Research

The Bhattacharya Lab focuses on both genomics methods development and applications of these methods to study complex traits and diseases using large molecular datasets through multi-group collaboration. We highlight manuscripts with primary contributions from our group and include work to which we’ve contributed.

Highlighted

2024

2023

2022

2021

2020

All

2024

Brain cell-type shifts in Alzheimer’s disease, autism, and schizophrenia interrogated using methylomics and genetics

Chloe X. Yap, Daniel D. Vo, Matthew G. Heffel, Arjun Bhattacharya, Cindy Wen, ..., Alexander Gusev, Bogdan Pasaniuc, Jonathan Mill, Chongyuan Luo, Michael J. Gandal

Science Advances   ·   24 May 2024   ·   doi:10.1126/sciadv.adn7655

Cross-ancestry atlas of gene, isoform, and splicing regulation in the developing human brain

Cindy Wen, Michael Margolis, Rujia Dai, Pan Zhang, Pawel F. Przytycki, ..., Yanqiong Zhang, Xiao Zhou, Ryan Ziffra, Zane R. Zeier, Trisha M. Zintel

Science   ·   24 May 2024   ·   doi:10.1126/science.adh0829

Novel ancestry-specific primary open-angle glaucoma loci and shared biology with vascular mechanisms and cell proliferation

Valeria Lo Faro, Arjun Bhattacharya, Wei Zhou, Dan Zhou, Ying Wang, ..., Eric R. Gamazon, Nomdo M. Jansonius, Karen Joos, Nancy J. Cox, Jibril Hirbo

Cell Reports Medicine   ·   01 Feb 2024   ·   doi:10.1016/j.xcrm.2024.101430

Polygenic scores for tobacco use provide insights into systemic health risks in a diverse EHR-linked biobank in Los Angeles

Vidhya Venkateswaran, Kristin Boulier, Yi Ding, Ruth Johnson, Arjun Bhattacharya, Bogdan Pasaniuc

Translational Psychiatry   ·   18 Jan 2024   ·   doi:10.1038/s41398-024-02743-z

2023

Isoform-level transcriptome-wide association uncovers genetic risk mechanisms for neuropsychiatric disorders in the human brain

Arjun Bhattacharya, Daniel D. Vo, Connor Jops, Minsoo Kim, Cindy Wen, Jonatan L. Hervoso, Bogdan Pasaniuc, Michael J. Gandal

Nature Genetics   ·   30 Nov 2023   ·   doi:10.1038/s41588-023-01560-2

Multi-ancestry genome-wide association study of cannabis use disorder yields insight into disease biology and public health implications

Daniel F. Levey, Marco Galimberti, Joseph D. Deak, Frank R. Wendt, Arjun Bhattacharya, ..., J. Michael Gaziano, Michael J. Gandal, Renato Polimanti, Murray B. Stein, Joel Gelernter

Nature Genetics   ·   20 Nov 2023   ·   doi:10.1038/s41588-023-01563-z

Interplay Of Serum Bilirubin and Tobacco Smoking with Lung and Head and Neck Cancers in a Diverse, EHR-linked Los Angeles Biobank

Vidhya Venkateswaran, Ella Petter, Kristin Boulier, Yi Ding, Arjun Bhattacharya, Bogdan Pasaniuc

Cold Spring Harbor Laboratory   ·   03 Oct 2023   ·   doi:10.1101/2023.09.29.23296364

Genotype error due to low-coverage sequencing induces uncertainty in polygenic scoring

Ella Petter, Yi Ding, Kangcheng Hou, Arjun Bhattacharya, Alexander Gusev, Noah Zaitlen, Bogdan Pasaniuc

The American Journal of Human Genetics   ·   01 Aug 2023   ·   doi:10.1016/j.ajhg.2023.06.015

Impact of cross-ancestry genetic architecture on GWASs in admixed populations

Rachel Mester, Kangcheng Hou, Yi Ding, Gillian Meeks, Kathryn S. Burch, Arjun Bhattacharya, Brenna M. Henn, Bogdan Pasaniuc

The American Journal of Human Genetics   ·   01 Jun 2023   ·   doi:10.1016/j.ajhg.2023.05.001

twas_sim, a Python-based tool for simulation and power analysis of transcriptome-wide association analysis

Xinran Wang, Zeyun Lu, Arjun Bhattacharya, Bogdan Pasaniuc, Nicholas Mancuso

Bioinformatics   ·   26 Apr 2023   ·   doi:10.1093/bioinformatics/btad288

Causal effects on complex traits are similar for common variants across segments of different continental ancestries within admixed individuals

Kangcheng Hou, Yi Ding, Ziqi Xu, Yue Wu, Arjun Bhattacharya, ..., Heather E. Wheeler, Genevieve L. Wojcik, Ying Zhou, Sriram Sankararaman, Bogdan Pasaniuc

Nature Genetics   ·   20 Mar 2023   ·   doi:10.1038/s41588-023-01338-6

Global Biobank analyses provide lessons for developing polygenic risk scores across diverse cohorts

Ying Wang, Shinichi Namba, Esteban Lopera, Sini Kerminen, Kristin Tsuo, ..., Sebastian Zöllner, Alicia R. Martin, Cristen J. Willer, Mark J. Daly, Benjamin M. Neale

Cell Genomics   ·   01 Jan 2023   ·   doi:10.1016/j.xgen.2022.100241

The UCLA ATLAS Community Health Initiative: Promoting precision health research in a diverse biobank

Ruth Johnson, Yi Ding, Arjun Bhattacharya, Sergey Knyazev, Alec Chiu, Clara Lajonchere, Daniel H. Geschwind, Bogdan Pasaniuc

Cell Genomics   ·   01 Jan 2023   ·   doi:10.1016/j.xgen.2022.100243

2022

Multi-ancestry meta-analysis of asthma identifies novel associations and highlights the value of increased power and diversity

Kristin Tsuo, Wei Zhou, Ying Wang, Masahiro Kanai, Shinichi Namba, ..., Takayuki Morisaki, Yukinori Okada, Benjamin M. Neale, Mark J. Daly, Alicia R. Martin

Cell Genomics   ·   01 Dec 2022   ·   doi:10.1016/j.xgen.2022.100212

Meta-analysis fine-mapping is often miscalibrated at single-variant resolution

Masahiro Kanai, Roy Elzur, Wei Zhou, Mark J. Daly, Hilary K. Finucane, ..., Uk Biobank, Alicia R. Martin, Cristen J. Willer, Mark J. Daly, Benjamin M. Neale

Cell Genomics   ·   01 Dec 2022   ·   doi:10.1016/j.xgen.2022.100210

Broad transcriptomic dysregulation occurs across the cerebral cortex in ASD

Michael J. Gandal, Jillian R. Haney, Brie Wamsley, Chloe X. Yap, Sepideh Parhami, ..., Vivek Swarup, T. Grant Belgard, Mark Gerstein, Bogdan Pasaniuc, Daniel H. Geschwind

Nature   ·   02 Nov 2022   ·   doi:10.1038/s41586-022-05377-7

Proteome-wide Mendelian randomization in global biobank meta-analysis reveals multi-ancestry drug targets for common diseases

Huiling Zhao, Humaria Rasheed, Therese Haugdahl Nøst, Yoonsu Cho, Yi Liu, ..., Ben Michael Brumpton, Wei Zhou, Benjamin M. Neale, Tom R. Gaunt, Jie Zheng

Cell Genomics   ·   01 Nov 2022   ·   doi:10.1016/j.xgen.2022.100195

Multivariate variance components analysis uncovers genetic architecture of brain isoform expression and novel psychiatric disease mechanisms

Minsoo Kim, Daniel D. Vo, Connor T. Jops, Cindy Wen, Ashok Patowary, Arjun Bhattacharya, Chloe X. Yap, Hua Zhou, Michael J. Gandal

Cold Spring Harbor Laboratory   ·   21 Oct 2022   ·   doi:10.1101/2022.10.18.22281204

Global Biobank Meta-analysis Initiative: Powering genetic discovery across human disease

Wei Zhou, Masahiro Kanai, Kuan-Han H. Wu, Humaira Rasheed, Kristin Tsuo, ..., Sebastian Zöllner, Alicia R. Martin, Cristen J. Willer, Mark J. Daly, Benjamin M. Neale

Cell Genomics   ·   01 Oct 2022   ·   doi:10.1016/j.xgen.2022.100192

A practical guideline of genomics-driven drug discovery in the era of global biobank meta-analysis

Shinichi Namba, Takahiro Konuma, Kuan-Han Wu, Wei Zhou, Yukinori Okada

Cell Genomics   ·   01 Oct 2022   ·   doi:10.1016/j.xgen.2022.100190

Leveraging global multi-ancestry meta-analysis in the study of idiopathic pulmonary fibrosis genetics

Juulia J. Partanen, Paavo Häppölä, Wei Zhou, Arto A. Lehisto, Mari Ainola, ..., Tarja Laitinen, Riitta Kaarteenaho, Marjukka Myllärniemi, Mark J. Daly, Jukka T. Koskela

Cell Genomics   ·   01 Oct 2022   ·   doi:10.1016/j.xgen.2022.100181

Best practices for multi-ancestry, meta-analytic transcriptome-wide association studies: Lessons from the Global Biobank Meta-analysis Initiative

Arjun Bhattacharya, Jibril B. Hirbo, Dan Zhou, Wei Zhou, Jie Zheng, Masahiro Kanai, Bogdan Pasaniuc, Eric R. Gamazon, Nancy J. Cox

Cell Genomics   ·   01 Oct 2022   ·   doi:10.1016/j.xgen.2022.100180

Leveraging genomic diversity for discovery in an electronic health record linked biobank: the UCLA ATLAS Community Health Initiative

Ruth Johnson, Yi Ding, Vidhya Venkateswaran, Arjun Bhattacharya, Kristin Boulier, ..., Sriram Sankararaman, Manish J. Butte, Clara Lajonchere, Daniel H. Geschwind, Bogdan Pasaniuc

Genome Medicine   ·   09 Sep 2022   ·   doi:10.1186/s13073-022-01106-x

Innovative computational approaches shed light on genetic mechanisms underlying cognitive impairment among children born extremely preterm

Weifang Liu, Quan Sun, Le Huang, Arjun Bhattacharya, Geoffery W. Wang, ..., Robert M. Joseph, T. Michael O’Shea, Rebecca C. Fry, Yun Li, Hudson P. Santos

Journal of Neurodevelopmental Disorders   ·   03 Mar 2022   ·   doi:10.1186/s11689-022-09429-x

Distal gene regulation mediated by non-coding RNAs contributes to germline risk for breast and prostate cancer

Nolan Cole, Paige Lee, Tommer Schwarz, Pan Zhang, Matthew L. Freedman, Alexander Gusev, Sara Lindström, Michael J. Gandal, Bogdan Pasaniuc, Arjun Bhattacharya

Cold Spring Harbor Laboratory   ·   09 Feb 2022   ·   doi:10.1101/2022.02.08.22270601

Placental genomics mediates genetic associations with complex health traits and disease

Arjun Bhattacharya, Anastasia N. Freedman, Vennela Avula, Rebeca Harris, Weifang Liu, ..., Carmen J. Marsit, Yun Li, T. Michael O’Shea, Rebecca C. Fry, Hudson P. Santos

Nature Communications   ·   04 Feb 2022   ·   doi:10.1038/s41467-022-28365-x

Racial differences in breast cancer outcomes by hepatocyte growth factor pathway expression

Gieira S. Jones, Katherine A. Hoadley, Halei Benefield, Linnea T. Olsson, Alina M. Hamilton, ..., Kevin P. Williams, Michael I. Love, Hazel B. Nichols, Andrew F. Olshan, Melissa A. Troester

Breast Cancer Research and Treatment   ·   16 Jan 2022   ·   doi:10.1007/s10549-021-06497-w

2021

On powerful GWAS in admixed populations

Kangcheng Hou, Arjun Bhattacharya, Rachel Mester, Kathryn S. Burch, Bogdan Pasaniuc

Nature Genetics   ·   25 Nov 2021   ·   doi:10.1038/s41588-021-00953-5

Gene-Level Germline Contributions to Clinical Risk of Recurrence Scores in Black and White Patients with Breast Cancer

Achal Patel, Montserrat García-Closas, Andrew F. Olshan, Charles M. Perou, Melissa A. Troester, Michael I. Love, Arjun Bhattacharya

Cancer Research   ·   28 Oct 2021   ·   doi:10.1158/0008-5472.CAN-21-1207

Hepatocyte growth factor pathway expression in breast cancer by race and subtype

Gieira S. Jones, Katherine A. Hoadley, Linnea T. Olsson, Alina M. Hamilton, Arjun Bhattacharya, ..., Jodie M. Fleming, Michael I. Love, Hazel B. Nichols, Andrew F. Olshan, Melissa A. Troester

Breast Cancer Research   ·   03 Aug 2021   ·   doi:10.1186/s13058-021-01460-5

MOSTWAS: Multi-Omic Strategies for Transcriptome-Wide Association Studies

Arjun Bhattacharya, Yun Li, Michael I. Love

PLOS Genetics   ·   08 Mar 2021   ·   doi:10.1371/journal.pgen.1009398

Biopsychosocial correlates of psychological distress in Latina mothers

Hudson P Santos, Harry Adynski, Rebeca Harris, Arjun Bhattacharya, Angela C Incollingo Rodriguez, Ryan Cali, Alessandra Torres Yabar, Benjamin C Nephew, Christopher Murgatroyd

Journal of Affective Disorders   ·   01 Mar 2021   ·   doi:10.1016/j.jad.2020.12.193

DeCompress: tissue compartment deconvolution of targeted mRNA expression panels using compressed sensing

Arjun Bhattacharya, Alina M Hamilton, Melissa A Troester, Michael I Love

Nucleic Acids Research   ·   01 Feb 2021   ·   doi:10.1093/nar/gkab031

2020

Evidence for the placenta-brain axis: multi-omic kernel aggregation predicts intellectual and social impairment in children born extremely preterm

Hudson P. Santos Jr, Arjun Bhattacharya, Robert M. Joseph, Lisa Smeester, Karl C. K. Kuban, Carmen J. Marsit, T. Michael O’Shea, Rebecca C. Fry

Molecular Autism   ·   01 Dec 2020   ·   doi:10.1186/s13229-020-00402-w

An approach for normalization and quality control for NanoString RNA expression data

Arjun Bhattacharya, Alina M Hamilton, Helena Furberg, Eugene Pietzak, Mark P Purdue, Melissa A Troester, Katherine A Hoadley, Michael I Love

Briefings in Bioinformatics   ·   13 Aug 2020   ·   doi:10.1093/bib/bbaa163

A framework for transcriptome-wide association studies in breast cancer in diverse study populations

Arjun Bhattacharya, Montserrat García-Closas, Andrew F. Olshan, Charles M. Perou, Melissa A. Troester, Michael I. Love

Genome Biology   ·   20 Feb 2020   ·   doi:10.1186/s13059-020-1942-6

2019

Epigenome-wide DNA methylation in placentas from preterm infants: association with maternal socioeconomic status

Hudson P. Santos, Arjun Bhattacharya, Elizabeth M. Martin, Kezia Addo, Matt Psioda, ..., Stephen R. Hooper, Jean A. Frazier, Karl C. Kuban, T.Michael O’Shea, Rebecca C. Fry

Epigenetics   ·   21 May 2019   ·   doi:10.1080/15592294.2019.1614743

2018

Discrimination exposure and DNA methylation of stress-related genes in Latina mothers

Hudson P. Santos, Benjamin C. Nephew, Arjun Bhattacharya, Xianming Tan, Laura Smith, Reema Abdulrahman S. Alyamani, Elizabeth M. Martin, Krista Perreira, Rebecca C. Fry, Christopher Murgatroyd

Psychoneuroendocrinology   ·   01 Dec 2018   ·   doi:10.1016/j.psyneuen.2018.08.014