Iuliana Ionita-Laza Department of Biostatistics, Columbia University

Irina Hannah

About

• Tianying Wang, Iuliana Ionita-Laza, Ying Wei, "A Unified Quantile Framework reveals nonlinear heterogeneous transcriptome-wide associations"


• 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", 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", 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", 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", 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", 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", 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", 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", 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", 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", 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", 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", 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", American Journal of Human Genetics 2006

- NIH-R01 (AG072272, 2021-2025)
- NIH-R21 (HG012345, 2021-2023)
- NIH-R25 (GM143298, 2021-2026)
- NIH-R01 (MH095797, 2012-2023)
- NIH-R01 (MH106910, 2016-2021)
- NIH-R21 (MH106888, 2015-2017)
- NSF (DMS-1100279, 2011-2015)
- NIH-R03 (HG005908, 2010-2013)

- I am an associate editor for Biometrics, and Statistics in Biosciences.

- Workshops organized: La Fondation des Treilles (France, 2024), Symposium on Advances in Genomics, Epidemiology and Statistics (Penn, 2015-present), 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).

- Upcoming conferences: ENAR (Nashville, March 2023), BIRS workshop on "Computational Biology meets Data Science" (Oaxaca, May 2023), School on Cancer Evolution (Como, Italy, May 2023), City University of Hong Kong (June 2023), WNAR (Anchorage, June 2023), The 6th International Conference on Econometrics and Statistics (Tokyo, August 2023).

Openings: I am recruiting students/postdocs. Please email me (ii2135@columbia.edu) if interested.