ד"ר ישי יהודה

2001-2006:

Yeshivat Hesder Petah Tikva

2004-2005:

Moreshet Yaakov Religious College of Education

Psychometric score: 768

2007-2009:

B.Sc. in the honors program “Etgar” in Life science.

Hebrew University, Faculty of Life Science.  

Dean’s List (2007,2008). With excellence. GPA: 93

2010:

M.Sc. in Microbiology & Molecular Genetics, specialization in Genomics & Bioinformatics.

Hebrew University, Faculty of Medicine

Moved to a “direct track” PhD program. GPA: 93

2011-2016:

PhD under the supervision of Prof. Itamar Simon.

Thesis title: "The Mammalian Genomic Organization of Replication".

Hebrew University, Faculty of Medicine.

2011-2015:

Teaching Assistant in the Faculty of Medicine, Hebrew University. course: Industrial Microbiology

2017:

Post-Doc under the supervision of Dr. Michael Berger (Immunology) and Prof. Itamar Simon (Genomics). Faculty of Medicine, Hebrew University.

2017-

Lecturer, Dept. of Bioinformatics, Jerusalem College of Technology.

2018-

Research associate and Lab manager, Dr. Tomer Kalisky lab, Faculty of Engineering, Bar Ilan University.

• Grant from Mifal Hapayis. (2007-2009)
• Grant from the National Student Organization. (2009)
• Grant from the Ministry of Science. (2010)
• Excellence grants from the Faculty of Medicine. (2010-2015)
• Bester prize for cancer research. (2012)
• Sudarsky prize for the "Best poster prize", Israel Bioinformatics Society conference. (2012)
• Special scholarship - HUJI friends in England (10,000£/year). (2013-2016)
• Travel grant from the Broad Institute of MIT and Harvard. (2016)
• The Hebrew University of Jerusalem travel grant. (2016)
• Hebrew University Postdoctoral fellowship (2017)
• Excellence in teaching award, Jerusalem College of Technology. (2019)

During my M.A. and Phd years I developed novel methods for better understanding of the genomic DNA replication program. Each genomic region replicates in a specific time along S and we consider this as the Replication Timing (RT) of the region. In collaboration with groups from Israel (Weizmann, and HUJI), Sweden and US, we showed that the RT changes the genomic sequence. This surprising finding also shed light on the long standing question of Isochore formation (the GC percent variation along the genome).

 I developed a novel method to map genome wide RT from a small number of cells (X100 fold less than what was previously used) enabling to map RT in many cell types that were unavailable till now. I initiated and led collaboration with 3 groups in HUJI, in order to map for the first time RT of In-vivo cells, both from the immune system and from germ cells. We mapped the first germline RT map, which enabled us to better understand the role of RT in affecting other genomic features like retrotransposon and gene density variation. This work will be sent to publication in the next few weeks. In collaboration with other groups in the US and HUJI (including Prof. Chaim Cedar and Prof. Yehudit Bergman) we mapped the a-synchronous RT of immune cell clones. This work allowed solving a basic question in the replication field since we clearly showed a lack of coordination between asynchronous replicating loci (in preparation). Besides the projects I led, I was involved in a few more projects that hopefully will be finished in the coming year: Understanding the changes in replication program during cancer transformation (we found that 15% of the genome changes RT while becoming cancerous), the effects of stress on replication, role of Cohesin in RT and more.

In the last two years I am positioned at the Faculy of BioEngineenirg at Bar-Ilan University as a research associate and lab manager of the Tomer Kalisky Lab. I am using state of the art single cell genomic methods for the study of kidney disease and development. I am developing new single cell experimental methods, cell dissociation techniques combined with new bioinformatics approaches. Two papers are published from this period and many ongoing projects on the pipeline.

Publications - Peer-Reviewed Papers in Refereed Journals "before last appointment"

1. Ephraim Kenigsberg*, Yishai Yehuda*, Lisette Marjavaara, Andrea Keszthelyi, Andrei Chabes, Amos Tanay, Itamar Simon. (2016) The mutation spectrum in genomic late replication domains shapes mammalian GC content. Nucleic Acids Res. (IF:11.5, Q1)

*Equal contribution

2. Yishai Yehuda, Britny Blumenfeld, Dan Lehmann, Itamar Simon. (2017) Genome-wide determination of mammalian replication timing by DNA content measurement. Vis. Exp. (IF:1.2, Q1)

Peer-Reviewed Papers in Refereed Journals "after last appointment"

1. Yishai Yehuda*, Britny Blumenfeld*, Nina Mayorek, Kirill Makedonski, Oriya Vardi, Leonor Cohen-Daniel, Yousef Mansour, Shulamit Baror-Sebban, Hagit Masika, Marganit Farago, Michael Berger, Shai Carmi, Yosef Buganim, Amnon Koren, Itamar Simon. (2018). Germline DNA replication timing shapes mammalian genome composition. Nucleic acids research, 46(16), 8299-8310. (IF:11.5, Q1)

*Equal contribution

2. Yishay Wineberg, Tali Bar-Lev, Anna Futorian, Nissim Ben-Haim, Leah Armon, Debby Ickowicz, Sarit Oriel, Efrat Bucris, Yishai Yehuda, Naomi Pode-Shakked, Shlomit Gilad, Sima Benjamin, Peter Hohenstein, Benjamin Dekel, Achia Urbach and Tomer Kalisky. (2020) Single-Cell RNA Sequencing Reveals mRNA Splice Isoform Switching during Kidney Development. J Am Soc Nephrol. 31.10 (2020): 2278-2291 (IF: 9.3, Q1)
3. Yishay Wineberg, Itamar Kanter, Nissim Ben-Haim, Naomi Pode-Shakked, Efrat Bucris, Tali Hana Bar-Lev, Sarit Oriel, Yishai Yehuda, Rotem Gershon, Rachel Shukrun, Dekel Dov Bar-Lev, Achia Urbach, Benjamin Dekel, Tomer Kalisky. (2019) Characterization of splice isoform switching during human kidney development. bioRxiv 816371; doi: https://doi.org/10.1101/816371

Invited Talks:

• GRBP, BioPhysics forum, Jerusalem. (2013)
• FISEB (Ilanit) 7th congress, Eilat. (2014)
• IMRIC 3rd Scientific Conference, and also a co-chair of a session "DEVELOPMENT AND GENE REGULATION", Dead sea. (2015)
• of Cell Biology seminar, Albert Einstein College of Medicine, N.Y. (2016) (invited by Prof. Eric Bouhassira)
• Special seminar at Kevin Strhul lab, Harvard Medical School, Boston (2016)

Poster Presentations and active participation in Conferences:

• JSLS, Nuclear Organization Dynamics and Activity, Jerusalem. (2011)
• FISEB (ILANIT) congress, Eilat. (2011)
• Israeli Bioinformatics Symposium, Jerusalem. (2012) – Best Poster Award.
• Epigenesys Systems Biology, Rehovot. (2012)
• Genome Stability meeting, Jerusalem. (2013)
• Systems Biology conference. Rehovot (2013)
• Frontiers in Genetics IX, Rehovot. (2015)
• Israeli Bioinformatics Symposium, Tel Aviv. (2015)
• Genome Regulation in 3D, Rehovot. (2015)
• Broad-ISF Cell Circuits Symposium, Jerusalem. (2015)
• Broad-ISF Cell Circuits Symposium, Boston. (2016)
• Israeli Bioinformatics Symposium, Haifa. (2016)
• EMBO-NEXT GEN IMMUNOLOGY, Rehovot. (2016)
• Israeli Bioinformatics Symposium, Rehovot. (2017)
• FISEB (ILANIT) congress, Eilat. (2017)
• RNA Biology and Processing meeting, Ramat Gan (2018)
• Faculty of Engineering Conference, Zefat (2018)
• International Workshop on Developmental Nephrology, Ein Gedi (2018)
• BINA conference, Neve Ilan (2018)
• Dynamic Processes in Living Systems, Jerusalem (2019)
• Faculty of Engineering Conference, Maalot (2019)
• Broad-ISF Cell Circuits Symposium, Jerusalem. (2019)
• BINA conference, Herzliya (2019)
• FISEB (ILANIT) congress, Eilat. (2020)
• Broad-ISF Cell Circuits Symposium, virtual. (2020)

• Journal refereeing for: NAR & Jove journals.
• Instructing students: instructed three lab technicians (Dr. Sharon Eden, Dr. Micha Ben-Zimra & Dr. Hagit Masika), one PhD student (andrew silvanus) and one M.Sc. student (Oriya Vardi, later continued to PhD) in learning genomic approaches, FACS, and next generation sequencing. Instructed three B.Sc. students (Kenas Wiskott (MD student), Ehud Dahan & Avraham Greenberg (B.Sc students)) in bioinformatics, genomics and molecular genetics methods. Instructed one Post-Doc (Dr. Sarit Oriel) and many B.Sc. students in Cell Culture techniques. Instructed dozens of PhD, M.A. and B.Sc. students in presentations and poster design.

2001-2006:

• Volunteer Tutor for a Jewish Ethiopian child in Petach Tikva
• Lead trips for youth movement guides and high school students
• Tour Instructor in the Old City of Jerusalem
• Trainers' course in “Yad Vashem”
• Volunteer in an after school program for kids at risk
• Volunteer work with the disabled

2007-2020:

• Volunteer Family guide in “Or Yarok” for Safer Driving in Israel (2007-2012)
• Volunteer with Holocaust survivors (2010-2012)
• Volunteer Tutor for children at risk
• Volunteer in the community: Chairman of the Internal absorption & communication committees; Adoption of new families & National Service Girls; Torah classes for youth and adults; Accommodation and care for soldiers in the region; Initiatives and organizing community events; Community support and community charity activities; The establishment and operation of a charitable loan fund for the needy