Johnson H, Lescarbeau RS, Gutierrez JA, White FM. Phosphotyrosine Profiling of
NSCLC cells in Response to EGF and HGF Reveals Network Specific Mediators of
Invasion. J Proteome Res. 2013 Feb 26. [Epub ahead of print] PubMed PMID:

Winter GE, Rix U, Carlson SM, Gleixner KV, Grebien F, Gridling M, Müller AC,
Breitwieser FP, Bilban M, Colinge J, Valent P, Bennett KL, White FM,
Superti-Furga G. Systems-pharmacology dissection of a drug synergy in
imatinib-resistant CML. Nat Chem Biol. 2012 Nov;8(11):905-12. doi:
10.1038/nchembio.1085. Epub 2012 Sep 30. PubMed PMID: 23023260.

Johnson H, Del Rosario AM, Bryson BD, Schroeder MA, Sarkaria JN, White FM.
Molecular characterization of EGFR and EGFRvIII signaling networks in human
glioblastoma tumor xenografts. Mol Cell Proteomics. 2012 Dec;11(12):1724-40. doi:
10.1074/mcp.M112.019984. Epub 2012 Sep 10. PubMed PMID: 22964225; PubMed Central
PMCID: PMC3518138.

Naegle KM, White FM, Lauffenburger DA, Yaffe MB. Robust co-regulation of
tyrosine phosphorylation sites on proteins reveals novel protein interactions.
Mol Biosyst. 2012 Oct;8(10):2771-82. doi: 10.1039/c2mb25200g. PubMed PMID:
22851037; PubMed Central PMCID: PMC3501258.

Bryson BD, White FM. Signaling for death: tyrosine phosphorylation in the
response to glucose deprivation. Mol Syst Biol. 2012 Jun 26;8:591. doi:
10.1038/msb.2012.27. PubMed PMID: 22735337; PubMed Central PMCID: PMC3397416.

Johnson H, White FM. Toward quantitative phosphotyrosine profiling in vivo.
Semin Cell Dev Biol. 2012 Oct;23(8):854-62. doi: 10.1016/j.semcdb.2012.05.008.
Epub 2012 Jun 5. PubMed PMID: 22677333; PubMed Central PMCID: PMC3496061.

Carlson SM, White FM. Labeling and identification of direct kinase substrates.
Sci Signal. 2012 Jun 5;5(227):pl3. doi: 10.1126/scisignal.2002568. PubMed PMID:

Jun HJ, Johnson H, Bronson RT, de Feraudy S, White F, Charest A. The oncogenic
lung cancer fusion kinase CD74-ROS activates a novel invasiveness pathway through
E-Syt1 phosphorylation. Cancer Res. 2012 Aug 1;72(15):3764-74. doi:
10.1158/0008-5472.CAN-11-3990. Epub 2012 Jun 1. PubMed PMID: 22659450.

Carlson SM, White FM. Expanding applications of chemical genetics in signal
transduction. Cell Cycle. 2012 May 15;11(10):1903-9. doi: 10.4161/cc.19956. Epub
2012 May 15. PubMed PMID: 22544320; PubMed Central PMCID: PMC3359120.

Hackel BJ, Neil JR, White FM, Wittrup KD. Epidermal growth factor receptor
downregulation by small heterodimeric binding proteins. Protein Eng Des Sel. 2012
Feb;25(2):47-57. doi: 10.1093/protein/gzr056. Epub 2011 Dec 9. PubMed PMID:
22160867; PubMed Central PMCID: PMC3286197.

Carlson SM, Chouinard CR, Labadorf A, Lam CJ, Schmelzle K, Fraenkel E, White
FM. Large-scale discovery of ERK2 substrates identifies ERK-mediated
transcriptional regulation by ETV3. Sci Signal. 2011 Oct 25;4(196):rs11. doi:
10.1126/scisignal.2002010. PubMed PMID: 22028470.

Hagen DR, Apgar JF, Witmer DK, White FM, Tidor B. Reply to Comment on "Sloppy
models, parameter uncertainty, and the role of experimental design". Mol Biosyst.
2011 Aug 1;7(8):2523-2524. PubMed PMID: 23148131; PubMed Central PMCID:

Naegle KM, Welsch RE, Yaffe MB, White FM, Lauffenburger DA. MCAM: multiple
clustering analysis methodology for deriving hypotheses and insights from
high-throughput proteomic datasets. PLoS Comput Biol. 2011 Jul;7(7):e1002119.
doi: 10.1371/journal.pcbi.1002119. Epub 2011 Jul 21. PubMed PMID: 21799663;
PubMed Central PMCID: PMC3140961.

White FM. The potential cost of high-throughput proteomics. Sci Signal. 2011
Feb 15;4(160):pe8. doi: 10.1126/scisignal.2001813. PubMed PMID: 21325204.

Liu H, Ong SE, Badu-Nkansah K, Schindler J, White FM, Hynes RO.
CUB-domain-containing protein 1 (CDCP1) activates Src to promote melanoma
metastasis. Proc Natl Acad Sci U S A. 2011 Jan 25;108(4):1379-84. doi:
10.1073/pnas.1017228108. Epub 2011 Jan 10. PubMed PMID: 21220330; PubMed Central
PMCID: PMC3029734.

Carlson SM, White FM. Using small molecules and chemical genetics to
interrogate signaling networks. ACS Chem Biol. 2011 Jan 21;6(1):75-85. doi:
10.1021/cb1002834. Epub 2010 Nov 29. Review. PubMed PMID: 21077690.

Lahesmaa-Korpinen AM, Carlson SM, White FM, Hautaniemi S. Integrated data
management and validation platform for phosphorylated tandem mass spectrometry
data. Proteomics. 2010 Oct;10(19):3515-24. doi: 10.1002/pmic.200900727. PubMed
PMID: 20827731; PubMed Central PMCID: PMC3017393.

Naegle KM, Gymrek M, Joughin BA, Wagner JP, Welsch RE, Yaffe MB,
Lauffenburger DA, White FM. PTMScout, a Web resource for analysis of high
throughput post-translational proteomics studies. Mol Cell Proteomics. 2010
Nov;9(11):2558-70. doi: 10.1074/mcp.M110.001206. Epub 2010 Jul 14. PubMed PMID:
20631208; PubMed Central PMCID: PMC2984232.

Spangler JB, Neil JR, Abramovitch S, Yarden Y, White FM, Lauffenburger DA,
Wittrup KD. Combination antibody treatment down-regulates epidermal growth factor
receptor by inhibiting endosomal recycling. Proc Natl Acad Sci U S A. 2010 Jul
27;107(30):13252-7. doi: 10.1073/pnas.0913476107. Epub 2010 Jul 7. PubMed PMID:
20616078; PubMed Central PMCID: PMC2922117.

Apgar JF, Witmer DK, White FM, Tidor B. Sloppy models, parameter uncertainty,
and the role of experimental design. Mol Biosyst. 2010 Oct;6(10):1890-900. doi:
10.1039/b918098b. Epub 2010 Jun 17. PubMed PMID: 20556289.

Huang PH, Miraldi ER, Xu AM, Kundukulam VA, Del Rosario AM, Flynn RA, Cavenee
WK, Furnari FB, White FM. Phosphotyrosine signaling analysis of site-specific
mutations on EGFRvIII identifies determinants governing glioblastoma cell growth.
Mol Biosyst. 2010 Jul;6(7):1227-37. doi: 10.1039/c001196g. Epub 2010 May 11.
PubMed PMID: 20461251; PubMed Central PMCID: PMC3291333.

Iwai LK, Benoist C, Mathis D, White FM. Quantitative phosphoproteomic
analysis of T cell receptor signaling in diabetes prone and resistant mice. J
Proteome Res. 2010 Jun 4;9(6):3135-45. doi: 10.1021/pr100035b. PubMed PMID:

Del Rosario AM, White FM. Quantifying oncogenic phosphotyrosine signaling
networks through systems biology. Curr Opin Genet Dev. 2010 Feb;20(1):23-30. doi:
10.1016/j.gde.2009.12.005. Epub 2010 Jan 13. Review. PubMed PMID: 20074929.

Huang PH, Xu AM, White FM. Oncogenic EGFR signaling networks in glioma. Sci
Signal. 2009 Sep 8;2(87):re6. doi: 10.1126/scisignal.287re6. Review. Erratum in:
Sci Signal. 2009 Sep 22;2(89):er7. PubMed PMID: 19738203.

Morel C, Carlson SM, White FM, Davis RJ. Mcl-1 integrates the opposing
actions of signaling pathways that mediate survival and apoptosis. Mol Cell Biol.
2009 Jul;29(14):3845-52. doi: 10.1128/MCB.00279-09. Epub 2009 May 11. PubMed
PMID: 19433446; PubMed Central PMCID: PMC2704749.

Nichols AM, White FM. Manual validation of peptide sequence and sites of
tyrosine phosphorylation from MS/MS spectra. Methods Mol Biol. 2009;492:143-60.
doi: 10.1007/978-1-59745-493-3_8. PubMed PMID: 19241031.

Stevens AL, Wishnok JS, White FM, Grodzinsky AJ, Tannenbaum SR. Mechanical
injury and cytokines cause loss of cartilage integrity and upregulate proteins
associated with catabolism, immunity, inflammation, and repair. Mol Cell
Proteomics. 2009 Jul;8(7):1475-89. doi: 10.1074/mcp.M800181-MCP200. Epub 2009 Feb
4. PubMed PMID: 19196708; PubMed Central PMCID: PMC2709180.

Joughin BA, Naegle KM, Huang PH, Yaffe MB, Lauffenburger DA, White FM. An
integrated comparative phosphoproteomic and bioinformatic approach reveals a
novel class of MPM-2 motifs upregulated in EGFRvIII-expressing glioblastoma
cells. Mol Biosyst. 2009 Jan;5(1):59-67. doi: 10.1039/b815075c. Epub 2008 Oct 30.
PubMed PMID: 19081932; PubMed Central PMCID: PMC2701618.

Huang PH, White FM. Phosphoproteomics: unraveling the signaling web. Mol
Cell. 2008 Sep 26;31(6):777-81. doi: 10.1016/j.molcel.2008.09.001. Review. PubMed
PMID: 18922462; PubMed Central PMCID: PMC2754874.

Nita-Lazar A, Saito-Benz H, White FM. Quantitative phosphoproteomics by mass
spectrometry: past, present, and future. Proteomics. 2008 Nov;8(21):4433-43. doi:
10.1002/pmic.200800231. Review. PubMed PMID: 18846511; PubMed Central PMCID:

Tedford NC, White FM, Radding JA. Illuminating signaling network functional
biology through quantitative phosphoproteomic mass spectrometry. Brief Funct
Genomic Proteomic. 2008 Sep;7(5):383-94. doi: 10.1093/bfgp/eln037. Epub 2008 Oct
4. PubMed PMID: 18836207.

White FM. Quantitative phosphoproteomic analysis of signaling network
dynamics. Curr Opin Biotechnol. 2008 Aug;19(4):404-9. doi:
10.1016/j.copbio.2008.06.006. Epub 2008 Jul 24. Review. PubMed PMID: 18619541;
PubMed Central PMCID: PMC2567239.

Apgar JF, Toettcher JE, Endy D, White FM, Tidor B. Stimulus design for model
selection and validation in cell signaling. PLoS Comput Biol. 2008 Feb;4(2):e30.
doi: 10.1371/journal.pcbi.0040030. PubMed PMID: 18282085; PubMed Central PMCID:

Huang PH, Cavenee WK, Furnari FB, White FM. Uncovering therapeutic targets
for glioblastoma: a systems biology approach. Cell Cycle. 2007 Nov
15;6(22):2750-4. Epub 2007 Aug 20. Review. PubMed PMID: 17986864.

White FM. Cell system perturbation for time-resolved quantification of
tyrosine phosphorylation in complex samples. Conf Proc IEEE Eng Med Biol Soc.
2006;1:51-2. PubMed PMID: 17946778.

White FM. On the iTRAQ of kinase inhibitors. Nat Biotechnol. 2007
Sep;25(9):994-6. PubMed PMID: 17846628.

Huang PH, Mukasa A, Bonavia R, Flynn RA, Brewer ZE, Cavenee WK, Furnari FB,
White FM. Quantitative analysis of EGFRvIII cellular signaling networks reveals a
combinatorial therapeutic strategy for glioblastoma. Proc Natl Acad Sci U S A.
2007 Jul 31;104(31):12867-72. Epub 2007 Jul 23. PubMed PMID: 17646646; PubMed
Central PMCID: PMC1937558.

Zhang Y, Wolf-Yadlin A, White FM. Quantitative proteomic analysis of
phosphotyrosine-mediated cellular signaling networks. Methods Mol Biol.
2007;359:203-12. PubMed PMID: 17484120.

Wolf-Yadlin A, Hautaniemi S, Lauffenburger DA, White FM. Multiple reaction
monitoring for robust quantitative proteomic analysis of cellular signaling
networks. Proc Natl Acad Sci U S A. 2007 Apr 3;104(14):5860-5. Epub 2007 Mar 26.
PubMed PMID: 17389395; PubMed Central PMCID: PMC1851582.

Wilker EW, van Vugt MA, Artim SA, Huang PH, Petersen CP, Reinhardt HC, Feng
Y, Sharp PA, Sonenberg N, White FM, Yaffe MB. 14-3-3sigma controls mitotic
translation to facilitate cytokinesis. Nature. 2007 Mar 15;446(7133):329-32.
PubMed PMID: 17361185.

Yaffe MB, White FM. Signaling netwErks get the global treatment. Genome Biol.
2007;8(1):202. PubMed PMID: 17274840; PubMed Central PMCID: PMC1839117.

Kumar N, Wolf-Yadlin A, White FM, Lauffenburger DA. Modeling HER2 effects on
cell behavior from mass spectrometry phosphotyrosine data. PLoS Comput Biol. 2007
Jan 5;3(1):e4. Epub 2006 Nov 21. PubMed PMID: 17206861; PubMed Central PMCID:

Tannenbaum SR, White FM. Regulation and specificity of S-nitrosylation and
denitrosylation. ACS Chem Biol. 2006 Nov 21;1(10):615-8. Review. PubMed PMID:

Albeck JG, MacBeath G, White FM, Sorger PK, Lauffenburger DA, Gaudet S.
Collecting and organizing systematic sets of protein data. Nat Rev Mol Cell Biol.
2006 Nov;7(11):803-12. Review. PubMed PMID: 17057751.

Wolf-Yadlin A, Kumar N, Zhang Y, Hautaniemi S, Zaman M, Kim HD, Grantcharova
V, Lauffenburger DA, White FM. Effects of HER2 overexpression on cell signaling
networks governing proliferation and migration. Mol Syst Biol. 2006;2:54. Epub
2006 Oct 3. PubMed PMID: 17016520; PubMed Central PMCID: PMC1682017.

Schmelzle K, Kane S, Gridley S, Lienhard GE, White FM. Temporal dynamics of
tyrosine phosphorylation in insulin signaling. Diabetes. 2006 Aug;55(8):2171-9.
PubMed PMID: 16873679.

Schmelzle K, White FM. Phosphoproteomic approaches to elucidate cellular
signaling networks. Curr Opin Biotechnol. 2006 Aug;17(4):406-14. Epub 2006 Jun
27. Review. PubMed PMID: 16806894.

Brar GA, Kiburz BM, Zhang Y, Kim JE, White F, Amon A. Rec8 phosphorylation
and recombination promote the step-wise loss of cohesins in meiosis. Nature. 2006
May 25;441(7092):532-6. Epub 2006 May 3. PubMed PMID: 16672979.

Kim JE, White FM. Quantitative analysis of phosphotyrosine signaling networks
triggered by CD3 and CD28 costimulation in Jurkat cells. J Immunol. 2006 Mar
1;176(5):2833-43. PubMed PMID: 16493040.

Moser K, White FM. Phosphoproteomic analysis of rat liver by high capacity
IMAC and LC-MS/MS. J Proteome Res. 2006 Jan;5(1):98-104. PubMed PMID: 16396499.

Behr JR, Matsumoto Y, White FM, Sasisekharan R. 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. PubMed PMID:

Kim JE, Tannenbaum SR, White FM. Global phosphoproteome of HT-29 human colon
adenocarcinoma cells. J Proteome Res. 2005 Jul-Aug;4(4):1339-46. PubMed PMID:

Chen WG, White FM. Proteomic analysis of cellular signaling. Expert Rev
Proteomics. 2004 Oct;1(3):343-54. Review. PubMed PMID: 15966830.

Zhang Y, Wolf-Yadlin A, Ross PL, Pappin DJ, Rush J, Lauffenburger DA, White
FM. Time-resolved mass spectrometry of tyrosine phosphorylation sites in the
epidermal growth factor receptor signaling network reveals dynamic modules. Mol
Cell Proteomics. 2005 Sep;4(9):1240-50. Epub 2005 Jun 11. PubMed PMID: 15951569.

Zarling AL, Luckey CJ, Marto JA, White FM, Brame CJ, Evans AM, Lehner PJ,
Cresswell P, Shabanowitz J, Hunt DF, Engelhard VH. Tapasin is a facilitator, not
an editor, of class I MHC peptide binding. J Immunol. 2003 Nov
15;171(10):5287-95. PubMed PMID: 14607930.

Saibil SD, Ohteki T, White FM, Luscher M, Zakarian A, Elford A, Shabanowitz
J, Nishina H, Hugo P, Penninger J, Barber B, Hunt DF, Ohashi PS. Weak agonist
self-peptides promote selection and tuning of virus-specific T cells. Eur J
Immunol. 2003 Mar;33(3):685-96. PubMed PMID: 12616489.

Ficarro S, Chertihin O, Westbrook VA, White F, Jayes F, Kalab P, Marto JA,
Shabanowitz J, Herr JC, Hunt DF, Visconti PE. Phosphoproteome analysis of
capacitated human sperm. Evidence of tyrosine phosphorylation of a
kinase-anchoring protein 3 and valosin-containing protein/p97 during
capacitation. J Biol Chem. 2003 Mar 28;278(13):11579-89. Epub 2002 Dec 30. PubMed
PMID: 12509440.

Lippolis JD, White FM, Marto JA, Luckey CJ, Bullock TN, Shabanowitz J, Hunt
DF, Engelhard VH. Analysis of MHC class II antigen processing by quantitation of
peptides that constitute nested sets. J Immunol. 2002 Nov 1;169(9):5089-97.
PubMed PMID: 12391225.

Gioeli D, Ficarro SB, Kwiek JJ, Aaronson D, Hancock M, Catling AD, White FM,
Christian RE, Settlage RE, Shabanowitz J, Hunt DF, Weber MJ. Androgen receptor
phosphorylation. Regulation and identification of the phosphorylation sites. J
Biol Chem. 2002 Aug 9;277(32):29304-14. Epub 2002 May 15. PubMed PMID: 12015328.

Flyer DC, Ramakrishna V, Miller C, Myers H, McDaniel M, Root K, Flournoy C,
Engelhard VH, Canaday DH, Marto JA, Ross MM, Hunt DF, Shabanowitz J, White FM.
Identification by mass spectrometry of CD8(+)-T-cell Mycobacterium tuberculosis
epitopes within the Rv0341 gene product. Infect Immun. 2002 Jun;70(6):2926-32.
PubMed PMID: 12010981; PubMed Central PMCID: PMC127998.

Ficarro SB, McCleland ML, Stukenberg PT, Burke DJ, Ross MM, Shabanowitz J,
Hunt DF, White FM. Phosphoproteome analysis by mass spectrometry and its
application to Saccharomyces cerevisiae. Nat Biotechnol. 2002 Mar;20(3):301-5.
PubMed PMID: 11875433.