Statistical treatment of data workshop. For first year graduate students in Molecular Biology (MOL) and Quantitative and Computational Biology (QCB). Princeton University
• 2011-09-15 to 2012-01-15. Assistant Instructor to Introduction to Genomics and Computational Molecular Biology (COS/MOL 455/551). Professors Mona Singh and Coleen Murphy. Princeton University. Molecular Biology and Computer Science.
• 2008-02-04 to 2008-05-22. Assistant Instructor to Core Laboratory (MOL 350). Professors Alison Gammie and Robyn Tanny. Princeton University. Molecular Biology.
• 2008-01-31 to 2008-02-01. Assistant Instructor Orientation to Teaching. An orientation to improve undergraduate instruction. Princeton University. McGraw Center for Teaching and Learning, and the Graduate School. Certificate of attendance
• 2005-06 to 2005-08. Calculus Teaching Assistant. MIT. OME Project Interphase
• 2004-06 to 2004-08. Calculus Teaching Assistant. MIT. MITE²S Program
• 2003-09 to 2004-06. Multivariable Calculus and Differential Equations Tutor. MIT. OME Seminar XL
• 2003-06 to 2003-08. Calculus Teaching Assistant. MIT. MITE²S Program
• 2002-06. Combinatorics Lessons. ITESM. Mexican Math Olympiad in Chihuahua
• 2002-01 to 2002-06. High School Algebra, Trigonometry, and Calculus tutoring. ITESM. Work-Study

Outreach

• 2017-06-09. Panelist at HISPA Latinos in College Conference. Princeton University. Program
• 2011-03-17. Science and Engineering Expo. HHMI and Princeton University. Certificate of appreciation
• 2010-09-19 to 2010-09-22. Ivy-plus recruiting fair at University of Puerto Rico campuses. Dean Redman invited Luis Othoniel and I to recruit Puerto Rican students to Princeton, in an event organized in conjunction with other universities. We covered the Río Piedras, Humacao, Cayey, and Mayagüez campuses.
• 2010-03-18. Science and Engineering Expo. HHMI and Princeton University. Certificate of appreciation
• 2009-03-19. Science and Engineering Expo. HHMI and Princeton University. Certificate of appreciation. I also appeared in a news article!
• 2008-03-19. Science and Engineering Expo. HHMI and Princeton University. Certificate of appreciation
• 2007-11-09. Helping Local High School Students with College Personal Statements. Princeton University. PUPP

Competitions

• 2003-12. Putnam Examination. National college-level mathematics. MIT. Cambridge, Massachusetts, United States of America
• 2002-12. Putnam Examination. National college-level mathematics. MIT. Cambridge, Massachusetts, United States of America
• 2002-05. Entrepeneurship fair. ITESM. Ciudad Juarez, Chihuahua, Mexico
• 2001-11. National Examination for the Mexican Math Olympiad. OMM. Oaxtepec, Morelos, Mexico. See awards above.
• 2001-07. State Examination for the Mexican Math Olympiad in Chihuahua. UACJ. Ciudad Juarez, Chihuahua, Mexico
• 2000-11. CreaTec (creativity fair). ITESM. Ciudad Juarez, Chihuahua, Mexico
• 2000-07-05. State Examination for the Mexican Math Olympiad in Chihuahua. UACH. Chihuahua, Chihuahua, Mexico. Diploma
• 2000-06-10. Regional Examination for the Mexican Math Olympiad in Chihuahua. UACJ. Ciudad Juarez, Chihuahua, Mexico. Recognition
• 1999-05. Applied Math Examination. Chihuahua State Government. Ciudad Juarez, Chihuahua, Mexico. Recognition

Special programs

• 2002-06 to 2002-08. Project Interphase. For admitted freshmen in their transition to MIT, who especially benefit from academic enrichment and support. MIT OME. Cambridge, Massachusetts, United States of America. Diploma
• 2002-06. Proyecto Abel. For distinguished high school seniors in Mathematics. UACJ. Ciudad Juarez, Chihuahua, Mexico. Diploma
• 2001-12 to 2002-03. National trainings for the Mexican Math Olympiad. OMM, CIMAT. Guanajuato, Guanajuato, Mexico
• 2001-08 to 2001-10. State trainings for the Mexican Math Olympiad in Chihuahua. UACJ. Ciudad Juarez, Chihuahua, Mexico

Skills

• Operating systems: Windows, Linux (Fedora/Red Hat)
• Programming and scripting: R, Perl, Bash, Java, C, Javascript
• Markup languages: LaTeX (incl. TikZ, Beamer), HTML, CSS, XML, YAML, R Markdown
• Version control systems: Git/GitHub, SVN
• Office suites: Microsoft Office (Word, Excel, PowerPoint), OpenOffice/LibreOffice
• Educational tools: Blackboard, Piazza
• Human languages:
  • Spanish (native, oral and written proficiency)
  • English (second language, oral and written proficiency)
  • French (conversational, proficient reading)
  • Partial understanding of Portuguese and Italian.
  • Learning Nahuatl, Latin
  • Interested in Maya, German, Hindi, and Persian.

Professional accounts online

• Linked-in (social network)
• GitHub (my public code)
• Google Scholar (publications and citations)
• Scopus (publications and citations)
• ORCID (research profile)
• Publons (peer review record)

Memberships

• 2011-09 to 2012-09. American Association for the Advancement of Science (AAAS). Accepted through the AAAS/Science Program for Excellence in Science.
• 2006-09 to 2010-09. Latino Graduate Student Association (LGSA). Board member, in the position of Technology Specialist 2007-2010 (in charge of website, email list, photos, calendar). Regular member first year. Princeton University.
• 2002-09 to 2006-05. Association of Puerto Rican students (APR). Regular member. MIT.

Interests

• Music: performance (guitar, bass, piano, voice), composition, listening
• Sports: ski, cycling, soccer
• Visual arts: photography, cinema, drawing
• Languages: see skills above
• Travel

Explanation of institutional acronyms

• CIMAT: Centro de Investigación en Matemáticas
• ITESM: Instituto Tecnológico y de Estudios Superiores de Monterrey, campus Ciudad Juárez
• MIT: Massachusetts Institute of Technology
• MITE²S: Minority Introduction to Engineering, Entrepreneurship, and Science (MIT)
• NSF: National Science Foundation
• OME: Office of Minority Education (MIT)
• OMM: Olimpiada Mexicana de Matemáticas
• PUPP: Princeton University Preparatory Program
• UACH: Universidad Autónoma de Chihuahua
• UACJ: Universidad Autónoma de Ciudad Juárez