94 questions in biology in general and the adaptive immune system in particular. The research activities of our group are divided into two: (1) developing statistical and machine learning-based tools to analyze high-throughput biological data, (2) mining big immunological datasets to extract new insights. Publications 2022 and 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 Pavlović � , Knut Dagestad Rand, Maria Chernigovskaya, Oz Pirvandy, Gur Yaari, Victor Greiff, Geir K Sandve. “sim. AIRR: simulation of adaptive immune repertoires with realistic receptor sequence sharing for benchmarking of immune state prediction methods”. GigaScience, 2023. • 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. • 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. • Jason T Smith, Juhi M Gupta, Alena Rudkouskaya, Shan Gao, Arin Ulku, Claudio Bruschini, Edoardo Charbon, Shimon Weiss, Margarida Barroso, Xavier Intes, Xavier Michalet. “Characterization of a large Gated SPAD camera for in vivo Macroscopic Fluorescence Lifetime Imaging”. Clinical and Translational Biophotonics, 2022. • Lion Morgenstein, Merav Tsubary, Ayelet Atkins, Asaf Grupi, Shimon Weiss. “Controlled membrane interactions by lipid coated quantum dots”. Biophysical Journal, 2022. • Paul David Harris, Alessandra Narducci, Christian Gebhardt, Thorben Cordes, Shimon Weiss, Eitan Lerner. “Multiparameter photon-by-photon hidden Markov modeling”. Nature communications, 2022. • SangYoon Chung, Yazan Alhadid, Maya Segal, Jookyung Lee, Sergei Borukhov, Shimon Weiss. “Single molecule activity assay for SARS-CoV-2 RNA dependent RNA polymerase”. Biophysical Journal, 2022. • Shimon Yudovich, Adan Marzouqe, Joseph Kantorovitsch, Eti Teblum, Tao Chen, Jörg Enderlein, Evan W Miller, Shimon Weiss. “Electrically Controlling and Optically Observing the Membrane Potential of Supported Lipid Bilayers”. Biophysical Journal, 2022. Prof. Yaari Gur Faculty of Engineering Member of BINA Nano-Biomedicine Center Nano & Advanced Materials Center Nano-Bioconvergence Center Nano-Cleantech Center Research Areas • Computational • immunology Systems biology • Machine Learning Abstract Computational Systems Immunology We are a data science-driven lab, combining experimental and computational expertise, aiming to address fundamental • 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, T homas C Mitchell, Gur Yaari, Robert P Sebra, Corey T Watson, Melissa L Smith. “Flairr-seq: A method for singlemolecule resolution of near full-length antibody H chain repertoires”. The Journal of Immunology, 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”. 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. • Modi Safra, Lael Werner, Ayelet Peres, Pazit Polak, 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. • Katherine JL Jackson, Justin T Kos, William Lees, William S Gibson, Melissa Laird Smith, Ayelet Peres, Gur Yaari, Martin Corcoran, Christian E Busse, Mats Ohlin, Corey T Watson, Andrew M Collins. “A BALB/c IGHV reference set, defined by haplotype analysis of long-read VDJ-c sequences from F1 (BALB/cx C57BL/6) mice”. Frontiers in Immunology, 2022. • Aviv Omer, Ayelet Peres, Oscar L Rodriguez, Corey T Watson, William Lees,
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