Forest M White

Forest M White

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High-fat diet in a mouse insulin-resistant model induces widespread rewiring of the phosphotyrosine signaling network.

Mol Syst Biol 2019 Aug;15(8):e8849

The David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA.

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http://dx.doi.org/10.15252/msb.20198849DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6674232PMC
August 2019

The Physics of Cancer.

Cancer Res 2019 May 24;79(9):2107-2110. Epub 2019 Apr 24.

Nancy E. and Peter C. Meinig School of Biomedical Engineering, Cornell University, Ithaca, New York.

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http://cancerres.aacrjournals.org/lookup/doi/10.1158/0008-54
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http://dx.doi.org/10.1158/0008-5472.CAN-18-3937DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6497564PMC
May 2019

Systemic analysis of tyrosine kinase signaling reveals a common adaptive response program in a HER2-positive breast cancer.

Sci Signal 2019 Jan 22;12(565). Epub 2019 Jan 22.

Department of Biochemistry, University of Zurich, Winterthurerstr. 190, 8057 Zurich, Switzerland.

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http://dx.doi.org/10.1126/scisignal.aau2875DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6546113PMC
January 2019

A Proteomics Approach to Profiling the Temporal Translational Response to Stress and Growth.

iScience 2018 Nov 5;9:367-381. Epub 2018 Nov 5.

Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; The Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Center for Precision Cancer Medicine, Massachusetts Institute of Technology, Cambridge, MA 02139, USA. Electronic address:

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http://dx.doi.org/10.1016/j.isci.2018.11.004DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6249402PMC
November 2018

Microtubule-Based Control of Motor-Clutch System Mechanics in Glioma Cell Migration.

Cell Rep 2018 11;25(9):2591-2604.e8

Department of Biomedical Engineering, University of Minnesota, Minneapolis, MN 55455, USA; Physical Sciences-Oncology Center, University of Minnesota, Minneapolis, MN 55455, USA. Electronic address:

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http://dx.doi.org/10.1016/j.celrep.2018.10.101DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6345402PMC
November 2018

Quantitative Analysis of Tyrosine Kinase Signaling Across Differentially Embedded Human Glioblastoma Tumors.

Methods Mol Biol 2018 ;1711:149-164

Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA.

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http://dx.doi.org/10.1007/978-1-4939-7493-1_8DOI Listing
October 2018

Src homology 2 domains enhance tyrosine phosphorylation by protecting binding sites in their target proteins from dephosphorylation.

J Biol Chem 2018 01 21;293(2):623-637. Epub 2017 Nov 21.

From the Raymond and Beverly Sackler Laboratory of Molecular Medicine, Department of Genetics and Genome Sciences, and the Richard D. Berlin Center for Cell Analysis and Modeling, University of Connecticut School of Medicine, Farmington, Connecticut 06030 and

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http://dx.doi.org/10.1074/jbc.M117.794412DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5767867PMC
January 2018

Hepatic Dysfunction Caused by Consumption of a High-Fat Diet.

Cell Rep 2017 Dec;21(11):3317-3328

Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA. Electronic address:

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http://dx.doi.org/10.1016/j.celrep.2017.11.059DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5734865PMC
December 2017

Characterization of Resistance to Osimertinib and JNJ-61186372, an EGFR/Met Bispecific Antibody, Reveals Unique and Consensus Mechanisms of Resistance.

Mol Cancer Ther 2017 11 22;16(11):2572-2585. Epub 2017 Aug 22.

Department of Biological Engineering and David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, Massachusetts.

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http://mct.aacrjournals.org/lookup/doi/10.1158/1535-7163.MCT
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http://dx.doi.org/10.1158/1535-7163.MCT-17-0413DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5669802PMC
November 2017

Measurement of Phosphorylated Peptides with Absolute Quantification.

Methods Mol Biol 2016 ;1410:281-92

Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA.

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http://dx.doi.org/10.1007/978-1-4939-3524-6_17DOI Listing
December 2016

Revealing disease-associated pathways by network integration of untargeted metabolomics.

Nat Methods 2016 09 1;13(9):770-6. Epub 2016 Aug 1.

Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA.

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http://dx.doi.org/10.1038/nmeth.3940DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5209295PMC
September 2016

Identification of Direct Kinase Substrates Using Analogue-Sensitive Alleles.

Methods Mol Biol 2016 ;1355:71-84

Whitehead Institute for Biomedical Research, Cambridge, MA, 02142, USA.

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http://dx.doi.org/10.1007/978-1-4939-3049-4_5DOI Listing
August 2016

A Thermodynamic-Based Interpretation of Protein Expression Heterogeneity in Different Glioblastoma Multiforme Tumors Identifies Tumor-Specific Unbalanced Processes.

J Phys Chem B 2016 07 12;120(26):5990-7. Epub 2016 Apr 12.

Department of Molecular and Medical Pharmacology, David Geffen School of Medicine and Department of Chemistry and Biochemistry, UCLA , Los Angeles, California 90095, United States.

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http://pubs.acs.org/doi/10.1021/acs.jpcb.6b01692
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http://dx.doi.org/10.1021/acs.jpcb.6b01692DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4937832PMC
July 2016

Methods for the Analysis of Protein Phosphorylation-Mediated Cellular Signaling Networks.

Annu Rev Anal Chem (Palo Alto Calif) 2016 06 30;9(1):295-315. Epub 2016 Mar 30.

Department of Genome Sciences, University of Washington, Seattle, Washington 98105; email:

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http://dx.doi.org/10.1146/annurev-anchem-071015-041542DOI Listing
June 2016

Quantitative Phosphoproteomics Reveals Wee1 Kinase as a Therapeutic Target in a Model of Proneural Glioblastoma.

Mol Cancer Ther 2016 06 17;15(6):1332-43. Epub 2016 May 17.

Department of Biological Engineering and David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, Massachusetts.

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http://dx.doi.org/10.1158/1535-7163.MCT-15-0692DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4893926PMC
June 2016

Network Modeling Identifies Patient-specific Pathways in Glioblastoma.

Sci Rep 2016 06 29;6:28668. Epub 2016 Jun 29.

Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, 02139, USA.

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http://dx.doi.org/10.1038/srep28668DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4926112PMC
June 2016

Quantitative Profiling of Lysine Acetylation Reveals Dynamic Crosstalk between Receptor Tyrosine Kinases and Lysine Acetylation.

PLoS One 2015 15;10(5):e0126242. Epub 2015 May 15.

Department of Biological Engineering, Massachusetts Institute of Technology (MIT), Cambridge, Massachusetts, United States of America; David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology (MIT), Cambridge, Massachusetts, United States of America.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0126242PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4433260PMC
April 2016

Time-resolved multimodal analysis of Src Homology 2 (SH2) domain binding in signaling by receptor tyrosine kinases.

Elife 2016 Apr 12;5:e11835. Epub 2016 Apr 12.

Raymond and Beverly Sackler Laboratory of Molecular Medicine, Department of Genetics and Genome Sciences, University of Connecticut School of Medicine, Farmington, United States.

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http://dx.doi.org/10.7554/eLife.11835DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4841779PMC
April 2016

Early signaling dynamics of the epidermal growth factor receptor.

Proc Natl Acad Sci U S A 2016 Mar 29;113(11):3114-9. Epub 2016 Feb 29.

Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139; Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139

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http://dx.doi.org/10.1073/pnas.1521288113DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4801278PMC
March 2016

CNS Anticancer Drug Discovery and Development Conference White Paper.

Neuro Oncol 2015 Nov;17 Suppl 6:vi1-26

Kaiser Permanente, Redwood City, California, USA (V.A.L.); University of Texas MD Anderson Cancer Center, Houston, TX, USA (V.A.L.); University of California, San Francisco, CA, USA (V.A.L.); SUNY Stony Brook University, Stony Brook, NY, USA (P.J.T.); Icahn School of Medicine at Mount Sinai, New York, NY, USA (J.M.G., M.R.B., A.C.D.); Columbia University Institute for Cancer Genetics, New York, NY, USA (A.I.); Fred Hutchinson Cancer Research Center, Seattle, WA, USA (P.J.P.); Genentech, Inc., South San Francisco, CA, USA (T.P.H.); University of Minnesota School of Pharmacy, Minneapolis, MN, USA (W.F.E.); Angiochem, Inc., Montreal, Quebec, Canada (J.E.L.); Pfizer Oncology, San Diego, CA, USA (T.W.J.); Massachusetts Institute of Technology, Cambridge, MA, USA (F.M.W.); US Food and Drug Administration, Silver Spring, MD, USA (J.S.); Texas Tech University School of Pharmacy, Amarillo, TX, USA (Q.R.S., R.S.); NewGen Therapeutics, Inc., Menlo Park, CA, USA (W.S.); Mayo Clinic, Rochester, MN, USA (J.N.S.); Dana-Farber Cancer Institute, Boston, MA, USA (P.Y.W.); University of Texas MD Anderson Cancer Center, Houston, TX, USA (D.A.B.); Celgene Avilomics Research, Bedford, MA, USA (R.C.P.).

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http://dx.doi.org/10.1093/neuonc/nov169DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4581696PMC
November 2015

Minor Changes in Expression of the Mismatch Repair Protein MSH2 Exert a Major Impact on Glioblastoma Response to Temozolomide.

Cancer Res 2015 Aug 29;75(15):3127-38. Epub 2015 May 29.

Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, Massachusetts. Center for Environmental Health Sciences, Massachusetts Institute of Technology, Cambridge, Massachusetts. Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts.

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http://dx.doi.org/10.1158/0008-5472.CAN-14-3616DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4526337PMC
August 2015

Engineered bromodomains to explore the acetylproteome.

Proteomics 2015 May 5;15(9):1470-5. Epub 2015 Mar 5.

Department of Biological Engineering, MIT, Cambridge, MA, USA; David H. Koch Institute for Integrative Cancer Research, MIT, Cambridge, MA, USA.

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http://dx.doi.org/10.1002/pmic.201400401DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4535431PMC
May 2015

Phosphotyrosine signaling analysis in human tumors is confounded by systemic ischemia-driven artifacts and intra-specimen heterogeneity.

Cancer Res 2015 Apr 10;75(7):1495-503. Epub 2015 Feb 10.

Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts. David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, Massachusetts.

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http://cancerres.aacrjournals.org/lookup/doi/10.1158/0008-54
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http://dx.doi.org/10.1158/0008-5472.CAN-14-2309DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4383696PMC
April 2015

MARQUIS: a multiplex method for absolute quantification of peptides and posttranslational modifications.

Nat Commun 2015 Jan 12;6:5924. Epub 2015 Jan 12.

1] Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA [2] Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA.

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http://dx.doi.org/10.1038/ncomms6924DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4293043PMC
January 2015

Quantitative analysis of signaling networks across differentially embedded tumors highlights interpatient heterogeneity in human glioblastoma.

J Proteome Res 2014 Nov 24;13(11):4581-93. Epub 2014 Jun 24.

Department of Biological Engineering, Massachusetts Institute of Technology , Cambridge, Massachusetts 02139, United States.

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http://dx.doi.org/10.1021/pr500418wDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4227552PMC
November 2014

SirT1 is required in the male germ cell for differentiation and fecundity in mice.

Development 2014 Sep 19;141(18):3495-504. Epub 2014 Aug 19.

Massachusetts Institute of Technology, Department of Biology, Glenn Laboratory for the Science of Aging, Cambridge, MA 02139, USA Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA

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http://dx.doi.org/10.1242/dev.110627DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4197722PMC
September 2014

System level dynamics of post-translational modifications.

Curr Opin Biotechnol 2014 Aug 15;28:83-7. Epub 2014 Jan 15.

Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA. Electronic address:

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http://dx.doi.org/10.1016/j.copbio.2013.12.009DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4097989PMC
August 2014

Adaptive protein and phosphoprotein networks which promote therapeutic sensitivity or acquired resistance.

Biochem Soc Trans 2014 Aug;42(4):758-64

‡Department of Biological Engineering and Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, U.S.A.

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http://dx.doi.org/10.1042/BST20140038DOI Listing
August 2014

Qualitatively different T cell phenotypic responses to IL-2 versus IL-15 are unified by identical dependences on receptor signal strength and duration.

J Immunol 2014 Jan 2;192(1):123-35. Epub 2013 Dec 2.

David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139;

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http://dx.doi.org/10.4049/jimmunol.1302291DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3950894PMC
January 2014

Computer aided manual validation of mass spectrometry-based proteomic data.

Methods 2013 Jun 13;61(3):219-26. Epub 2013 Mar 13.

Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.

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http://dx.doi.org/10.1016/j.ymeth.2013.03.004DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3700613PMC
June 2013

Phosphotyrosine profiling of NSCLC cells in response to EGF and HGF reveals network specific mediators of invasion.

J Proteome Res 2013 Apr 11;12(4):1856-67. Epub 2013 Mar 11.

Department of Biological Engineering, Massachusetts Institute of Technology , Cambridge, Massachusetts, United States.

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http://dx.doi.org/10.1021/pr301192tDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3950895PMC
April 2013

Molecular characterization of EGFR and EGFRvIII signaling networks in human glioblastoma tumor xenografts.

Mol Cell Proteomics 2012 Dec 10;11(12):1724-40. Epub 2012 Sep 10.

Department of Bioengineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA.

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http://dx.doi.org/10.1074/mcp.M112.019984DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3518138PMC
December 2012

Toward quantitative phosphotyrosine profiling in vivo.

Semin Cell Dev Biol 2012 Oct 5;23(8):854-62. Epub 2012 Jun 5.

Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, United States.

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http://dx.doi.org/10.1016/j.semcdb.2012.05.008DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3496061PMC
October 2012

Robust co-regulation of tyrosine phosphorylation sites on proteins reveals novel protein interactions.

Mol Biosyst 2012 Oct;8(10):2771-82

The David H. Koch Institute for Integrative Cancer Research, Washington University in St. Louis, St. Louis, MO 63130, USA.

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http://xlink.rsc.org/?DOI=c2mb25200g
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http://dx.doi.org/10.1039/c2mb25200gDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3501258PMC
October 2012

Labeling and identification of direct kinase substrates.

Sci Signal 2012 Jun 5;5(227):pl3. Epub 2012 Jun 5.

Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA.

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http://dx.doi.org/10.1126/scisignal.2002568DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3690949PMC
June 2012

Expanding applications of chemical genetics in signal transduction.

Cell Cycle 2012 May 15;11(10):1903-9. Epub 2012 May 15.

Department of Biological Engineering; Massachusetts Institute of Technology; Cambridge, MA, USA.

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http://dx.doi.org/10.4161/cc.19956DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3359120PMC
May 2012

Epidermal growth factor receptor downregulation by small heterodimeric binding proteins.

Protein Eng Des Sel 2012 Feb 9;25(2):47-57. Epub 2011 Dec 9.

Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.

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http://dx.doi.org/10.1093/protein/gzr056DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3286197PMC
February 2012

Large-scale discovery of ERK2 substrates identifies ERK-mediated transcriptional regulation by ETV3.

Sci Signal 2011 Oct 25;4(196):rs11. Epub 2011 Oct 25.

Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.

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http://dx.doi.org/10.1126/scisignal.2002010DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3779841PMC
October 2011

Reply to Comment on "Sloppy models, parameter uncertainty, and the role of experimental design"

Mol Biosyst 2011 Aug;7(8):2523-2524

Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA ; Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA.

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http://dx.doi.org/10.1039/C1MB05200DDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3495004PMC
August 2011

MCAM: multiple clustering analysis methodology for deriving hypotheses and insights from high-throughput proteomic datasets.

PLoS Comput Biol 2011 Jul 21;7(7):e1002119. Epub 2011 Jul 21.

Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA.

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http://dx.plos.org/10.1371/journal.pcbi.1002119
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http://dx.doi.org/10.1371/journal.pcbi.1002119DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3140961PMC
July 2011

The potential cost of high-throughput proteomics.

Authors:
Forest M White

Sci Signal 2011 Feb 15;4(160):pe8. Epub 2011 Feb 15.

Department of Biological Engineering and Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.

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http://dx.doi.org/10.1126/scisignal.2001813DOI Listing
February 2011

Using small molecules and chemical genetics to interrogate signaling networks.

ACS Chem Biol 2011 Jan 29;6(1):75-85. Epub 2010 Nov 29.

Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, 02139, United States.

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http://dx.doi.org/10.1021/cb1002834DOI Listing
January 2011

CUB-domain-containing protein 1 (CDCP1) activates Src to promote melanoma metastasis.

Proc Natl Acad Sci U S A 2011 Jan 10;108(4):1379-84. Epub 2011 Jan 10.

Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.

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http://dx.doi.org/10.1073/pnas.1017228108DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3029734PMC
January 2011

PTMScout, a Web resource for analysis of high throughput post-translational proteomics studies.

Mol Cell Proteomics 2010 Nov 14;9(11):2558-70. Epub 2010 Jul 14.

Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA.

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http://dx.doi.org/10.1074/mcp.M110.001206DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2984232PMC
November 2010

Sloppy models, parameter uncertainty, and the role of experimental design.

Mol Biosyst 2010 Oct 17;6(10):1890-900. Epub 2010 Jun 17.

Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA.

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http://dx.doi.org/10.1039/b918098bDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3505121PMC
October 2010

Integrated data management and validation platform for phosphorylated tandem mass spectrometry data.

Proteomics 2010 Oct;10(19):3515-24

Genome-Scale Biology Program, Institute of Biomedicine, University of Helsinki, Helsinki, Finland.

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http://dx.doi.org/10.1002/pmic.200900727DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3017393PMC
October 2010

Combination antibody treatment down-regulates epidermal growth factor receptor by inhibiting endosomal recycling.

Proc Natl Acad Sci U S A 2010 Jul 7;107(30):13252-7. Epub 2010 Jul 7.

Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.

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http://dx.doi.org/10.1073/pnas.0913476107DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2922117PMC
July 2010

Quantitative phosphoproteomic analysis of T cell receptor signaling in diabetes prone and resistant mice.

J Proteome Res 2010 Jun;9(6):3135-45

Department of Pathology, Harvard Medical School and Section on Immunology and Immunogenetics, Joslin Diabetes Center, Boston, Massachusetts, USA.

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http://dx.doi.org/10.1021/pr100035bDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3603002PMC
June 2010

Quantifying oncogenic phosphotyrosine signaling networks through systems biology.

Curr Opin Genet Dev 2010 Feb 13;20(1):23-30. Epub 2010 Jan 13.

Department of Biological Engineering, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, USA.

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http://dx.doi.org/10.1016/j.gde.2009.12.005DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3694410PMC
February 2010

Oncogenic EGFR signaling networks in glioma.

Sci Signal 2009 Sep 8;2(87):re6. Epub 2009 Sep 8.

Protein Networks Team, Section of Cell and Molecular Biology, Institute of Cancer Research, London, UK.

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http://dx.doi.org/10.1126/scisignal.287re6DOI Listing
September 2009

Mechanical injury and cytokines cause loss of cartilage integrity and upregulate proteins associated with catabolism, immunity, inflammation, and repair.

Mol Cell Proteomics 2009 Jul 4;8(7):1475-89. Epub 2009 Feb 4.

Biological Engineering Department, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA.

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http://dx.doi.org/10.1074/mcp.M800181-MCP200DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2709180PMC
July 2009

Mcl-1 integrates the opposing actions of signaling pathways that mediate survival and apoptosis.

Mol Cell Biol 2009 Jul 11;29(14):3845-52. Epub 2009 May 11.

Howard Hughes Medical Institute and Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA 01605, USA.

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http://dx.doi.org/10.1128/MCB.00279-09DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2704749PMC
July 2009

Manual validation of peptide sequence and sites of tyrosine phosphorylation from MS/MS spectra.

Methods Mol Biol 2009 ;492:143-60

Biological Engineering Department, Massachusetts Institute of Technology, Cambridge, MA, USA.

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http://dx.doi.org/10.1007/978-1-59745-493-3_8DOI Listing
March 2009

Quantitative phosphoproteomics by mass spectrometry: past, present, and future.

Proteomics 2008 Nov;8(21):4433-43

Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.

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http://dx.doi.org/10.1002/pmic.200800231DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2701620PMC
November 2008

Illuminating signaling network functional biology through quantitative phosphoproteomic mass spectrometry.

Brief Funct Genomic Proteomic 2008 Sep 4;7(5):383-94. Epub 2008 Oct 4.

Epitome Biosystems, 100 Beaver St., Waltham, MA 02453, USA.

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http://dx.doi.org/10.1093/bfgp/eln037DOI Listing
September 2008

Phosphoproteomics: unraveling the signaling web.

Mol Cell 2008 Sep;31(6):777-81

Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2754874PMC
September 2008

Quantitative phosphoproteomic analysis of signaling network dynamics.

Authors:
Forest M White

Curr Opin Biotechnol 2008 Aug 24;19(4):404-9. Epub 2008 Jul 24.

Department of Biological Engineering and David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Building 56-787a, 77 Massachusetts Avenue, Cambridge, MA 02139, United States.

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http://dx.doi.org/10.1016/j.copbio.2008.06.006DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2567239PMC
August 2008

Cell system perturbation for time-resolved quantification of tyrosine phosphorylation in complex samples.

Authors:
Forest M White

Conf Proc IEEE Eng Med Biol Soc 2006 ;1:51-2

Biological Engineering, MIT.

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March 2008

Stimulus design for model selection and validation in cell signaling.

PLoS Comput Biol 2008 Feb;4(2):e30

Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2323406PMC
February 2008

Uncovering therapeutic targets for glioblastoma: a systems biology approach.

Cell Cycle 2007 Nov 20;6(22):2750-4. Epub 2007 Aug 20.

Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA.

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http://dx.doi.org/10.4161/cc.6.22.4922DOI Listing
November 2007

On the iTRAQ of kinase inhibitors.

Authors:
Forest M White

Nat Biotechnol 2007 Sep;25(9):994-6

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http://dx.doi.org/10.1038/nbt0907-994DOI Listing
September 2007

Quantitative analysis of EGFRvIII cellular signaling networks reveals a combinatorial therapeutic strategy for glioblastoma.

Proc Natl Acad Sci U S A 2007 Jul 23;104(31):12867-72. Epub 2007 Jul 23.

Department of Biological Engineering and Center for Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.

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http://dx.doi.org/10.1073/pnas.0705158104DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1937558PMC
July 2007

Quantitative proteomic analysis of phosphotyrosine-mediated cellular signaling networks.

Methods Mol Biol 2007 ;359:203-12

Biological Engineering Division, MIT, Cambridge, MA, USA.

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June 2007

Signaling netwErks get the global treatment.

Genome Biol 2007 ;8(1):202

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

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1839117PMC
April 2007

Multiple reaction monitoring for robust quantitative proteomic analysis of cellular signaling networks.

Proc Natl Acad Sci U S A 2007 Apr 26;104(14):5860-5. Epub 2007 Mar 26.

Biological Engineering Division, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.

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http://dx.doi.org/10.1073/pnas.0608638104DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1851582PMC
April 2007

14-3-3sigma controls mitotic translation to facilitate cytokinesis.

Nature 2007 Mar;446(7133):329-32

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

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http://dx.doi.org/10.1038/nature05584DOI Listing
March 2007

Modeling HER2 effects on cell behavior from mass spectrometry phosphotyrosine data.

PLoS Comput Biol 2007 Jan 21;3(1):e4. Epub 2006 Nov 21.

Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America.

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http://dx.doi.org/10.1371/journal.pcbi.0030004DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1761044PMC
January 2007

Collecting and organizing systematic sets of protein data.

Nat Rev Mol Cell Biol 2006 Nov;7(11):803-12

Center for Cell Decision Processes, Department of Biological Engineering, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, USA.

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November 2006

Regulation and specificity of S-nitrosylation and denitrosylation.

ACS Chem Biol 2006 Nov;1(10):615-8

Division of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA.

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http://dx.doi.org/10.1021/cb600439hDOI Listing
November 2006

Phosphoproteomic approaches to elucidate cellular signaling networks.

Curr Opin Biotechnol 2006 Aug 27;17(4):406-14. Epub 2006 Jun 27.

Biological Engineering Division, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.

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http://dx.doi.org/10.1016/j.copbio.2006.06.004DOI Listing
August 2006

Temporal dynamics of tyrosine phosphorylation in insulin signaling.

Diabetes 2006 Aug;55(8):2171-9

Biological Engineering Division, Massachusetts Institute of Technology, Cambridge, USA.

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http://dx.doi.org/10.2337/db06-0148DOI Listing
August 2006

Quantification of isomers from a mixture of twelve heparin and heparan sulfate disaccharides using tandem mass spectrometry.

Rapid Commun Mass Spectrom 2005 ;19(18):2553-62

Biological Engineering Division, 77 Massachusetts Ave., Massachusetts Institute of Technology, Cambridge, MA 02139, USA.

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http://dx.doi.org/10.1002/rcm.2079DOI Listing
March 2006

Quantitative analysis of phosphotyrosine signaling networks triggered by CD3 and CD28 costimulation in Jurkat cells.

J Immunol 2006 Mar;176(5):2833-43

Biological Engineering Division, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.

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http://dx.doi.org/10.4049/jimmunol.176.5.2833DOI Listing
March 2006

Phosphoproteomic analysis of rat liver by high capacity IMAC and LC-MS/MS.

J Proteome Res 2006 Jan;5(1):98-104

Biological Engineering Division, MIT, Cambridge, Massachusetts 02139, USA.

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http://dx.doi.org/10.1021/pr0503073DOI Listing
January 2006

Global phosphoproteome of HT-29 human colon adenocarcinoma cells.

J Proteome Res 2005 Jul-Aug;4(4):1339-46

Biological Engineering Division, Massachusetts Institute of Technology, 77 Massassachusetts Avenue, Cambridge, MA 02139, USA.

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http://dx.doi.org/10.1021/pr050048hDOI Listing
October 2005

Time-resolved mass spectrometry of tyrosine phosphorylation sites in the epidermal growth factor receptor signaling network reveals dynamic modules.

Mol Cell Proteomics 2005 Sep 11;4(9):1240-50. Epub 2005 Jun 11.

Biological Engineering Division, Massachusetts Institute of Technnology, Cambridge, Massachusetts 02139, USA.

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http://dx.doi.org/10.1074/mcp.M500089-MCP200DOI Listing
September 2005

Proteomic analysis of cellular signaling.

Expert Rev Proteomics 2004 Oct;1(3):343-54

Department of Biological Engineering, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, USA.

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http://dx.doi.org/10.1586/14789450.1.3.343DOI Listing
October 2004

Tapasin is a facilitator, not an editor, of class I MHC peptide binding.

J Immunol 2003 Nov;171(10):5287-95

Carter Immunology Center and Department of Microbiology, University of Virginia, Charlottesville, VA 22908, USA.

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http://dx.doi.org/10.4049/jimmunol.171.10.5287DOI Listing
November 2003

Weak agonist self-peptides promote selection and tuning of virus-specific T cells.

Eur J Immunol 2003 Mar;33(3):685-96

Departments of Medical Biophysics and Immunology, University Health Network, Ontario Cancer Institute, 610 University Avenue, Toronto, Ontario M5G 2M9, Canada.

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http://doi.wiley.com/10.1002/eji.200323143
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March 2003

Analysis of MHC class II antigen processing by quantitation of peptides that constitute nested sets.

J Immunol 2002 Nov;169(9):5089-97

Department of Microbiology and Carter Immunology Center, University of Virginia, Charlottesville 22908, USA.

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November 2002

Androgen receptor phosphorylation. Regulation and identification of the phosphorylation sites.

J Biol Chem 2002 Aug 15;277(32):29304-14. Epub 2002 May 15.

Department of Microbiology and Cancer Center, University of Virginia Health Sciences Center, Charlottesville, Virginia 22908, USA.

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http://www.jbc.org/lookup/doi/10.1074/jbc.M204131200
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August 2002

Phosphoproteome analysis by mass spectrometry and its application to Saccharomyces cerevisiae.

Nat Biotechnol 2002 Mar;20(3):301-5

Department of Chemistry, University of Virginia, Charlottesville, VA 22901, USA.

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March 2002