• 2019
• 2018
• 2017
• 2016
• 2015
• 2014
• 2013
• 2012
• 2011
• 2010
• 2009 and earlier

2019

• Patterson JC, Joughin BA, van de Kooij B, Lim DC, Lauffenburger DA, Yaffe MB. 2019. ROS and Oxidative Stress Are Elevated in Mitosis during Asynchronous Cell Cycle Progression and Are Exacerbated by Mitotic Arrest. Cell Syst 8: 163-167.e2.
• Rohani N, Hao L, Alexis MS, Joughin BA, Krismer K, Moufarrej MN, Soltis AR, Lauffenburger DA, Yaffe MB, Burge CB, Bhatia SN, Gertler FB. 2019. Acidification of tumor at stromal boundaries drives transcriptome alterations associated with aggressive phenotypes. Cancer Res. 
• Barrett CD, Moore HB, Kong Y-W, Chapman MP, Sriram G, Lim D, Moore EE, Yaffe MB. 2019. Tranexamic acid mediates proinflammatory and anti-inflammatory signaling via complement C5a regulation in a plasminogen activator-dependent manner. J Trauma Acute Care Surg 86: 101–107.
• Yaffe MB. 2019. Why geneticists stole cancer research even though cancer is primarily a signaling disease. Sci Signal 12.
• Hwang J-H, Kim AR, Kim KM, Il Park J, Oh HT, Moon SA, Byun MR, Jeong H, Kim HK, Yaffe MB, Hwang ES, Hong JH. 2019. TAZ couples Hippo/Wnt signalling and insulin sensitivity through Irs1 expression. Nat Commun 10: 421.

2018

• Barrett CD, Hsu AT, Ellson CD, Y Miyazawa B, Kong Y-W, Greenwood JD, Dhara S, Neal MD, Sperry JL, Park MS, Cohen MJ, Zuckerbraun BS, Yaffe MB. 2018. Blood clotting and traumatic injury with shock mediates complement-dependent neutrophil priming for extracellular ROS, ROS-dependent organ injury and coagulopathy. Clin Exp Immunol 194: 103–117
• Creixell P, Pandey JP, Palmeri A, Bhattacharyya M, Creixell M, Ranganathan R, Pincus D, Yaffe MB. 2018. Hierarchical Organization Endows the Kinase Domain with Regulatory Plasticity. Cell Systems 7: 371-383.e4.
• Hymel D, Grant RA, Tsuji K, Yaffe MB, Burke TR. 2018. Histidine N(τ)-cyclized macrocycles as a new genre of polo-like kinase 1 polo-box domain-binding inhibitors. Bioorganic & Medicinal Chemistry Letters 28: 3202–3205.
• Alkan O, Schoeberl B, Shah M, Koshkaryev A, Heinemann T, Drummond DC, Yaffe MB, Raue A. 2018. Modeling chemotherapy-induced stress to identify rational combination therapies in the DNA damage response pathway. Sci Signal 11: eaat0229.
• Kaczmarek E, Hauser CJ, Kwon WY, Rica I, Chen L, Sandler N, Otterbein LE, Campbell Y, Cook CH, Yaffe MB, Marusich M, Itagaki K. 2018. A subset of five human mitochondrial formyl peptides mimics bacterial peptides and functionally deactivates human neutrophils. J Trauma Acute Care Surg. 85(5):936-943.
• Lam FC, Morton SW, Wyckoff J, Vu Han TL, Hwang MK, Maffa A, Balkanska-Sinclair E, Yaffe MB, Floyd SR, Hammond PT. 2018. Enhances efficacy of combined temozolomide and bromodomain inhibitor therapy for gliomas using targeted nanoparticles. Nat Commun. 19(1): 1191.
• Suarez-Lopez L, Sriram G, Kong YW, Morandell S, Merrick KA, Hernandez Y, Haigis KM, Yaffe MB. 2018. MK2 contributes to tumor progression by promoting M2 macrophage polarization and tumor angiogenesis. PNAS. 115(18): E4236-44.
• Dreaden EC, Kong YW,Quadir MA, Correa S, Barberio AE, Hwang MK, Shi AC, Oberlton B, Gallagher PN, Shopsowitz KE, Elias KM, Yaffe MB, Hammond PT. 2018. RNA-Peptide nanoplexes drug DNA damage pathways in high-grade serous ovarian tumors. Bioeng Transl Med. 3: 26–36.
• Moya CM, Zaballos MA, Garzón L, Luna C, Simón R, Yaffe MB, Gallego E, Santisteban P, Moreno JC. 2018. TAZ/WWTR1 Mediates the Pulmonary Effects of NKX2-1 Mutations in Brain-Lung-Thyroid Syndrome. J Clin Endocrinol Metab. 103: 839–852.
• Yaffe MB. 2018. Predicting the future of signaling for 2018. Sci Signal. 11(511). pii:eaar7429.

2017

2016

• Lee MJ, Yaffe MB. 2016. Protein Regulation in Signal Transduction. Cold Spring Harb Perspect Biol. 8(6). pii: a005918. 
• Lam FC, Yaffe MB.  2016. Kicking Genomic Profiling to the Curb: How Re-wiring the Phosphoproteome Can Explain Treatment Resistance in Glioma. Cancer Cell. 29(4):435-6.
• Yaffe MB, Gough NR. 2016. Leveraging signaling research to understand and treat disease. Science Signaling. 9:eg4. 

2015

• Qian WJ, Park JE, Grant R, Lai CC, Kelley JA, Yaffe MB, Lee KS, Burke TR. 2015. Neighbor-directed Histidine N(τ)-Alkylation: A Route to Imidazolium-containing Phosphopeptide Macrocycles. Biopolymers. 104(6): 663-73.
• Dreaden EC, Kong YW, Morton SW, Correa S, Choi KY, Shopsowitz KE, Renggli K, Drapkin R, Yaffe MB, Hammond PT. 2015. Tumor-Targeted Synergistic Blockade of MAPK and PI3K From a Layer-by-Layer Nanoparticle. Clin Cancer Res. 21(19): 4410-9.
• Hsu AT, Barrett CD, DeBusk GM, Ellson CD, Gautam S, Talmor DS, Gallagher DC, Yaffe MB. 2015. Kinetics and Role of Plasma Matrix Metalloproteinase-9 Expression in Acute Lung Injury and the Acute Respiratory Distress Syndrome. Shock. 44(2):128-36. 
• Rameseder J, Krismer K, Dayma Y, Ehrenberger T, Hwang MK, Airoldi EM, Floyd SR, Yaffe MB. 2015. A Multivariate Computational Method to Analyze High-Content RNAi Screening Data. J Biomol Screen. 20(8): 985-97.
• Ehrenberger T, Cantley LC, Yaffe MB. 2015. Computational prediction of protein-protein interactions. Methods Mol Biol. 1278: 57-75. 
• Naegle K, Gough NR, Yaffe MB. 2015. Criteria for biological reproducibility: what does "n" mean? Sci Signal. 8(371):fs7.
• Lunt SY, Muralidhar V, Hosios AM, Israelsen WJ, Gui DY, Newhouse L, Ogrodzinski M, Hecht V, Xu K, Acevedo PN, Hollern DP, Bellinger G, Dayton TL, Christen S, Elia I, Dinh AT, Stephanopoulos G, Manalis SR, Yaffe MB, Andrechek ER, Fendt SM, Vander Heiden MG. 2015. Pyruvate kinase isoform expression alters nucleotide synthesis to impact cell proliferation. Molecular Cell. 57:95-107. 
• Bryson BD, Del Rosario AM, Gootenberg JS, Yaffe MB, White FM.  2015. Engineered bromodomains to explore the acetylproteome. Proteomics. 15:1470-5. 
• Zhu EF, Gai SA, Opel CF, Kwan BH, Surana R, Mihm MC, Kauke MJ, Moynihan KD, Angelini A, Williams RT, Stephan MT, Kim JS, Yaffe MB, Irvine DJ, Weiner LM, Dranoff G, Wittrup KD. 2015. Synergistic innate and adaptive immune response to combination immunotherapy with anti-tumor antigen antibodies and extended serum half-life IL-2. Cancer Cell. 27:489-501. 
• Cannell IG, Merrick KA, Morandell S, Zhu CQ, Braun CJ, Grant RA, Cameron ER, Tsao MS, Hemann MT, Yaffe MB. 2015. A Pleiotropic RNA-Binding Protein Controls Distinct Cell Cycle Checkpoints to Drive Resistance of p53-Defective Tumors to Chemotherapy. Cancer Cell. 28:623-37.

2014

• Shaul YD, Freinkman E, Comb WC, Cantor JR, Tam WL, Thiru P, Kim D, Kanarek N, Pacold ME, Chen WW, Bierie B, Possemato R, Reinhardt F, Weinberg RA, Yaffe MB, Sabatini DM. 2014. Dihydropyrimidine accumulation is required for the epithelial-mesenchymal transition. Cell.158(5):1094-109. 
• Peterson LB, Yaffe MB, Imperiali B. 2014. Selective mitogen activated protein kinase activity sensors through the application of directionally programmable D domain motifs. Biochemistry. 53(36):5771-8.
• Morton SW, Lee MJ, Deng ZJ, Dreaden EC, Siouve E, Shopsowitz KE, Shah NJ, Yaffe MB, Hammond PT. 2014. A nanoparticle-based combination chemotherapy delivery system for enhanced tumor killing by dynamic rewiring of signaling pathways. Sci Signal. 7(325):ra44.

2013

• Morandell S, Reinhardt HC, Cannell IG, Kim JS, Ruf DM, Mitra T, Couvillon AD, Jacks T, Yaffe MB. 2013. A reversible gene-targeting strategy identifies synthetic lethal interactions between MK2 and p53 in the DNA damage response in vivo. Cell Rep. 5(4):868-77. 
• Floyd SR, Pacold ME, Huang 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. 2013. The bromodomain protein Brd4 insulates chromatin from DNA damage signalling. Nature. 498(7453): 246-50. 
• Rock JM, Lim D, Stach L, Ogrodowicz RW, Keck JM, Jones MH, Wong CC, Yates JR 3rd, Winey M, Smerdon SJ, Yaffe MB, Amon A. 2013. Activation of the yeast Hippo pathway by phosphorylation-dependent assembly of signaling complexes. Science. 340(6134): 871-5. 
• Weingeist DM, Ge J, Wood DK, Mutamba JT, Huang Q, Rowland EA, Yaffe MB, Floyd S, Engelward BP. 2013. Single-cell microarray enables high-throughput evaluation of DNA double-strand breaks and DNA repair inhibitors. Cell Cycle. 12(6): 907-15.

​2012

• 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. 2012. AATF/Che-1 acts as a phosphorylation-dependent molecular modulator to repress p53-driven apoptosis. EMBO J. 31(20):3961-75. doi: 10.1038/emboj.2012.236. 
• Singh N, Basnet H, Wiltshire TD, Mohammad DH, Thompson JR, Héroux A, Botuyan MV, Yaffe MB, Couch FJ, Rosenfeld MG, Mer G. 2012. Dual recognition of phosphoserine and phosphotyrosine in histone variant H2A.X by DNA damage response protein MCPH1. PNAS. 109(36):14381-6. doi: 10.1073/pnas.1212366109. 
• Joughin BA, Liu C, Lauffenburger DA, Hogue CW, Yaffe MB. 2012. Protein kinases display minimal interpositional dependence on substrate sequence: potential implications for the evolution of signalling networks. Philos Trans R Soc Lond B Biol Sci. 367(1602): 2574-83. doi: 10.1098/rstb.2012.0010.
• Naegle KM, White FM, Lauffenburger DA, Yaffe MB. 2012. Robust co-regulation of tyrosine phosphorylation sites on proteins reveals novel protein interactions. Mol Biosyst. 8(10): 2771-82. doi: 10.1039/c2mb25200g.
• Lee MJ, Ye AS, Gardino AK, Heijink AM, Sorger PK, MacBeath G, Yaffe MB. 2012. Sequential application of anticancer drugs enhances cell death by rewiring apoptotic signaling networks. Cell. 149(4):780-94. doi: 10.1016/j.cell.2012.03.031.
• Mohammad DH, Yaffe MB. 2012. Fixin' to divide. Mol Cell. 45(3):273-5. doi: 10.1016/j.molcel.2012.01.022.
• Tentner AR, Lee MJ, Ostheimer GJ, Samson LD, Lauffenburger DA, Yaffe MB. 2012. 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. 8:568. doi: 10.1038/msb.2012.1.
• Liu F, Park JE, Qian WJ, Lim D, Scharow A, Berg T, Yaffe MB, Lee KS, Burke TR Jr. 2012. Identification of high affinity polo-like kinase 1 (Plk1) polo-box domain binding peptides using oxime-based diversification. ACS Chem Biol. 7(5):805-10. 

2011

• 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. 2011. Systematic phosphorylation analysis of human mitotic protein complexes. Sci Signal. 4(198):rs12. doi: 10.1126/scisignal.2001993.
• 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. 2011. Quantitative phospho-proteomics to investigate the polo-like kinase 1-dependent phospho-proteome. Mol Cell Proteomics. 10(11):M111.008540. doi: 10.1074/mcp.M111.008540. 
• Naegle KM, Welsch RE, Yaffe MB, White FM, Lauffenburger DA. 2011. MCAM: multiple clustering analysis methodology for deriving hypotheses and insights from high-throughput proteomic datasets. PLoS Comput Biol. 7(7):e1002119. doi: 10.1371/journal.pcbi.1002119. 
• Liu F, Park JE, Qian WJ, Lim D, Gräber M, Berg T, Yaffe MB, Lee KS, Burke TR Jr. 2011. Serendipitous alkylation of a Plk1 ligand uncovers a new binding channel. Nat Chem Biol. 7(9):595-601. doi: 10.1038/nchembio.614.
• 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. 2011. Spatial exclusivity combined with positive and negative selection of phosphorylation motifs is the basis for context-dependent mitotic signaling. Sci Signal. 4(179):ra42. doi: 10.1126/scisignal.2001796.
• Cannell IG, Yaffe MB. 2011. Salvaging the septic heart through targeting the interleukin-6/p38 mitogen-activated protein kinase signaling network. Crit Care Med. 39(7): 1836-7. doi: 10.1097/CCM.0b013e3182204ad1. 

2010

• Pennell S, Westcott S, Ortiz-Lombardía M, Patel D, Li J, Nott TJ, Mohammed D, Buxton RS, Yaffe MB, Verma C, Smerdon SJ. 2010. Structural and functional analysis of phosphothreonine-dependent FHA domain interactions. Mol Cell. 40(1):34-49. doi: 10.1016/j.molcel.2010.09.018.
• Reinhardt HC, Hasskamp P, Schmedding I, Morandell S, van Vugt MA, Wang X, Linding R, Ong SE, Weaver D, Carr SA, Yaffe MB. 2010. DNA damage activates a spatially distinct late cytoplasmic cell-cycle checkpoint network controlled by MK2-mediated RNA stabilization. Mol Cell. 40(1):34-49. doi: 10.1016/j.molcel.2010.09.018.
• Naegle KM, Gymrek M, Joughin BA, Wagner JP, Welsch RE, Yaffe MB, Lauffenburger DA, White FM. 2010. PTMScout, a Web resource for analysis of high throughput post-translational proteomics studies. Mol Cell Proteomics. 9(11):2558-70. doi: 10.1074/mcp.M110.001206.
• Jeong H, Bae S, An SY, Byun MR, Hwang JH, Yaffe MB, Hong JH, Hwang ES. 2010. TAZ as a novel enhancer of MyoD-mediated myogenic differentiation. FASEB J. 24(9):3310-20. doi: 10.1096/fj.09-151324. 
• 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. 2010. A mitotic phosphorylation feedback network connects Cdk1, Plk1, 53BP1, and Chk2 to inactivate the G(2)/M DNA damage checkpoint. PLoS Biol. 8(1):e1000287. doi: 10.1371/journal.pbio.1000287.
• Wen J, Wilker EW, Yaffe MB, Jensen KF. 2010. Microfluidic preparative free-flow isoelectric focusing: system optimization for protein complex separation. Anal Chem. 82(4):1253-60. doi: 10.1021/ac902157e.

2009 and earlier

• article