Publications

Polygenic Risk Scores and HLA Class II Variants are Biomarkers of Corticosteroid Response in Childhood Nephrotic Syndrome
Tiffany Tu, Alejandro Ochoa, Amika Sood, Ashley Drabik, Megan Chryst-Stangl, Brandon M Lane, Guanghong Wu, Frank Donovan, Ursula Harper, Settara Chandrasekharappa, Christopher Esezobor, Adaobi Solarin, David Hooper, Christine Sethna, Sandra Amaral, Mahmoud Kallash, Michelle Rheault, Priya Verghese, Vikas Dharnidharka, Eloise Salmon, Patricia Weng, Tarak Srivastava, Michael E. Seifert, Cozumel Pruette, David Selewski, Keisha Gibson, Tracy Hunley, Asiri Abeyagunawardena, Shenal Thalgahagoda, Arvind Bagga, Aditi Sinha, Nicholas Webb, Larry Greenbaum, Ali Gharavi, Krzysztof Kiryluk, Mathias Kretzler, Lisa Guay-Woodford, Simone Sanna-Cherchi, Agnieszka Bierzynska, Ania Koziell, Gavin Welsh, Moin Saleem, Charles Rotimi, Eileen T Chambers, Cliburn Chan, CureGN Consortium, PNRC Glomerular disease group, CIBMTR/NMDP Consortium, Annette M Jackson, Adebowale Adeyemo, Rasheed Gbadegesin
medRxiv doi:10.1101/2025.08.01.25332825. 2025-08-07

Kinship estimation bias carries over to heritability estimation bias using variance components
Zhuoran Hou, Alejandro Ochoa
bioRxiv doi:10.1101/2025.05.13.653659. 2025-05-15

Genetic association meta-analysis is susceptible to confounding by between-study cryptic relatedness
Tiffany Tu, Alejandro Ochoa
bioRxiv doi:10.1101/2025.05.10.653279. 2025-05-12

Genetic risk variants for childhood nephrotic syndrome and corticosteroid response
Rachel Kate Cason, Eileen T Chambers, Tiffany Tu, Megan Chryst-Stangl, Kinsie Huggins, Brandon M Lane, Alejandro Ochoa, Annette M Jackson, Rasheed Gbadegesin
Frontiers in Pediatrics 11:1248733. 2023-10-06

Limitations of principal components in quantitative genetic association models for human studies
Yiqi Yao, Alejandro Ochoa
eLife 79238. 2023-05-04

Genetic association models are robust to common population kinship estimation biases
Zhuoran Hou, Alejandro Ochoa
Genetics iyad030. 2023-02-27

CLVS1, a candidate gene for steroid sensitive nephrotic syndrome, regulates podocyte oxidative stress and endocytosis
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
JCI Insight 7(2) e152102. 2021-12-07

HLA Loci and Recurrence of Focal Segmental Glomerulosclerosis In Pediatric Kidney Transplantation
Brian I Shaw, Alejandro Ochoa, Cliburn Chan, Chloe Nobuhara, Rasheed Gbadegesin, Annette M Jackson, Eileen T Chambers
Transplant Direct 7(10) e748. 2021-08-26

Correcting signal biases and detecting regulatory elements in STARR-seq data
Young-Sook Kim, Graham D Johnson, Jungkyun Seo, Alejandro Barrera, Thomas N. Cowart, William H Majoros, Alejandro Ochoa, Andrew S Allen, Timothy E Reddy
Genome Res 31(5) 877-889. 2021-05-01

Estimating F_ST and kinship for arbitrary population structures
Alejandro Ochoa, John D Storey
PLoS Genet 17(1) e1009241. 2021-01-19

New kinship and F_ST estimates reveal higher levels of differentiation in the global human population
Alejandro Ochoa, John D Storey
bioRxiv doi:10.1101/653279. 2019-05-30

Domain prediction with probabilistic directional context
Alejandro Ochoa, Mona Singh
Bioinf 33(16) 2471-8. 2017-04-12

F_ST and kinship for arbitrary population structures I: Generalized definitions
Alejandro Ochoa, John D Storey
bioRxiv doi:10.1101/083915. 2016-10-27

Proteome-wide analysis reveals widespread lysine acetylation of major protein complexes in the malaria parasite
Simon A Cobbold, Joana M Santos, Alejandro Ochoa, David H Perlman, Manuel Llinás
Sci Rep 2016;6:19722. 2016-01-27

Beyond the E-value: stratified statistics for protein domain prediction
Alejandro Ochoa, John D Storey, Manuel Llinás, Mona Singh
PLoS Comput Biol 11 e1004509. 2015-11-17

Evolution and diversity in human herpes simplex virus genomes
Moriah L Szpara, Derek Gatherer, Alejandro Ochoa, Benjamin Greenbaum, Aidan Dolan, Rory J Bowden, Lynn W Enquist, Matthieu Legendre, Andrew J Davison
J Virol 88:1209-27. 2013-11-13

Using context to improve protein domain identification
Alejandro Ochoa, Manuel Llinás, Mona Singh
BMC Bioinformatics 12(1) 90. 2011-03-31

Computing van der Waals energies in the context of the rotamer approximation
Gevorg Grigoryan, Alejandro Ochoa, Amy E Keating
Proteins 68(4) 863-78. 2007-11-01