| 88 | 2024 Annual Report Illustration of a novel T-cell receptor beta repertoire encoding approach using lossless string compression. Publications 2023 and 2024 • Eric Engelbrecht, Oscar L Rodriguez, Kaitlyn Shields, Steven Schultze, David Tieri, Uddalok Jana, Gur Yaari, William D Lees, Melissa L Smith, Corey T Watson. “Resolving Haplotype Variation and Complex Genetic Architecture in the Human Immunoglobulin Kappa Chain Locus in Individuals of Diverse Ancestry.” Genes & Immunity, 2024. • Ayelet Peres, Vered Klein, Boaz Frankel, William Lees, Pazit Polak, Mark Meehan, Artur Rocha, João Correia Lopes, Gur Yaari. “Guidelines for Reproducible Analysis of Adaptive Immune Receptor Repertoire Sequencing Data.” Briefings in Bioinformatics, 2024. • William D Lees, Swati Saha, Gur Yaari, Corey T Watson. “Digger: Directed Annotation of Immunoglobulin and T Cell Receptor V, D, and J Gene Sequences and Assemblies.” Bioinformatics, 2024. • Andrew M Collins, Mats Ohlin, Martin Corcoran, James M Heather, Duncan Ralph, Mansun Law, Jesus MartínezBarnetche, Jian Ye, Eve Richardson, William S Gibson, Oscar L Rodriguez, Ayelet Peres, Gur Yaari, Corey T Watson, William D Lees. “AIRR-C IG Reference Sets: Curated Sets of Immunoglobulin Heavy and Light Chain Germline Genes.” Frontiers in Immunology, 2024. • Modi Safra, Lael Werner, Pazit Polak, Ayelet Peres, Naomi Salamon, Michael Schvimer, Batia Weiss, Iris Barshack, Dror S Shouval, Gur Yaari. “A Somatic Hypermutation–Based Machine Learning Model Stratifies Individuals with Crohn's Disease and Controls.” Genome Research, 2023. • Ayelet Peres, William D Lees, Oscar L Rodriguez, Noah Y Lee, Pazit Polak, Ronen Hope, Meirav Kedmi, Andrew M Collins, Mats Ohlin, Steven H Kleinstein, Corey T Watson, Gur Yaari. “IGHV Allele Similarity Clustering Improves Genotype Inference from Adaptive Immune Receptor Repertoire Sequencing Data.” Nucleic Acids Research, 2023. • Miriam I Rosenberg, Erez Greenstein, Martin Buchkovich, Ayelet Peres, Eric Santoni-Rugiu, Lei Yang, Martin Mikl, Zalman Vaksman, David L Gibbs, Dan Reshef, Amy Salovin, Meredith S Irwin, Arlene Naranjo, Igor Ulitsky, Pedro A de Alarcon, Katherine K Matthay, Victor Weigman, Gur Yaari, Jessica A Panzer, Nir Friedman, John M Maris. “Polyclonal Lymphoid Expansion Drives Paraneoplastic Autoimmunity in Neuroblastoma.” Cell reports, 2023. • Liat Stoler-Barak, Ethan Harris, Ayelet Peres, Hadas Hezroni, Mirela Kuka, Amalie Grenov, Neta Gurwicz, Meital Kupervaser, Bon Ham Yip, Matteo Iannacone, Gur Yaari, John Crispino, Ziv Shulman. “B Cell Class Switch Recombination is Regulated by DYRK1A through MSH6 Phosphorylation.” Nature Communications, 2023. • Chakravarthi Kanduri, Lonneke Scheffer, Milena Pavlovi , Knut Dagestad Rand, Maria Chernigovskaya, Oz Pirvandy, Gur Yaari, Victor Greiff, Geir K Sandve. “SimAIRR: Simulation of Adaptive Immune Repertoires with Realistic Receptor Sequence Sharing for Benchmarking of Immune State Prediction Methods.” GigaScience, 2023. • William D Lees, Scott Christley, Ayelet Peres, Justin T Kos, Brian Corrie, Duncan Ralph, Felix Breden, Lindsay G Cowell, Gur Yaari, Martin Corcoran, Gunilla B Karlsson Hedestam, Mats Ohlin, Andrew M Collins, Corey T Watson, Christian E Busse. “AIRR Community Curation and Standardised Representation for Immunoglobulin and T Cell Receptor Germline Sets.” ImmunoInformatics, 2023. • Modi Safra, Zvi Tamari, Pazit Polak, Shachaf Shiber, Moshe Matan, Hani Karameh, Yigal Helviz, Adva Levy-Barda, Vered Yahalom, Avi Peretz, Eli BenChetrit, B aruch Brenner, Tamir Tuller, Meital Gal-Tanamy, Gur Yaari. “Altered Somatic Hypermutation Patterns in COVID-19 Patients Classifies Disease Severity.” Frontiers in Immunology, 2023. • Easton E Ford, David Tieri, Oscar L Rodriguez, Nancy J Francoeur, Juan Soto, Justin T Kos, Ayelet Peres, William S Gibson, Catherine A Silver, Gintaras Deikus, Elizabeth Hudson, Cassandra R Woolley, Noam Beckmann, Alexander Charney, Thomas C Mitchell, Gur Yaari, Robert P Sebra, Corey T Watson, Melissa L Smith. “FLAIRR-Seq: A Method for Single-Molecule Resolution of Near FullLength Antibody H Chain Repertoires.” The Journal of Immunology, 2023. • Shira Perez, Anat Lavi-Itzkovitz, Moriah Gidoni, Tom Domovitz, Roba Dabour, Ishant Khurana, Ateret Davidovich, Ana Tobar, Alejandro Livoff, Evgeny Solomonov, Yaakov Maman, Assam ElOsta, Yishan Tsai, Ming-Lung Yu, Salomon M Stemmer, Izhak Haviv, Gur Yaari, Meital Gal-Tanamy. “High-Resolution Genomic Profiling of Liver Cancer Links Etiology With Mutation and Epigenetic Signatures.” Cellular and Molecular Gastroenterology and Hepatology, 2023. Dr. Yadid Moran Faculty of Medicine Bioengineering and Regenerative Medicine Research Areas • Bioengineering • Regenerative medicine • Human organs-on-chips • Extracellular vesicles • Cardiovascular physiology and disease • Cellular stress Abstract In our lab, we use organs-on-chips, which are advanced in vitro models based on human cells, to study organ-organ interactions in health and disease. We use tissue engineering and stem cell technology to build the components of the cardiovascular system, allowing us to study the roles of the endothelium in regulating tissues function under various conditions. We study extracellular vesicles (EVs) and how they modulate cells and tissues' response to metabolic stress, with the goal of developing novel bio-inspired therapeutics. Our multidisciplinary lab employs engineering, biology, and material sciences to study human physiology and develop new regenerative medicine approaches.
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