Publications by authors named "John Doench"

97Publications

CRISPR-Cas9 Genome-Wide Knockout Screen Identifies Mechanism of Selective Activity of Dehydrofalcarinol in Mesenchymal Stem-like Triple-Negative Breast Cancer Cells.

J Nat Prod 2020 Oct 6;83(10):3080-3092. Epub 2020 Oct 6.

Natural Products Discovery Group, Institute for Natural Products Applications and Research Technologies, Department of Chemistry & Biochemistry, Stephenson Life Science Research Center, University of Oklahoma, Norman, Oklahoma 73019, United States.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1021/acs.jnatprod.0c00642DOI Listing
October 2020

Illuminating Host-Mycobacterial Interactions with Genome-wide CRISPR Knockout and CRISPRi Screens.

Cell Syst 2020 Sep;11(3):239-251.e7

Antimicrobial Resistance Interdisciplinary Research Group, Singapore-MIT Alliance for Research and Technology, Singapore 138602, Singapore; Synthetic Biology Group, MIT Synthetic Biology Center, Massachusetts Institute of Technology (MIT), Cambridge, MA 02139, USA; Research Laboratory of Electronics, MIT, Cambridge, MA 02139, USA; Broad Institute, Cambridge, MA 02139, USA; Department of Electrical Engineering and Computer Science, MIT, Cambridge, MA 02139, USA; Harvard-MIT Division of Health Sciences and Technology, Cambridge, MA 02139, USA; Department of Biological Engineering, MIT, Cambridge, MA 02139, USA. Electronic address:

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1016/j.cels.2020.08.010DOI Listing
September 2020

DNA methylation enzymes and PRC1 restrict B-cell Epstein-Barr virus oncoprotein expression.

Nat Microbiol 2020 Aug 18;5(8):1051-1063. Epub 2020 May 18.

Division of Infectious Diseases, Department of Medicine, Brigham and Women's Hospital, Boston, MA, USA.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1038/s41564-020-0724-yDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7462085PMC
August 2020

MYC Controls the Epstein-Barr Virus Lytic Switch.

Mol Cell 2020 05 20;78(4):653-669.e8. Epub 2020 Apr 20.

Division of Infectious Disease, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA; Department of Microbiology, Harvard Medical School, Boston, MA 02115, USA; Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA; Harvard Graduate Program in Virology, Boston, MA 02115, USA. Electronic address:

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1016/j.molcel.2020.03.025DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7245572PMC
May 2020

Design and analysis of CRISPR-Cas experiments.

Nat Biotechnol 2020 07 13;38(7):813-823. Epub 2020 Apr 13.

Broad Institute of Harvard and MIT, Cambridge, MA, USA.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1038/s41587-020-0490-7DOI Listing
July 2020

Cytochrome P450 oxidoreductase contributes to phospholipid peroxidation in ferroptosis.

Nat Chem Biol 2020 03 17;16(3):302-309. Epub 2020 Feb 17.

Chemical Biology and Therapeutics Science Program, Broad Institute, Cambridge, MA, USA.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1038/s41589-020-0472-6DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7353921PMC
March 2020

Genetic screens in isogenic mammalian cell lines without single cell cloning.

Nat Commun 2020 02 6;11(1):752. Epub 2020 Feb 6.

Genetic Perturbation Platform, Broad Institute of MIT and Harvard, 75 Ames Street, Cambridge, MA, 02142, USA.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1038/s41467-020-14620-6DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7005275PMC
February 2020

Genome-wide In Vivo CNS Screening Identifies Genes that Modify CNS Neuronal Survival and mHTT Toxicity.

Neuron 2020 04 30;106(1):76-89.e8. Epub 2020 Jan 30.

Department of Brain and Cognitive Sciences, MIT, Cambridge, MA 02139, USA; Picower Institute for Learning and Memory, Cambridge, MA 02139, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA. Electronic address:

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1016/j.neuron.2020.01.004DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7181458PMC
April 2020

CRISPR-Switch regulates sgRNA activity by Cre recombination for sequential editing of two loci.

Nat Commun 2019 11 29;10(1):5454. Epub 2019 Nov 29.

Institute of Molecular Biotechnology of the Austrian Academy of Science (IMBA), Vienna Biocenter (VBC), Dr. Bohr Gasse 3, 1030, Vienna, Austria.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1038/s41467-019-13403-yDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6884486PMC
November 2019

A Compendium of Genetic Modifiers of Mitochondrial Dysfunction Reveals Intra-organelle Buffering.

Cell 2019 11;179(5):1222-1238.e17

Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA; Howard Hughes Medical Institute, Massachusetts General Hospital, Boston, MA 02114, USA, Massachusetts General Hospital, Boston, MA 02114, USA; Department of Molecular Biology, Massachusetts General Hospital, Boston, MA 02114, USA. Electronic address:

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1016/j.cell.2019.10.032DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7053407PMC
November 2019

CRISPR/Cas9 Screens Reveal Multiple Layers of B cell CD40 Regulation.

Cell Rep 2019 07;28(5):1307-1322.e8

Division of Infectious Diseases, Department of Medicine, Brigham and Women's Hospital, 181 Longwood Avenue, Boston, MA 02115, USA; Department of Microbiology, Harvard Medical School, Boston, MA 02115, USA; Department of Biostatistics and Bioinformatics, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL 33612, USA; Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA. Electronic address:

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1016/j.celrep.2019.06.079DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6684324PMC
July 2019

6-Phosphogluconate Dehydrogenase Links Cytosolic Carbohydrate Metabolism to Protein Secretion via Modulation of Glutathione Levels.

Cell Chem Biol 2019 09 13;26(9):1306-1314.e5. Epub 2019 Jun 13.

Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA; Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138, USA. Electronic address:

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1016/j.chembiol.2019.05.006DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6754299PMC
September 2019

CRISPR-suppressor scanning reveals a nonenzymatic role of LSD1 in AML.

Nat Chem Biol 2019 05 15;15(5):529-539. Epub 2019 Apr 15.

Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1038/s41589-019-0263-0DOI Listing
May 2019

A FACS-Based Genome-wide CRISPR Screen Reveals a Requirement for COPI in Chlamydia trachomatis Invasion.

iScience 2019 Jan 14;11:71-84. Epub 2018 Dec 14.

Howard Hughes Medical Institute, Boston, MA 02215, USA; Department of Microbiology and Immunobiology, Harvard Medical School, Boston, MA 02115, USA; Division of Infectious Diseases, Brigham & Women's Hospital, Boston 02115, MA, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA. Electronic address:

View Article

Download full-text PDF

Source
https://linkinghub.elsevier.com/retrieve/pii/S25890042183024
Publisher Site
http://dx.doi.org/10.1016/j.isci.2018.12.011DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6308251PMC
January 2019

Identification of Antinorovirus Genes in Human Cells Using Genome-Wide CRISPR Activation Screening.

J Virol 2019 01 10;93(1). Epub 2018 Dec 10.

Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, Missouri, USA

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1128/JVI.01324-18DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6288323PMC
January 2019

A case of mistaken identity.

Nat Biotechnol 2018 09;36(9):802-804

Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1038/nbt.4208DOI Listing
September 2018

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

Cell Rep 2018 07;24(4):838-850

Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Molecular Biology, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA; Gastrointestinal Unit and Center for the Study of Inflammatory Bowel Disease, Massachusetts General Hospital, Boston, MA 02114, USA; Harvard Medical School, Boston, MA 02114, USA; Center for Microbiome Informatics and Therapeutics, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Center for Computational and Integrative Biology, Massachusetts General Hospital, Boston, MA 02114, USA. Electronic address:

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1016/j.celrep.2018.06.081DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6156773PMC
July 2018

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

PLoS One 2018 25;13(5):e0197547. Epub 2018 May 25.

Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America.

View Article

Download full-text PDF

Source
http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0197547PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5969736PMC
December 2018

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

Authors:
John G Doench

Nat Rev Genet 2018 02 4;19(2):67-80. Epub 2017 Dec 4.

Genetic Perturbation Platform, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, 02142, USA.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1038/nrg.2017.97DOI Listing
February 2018

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

PLoS Genet 2017 Jul 12;13(7):e1006891. Epub 2017 Jul 12.

Interdisciplinary Biological Sciences Program, Northwestern University, Evanston, Illinois, United States of America.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1371/journal.pgen.1006891DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5529024PMC
July 2017

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

Cell Host Microbe 2017 May;21(5):580-591.e7

Division of Infectious Diseases, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA; Program in Virology, Harvard Medical School, Boston, MA 02115, USA; Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA. Electronic address:

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1016/j.chom.2017.04.005DOI Listing
May 2017

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

Nat Commun 2017 04 27;8:15110. Epub 2017 Apr 27.

Department of Medical Oncology, Dana-Farber Cancer Institute, 450 Brookline Avenue, Boston, Massachusetts 02215, USA.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1038/ncomms15110DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5414184PMC
April 2017

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

Cell Rep 2017 02;18(6):1543-1557

Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA; Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA. Electronic address:

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1016/j.celrep.2017.01.031DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5313047PMC
February 2017

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

Cell Syst 2016 09;3(3):302-316.e4

Broad Institute of Harvard and MIT, 415 Main Street, Cambridge, MA 02142, USA; Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, 450 Brookline Avenue, Boston, MA 02215, USA. Electronic address:

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1016/j.cels.2016.09.001DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5455996PMC
September 2016

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

Cell Metab 2016 12 22;24(6):875-885. Epub 2016 Sep 22.

Department of Molecular Biology and Howard Hughes Medical Institute, Massachusetts General Hospital, Boston, MA 02114, USA; Department of Systems Biology, Harvard Medical School, Boston, MA 02115, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA. Electronic address:

View Article

Download full-text PDF

Source
http://www.cell.com/cell-metabolism/pdf/S1550-4131(16)30433-
Web Search
http://www.cell.com/cms/attachment/2064501967/2065983246/mmc
Web Search
http://dx.doi.org/10.1016/j.cmet.2016.08.017DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5474757PMC
December 2016

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

Mol Cell 2016 10 22;64(1):163-175. Epub 2016 Sep 22.

Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA 02215; Department of Cell Biology, Harvard Medical School, Boston, MA, USA 02215; Broad Institute of MIT and Harvard, Cambridge, MA, USA 02142. Electronic address:

View Article

Download full-text PDF

Source
https://linkinghub.elsevier.com/retrieve/pii/S10972765163046
Publisher Site
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5055448PMC
http://dx.doi.org/10.1016/j.molcel.2016.08.023DOI Listing
October 2016

CRISPR/Cas9 gene editing special issue.

Authors:
John G Doench

FEBS J 2016 09;283(17):3160-1

Broad Institute of MIT and Harvard, Cambridge, MA, USA.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1111/febs.13823DOI Listing
September 2016

Discovery of a proteinaceous cellular receptor for a norovirus.

Science 2016 08 18;353(6302):933-6. Epub 2016 Aug 18.

Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110, USA.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1126/science.aaf1220DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5484048PMC
August 2016

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

Cell Host Microbe 2016 Aug 21;20(2):226-37. Epub 2016 Jul 21.

Division of Infectious Diseases, Brigham and Women's Hospital, Boston, MA 02115, USA; Department of Microbiology and Immunobiology, Harvard Medical School, Boston, MA 02115, USA; Howard Hughes Medical Institute, Boston, MA 02115, USA. Electronic address:

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1016/j.chom.2016.06.010DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4982808PMC
August 2016

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

Cell 2015 Jul;162(2):412-424

Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138, USA; Broad Institute, Cambridge, MA 02142, USA; Harvard Stem Cell Institute, Harvard University, Cambridge, MA 02138, USA. Electronic address:

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1016/j.cell.2015.06.016DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4511597PMC
July 2015

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

Proc Natl Acad Sci U S A 2015 May 20;112(18):5708-13. Epub 2015 Apr 20.

Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115;

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1073/pnas.1505979112DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4426412PMC
May 2015

Genetic screens and functional genomics using CRISPR/Cas9 technology.

FEBS J 2015 Apr 16;282(8):1383-93. Epub 2015 Mar 16.

Department of Molecular and Cellular Biology, University of California Berkeley, Berkeley, CA, USA.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1111/febs.13248DOI Listing
April 2015

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

Haematologica 2014 Jul 18;99(7):1157-67. Epub 2014 Apr 18.

Department of Pathology, Feinberg School of Medicine, Northwestern University, Chicago, IL

View Article

Download full-text PDF

Source
http://dx.doi.org/10.3324/haematol.2014.105809DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4077076PMC
July 2014

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

Science 2014 Jan 12;343(6166):84-87. Epub 2013 Dec 12.

Broad Institute of MIT and Harvard, 7 Cambridge Center, MA 02142, USA.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1126/science.1247005DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4089965PMC
January 2014

Kinase requirements in human cells: I. Comparing kinase requirements across various cell types.

Proc Natl Acad Sci U S A 2008 Oct 23;105(43):16472-7. Epub 2008 Oct 23.

Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, 240 Longwood Avenue, Boston, MA 02115, USA.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1073/pnas.0808019105DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2575444PMC
October 2008

Analysis of microRNA effector functions in vitro.

Methods 2007 Oct;43(2):91-104

Cancer Immunology and AIDS, Dana-Farber Cancer Institute, and Department of Pathology, Harvard Medical School, Boston, MA 02115, USA.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1016/j.ymeth.2007.04.003DOI Listing
October 2007

Comparison of siRNA-induced off-target RNA and protein effects.

RNA 2007 Mar 19;13(3):385-95. Epub 2007 Jan 19.

Center for Cancer Research, Massachusetts Institute of Technology, Cambridge 02139, USA,

View Article

Download full-text PDF

Source
http://educationgroup.mit.edu/HHMIEducationGroup/wp-content/
Web Search
http://www.rnajournal.org/cgi/doi/10.1261/rna.352507
Publisher Site
http://dx.doi.org/10.1261/rna.352507DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1800510PMC
March 2007

Recapitulation of short RNA-directed translational gene silencing in vitro.

Mol Cell 2006 May;22(4):553-60

Department of Cancer Immunology and AIDS, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts 02115, USA.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1016/j.molcel.2006.03.034DOI Listing
May 2006

RNA interference of Xenopus NMDAR NR1 in vitro and in vivo.

J Neurosci Methods 2006 Apr 22;152(1-2):65-73. Epub 2005 Sep 22.

McGovern Institute for Brain Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1016/j.jneumeth.2005.08.010DOI Listing
April 2006

Specificity of microRNA target selection in translational repression.

Genes Dev 2004 Mar 10;18(5):504-11. Epub 2004 Mar 10.

Center for Cancer Research, Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA.

View Article

Download full-text PDF

Source
http://www.genesdev.org/cgi/doi/10.1101/gad.1184404
Publisher Site
http://dx.doi.org/10.1101/gad.1184404DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC374233PMC
March 2004

siRNAs can function as miRNAs.

Genes Dev 2003 Feb;17(4):438-42

Center for Cancer Research, Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA.

View Article

Download full-text PDF

Source
http://www.genesdev.org/cgi/doi/10.1101/gad.1064703
Publisher Site
http://dx.doi.org/10.1101/gad.1064703DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC195999PMC
February 2003