111 Prof. Yaari Gur Faculty of Engineering Member of BINA Nano-Medicine & Nano-Materials 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 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 2020 and 2021 • Miri Ostrovsky-Berman, Boaz Frankel, Pazit Polak, Gur Yaari. “Immune2vec: Embedding B/T Cell Receptor Sequences in ℝN Using Natural Language Processing”. Frontiers in Immunology, 2021. • Andrew M Collins, Ayelet Peres, Martin M Corcoran, Corey T Watson, Gur Yaari, William D Lees, Mats Ohlin. “Commentary Single-particle membrane potential optical recordings from NDTF,Cy5-Ab-avidin complex targeting GABAAR and DPA in cultured cortical neurons. Publications 2020 and 2021 • Un Seng Chio, Yumeng Liu, SangYoon Chung, Woo Jun Shim, Sowmya Chandrasekar, Shimon Weiss, Shuou Shan. “Subunit cooperation in the Get1/2 receptor promotes tail-anchored membrane protein insertion”. Journal of Cell Biology, 2021. • Asaf Grupi, Zehavit Shapira, Shimon Yudovich, Nurit Degani-Katzav, Shimon Weiss. “Point-localized, site-specific membrane potential optical recording by single fluorescent nanodiscs”. Biophysical Reports, 2021. • Simon Sehayek, Xiyu Yi, Shimon Weiss, Paul W Wiseman. “Rapid ensemble measurement of protein diffusion and probe blinking dynamics in cells”. Biophysical Reports, 2021. • Soma Ghosh, Nishanth Belugali Nataraj, Ashish Noronha, Sushant Patkar, Arunachalam Sekar, Saptaparna Mukherjee, Sabina Winograd-Katz, Lior Kramarski, Aakanksha Verma, Moshit Lindzen, Diana Drago Garcia, Joseph Green, Galit Eisenberg, Hava Gil-Henn, Arkaprabha Basu, Yan Lender, Shimon Weiss, Moshe Oren, Michal Lotem, Benjamin Geiger, Eytan Ruppin, Yosef Yarden. “PD-L1 recruits phospholipase C and enhances tumorigenicity of lung tumors harboring mutant forms of EGFR”. Cell Reports, 2021. • Jae Ho Lee, Ahmad Jomaa, SangYoon Chung, Yu-Hsien Hwang Fu, Ruilin Qian, Xuemeng Sun, Hao-Hsuan Hsieh, Sowmya Chandrasekar, Xiaotian Bi, Simone Mattei, Daniel Boehringer, Shimon Weiss, Nenad Ban, Shu-ou Shan. “Receptor compaction and GTPase rearrangement drive SRP-mediated cotranslational protein translocation into the ER”. Science Advances, 2021. • Eitan Lerner, Anders Barth, Jelle Hendrix, Benjamin Ambrose, Victoria Birkedal, Scott C Blanchard, Richard Börner, Hoi Sung Chung, Thorben Cordes, Timothy D Craggs, Ashok A Deniz, Jiajie Diao, Jingyi Fei, Ruben L Gonzalez, Irina V Gopich, Taekjip Ha, Christian A Hanke, Gilad Haran, Nikos S Hatzakis, Sungchul Hohng, Seok-Cheol Hong,Thorsten Hugel, Antonino Ingargiola, Chirlmin Joo, Achillefs N Kapanidis, Harold D Kim, Ted Laurence,Nam Ki Lee, Tae-Hee Lee, Edward A Lemke, Emmanuel Margeat, Jens Michaelis ,Xavier Michalet, Sua Myong, Daniel Nettels, Thomas-Otavio Peulen, Evelyn Ploetz, Yair Razvag, Nicole C Robb, Benjamin Schuler, Hamid Soleimaninejad, Chun Tang, Reza Vafabakhsh, Don C Lamb, Claus AM Seidel, Shimon Weiss. “FRET-based dynamic structural biology: Challenges, perspectives and an appeal for openscience practices”. Elife 10, e60416, 2021. • Arkaprabha Basu, Manash K Paul, Mitchel Alioscha-Perez, Anna Grosberg, Hichem Sahli, Steven Dubinett, Shimon Weiss. “Quantitative Analysis of Actin Cytoskeleton’s Morphological Changes during EMT in Lung Cancer and PreCancer Cell Lines”. Biophysical Journal, 2021. • Dana Adler, Zehavit Shapira, Shimon Weiss, Asher Shainberg, Abram Katz. “Weak Electromagnetic Fields Accelerate Fusion of Myoblasts”. International journal of molecular sciences, 2021. • Anastasia Ludwig, Pablo Serna, Lion Morgenstein, Gaoling Yang, Omri BarElli, Gloria Ortiz, Evan Miller, Dan Oron, Asaf Grupi, Shimon Weiss, Antoine Triller. “Development of lipid-coated semiconductor nanosensors for recording of membrane potential in neurons”. ACS Photonics, 2020. • Ludwig, A.; Serna, P.; Morgenstein, L.; Yang, G.; Bar-Elli, O.; Ortiz, G.; Miller, E.; Oron, D., Grupi, A.; Weiss, S.; Triller, A.; “Feasibility analysis of semiconductor voltage nanosensors for neuronal membrane potential sensing”. ACS Photonics, 2020, 7, 1141−1152.
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