preprints (before publications):

Selected publications:

Efficient and flexible tagging of endogenous genes by homology-independent intron targeting

Serebrenik YV*, Sansbury SE*, Santhosh Kumar S, Henao-Mejia J, Shalem O.

Genome Res. 2019 Jun 25

Systematic dissection of the sequence determinants of gene 3’ end mediated expression control.

Shalem O*, Sharon E*, Lubliner S, Regev I, Lotan-Pompan M, Yakhini Z and Segal E. PLoS Genet. 2015 Apr

High-throughput functional genomics using CRISPR-Cas9.

Shalem O‡, Sanjana NE and Zhang F‡. Nature Rev Genet. 2015 Apr (‡ corresponding authors)

Improved lentiviral vectors and genome-wide libraries for genetic screening in human and mouse cells using the CRISPR nuclease Cas9.

Sanjana NE*, Shalem O* and Zhang F. Nature Methods. 2014 Aug

Genome-scale CRISPR-Cas9 knockout screening in human cells.

Shalem O*, Sanjana NE*, Hartenian E, Shi X, Scott DA, Mikkelsen TS, Heckl D, Ebert BL, Root DE, Doench JG, Zhang F. Science 2014 Jan (Science research highlightsNature research highlightsNature Genetics research highlightsNature Methods research highlights)

Full list:

The Hyaluronidase, TMEM2, Promotes ER Homeostasis and Longevity Independent of the UPR-ER

Schinzel TR*, Higuchi-Sanabria R*, Shalem O*, Moehle EA, Webster BM, Joe L, Bar-Ziv R, Frankino PA, Durieux J, Pender C, Kelet N, Santhosh Kumar S, Savalia N, Chi H, Simic M, Nguyen NT and Dillin A.
Cell, 2019 Nov

Efficient and flexible tagging of endogenous genes by homology-independent intron targeting

Serebrenik YV*, Sansbury SE*, Santhosh Kumar S, Henao-Mejia J, Shalem O.

Genome Res. 2019 Jun 25

CRISPR mutagenesis screening of mice

Serebrenik YV, Shalem O.

Nat Cell Biol. 2018 Nov

Integrated design, execution, and analysis of arrayed and pooled CRISPR genome-editing experiments.

Canver MC, Haeussler M, Bauer DE, Orkin SH, Sanjana NE, Shalem O, Yuan GC, Zhang F, Concordet JP, Pinello L.

Nat Protoc. 2018 May

Identification of essential genes for cancer immunotherapy.
Patel SJ, Sanjana NE, Kishton RJ, Eidizadeh A, Vodnala SK, Cam M, Gartner JJ, Jia L, Steinberg SM, Yamamoto TN, Merchant AS, Mehta GU, Chichura A, Shalem O, Tran E, Eil R, Sukumar M, Guijarro EP, Day CP, Robbins P, Feldman S, Merlino G, Zhang F, Restifo NP.
Nature. 2017 Aug 7.

CRISPRing the Regulatory Genome, the Challenge Ahead.
Sansbury SE, Sweeney KM, Shalem O.
Trends Genet. 2017 Jul 29. 

Transcription control by the ENL YEATS domain in acute leukaemia.
Erb MA, Scott TG, Li BE, Xie H, Paulk J, Seo HS, Souza A, Roberts JM, Dastjerdi S, Buckley DL, Sanjana NE, Shalem O, Nabet B, Zeid R, Offei-Addo NK, Dhe-Paganon S, Zhang F, Orkin SH, Winter GE, Bradner JE.
Nature 2017 Mar 

High-resolution interrogation of functional elements in the noncoding genome
Sanjana NE*, Wright JB*, Zheng K, Shalem O, Fontanillas P, Joung J, Cheng C, Regev A, Zhang F. Science Sep 2016.

Hypoxia as a therapy for mitochondrial disease.

Jain IH, Zazzeron L, Goli R, Alexa K, Schatzman-Bone S, Dhillon H, Goldberger O, Peng J, Shalem O, Sanjana NE, Zhang F, Goessling W, Zapol WM, Mootha VK. Science. 2016 Apr.

BCL11A enhancer dissection by Cas9-mediated in situ saturating mutagenesis.
Canver MC*, Smith EC*, Sher F*, Pinello L*, Sanjana NE*, Shalem O, Chen DD, Schupp PG, Vinjamur DS, Garcia SP, Luc S, Kurita R, Nakamura Y, Fujiwara Y, Maeda T, Yuan GC, Zhang F, Orkin SH, Bauer DE. Nature. 2015 Nov

A Genome-wide CRISPR Screen in Primary Immune Cells to Dissect Regulatory Networks.
Parnas O, Jovanovic M, Eisenhaure TM, Herbst RH, Dixit A, Ye CJ, Przybylski D, Platt RJ, Tirosh I, Sanjana NE, Shalem O, Satija R, Raychowdhury R, Mertins P, Carr SA, Zhang F, Hacohen N, Regev A. Cell. 2015 Jul

Systematic dissection of the sequence determinants of gene 3’ end mediated expression control.
Shalem O*, Sharon E*, Lubliner S, Regev I, Lotan-Pompan M, Yakhini Z and Segal E. PLoS Genet. 2015 Apr

High-throughput functional genomics using CRISPR-Cas9.
Shalem O‡, Sanjana NE and Zhang F‡. Nature Rev Genet. 2015 Apr (‡ corresponding authors)

In vivo genome editing using Staphylococcus aureus Cas9.
Ran FA*, Cong L*, Yan WX*, Scott DA, Gootenberg JS, Kriz AJ, Zetsche B, Shalem O, Wu X, Makarova KS, Koonin EV, Sharp PA, Zhang F. Nature 2015 Apr

Genome-wide CRISPR Screen in a Mouse Model of Tumor Growth and Metastasis.
Chen S*, Sanjana NE*, Zheng K, Shalem O, Lee K, Shi X, Scott DA, Song J, Pan JQ, Weissleder R, Lee H, Zhang F, Sharp PA. Cell 2015 Mar

Improved lentiviral vectors and genome-wide libraries for genetic screening in human and mouse cells using the CRISPR nuclease Cas9.
Sanjana NE*, Shalem O* and Zhang F. Nature Methods. 2014 Aug

Genome-scale CRISPR-Cas9 knockout screening in human cells.
Shalem O*, Sanjana NE*, Hartenian E, Shi X, Scott DA, Mikkelsen TS, Heckl D, Ebert BL, Root DE, Doench JG, Zhang F. Science 2014 Jan (Science research highlightsNature research highlightsNature Genetics research highlightsNature Methods research highlights)

 

DNA targeting specificity of RNA-guided Cas9 nucleases.
Hsu PD*, Scott DA*, Weinstein JA, Ran FA, Konermann S, Agarwala V, Li Y, Fine EJ, Wu X, Shalem O, Cradick TJ, Marraffini LA, Bao G, Zhang F. Nat Biotechnol. 2013 Sep

 

Measurements of the impact of 3′ end sequences on gene expression reveal wide range and sequence dependent effects.
Shalem O, Carey L, Zeevi D, Sharon E, Keren L, Weinberger A, Dahan O, Pilpel Y, Segal E. PLoS Comput Biol. 2013

 

Widespread promoter-mediated coordination of transcription and mRNA degradation.
Dori-Bachash M*, Shalem O*, Manor YS, Pilpel Y, Tirosh I. Genome Biol. 2012 Dec

 

Axonal transcription factors signal retrogradely in lesioned peripheral nerve.
Ben-Yaakov K, Dagan SY, Segal-Ruder Y, Shalem O, Vuppalanchi D, Willis DE, Yudin D, Rishal I, Rother F, Bader M, Blesch A, Pilpel Y, Twiss JL, Fainzilber M. EMBO J 2012 Mar

 

Transcriptome kinetics is governed by a genome-wide coupling of mRNA production and degradation: a role for RNA Pol II.
Shalem O, Groisman B, Choder M, Dahan O, Pilpel Y. PLoS Genet. 2011 Sep

 

Signaling to transcription networks in the neuronal retrograde injury response.
Michaelevski I, Segal-Ruder Y, Rozenbaum M, Medzihradszky KF, Shalem O, Coppola G, Horn-Saban S, Ben-Yaakov K, Dagan SY, Rishal I, Geschwind DH, Pilpel Y, Burlingame AL, Fainzilber M.
Science Signal. 2010 Jul 13

 

Transient transcriptional responses to stress are generated by opposing effects of mRNA production and degradation.
Shalem O, Dahan O, Levo M, Martinez MR, Furman I, Segal E, Pilpel Y. Mol Syst Biol. 2008 (F1000 review)

Shalem Lab

Functional Genomics

Protein Quality Control

and Neurodegeneration