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Items: 1 to 50 of 62

1.

Mutational processes shape the landscape of TP53 mutations in human cancer.

Giacomelli AO, Yang X, Lintner RE, McFarland JM, Duby M, Kim J, Howard TP, Takeda DY, Ly SH, Kim E, Gannon HS, Hurhula B, Sharpe T, Goodale A, Fritchman B, Steelman S, Vazquez F, Tsherniak A, Aguirre AJ, Doench JG, Piccioni F, Roberts CWM, Meyerson M, Getz G, Johannessen CM, Root DE, Hahn WC.

Nat Genet. 2018 Sep 17. doi: 10.1038/s41588-018-0204-y. [Epub ahead of print]

PMID:
30224644
2.

A case of mistaken identity.

Hanna RE, Doench JG.

Nat Biotechnol. 2018 Sep 6;36(9):802-804. doi: 10.1038/nbt.4208. No abstract available.

PMID:
30188534
3.

An alternative splicing switch in FLNB promotes the mesenchymal cell state in human breast cancer.

Li J, Choi PS, Chaffer CL, Labella K, Hwang JH, Giacomelli AO, Kim JW, Ilic N, Doench JG, Ly SH, Dai C, Hagel K, Hong AL, Gjoerup O, Goel S, Ge JY, Root DE, Zhao JJ, Brooks AN, Weinberg RA, Hahn WC.

Elife. 2018 Jul 30;7. pii: e37184. doi: 10.7554/eLife.37184.

4.

Nitric Oxide Engages an Anti-inflammatory Feedback Loop Mediated by Peroxiredoxin 5 in Phagocytes.

Graham DB, Jasso GJ, Mok A, Goel G, Ng ACY, Kolde R, Varma M, Doench JG, Root DE, Clish CB, Carr SA, Xavier RJ.

Cell Rep. 2018 Jul 24;24(4):838-850. doi: 10.1016/j.celrep.2018.06.081.

5.

Prediction of off-target activities for the end-to-end design of CRISPR guide RNAs.

Listgarten J, Weinstein M, Kleinstiver BP, Sousa AA, Joung JK, Crawford J, Gao K, Hoang L, Elibol M, Doench JG, Fusi N.

Nat Biomed Eng. 2018 Jan;2(1):38-47. doi: 10.1038/s41551-017-0178-6. Epub 2018 Jan 10.

6.

miR-196b target screen reveals mechanisms maintaining leukemia stemness with therapeutic potential.

Meyer SE, Muench DE, Rogers AM, Newkold TJ, Orr E, O'Brien E, Perentesis JP, Doench JG, Lal A, Morris PJ, Thomas CJ, Lieberman J, McGlinn E, Aronow BJ, Salomonis N, Grimes HL.

J Exp Med. 2018 Aug 6;215(8):2115-2136. doi: 10.1084/jem.20171312. Epub 2018 Jul 11.

PMID:
29997117
7.

PPM1D-truncating mutations confer resistance to chemotherapy and sensitivity to PPM1D inhibition in hematopoietic cells.

Kahn JD, Miller PG, Silver AJ, Sellar RS, Bhatt S, Gibson C, McConkey M, Adams D, Mar B, Mertins P, Fereshetian S, Krug K, Zhu H, Letai A, Carr SA, Doench J, Jaiswal S, Ebert BL.

Blood. 2018 Sep 13;132(11):1095-1105. doi: 10.1182/blood-2018-05-850339. Epub 2018 Jun 28.

PMID:
29954749
8.

CRISPR Screen Reveals that EHEC's T3SS and Shiga Toxin Rely on Shared Host Factors for Infection.

Pacheco AR, Lazarus JE, Sit B, Schmieder S, Lencer WI, Blondel CJ, Doench JG, Davis BM, Waldor MK.

MBio. 2018 Jun 19;9(3). pii: e01003-18. doi: 10.1128/mBio.01003-18.

9.

The Canonical Wnt Pathway Drives Macropinocytosis in Cancer.

Redelman-Sidi G, Binyamin A, Gaeta I, Palm W, Thompson CB, Romesser PB, Lowe SW, Bagul M, Doench JG, Root DE, Glickman MS.

Cancer Res. 2018 Aug 15;78(16):4658-4670. doi: 10.1158/0008-5472.CAN-17-3199. Epub 2018 Jun 5.

PMID:
29871936
10.

Uncoupling of sgRNAs from their associated barcodes during PCR amplification of combinatorial CRISPR screens.

Hegde M, Strand C, Hanna RE, Doench JG.

PLoS One. 2018 May 25;13(5):e0197547. doi: 10.1371/journal.pone.0197547. eCollection 2018.

11.

A major chromatin regulator determines resistance of tumor cells to T cell-mediated killing.

Pan D, Kobayashi A, Jiang P, Ferrari de Andrade L, Tay RE, Luoma AM, Tsoucas D, Qiu X, Lim K, Rao P, Long HW, Yuan GC, Doench J, Brown M, Liu XS, Wucherpfennig KW.

Science. 2018 Feb 16;359(6377):770-775. doi: 10.1126/science.aao1710. Epub 2018 Jan 4.

12.

Orthologous CRISPR-Cas9 enzymes for combinatorial genetic screens.

Najm FJ, Strand C, Donovan KF, Hegde M, Sanson KR, Vaimberg EW, Sullender ME, Hartenian E, Kalani Z, Fusi N, Listgarten J, Younger ST, Bernstein BE, Root DE, Doench JG.

Nat Biotechnol. 2018 Feb;36(2):179-189. doi: 10.1038/nbt.4048. Epub 2017 Dec 18.

13.

High-throughput Phenotyping of Lung Cancer Somatic Mutations.

Berger AH, Brooks AN, Wu X, Shrestha Y, Chouinard C, Piccioni F, Bagul M, Kamburov A, Imielinski M, Hogstrom L, Zhu C, Yang X, Pantel S, Sakai R, Watson J, Kaplan N, Campbell JD, Singh S, Root DE, Narayan R, Natoli T, Lahr DL, Tirosh I, Tamayo P, Getz G, Wong B, Doench J, Subramanian A, Golub TR, Meyerson M, Boehm JS.

Cancer Cell. 2017 Dec 11;32(6):884. doi: 10.1016/j.ccell.2017.11.008. No abstract available.

PMID:
29232558
14.

Am I ready for CRISPR? A user's guide to genetic screens.

Doench JG.

Nat Rev Genet. 2018 Feb;19(2):67-80. doi: 10.1038/nrg.2017.97. Epub 2017 Dec 4. Review.

PMID:
29199283
15.

A Next Generation Connectivity Map: L1000 Platform and the First 1,000,000 Profiles.

Subramanian A, Narayan R, Corsello SM, Peck DD, Natoli TE, Lu X, Gould J, Davis JF, Tubelli AA, Asiedu JK, Lahr DL, Hirschman JE, Liu Z, Donahue M, Julian B, Khan M, Wadden D, Smith IC, Lam D, Liberzon A, Toder C, Bagul M, Orzechowski M, Enache OM, Piccioni F, Johnson SA, Lyons NJ, Berger AH, Shamji AF, Brooks AN, Vrcic A, Flynn C, Rosains J, Takeda DY, Hu R, Davison D, Lamb J, Ardlie K, Hogstrom L, Greenside P, Gray NS, Clemons PA, Silver S, Wu X, Zhao WN, Read-Button W, Wu X, Haggarty SJ, Ronco LV, Boehm JS, Schreiber SL, Doench JG, Bittker JA, Root DE, Wong B, Golub TR.

Cell. 2017 Nov 30;171(6):1437-1452.e17. doi: 10.1016/j.cell.2017.10.049.

PMID:
29195078
16.

Evaluation of RNAi and CRISPR technologies by large-scale gene expression profiling in the Connectivity Map.

Smith I, Greenside PG, Natoli T, Lahr DL, Wadden D, Tirosh I, Narayan R, Root DE, Golub TR, Subramanian A, Doench JG.

PLoS Biol. 2017 Nov 30;15(11):e2003213. doi: 10.1371/journal.pbio.2003213. eCollection 2017 Nov.

17.

Correction: KEAP1 loss modulates sensitivity to kinase targeted therapy in lung cancer.

Krall EB, Wang B, Munoz DM, Ilic N, Raghavan S, Niederst MJ, Yu K, Ruddy DA, Aguirre AJ, Kim JW, Redig AJ, Gainor JF, Williams JA, Asara JM, Doench JG, Janne PA, Shaw AT, McDonald Iii RE, Engelman JA, Stegmeier F, Schlabach MR, Hahn WC.

Elife. 2017 Oct 31;6. pii: e33173. doi: 10.7554/eLife.33173. No abstract available.

18.

Decomposing Oncogenic Transcriptional Signatures to Generate Maps of Divergent Cellular States.

Kim JW, Abudayyeh OO, Yeerna H, Yeang CH, Stewart M, Jenkins RW, Kitajima S, Konieczkowski DJ, Medetgul-Ernar K, Cavazos T, Mah C, Ting S, Van Allen EM, Cohen O, Mcdermott J, Damato E, Aguirre AJ, Liang J, Liberzon A, Alexe G, Doench J, Ghandi M, Vazquez F, Weir BA, Tsherniak A, Subramanian A, Meneses-Cime K, Park J, Clemons P, Garraway LA, Thomas D, Boehm JS, Barbie DA, Hahn WC, Mesirov JP, Tamayo P.

Cell Syst. 2017 Aug 23;5(2):105-118.e9. doi: 10.1016/j.cels.2017.08.002.

19.

In vivo CRISPR screening identifies Ptpn2 as a cancer immunotherapy target.

Manguso RT, Pope HW, Zimmer MD, Brown FD, Yates KB, Miller BC, Collins NB, Bi K, LaFleur MW, Juneja VR, Weiss SA, Lo J, Fisher DE, Miao D, Van Allen E, Root DE, Sharpe AH, Doench JG, Haining WN.

Nature. 2017 Jul 27;547(7664):413-418. doi: 10.1038/nature23270. Epub 2017 Jul 19.

20.

Natural variation in a single amino acid substitution underlies physiological responses to topoisomerase II poisons.

Zdraljevic S, Strand C, Seidel HS, Cook DE, Doench JG, Andersen EC.

PLoS Genet. 2017 Jul 12;13(7):e1006891. doi: 10.1371/journal.pgen.1006891. eCollection 2017 Jul.

21.

Dependency of a therapy-resistant state of cancer cells on a lipid peroxidase pathway.

Viswanathan VS, Ryan MJ, Dhruv HD, Gill S, Eichhoff OM, Seashore-Ludlow B, Kaffenberger SD, Eaton JK, Shimada K, Aguirre AJ, Viswanathan SR, Chattopadhyay S, Tamayo P, Yang WS, Rees MG, Chen S, Boskovic ZV, Javaid S, Huang C, Wu X, Tseng YY, Roider EM, Gao D, Cleary JM, Wolpin BM, Mesirov JP, Haber DA, Engelman JA, Boehm JS, Kotz JD, Hon CS, Chen Y, Hahn WC, Levesque MP, Doench JG, Berens ME, Shamji AF, Clemons PA, Stockwell BR, Schreiber SL.

Nature. 2017 Jul 27;547(7664):453-457. doi: 10.1038/nature23007. Epub 2017 Jul 5.

22.

Corrigendum: PARP3 is a promoter of chromosomal rearrangements and limits G4 DNA.

Day TA, Layer JV, Cleary JP, Guha S, Stevenson KE, Tivey T, Kim S, Schinzel AC, Izzo F, Doench J, Root DE, Hahn WC, Price BD, Weinstock DM.

Nat Commun. 2017 Jun 13;8:15918. doi: 10.1038/ncomms15918.

23.

Synergistic interactions with PI3K inhibition that induce apoptosis.

Zwang Y, Jonas O, Chen C, Rinne ML, Doench JG, Piccioni F, Tan L, Huang HT, Wang J, Ham YJ, O'Connell J, Bhola P, Doshi M, Whitman M, Cima M, Letai A, Root DE, Langer RS, Gray N, Hahn WC.

Elife. 2017 May 31;6. pii: e24523. doi: 10.7554/eLife.24523.

24.

CRISPR/Cas9 Screens Reveal Epstein-Barr Virus-Transformed B Cell Host Dependency Factors.

Ma Y, Walsh MJ, Bernhardt K, Ashbaugh CW, Trudeau SJ, Ashbaugh IY, Jiang S, Jiang C, Zhao B, Root DE, Doench JG, Gewurz BE.

Cell Host Microbe. 2017 May 10;21(5):580-591.e7. doi: 10.1016/j.chom.2017.04.005.

25.

PARP3 is a promoter of chromosomal rearrangements and limits G4 DNA.

Day TA, Layer JV, Cleary JP, Guha S, Stevenson KE, Tivey T, Kim S, Schinzel AC, Izzo F, Doench J, Root DE, Hahn WC, Price BD, Weinstock DM.

Nat Commun. 2017 Apr 27;8:15110. doi: 10.1038/ncomms15110. Erratum in: Nat Commun. 2017 Jun 13;8:15918.

26.

Functional screen of MSI2 interactors identifies an essential role for SYNCRIP in myeloid leukemia stem cells.

Vu LP, Prieto C, Amin EM, Chhangawala S, Krivtsov A, Calvo-Vidal MN, Chou T, Chow A, Minuesa G, Park SM, Barlowe TS, Taggart J, Tivnan P, Deering RP, Chu LP, Kwon JA, Meydan C, Perales-Paton J, Arshi A, Gönen M, Famulare C, Patel M, Paietta E, Tallman MS, Lu Y, Glass J, Garret-Bakelman FE, Melnick A, Levine R, Al-Shahrour F, Järås M, Hacohen N, Hwang A, Garippa R, Lengner CJ, Armstrong SA, Cerchietti L, Cowley GS, Root D, Doench J, Leslie C, Ebert BL, Kharas MG.

Nat Genet. 2017 Jun;49(6):866-875. doi: 10.1038/ng.3854. Epub 2017 Apr 24.

27.

ATXN1L, CIC, and ETS Transcription Factors Modulate Sensitivity to MAPK Pathway Inhibition.

Wang B, Krall EB, Aguirre AJ, Kim M, Widlund HR, Doshi MB, Sicinska E, Sulahian R, Goodale A, Cowley GS, Piccioni F, Doench JG, Root DE, Hahn WC.

Cell Rep. 2017 Feb 7;18(6):1543-1557. doi: 10.1016/j.celrep.2017.01.031.

28.

KEAP1 loss modulates sensitivity to kinase targeted therapy in lung cancer.

Krall EB, Wang B, Munoz DM, Ilic N, Raghavan S, Niederst MJ, Yu K, Ruddy DA, Aguirre AJ, Kim JW, Redig AJ, Gainor JF, Williams JA, Asara JM, Doench JG, Janne PA, Shaw AT, McDonald Iii RE, Engelman JA, Stegmeier F, Schlabach MR, Hahn WC.

Elife. 2017 Feb 1;6. pii: e18970. doi: 10.7554/eLife.18970. Erratum in: Elife. 2017 Oct 31;6:.

29.

Creation of Novel Protein Variants with CRISPR/Cas9-Mediated Mutagenesis: Turning a Screening By-Product into a Discovery Tool.

Donovan KF, Hegde M, Sullender M, Vaimberg EW, Johannessen CM, Root DE, Doench JG.

PLoS One. 2017 Jan 24;12(1):e0170445. doi: 10.1371/journal.pone.0170445. eCollection 2017.

30.

Genetic and Proteomic Interrogation of Lower Confidence Candidate Genes Reveals Signaling Networks in β-Catenin-Active Cancers.

Rosenbluh J, Mercer J, Shrestha Y, Oliver R, Tamayo P, Doench JG, Tirosh I, Piccioni F, Hartenian E, Horn H, Fagbami L, Root DE, Jaffe J, Lage K, Boehm JS, Hahn WC.

Cell Syst. 2016 Sep 28;3(3):302-316.e4. doi: 10.1016/j.cels.2016.09.001.

31.

A Genome-wide CRISPR Death Screen Identifies Genes Essential for Oxidative Phosphorylation.

Arroyo JD, Jourdain AA, Calvo SE, Ballarano CA, Doench JG, Root DE, Mootha VK.

Cell Metab. 2016 Dec 13;24(6):875-885. doi: 10.1016/j.cmet.2016.08.017. Epub 2016 Sep 22.

32.

Bromodomain Inhibitors Correct Bioenergetic Deficiency Caused by Mitochondrial Disease Complex I Mutations.

Barrow JJ, Balsa E, Verdeguer F, Tavares CD, Soustek MS, Hollingsworth LR 4th, Jedrychowski M, Vogel R, Paulo JA, Smeitink J, Gygi SP, Doench J, Root DE, Puigserver P.

Mol Cell. 2016 Oct 6;64(1):163-175. doi: 10.1016/j.molcel.2016.08.023. Epub 2016 Sep 22.

33.

CRISPR/Cas9 gene editing special issue.

Doench JG.

FEBS J. 2016 Sep;283(17):3160-1. doi: 10.1111/febs.13823.

34.

Discovery of a proteinaceous cellular receptor for a norovirus.

Orchard RC, Wilen CB, Doench JG, Baldridge MT, McCune BT, Lee YC, Lee S, Pruett-Miller SM, Nelson CA, Fremont DH, Virgin HW.

Science. 2016 Aug 26;353(6302):933-6. doi: 10.1126/science.aaf1220. Epub 2016 Aug 18.

35.

High-throughput Phenotyping of Lung Cancer Somatic Mutations.

Berger AH, Brooks AN, Wu X, Shrestha Y, Chouinard C, Piccioni F, Bagul M, Kamburov A, Imielinski M, Hogstrom L, Zhu C, Yang X, Pantel S, Sakai R, Watson J, Kaplan N, Campbell JD, Singh S, Root DE, Narayan R, Natoli T, Lahr DL, Tirosh I, Tamayo P, Getz G, Wong B, Doench J, Subramanian A, Golub TR, Meyerson M, Boehm JS.

Cancer Cell. 2016 Aug 8;30(2):214-228. doi: 10.1016/j.ccell.2016.06.022. Epub 2016 Jul 28. Erratum in: Cancer Cell. 2017 Dec 11;32(6):884.

36.

CRISPR/Cas9 Screens Reveal Requirements for Host Cell Sulfation and Fucosylation in Bacterial Type III Secretion System-Mediated Cytotoxicity.

Blondel CJ, Park JS, Hubbard TP, Pacheco AR, Kuehl CJ, Walsh MJ, Davis BM, Gewurz BE, Doench JG, Waldor MK.

Cell Host Microbe. 2016 Aug 10;20(2):226-37. doi: 10.1016/j.chom.2016.06.010. Epub 2016 Jul 21.

37.

Systematic Functional Interrogation of Rare Cancer Variants Identifies Oncogenic Alleles.

Kim E, Ilic N, Shrestha Y, Zou L, Kamburov A, Zhu C, Yang X, Lubonja R, Tran N, Nguyen C, Lawrence MS, Piccioni F, Bagul M, Doench JG, Chouinard CR, Wu X, Hogstrom L, Natoli T, Tamayo P, Horn H, Corsello SM, Lage K, Root DE, Subramanian A, Golub TR, Getz G, Boehm JS, Hahn WC.

Cancer Discov. 2016 Jul;6(7):714-26. doi: 10.1158/2159-8290.CD-16-0160. Epub 2016 May 4.

38.

Optimized sgRNA design to maximize activity and minimize off-target effects of CRISPR-Cas9.

Doench JG, Fusi N, Sullender M, Hegde M, Vaimberg EW, Donovan KF, Smith I, Tothova Z, Wilen C, Orchard R, Virgin HW, Listgarten J, Root DE.

Nat Biotechnol. 2016 Feb;34(2):184-191. doi: 10.1038/nbt.3437. Epub 2016 Jan 18.

39.

Morphological Profiles of RNAi-Induced Gene Knockdown Are Highly Reproducible but Dominated by Seed Effects.

Singh S, Wu X, Ljosa V, Bray MA, Piccioni F, Root DE, Doench JG, Boehm JS, Carpenter AE.

PLoS One. 2015 Jul 21;10(7):e0131370. doi: 10.1371/journal.pone.0131370. eCollection 2015.

40.

Functional genomics identifies negative regulatory nodes controlling phagocyte oxidative burst.

Graham DB, Becker CE, Doan A, Goel G, Villablanca EJ, Knights D, Mok A, Ng AC, Doench JG, Root DE, Clish CB, Xavier RJ.

Nat Commun. 2015 Jul 21;6:7838. doi: 10.1038/ncomms8838.

41.

Integrative Analyses of Human Reprogramming Reveal Dynamic Nature of Induced Pluripotency.

Cacchiarelli D, Trapnell C, Ziller MJ, Soumillon M, Cesana M, Karnik R, Donaghey J, Smith ZD, Ratanasirintrawoot S, Zhang X, Ho Sui SJ, Wu Z, Akopian V, Gifford CA, Doench J, Rinn JL, Daley GQ, Meissner A, Lander ES, Mikkelsen TS.

Cell. 2015 Jul 16;162(2):412-424. doi: 10.1016/j.cell.2015.06.016.

42.

Malaria. A forward genetic screen identifies erythrocyte CD55 as essential for Plasmodium falciparum invasion.

Egan ES, Jiang RH, Moechtar MA, Barteneva NS, Weekes MP, Nobre LV, Gygi SP, Paulo JA, Frantzreb C, Tani Y, Takahashi J, Watanabe S, Goldberg J, Paul AS, Brugnara C, Root DE, Wiegand RC, Doench JG, Duraisingh MT.

Science. 2015 May 8;348(6235):711-4. doi: 10.1126/science.aaa3526.

43.

Alternative to the soft-agar assay that permits high-throughput drug and genetic screens for cellular transformation.

Rotem A, Janzer A, Izar B, Ji Z, Doench JG, Garraway LA, Struhl K.

Proc Natl Acad Sci U S A. 2015 May 5;112(18):5708-13. doi: 10.1073/pnas.1505979112. Epub 2015 Apr 20.

44.

DOT1L inhibits SIRT1-mediated epigenetic silencing to maintain leukemic gene expression in MLL-rearranged leukemia.

Chen CW, Koche RP, Sinha AU, Deshpande AJ, Zhu N, Eng R, Doench JG, Xu H, Chu SH, Qi J, Wang X, Delaney C, Bernt KM, Root DE, Hahn WC, Bradner JE, Armstrong SA.

Nat Med. 2015 Apr;21(4):335-43. doi: 10.1038/nm.3832. Epub 2015 Mar 30.

45.

Genetic screens and functional genomics using CRISPR/Cas9 technology.

Hartenian E, Doench JG.

FEBS J. 2015 Apr;282(8):1383-93. doi: 10.1111/febs.13248. Epub 2015 Mar 16. Review.

46.

HDAC5 controls MEF2C-driven sclerostin expression in osteocytes.

Wein MN, Spatz J, Nishimori S, Doench J, Root D, Babij P, Nagano K, Baron R, Brooks D, Bouxsein M, Pajevic PD, Kronenberg HM.

J Bone Miner Res. 2015 Mar;30(3):400-11. doi: 10.1002/jbmr.2381.

47.

Rational design of highly active sgRNAs for CRISPR-Cas9-mediated gene inactivation.

Doench JG, Hartenian E, Graham DB, Tothova Z, Hegde M, Smith I, Sullender M, Ebert BL, Xavier RJ, Root DE.

Nat Biotechnol. 2014 Dec;32(12):1262-7. doi: 10.1038/nbt.3026. Epub 2014 Sep 3.

48.

Targeted shRNA screening identified critical roles of pleckstrin-2 in erythropoiesis.

Zhao B, Keerthivasan G, Mei Y, Yang J, McElherne J, Wong P, Doench JG, Feng G, Root DE, Ji P.

Haematologica. 2014 Jul;99(7):1157-67. doi: 10.3324/haematol.2014.105809. Epub 2014 Apr 18.

49.

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

Shalem O, Sanjana NE, Hartenian E, Shi X, Scott DA, Mikkelson T, Heckl D, Ebert BL, Root DE, Doench JG, Zhang F.

Science. 2014 Jan 3;343(6166):84-87. doi: 10.1126/science.1247005. Epub 2013 Dec 12.

50.

Discovery and characterization of super-enhancer-associated dependencies in diffuse large B cell lymphoma.

Chapuy B, McKeown MR, Lin CY, Monti S, Roemer MG, Qi J, Rahl PB, Sun HH, Yeda KT, Doench JG, Reichert E, Kung AL, Rodig SJ, Young RA, Shipp MA, Bradner JE.

Cancer Cell. 2013 Dec 9;24(6):777-90. doi: 10.1016/j.ccr.2013.11.003. Erratum in: Cancer Cell. 2014 Apr 14;25(4):545-6.

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