Author

Yi‐Fan Chou

University of PennsylvaniaORCID 0000-0002-9932-7091Unclaimed ORCID profile · follow to get notified of new preprints

Biology Disciplines

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Signature Assays, Organisms & Methods

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Organism:human· 4 Approach:statistical model· 4 Assay:GWAS summary statistics· 2 Research Focus:variant calling· 2 Assay:whole-exome sequencing· 2 Research Focus:eQTL / molecular QTL mapping· 1 Research Focus:gene regulatory network inference· 1 Research Focus:variant effect prediction· 1

Frequent Co-Authors

Li‐San WangiD· 4 shared Yuk Yee LeungiD· 4 shared Amanda B KuzmaiD· 3 shared Gerard D. SchellenbergiD· 3 shared Otto ValladaresiD· 3 shared Prabhakaran Gangadharan· 3 shared Alexandre Amlie‐WolfiD· 2 shared Elisabeth E. MlynarskiiD· 2 shared

Activity by Year

2018-2022 · peak 1/yr

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10 top collaborators · 45 mutual co-author links

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4 shared papersBioinformatics

Li‐San WangORCID

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4 papers

Recent·Most cited

Data Descriptor: Human whole exome genotype data for Alzheimer's Disease

Yuk Yee Leung, Adam Christian Naj, Yi‐Fan Chou, Otto Valladares, Nicholas R. Wheeler, Honghuang Lin, Prabhakaran Gangadharan, Liming Qu, Kaylyn Clark, Laura B. Cantwell, Heather Issen Nicaretta, the Alzheimer’s Disease Sequencing Project, Sudha S. Seshadri, Zoran Brkanac, Carlos Cruchaga, , Li‐San Wang

This paper presents a strategy to jointly analyze 20,504 whole-exome sequencing samples from nine studies, generating high-quality variant calls and addressing batch effects from different capture kits.

bioRxiv · Oct 11, 2022 · PreprintGenetics

SparkINFERNO: A scalable high-throughput pipeline for inferring molecular mechanisms of non-coding genetic variants

Pavel P. Kuksa, Chien‐Yueh Lee, Alexandre Amlie‐Wolf, Prabhakaran Gangadharan, Elisabeth E. Mlynarski, Yi‐Fan Chou, Han‐Jen Lin, Heather Issen Nicaretta, Emily Greenfest‐Allen, Otto Valladares, Yuk Yee Leung, Li‐San Wang

SparkINFERNO efficiently identifies causal non-coding genetic variants and their molecular mechanisms using GWAS data and functional genomics datasets.

Bioinformatics · Apr 17, 2020Peer-reviewedBioinformatics

Inferring the molecular mechanisms of noncoding Alzheimer’s disease-associated genetic variants

Alexandre Amlie‐Wolf, Mitchell Tang, Jessica Way, Beth A. Dombroski, Jiang Ming, Nicholas Vrettos, Yi‐Fan Chou, Yi Zhao, Amanda B Kuzma, Elisabeth E. Mlynarski, Yuk Yee Leung, Christopher D. Brown, Li‐San Wang, Gerard D. Schellenberg

The paper identifies enhancer dysregulation and target genes for noncoding Alzheimer's disease-associated variants using GWAS and eQTL data.

Journal of Alzheimer s Disease · Sep 24, 2019Peer-reviewedBioinformatics

VCPA: genomic variant calling pipeline and data management tool for Alzheimer’s Disease Sequencing Project

Yuk Yee Leung, Otto Valladares, Yi‐Fan Chou, Han‐Jen Lin, Amanda B Kuzma, Laura B. Cantwell, Liming Qu, Prabhakaran Gangadharan, Alzheimer's Disease Sequencing Project, William J. Salerno, Gerard D. Schellenberg, Li‐San Wang

VCPA is a genomic variant calling pipeline and data management tool for Alzheimer’s Disease Sequencing Project, providing variant calling and job tracking for WGS/WES data on Amazon cloud.

Bioinformatics · Oct 22, 2018Peer-reviewedBioinformatics