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Selected Publications

Pan-viral ORFs discovery using Massively Parallel Ribosome Profiling

Weingarten-Gabbay S, Bauer MR, Stanton AC, Klaeger S, Verzani EK, López D, Clauser KR, Carr SA, Abelin JG, Rice CM,

Sabeti PC. Pan-viral ORFs discovery using Massively Parallel Ribosome Profiling. bioRxiv. 2023

The HLA-II immunopeptidome of SARS-CoV-2

Weingarten-Gabbay S*✉, Chen D-Y*, Sarkizova S*, Taylor HB, Gentili M, Pearlman LR, Bauer MR, Rice CM, Clauser KR, Hachoen N, Carr SA, Abelin JG, Saeed M, Sabeti PC. Cell Reports. 2023

HLA-I immunopeptidome profiling of human cells infected with high-containment enveloped viruses

Weingarten-Gabbay S*✉, Pearlman LR*, Chen D-Y, Klaeger S, Taylor HB, Welch NL, Keskin DB, Carr SA, Abelin JG, Saeed M, Sabeti PC. STAR protocols. 2022

Profiling SARS-CoV-2 HLA-I peptidome reveals T cell epitopes from out-of-frame ORFs

Weingarten-Gabbay S*✉, Klaeger S*✉, Sarkizova S*, Pearlman LR, Chen D-Y, …, Hacohen N, Carr SA, Abelin JG, Saeed M✉, Sabeti PC. Cell. 2021

> Featured on Cell’s cover, HFSP highlight, Broad Institute news, Boston University news

Systematic interrogation of human promoters

Weingarten-Gabbay S*✉, Nir R*, Lubliner S, Sharon E, Kalma Y, Weinberger A and Segal E✉. Genome Research. 2019

Sequence features of viral and human internal ribosome entry sites predictive of their activity

Gritsenko AA*, Weingarten-Gabbay S*, Elias-Kirma S, Nir R, de Ridder D and Segal E. PLoS Comp Biol. 2017

Systematic discovery of cap-independent translation sequences in human and viral genomes

Weingarten-Gabbay S, Elias-Kirma S, Nir R, Gritsenko AA, Yakhini Z, Stern-Ginossar N, Weinberger A and Segal E. Science. 2016

>Perspective in Science, Highlight in Cell Systems, Faculty of 1000 review

Toward a systematic understanding of translational regulatory elements in human and viruses

Weingarten-Gabbay S and Segal E. RNA Biology. 2016.

The grammar of transcriptional regulation

Weingarten-Gabbay S and Segal E. Human Genetics. 2014

A shared architecture for promoters and enhancers

Weingarten-Gabbay S and Segal E. Nature Genetics. 2014 (News and Views on Core et al)

The translation initiation factor DAP5 promotes IRES-driven translation of p53 mRNA

Weingarten-Gabbay S*, Khan D*, Liberman N, Yoffe Y, Bialik S, Das S, Oren M and Kimchi A. Oncogene. 2013

* co-first author  ✉ corresponding author

Additional Publications

Functional analysis of the AUG initiator codon context reveals novel conserved sequences that disfavor mRNA translation in eukaryotes

Hernández G, García A, Weingarten-Gabbay S, Mishra RK, Hussain T, Amiri M, Moreno-Hagelsieb G, Montiel-Dávalos A, Lasko P, Sonenberg N. NAR. 2023

DAP5 drives translation of specific mRNA targets with upstream ORFs in human embryonic stem cells

David M, Olender T, Mizrahi O, Weingarten-Gabbay S, Friedlander G, Savidor A, Levin Y, Salomon V, Stern-Ginossar N, Bialik S and Kimchi A. RNA. 2022

Structured elements drive extensive circular RNA translation

Chen CK, Cheng R, Demeter J, Chen J, Weingarten-Gabbay S, Jiang L, Snyder MP, Weissman JS, Segal E, Jackson PK and Chang HY. Molecular Cell. 2021.

MS-based HLA-II peptidomics combined with multi-omics will aid the development of future immunotherapies

Taylor HB, Klaeger S, Clauser KR, Sarkizova S, Weingarten-Gabbay S, Graham DB, Carr SA, Abelin JG. Mol Cell Proteomics. 2021

The coding capacity of SARS-CoV-2

Finkel Y*, Mizrahi O*, Nachshon A, Weingarten-Gabbay S, Yahalom-Ronen Y, Tamir H, Achdout H, Melamed S, Weiss S, Israely T, Paran N, Schwartz M and Stern-Ginossar N. Nature. 2020


Unraveling the determinants of microRNA mediated regulation using a massively parallel reporter assay

Vainberg Slutskin I, Weingarten-Gabbay S, Nir R, Weinberger A and Segal E. Nature Communications. 2018

Noise in gene expression is coupled to growth rate

Keren L*, van Dijk D*, Weingarten-Gabbay S, Davidi D, Jona G, Weinberger A, Milo R and Segal E. Genome Research. 2015

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