CURRICULUM VITAE
David H. Koch Professor of Science
Koch Institute for Integrative Cancer Biology
Departments of Biology and Biological Engineering
Senior Associate Member, Broad Institute
Massachusetts Institute of Technology,
Cambridge, MA 02139
Attending Surgeon and Instructor
Division of Acute Care Surgery
Department of Surgery
Beth Israel Deaconess Medical Center
Harvard Medical School
Boston, MA
Education
1977-1981 B.S. with distinction, Cornell University, Department of
Materials Science and Engineering, Ithaca, N.Y.
Concentration: Solid-State and Polymer Physics.
1983-1987 Ph.D., Biophysical Chemistry, Case Western Reserve University,
Department of Pharmacology, Cleveland, OH
Thesis Title: Biophysical and Biochemical Properties of Tubulin
 -Chain,
1981-1983 and M.D., Case Western Reserve University School of Medicine,
1983-1989 Cleveland, OH
Positions Held
1989-1990
1990-1991
Intern in Surgery, Deaconess Hospital/Harvard Medical School
Boston, MA
Postdoctoral Fellow, Department of Physiology and Biophysics,
Case Western Reserve University, Cleveland, OH
1991-1995
1995 - 1996
Junior Resident, Resident, Senior Resident and Chief Resident in
General Surgery/Surgical Oncology, University Hospitals of
Cleveland, Cleveland, OH & Deaconess Hospital/Harvard
Medical, School, Boston, MA
Fellow in Surgical Critical Care, Harvard-Longwood Critical
Care Program, Harvard Medical School, Boston, MA

M. Yaffe (Continued)
1996-1998 Postdoctoral Fellow, (Laboratory of Lewis Cantley) Department of
Cell Biology, Harvard Medical School, and Division of Signal
Transduction, Beth Israel Deaconess Medical Center, Boston, MA
1998-2000 Instructor in Surgery and Medicine, Harvard Medical School,
Division of Signal Transduction, Beth Israel Deaconess Medical
Center, Boston, MA
2000-present
2000-2003
Instructor in Surgery and Anesthesiology, Attending Surgeon,
Beth Israel Deaconess Hospital Surgical Intensive Care Unit,
Department of Surgery, Harvard Medical School, Boston, MA
Assistant Professor, Center for Cancer Research, Department of
Biology. Affiliate – Division of Biological Engineering
Massachusetts Institute of Technology, Cambridge, MA
July 2003-June, 2009 Howard S. and Linda B. Stern Associate Professor, Center for Cancer
(tenured in 2006) Research, Departments of Biology and Biological Engineering
Massachusetts Institute of Technology, Cambridge, MA
Associate Member and Chair, Cell Circuits Program, Broad Institute.
July 2009-Sept, 2011 Professor, Koch Institute for Integrative Cancer Biology
Departments of Biology and Biological Engineering
Massachusetts Institute of Technology, Cambridge, MA
Senior Associate Member and Chair, Cell Circuits Program,
Broad Institute.
October 2011-present David H. Koch Professor of Science
Koch Institute for Integrative Cancer Biology
Departments of Biology and Biological Engineering
Massachusetts Institute of Technology, Cambridge, MA
Senior Associate Member and Chair, Cell Circuits Program,
Broad Institute.
Medical Licensure and Board Certification
1995-present Massachusetts Medical License, Registration # 151835
1996, 2012
1999, 2008
Diplomate, American Board of Surgery, Certificate # 41699
Certification in Surgical Critical Care, American Board of
Surgery
Awards and Honors
1979
1979
1988
Elected Tau Beta Pi (Engineering Honorary Society)
Elected Alpha Sigma Mu (Materials Science Honorary Society)
Elected Alpha Omega Alpha (Medical Honorary Society)
2

M. Yaffe (Continued)
1989
1989
1994
1995
1998
1999
2003
2010
Martin Wahl Award for excellence in research and clinical
skills, Case Western Reserve University
William Holden Award in Surgery, Case Western Reserve
University
Junior Resident Teaching Award, Univ. Hospitals of Cleveland
Senior Resident Reaching Award, Univ. Hospitals of Cleveland
Howard Hughes Physician Scientist Award
Burroughs Wellcome Career Development Award
Howard S. and Linda B. Stern Chair in Biology
MIT School of Science faculty Teaching Prize
2011 David H. Koch Chair of Science in Cancer Research
Major Research Interests
• Systems biology studies of cell signaling, with a focus on cancer biology, sepsis, and inflammation.
• Systems approaches to targeted cancer therapy.
• Protein-protein interactions and modular protein domains in signal transduction.
• Protein kinase signaling pathways involved in cell cycle control, DNA damage and inflammation.
• Novel drug design using nanoparticles and peptide libraries.
• Engineering approaches to improve trauma resuscitation and wound healing
Patents/Commercial Ventures
US Patent 6,462,173 “Inhibitors of phosphoserine and phosphothreonine-prolinespecific isomerases” Inventors: Kun P. Lu, Lewis C. Cantley, Michael B. Yaffe, and
Gunther Fischer, Issued October 8, 2002.
US Patent 7,083,938 “Cell-based screening methods” Inventors: Michael H. Cardone and Michael B. Yaffe. Issued May 4, 2004.
US Patent 6,730,492 “Cell-based screening methods” Inventors: Michael H. Cardone and Michael B. Yaffe. Issued May 4, 2004.
“Binding Compounds Targeting the Non-Kinase Domain Segment of Polo-Like
Kinases” Inventors: Michael B. Yaffe Andrew E.H. Elia, Peter Rellos, Lewis C.
Cantley, and Stephen J. Smerdon. Application filed July 8, 2003
“Products and Processes for Modulating Peptide-Peptide Binding Domain
Interactions” Inventors: Michael B. Yaffe Andrew E.H. Elia, Peter Rellos, Lewis C.
Cantley, Stephen J. Smerdon, and Isaac A. Manke. Application filed November 14,
2003
3

M. Yaffe (Continued)
“Methods and Compositions for Cancer Treatment Related to BRCA1 BRCT domain
Recognition of Phosphorylated BACH1” Inventors: Isaac Manke, Julie Clapperton,
Stephen J. Smerdon, Michael B. Yaffe” Application filed May, 2004.
“MAPKAP Kinase-2 as a Specific Marker for Predicting the Response of Tumors to
DNA-Damaging Therapies.” Inventors: H. Christian Reinhardt, and Michael B.
Yaffe, Application filed May, 2007.
“Brd4 as a Prognostic Indicator and Modulator of Method Cell Response to DNA
Damage.” Inventors: Scott Floyd and Michael B. Yaffe, Application filed January,
2010.
Companies/Industry Activities:
Co-Founder and Member of Scientific Advisory Board, Merrimac Pharmeuticals.
Co-Founder and Member of Scientific Advisory Board, On-Q-Ity.
Member of Scientific Advisory Board, Cell Signaling Technologies.
Professional Societies:
Member, American Association for the Advancement of Science
Member, American Society for Microbiology
Member, American Society for Biochemistry and Molecular Biology
Member, American Society for Cell Biology
Member, American Chemical Society, Divisions of Medicinal Chemistry and
Biochemistry
Member, American Crystallographic Association
Member, Massachusetts Medical Society
Member, Surgical Biology Club section of American College of Surgeons
Member, Society of University Surgeons.
Member, Society of Critical Care Medicine
Member, American Association for Cancer Research
Member, International Society for Systems Biology
Scientific Journals and Editorial Boards
Scientific Editor-in Chief of Science Signaling
Editorial Board member for Molecular and Cellular Biology,
Molecular and Cellular Proteomics and Cell Cycle
Publications Committee Member for American Society of Biochemistry and Molecular
Biology
Reviewer for Cell, Science, Nature, Molecular Cell, Nature Cell Biology, Nature
Methods, Nature Biotechnology, Nature Reviews in Molecular Cell Biology, Journal
4

M. Yaffe (Continued) of Biological Chemistry, Journal of Cell Biology, EMBO J., Biochemical Journal,
Biochemistry, Cancer Research, Bioinformatics, Critical Care Medicine, among others.
Scientific Service
Member, Scientific Advisory Board – Boston Biomedical Research Institute, Boston,
MA 2007-2010
Ad-hoc member, NIH Study Section Erythrocyte and Leukocyte Biology 2006
Ad-hoc member, NIH Study Section Cell Signaling and Regulatory Systems 2006
NIH Study Section Member, Cell Signaling and Regulatory Systems (CSRS) 2007-2012
External Advisory Board Member, Division of Radiation Oncology Research, Dana-
Farber Cancer Institute, Harvard Medical School, Boston, MA 2008-present.
Organizer, GRC Growth Factors and Signaling Meeting 2004, 2006.
Organizer, GRC Molecular and Genetic Basis of Cell Proliferation Meeting 2005, 2007
Organizer, FASEB Protein Kinases and Protein Phosphorylation Meeting, 2009, 2011
Organizer, KEYSTONE Genomic Instability and DNA Repair Meeting, 2011
Co-Organizer ASBMB Annual Meeting, 2006, 2007
Co-Organizer, AACR Annual Meeting 2012 q-Bio-7 Annual Conference Planning Committee – 2012
Society of Critical Care Medicine Annual Conference Program Committee - 2012
Military Service (2008-present)
Lieutenant Colonel, US Army Reserve Medical Corps
Current Duty Station: US Army Institute for Surgical Research, Combat Casualty
Care, Medical Research and Materiel Command, Fort Sam Houston, Texas.
Teaching and Instruction
2000-current: Primary Instructor in 7.05 Biochemistry (~210 students)
2002-2007: Primary Instructor in Introduction to Computational and Systems Biology
(~75 students)
2008-current: Primary Instructor in 7.10/20.111/5.60 – Physical Chemistry of
Biomolecular Systems
5

M. Yaffe (Continued)
Publications of Michael B. Yaffe
1. Books
1. Cesareni, G, Gimona, M, Sudol, M, and Yaffe, M. editors. Modular Protein
Domains, Wiley-VCH, in publication.
2. Papers in Refereed Journals
1. Yaffe MB, Kramer EJ. Plasticization effects on environmental craze microstructure. J Materials Science 1981; 16:2130-2136.
2. Szasz J, Yaffe MB, Elzinga M, Blank GS, Sternlicht H. Microtubule assembly is dependent on a cluster of basic residues in alpha tubulin. Biochemistry
1986; 25:4572-4582.
3. Sternlicht H, Yaffe MB, Farr GW. A model of the nucleotide binding site in tubulin. FEBS Lett 1987; 214:226-235.
4. Yaffe MB, Levison BS, Szasz J, Sternlicht H. Expression of a human alphatubulin: properties of the isolated subunit. Biochemistry 1988; 27: 1869-
1880.
5. Yaffe MB, Farr GW, Sternlicht H. Translation of beta-tubulin mRNA in vitro generates multiple molecular forms. J Biol Chem 1988; 263:16023-16031.
6. Yaffe MB, Farr GW, Sternlicht H. Kinetics of beta-tubulin exchange following translation: evidence of a slow conformational change in betatubulin necessary for incorporation into heterodimers. J Biol Chem 1989;
265:19045-19051.
7. Farr GW, Yaffe MB, Sternlicht H. Alpha tubulin influences nucleotide binding to beta-tubulin: an assay using picomoles of unpurified protein.
Proc Natl Acad Sci USA 1990; 87:5041-5045.
8. Yaffe MB, Beegen H, Eckert RL. Biophysical characterization of involucrin reveals a molecule ideally suited to function as an intermolecular cross bridge of the keratinocyte cornified envelope. J Biol Chem 1992; 267:12233-
12238.
9. Hoffman PA, Yaffe MB, Hoffman BL, Yei SP, Wold WSM, Feider S, Carlin
CR. Characterization of the adenovirus E3 protein that downregulates the epidermal growth factor receptor reveals an integral plasma membrane
6

M. Yaffe (Continued) protein whose function depends on receptor cytosolic sequences. J Biol
Chem 1992; 267:13480-13487.
10. Yaffe MB, Farr GW, Miklos D, Horwich AL, Sternlicht ML,, Sternlicht H.
TCP1 complex is a molecular chaperone in tubulin biogenesis. Nature 1992;
358:245-248.
11. Yaffe MB, Murthy S, Eckert RL. Evidence that involucrin is a covalently linked constituent of highly purified cultured keratinocyte cornified envelopes. J Invest Derm 1993; 100:3-9.
12. Eckert RL, Yaffe MB, Crisch JS, Murthy S, Rorke EA, Welter JS. Involucrin - structure and role in envelope assembly. J Invest Derm 1993; 100:613-617.
13. Szasz J, Yaffe MB, Sternlicht H. Site directed mutagenesis of alpha tubulin: reductive methylation studies of the lys-394 region. Biophys J 1993; 64:792-
802.
14. Sternlicht H, Farr GW, Sternlicht ML, Driscoll JK, Willison K, Yaffe MB. The tcomplex polypeptide 1 complex is a chaperonin for tubulin and actin in vivo.
Proc Natl Acad Sci USA 1993; 90:9422-9426.
15. Burke PA, Drotar M, Luo M, Yaffe MB, Forse R. Rapid modulation of liver specific transcription factors after injury. Surgery 1994; 116:285-293.
16. Burke PA, Luo M, Zhu J, Yaffe MB, Forse RA. Injury induces rapid changes in hepatocyte nuclear factor-1:DNA binding. Surgery 1996;120:374-380.
17. Akhrass R, Yaffe MB, Fischer C, Ponsky J, Shuck JM. Small Bowel
Diverticulosis - perceptions and reality. J Am Coll Surg 1997; 184:383-388.
18. Akhrass R, Yaffe MB, Kyung K, Fallon W, Malangoni M. Management of pancreatic trauma - a multi-institutional series. Am Surg 1997; 63:598-604.
19. Yaffe MB, Fink ML. Hospital acquired pneumonia in the postoperative setting. Sem Resp Crit Care Med 1997; 18:121-132.
20. Algenstaedt P, Antometti DA, Yaffe MB, Kahn CR. IRS proteins create a link between the tyrosine phosphorylation cascade and the Ca 2+ -ATPases in muscle and heart. J Biol Chem 1997; 272:23696-23702.
21. Yaffe MB, Schutkowski M, Shen M, Zhou XZ, Stukenberg PT, Rahfeld J-U,
Xu J, Terada N, Kuang J, Kirschner MW, Fischer G, Cantley LC, Lu KP.
7

M. Yaffe (Continued)
Sequence-specific and phosphorylation-dependent proline isomerization: A potential novel mitotic regulatory mechanism. Science 1997; 278:1957-1960.
22. Yaffe MB, Rittinger K, Volinia, S, Caron PR, Aitken A, Leffers, H, Gamblin SJ,
Smerdon SJ, Cantley LC. The structural basis for 14-3-3:phosphopeptide binding specificity. Cell 1997; 91:961-971.
23. Parker D, Jhala US, Radhakrishnan I, Yaffe MB, Reyes C, Shulman AI,
Cantley LC, Wright PE, Montminy M. Analysis of an activator:coactivator complex reveals an essential role for secondary structure in transcriptional activation. Molecular Cell 1998;2:353-9.
24. Yaffe MB, Xu J, Burke PA, Forse RA, Brown GE. Priming of the neutrophil respiratory burst is species dependent and involves MAP kinase activation.
Surgery 1999;126:248-54.
25. Rittinger K, Budman J, Xu J, Volinia S, Cantley LC, Smerdon SJ, Gamblin SJ,
Yaffe MB. Structural analysis of 14-3-3 phosphopeptide complexes identifies a dual role for the nuclear export signal of 14-3-3 in ligand binding.
Molecular Cell 1999;4:153-166.
26. Aramburu J, Yaffe MB, Lopez-Rodriguez C, Cantley LC, Hogan PG, Rao A.
Affinity-driven optimisation of protein-protein interactions: evolution of a high affinity NFAT inhibitor more selective than cyclosporin A. Science
1999; l285:2129-33.
27. Poy F, Yaffe MB, Sayos J, Saxena K, Morra M, Samugi J, Cantley LC, Terhorst
C, Eck MJ. Crystal structures of the XLP protein SAP reveal a class of SH2 domains with extended phosphotyrosine-independent sequence recognition.
Molecular Cell 1999;4:555-561.
28. Bunnell SC, Diehn M, Yaffe MB, Findell PR, Cantley LC, Berg LJ. Biochemical interactions integrating Itk with the T Cell receptor-initiated signaling cascade. J Biol Chem. 2000; 275:2219-2230.
29. Bedford M, Sarbassova D, Xu J, Leder P, Yaffe MB. A Novel Pro-Arg motif recognized by WW domains. J Biol Chem 2000;275:10359-69.
30.
Bedford MT, Frankel A, Yaffe MB, Clarke S, Leder P, Richard S. Arginine methylation inhibits the binding of proline-rich ligands to SH3, but not WW domains. J Biol Chem 2000;275: 16030-16036.
31. Benzing T, Yaffe MB, Arnould T, Sellin L, Schilling B, Schreiber R,
Kunzelmann K, Leparc GG, Kim E and Walz G. 14-3-3 interacts with
8

M. Yaffe (Continued) regulator of G protein signaling proteins and modulates their activity. J Biol
Chem 2000 275:28167-28172.
32. Datta SR, Katsov A, Hu L, Petros A, Fesik SW, Yaffe MB, Greenberg ME.
14-3-3 Proteins and Survival Kinases Cooperate to Inactivate BAD by BH3
Domain Phosphorylation. Molecular Cell 2000 6:41-51.
33. Obata T, Yaffe MB, Leparc GG, Piro ET, Maegawa H, Kashiwagi A, Kikkawa
R, Cantley LC. Peptide and protein library screening defines optimal substrate motifs for AKT/PKB. J Biol Chem 2000 275:36108-36115.
34. Nishikawa K, Sawasdikosol S, Burakoff SJ, Fruman DA, Lai J, Songyang Z,
Yaffe MB and Cantley LC. A Peptide Library Approach Identifies a Specific
Inhibitor for the ZAP-70 Protein-Tyr Kinase. Molecular Cell 2000 6:969-974.
35. Durocher D, Taylor IA, Sarbassova D, Haire LH, Jackson SP, Smerdon SJ, and Yaffe MB. The Molecular Basis of FHA Domain:Phosphopeptide Binding
Specificity and Implications For the Evolution of Phosphodependent
Signaling Mechanisms. Molecular Cell 2000 6:1169-82.
36. Kanai F, Marignani PA, Sarbasova D, Yagi R, Hall RA, Donowitz M,
Hisaminato A, Fujiwara T, Ito Y, Cantley LC and Yaffe MB. TAZ; A Novel
Transcriptional Co-activator Regulated by Interactions with 14-3-3 and PDZdomain Proteins. EMBO J 2000 19:6778-6791.
37. Yaffe MB, Leparc GG, Lai J, Obata T, Volinia S and Cantley LC. A Motif-
Based Profile Scanning Approach for Genome Wide Prediction of Signaling
Pathways. Nature Biotech 2001 19:348-353.
38. Kanai F, Liu H, Field SJ, Akbary H, Matsuo T, Brown GE, Cantley LC and
Yaffe MB. The PX domains of p47phox and p40phox bind to lipid products of PI(3)K. Nature Cell Biol 2001 3:675-678.
39. He J, Lau AG, Yaffe MB, Hall RA. Phosphorylation and cell cycle-dependent regulation of Na+/H+ exchanger regulatory factor-1 by Cdc2 kinase. J Biol
Chem 2001 276:41559-21565.
40. Morra M, Lu J, Poy F, Martin M, Sayos J, Calpe S, Gullo C, Howie D, Rietdijk
S, Thompson A, Coyle AJ, Denny C, Yaffe MB, Engel P, Eck MJ, Terhorst C.
Structural basis for the interaction of the free SH2 domain EAT-2 with SLAM receptors in hematopoietic cells. EMBO J 2001 20:5840-5852.
41. Brunet A, Kanai F, Stehn J, Xu J, Sarbassova D, Frangioni JV, Dalal SN,
DeCaprio JA, Greenberg ME, Yaffe MB. 14-3-3 transits to the nucleus and
9

M. Yaffe (Continued) participates in dynamic nucleocytoplasmic transport. J Cell Biol 2002
156:817-828.
42. Johnson BA, Stehn JR, Yaffe MB, Blackwell TK. Cytoplasmic localization of
Tristetraprolin involves 14-3-3-dependent and -independent mechanisms. J
Biol Chem 2002 277:18029-18036.
43. Yaffe MB. How do 14-3-3 proteins work? - Gatekeeper phosphorylation and the molecular anvil hypothesis. FEBS Lett 2002 513:53-57.
44. Li Jeijin, Williams, B.L., Haire, L.F., Goldberg, M., Wilker, E., Durocher, D.,
Yaffe, M.B., Jackson, S.P., Smerdon, S.J. Structural and Functional Versatility of the FHA Domain in DNA-Damage Signaling by the Tumor Suppressor
Kinase Chk2. Molecular Cell 2002 9:1045-1054.
45. Brown GE, Stewart MQ, Liu H, Ha VL, Yaffe MB. A Novel Assay System
Implicates PtdIns(3,4)P(2), PtdIns(3)P, and PKCdelta in Intracellular
Production of Reactive Oxygen Species by the NADPH Oxidase. Molecular
Cell 2003 11:35-47.
46. Elia AE, Cantley LC, Yaffe MB. Proteomic screen finds pSer/pThr-binding domain localizing Plk1 to mitotic substrates. Science 2003 299:1228-31.*
47. Obenauer JC, Cantley LC, Yaffe MB. Scansite 2.0: Proteome-wide prediction of cell signaling interactions using short sequence motifs. Nucleic Acids Res
2003 31:3635-41.
48. Powell DW, Rane MJ, Joughin BA, Kalmukova R, Hong JH, Tidor B, Dean
WL, Pierce WM, Klein JB, Yaffe MB, McLeish KR. Proteomic identification of
14-3-3zeta as a mitogen-activated protein kinase-activated protein kinase 2 substrate: role in dimer formation and ligand binding. Mol Cell Biol 2003
23:5376-87.*
49. Janes KA, Albeck JG, Peng LX, Sorger PK, Lauffenburger DA and Yaffe MB.
A High-Throughput Quantitative Multiplex Kinase Assay for Monitoring
Information Flow in Signaling Networks: Application to Sepsis-Apoptosis.
Molecular and Cellular Proteomics 2003 2:463-73.*
50. Vazquez ME, Nitz M, Stehn J, Yaffe MB, Imperiali B. Fluorescent caged phosphoserine peptides as probes to investigate phosphorylation-dependent protein associations. J Am Chem Soc 2003 125:10150-1.
51. Elia AEH, Rellos P, Haire LF, Chao JW, Ivins FJ, Hoepker K, Mohammad D,
Cantley LC, Smerdon SJ and Yaffe MB. The molecular basis of
10

M. Yaffe (Continued) phosphodependent substrate targeting and regulation of Plks by the Polo-
Box domain. Cell 2003 115:83-95.*
52. Manke IA, Lowery DM, Nguyen A and Yaffe MB. BRCT repeats as phosphopeptide binding modules involved in protein targeting.
Science 2003 302:636-639.*
53. Kissel JL, Wilker EW, Johnson KC, Eckman MS, Yaffe MB, Jacks T. Merlin the product of Nf2 tumor suppressor gene, is an inhibitor of the p21activated kinase, pak 1. Molecular Cell 2003 4:841-849.
54. Lowery DW, Mohammad DH, Elia AE, Yaffe MB. The Polo-box domain: a molecular integrator of mitotic kinase cascades and Polo-like kinase function.
Cell Cycle 2004 2:128-31.*
55. Park KS, Whitsett JA, DiPalma T, Hong JH, Yaffe MB, Zannini M. TAZ interacts with TTF-1 and regulates expression of surfactant protein-C. J Biol
Chem 2004 17:17384-90.
56. Brown GE, Stewart MQ, Bissonnette SA, Elia AE, Wilker E, Yaffe MB.
Distinct ligand-dependent roles for p38 MAPK in priming and activation of the neutrophil NADPH oxidase. J Biol Chem 2004 279:27059-68.*
57. Dalal SN, Yaffe MB, DeCaprio JA. 14-3-3 Family Members Act Coordinately to Regulate Mitotic Progression. Cell Cycle 2004 3:672-7.
58. Clapperton JA, Manke IA, Lowery DM, Ho T, Haire LF, Yaffe MB, Smerdon
SJ . Structure and mechanism of BRCA1 BRCT domain recognition of phosphorylated BACH1 with implications for cancer. Nat. Struct. Mol. Biol.
2004 11:512-8.*
59.
Nguyen A, Rothman DM, Stehn J, Imperiali B, Yaffe MB. Caged phosphopeptides reveal a temporal role for 14-3-3 in G1 arrest and S-phase checkpoint function. Nat. Biotech. 2004 22:993-1000.
60.
Krause M, Leslie JD, Stewart M, Lafuente EM, Valderrama F, Jagannathan R,
Strasser GA, Rubinson DA, Liu H, Way M, Yaffe MB, Boussiotis VA, Gertler
FB. Lamellipodin, an Ena/VASP ligand, is implicated in the regulation of lamellipodial dynamics. Dev Cell. 2004 7:571-83.
61.
Rubin BB, Downey GP, Koh A, Degousee N, Ghomashchi F, Nallan L,
Stefanski E, Smart BP, Lindsay TF, Cherepanov V, Vachon E, Kelvin D,
Sadilek M, Brown GE, Yaffe MB, Plumb J, Grinstein S, Glogauer M, Gelb
MH. Cytosolic phospholipase A2-alpha is necessary for platelet activating
11

M. Yaffe (Continued) factor biosynthesis, efficient neutrophil mediated bacterial killing and the innate immune response to pulmonary infection. J Biol Chem. 2005
280:7519-7529 .
62.
Joughin BA, Tidor B, Yaffe MB. A computational method for the analysis and prediction of protein:phosphopeptide-binding sites. Protein Sci. 2005
14:131-9.
*
63.
Mahoney WM, Hong JH, Yaffe MB, Farrance IK. Transcriptional co-activator
TAZ interacts differentially with Transcriptional Enhancer Factor -1 (TEF-1) family members. Biochem J. 2005 388:217-25.
64.
Manke IA, Nguyen A, Lim D, Stewart MQ, Elia AE, Yaffe MB. MAPKAP kinase-2 is a cell cycle checkpoint kinase that regulates the G2/M transition and S phase progression in response to UV irradiation. Mol Cell. 2005 17:37-
48.
*
65.
Blander G, Olejnik J, Krzymanska-Olejnik E, McDonagh T, Haigis M, Yaffe
MB, Guarente L. SIRT1 shows no substrate specificity in vitro. J Biol Chem.
2005 80:9780-5 .
66.
Lowery DM, Lim D, Yaffe MB. Structure and function of Polo-like kinases.
Oncogene. 2005 24:248-59.
*
67.
Wilker EW, Grant RA, Artim SC, Yaffe MB. A structural basis for 14-3-3 sigma functional specificity. J Biol Chem. 2005 280:18891-8 .
68.
Ahonen LJ, Kallio MJ, Daum JR, Bolton M, Manke IA, Yaffe MB, Stukenberg
PT, Gorbsky GJ. Polo-like kinase 1 creates the tension-sensing 3F3/2 phosphoepitope and modulates the association of spindle-checkpoint proteins at kinetochores. Curr Biol. 2005 15:1078-89.
69.
Hong JH, Hwang ES, McManus MT, Amsterdam A, Tian Y, Kalmukova R,
Mueller E, Benjamin T, Spiegelman BM, Sharp PA, Hopkins N, Yaffe MB.
TAZ, a transcriptional modulator of mesenchymal stem cell differentiation.
Science. 2005 309:1074-8.
70.
Russ WP, Lowery DM, Mishra P, Yaffe MB, Ranganathan R. Natural-like function in artificial WW domains. Nature. 2005 437:579-83.
*
71.
Mah AS, Elia AE, Devgan G, Ptacek J, Schutkowski M, Snyder M, Yaffe MB,
Deshaies RJ. Substrate specificity analysis of protein kinase complex Dbf2-
Mob1 by peptide library and proteome array screening. BMC Biochem. 2005
6:22, 1-11. *
12

M. Yaffe (Continued)
72. Macdonald N, Welburn JP, Noble ME, Nguyen A, Yaffe MB, Clynes D, Moggs
JG, Orphanides G, Thomson S, Edmunds JW, Clayton AL, Endicott JA,
Mahadevan LC. Molecular basis for the recognition of phosphorylated and phosphoacetylated histone h3 by 14-3-3. Mol Cell. 2005 20:199-211.
73. Janes KA, Albeck JG, Gaudet S, Sorger PK, Lauffenburger DA, Yaffe MB. A systems model of signaling identifies a molecular basis set for cytokineinduced apoptosis. Science. 2005 310:1646-53. *
74. Stucki M, Clapperton JA, Mohammad D, Yaffe MB, Smerdon SJ, Jackson SP.
MDC1 Directly Binds Phosphorylated Histone H2AX to Regulate Cellular
Responses to DNA Double-Strand Breaks. Cell. 2005 123:1213-26.*
75. Weiner OD, Rentel MC, Ott A, Brown GE, Jedrychowski M, Yaffe MB, Gygi
SP, Cantley LC, Bourne HR, Kirschner MW. Hem-1 complexes are essential for Rac activation, actin polymerization, and myosin regulation during neutrophil chemotaxis. PLoS Biol. 2006 4:e38.
76. Gardino AK, Smerdon SJ, Yaffe MB. Structural determinants of 14-3-3 binding specificities and regulation of subcellular localization of 14-3-3ligand complexes: A comparison of the X-ray crystal structures of all human
14-3-3 isoforms. Semin Cancer Biol. 2006 16:173-82.
77. Yoshida S, Kono K, Lowery DM, Bartolini S, Yaffe MB, Ohya Y, Pellman D.
Polo-like kinase Cdc5 controls the local activation of Rho1 to promote cytokinesis. Science. 2006 313:108-11. *
78. Cheng C, Yaffe MB, Sharp PA. A positive feedback loop couples Ras activation and CD44 alternative splicing. Genes Dev. 2006 20:1715-20.
79. Suh CI, Stull ND, Li XJ, Tian W, Price MO, Grinstein S, Yaffe MB, Atkinson S,
Dinauer MC. The phosphoinositide-binding protein p40phox activates the
NADPH oxidase during FcgammaIIA receptor-induced phagocytosis. J Exp
Med. 2006 203:1915-25.
80. Charest A, Wilker EW, McLaughlin ME, Lane K, Gowda R, Coven S,
McMahon K, Kovach S, Feng Y, Yaffe MB, Jacks T, Housman D. ROS fusion tyrosine kinase activates a SH2 domain-containing phosphatase-2/ phosphatidylinositol 3-kinase/mammalian target of rapamycin signaling axis to form glioblastoma in mice. Cancer Res. 2006 66:7473-81.
13

M. Yaffe (Continued)
81. Nishikawa K, Watanabe M, Kita E, Igai K, Omata K, Yaffe MB, Natori Y. A multivalent peptide library approach identifies a novel Shiga toxin inhibitor that indices aberrant cellular transport of the toxin. FASEB J. 2006 20:2597-9.
83. Reinhardt HC, Aslanian AS, Lees JA, Yaffe MB. p53-deficient cells rely on
ATM- and ATR-mediated checkpoint signaling through the p38MAPK/MK2 pathway for survival after DNA damage. Cancer Cell. 2007 11:175-89.
84.
Wilker EW, van Vugt MA, Artim SA, Huang PH, Petersen CP, Reinhardt
HC, Feng Y, Sharp PA, Sonenberg N, White FM, Yaffe MB. 14-3-3 sigma controls mitotic translation to facilitate cytokinesis. Nature. 2007 446:329-32 .
85. Lowery DM, Clauser KR, Hjerrild M, Lim D, Alexander J, Kishi K, Ong SE,
Gammeltoft S, Carr SA, Yaffe MB. Proteomic screen defines the Polo-box domain interactome and identifies Rock2 as a Plk1 substrate. EMBO J 2007
26:2262-73.*
86. Linding R, Jensen LJ, Ostheimer GJ, van Vugt MA, Jorgensen C, Miron IM,
Diella F, Colwill K, Taylor L, Elder K, Metalnikov P, Nguyen V, Pasculescu
A, Jin J, Park JG, Samson LD, Woodgett JR, Russell RB, Bork P, Yaffe MB,
Pawson T. Systematic discovery of in vivo phosphorylation networks.
Cell 2007 129:1415-26.
87. Tian Y, Kolb R, Hong JH, Carroll J, Li D, You J, Bronson R, Yaffe MB, Zhou J,
Benjamin T. TAZ promotes PC2 degradation through a SCFbeta-Trcp E3 ligase complex. Mol Cell Biol. 2007 27:6383-95.
88. Dai S, Zhang Y, Weimbs T, Yaffe MB, Zhou D. Bacteria-generated PtdIns(3)P recruits VAMP8 to facilitate phagocytosis. Traffic. 2007 8:1365-74.
89. Huen MS, Grant R, Manke I, Minn K, Yu X, Yaffe MB, Chen J. RNF8 transduces the DNA-damage signal via histone ubiquitylation and checkpoint protein assembly. Cell. 2007 131:901-14.
90. Snead JL, Sullivan M, Lowery DM, Cohen MS, Zhang C, Randle DH, Taunton
J, Yaffe MB, Morgan DO, Shokat KM. A coupled chemical-genetic and bioinformatic approach to Polo-like kinase pathway exploration. Chem Biol.
2007 14:1261-72.
91. Bissonnette SA, Glazier CM, Stewart MQ, Brown GE, Ellson DE, Yaffe MB.
Phosphatidylinositol 3-phoshate-dependent and -independent functions of p40phox in activation of the NADPH oxidase. J. Biol. Chem. 2008 283:2108-
19.*
14

M. Yaffe (Continued)
92. Varelas X, Sakuma R, Samavarchi-Tehrani P, Peerani R, Rao BM, Dembowy J,
Yaffe MB, Zandstra PW, Wrana JL. TAZ controls Smad nucleocytoplasmic shuttling and regulates human embryonic stem-cell self-renewal. Nat Cell
Biol. 2008 10:837-48.
93. Linding R, Jensen LJ, Pasculescu A, Olhovsky M, Colwill K, Bork P, Yaffe MB,
Pawson T. NetworKIN: a resource for exploring cellular phosphorylation networks. Nucleic Acids Res. 2008 36:D695-9.
94. Mazanka E, Alexander J, Yeh BJ, Charoenpong P, Lowery DM, Yaffe M, Weiss
EL. The NRD/LATS family kinase Cbk1 directly controls transcriptional asymmetry. PloS Biology 2008 6:1778-90.*
95. Macůrek L, Lindqvist A, Lim D, Lampson MA, Klompmaker R, Freire R,
Clouin C, Taylor SS, Yaffe MB, Medema RH. Polo-like kinase-1 is activated by aurora A to promote checkpoint recovery. Nature 2008 455:119-23.
96. Tian W, Li XJ, Stull ND, Ming W, Suh CI, Bissonnette SA, Yaffe MB, Grinstein
S, Atkinson SJ, Dinauer MC. Fc{gamma}R-stimulated activation of the
NADPH oxidase: phosphoinositide-binding protein p40phox regulates
NADPH oxidase activity after enzyme assembly on the phagosome. Blood.
2008 112:3867-77.*
97. Miller ML, Jensen LJ, Diella F, Jørgensen C, Tinti M, Li L, Hsiung M, Parker
SA, Bordeaux J, Sicheritz-Ponten T, Olhovsky M, Pasculescu A, Alexander J,
Knapp S, Blom N, Bork P, Li S, Cesareni G, Pawson T, Turk BE, Yaffe MB*,
Brunak S*, Linding R*. Linear motif atlas for phosphorylation-dependent signaling. Sci Signal 2008 1:ra2.
98. Yi C, Wilker EW, Yaffe MB, Stemmer-Rachamimov A, Kissil JL. Validation of the p21-activated kinases as targets for inhibition in neurofibromatosis type
2. Cancer Res 2008 68:7932-7.
99. Janes KA, Reinhardt HC, Yaffe MB. Cytokine-induced signaling networks prioritize dynamic range over signal strength. Cell 2008 135:343-54.
100. Mazanka E, Alexander J, Yeh BJ, Charoenpong P, Lowery DM, Yaffe M,
Weiss EL. The NDR/LATS family kinase Cbk1 directly controls transcriptional asymmetry. PLoS Biol. 2008 6(8):e203
101. Edbauer D, Cheng D, Batterton MN, Wang CF, Duong DM, Yaffe MB, Peng J,
Sheng M. Identification and characterization of neuronal mitogen-activated
15

M. Yaffe (Continued) protein kinase substrates using a specific phosphomotif antibody. Mol Cell
Proteomics. 2009 8:681-95.
102. 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 EGFRvIIIexpressing glioblastoma cells. Mol Biosyst. 2009 5:59-67.*
103. Toettcher JE, Loewer A, Ostheimer GJ, Yaffe MB, Tidor B, Lahav G. Distinct mechanisms act in concert to mediate cell cycle arrest. Proc Natl Acad Sci U
S A. 2009 Jan 20;106(3):785-90.
104. Kishi K, van Vugt MA, Okamoto K, Hayashi Y, Yaffe MB. Functional dynamics of Polo-like kinase 1 at the centrosome. Mol Cell Biol. 2009
29:3134-50.
105. van Leuken R, Clijsters L, van Zon W, Lim D, Yao X, Wolthuis RM, Yaffe
MB, Medema RH, van Vugt MA. Polo-like kinase-1 controls Aurora A destruction by activating APC/C-Cdh1. PLoS ONE. 2009;4(4):e5282.
106. Burkard ME, Maciejowski J, Rodriguez-Bravo V, Repka M, Lowery DM,
Clauser KR, Zhang C, Shokat KM, Carr SA, Yaffe MB, Jallepalli PV. Plk1 selforganization and priming phosphorylation of HsCYK-4 at the spindle midzone regulate the onset of division in human cells. PLoS Biol. 2009 May
5;7(5):e1000111.*
107. Reinhardt HC, Yaffe MB. Kinases that control the cell cycle in response to
DNA damage: Chk1, Chk2, and MK2. Curr Opin Cell Biol. 2009 21:245-55.
108. Mohammad DH, Yaffe MB. 14-3-3 proteins, FHA domains and BRCT domains in the DNA damage response. DNA Repair. 2009 8:1009-17.*
109. Smith A, Blois J, Yuan H, Aikawa E, Ellson C, Figueiredo JL, Weissleder R,
Kohler R, Yaffe MB, Cantley LC, Josephson L. The antiproliferative cytostatic effects of a self-activating viridin prodrug. Mol Cancer Ther. 2009 8:1666-75.
110. Yun SM, Moulaei T, Lim D, Bang JK, Park JE, Shenoy SR, Liu F, Kang YH,
Liao C, Soung NK, Lee S, Yoon DY, Lim Y, Lee DH, Otaka A, Appella E,
McMahon JB, Nicklaus MC, Burke TR Jr, Yaffe MB, Wlodawer A, Lee KS.
Structural and functional analyses of minimal phosphopeptides targeting the polo-box domain of polo-like kinase 1. Nat Struct Mol Biol. 2009 16:876-82.
16

M. Yaffe (Continued)
111. Jiang H, Reinhardt HC, Bartkova J, Tommiska J, Blomqvist C, Nevanlinna H,
Bartek J, Yaffe MB, Hemann MT. The combined status of ATM and p53 link tumor development with therapeutic response. Genes Dev. 2009 23:1895-909.
112. Stangenberg L, Ellson C, Cortez-Retamozo V, Ortiz-Lopez A, Yuan H, Blois J,
Smith RA, Yaffe MB, Weissleder R, Benoist C, Mathis D, Josephson L,
Mahmood U. Abrogation of antibody-induced arthritis in mice by a selfactivating viridin prodrug and association with impaired neutrophil and endothelial cell function. Arthritis Rheum. 2009 60:2314-24.
113. Reinhardt HC, Jiang H, Hemann MT, Yaffe MB. Exploiting synthetic lethal interactions for targeted cancer therapy. Cell Cycle. 2009 8:3112-98.
114. Asaoka Y, Kanai F, Ichimura T, Tateishi K, Tanaka Y, Ohta M, Seto M, Tada
M, Ijichi H, Ikenoue T, Kawabe T, Isobe T, Yaffe MB, Omata M. Identification of a suppressive mechanism for Hedgehog signaling through a novel interaction of Gli with 14-3-3. J Biol Chem. 2010 285:4185-94.
115. Wen J, Wilker EW, Yaffe MB, Jensen KF. Microfluidic preparative free-flow isoelectric focusing: system optimization for protein complex separation.
Anal Chem. 2010 82:1253-60.*
116. van Vugt MA, Gardino AK, Linding R, Ostheimer GJ, Reinhardt HC, Ong SE,
Tan CS, Miao H, Keezer SM, Li J, Pawson T, Lewis TA, Carr SA, Smerdon SJ,
Brummelkamp TR, Yaffe MB. A mitotic phosphorylation feedback network connects Cdk1, Plk1, 53BP1, and Chk2 to inactivate the G(2)/M DNA damage checkpoint. PLoS Biol. 2010 8:e1000287.
117. Lazzara MJ, Lane K, Chan R, Jasper PJ, Yaffe MB, Sorger PK, Jacks T, Neel
BG, Lauffenburger DA. Impaired SHP2-mediated extracellular signalregulated kinase activation contributes to gefitinib sensitivity of lung cancer cells with epidermal growth factor receptor-activating mutations. Cancer
Res. 2010 70:3843-50.
118. Jeong H, Bae S, An SY, Byun MR, Hwang JH, Yaffe MB, Hong JH, Hwang ES.
TAZ as a novel enhancer of MyoD-mediated myogenic differentiation.
FASEB J. 2010 24:3310-20.
119. van Vugt MA, Yaffe MB. Cell cycle re-entry mechanisms after DNA damage checkpoints: Giving it some gas to shut off the breaks! Cell Cycle. 2010
9:2097-101.
17

M. Yaffe (Continued)
120. Jiang Y, Puliyappadamba VT, Zhang L, Wu W, Wali A, Yaffe MB, Fontana JA,
Rishi AK. A novel mechanism of cell growth regulation by Cell Cycle and
Apoptosis Regulatory Protein (CARP)-1. J Mol Signal. 2010 5:7.
121. 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 proteomic studies. Mol Cell Proteomics.
2010 9:2558-7.*
122. Reinhardt HC, Hasskamp P, Schmedding I, Morandell S, van Vugt MA,
Wang X, Linding R, Ong SE, Weaver D, Carr SA, Yaffe MB. DNA damage activates a spatially distinct late cytoplasmic cell-cycle checkpoint network controlled by MK2-mediated RNA stabilization. Molecular Cell 2010 40:34-
49.
123. Pennell S, Westcott S, Ortiz-Lombardía M, Patel D, Li J, Nott TJ, Mohammed
D, Buxton RS, Yaffe MB, Verma C, Smerdon SJ. Structural and functional analysis of phosphothreonine-dependent FHA domain interactions.
Structure 2010 18:1587-95.
124. Reinhardt HC, Cannell IG, Morandell S, Yaffe MB. Is post-transcriptional stabilization, splicing and translation of selective mRNAs a key to the DNA damage response? Cell Cycle 2011 10:23-7.
125. Hsu PP, Kang SA, Rameseder J, Zhang Y, Ottina KA, Lim D, Peterson TR,
Choi Y, Gray NS, Yaffe MB, Marto JA, Sabatini DM. The mTOR-regulated phosphoproteome reveals a mechanism of mTORC1-mediated inhibition of growth factor signaling. Science 2011 332:1317-22. *
126. Cannell IG, Yaffe MB. Salvaging the septic heart through targeting the interleukin-6/p38 mitogen-activated protein kinase signaling network. Crit
Care Med. 2011 39:1836-7.
127. Alexander J, Lim D, Joughin BA, Hegemann B, Hutchins JR, Ehrenberger T,
Ivins F, Sessa F, Hudecz O, Nigg EA, Fry AM, Musacchio A, Stukenberg PT,
Mechtler K, Peters JM, Smerdon SJ, Yaffe MB. Spatial exclusivity combined with positive and negative selection of phosphorylation motifs is the basis for context-dependent mitotic signaling. Science Signal. 2011 4:ra42. *
128. Liu F, Park JE, Qian WJ, Lim D, Gräber M, Berg T, Yaffe MB, Lee KS, Burke
TR Jr. Serendipitous alkylation of a Plk1 ligand uncovers a new binding channel. Nat Chem Biol. 2011 7:595-60
18

M. Yaffe (Continued)
129. 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. 7:e100211.*
130. Grosstessner-Hain K, Hegemann B, Novatchkova M, Rameseder J, Joughin
BA, Hudecz O, Roitinger E, Pichler P, Kraut N, Yaffe MB, Peters JM,
Mechtler K. Quantitative phospho-proteomics to investigate the Polo-like kinase 1-dependent phospho-proteome. Mol Cell Proteomics. 2011: 10:M111.
131. Gardino AK, Yaffe MB. 14-3-3 proteins as signaling integration points for cell cycle control and apoptosis. Semin Cell Dev Biol. 2011 22:688-9.
132. Hegemann B, Hutchins JR, Hudecz O, Novatchkova M, Rameseder J, Sykora
MM, Liu S, Mazanek M, Lénárt P, Hériché JK, Poser I, Kraut N, Hyman AA,
Yaffe MB, Mechtler K, Peters JM. Systematic phosphorylation analysis of human mitotic protein complexes. Science Signal. 2011 4:rs12.
133. Valenti F, Fausti F, Biagioni F, Shay T, Fontemaggi G, Domany E, Yaffe MB,
Strano S, Blandino G, Di Agostino S. Mutant p53 oncogenic functions are sustained by Plk2 kinase through an autoregulatory feedback loop. Cell
Cycle. 2011 Dec 15;10(24). [Epub ahead of print]
134. Banko MR, Allen JJ, Schaffer BE, Wilker EW, Tsou P, White JL, Villén J, Wang
B, Kim SR, Sakamoto K, Gygi SP, Cantley LC, Yaffe MB, Shokat KM, Brunet
A. Chemical Genetic Screen for AMPK α 2 Substrates Uncovers a Network of
Proteins Involved in Mitosis. Molecular Cell. 2011 44:878-92.
135. Lee CH, Ou WB, Mariño-Enriquez A, Zhu M, Mayeda M, Wang Y, Guo X,
Brunner AL, Amant F, French CA, West RB, McAlpine JN, Gilks CB, Yaffe
MB, Prentice LM, McPherson A, Jones SJ, Marra MA, Shah SP, van de Rijn M,
Huntsman DG, Dal Cin P, Debiec-Rychter M, Nucci MR, Fletcher JA. 14-3-3 fusion oncogenes in high-grade endometrial stromal sarcoma. Proc Natl
Acad Sci USA. 2012 109:929-34.
136. Kholodenko B, Yaffe MB, Kolch W.Computational approaches for analyzing information flow in biological networks. Sci Signal. 2012 Apr 17;5(220):re1
137. Liu F, Park JE, Qian WJ, Lim D, Scharow A, Berg T, Yaffe MB, Lee KS, Burke
TR. Identification of High Affinity Polo-like Kinase 1 (Plk1) Polo-box Domain
Binding Peptides Using Oxime-based Diversification. ACS Chem Biol. 2012
Jan 31. [Epub ahead of print]
138. Tentner AR, Lee MJ, Ostheimer GJ, Samson LD, Lauffenburger DA, Yaffe MB.
19

M. Yaffe (Continued)
Combined experimental and computational analysis of DNA damage signaling reveals context-dependent roles for Erk in apoptosis and G1/S arrest after genotoxic stress. Mol Syst Biol. 2012 Jan 31;8:568.*
139. Joughin BA, Liu C, Lauffenburger DA, Hogue CWV, Yaffe MB. Protein kinases display minimal interpositional dependence on substrate sequence: potential implications for the evolution of signaling networks. Phil. Trans.
Royal Soc. London 2012 367:2574-83.
140. Lee MJ, Ye AS, Gardino AK, Heijink AM, Sorger PK, MacBeath G, Yaffe MB.
Sequential application of anti-cancer drugs enhances cell death by re-wiring apoptotic signaling networks. Cell 2012 149:780-94.
141. Morandell S, Yaffe MB.Exploiting synthetic lethal interactions between DNA damage signaling, checkpoint control, and p53 for targeted cancer therapy.
Prog Mol Biol Transl Sci. 2012 110:289-314.
142. Niedelman W, Gold DA, Rosowski EE, Sprokholt JK, Lim D, Farid Arenas A,
Melo MB, Spooner E, Yaffe MB, Saeij JP. The rhoptry proteins ROP18 and
ROP5 mediate Toxoplasma gondii evasion of the murine, but not the human, interferon-gamma response. PLoS Pathog. 2012 8:e1002784*.
143. Naegle KM, White FM, Lauffenburger DA, Yaffe MB. Robust co-regulation of tyrosine phosphorylation sites on proteins reveals novel protein interactions.
Mol Biosyst. 2012 8:2771-82.
144. Noonan EM, Shah D, Yaffe MB, Lauffenburger DA, Samson LD. O(6)-
Methylguanine DNA lesions induce an intra-S-phase arrest from which cells exit into apoptosis governed by early and late multi-pathway signaling network activation. Integr Biol (Camb). 2012 4:1237-55*.
145. Singh N, Basnet H, Wiltshire TD, Mohammad DH, Thompson JR, Héroux A,
Botuyan MV, Yaffe MB, Couch FJ, Rosenfeld MG, Mer G. Dual recognition of phosphoserine and phosphotyrosine in histone variant H2A.X by DNA damage response protein MCPH1. Proc Natl Acad Sci USA. 2012 109:14381-
6.
146. Höpker K, Hagmann H, Khurshid S, Chen S, Hasskamp P, Seeger-Nukpezah
T, Schilberg K, Heukamp L, Lamkemeyer T, Sos ML, Thomas RK, Lowery D,
Roels F, Fischer M, Liebau MC, Resch U, Kisner T, Röther F, Bartram MP,
Müller RU, Fabretti F, Kurschat P, Schumacher B, Gaestel M, Medema RH,
Yaffe MB, Schermer B, Reinhardt HC, Benzing T. AATF/Che-1 acts as a phosphorylation-dependent molecular modulator to repress p53-driven apoptosis.
EMBO J. 2012 31:3961-3975.
20

M. Yaffe (Continued)
147. Weingeist DM, Ge J, Wood DK, Mutamba JT, Huang Q, Rowland EA, Yaffe
MB, Floyd S, Engelward BP. Single-cell microarray enables high-throughput evaluation of DNA double-strand breaks and DNA repair inhibitors. Cell
Cycle. 2013 12: 907-15.
148. Murugan RN, Park JE, Lim D, Ahn M, Cheong C, Kwon T, Nam KY, Choi SH,
Kim BY, Yoon DY, Yaffe MB, Yu DY, Lee KS, Bang JK. Development of cyclic peptomer inhibitors targeting the polo-box domain of polo-like kinase 1.
Bioorg Med Chem. 2013 Feb 27. [Epub ahead of print]
149. Rock, JM, Lim D, Stach L, Ogrodowowicz RW, Keck JM, Jones MH, Wong
CLC, Yates JR, Winey M, Smerdon SJ, Yaffe MB, Amon A. Activation of the yeast Hippo pathway by phosphorylation-dependent assembly of signaling complexes. Science 2013 (April 11, Epub ahead of print)*.
150. Floyd SR, Pacold ME, Huan Q, Clarke SM, Lam FC, Cannell IG, Bryson BD,
Rameseder J, Lee MJ, Blake EJ, Fydrych A, Ho R, Greenberger BA, Chen GC,
Maffa A, Del Rosario AM, Root DE, Carpenter AE, Hahn WC, Sabatini DM,
Chen CC, White FM, Bradner JE, Yaffe MB. The Bromodomain Protein Brd4
Insulates Chromatin from DNA Damage Signaling. Nature 2013 (in press).
* denotes manuscript arising from MIT supervised thesis or UROP research
Reviews and Summaries
1.
Yaffe MB, Cantley LC. Grabbing Phosphoproteins. Nature 1999; 402:30-31.
2. Obata T, Brown GE, Yaffe MB. MAP kinase pathways activated by stress: the p38 MAPK pathway. Crit Care Med 2000;28:67-77.
3. Durocher D, Smerdon SJ, Yaffe MB, Jackson SP. The FHA domain in DNA repair and checkpoint signaling. Cold Spring Harb Symp Quant Biol.
2000;65:423-31.
4. Yaffe MB, and Elia AEH. Phosphoserine/threonine binding domains. Curr
Opin in Cell Biol 2001 13:131-138.
5. Yaffe MB, and Smerdon SJ. Phosphoserine?Threonine Binding Domains –
You Can’t pSERious? Structure 2001 9:R33-R38.
6. Yaffe MB. MAGUK SH3 Domains-Swapped and Stranded by Their Kinases?
Structure 2002 10:3-5.
21

M. Yaffe (Continued)
7.
Yaffe MB. Phosphotyrosine-binding domains in signal transduction. Nat Rev
Mol Cell Biol 2002 3:177-186.
8. Yaffe M.. The p47phox PX Domain. Two Heads Are Better Than One!
Structure 2002 10:1288-1291.
9. Nguyen A, Yaffe MB. Proteomics and systems biology approaches to signal transduction in sepsis. Crit Care Med 2003 1:S1-6.
10.
Manke IA, Yaffe MB. Chk'n Out in Mitosis. Cell Cycle 2003 2:236-7.
11. Endy D., Yaffe MB. Signal transduction: Molecular Monogamy. Nature 2003
6967: 614-615.
12. Yaffe MB. Master of all things Phosphorylated. Biochem J 2004 379:e1-2.
13.
Wilker E, Yaffe MB. 14-3-3 Proteins--a focus on cancer and human disease.
J Mol Cell Cardiol 2004 37:633-42.
14. Yaffe MB, Smerdon SJ. The use of in vitro peptide-library screens in the analysis of phosphoserine/threonine-binding domain structure and function. Ann Rev Biophys Biomol Struct 2004 33:225-44.
15.
Yaffe MB. Novel at the library. Nat Methods 2004 1:13-4.
16. Yaffe MB. X-ray crystallography and structural biology. Crit Care Med 2005
33:S435-40.
17. Hong JH, Yaffe MB. TAZ, a beta-catenin-like molecule that regulates mesenchymal stem cell differentiation. Cell Cycle 2006 5:176-9.
18. Yaffe MB. Bits and Pieces. Sci STKE 2006 pe278.
19. Yaffe MB, White FM. Signaling netwErks get the global treatment.
Genome Biol . 2007 8:202-205.
20. Janes KA, Yaffe MB. Data-driven modelling of signal transduction networks.
Nat. Rev. Mol. Cell Biol. 2006 7:820-8.
21. Blandino G, Shaul Y, Strano S, Sudol M, Yaffe M. The Hippo tumor suppressor pathway: a brainstorming workshop. Sci Signal. 2009 2(95):mr6.
22. Mohammad DH, Yaffe MB. Fixin' to divide. Molecular Cell. 2012 45:273-5.
22

M. Yaffe (Continued)
3. Proceedings of Refereed Conferences
1. Yaffe MB, Kramer EJ. Morphology of solvent crazes in polystyrene. Bull
Am Phys Soc 1980; 31:2175.
2. MacAfee PC, Wilson WL, Bohlman HH, Forcier P, Yaffe MB, Balourdes G.
The triple wire fixation technique for stabilization of acute cervical fracturedislocations: a biomechanical analysis. Trans Ortho Res Soc 1985; 10:232.
3. Wilson WL, MacAfee PC, Bohlman HH, Yaffe MB, Balourdes, Bahniuk E. A new method for determining the load-deformation properties of the intact cervical spine and the biomechanical properties of spinal fixation. Trans
Ortho Res Soc 1985; 10:233.
4. Blank GS, Yaffe MB, Szasz J, George E, Rosenberry TL, Sternlicht H. The role of lys-394 in microtubule assembly. Ann NY Acad Sci 1986; 466:467-481.
4. Other Major Publications
1. Yaffe MB, Fink MP. Cellular signaling in critical care--putting the pieces together. Crit Care Med 2000; 28:1-2.
2. Yaffe MB, Cantley LC. Random peptide libraries for mapping specificity determinants for protein-protein association. Methods Enzymol 2000
328:157-70.
3. Yaffe MB. Studying the optimal Peptide substrate motifs of protein kinase C using oriented Peptide libraries. Methods Mol Biol 2003;233:273-86.
4. Yaffe MB. Study of substrate specificity of MAPK’s using oriented peptide libraries. Methods Mol Biol 2004 250:237-250.
5. Obenauer JC, Yaffe MB. Computational prediction of protein-protein interactions. Methods Mol Biol 2004 261:445-468.
6. Yaffe MB. 14-3-3 Proteins. Encyclopedia of Molecular Medicine, T.E.
Creighton, ed. John Wiley and Sons. 2001.
7. Kanai F, Yaffe MB and Stukenberg PT. Small Pool Expression Cloning.
Protein-Protein Interactions-A Molecular Cloning Manual. E. Golemis, ed.
Cold Spring Harbor Press, 2002.
23

M. Yaffe (Continued)
8. Liu H , Yaffe MB. PX Domains. Handbook of Cell Signaling, R. Bradshaw and E. Dennis, eds. Academic Press 2004 Volume 2, 171-175.
9. Smerdon SJ, Yaffe MB. Recognition of Phospho-Serine/Threonine
Phosphorylated Proteins. Handbook of Cell Signaling, R. Bradshaw and E.
Dennis, eds. Academic Press 2004 Volume 1, 505-511.
10. Obenauer JC, Yaffe MB. Computational prediction of protein-protein interactions. Protein-Protein Interactions, H. Fu ed. Humana Press 2004
445-467.
11. Yaffe MB, Smerdon SJ. The use of in vitro peptide-library screens in the analysis of phosphoserine/threonine-binding domain structure and function. Ann. Rev Biophys Biomol Struct. 2004;33:225-44.
12.
Stehn J, Yaffe MB. Protemics approaches to studying phosphoerine/threonine-binding domains: Application to 14-3-3 protein complexes. Functional Proteomics: Principles and Practical Applications, P.
Ping, ed. Humana Press 2005.
13.
Manke IA, Yaffe MB. Screening kinase phosphorylation motifs using Peptide libraries. CSH Protoc. 2007 doi: 10.1101/pdb.prot4640.
14.
Janes KA, Reinhardt HC, Yaffe MB. The apoptotic signaling network dynamically interprets the outputs of individual signaling pathways in an early analog and late digital manner. Systems Biology: The Challenge of
Complexity. S. Nakanishi and R. Kageyama, eds. Springer-Verlag Berlin,
2009.
24