100 Sood Amika
Posts by Collection
alumni
300 Yao Yiqi
302 Shen Jiajie
400 Emmanuel Mokel
401 Danielle Mensah
people
000 Ochoa Alejandro
200 Tu Tiffany
201 Pornmongkolsuk Rp
202 Hou Zhuoran
99 You
publications
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 12:90. 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
FST 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 FST 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 FST 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
software_package_major
DomStratStats
RandProt
dPUC2
bnpsd
popkin
simtrait
genio
lfa
gcatest
jackstraw
simfam
popgeninfer
software_package_minor
kinshipsymbols
popkinsuppl
ligera
genbin
simgenphen
software_paper
human-differentiation-manuscript
pca-assoc-paper
data
bias-herit-paper
bias-assoc-paper
meta-gwas-cryptic-inflation
talks
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
FST generalized for arbitrary population structures
FST 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