Posts by Collection

100 Sood Amika

200 Tu Tiffany

300 Yao Yiqi

302 Shen Jiajie

400 Emmanuel Mokel

401 Danielle Mensah

000 Ochoa Alejandro

201 Pornmongkolsuk Rp

202 Hou Zhuoran

203 Kennedy Gabriel

204 Chen Bide

303 Xu Izzi

99 You

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

DomStratStats

RandProt

dPUC2

bnpsd

popkin

simtrait

genio

lfa

gcatest

jackstraw

simfam

popgeninfer

kinshipsymbols

popkinsuppl

ligera

genbin

simgenphen

domrec

human-differentiation-manuscript

pca-assoc-paper

data

bias-herit-paper

bias-assoc-paper

meta-gwas-cryptic-inflation

La Biología Molecular

Domain Prediction Using Context in Plasmodium falciparum

Forget the E-value: family-based q-values for protein domain prediction, and empirical error detection

Forget the E-value: q-values for domains (poster blitz)

Forget the E-value: family-based q-values for protein domain prediction, and empirical error detection

Beyond the E-value: stratified statistics for protein domain prediction

F_ST generalized for arbitrary population structures

F_ST and kinship for arbitrary population structures

Measuring relatedness in human populations from DNA

Relatedness and differentiation in arbitrary population structures

Relatedness and differentiation in arbitrary population structures

Relatedness and differentiation in arbitrary population structures

Relatedness and differentiation in arbitrary population structures

Relatedness and differentiation in arbitrary population structures (lightning talk)

Relatedness and differentiation in arbitrary population structures

Modeling Relatedness in Genetic Association Studies

Population Kinship and Differentiation in Human Studies

Estimating ancestry from a population kinship matrix under arbitrary ancestral subpopulation structure

Master's Student Research in the Ochoa Lab

Statistical models and methods for human genetic data

Defining the Landscape of HLA Risk Alleles in Primary Nephrotic Syndrome and Post Kidney Transplant Recurrence

HLA Antigens And Recurrence Of Focal Segmental Glomerulosclerosis In Pediatric Kidney Transplantation.

Statistical Genetics Research: Kinship, Bias, Admixture

Defining the Landscape of HLA Risk Alleles in Primary Nephrotic Syndrome and Post Kidney Transplant Recurrence

Statistical Genetics Research: Kinship, Bias, Admixture

Statistical Genetics Research: Kinship, Bias, Admixture

Genetic association models for related samples and population structure

HLA Antigens And Recurrence Of Focal Segmental Glomerulosclerosis In Pediatric Kidney Transplantation

Inference of admixture model parameters from genetic covariance

Development of Genomic Resource Modules for a Diverse Workforce

Defining the Landscape of HLA Risk Alleles in Primary Nephrotic Syndrome and Post Kidney Transplant Recurrence

Admixture and genetic association models for complex populations with cryptic relatedness

Outreach activities: Duke Genomic Scholars Program

Genetic association and heritability estimation in structured populations

Models for diverse human genetic data

The presence of cryptic relatedness creates inflation in meta-analyses of genome-wide association studies

Defining the Landscape of HLA Risk Alleles in Primary Nephrotic Syndrome and Post Kidney Transplant Recurrence

Models for diverse human genetic data

Improving modeling of linkage disequilibrium in genetically diverse populations

Improving modeling of linkage disequilibrium in genetically diverse populations