Scholars@Duke

• Background
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  Education, Training, & Certifications

  • Ph.D., Princeton University 2013
• Recognition
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  Awards & Honors

  • Whitehead Scholars. Whitehead Charitable Foundation. January 13, 2020
• Expertise
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  Subject Headings

  • Computational Biology
  • Genetics--Statistical methods
  • Genome-Wide Association Study
  • Human population genetics
  • Kinship
  • Method of moments
  • Muser Mentor
  • Population genetics
  • Statistics, Nonparametric
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  Global Scholarship

  • Expertise

    • Mexico (Country) 
• Research
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  Selected Grants

  • REGULATORS OF CALCINEURIN PATHWAYS AS DIAGNOSTIC AND THERAPEUTIC TARGETS FOR NEPHROTIC SYNDROME awarded by National Institutes of Health 2023 - 2026
  • Genetic and Genomics Training Grant awarded by National Institutes of Health 2020 - 2025
  • Defining the Landscape of HLA Risk Alleles in Primary Nephrotic Syndrome and Post Kidney Transplant Recurrence awarded by National Institutes of Health 2020 - 2025
  • The Duke FUNCTION Center: Pioneering the comprehensive identification of combinatorial noncoding causes of disease awarded by National Institutes of Health 2020 - 2023
  • Bioinformatics and Computational Biology Training Program awarded by National Institutes of Health 2005 - 2021
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  External Relationships

  • NC State University
• Publications & Artistic Works
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  Selected Publications

  • Academic Articles

    • Lane, Brandon M., Megan Chryst-Stangl, Guanghong Wu, Mohamed Shalaby, Sherif El Desoky, Claire C. Middleton, Kinsie Huggins, et al. “Steroid-sensitive nephrotic syndrome candidate gene CLVS1 regulates podocyte oxidative stress and endocytosis.” Jci Insight 7, no. 2 (January 25, 2022). https://doi.org/10.1172/jci.insight.152102.
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    • Shaw, Brian I., Alejandro Ochoa, Cliburn Chan, Chloe Nobuhara, Rasheed Gbadegesin, Annette M. Jackson, and Eileen T. Chambers. “HLA Loci and Recurrence of Focal Segmental Glomerulosclerosis in Pediatric Kidney Transplantation.” Transplant Direct 7, no. 10 (October 2021): e748. https://doi.org/10.1097/TXD.0000000000001201.
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    • Kim, Young-Sook, Graham D. Johnson, Jungkyun Seo, Alejandro Barrera, Thomas N. Cowart, William H. Majoros, Alejandro Ochoa, Andrew S. Allen, and Timothy E. Reddy. “Correcting signal biases and detecting regulatory elements in STARR-seq data.” Genome Res 31, no. 5 (May 2021): 877–89. https://doi.org/10.1101/gr.269209.120.
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    • Ochoa, Alejandro, and John D. Storey. “Estimating FST and kinship for arbitrary population structures.” Plos Genet 17, no. 1 (January 2021): e1009241. https://doi.org/10.1371/journal.pgen.1009241.
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    • Ochoa, Alejandro, and John Storey. “New kinship andF_STestimates reveal higher levels of differentiation in the global human population,” 2019. https://doi.org/10.1101/653279.
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    • Yao, Yiqi, and Alejandro Ochoa. “Testing the effectiveness of principal components in adjusting for relatedness in genetic association studies,” 2019. https://doi.org/10.1101/858399.
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    • Ochoa, Alejandro, and Mona Singh. “Domain prediction with probabilistic directional context.” Bioinformatics 33, no. 16 (August 15, 2017): 2471–78. https://doi.org/10.1093/bioinformatics/btx221.
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    • Cobbold, Simon A., Joana M. Santos, Alejandro Ochoa, David H. Perlman, and Manuel Llinás. “Proteome-wide analysis reveals widespread lysine acetylation of major protein complexes in the malaria parasite.” Sci Rep 6 (January 27, 2016): 19722. https://doi.org/10.1038/srep19722.
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    • Ochoa, Alejandro, and John Storey. “F_STand kinship for arbitrary population structures I: Generalized definitions,” 2016. https://doi.org/10.1101/083915.
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    • Ochoa, Alejandro, and John Storey. “F_STand kinship for arbitrary population structures II: Method-of-moments estimators,” 2016. https://doi.org/10.1101/083923.
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    • Ochoa, Alejandro, and Mona Singh. “Domain prediction with probabilistic directional context,” 2016. https://doi.org/10.1101/094284.
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    • Ochoa, Alejandro, John D. Storey, Manuel Llinás, and Mona Singh. “Beyond the E-Value: Stratified Statistics for Protein Domain Prediction.” Plos Comput Biol 11, no. 11 (November 2015): e1004509. https://doi.org/10.1371/journal.pcbi.1004509.
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    • Szpara, Moriah L., Derek Gatherer, Alejandro Ochoa, Benjamin Greenbaum, Aidan Dolan, Rory J. Bowden, Lynn W. Enquist, Matthieu Legendre, and Andrew J. Davison. “Evolution and diversity in human herpes simplex virus genomes.” J Virol 88, no. 2 (January 2014): 1209–27. https://doi.org/10.1128/JVI.01987-13.
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    • Ochoa, Alejandro, Manuel Llinás, and Mona Singh. “Using context to improve protein domain identification.” Bmc Bioinformatics 12 (March 31, 2011): 90. https://doi.org/10.1186/1471-2105-12-90.
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    • Grigoryan, Gevorg, Alejandro Ochoa, and Amy E. Keating. “Computing van der Waals energies in the context of the rotamer approximation.” Proteins 68, no. 4 (September 1, 2007): 863–78. https://doi.org/10.1002/prot.21470.
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  • Conference Papers

    • Shaw, B. I., A. Ochoa, C. Chan, R. A. Gbadegesin, A. M. Jackson, and E. T. Chambers. “Hla Antigens and Recurrence of Focal Segmental Glomerulosclerosis in Pediatric Kidney Transplantation.” In American Journal of Transplantation, 21:321–22, 2021.
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    • Gottipati, Srikanth, Alejandro Ochoa, Bharath Ramaswamy, Merzu Belete, and John Storey. “T73GENOME-WIDE ASSOCIATION STUDY FOR PSYCHIATRIC RESPONSE TO ANTI-PSYCHOTIC TREATMENT.” In European Neuropsychopharmacology, 29:S254–S254. Elsevier BV, 2019. https://doi.org/10.1016/j.euroneuro.2019.08.272.
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  • Preprints

    • Hou, Zhuoran, and Alejandro Ochoa. “Genetic association models are robust to common population kinship estimation biases.” Cold Spring Harbor Laboratory, November 8, 2022. https://doi.org/10.1101/2022.11.07.515490.
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    • Yao, Yiqi, and Alejandro Ochoa. “Limitations of principal components in quantitative genetic association models for human studies.” BioRxiv, 2022. https://doi.org/10.1101/2022.03.25.485885.
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• Teaching & Mentoring
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  Recent Courses

  • UPGEN 778A: University Program in Genetics and Genomics Biological Solutions Module I 2022
  • UPGEN 778C: University Program in Genetics and Genomics Biological Solutions Module Ill 2021

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