Publications by authors named "Paul A Clemons"

97Publications

Addendum: High-resolution specificity profiling and off-target prediction for site-specific DNA recombinases.

Nat Commun 2019 07 2;10(1):3003. Epub 2019 Jul 2.

Merkin Institute of Transformative Technologies in Healthcare, Broad Institute of Harvard and MIT, Cambridge, MA, 02142, USA.

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http://dx.doi.org/10.1038/s41467-019-10892-9DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6606619PMC
July 2019

DNA Barcoding a Complete Matrix of Stereoisomeric Small Molecules.

J Am Chem Soc 2019 07 25;141(26):10225-10235. Epub 2019 Jun 25.

Department of Chemistry and Chemical Biology , Harvard University , 12 Oxford Street , Cambridge , Massachusetts 02138 , United States.

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http://dx.doi.org/10.1021/jacs.9b01203DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6681660PMC
July 2019

A High-Throughput Platform to Identify Small-Molecule Inhibitors of CRISPR-Cas9.

Cell 2019 05;177(4):1067-1079.e19

Chemical Biology and Therapeutics Science Program, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Medicine, Harvard Medical School, Boston, MA 02115, USA; Divisions of Renal Medicine and Engineering, Brigham and Women's Hospital, Boston, MA 02115, USA. Electronic address:

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http://dx.doi.org/10.1016/j.cell.2019.04.009DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7182439PMC
May 2019

High-resolution specificity profiling and off-target prediction for site-specific DNA recombinases.

Nat Commun 2019 04 26;10(1):1937. Epub 2019 Apr 26.

Merkin Institute of Transformative Technologies in Healthcare, Broad Institute of Harvard and MIT, Cambridge, MA, 02142, USA.

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http://dx.doi.org/10.1038/s41467-019-09987-0DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6486577PMC
April 2019

Stabilization of the Max Homodimer with a Small Molecule Attenuates Myc-Driven Transcription.

Cell Chem Biol 2019 05 14;26(5):711-723.e14. Epub 2019 Mar 14.

David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02142, USA; Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; MIT Center for Precision Cancer Medicine, Massachusetts Institute of Technology, Cambridge, MA 02142, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA. Electronic address:

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http://dx.doi.org/10.1016/j.chembiol.2019.02.009DOI Listing
May 2019

Chemical Space Overlap with Critical Protein-Protein Interface Residues in Commercial and Specialized Small-Molecule Libraries.

ChemMedChem 2019 01 20;14(1):119-131. Epub 2018 Dec 20.

Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, IN, 46202, USA.

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http://dx.doi.org/10.1002/cmdc.201800537DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7175409PMC
January 2019

Computational Analyses Connect Small-Molecule Sensitivity to Cellular Features Using Large Panels of Cancer Cell Lines.

Methods Mol Biol 2019 ;1888:233-254

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

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http://link.springer.com/10.1007/978-1-4939-8891-4_14
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http://dx.doi.org/10.1007/978-1-4939-8891-4_14DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6563933PMC
June 2019

Modeling the impact of drug interactions on therapeutic selectivity.

Nat Commun 2018 08 27;9(1):3452. Epub 2018 Aug 27.

Faculty of Engineering and Natural Sciences, Sabanci University, 34956, Istanbul, Turkey.

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http://dx.doi.org/10.1038/s41467-018-05954-3DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6110842PMC
August 2018

Synergistic Effects of Stereochemistry and Appendages on the Performance Diversity of a Collection of Synthetic Compounds.

J Am Chem Soc 2018 09 6;140(37):11784-11790. Epub 2018 Sep 6.

Department of Chemistry and Chemical Biology , Harvard University , Cambridge , Massachusetts 02138 , United States.

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http://pubs.acs.org/doi/10.1021/jacs.8b07319
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http://dx.doi.org/10.1021/jacs.8b07319DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6644712PMC
September 2018

RWEN: response-weighted elastic net for prediction of chemosensitivity of cancer cell lines.

Bioinformatics 2018 10;34(19):3332-3339

Chemical Biology & Therapeutics Science Program, Broad Institute of Harvard and MIT, Cambridge, MA, USA.

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http://dx.doi.org/10.1093/bioinformatics/bty199DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6157095PMC
October 2018

Inhibition of Dihydroorotate Dehydrogenase Overcomes Differentiation Blockade in Acute Myeloid Leukemia.

Cell 2016 Sep 15;167(1):171-186.e15. Epub 2016 Sep 15.

Center for Regenerative Medicine, Massachusetts General Hospital, Boston, MA 02114, USA; Cancer Center, Massachusetts General Hospital, Boston, MA 02114, USA; Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138, USA; Harvard Stem Cell Institute, Cambridge, MA 02138, USA. Electronic address:

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https://linkinghub.elsevier.com/retrieve/pii/S00928674163115
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http://dx.doi.org/10.1016/j.cell.2016.08.057DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7360335PMC
September 2016

Real-Time Biological Annotation of Synthetic Compounds.

J Am Chem Soc 2016 07 11;138(28):8920-7. Epub 2016 Jul 11.

Department of Chemistry and Chemical Biology, Harvard University , 12 Oxford Street, Cambridge, Massachusetts 02138, United States.

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http://dx.doi.org/10.1021/jacs.6b04614DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4976700PMC
July 2016

Small-molecule enhancers of autophagy modulate cellular disease phenotypes suggested by human genetics.

Proc Natl Acad Sci U S A 2015 Aug 20;112(31):E4281-7. Epub 2015 Jul 20.

Center for Computational and Integrative Biology, Massachusetts General Hospital, Boston, MA 02114; Program in Medical and Population Genetics, Broad Institute, Cambridge, MA 02142; Center for the Study of Inflammatory Bowel Disease, Massachusetts General Hospital, Boston, MA 02114;

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http://dx.doi.org/10.1073/pnas.1512289112DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4534235PMC
August 2015

High-throughput luminescent reporter of insulin secretion for discovering regulators of pancreatic Beta-cell function.

Cell Metab 2015 Jan;21(1):126-37

Diabetes Unit of the Department of Medicine, Massachusetts General Hospital, Boston, MA 02114, USA; Center for Human Genetic Research, Massachusetts General Hospital, Boston, MA 02114, USA; Department of Molecular Biology, Massachusetts General Hospital, Boston, MA 02114, USA; Department of Genetics, Harvard Medical School, Boston, MA 02115, USA; Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02142, USA; Medical and Population Genetics Program, Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA.

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http://dx.doi.org/10.1016/j.cmet.2014.12.010DOI Listing
January 2015

Integrating phenotypic small-molecule profiling and human genetics: the next phase in drug discovery.

Trends Genet 2015 Jan 12;31(1):16-23. Epub 2014 Dec 12.

Center for the Science of Therapeutics, Broad Institute of Harvard and MIT, Cambridge, MA, USA. Electronic address:

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http://dx.doi.org/10.1016/j.tig.2014.11.002DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4281276PMC
January 2015

Predicting cancer-specific vulnerability via data-driven detection of synthetic lethality.

Cell 2014 Aug;158(5):1199-1209

The Blavatnik School of Computer Science, Tel Aviv University, Tel Aviv 6997801, Israel; The Sackler School of Medicine, Tel Aviv University, Tel Aviv 6997801, Israel. Electronic address:

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http://dx.doi.org/10.1016/j.cell.2014.07.027DOI Listing
August 2014

Evolving BioAssay Ontology (BAO): modularization, integration and applications.

J Biomed Semantics 2014 3;5(Suppl 1 Proceedings of the Bio-Ontologies Spec Interest G):S5. Epub 2014 Jun 3.

Center for Computational Science, University of Miami, 1320 S. Dixie Highway, Gables One Tower, 33146 Coral Gables, FL, USA ; Department of Molecular and Cellular Pharmacology, University of Miami School of Medicine, 1120 NW 14th Street, CRB 650 (M-857), 33136 Miami, FL, USA.

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http://dx.doi.org/10.1186/2041-1480-5-S1-S5DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4108877PMC
August 2014

NAMPT is the cellular target of STF-31-like small-molecule probes.

ACS Chem Biol 2014 Oct 7;9(10):2247-54. Epub 2014 Aug 7.

Center for the Science of Therapeutics and ∥Howard Hughes Medical Institute, Broad Institute , 7 Cambridge Center, Cambridge, Massachusetts 02142, United States.

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http://dx.doi.org/10.1021/cb500347pDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4201331PMC
October 2014

Knowledge from Small-Molecule Screening and Profiling Data.

J Biomol Screen 2014 Jun;19(5):611-3

Chemical Biology Program, Cambridge, MA, USA.

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http://dx.doi.org/10.1177/1087057114531209DOI Listing
June 2014

Regulation of ferroptotic cancer cell death by GPX4.

Cell 2014 Jan;156(1-2):317-331

Department of Biological Sciences, Columbia University, 1208 Northwest Corner Building, 12 Floor, 550 West 120 Street, MC 4846, New York, NY 10027, USA.

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http://dx.doi.org/10.1016/j.cell.2013.12.010DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4076414PMC
January 2014

Target identification and mechanism of action in chemical biology and drug discovery.

Nat Chem Biol 2013 Apr;9(4):232-40

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

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http://dx.doi.org/10.1038/nchembio.1199DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5543995PMC
April 2013

Utility-aware screening with clique-oriented prioritization.

J Chem Inf Model 2012 Jan 20;52(1):29-37. Epub 2011 Dec 20.

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

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http://dx.doi.org/10.1021/ci2003285DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3264765PMC
January 2012

Enhancing the rate of scaffold discovery with diversity-oriented prioritization.

Bioinformatics 2011 Aug 17;27(16):2271-8. Epub 2011 Jun 17.

Division of Laboratory and Genomic Medicine, Department of Pathology and Immunology, Washington University School of Medicine, St Louis, MO, USA.

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https://academic.oup.com/bioinformatics/article-lookup/doi/1
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http://dx.doi.org/10.1093/bioinformatics/btr369DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3150035PMC
August 2011

Master data management: getting your house in order.

Comb Chem High Throughput Screen 2011 Nov;14(9):749-56

The Broad Institute, Chemical Biology Program, Cambridge, MA 02140, USA.

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http://dx.doi.org/10.2174/138620711796957189DOI Listing
November 2011

Route to three-dimensional fragments using diversity-oriented synthesis.

Proc Natl Acad Sci U S A 2011 Apr 11;108(17):6799-804. Epub 2011 Apr 11.

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

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http://dx.doi.org/10.1073/pnas.1015271108DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3084099PMC
April 2011

The binding of fluorophores to proteins depends on the cellular environment.

Angew Chem Int Ed Engl 2011 Mar 2;50(12):2761-3. Epub 2011 Mar 2.

Department of Chemistry, National University of Singapore, Singapore.

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http://dx.doi.org/10.1002/anie.201007626DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4758120PMC
March 2011

Disease allele-dependent small-molecule sensitivities in blood cells from monogenic diabetes.

Proc Natl Acad Sci U S A 2011 Jan 23;108(2):492-7. Epub 2010 Dec 23.

Center for Systems Biology, Massachusetts General Hospital, 185 Cambridge Street, Boston, MA 02114, USA.

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http://dx.doi.org/10.1073/pnas.1016789108DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3021060PMC
January 2011

Expanding stereochemical and skeletal diversity using petasis reactions and 1,3-dipolar cycloadditions.

Org Lett 2010 Nov 26;12(22):5230-3. Epub 2010 Oct 26.

Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts 02138, United States.

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http://dx.doi.org/10.1021/ol102266jDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2979010PMC
November 2010

Small-molecule inducers of insulin expression in pancreatic alpha-cells.

Proc Natl Acad Sci U S A 2010 Aug 9;107(34):15099-104. Epub 2010 Aug 9.

Howard Hughes Medical Institute, Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, MA 02142.

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http://dx.doi.org/10.1073/pnas.1010018107DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2930573PMC
August 2010

Distinct biological network properties between the targets of natural products and disease genes.

J Am Chem Soc 2010 Jul;132(27):9259-61

Broad Institute of Harvard and MIT, 7 Cambridge Center, Cambridge, Massachusetts 02143, USA.

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http://dx.doi.org/10.1021/ja102798tDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2898216PMC
July 2010

An economic framework to prioritize confirmatory tests after a high-throughput screen.

J Biomol Screen 2010 Jul 14;15(6):680-6. Epub 2010 Jun 14.

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

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http://dx.doi.org/10.1177/1087057110372803DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3069998PMC
July 2010

Stereochemical and skeletal diversity arising from amino propargylic alcohols.

Org Lett 2010 Jun;12(12):2822-5

Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts 02138, USA.

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http://dx.doi.org/10.1021/ol100914bDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2883853PMC
June 2010

Unbiased discovery of in vivo imaging probes through in vitro profiling of nanoparticle libraries.

Integr Biol (Camb) 2009 Apr 9;1(4):311-7. Epub 2009 Feb 9.

Center for Molecular Imaging, Massachusetts General Hospital, Harvard Medical School, 149 13th St., Rm 5420, Charlestown, MA 02129, USA.

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http://dx.doi.org/10.1039/b821775kDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2748356PMC
April 2009

Connecting synthetic chemistry decisions to cell and genome biology using small-molecule phenotypic profiling.

Curr Opin Chem Biol 2009 Dec 12;13(5-6):539-48. Epub 2009 Oct 12.

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

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http://dx.doi.org/10.1016/j.cbpa.2009.09.018DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2787914PMC
December 2009

Alpha shapes applied to molecular shape characterization exhibit novel properties compared to established shape descriptors.

J Chem Inf Model 2009 Oct;49(10):2231-41

Chemical Biology Program, Broad Institute of Harvard and MIT, 7 Cambridge Center, Cambridge, Massachusetts 02142, USA.

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http://dx.doi.org/10.1021/ci900190zDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3158582PMC
October 2009

Using biological performance similarity to inform disaccharide library design.

J Am Chem Soc 2009 Apr;131(14):5075-83

Department of Chemistry and Chemical Biology, Harvard University, 12 Oxford Street, Cambridge, Massachusetts 02138, USA.

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http://dx.doi.org/10.1021/ja806583yDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2730776PMC
April 2009

Using ChemBank to probe chemical biology.

Curr Protoc Bioinformatics 2008 Jun;Chapter 14:Unit 14.5

Chemical Biology Program and Platform, Broad Institute of Harvard and MIT, Cambridge, Massachusetts, USA.

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http://dx.doi.org/10.1002/0471250953.bi1405s22DOI Listing
June 2008

Small-molecule fluorophores to detect cell-state switching in the context of high-throughput screening.

J Am Chem Soc 2008 Apr 8;130(13):4208-9. Epub 2008 Mar 8.

Chemical Biology Program, Broad Institute of Harvard and MIT, Cambridge, Massachusetts 02142, USA.

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http://dx.doi.org/10.1021/ja077656dDOI Listing
April 2008

Chemogenomic data analysis: prediction of small-molecule targets and the advent of biological fingerprint.

Comb Chem High Throughput Screen 2007 Sep;10(8):719-31

Lead Discovery Informatics, Novartis Institutes for BioMedical Research Inc., 250 Massachusetts Ave., Cambridge, MA 02139, USA.

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http://dx.doi.org/10.2174/138620707782507313DOI Listing
September 2007

ChemBank: a small-molecule screening and cheminformatics resource database.

Nucleic Acids Res 2008 Jan 18;36(Database issue):D351-9. Epub 2007 Oct 18.

Chemical Biology Program and Platform, Broad Institute of Harvard and MIT, 7 Cambridge Center, Cambridge, MA 02142, USA.

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http://dx.doi.org/10.1093/nar/gkm843DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2238881PMC
January 2008

A pipeline for ligand discovery using small-molecule microarrays.

Curr Opin Chem Biol 2007 Feb 13;11(1):74-82. Epub 2006 Dec 13.

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

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http://dx.doi.org/10.1016/j.cbpa.2006.11.031DOI Listing
February 2007

High-throughput identification of phage-derived imaging agents.

Mol Imaging 2006 Jan-Mar;5(1):24-30

Massachusetts General Hospital and Harvard Medical School, Charlestown 02129, USA.

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July 2006

SpectralNET--an application for spectral graph analysis and visualization.

BMC Bioinformatics 2005 Oct 19;6:260. Epub 2005 Oct 19.

The Broad Institute of MIT & Harvard University, Cambridge, MA 02141, USA.

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http://dx.doi.org/10.1186/1471-2105-6-260DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1276787PMC
October 2005

Mapping chemical space using molecular descriptors and chemical genetics: deacetylase inhibitors.

Comb Chem High Throughput Screen 2004 Nov;7(7):669-76

The Eli and Edythe L. Broad Institute, Massachusetts Institute of Technology and Harvard University, 320 Charles Street, Cambridge, MA 02141, USA.

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http://dx.doi.org/10.2174/1386207043328319DOI Listing
November 2004

Relationship of stereochemical and skeletal diversity of small molecules to cellular measurement space.

J Am Chem Soc 2004 Nov;126(45):14740-5

Howard Hughes Medical Institute, Department of Chemistry and Chemical Biology, and The Eli and Edythe Broad Institute, Program in Chemical Biology, Harvard University, 12 Oxford Street, Cambridge, MA 02138, USA.

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http://dx.doi.org/10.1021/ja048170pDOI Listing
November 2004

Chemical genomics: probing protein function using small molecules.

Am J Pharmacogenomics 2004 ;4(5):313-20

The Eli and Edythe L. Broad Institute, Massachusetts Institute of Technology & Harvard University, Institute of Chemistry & Cell Biology (ICCB), Initiative for Chemical Genetics, Cambridge, Massachusetts, USA.

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http://dx.doi.org/10.2165/00129785-200404050-00004DOI Listing
December 2004

Complex phenotypic assays in high-throughput screening.

Authors:
Paul A Clemons

Curr Opin Chem Biol 2004 Jun;8(3):334-8

Initiative for Chemical Genetics, ICCB-Broad Institute, Harvard University, 320 Charles Street, Room 184, Cambridge, Massachusetts 02141, USA.

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http://linkinghub.elsevier.com/retrieve/pii/S136759310400048
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http://dx.doi.org/10.1016/j.cbpa.2004.04.002DOI Listing
June 2004

Chemical genomic profiling of biological networks using graph theory and combinations of small molecule perturbations.

J Am Chem Soc 2003 Sep;125(35):10543-5

Departments of Chemistry and Chemical Biology and of Molecular and Cellular Biology, Howard Hughes Medical Institute, Harvard Institute of Chemistry & Cell Biology, Harvard University, 12 Oxford Street, Cambridge, MA 02138, USA.

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http://pubs.acs.org/doi/abs/10.1021/ja035413p
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http://dx.doi.org/10.1021/ja035413pDOI Listing
September 2003

Uncleaved BAP31 in association with A4 protein at the endoplasmic reticulum is an inhibitor of Fas-initiated release of cytochrome c from mitochondria.

J Biol Chem 2003 Apr 15;278(16):14461-8. Epub 2003 Jan 15.

Department of Biochemistry, McGill University, Montreal, Quebec H3G 1Y, Canada.

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http://dx.doi.org/10.1074/jbc.M209684200DOI Listing
April 2003

Synthesis of calcineurin-resistant derivatives of FK506 and selection of compensatory receptors.

Chem Biol 2002 Jan;9(1):49-61

Howard Hughes Medical Institute at Harvard University, Cambridge, MA 02138, USA.

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http://dx.doi.org/10.1016/s1074-5521(02)00085-6DOI Listing
January 2002