The Bhattacharya Lab for Computational Genomics Computational genetic and molecular epidemiology for cancer and development

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

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
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
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

2022

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
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
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

2021

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
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
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

All

2024

Brain cell-type shifts in Alzheimer’s disease, autism, and schizophrenia interrogated using methylomics and genetics
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
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
Polygenic scores for tobacco use provide insights into systemic health risks in a diverse EHR-linked biobank in Los Angeles
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
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
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
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
Impact of cross-ancestry genetic architecture on GWASs in admixed populations
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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

Genome-wide association meta-analysis identifies novel ancestry-specific primary open-angle glaucoma loci and shared biology with vascular mechanisms and cell proliferation
Genome-wide association meta-analysis identifies 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
Cold Spring Harbor Laboratory   ·   17 Dec 2021   ·   doi:10.1101/2021.12.16.21267891
On powerful GWAS in admixed populations
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
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
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
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
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
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
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
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
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
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
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