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Iuliana Ionita-Laza
Department of Biostatistics, Columbia University
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Irina
Hannah
About
I am a professor in the Department of Biostatistics at Columbia University and a visiting professor in the Department of Statistics at Lund University in Sweden. During AY 2023-2024 I visited the Department of Biostatistics at Université Paris-Saclay and Institut Pasteur.
My main research interests lie at the interface between statistics and genomics. I am particularly interested in developing statistical and machine learning methods for the analysis of high-dimensional genetic and functional genomics data. I am also involved in applications of such methods to understand the genetic basis of complex diseases and traits, including autism spectrum disorders, schizophrenia and Alzheimer's disease. I am co-director of Career MODE, an NIH funded mentoring program for early career biomedical scientists. I also lead the Genomics@Columbia Program, an initiative to bring together an interdisciplinary group of people from multiple departments across Columbia University with diverse research expertise in statistical/computational genomics and other omics, computational biology, biomedical informatics, and interested in understanding biology and human health.
I organize a monthly genomics seminar:
2024-2025.
In November 2024, I organized a workshop at La Fondation des Treilles on "Causality in Genetics" (image).
Upcoming travel: University of Wrocław (Poland, June 2025), BIRS workshop (Canada, July 2025), UCLA Computational Genomics Summer Institute (July 2025), RIKEN/Kyoto University (Japan, August 2025), UNC Chapel Hill (October 2025), Inserm conference on "Genomic Variability in Health and Disease" (Marseille, France, November 2025), IMS ICSDS conference (Seville, Spain, December 2025).
Selected papers
- Hanqing Wu, Hyunkyu Lee, Najmeh Abiri, Iuliana Ionita-Laza, "Domain-aware matrix completion for predicting phenotypes from Electronic Health Record data with applications in genomic research", biorxiv, 2025
- Fan Wang, Chen Wang, Tianying Wang, Marco Masala, Edoardo Fiorillo, Marcella Devoto, Francesco Cucca, Iuliana Ionita-Laza, "Regenie.QRS: computationally efficient whole-genome quantile regression at biobank scale", biorxiv, 2025
- Zihuai He, Benjamin Chu, James Yang, Jiaqi Gu, Zhaomeng Chen, Linxi Liu, Tim Morrison, Michael E Belloy, Xinran Qi, Nima Hejazi, Maya Mathur, Yann Le Guen, Hua Tang, Trevor Hastie, Iuliana Ionita-Laza, Emmanuel Candès, Chiara Sabatti, "Beyond guilty by association at scale: Searching for causal variants on the basis of genome-wide summary statistics", biorxiv, 2025
- Xiaoxia Liu, Jiaqi Gu, Zhaomeng Chen, Benjamin Chu, Linxi Liu, Tim Morrison, Robert R Butler III, Jacob Edelson, Jinzhou Li, Frank M Longo, Hua Tang, Iuliana Ionita-Laza, Chiara Sabatti, Emmanuel Candès, Zihuai He, "Uncovering Heterogeneous Effects via Localized Feature Selection", biorxiv, 2025
- Chen Wang, Marco Masala, Edoardo Fiorillo, Marcella Devoto, Francesco Cucca, Iuliana Ionita-Laza, "Quantile-specific confounding: correction for subtle population stratification via quantile regression", Genetics, 2025
- Zikun Yang, Chen Wang, Yuridia Selene Posadas Garcia, Valeria Anorve Garibay, Badri Vardarajan, Andres Moreno Estrada, Mashaal Sohail, Richard Mayeux, Iuliana Ionita-Laza, "Fine-mapping in admixed populations with applications to Latin American studies", The American Journal of Human Genetics, 2025
- Bruxel et al., "Psychiatric Genetics in the Diverse Landscape of Latin American Populations", Nature Genetics, 2025
- Hyunkyu Lee, Atlas Khan, Chen Wang, Chunhua Weng, Joseph D. Buxbaum, Krzysztof Kiryluk, Iuliana Ionita-Laza, "Liability threshold model-based disease risk prediction based on Electronic Health Record phenotypes", Nature Genetics, to appear
- Tianying Wang, Iuliana Ionita-Laza, Ying Wei, "A unified quantile framework for nonlinear heterogeneous transcriptome-wide associations", Annals of Applied Statistics, 2024
- Shiyang Ma, Fan Wang, Richard Border, Joseph Buxbaum, Noah Zaitlen, Iuliana Ionita-Laza, "Local genetic correlation via knockoffs reduces confounding due to cross-trait assortative mating", The American Journal of Human Genetics, 2024
- Chen Wang, Tianying Wang, Krzysztof Kiryluk, Ying Wei, Hugues Aschard, Iuliana Ionita-Laza, "Genome-wide analysis at biobank scale of biomarkers using quantile regression", Nature Communications, 2024
- Yi Yang, Qi Wang, Chen Wang, Joseph Buxbaum, Iuliana Ionita-Laza, "KnockoffHybrid: A knockoff framework for hybrid analysis of trio and population designs in genome-wide association studies", The American Journal of Human Genetics, 2024
- Zikun Yang, Chen Wang, Linxi Liu, Atlas Khan, Annie Lee, Badri Vardarajan, Richard Mayeux, Krzysztof Kiryluk, Iuliana Ionita-Laza, "CARMA: Novel Bayesian model for fine-mapping in meta-analysis studies", Nature Genetics, 2023
- Shiyang Ma, Chen Wang, Atlas Khan, Linxi Liu, James Dalgleish, Krzysztof Kiryluk, Zihuai He, Iuliana Ionita-Laza, "Fine-mapping gene-based associations via knockoff analysis of biobank-scale data with applications to UK Biobank", Genome Biology, 2023
- Krzysztof Kiryluk et al. "GWAS defines pathogenic signaling pathways and prioritizes drug targets for IgA nephropathy", Nature Genetics, 2023
- Yi Yang, Chen Wang, Linxi Liu, Joseph Buxbaum, Zihuai He, Iuliana Ionita-Laza, "KnockoffTrio: A knockoff framework for the identification of putative causal variants in genome-wide association studies with trio design", The American Journal of Human Genetics, 2022
- Tianying Wang, Iuliana Ionita-Laza, Ying Wei,
"Integrated Quantile RAnk Test (iQRAT) for gene-level associations in sequencing studies", Annals of Applied Statistics, 2022
- Zihuai He, Linxi Liu, Michael E. Belloy, Yann Le Guen, Aaron Sossin, Xiaoxia Liu, Xinran Qi, Shiyang Ma, Tony Wyss-Coray, Hua Tang, Chiara Sabatti, Emmanuel Candès, Michael D. Greicius, Iuliana Ionita-Laza, "Summary statistics knockoff inference empowers identification of putative causal variants in genome-wide association studies", Nature Communications, 2022
- Xihao Li, Godwin Yung, Hufeng Zhou, Ryan Sun, Zilin Li, Yaowu Liu,
Iuliana Ionita-Laza, Xihong Lin, "A Multi-dimensional Integrative
Scoring Framework for Predicting Functional Regions in the Human
Genome", The American Journal of Human Genetics, 2022
- Atlas Khan et al. "Genome-wide polygenic score with APOL1 risk genotypes predicts chronic kidney disease across major continental ancestries", Nature Medicine, 2022
- Tristan Hayeck, Nicholas Stong, Evan Baugh, Ryan Dhindsa, Tychele Turner, Ayan Malakar, Timothy Mosbruger, Yuncheng Duan, Iuliana Ionita-Laza, David Goldstein, Andrew Allen, "Ancestry adjustment improves genome-wide estimates of regional intolerance", Genetics, 2022
- Shiyang Ma, James Dalgleish, Justin Lee, Chen Wang, Linxi Liu, Richard Gill, Joseph Buxbaum, Wendy Chung, Hugues Aschard, Edwin K. Silverman, Michael H. Cho, Zihuai He, Iuliana Ionita-Laza, "Powerful gene-based testing by integrating long-range chromatin interactions and knockoff genotypes", Applications to UK/Japan Biobank , Proceedings of the National Academy
of Sciences USA, 2021
- Zihuai He, Yann Le Guen, Linxi Liu, Justin Lee, Shiyang Ma, Andrew C. Yang, Xiaoxia Liu, Jarod Rutledge, Patricia Moran Losada, Bowen Song, Robert Butler, Frank Longo, Hua Tang, Elizabeth Mormino, Tony Wyss-Coray, Michael Greicius, Iuliana Ionita-Laza, "Genome-wide analysis of common and rare variants via multiple knockoffs at biobank-scale: methods and applications", The American Journal of Human Genetics, 2021
- Zihuai He, Linxi Liu, Chen Wang, Yann Le Guen, Justin Lee, Stephanie Gogarten, Fred Lu, Stephen Montgomery, Hua Tang, Edwin K. Silverman, Michael H. Cho, Michael Greicius, Iuliana Ionita-Laza, "KnockoffScreen: A powerful method for the identification of putative causal loci in whole-genome sequencing data via knockoff statistics", Nature Communications, 2021
- Zikun Yang, Chen Wang, Lynn Petukhova, Angela Christiano, Iuliana Ionita-Laza, "A robust presence-only model to predict regulatory effects of genetic variants at single nucleotide resolution by integrating epigenetic information and massively parallel reporter assays", Bioinformatics, 2021
- Danqing Xu, Chen Wang, Atlas Khan, Ning Shang, Zihuai He, Ali Gharavi, Krzysztof Kiryluk, Chunhua Weng, Iuliana Ionita-Laza, "Deriving quantitative disease risk scores for common diseases from Electronic Health Records, with applications to clinical risk stratification and genetic association studies", npj Digital Medicine, 2021
- COVID-19 Host Genetics Initiative, "Mapping the human genetic architecture of COVID-19" Nature, 2021
- Stephanie O. Erjavec, Sahar Gelfman, Alexa R. Abdelaziz, Eunice Y. Lee, Isha Monga, Anna Alkelai, Iuliana Ionita-Laza, Lynn M. Petukhova, Angela M. Christiano, "Whole exome sequencing in Alopecia Areata identifies rare mutations in KRT82", Nature Communications, 2021
- Hanna Julienne, Vincent Laville, Zachary R. McCaw, Zihuai He, Vincent Guillemot, Carla Lasry, Andrey Ziyatdinov, Cyril Nerin, Amaury Vaysse, Pierre Lechat, Hervé Ménager, Wilfried Le Goff, Marie-Pierre Dube, Peter Kraft, Iuliana Ionita-Laza, Bjarni J. Vilhjálmsson, Hugues Aschard, "Multitrait GWAS to connect disease variants and biological mechanisms", PLOS Genetics, 2021
- Zekavat M et al., "Hematopoietic mosaic chromosomal alterations and risk for infection among 767,891 individuals without blood cancer", Nature Medicine, 2021
- Danqing Xu, Chen Wang, Krzysztof Kiryluk, Joseph D. Buxbaum,
Iuliana Ionita-Laza, "Co-localization between sequence constraint and
epigenomic information improves interpretation of whole genome
sequencing data", The American Journal of Human Genetics, 2020, Co-localization webpage
- Zihuai He, Bin Xu, Joseph Buxbaum, Iuliana Ionita-Laza, "WGScan:
a genome-wide scan statistic framework for whole-genome sequence data
analysis with applications to data from the Simons Simplex Collection", Nature Communications, 2019, WGScan R package on CRAN
- Satterstrom et al., "Novel genes for autism implicate both
excitatory and inhibitory cell lineages in risk", Cell, to appear,
2019
- N Steers et al., "Genomic Mismatch at LIMS1 Locus is Associated with Kidney Allograft Rejection", New England Journal of Medicine, 2019
- Zihuai He, Linxi Liu, Kai Wang, Iuliana Ionita-Laza, "A
semi-supervised approach for predicting cell type/tissue specific
functional consequences of non-coding variation using massively parallel
reporter assays", Nature Communications 2018, GenoNet scores
- Daniel Backenroth, Zihuai He, Krzysztof Kiryluk, Valentina Boeva,
Lynn Pethukova, Ekta Khurana, Angela Christiano, Joseph Buxbaum, Iuliana
Ionita-Laza, "FUN-LDA: A latent Dirichlet allocation model for predicting tissue-specific functional effects of noncoding variation", The American Journal of Human Genetics, 2018, FUN-LDA scores
- Fernanda Polubriaginof et al., "Estimate of disease heritability using 7.4 million familial relationships inferred from electronic health records", Cell, 2018
- Yuwen Liu et al., "A statistical framework for mapping risk genes from de novo mutations in whole-genome sequencing studies", The American Journal of Human Genetics, 2018
- Zihuai He, Bin Xu, Seunggeun Lee, Iuliana Ionita-Laza, "Unified
sequence-based association tests allowing for multiple functional
annotation scores, and applications to meta-analysis of noncoding
variation in Metabochip data", The American Journal of Human Genetics, 2017, FST R package on CRAN
- Zihuai He, Seunggeun Lee, Min Zhang, Jennifer Smith, Xiuqing Guo,
Walter Palmas, Sharon Kardia, Iuliana Ionita-Laza, Bhramar Mukherjee, "Rare-variant
association tests in longitudinal studies, with an application to the
Multi-Ethnic Study of Atherosclerosis (MESA)", Genetic Epidemiology, 2017
- Xiaoyu Song, Gen Li, Zhenwei Zhou, Xianling Wang, Iuliana Ionita-Laza, Ying Wei, "QRank: A novel quantile regression tool for eQTL discovery", Bioinformatics, 2017, QRank R package on CRAN
- Lim et al., "Rates, distribution and implications of postzygotic mosaic mutations in autism spectrum disorder", Nature Neuroscience, 2017
- Simone Sanna-Cherchi et al.,"Exome-wide Association Study Identifies GREB1L Mutations in Congenital Kidney Malformations", The American Journal of Human Genetics, 2017
- Krzysztof Kiryluk et al., "GWAS for serum galactose-deficient IgA1 implicates critical genes of the O-glycosylation pathway", PloS Genetics, 2017
- Iuliana Ionita-Laza, Kenneth McCallum, Bin Xu, Joseph Buxbaum, "A spectral approach integrating functional genomic annotations for coding and noncoding variants", Nature Genetics, 2016, Eigen scores (research highlighted here in Nature Methods)
- Atsushi Takata, Iuliana Ionita-Laza, Joseph
Gogos, Bin Xu, Maria Karayiorgou, "De Novo Synonymous Mutations in Regulatory Elements Contribute to the Genetic
Etiology of Autism and Schizophrenia", Neuron, 2016
- Xiaoyu Song, Iuliana Ionita-Laza, Mengling Liu, Joan Reibman, Ying Wei, "A new estimating equation approach for secondary trait analyses in genetic case-control studies", Genetics, 2016
- Kenneth McCallum, Iuliana Ionita-Laza, "Empirical Bayes scan
statistics for detecting clusters of disease risk variants in genetic
studies", Biometrics, 2015, Source Code
- Ying Wei, Xiaoyu Song, Mengling Liu, Iuliana Ionita-Laza, Joan
Reibman, "Secondary Case-Control Quantile analysis with applications to
GWAS", Journal of the American Statistical Association, 2015
- Iuliana Ionita-Laza, Marinela Capanu, Silvia De Rubeis, Kenneth
McCallum, Joseph Buxbaum, "Identification of rare causal variants in
sequence-based studies: methods and applications", PloS Genetics, 2014, Software
- Silvia De Rubeis et al., "Synaptic, transcriptional, and chromatin genes disrupted in autism", Nature, 2014
- Iuliana Ionita-Laza, Bin Xu, V Makarov, Joseph Buxbaum, J. Louw
Roos, Joseph Gogos, Maria Karayiorgou, "A Scan-Statistic Based Analysis
of Exome Sequencing Data Identifies FAN1 at 15q13.3 as a Susceptibility
Gene for Schizophrenia and Autism", Proceedings of the National Academy
of Sciences USA, 2014
- Atsushi Takata, Bin Xu, Iuliana Ionita-Laza, J. Louw Roos, Joseph
Gogos, Maria Karayiorgou, "Loss-of-Function Variants in Schizophrenia
Risk and SETD1A as a Candidate Susceptibility Gene", Neuron, 2014
- Iuliana Ionita-Laza, Seunggeun Lee, Vlad Makarov, Joseph Buxbaum,
Xihong Lin "Sequence kernel association tests for the combined effect of
rare and common variants", The American Journal of Human Genetics, 2013, Software, (brief SFARI story)
- Iuliana Ionita-Laza, Seunggeun Lee, Vlad Makarov, Joseph Buxbaum,
Xihong Lin "General class of family-based association tests for sequence
data, and comparisons with population-based association tests",
European Journal of Human Genetics, 2013, Source Code
- Bin Xu, Iuliana Ionita-Laza, J Louw Roos, Braden Boone, Scarlet
Woodrick, Yan Sun, Shawn Levy, Joseph A Gogos, Maria Karayiorgou "De
novo gene mutations highlight patterns of genetic and neural complexity
in schizophrenia", Nature Genetics, 2012
- Iuliana Ionita-Laza, Vlad Makarov, the AASC, Joseph Buxbaum
"Scan-statistic approach identifies clusters of rare disease variants in
three independent datasets in LRP2, a gene linked and associated with
autism spectrum disorders", The American Journal of Human Genetics, in
press, 2012 (SFARI news story)
- Iuliana Ionita-Laza, Michael Cho, Nan Laird "Statistical challenges
in sequence-based association studies with population- and family-based
designs", Statistics in Biosciences, 2012 (invited article)
- Iuliana Ionita-Laza, Vlad Makarov, Seungtai Yoon, Benjamin Raby,
Joseph Buxbaum, Dan Nicolae, Xihong Lin "Finding genes in Mendelian
disorders using sequence data: methods and applications", The American
Journal of Human Genetics, 2011, Source Code, Simulated Example (highlighted in Nature Genetics)
- Iuliana Ionita-Laza and Ruth Ottman "Design of association studies with rare variants" Genetics, 2011, Source Code (EPV), and Source Code (Power), and Documentation
- Omer Gokcumen et al. "Refinement of primate copy number variation hotspots identifies candidate genomic regions evolving under positive selection", Genome Biology, 2011
- Iuliana Ionita-Laza, Joseph Buxbaum, Nan Laird and Christoph Lange
"A new testing strategy to identify rare variants with either risk or
protective effect on disease" PloS Genetics, 2011 -- Source Code and Documentation
- Iuliana Ionita-Laza, Angela Rogers, Christoph Lange, Benjamin Raby,
Charles Lee "Genetic association analysis of copy number variation in
human disease pathogenesis", Genomics 2009
- Iuliana Ionita-Laza, Nan Laird "On the optimal design of genetic
variant discovery studies", Statistical Applications in Genetics and
Molecular Biology, 2010
- David Fardo, Iuliana Ionita-Laza, Christoph Lange "On
quality control measures in genome-wide association studies: a test to
assess the genotyping quality of individual probands in family-based
association studies and an application to the HapMap data", PloS Genetics 2009
- Iuliana Ionita-Laza, Christoph Lange, Nan Laird "On a method to
count the number of unseen variants in the human genome", Proceedings of
the National Academy of Sciences 2009 (story)
- Iuliana Ionita-Laza, Nan Laird, Benjamin Raby, Scott Weiss,
Christoph Lange "On the frequency of copy number variants", Bioinformatics 2008
- Iuliana Ionita-Laza, George Perry, Benjamin Raby, Barbara
Klanderman, Charles Lee, Nan Laird, Scott Weiss, Christoph Lange (2007)
"On the analysis
of copy-number variations in genome-wide association studies: a
translation of the family-based association test", Genetic Epidemiology 2008
- Iuliana Ionita-Laza, Matthew McQueen, Nan Laird, Christoph Lange
"Genomewide Weighted Hypothesis Testing in Family-Based Association
Studies, with an Application to a 100K Scan", The American Journal of Human
Genetics 2007
- Iuliana Ionita, Raul-Sam Daruwala, Bud Mishra "Mapping Tumor
Suppressor Genes using Multipoint Statistics from Copy-Number Variation
Data", The American Journal of Human Genetics 2006
Funding (as PI/MPI)
- NIH-R01 (AG072272, 2021-2026)
- NIH-R01 (MH095797, 2012-2024)
- NIH-R01 (AG087496, 2024-2029)
- NIH-R25 (GM143298, 2021-2026)
- NIH-R21 (HG012345, 2021-2024)
- NIH-R01 (MH106910, 2016-2021)
- NIH-R21 (MH106888, 2015-2017)
- NSF (DMS-1100279, 2011-2015)
- NIH-R03 (HG005908, 2010-2013)
Some professional activities
- Workshops organized: La Fondation des Treilles (France, 2024), Symposium on Advances in Genomics, Epidemiology and Statistics (Penn, 2015-2019), BIRS workshop on deep learning methods in genomics (Canada, 2022), BIRS workshop on genomics and microbiome (Canada, February 2019), Oberwolfach Workshop in Statistical Genomics (Germany, 2015).
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