Publications By Our Scientists

Publications & Posters

CST scientists continually work to propel biological discovery forward, not only by providing tools, reagents, and services to our fellow scientists, but also through their own scientific advancements. Our studies often involve the development of new technologies that enable signaling pathway analysis and mechanistic biology research.

CST scientists are indicated in bold.

2023 Publications

Jean-Pierre Bellier, Yuqi Cai, Sarah M. Alam, Thorsten Wiederhold, Arica Aiello, Jonathan S. Vogelgsang, Sabina Berretta, Jasmeer P. Chhatwal, Dennis J. Selkoe, Lei Liu. Uncovering elevated tau TPP motif phosphorylation in the brain of Alzheimer's disease patients Alzheimer’s & Dementia
Ellen M. Quardokus, Diane C. Saunders, Elizabeth McDonough, John W. Hickey, Christopher Werlein, Christine Surrette, Presha Rajbhandari, Anna Martinez Casals, Hua Tian, Lisa Lowery, Elizabeth K. Neumann, Frida Björklund, Taruna V. Neelakantan, Josh Croteau, Anne E. Wiblin, Jeremy Fisher, April J. Livengood, Karen G. Dowell, Jonathan C. Silverstein, Jeffrey M. Spraggins, Gloria S. Pryhuber, Gail Deutsch, Fiona Ginty, Garry P. Nolan, Simon Melov, Danny Jonigk, Michael A. Caldwell, Ioannis S. Vlachos, Werner Muller, Nils Gehlenborg, Brent R. Stockwell, Emma Lundberg, Michael P. Snyder, Ronald N. Germain, Jeannie M. Camarillo, Neil L. Kelleher, Katy Börner & Andrea J. Radtke Organ Mapping Antibody Panels: a community resource for standardized multiplexed tissue imaging ??— Nature Methods.2023

2021 Publications

Khbouz B, Rowart P, Poma L, Dahlke E, Bottner M, Stokes M, Bolen G, Rahmouni S, Theilig F, Jouret F. The genetic deletion of the Dual Specificity Phosphatase 3 (DUSP3) attenuates kidney damage and inflammation following ischemia/reperfusion injury in mouse Acta Physiol (Oxf). 2021;e13735
Hickey JW, Neumann EK, Radtke AJ, Camarillo JM, Beuschel RT, Albanese A, McDonough E, Hatler J, Wiblin AE, Fisher J, Croteau J, Small EC, Sood A, Caprioli RM, Angelo MR, Nolan GP, Chung K, Hewitt SM, Germain RN, Spraggins JM, Lundberg E, Snyder MP, Kelleher NL, Saka SK. Spatial mapping of protein composition and tissue organization: a primer for multiplexed antibody-based imaging Nature Methods. 2021

2020 Publications

Crosby K, Wood AW, Simendinger J, Grange C, Carr L, Costa-Grant K, Roller CJ, Polakiewicz RD. YAP vs. TAZ: differences in expression revealed through rigorous validation of target-specific monoclonal antibodies Journal of Histotechnology. 2020

2019 Publications

2018 Publications

2017 Publications

Gu H, Ren J, Jia X, Stokes MP (2017) Identification of Post-Translational Modifications from Serum/Plasma by Immunoaffinity Enrichment and LC-MS/MS Analysis Without Depletion of Abundant Proteins. Methods Mol. Biol. 1619, 119–125.
Dogan T, Gnad F, Chan J, Phu L, Young A, Chen MJ, Doll S, Stokes MP, Belvin M, Friedman LS, Kirkpatrick DS, Hoeflich KP, Hatzivassiliou G (2017) Role of the E3 ubiquitin ligase RNF157 as a novel downstream effector linking PI3K and MAPK signaling to the cell cycle. J. Biol. Chem. [Epub ahead of print].
Lee G, Zheng Y, Cho S, Jang C, England C, Dempsey JM, Yu Y, Liu X, He L, Cavaliere PM, Chavez A, Zhang E, Isik M, Couvillon A, Dephoure NE, Blackwell TK, Yu JJ, Rabinowitz JD, Cantley LC, Blenis J. Post-transcriptional Regulation of De Novo Lipogenesis by mTORC1-S6K1-SRPK2 Signaling. Cell. 2017.
Hershberger KA, Abraham DM, Martin AS, Mao L, Liu J, Gu H, Locasale JW, Hirschey MD. Sirtuin 5 is required for mouse survival in response to cardiac pressure overload. J Biol Chem. 2017.
Lumpkin RJ, Gu H, Zhu Y, Leonard M, Ahmad AS, Clauser KR, Meyer JG, Bennett EJ, Komives EA. Site-specific identification and quantitation of endogenous SUMO modifications under native conditions. Nat Commun. 2017.
Ying L, Yan F, Meng Q, Yuan X, Yu L, Williams BRG, Chan DW, Shi L, Tu Y, Ni P, Wang X, Xu D, Hu Y. Understanding immune phenotypes in human gastric disease tissues by multiplexed immunohistochemistry. J Transl Med. 2017.
Fernandez NF, Gundersen GW, Rahman A, Grimes ML, Rikova K, Hornbeck P, Ma'ayan A. Clustergrammer, a web-based heatmap visualization and analysis tool for high-dimensional biological data. Sci Data. 2017.
Takada M, Zhang W, Suzuki A, Kuroda TS, Yu Z, Inuzuka H, Gao D, Wan L, Zhuang M, Hu L, Zhai B, Fry CJ, Bloom K, Li G, Karpen GH, Wei W, Zhang Q. FBW7 Loss Promotes Chromosomal Instability and Tumorigenesis via Cyclin E1/CDK2-Mediated Phosphorylation of CENP-A. Cancer Res. 2017.
Dogan T, Gnad F, Chan J, Phu L, Young A, Chen MJ, Doll S, Stokes MP, Belvin M, Friedman LS, Kirkpatrick DS, Hoeflich KP, Hatzivassiliou G. Role of the E3 ubiquitin ligase RNF157 as a novel downstream effector linking PI3K and MAPK signaling pathways to the cell cycle. J Biol Chem. 2017.
Chen R, Lai LA, Sullivan Y, Wong M, Wang L, Riddell J, Jung L, Pillarisetty VG, Brentnall TA, Pan S. Disrupting glutamine metabolic pathways to sensitize gemcitabine-resistant pancreatic cancer. Sci Rep. 2017.
Everley RA, Huttlin EL, Erickson AR, Beausoleil SA, Gygi SP. Neutral Loss Is a Very Common Occurrence in Phosphotyrosine-Containing Peptides Labeled with Isobaric Tags. J Proteome Res. 2017.
Shimizu K, Fukushima H, Ogura K, Lien EC, Nihira NT, Zhang J, North BJ, Guo A, Nagashima K, Nakagawa T, Hoshikawa S, Watahiki A, Okabe K, Yamada A, Toker A, Asara JM, Fukumoto S, Nakayama KI, Nakayama K, Inuzuka H, Wei W. The SCFΒ-TRCP E3 ubiquitin ligase complex targets Lipin1 for ubiquitination and degradation to promote hepatic lipogenesis. Sci Signal. 2017.
Gu H, Ren J, Jia X, Stokes MP. Identification of Post-Translational Modifications from Serum/Plasma by Immunoaffinity Enrichment and LC-MS/MS Analysis Without Depletion of Abundant Proteins. Methods Mol Biol. 2017.
Tsanov KM, Pearson DS, Wu Z, Han A, Triboulet R, Seligson MT, Powers JT, Osborne JK, Kane S, Gygi SP, Gregory RI, Daley GQ. LIN28 phosphorylation by MAPK/ERK couples signalling to the post-transcriptional control of pluripotency. Nat Cell Biol. 2017.

2016 Publications

Lohmueller JJ, Sato S, Popova L, Chu IM, Tucker MA, Barberena R, Innocenti GM, Cudic M, Ham JD, Cheung WC, Polakiewicz RD, Finn OJ (2016) Antibodies elicited by the first non-viral prophylactic cancer vaccine show tumor-specificity and immunotherapeutic potential. Sci Rep 6, 31740.
Gnad F, Wallin J, Edgar K, Doll S, Arnott D, Robillard L, Kirkpatrick DS, Stokes MP, Vijapurkar U, Hatzivassiliou G, Friedman LS, Belvin M (2016) Quantitative phosphoproteomic analysis of the PI3K-regulated signaling network. Proteomics 16(14), 1992-7.
Gnad F, Doll S, Song K, Stokes MP, Moffat J, Liu B, Arnott D, Wallin J, Friedman LS, Hatzivassiliou G, Belvin M (2016) Phosphoproteome analysis of the MAPK pathway reveals previously undetected feedback mechanisms. Proteomics 16(14), 1998-2004.
Li MO, Rudensky AY (2016) T cell receptor signalling in the control of regulatory T cell differentiation and function. Nat. Rev. Immunol. 16(4), 220–33.
Gu H, Ren JM, Jia X, Levy T, Rikova K, Yang V, Lee KA, Stokes MP, Silva JC (2016) Quantitative Profiling of Post-translational Modifications by Immunoaffinity Enrichment and LC-MS/MS in Cancer Serum without Immunodepletion. Mol. Cell Proteomics 15(2), 692–702.
Stokes M., et al. Antibody-Based Proteomic Analysis of Apoptosis Signaling. In: Perpetua M. (Ed.) Apoptosis Methods in Toxicology. New York, NY: Humana Press; 2016: 163-178.
Gu H, Stokes MP, Silva JC. Proteomic Analysis of Post-Translational Modifications in Neurobiology. In: Grant J, Hong L (Eds.) Analysis of Post-Translation Modifications and Proteolysis in Neuroscience. Vol. 114. New York, NY: Humana Press; 2016: TBD.
Rose CM, Isasa M, Ordureau A, Prado MA, Beausoleil SA, Jedrychowski MP, Finley DJ, Harper JW, Gygi SP. Highly Multiplexed Quantitative Mass Spectrometry Analysis of Ubiquitylomes. Cell Syst. 2016.
Beckerman R, Yoh K, Mattia-Sansobrino M, Zupnick A, Laptenko O, Karni-Schmidt O, Ahn J, Byeon IJ, Keezer S, Prives C. Lysines in the tetramerization domain of p53 selectively modulate G1 arrest. Cell Cycle. 2016.
Massey KJ, Li Q, Rossi NF, Keezer SM, Mattingly RR, Yingst DR. Phosphorylation of rat kidney Na-K pump at Ser938 is required for rapid angiotensin II-dependent stimulation of activity and trafficking in proximal tubule cells. Am J Physiol Cell Physiol. 2016.

2015 Publications

Morvan MG, Lanier LL (2015) NK cells and cancer: you can teach innate cells new tricks. Nat Rev Cancer 16(1), 7-19.
Childs RW, Carlsten M (2015) Therapeutic approaches to enhance natural killer cell cytotoxicity against cancer: the force awakens. Nat Rev Drug Discov 14(7), 487-98.
Kumar S, Lu B, Dixit U, Hossain S, Liu Y, Li J, Hornbeck P, Zheng W, Sowalsky AG, Kotula L, Birge RB (2015) Reciprocal regulation of Abl kinase by Crk Y251 and Abi1 controls invasive phenotypes in glioblastoma. Oncotarget 6(35), 37792–807.
Sriram G, Jankowski W, Kasikara C, Reichman C, Saleh T, Nguyen KQ, Li J, Hornbeck P, Machida K, Liu T, Li H, Kalodimos CG, Birge RB (2015) Iterative tyrosine phosphorylation controls non-canonical domain utilization in Crk. Oncogene 34(32), 4260–9.
Hornbeck PV (2015) Enzyme-Linked Immunosorbent Assays. Curr Protoc Immunol 110, 2.1.1–23.
Gray LR, Sultana MR, Rauckhorst AJ, Oonthonpan L, Tompkins SC, Sharma A, Fu X, Miao R, Pewa AD, Brown KS, Lane EE, Dohlman A, Zepeda-Orozco D, Xie J, Rutter J, Norris AW, Cox JE, Burgess SC, Potthoff MJ, Taylor EB (2015) Hepatic Mitochondrial Pyruvate Carrier 1 Is Required for Efficient Regulation of Gluconeogenesis and Whole-Body Glucose Homeostasis. Cell Metab. 22(4), 669–81.
Wimberly H, Brown JR, Schalper K, Haack H, Silver MR, Nixon C, Bossuyt V, Pusztai L, Lannin DR, Rimm DL (2015) PD-L1 Expression Correlates with Tumor-Infiltrating Lymphocytes and Response to Neoadjuvant Chemotherapy in Breast Cancer. Cancer Immunol Res 3(4), 326–32.
Kee JM, Oslund RC, Couvillon AD, Muir TW (2015) A second-generation phosphohistidine analog for production of phosphohistidine antibodies. Org. Lett. 17(2), 187–9.
Honda T, Obara Y, Yamauchi A, Couvillon AD, Mason JJ, Ishii K, Nakahata N (2015) Phosphorylation of ERK5 on Thr732 is associated with ERK5 nuclear localization and ERK5-dependent transcription. PLoS ONE 10(2), e0117914.
Werner S, Brors B, Eick J, Marques E, Pogenberg V, Parret A, Kemming D, Wood AW, Edgren H, Neubauer H, Streichert T, Riethdorf S, Bedi U, Baccelli I, Jucker M, Eils R, Fehm T, Trumpp A, Johnsen SA, Klefstrom J, Wilmanns M, Muller V, Pantel K, Wikman H (2015) Suppression of early hematogenous dissemination of human breast cancer cells to bone marrow by retinoic acid induced 2. Cancer Discov [Epub ahead of print].
Lawan A, Zhang L, Gatzke F, Min K, Jurczak MJ, Al-Mutairi M, Richter P, Camporez JP, Couvillon A, Pesta D, Roth Flach RJ, Shulman GI, Bennett AM (2015) Hepatic mitogen-activated protein kinase phosphatase 1 selectively regulates glucose metabolism and energy homeostasis. Mol. Cell. Biol. 35(1), 26–40.
Hornbeck PV, Zhang B, Murray B, Kornhauser JM, Latham V, Skrzypek E (2015) PhosphoSitePlus, 2014: mutations, PTMs and recalibrations. Nucleic Acids Res. 43(Database issue), D512–20.
Paulo JA, McAllister FE, Everley RA, Beausoleil SA, Banks AS, Gygi SP (2015) Effects of MEK inhibitors GSK1120212 and PD0325901 in vivo using 10-plex quantitative proteomics and phosphoproteomics. Proteomics 15(2-3), 462–73.
Lin R, Elf S, Shan C, Kang HB, Ji Q, Zhou L, Hitosugi T, Zhang L, Zhang S, Seo JH, Xie J, Tucker M, Gu TL, Sudderth J, Jiang L, Mitsche M, DeBerardinis RJ, Wu S, Li Y, Mao H, Chen PR, Wang D, Chen GZ, Hurwitz SJ, Lonial S, Arellano ML, Khoury HJ, Khuri FR, Lee BH, Lei Q, Brat DJ, Ye K, Boggon TJ, He C, Kang S, Fan J, Chen J (2015) 6-Phosphogluconate dehydrogenase links oxidative PPP, lipogenesis and tumour growth by inhibiting LKB1-AMPK signalling. Nat. Cell Biol. 17(11), 1484–96.
Patterson HC, Gerbeth C, Thiru P, Vögtle NF, Knoll M, Shahsafaei A, Samocha KE, Huang CX, Harden MM, Song R, Chen C, Kao J, Shi J, Salmon W, Shaul YD, Stokes MP, Silva JC, Bell GW, MacArthur DG, Ruland J, Meisinger C, Lodish HF (2015) A respiratory chain controlled signal transduction cascade in the mitochondrial intermembrane space mediates hydrogen peroxide signaling. Proc. Natl. Acad. Sci. U.S.A. 112(42), E5679–88.
Barrows D, Schoenfeld SM, Hodakoski C, Silkov A, Honig B, Couvillon A, Shymanets A, Nuernberg B, Asara JM, Parsons R (2015) PAK kinases mediate the phosphorylation of PREX2 to initiate feedback inhibition of Rac1. J. Biol. Chem. [Epub ahead of print].
Lawan A, Zhang L, Gatzke F, Min K, Jurczak MJ, Al-Mutairi M, Richter P, Camporez JP, Couvillon A, Pesta D, Roth Flach RJ, Shulman GI, Bennett AM (2015) Hepatic mitogen-activated protein kinase phosphatase 1 selectively regulates glucose metabolism and energy homeostasis. Mol. Cell. Biol. 35(1), 26–40.
Zhang L, Tran NT, Su H, Wang R, Lu Y, Tang H, Aoyagi S, Guo A , Khodadadi-Jamayran A, Zhou D, Qian K, Hricik T, Côté J, Han X, Zhou W, Laha S, Abdel-Wahab O, Levine RL, Raffel G, Liu Y, Chen D, Li H, et al. Cross-talk between PRMT1-mediated methylation and ubiquitylation on RBM15 controls RNA splicing. Elife 2015.

2014 Publications

Shan C, Elf S, Ji Q, Kang HB, Zhou L, Hitosugi T, Jin L, Lin R, Zhang L, Seo JH, Xie J, Tucker M, Gu TL, Sudderth J, Jiang L, DeBerardinis RJ, Wu S, Li Y, Mao H, Chen PR, Wang D, Chen GZ, Lonial S, Arellano ML, Khoury HJ, Khuri FR, Lee BH, Brat DJ, Ye K, Boggon TJ, He C, Kang S, Fan J, Chen J (2014) Lysine acetylation activates 6-phosphogluconate dehydrogenase to promote tumor growth. Mol. Cell 55(4), 552–65.
Mulherkar S, Uddin MD, Couvillon AD, Sillitoe RV, Tolias KF (2014) The small GTPases RhoA and Rac1 regulate cerebellar development by controlling cell morphogenesis, migration and foliation. Dev. Biol. 394(1), 39–53.
Oslund RC, Kee JM, Couvillon AD, Bhatia VN, Perlman DH, Muir TW (2014) A phosphohistidine proteomics strategy based on elucidation of a unique gas-phase phosphopeptide fragmentation mechanism. J. Am. Chem. Soc. 136(37), 12899–911.
Lauriol J, Keith K, Jaffré F, Couvillon A, Saci A, Goonasekera SA, McCarthy JR, Kessinger CW, Wang J, Ke Q, Kang PM, Molkentin JD, Carpenter C, Kontaridis MI (2014) RhoA signaling in cardiomyocytes protects against stress-induced heart failure but facilitates cardiac fibrosis. Sci Signal 7(348), ra100.
Fan J, Kang HB, Shan C, Elf S, Lin R, Xie J, Gu TL, Aguiar M, Lonning S, Chung TW, Arellano M, Khoury HJ, Shin DM, Khuri FR, Boggon TJ, Kang S, Chen J (2014) Tyr-301 phosphorylation inhibits pyruvate dehydrogenase by blocking substrate binding and promotes the Warburg effect. J. Biol. Chem. 289(38), 26533–41.
Fan J, Shan C, Kang HB, Elf S, Xie J, Tucker M, Gu TL, Aguiar M, Lonning S, Chen H, Mohammadi M, Britton LM, Garcia BA, Alečković M, Kang Y, Kaluz S, Devi N, Van Meir EG, Hitosugi T, Seo JH, Lonial S, Gaddh M, Arellano M, Khoury HJ, Khuri FR, Boggon TJ, Kang S, Chen J (2014) Tyr phosphorylation of PDP1 toggles recruitment between ACAT1 and SIRT3 to regulate the pyruvate dehydrogenase complex. Mol. Cell 53(4), 534–48.
Guo A, Gu H, Zhou J, Mulhern D, Wang Y, Lee KA, Yang V, Aguiar M, Kornhauser J, Jia X, Ren J, Beausoleil SA, Silva JC, Vemulapalli V, Bedford MT, Comb MJ (2014) Immunoaffinity enrichment and mass spectrometry analysis of protein methylation. Mol. Cell Proteomics 13(1), 372–87.
Wang L, Zhao Z, Meyer MB, Saha S, Yu M, Guo A, Wisinski KB, Huang W, Cai W, Pike JW, Yuan M, Ahlquist P, Xu W (2014) CARM1 methylates chromatin remodeling factor BAF155 to enhance tumor progression and metastasis. Cancer Cell 25(1), 21–36.
Sanidas I, Polytarchou C, Hatziapostolou M, Ezell SA, Kottakis F, Hu L, Guo A, Xie J, Comb MJ, Iliopoulos D, Tsichlis PN (2014) Phosphoproteomics screen reveals akt isoform-specific signals linking RNA processing to lung cancer. Mol. Cell 53(4), 577–90.
Schell JC, Olson KA, Jiang L, Hawkins AJ, Van Vranken JG, Xie J, Egnatchik RA, Earl EG, DeBerardinis RJ, Rutter J (2014) A role for the mitochondrial pyruvate carrier as a repressor of the warburg effect and colon cancer cell growth. Mol. Cell 56(3), 400–13.
Paardekooper Overman J, Yi JS, Bonetti M, Soulsby M, Preisinger C, Stokes MP, Hui L, Silva JC, Overvoorde J, Giansanti P, Heck AJ, Kontaridis MI, den Hertog J, Bennett AM (2014) PZR coordinates Shp2 Noonan and LEOPARD syndrome signaling in zebrafish and mice. Mol. Cell. Biol. 34(15), 2874–89.
Li N, Fassl A, Chick J, Inuzuka H, Li X, Mansour MR, Liu L, Wang H, King B, Shaik S, Gutierrez A, Ordureau A, Otto T, Kreslavsky T, Baitsch L, Bury L, Meyer CA, Ke N, Mulry KA, Kluk MJ, Roy M, Kim S, Zhang X, Geng Y, Zagozdzon A, Jenkinson S, Gale RE, Linch DC, Zhao JJ, Mullighan CG, Harper JW, Aster JC, Aifantis I, von Boehmer H, Gygi SP, Wei W, Look AT, Sicinski P (2014) Cyclin C is a haploinsufficient tumour suppressor. Nat. Cell Biol. 16(11), 1080–91.
Nifoussi SK, Ratcliffe NR, Ornstein DL, Kasof G, Strack S, Craig RW (2014) Inhibition of protein phosphatase 2A (PP2A) prevents Mcl-1 protein dephosphorylation at the Thr-163/Ser-159 phosphodegron, dramatically reducing expression in Mcl-1-amplified lymphoma cells. J. Biol. Chem. 289(32), 21950–9.
Gerhardt DM, Pajcini KV, D'altri T, Tu L, Jain R, Xu L, Chen MJ, Rentschler S, Shestova O, Wertheim GB, Tobias JW, Kluk M, Wood AW, Aster JC, Gimotty PA, Epstein JA, Speck N, Bigas A, Pear WS (2014) The Notch1 transcriptional activation domain is required for development and reveals a novel role for Notch1 signaling in fetal hematopoietic stem cells. Genes Dev. 28(6), 576–93.
Semenova I, Ikeda K, Resaul K, Kraikivski P, Aguiar M, Gygi S, Zaliapin I, Cowan A, Rodionov V (2014) Regulation of microtubule-based transport by MAP4. Mol. Biol. Cell 25(20), 3119–32.
Liew GM, Ye F, Nager AR, Murphy JP, Lee JS, Aguiar M, Breslow DK, Gygi SP, Nachury MV (2014) The Intraflagellar Transport Protein IFT27 Promotes BBSome Exit from Cilia through the GTPase ARL6/BBS3. Dev. Cell 31(3), 265–78.
Verma R, Su S, McCrann DJ, Green JM, Leu K, Young PR, Schatz PJ, Silva JC, Stokes MP, Wojchowski DM (2014) RHEX, a novel regulator of human erythroid progenitor cell expansion and erythroblast development. J. Exp. Med. 211(9), 1715–22.
Shan C, Kang HB, Elf S, Xie J, Gu TL, Aguiar M, Lonning S, Hitosugi T, Chung TW, Arellano M, Khoury HJ, Shin DM, Khuri FR, Boggon TJ, Fan J (2014) Tyr-94 phosphorylation inhibits pyruvate dehydrogenase phosphatase 1 and promotes tumor growth. J. Biol. Chem. 289(31), 21413–22.
Ordureau A, Sarraf SA, Duda DM, Heo JM, Jedrychowski MP, Sviderskiy VO, Olszewski JL, Koerber JT, Xie T, Beausoleil SA, Wells JA, Gygi SP, Schulman BA, Harper JW (2014) Quantitative Proteomics Reveal a Feedforward Mechanism for Mitochondrial PARKIN Translocation and Ubiquitin Chain Synthesis. Mol. Cell 56(3), 360–75.
Gray VE, Liu L, Nirankari R, Hornbeck PV, Kumar S (2014) Signatures of natural selection on mutations of residues with multiple posttranslational modifications. Mol. Biol. Evol. 31(7), 1641–5.
Sriram G, Jankowski W, Kasikara C, Reichman C, Saleh T, Nguyen KQ, Li J, Hornbeck P, Machida K, Liu T, Li H, Kalodimos CG, Birge RB (2014) Iterative tyrosine phosphorylation controls non-canonical domain utilization in Crk. Oncogene [Epub ahead of print].
Plattner F, Hernández A, Kistler TM, Pozo K, Zhong P, Yuen EY, Tan C, Hawasli AH, Cooke SF, Nishi A, Guo A, Wiederhold T, Yan Z, Bibb JA (2014) Memory enhancement by targeting Cdk5 regulation of NR2B. Neuron 81(5), 1070–83.
Yang L, Rozenfeld R, Wu D, Devi LA, Zhang Z, Cederbaum A (2014) Cannabidiol protects liver from binge alcohol-induced steatosis by mechanisms including inhibition of oxidative stress and increase in autophagy. Free Radic. Biol. Med. 68, 260–7.

2013 Publications

Dhar S, Vemulapalli V, Patananan AN, Huang GL, Di Lorenzo A, Richard S, Comb MJ, Guo A, Clarke SG, Bedford MT (2013) Loss of the major Type I arginine methyltransferase PRMT1 causes substrate scavenging by other PRMTs. Sci Rep 3, 1311.
Xin X, Gfeller D, Cheng J, Tonikian R, Sun L, Guo A, Lopez L, Pavlenco A, Akintobi A, Zhang Y, Rual JF, Currell B, Seshagiri S, Hao T, Yang X, Shen YA, Salehi-Ashtiani K, Li J, Cheng AT, Bouamalay D, Lugari A, Hill DE, Grimes ML, Drubin DG, Grant BD, Vidal M, Boone C, Sidhu SS, Bader GD (2013) SH3 interactome conserves general function over specific form. Mol. Syst. Biol. 9(Nucleic Acids Res. 2008 Jan;36(Database issue):D637-40), 652.
Swaney DL, Beltrao P, Starita L, Guo A, Rush J, Fields S, Krogan NJ, Villén J (2013) Global analysis of phosphorylation and ubiquitylation cross-talk in protein degradation. Nat. Methods 10(7), 676–82.
Pozo K, Castro-Rivera E, Tan C, Plattner F, Schwach G, Siegl V, Meyer D, Guo A, Gundara J, Mettlach G, Richer E, Guevara JA, Ning L, Gupta A, Hao G, Tsai LH, Sun X, Antich P, Sidhu S, Robinson BG, Chen H, Nwariaku FE, Pfragner R, Richardson JA, Bibb JA (2013) The role of Cdk5 in neuroendocrine thyroid cancer. Cancer Cell 24(4), 499–511.
Rardin MJ, He W, Nishida Y, Newman JC, Carrico C, Danielson SR, Guo A, Gut P, Sahu AK, Li B, Uppala R, Fitch M, Riiff T, Zhu L, Zhou J, Mulhern D, Stevens RD, Ilkayeva OR, Newgard CB, Jacobson MP, Hellerstein M, Goetzman ES, Gibson BW, Verdin E (2013) SIRT5 regulates the mitochondrial lysine succinylome and metabolic networks. Cell Metab. 18(6), 920–33.
Kim SE, Huang H, Zhao M, Zhang X, Zhang A, Semonov MV, MacDonald BT, Zhang X, Garcia Abreu J, Peng L, He X (2013) Wnt stabilization of β-catenin reveals principles for morphogen receptor-scaffold assemblies. Science 340(6134), 867–70.
Mielcarek M, Seredenina T, Stokes MP, Osborne GF, Landles C, Inuabasi L, Franklin SA, Silva JC, Luthi-Carter R, Beaumont V, Bates GP (2013) HDAC4 does not act as a protein deacetylase in the postnatal murine brain in vivo. PLoS ONE 8(11), e80849.
Giansanti P, Stokes MP, Silva JC, Scholten A, Heck AJ (2013) Interrogating cAMP-dependent kinase signaling in Jurkat T cells via a protein kinase A targeted immune-precipitation phosphoproteomics approach. Mol. Cell Proteomics 12(11), 3350–9.
Gnad F, Young A, Zhou W, Lyle K, Ong CC, Stokes MP, Silva JC, Belvin M, Friedman LS, Koeppen H, Minden A, Hoeflich KP (2013) Systems-wide analysis of K-Ras, Cdc42, and PAK4 signaling by quantitative phosphoproteomics. Mol. Cell Proteomics 12(8), 2070–80.
Zhang P, Guo A, Possemato A, Wang C, Beard L, Carlin C, Markowitz SD, Polakiewicz RD, Wang Z (2013) Identification and functional characterization of p130Cas as a substrate of protein tyrosine phosphatase nonreceptor 14. Oncogene 32(16), 2087–95.
Hernández-Gea V, Hilscher M, Rozenfeld R, Lim MP, Nieto N, Werner S, Devi LA, Friedman SL (2013) Endoplasmic reticulum stress induces fibrogenic activity in hepatic stellate cells through autophagy. J. Hepatol. 59(1), 98–104.
Miller RA, Chu Q, Xie J, Foretz M, Viollet B, Birnbaum MJ (2013) Biguanides suppress hepatic glucagon signalling by decreasing production of cyclic AMP. Nature 494(7436), 256–60.
Ling H, Roux E, Hempel D, Tao J, Smith M, Lonning S, Zuk A, Arbeeny C, Ledbetter S (2013) Transforming growth factor β neutralization ameliorates pre-existing hepatic fibrosis and reduces cholangiocarcinoma in thioacetamide-treated rats. PLoS ONE 8(1), e54499.
Mulherkar S, Liu F, Chen Q, Narayanan A, Couvillon AD, Shine HD, Tolias KF (2013) The Small GTPase RhoA Is Required for Proper Locomotor Circuit Assembly. PLoS ONE 8(6), e67015.
Israelsen WJ, Dayton TL, Davidson SM, Fiske BP, Hosios AM, Bellinger G, Li J, Yu Y, Sasaki M, Horner JW, Burga LN, Xie J, Jurczak MJ, Depinho RA, Clish CB, Jacks T, Kibbey RG, Wulf GM, Di Vizio D, Mills GB, Cantley LC, Vander Heiden MG (2013) PKM2 Isoform-Specific Deletion Reveals a Differential Requirement for Pyruvate Kinase in Tumor Cells. Cell 155(2), 397–409.
Hitosugi T, Zhou L, Fan J, Elf S, Zhang L, Xie J, Wang Y, Gu TL, Alečković M, LeRoy G, Kang Y, Kang HB, Seo JH, Shan C, Jin P, Gong W, Lonial S, Arellano ML, Khoury HJ, Chen GZ, Shin DM, Khuri FR, Boggon TJ, Kang S, He C, Chen J (2013) Tyr26 phosphorylation of PGAM1 provides a metabolic advantage to tumours by stabilizing the active conformation. Nat Commun 4, 1790.
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.

2012 Publications

Janas MM, Wang B, Harris AS, Aguiar M, Shaffer JM, Subrahmanyam YV, Behlke MA, Wucherpfennig KW, Gygi SP, Gagnon E, Novina CD (2012) Alternative RISC assembly: binding and repression of microRNA-mRNA duplexes by human Ago proteins. RNA 18(11), 2041–55.
Hernández-Gea V, Ghiassi-Nejad Z, Rozenfeld R, Gordon R, Fiel MI, Yue Z, Czaja MJ, Friedman SL (2012) Autophagy releases lipid that promotes fibrogenesis by activated hepatic stellate cells in mice and in human tissues. Gastroenterology 142(4), 938–46.
Rozenfeld R, Bushlin I, Gomes I, Tzavaras N, Gupta A, Neves S, Battini L, Gusella GL, Lachmann A, Ma'ayan A, Blitzer RD, Devi LA (2012) Receptor heteromerization expands the repertoire of cannabinoid signaling in rodent neurons. PLoS ONE 7(1), e29239.
Hornbeck PV, Kornhauser JM, Tkachev S, Zhang B, Skrzypek E, Murray B, Latham V, Sullivan M (2012) PhosphoSitePlus: a comprehensive resource for investigating the structure and function of experimentally determined post-translational modifications in man and mouse. Nucleic Acids Res. 40(1), D261–70.
Katayama R, Shaw AT, Khan TM, Mino-Kenudson M, Solomon BJ, Halmos B, Jessop NA, Wain JC, Yeo AT, Benes C, Drew L, Saeh JC, Crosby K, Sequist LV, Iafrate AJ, Engelman JA (2012) Mechanisms of acquired crizotinib resistance in ALK-rearranged lung Cancers. Sci Transl Med 4(120), 120ra17.
Feng H, Hu B, Jarzynka MJ, Li Y, Keezer S, Johns TG, Tang CK, Hamilton RL, Vuori K, Nishikawa R, Sarkaria JN, Fenton T, Cheng T, Furnari FB, Cavenee WK, Cheng SY (2012) Phosphorylation of dedicator of cytokinesis 1 (Dock180) at tyrosine residue Y722 by Src family kinases mediates EGFRvIII-driven glioblastoma tumorigenesis. Proc. Natl. Acad. Sci. U.S.A. 109(8), 3018–23.
Garnett MJ, Edelman EJ, Heidorn SJ, Greenman CD, Dastur A, Lau KW, Greninger P, Thompson IR, Luo X, Soares J, Liu Q, Iorio F, Surdez D, Chen L, Milano RJ, Bignell GR, Tam AT, Davies H, Stevenson JA, Barthorpe S, Lutz SR, Kogera F, Lawrence K, McLaren-Douglas A, Mitropoulos X, Mironenko T, Thi H, Richardson L, Zhou W, Jewitt F, Zhang T, O'Brien P, Boisvert JL, Price S, Hur W, Yang W, Deng X, Butler A, Choi HG, Chang JW, Baselga J, Stamenkovic I, Engelman JA, Sharma SV, Delattre O, Saez-Rodriguez J, Gray NS, Settleman J, Futreal PA, Haber DA, Stratton MR, Ramaswamy S, McDermott U, Benes CH (2012) Systematic identification of genomic markers of drug sensitivity in cancer cells. Nature 483(7391), 570–5.
Cheung WC, Beausoleil SA, Zhang X, Sato S, Schieferl SM, Wieler JS, Beaudet JG, Ramenani RK, Popova L, Comb MJ, Rush J, Polakiewicz RD (2012) A proteomics approach for the identification and cloning of monoclonal antibodies from serum. Nat. Biotechnol. 30(5), 447–52.
Stokes MP, Farnsworth CL, Moritz A, Silva JC, Jia X, Lee KA, Guo A, Polakiewicz RD, Comb MJ (2012) PTMScan direct: identification and quantification of peptides from critical signaling proteins by immunoaffinity enrichment coupled with LC-MS/MS. Mol. Cell Proteomics 11(5), 187–201.
Ren H, Tan ZP, Zhu X, Crosby K, Haack H, Ren JM, Beausoleil S, Moritz A, Innocenti G, Rush J, Zhang Y, Zhou XM, Gu TL, Yang YF, Comb MJ (2012) Identification of anaplastic lymphoma kinase as a potential therapeutic target in ovarian cancer. Cancer Res. 72(13), 3312–23.
Rimkunas VM, Crosby KE, Li D, Hu Y, Kelly ME, Gu TL, Mack JS, Silver MR, Zhou X, Haack H (2012) Analysis of Receptor Tyrosine Kinase ROS1-Positive Tumors in Non-Small Cell Lung Cancer: Identification of a FIG-ROS1 Fusion. Clin. Cancer Res. 18(16), 4449–57.
Xu W, Mollapour M, Prodromou C, Wang S, Scroggins BT, Palchick Z, Beebe K, Siderius M, Lee MJ, Couvillon A, Trepel JB, Miyata Y, Matts R, Neckers L (2012) Dynamic tyrosine phosphorylation modulates cycling of the HSP90-P50(CDC37)-AHA1 chaperone machine. Mol. Cell 47(3), 434–43.
Hardee ME, Marciscano AE, Medina-Ramirez CM, Zagzag D, Narayana A, Lonning SM, Barcellos-Hoff MH (2012) Resistance of glioblastoma-initiating cells to radiation mediated by the tumor microenvironment can be abolished by inhibiting transforming growth factor-β. Cancer Res. 72(16), 4119–29.
Hezel AF, Deshpande V, Zimmerman SM, Contino G, Alagesan B, O'Dell MR, Rivera LB, Harper J, Lonning S, Brekken RA, Bardeesy N (2012) TGF-β and αvβ6 integrin act in a common pathway to suppress pancreatic cancer progression. Cancer Res. 72(18), 4840–5.
Hitosugi T, Zhou L, Elf S, Fan J, Kang HB, Seo JH, Shan C, Dai Q, Zhang L, Xie J, Gu TL, Jin P, Alečković M, Leroy G, Kang Y, Sudderth JA, Deberardinis RJ, Luan CH, Chen GZ, Muller S, Shin DM, Owonikoko TK, Lonial S, Arellano ML, Khoury HJ, Khuri FR, Lee BH, Ye K, Boggon TJ, Kang S, He C, Chen J (2012) Phosphoglycerate mutase 1 coordinates glycolysis and biosynthesis to promote tumor growth. Cancer Cell 22(5), 585–600.
Sato S, Beausoleil SA, Popova L, Beaudet JG, Ramenani RK, Zhang X, Wieler JS, Schieferl SM, Cheung WC, Polakiewicz RD (2012) Proteomics-directed cloning of circulating antiviral human monoclonal antibodies. Nat. Biotechnol. 30(11), 1039–43.
Buckley SM, Aranda-Orgilles B, Strikoudis A, Apostolou E, Loizou E, Moran-Crusio K, Farnsworth CL, Koller AA, Dasgupta R, Silva JC, Stadtfeld M, Hochedlinger K, Chen EI, Aifantis I (2012) Regulation of pluripotency and cellular reprogramming by the ubiquitin-proteasome system. Cell Stem Cell 11(6), 783-98
Stokes MP, Silva JC, Jia X, Lee KA, Polakiewicz RD, Comb MJ (2012) Quantitative Profiling of DNA Damage and Apoptotic Pathways in UV Damaged Cells Using PTMScan Direct. Int J Mol Sci 14(1), 286–307.
Foulkes-Murzycki JE, Rosi C, Kurt Yilmaz N, Shafer RW, Schiffer CA (2012) Cooperative Effects of Drug-Resistance Mutations in the Flap Region of HIV-1 Protease. ACS Chem. Biol. 8(3), 513-8.
Li Z, Pang Y, Gara SK, Achyut BR, Heger C, Goldsmith PK, Lonning S, Yang L (2012) Gr-1+CD11b+ cells are responsible for tumor promoting effect of TGF-β in breast cancer progression. Int. J. Cancer 131(11), 2584–95.

2011 Publications

Sliter DA, Aguiar M, Gygi SP, Wojcikiewicz RJ (2011) Activated inositol 1,4,5-trisphosphate receptors are modified by homogeneous Lys-48- and Lys-63-linked ubiquitin chains, but only Lys-48-linked chains are required for degradation. J. Biol. Chem. 286(2), 1074–82.
Sriram G, Reichman C, Tunceroglu A, Kaushal N, Saleh T, Machida K, Mayer B, Ge Q, Li J, Hornbeck P, Kalodimos CG, Birge RB (2011) Phosphorylation of Crk on tyrosine 251 in the RT loop of the SH3C domain promotes Abl kinase transactivation. Oncogene 30(46), 4645–55.
Groeneweg JW, White YA, Kokel D, Peterson RT, Zukerberg LR, Berin I, Rueda BR, Wood AW (2011) cables1 is required for embryonic neural development: molecular, cellular, and behavioral evidence from the zebrafish. Mol. Reprod. Dev. 78(1), 22–32.
White YA, Woods DC, Wood AW (2011) A transgenic zebrafish model of targeted oocyte ablation and de novo oogenesis. Dev. Dyn. 240(8), 1929–37.
Lim MP, Devi LA, Rozenfeld R (2011) Cannabidiol causes activated hepatic stellate cell death through a mechanism of endoplasmic reticulum stress-induced apoptosis. Cell Death Dis 2, e170.
Rozenfeld R, Gupta A, Gagnidze K, Lim MP, Gomes I, Lee-Ramos D, Nieto N, Devi LA (2011) AT1R-CB₁R heteromerization reveals a new mechanism for the pathogenic properties of angiotensin II. EMBO J. 30(12), 2350–63.
Rozenfeld R, Devi LA (2011) Exploring a role for heteromerization in GPCR signalling specificity. Biochem. J. 433(1), 11–8.
Rozenfeld R (2011) Type I cannabinoid receptor trafficking: all roads lead to lysosome. Traffic 12(1), 12–8.
Hülper P, Schulz-Schaeffer W, Dullin C, Hoffmann P, Harper J, Kurtzberg L, Lonning S, Kugler W, Lakomek M, Erdlenbruch B (2011) Tumor localization of an anti-TGF-β antibody and its effects on gliomas. Int. J. Oncol. 38(1), 51–9.
Gu TL, Deng X, Huang F, Tucker M, Crosby K, Rimkunas V, Wang Y, Deng G, Zhu L, Tan Z, Hu Y, Wu C, Nardone J, MacNeill J, Ren J, Reeves C, Innocenti G, Norris B, Yuan J, Yu J, Haack H, Shen B, Peng C, Li H, Zhou X, Liu X, Rush J, Comb MJ (2011) Survey of tyrosine kinase signaling reveals ROS kinase fusions in human cholangiocarcinoma. PLoS ONE 6(1), e15640.
Kettenbach AN, Rush J, Gerber SA (2011) Absolute quantification of protein and post-translational modification abundance with stable isotope-labeled synthetic peptides. Nat Protoc 6(2), 175–86.
Verstraeten VL, Peckham LA, Olive M, Capell BC, Collins FS, Nabel EG, Young SG, Fong LG, Lammerding J (2011) Protein farnesylation inhibitors cause donut-shaped cell nuclei attributable to a centrosome separation defect. Proc. Natl. Acad. Sci. U.S.A. 108(12), 4997–5002.
Dammer EB, Na CH, Xu P, Seyfried NT, Duong DM, Cheng D, Gearing M, Rees H, Lah JJ, Levey AI, Rush J, Peng J (2011) Polyubiquitin linkage profiles in three models of proteolytic stress suggest the etiology of Alzheimer disease. J. Biol. Chem. 286(12), 10457–65.
Brave SR, Ratcliffe K, Wilson Z, James NH, Ashton S, Wainwright A, Kendrew J, Dudley P, Broadbent N, Sproat G, Taylor S, Barnes C, Silva JC, Farnsworth CL, Hennequin L, Ogilvie DJ, Jürgensmeier JM, Shibuya M, Wedge SR, Barry ST (2011) Assessing the activity of cediranib, a VEGFR-2/3 tyrosine kinase inhibitor, against VEGFR-1 and members of the structurally related PDGFR family. Mol. Cancer Ther. 10(5), 861–73.
Pighi C, Gu TL, Dalai I, Barbi S, Parolini C, Bertolaso A, Pedron S, Parisi A, Ren J, Cecconi D, Chilosi M, Menestrina F, Zamò A (2011) Phospho-proteomic analysis of mantle cell lymphoma cells suggests a pro-survival role of B-cell receptor signaling. Cell Oncol (Dordr) 34(2), 141–53.
Gu TL, Nardone J, Wang Y, Loriaux M, Villén J, Beausoleil S, Tucker M, Kornhauser J, Ren J, MacNeill J, Gygi SP, Druker BJ, Heinrich MC, Rush J, Polakiewicz RD (2011) Survey of activated FLT3 signaling in leukemia. PLoS ONE 6(4), e19169.
Yadav H, Quijano C, Kamaraju AK, Gavrilova O, Malek R, Chen W, Zerfas P, Zhigang D, Wright EC, Stuelten C, Sun P, Lonning S, Skarulis M, Sumner AE, Finkel T, Rane SG (2011) Protection from obesity and diabetes by blockade of TGF-β/Smad3 signaling. Cell Metab. 14(1), 67–79.
Kremer KN, Clift IC, Miamen AG, Bamidele AO, Qian NX, Humphreys TD, Hedin KE (2011) Stromal Cell-Derived Factor-1 Signaling via the CXCR4-TCR Heterodimer Requires Phospholipase C-{beta}3 and Phospholipase C-{gamma}1 for Distinct Cellular Responses. J. Immunol. 187(3), 1440–7.
Zhang Q, Chen L, Helfand BT, Jang TL, Sharma V, Kozlowski J, Kuzel TM, Zhu LJ, Yang XJ, Javonovic B, Guo Y, Lonning S, Harper J, Teicher BA, Brendler C, Yu N, Catalona WJ, Lee C (2011) TGF-β regulates DNA methyltransferase expression in prostate cancer, correlates with aggressive capabilities, and predicts disease recurrence. PLoS ONE 6(9), e25168.
Kim W, Bennett EJ, Huttlin EL, Guo A, Li J, Possemato A, Sowa ME, Rad R, Rush J, Comb MJ, Harper JW, Gygi SP (2011) Systematic and quantitative assessment of the ubiquitin-modified proteome. Mol. Cell 44(2), 325–40.
Emanuele MJ, Elia AE, Xu Q, Thoma CR, Izhar L, Leng Y, Guo A, Chen YN, Rush J, Hsu PW, Yen HC, Elledge SJ (2011) Global Identification of Modular Cullin-RING Ligase Substrates. Cell 147(2), 459–74.
Feng H, Hu B, Liu KW, Li Y, Lu X, Cheng T, Yiin JJ, Lu S, Keezer S, Fenton T, Furnari FB, Hamilton RL, Vuori K, Sarkaria JN, Nagane M, Nishikawa R, Cavenee WK, Cheng SY (2011) Activation of Rac1 by Src-dependent phosphorylation of Dock180Y1811 mediates PDGFRα-stimulated glioma tumorigenesis in mice and humans. J. Clin. Invest. 121(12), 4670–84.
Biswas S, Nyman JS, Alvarez J, Chakrabarti A, Ayres A, Sterling J, Edwards J, Rana T, Johnson R, Perrien DS, Lonning S, Shyr Y, Matrisian LM, Mundy GR (2011) Anti-transforming growth factor ß antibody treatment rescues bone loss and prevents breast cancer metastasis to bone. PLoS ONE 6(11), e27090.
Bouquet F, Pal A, Pilones KA, Demaria S, Hann B, Akhurst RJ, Babb JS, Lonning SM, DeWyngaert JK, Formenti SC, Barcellos-Hoff MH (2011) TGFβ1 inhibition increases the radiosensitivity of breast cancer cells in vitro and promotes tumor control by radiation in vivo. Clin. Cancer Res. 17(21), 6754–65.
Fan J, Hitosugi T, Chung TW, Xie J, Ge Q, Gu TL, Polakiewicz RD, Chen GZ, Boggon TJ, Lonial S, Khuri FR, Kang S, Chen J (2011) Tyrosine Phosphorylation of Lactate Dehydrogenase A Is Important for NADH/NAD+ Redox Homeostasis in Cancer Cells. Mol. Cell. Biol. 31(24), 4938-50.
Hitosugi T, Fan J, Chung TW, Lythgoe K, Wang X, Xie J, Ge Q, Gu TL, Polakiewicz RD, Roesel JL, Chen GZ, Boggon TJ, Lonial S, Fu H, Khuri FR, Kang S, Chen J (2011) Tyrosine phosphorylation of mitochondrial pyruvate dehydrogenase kinase 1 is important for cancer metabolism. Mol. Cell 44(6), 864-77.
Lee KA, Hammerle LP, Andrews PS, Stokes MP, Mustelin T, Silva JC, Black RA, Doedens JR (2011) Ubiquitin ligase substrate identification through quantitative proteomics at both the protein and peptide levels. J. Biol. Chem. 286(48), 41530–8.
Lonning S, Mannick J, McPherson JM (2011) Antibody targeting of TGF-β in cancer patients. Curr Pharm Biotechnol 12(12), 2176–89.

2010 Publications

Jin H, White SR, Shida T, Schulz S, Aguiar M, Gygi SP, Bazan JF, Nachury MV (2010) The conserved Bardet-Biedl syndrome proteins assemble a coat that traffics membrane proteins to cilia. Cell 141(7), 1208–19.
Demir E, Cary MP, Paley S, Fukuda K, Lemer C, Vastrik I, Wu G, D'Eustachio P, Schaefer C, Luciano J, Schacherer F, Martinez-Flores I, Hu Z, Jimenez-Jacinto V, Joshi-Tope G, Kandasamy K, Lopez-Fuentes AC, Mi H, Pichler E, Rodchenkov I, Splendiani A, Tkachev S, Zucker J, Gopinath G, Rajasimha H, Ramakrishnan R, Shah I, Syed M, Anwar N, Babur O, Blinov M, Brauner E, Corwin D, Donaldson S, Gibbons F, Goldberg R, Hornbeck P, Luna A, Murray-Rust P, Neumann E, Ruebenacker O, Reubenacker O, Samwald M, van Iersel M, Wimalaratne S, Allen K, Braun B, Whirl-Carrillo M, Cheung KH, Dahlquist K, Finney A, Gillespie M, Glass E, Gong L, Haw R, Honig M, Hubaut O, Kane D, Krupa S, Kutmon M, Leonard J, Marks D, Merberg D, Petri V, Pico A, Ravenscroft D, Ren L, Shah N, Sunshine M, Tang R, Whaley R, Letovksy S, Buetow KH, Rzhetsky A, Schachter V, Sobral BS, Dogrusoz U, McWeeney S, Aladjem M, Birney E, Collado-Vides J, Goto S, Hucka M, Le Novère N, Maltsev N, Pandey A, Thomas P, Wingender E, Karp PD, Sander C, Bader GD (2010) The BioPAX community standard for pathway data sharing. Nat. Biotechnol. 28(9), 935–42.
Rozenfeld R, Devi LA (2010) Receptor heteromerization and drug discovery. Trends Pharmacol. Sci. 31(3), 124–30.
Bushlin I, Rozenfeld R, Devi LA (2010) Cannabinoid-opioid interactions during neuropathic pain and analgesia. Curr Opin Pharmacol 10(1), 80–6.
Moritz A, Li Y, Guo A, Villén J, Wang Y, MacNeill J, Kornhauser J, Sprott K, Zhou J, Possemato A, Ren JM, Hornbeck P, Cantley LC, Gygi SP, Rush J, Comb MJ (2010) Akt-RSK-S6 kinase signaling networks activated by oncogenic receptor tyrosine kinases. Sci Signal 3(136), ra64. More Information.
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.
Gu TL, Cherry J, Tucker M, Wu J, Reeves C, Polakiewicz RD (2010) Identification of activated Tnk1 kinase in Hodgkin's lymphoma. Leukemia 24(4), 861-5.
Pecquet C, Staerk J, Chaligné R, Goss V, Lee KA, Zhang X, Rush J, Van Hees J, Poirel HA, Scheiff JM, Vainchenker W, Giraudier S, Polakiewicz RD, Constantinescu SN (2010) Induction of myeloproliferative disorder and myelofibrosis by thrombopoietin receptor W515 mutants is mediated by cytosolic tyrosine 112 of the receptor. Blood 115(5), 1037-48.
Nishimura EK, Suzuki M, Igras V, Du J, Lonning S, Miyachi Y, Roes J, Beermann F, Fisher DE (2010) Key roles for transforming growth factor beta in melanocyte stem cell maintenance. Cell Stem Cell 6(2), 130–40.
Hudon V, Sabourin S, Dydensborg AB, Kottis V, Ghazi A, Paquet M, Crosby K, Pomerleau V, Uetani N, Pause A (2010) Renal tumour suppressor function of the Birt-Hogg-Dubé syndrome gene product folliculin. J. Med. Genet. 47(3), 182-9.
Hirschey MD, Shimazu T, Goetzman E, Jing E, Schwer B, Lombard DB, Grueter CA, Harris C, Biddinger S, Ilkayeva OR, Stevens RD, Li Y, Saha AK, Ruderman NB, Bain JR, Newgard CB, Farese RV, Alt FW, Kahn CR, Verdin E (2010) SIRT3 regulates mitochondrial fatty-acid oxidation by reversible enzyme deacetylation. Nature 464(7285), 121-5.
Schoeberl B, Faber AC, Li D, Liang MC, Crosby K, Onsum M, Burenkova O, Pace E, Walton Z, Nie L, Fulgham A, Song Y, Nielsen UB, Engelman JA, Wong KK (2010) An ErbB3 antibody, MM-121, is active in cancers with ligand-dependent activation. Cancer Res. 70(6), 2485-94.
Ghosh R, Graham H, Rivas P, Tan XJ, Crosby K, Bhaskaran S, Schoolfield J, Banu J, Fernandes G, Yeh IT, Kumar AP (2010) Phellodendron amurense bark extract prevents progression of prostate tumors in transgenic adenocarcinoma of mouse prostate: potential for prostate cancer management. Anticancer Res. 30(3), 857-65.
Kang S, Elf S, Lythgoe K, Hitosugi T, Taunton J, Zhou W, Xiong L, Wang D, Muller S, Fan S, Sun SY, Marcus AI, Gu TL, Polakiewicz RD, Chen ZG, Khuri FR, Shin DM, Chen J (2010) p90 ribosomal S6 kinase 2 promotes invasion and metastasis of human head and neck squamous cell carcinoma cells. J. Clin. Invest. 120(4), 1165-77.
Ganapathy V, Ge R, Grazioli A, Xie W, Banach-Petrosky W, Kang Y, Lonning S, McPherson J, Yingling JM, Biswas S, Mundy GR, Reiss M (2010) Targeting the Transforming Growth Factor-beta pathway inhibits human basal-like breast cancer metastasis. Mol. Cancer 9, 122.
Takaku S, Terabe M, Ambrosino E, Peng J, Lonning S, McPherson JM, Berzofsky JA (2010) Blockade of TGF-beta enhances tumor vaccine efficacy mediated by CD8(+) T cells. Int. J. Cancer 126(7), 1666–74.
Bonnette PC, Robinson BS, Silva JC, Stokes MP, Brosius AD, Baumann A, Buckbinder L (2010) Phosphoproteomic characterization of PYK2 signaling pathways involved in osteogenesis. J Proteomics 73(7), 1306-20.
Aguiar M, Haas W, Beausoleil SA, Rush J, Gygi SP (2010) Gas-Phase Rearrangements Do Not Affect Site Localization Reliability in Phosphoproteomics Data Sets. J Proteome Res 9(6), 3103-7.
Carretero J, Shimamura T, Rikova K, Jackson AL, Wilkerson MD, Borgman CL, Buttarazzi MS, Sanofsky BA, McNamara KL, Brandstetter KA, Walton ZE, Gu TL, Silva JC, Crosby K, Shapiro GI, Maira SM, Ji H, Castrillon DH, Kim CF, García-Echeverría C, Bardeesy N, Sharpless NE, Hayes ND, Kim WY, Engelman JA, Wong KK (2010) Integrative genomic and proteomic analyses identify targets for Lkb1-deficient metastatic lung tumors. Cancer Cell 17(6), 547-59.
Andersen JN, Sathyanarayanan S, Di Bacco A, Chi A, Zhang T, Chen AH, Dolinski B, Kraus M, Roberts B, Arthur W, Klinghoffer RA, Gargano D, Li L, Feldman I, Lynch B, Rush J, Hendrickson RC, Blume-Jensen P, Paweletz CP (2010) Pathway-based identification of biomarkers for targeted therapeutics: personalized oncology with PI3K pathway inhibitors. Sci Transl Med 2(43), 43ra55.
Buel GR, Rush J, Ballif BA (2010) Fyn promotes phosphorylation of collapsin response mediator protein 1 at tyrosine 504, a novel, isoform-specific regulatory site. J Cell Biochem 111(1), 20-8.
Knowlton ML, Selfors LM, Wrobel CN, Gu TL, Ballif BA, Gygi SP, Polakiewicz R, Brugge JS (2010) Profiling Y561-dependent and -independent substrates of CSF-1R in epithelial cells. PLoS ONE 5(10), e13587.
Edwards JR, Nyman JS, Lwin ST, Moore MM, Esparza J, O'Quinn EC, Hart AJ, Biswas S, Patil CA, Lonning S, Mahadevan-Jansen A, Mundy GR (2010) Inhibition of TGF-β signaling by 1D11 antibody treatment increases bone mass and quality in vivo. J. Bone Miner. Res. 25(11), 2419–26.
Heo JM, Livnat-Levanon N, Taylor EB, Jones KT, Dephoure N, Ring J, Xie J, Brodsky JL, Madeo F, Gygi SP, Ashrafi K, Glickman MH, Rutter J (2010) A stress-responsive system for mitochondrial protein degradation. Mol. Cell 40(3), 465-80.
Emek Demir, Michael P Cary, Sasha Tkachev, Peter Hornbeck, Chris Sander, Gary D Bader, & 82 others. (2010) The BioPAX community standard for pathway data sharing. Nature Biotechnology 28, 935-942.
Bennett EJ, Rush J, Gygi SP, Harper JW (2010) Dynamics of cullin-RING ubiquitin ligase network revealed by systematic quantitative proteomics. Cell 143(6), 951–65.

2009 Publications

Yu J, Kane S, Wu J, Benedettini E, Li D, Reeves C, Innocenti G, Wetzel R, Crosby K, Becker A, Ferrante M, Cheung WC, Hong X, Chirieac LR, Sholl LM, Haack H, Smith BL, Polakiewicz RD, Tan Y, Gu TL, Loda M, Zhou X, Comb MJ (2009) Mutation-specific antibodies for the detection of EGFR mutations in non-small-cell lung cancer. Clin. Cancer Res. 15(9), 3023–8.
Fowler JD, Johnson ND, Haroldson TA, Brintnall JA, Herrera JE, Katz SA, Bernlohr DA (2009) Regulated renin release from 3T3-L1 adipocytes. Am. J. Physiol. Endocrinol. Metab. 296(6), E1383–91.
Medeiros RB, Papenfuss KJ, Hoium B, Coley K, Jadrich J, Goh SK, Elayaperumal A, Herrera JE, Resnik E, Ni HT (2009) Novel sequential ChIP and simplified basic ChIP protocols for promoter co-occupancy and target gene identification in human embryonic stem cells. BMC Biotechnol. 9, 59.
White YA, Kyle JT, Wood AW (2009) Targeted gene knockdown in zebrafish reveals distinct intraembryonic functions for insulin-like growth factor II signaling. Endocrinology 150(9), 4366–75.
Alfaras-Melainis K, Gomes I, Rozenfeld R, Zachariou V, Devi L (2009) Modulation of opioid receptor function by protein-protein interactions. Front Biosci (Landmark Ed) 14, 3594–607.
Claperon C, Banegas-Font I, Iturrioz X, Rozenfeld R, Maigret B, Llorens-Cortes C (2009) Identification of threonine 348 as a residue involved in aminopeptidase A substrate specificity. J. Biol. Chem. 284(16), 10618–26.
Vitsky A, Waire J, Pawliuk R, Bond A, Matthews D, Lacasse E, Hawes ML, Nelson C, Richards S, Piepenhagen PA, Garman RD, Andrews L, Thurberg BL, Lonning S, Ledbetter S, Ruzek MC (2009) Homeostatic role of transforming growth factor-beta in the oral cavity and esophagus of mice and its expression by mast cells in these tissues. Am. J. Pathol. 174(6), 2137–49.
Terabe M, Ambrosino E, Takaku S, O'Konek JJ, Venzon D, Lonning S, McPherson JM, Berzofsky JA (2009) Synergistic enhancement of CD8+ T cell-mediated tumor vaccine efficacy by an anti-transforming growth factor-beta monoclonal antibody. Clin. Cancer Res. 15(21), 6560–9.
Ueda R, Fujita M, Zhu X, Sasaki K, Kastenhuber ER, Kohanbash G, McDonald HA, Harper J, Lonning S, Okada H (2009) Systemic inhibition of transforming growth factor-beta in glioma-bearing mice improves the therapeutic efficacy of glioma-associated antigen peptide vaccines. Clin. Cancer Res. 15(21), 6551–9.
Gordus A, Krall JA, Beyer EM, Kaushansky A, Wolf-Yadlin A, Sevecka M, Chang BH, Rush J, MacBeath G (2009) Linear combinations of docking affinities explain quantitative differences in RTK signaling. Mol. Syst. Biol. 5, 235.
Hitosugi T, Kang S, Vander Heiden MG, Chung TW, Elf S, Lythgoe K, Dong S, Lonial S, Wang X, Chen GZ, Xie J, Gu TL, Polakiewicz RD, Roesel JL, Boggon TJ, Khuri FR, Gilliland DG, Cantley LC, Kaufman J, Chen J (2009) Tyrosine phosphorylation inhibits PKM2 to promote the Warburg effect and tumor growth. Sci Signal 2(97), ra73.
Harrington MG, Fonteh AN, Oborina E, Liao P, Cowan RP, McComb G, Chavez JN, Rush J, Biringer RG, Hühmer AF (2009) The morphology and biochemistry of nanostructures provide evidence for synthesis and signaling functions in human cerebrospinal fluid. Cerebrospinal Fluid Res 6, 10.
Pan S, Aebersold R, Chen R, Rush J, Goodlett DR, McIntosh MW, Zhang J, Brentnall TA (2009) Mass spectrometry based targeted protein quantification: methods and applications. J. Proteome Res. 8(2), 787-97.
Boccalatte FE, Voena C, Riganti C, Bosia A, D'Amico L, Riera L, Cheng M, Ruggeri B, Jensen ON, Goss VL, Lee K, Nardone J, Rush J, Polakiewicz RD, Comb MJ, Chiarle R, Inghirami G (2009) The enzymatic activity of 5-aminoimidazole-4-carboxamide ribonucleotide formyltransferase/IMP cyclohydrolase is enhanced by NPM-ALK: new insights in ALK-mediated pathogenesis and the treatment of ALCL. Blood 113(12), 2776-90.
Kang S, Elf S, Dong S, Hitosugi T, Lythgoe K, Guo A, Ruan H, Lonial S, Khoury HJ, Williams IR, Lee BH, Roesel JL, Karsenty G, Hanauer A, Taunton J, Boggon TJ, Gu TL, Chen J (2009) Fibroblast growth factor receptor 3 associates with and tyrosine phosphorylates p90 RSK2, leading to RSK2 activation that mediates hematopoietic transformation. Mol. Cell. Biol. 29(8), 2105-17.
ten Klooster JP, Jansen M, Yuan J, Oorschot V, Begthel H, Di Giacomo V, Colland F, de Koning J, Maurice MM, Hornbeck P, Clevers H (2009) Mst4 and Ezrin induce brush borders downstream of the Lkb1/Strad/Mo25 polarization complex. Dev. Cell 16(4), 551–62.
Xu P, Duong DM, Seyfried NT, Cheng D, Xie Y, Robert J, Rush J, Hochstrasser M, Finley D, Peng J (2009) Quantitative proteomics reveals the function of unconventional ubiquitin chains in proteasomal degradation. Cell 137(1), 133-45.
Haack H, Johnson LA, Fry CJ, Crosby K, Polakiewicz RD, Stelow EB, Hong SM, Schwartz BE, Cameron MJ, Rubin MA, Chang MC, Aster JC, French CA (2009) Diagnosis of NUT midline carcinoma using a NUT-specific monoclonal antibody. Am. J. Surg. Pathol. 33(7), 984-91.
Yu Y, Anjum R, Kubota K, Rush J, Villen J, Gygi SP (2009) A site-specific, multiplexed kinase activity assay using stable-isotope dilution and high-resolution mass spectrometry. Proc. Natl. Acad. Sci. U.S.A. 106(28), 11606-11.
Kasyapa C, Gu TL, Nagarajan L, Natarajan L, Polakiewicz R, Cowell JK (2009) Phosphorylation of the SSBP2 and ABL proteins by the ZNF198-FGFR1 fusion kinase seen in atypical myeloproliferative disorders as revealed by phosphopeptide-specific MS. Proteomics 9(16), 3979-88.
Schwer B, Eckersdorff M, Li Y, Silva JC, Fermin D, Kurtev MV, Giallourakis C, Comb MJ, Alt FW, Lombard DB (2009) Calorie restriction alters mitochondrial protein acetylation. Aging Cell 8(5), 604-6.
Kubota K, Anjum R, Yu Y, Kunz RC, Andersen JN, Kraus M, Keilhack H, Nagashima K, Krauss S, Paweletz C, Hendrickson RC, Feldman AS, Wu CL, Rush J, Villén J, Gygi SP (2009) Sensitive multiplexed analysis of kinase activities and activity-based kinase identification. Nat. Biotechnol. 27(10), 933-40.
Ji H, Wang J, Nika H, Hawke D, Keezer S, Ge Q, Fang B, Fang X, Fang D, Litchfield DW, Aldape K, Lu Z (2009) EGF-induced ERK activation promotes CK2-mediated disassociation of alpha-Catenin from beta-Catenin and transactivation of beta-Catenin. Mol. Cell 36(4), 547-59.
Lechtreck KF, Johnson EC, Sakai T, Cochran D, Ballif BA, Rush J, Pazour GJ, Ikebe M, Witman GB (2009) The Chlamydomonas reinhardtii BBSome is an IFT cargo required for export of specific signaling proteins from flagella. J. Cell Biol. 187(7), 1117-32.

2008 Publications

Ménétret JF, Hegde RS, Aguiar M, Gygi SP, Park E, Rapoport TA, Akey CW (2008) Single copies of Sec61 and TRAP associate with a nontranslating mammalian ribosome. Structure 16(7), 1126–37.
Sakamoto H, Friel AM, Wood AW, Guo L, Ilic A, Seiden MV, Chung DC, Lynch MP, Serikawa T, Munro E, Oliva E, Orsulic S, Kirley SD, Foster R, Zukerberg LR, Rueda BR (2008) Mechanisms of Cables 1 gene inactivation in human ovarian cancer development. Cancer Biol. Ther. 7(2), 180–88.
Sang X, Curran MS, Wood AW (2008) Paracrine insulin-like growth factor signaling influences primordial germ cell migration: in vivo evidence from the zebrafish model. Endocrinology 149(10), 5035–42.
Décaillot FM, Rozenfeld R, Gupta A, Devi LA (2008) Cell surface targeting of mu-delta opioid receptor heterodimers by RTP4. Proc. Natl. Acad. Sci. U.S.A. 105(41), 16045–50.
Claperon C, Rozenfeld R, Iturrioz X, Inguimbert N, Okada M, Roques B, Maigret B, Llorens-Cortes C (2008) Asp218 participates with Asp213 to bind a Ca2+ atom into the S1 subsite of aminopeptidase A: a key element for substrate specificity. Biochem. J. 416(1), 37–46.
Gagnidze K, Sachchidanand , Rozenfeld R, Mezei M, Zhou MM, Devi LA (2008) Homology modeling and site-directed mutagenesis to identify selective inhibitors of endothelin-converting enzyme-2. J. Med. Chem. 51(12), 3378–87.
Rozenfeld R, Devi LA (2008) Regulation of CB1 cannabinoid receptor trafficking by the adaptor protein AP-3. FASEB J. 22(7), 2311–22.
Fattouh R, Midence NG, Arias K, Johnson JR, Walker TD, Goncharova S, Souza KP, Gregory RC, Lonning S, Gauldie J, Jordana M (2008) Transforming growth factor-beta regulates house dust mite-induced allergic airway inflammation but not airway remodeling. Am. J. Respir. Crit. Care Med. 177(6), 593–603.
Perry K, Wong L, Liu V, Park I, Zhang Q, Rejen V, Huang X, Smith ND, Jovanovic B, Lonning S, Teicher BA, Lee C (2008) Treatment of transforming growth factor-beta-insensitive mouse Renca tumor by transforming growth factor-beta elimination. Urology 72(1), 225–9.
Nam JS, Terabe M, Mamura M, Kang MJ, Chae H, Stuelten C, Kohn E, Tang B, Sabzevari H, Anver MR, Lawrence S, Danielpour D, Lonning S, Berzofsky JA, Wakefield LM (2008) An anti-transforming growth factor beta antibody suppresses metastasis via cooperative effects on multiple cell compartments. Cancer Res. 68(10), 3835–43.
Nam JS, Terabe M, Kang MJ, Chae H, Voong N, Yang YA, Laurence A, Michalowska A, Mamura M, Lonning S, Berzofsky JA, Wakefield LM (2008) Transforming growth factor beta subverts the immune system into directly promoting tumor growth through interleukin-17. Cancer Res. 68(10), 3915–23.
Frantz S, Hu K, Adamek A, Wolf J, Sallam A, Maier SK, Lonning S, Ling H, Ertl G, Bauersachs J (2008) Transforming growth factor beta inhibition increases mortality and left ventricular dilatation after myocardial infarction. Basic Res. Cardiol. 103(5), 485–92.
Guo A, Villén J, Kornhauser J, Lee KA, Stokes MP, Rikova K, Possemato A, Nardone J, Innocenti G, Wetzel R, Wang Y, MacNeill J, Mitchell J, Gygi SP, Rush J, Polakiewicz RD, Comb MJ (2008) Signaling networks assembled by oncogenic EGFR and c-Met. Proc. Natl. Acad. Sci. U.S.A. 105(2), 692-7.
Pan S, Rush J, Peskind ER, Galasko D, Chung K, Quinn J, Jankovic J, Leverenz JB, Zabetian C, Pan C, Wang Y, Oh JH, Gao J, Zhang J, Montine T, Zhang J (2008) Application of targeted quantitative proteomics analysis in human cerebrospinal fluid using a liquid chromatography matrix-assisted laser desorption/ionization time-of-flight tandem mass spectrometer (LC MALDI TOF/TOF) platform. J. Proteome Res. 7(2), 720-30.
Kang S, Dong S, Guo A, Ruan H, Lonial S, Khoury HJ, Gu TL, Chen J (2008) Epidermal growth factor stimulates RSK2 activation through activation of the MEK/ERK pathway and src-dependent tyrosine phosphorylation of RSK2 at Tyr-529. J. Biol. Chem. 283(8), 4652-7.
Li K, Casta A, Wang R, Lozada E, Fan W, Kane S, Ge Q, Gu W, Orren D, Luo J (2008) Regulation of WRN protein cellular localization and enzymatic activities by SIRT1-mediated deacetylation. J. Biol. Chem. 283(12), 7590-8.
Dentin R, Hedrick S, Xie J, Yates J, Montminy M (2008) Hepatic glucose sensing via the CREB coactivator CRTC2. Science 319(5868), 1402-5.
Taylor EB, An D, Kramer HF, Yu H, Fujii NL, Roeckl KS, Bowles N, Hirshman MF, Xie J, Feener EP, Goodyear LJ (2008) Discovery of TBC1D1 as an insulin-, AICAR-, and contraction-stimulated signaling nexus in mouse skeletal muscle. J. Biol. Chem. 283(15), 9787-96.
Miyake Z, Takekawa M, Ge Q, Saito H (2007) Activation of MTK1/MEKK4 by GADD45 through induced N-C dissociation and dimerization-mediated trans autophosphorylation of the MTK1 kinase domain. Mol. Cell. Biol. 27(7), 2765-76.
Li Y, Zhang X, Polakiewicz RD, Yao TP, Comb MJ (2008) HDAC6 is required for epidermal growth factor-induced beta-catenin nuclear localization. J. Biol. Chem. 283(19), 12686-90.
Kaushansky A, Gordus A, Chang B, Rush J, MacBeath G (2008) A quantitative study of the recruitment potential of all intracellular tyrosine residues on EGFR, FGFR1 and IGF1R. Mol Biosyst 4(6), 643-53.
Kaushansky A, Gordus A, Budnik BA, Lane WS, Rush J, MacBeath G (2008) System-wide investigation of ErbB4 reveals 19 sites of Tyr phosphorylation that are unusually selective in their recruitment properties. Chem. Biol. 15(8), 808-17.
Pan W, Choi SC, Wang H, Qin Y, Volpicelli-Daley L, Swan L, Lucast L, Khoo C, Zhang X, Li L, Abrams CS, Sokol SY, Wu D (2008) Wnt3a-mediated formation of phosphatidylinositol 4,5-bisphosphate regulates LRP6 phosphorylation. Science 321(5894), 1350-3.
Altarejos JY, Goebel N, Conkright MD, Inoue H, Xie J, Arias CM, Sawchenko PE, Montminy M (2008) The Creb1 coactivator Crtc1 is required for energy balance and fertility. Nat. Med. 14(10), 1112-7.
Stratford AL, Fry CJ, Desilets C, Davies AH, Cho YY, Li Y, Dong Z, Berquin IM, Roux PP, Dunn SE (2008) Y-box binding protein-1 serine 102 is a downstream target of p90 ribosomal S6 kinase in basal-like breast cancer cells. Breast Cancer Res. 10(6), R99.
Stokes MP, Rush J, Macneill J, Ren JM, Sprott K, Nardone J, Yang V, Beausoleil SA, Gygi SP, Livingstone M, Zhang H, Polakiewicz RD, Comb MJ (2007) Profiling of UV-induced ATM/ATR signaling pathways. Proc. Natl. Acad. Sci. U.S.A. 104(50), 19855-60.
Engelman JA, Chen L, Tan X, Crosby K, Guimaraes AR, Upadhyay R, Maira M, McNamara K, Perera SA, Song Y, Chirieac LR, Kaur R, Lightbown A, Simendinger J, Li T, Padera RF, García-Echeverría C, Weissleder R, Mahmood U, Cantley LC, Wong KK (2008) Effective use of PI3K and MEK inhibitors to treat mutant Kras G12D and PIK3CA H1047R murine lung cancers. Nat. Med. 14(12), 1351-6.

2007 Publications

Schlueter PJ, Sang X, Duan C, Wood AW (2007) Insulin-like growth factor receptor 1b is required for zebrafish primordial germ cell migration and survival. Dev. Biol. 305(1), 377–87.
Rozenfeld R, Abul-Husn NS, Gomez I, Devi LA (2007) An emerging role for the delta opioid receptor in the regulation of mu opioid receptor function. ScientificWorldJournal 7, 64–73.
Rozenfeld R, Devi LA (2007) Receptor heterodimerization leads to a switch in signaling: beta-arrestin2-mediated ERK activation by mu-delta opioid receptor heterodimers. FASEB J. 21(10), 2455–65.
Morón JA, Abul-Husn NS, Rozenfeld R, Dolios G, Wang R, Devi LA (2007) Morphine administration alters the profile of hippocampal postsynaptic density-associated proteins: a proteomics study focusing on endocytic proteins. Mol. Cell Proteomics 6(1), 29–42.
Liu VC, Wong LY, Jang T, Shah AH, Park I, Yang X, Zhang Q, Lonning SM, Teicher BA, Lee C (2007) Tumor evasion of the immune system by converting CD4+CD25- T cells into CD4+CD25+ T regulatory cells: role of tumor-derived TGF-beta. J. Immunol. 178(5), 2883–92.
Nakanishi H, Sugiura T, Streisand JB, Lonning SM, Roberts JD (2007) TGF-beta-neutralizing antibodies improve pulmonary alveologenesis and vasculogenesis in the injured newborn lung. Am. J. Physiol. Lung Cell Mol. Physiol. 293(1), L151–61.
Gerber SA, Kettenbach AN, Rush J, Gygi SP (2007) The absolute quantification strategy: application to phosphorylation profiling of human separase serine 1126. Methods Mol. Biol. 359, 71-86.
Gu TL, Popova L, Reeves C, Nardone J, Macneill J, Rush J, Nimer SD, Polakiewicz RD (2007) Phosphoproteomic analysis identifies the M0-91 cell line as a cellular model for the study of TEL-TRKC fusion-associated leukemia. Leukemia 21(3), 563-6.
Li X, Monks B, Ge Q, Birnbaum MJ (2007) Akt/PKB regulates hepatic metabolism by directly inhibiting PGC-1alpha transcription coactivator. Nature 447(7147), 1012-6.
Dong S, Kang S, Gu TL, Kardar S, Fu H, Lonial S, Khoury HJ, Khuri F, Chen J (2007) 14-3-3 Integrates prosurvival signals mediated by the AKT and MAPK pathways in ZNF198-FGFR1-transformed hematopoietic cells. Blood 110(1), 360-9.
Gu TL, Mercher T, Tyner JW, Goss VL, Walters DK, Cornejo MG, Reeves C, Popova L, Lee K, Heinrich MC, Rush J, Daibata M, Miyoshi I, Gilliland DG, Druker BJ, Polakiewicz RD (2007) A novel fusion of RBM6 to CSF1R in acute megakaryoblastic leukemia. Blood 110(1), 323-33.
Kang S, Dong S, Gu TL, Guo A, Cohen MS, Lonial S, Khoury HJ, Fabbro D, Gilliland DG, Bergsagel PL, Taunton J, Polakiewicz RD, Chen J (2007) FGFR3 activates RSK2 to mediate hematopoietic transformation through tyrosine phosphorylation of RSK2 and activation of the MEK/ERK pathway. Cancer Cell 12(3), 201-14.
Kass EM, Ahn J, Tanaka T, Freed-Pastor WA, Keezer S, Prives C (2007) Stability of checkpoint kinase 2 is regulated via phosphorylation at serine 456. J. Biol. Chem. 282(41), 30311-21.
Rikova K, Guo A, Zeng Q, Possemato A, Yu J, Haack H, Nardone J, Lee K, Reeves C, Li Y, Hu Y, Tan Z, Stokes M, Sullivan L, Mitchell J, Wetzel R, Macneill J, Ren JM, Yuan J, Bakalarski CE, Villen J, Kornhauser JM, Smith B, Li D, Zhou X, Gygi SP, Gu TL, Polakiewicz RD, Rush J, Comb MJ (2007) Global survey of phosphotyrosine signaling identifies oncogenic kinases in lung cancer. Cell 131(6), 1190-203.

2006 Publications

Aguiar M, Masse R, Gibbs BF (2006) Mass spectrometric quantitation of C-reactive protein using labeled tryptic peptides. Anal. Biochem. 354(2), 175–81.
Schmelzle K, Kane S, Gridley S, Lienhard GE, White FM (2006) Temporal dynamics of tyrosine phosphorylation in insulin signaling. Diabetes 55(8), 2171–9.
Benlhabib H, Herrera JE (2006) Expression of the Op18 gene is maintained by the CCAAT-binding transcription factor NF-Y. Gene 377, 177–85.
Pignatari GC, Rozenfeld R, Ferro ES, Oliveira L, Paiva AC, Devi LA (2006) A role for transmembrane domains V and VI in ligand binding and maturation of the angiotensin II AT1 receptor. Biol. Chem. 387(3), 269–76.
Nam JS, Suchar AM, Kang MJ, Stuelten CH, Tang B, Michalowska AM, Fisher LW, Fedarko NS, Jain A, Pinkas J, Lonning SM, Wakefield LM (2006) Bone sialoprotein mediates the tumor cell-targeted prometastatic activity of transforming growth factor beta in a mouse model of breast cancer. Cancer Res. 66(12), 6327–35.
Steen H, Jebanathirajah JA, Rush J, Morrice N, Kirschner MW (2006) Phosphorylation analysis by mass spectrometry: myths, facts, and the consequences for qualitative and quantitative measurements. Mol. Cell Proteomics 5(1), 172-81.
Shalizi A, Gaudillière B, Yuan Z, Stegmüller J, Shirogane T, Ge Q, Tan Y, Schulman B, Harper JW, Bonni A (2006) A calcium-regulated MEF2 sumoylation switch controls postsynaptic differentiation. Science 311(5763), 1012-7.
Kling DE, Brandon KL, Sollinger CA, Cavicchio AJ, Ge Q, Kinane TB, Donahoe PK, Schnitzer JJ (2006) Distribution of ERK1/2 and ERK3 during normal rat fetal lung development. Anat. Embryol. 211(2), 139-53.
Goss VL, Lee KA, Moritz A, Nardone J, Spek EJ, MacNeill J, Rush J, Comb MJ, Polakiewicz RD (2006) A common phosphotyrosine signature for the Bcr-Abl kinase. Blood 107(12), 4888-97.
Cheng D, Hoogenraad CC, Rush J, Ramm E, Schlager MA, Duong DM, Xu P, Wijayawardana SR, Hanfelt J, Nakagawa T, Sheng M, Peng J (2006) Relative and absolute quantification of postsynaptic density proteome isolated from rat forebrain and cerebellum. Mol. Cell Proteomics 5(6), 1158-70.
Kirkpatrick DS, Hathaway NA, Hanna J, Elsasser S, Rush J, Finley D, King RW, Gygi SP (2006) Quantitative analysis of in vitro ubiquitinated cyclin B1 reveals complex chain topology. Nat. Cell Biol. 8(7), 700-10.
Walters DK, Mercher T, Gu TL, O'Hare T, Tyner JW, Loriaux M, Goss VL, Lee KA, Eide CA, Wong MJ, Stoffregen EP, McGreevey L, Nardone J, Moore SA, Crispino J, Boggon TJ, Heinrich MC, Deininger MW, Polakiewicz RD, Gilliland DG, Druker BJ (2006) Activating alleles of JAK3 in acute megakaryoblastic leukemia. Cancer Cell 10(1), 65-75.
Griswold IJ, MacPartlin M, Bumm T, Goss VL, O'Hare T, Lee KA, Corbin AS, Stoffregen EP, Smith C, Johnson K, Moseson EM, Wood LJ, Polakiewicz RD, Druker BJ, Deininger MW (2006) Kinase domain mutants of Bcr-Abl exhibit altered transformation potency, kinase activity, and substrate utilization, irrespective of sensitivity to imatinib. Mol. Cell. Biol. 26(16), 6082-93.
Walters DK, Goss VL, Stoffregen EP, Gu TL, Lee K, Nardone J, McGreevey L, Heinrich MC, Deininger MW, Polakiewicz R, Druker BJ (2006) Phosphoproteomic analysis of AML cell lines identifies leukemic oncogenes. Leuk. Res. 30(9), 1097-104.
Mercher T, Wernig G, Moore SA, Levine RL, Gu TL, Fröhling S, Cullen D, Polakiewicz RD, Bernard OA, Boggon TJ, Lee BH, Gilliland DG (2006) JAK2T875N is a novel activating mutation that results in myeloproliferative disease with features of megakaryoblastic leukemia in a murine bone marrow transplantation model. Blood 108(8), 2770-9.
Beausoleil SA, Villén J, Gerber SA, Rush J, Gygi SP (2006) A probability-based approach for high-throughput protein phosphorylation analysis and site localization. Nat. Biotechnol. 24(10), 1285-92.
Gu TL, Goss VL, Reeves C, Popova L, Nardone J, Macneill J, Walters DK, Wang Y, Rush J, Comb MJ, Druker BJ, Polakiewicz RD (2006) Phosphotyrosine profiling identifies the KG-1 cell line as a model for the study of FGFR1 fusions in acute myeloid leukemia. Blood 108(13), 4202-4.

2005 Publications

Aguiar M, Masse R, Gibbs BF (2005) Regulation of cytochrome P450 by posttranslational modification. Drug Metab. Rev. 37(2), 379–404.
Aguiar M, Gibbs BF, Massé R (2005) Sensitive capillary chromatography mass spectrometric methods for the determination of salcatonin in human biological matrices. J. Chromatogr. B Analyt. Technol. Biomed. Life Sci. 818(2), 301–8.
Ewart MA, Clarke M, Kane S, Chamberlain LH, Gould GW (2005) Evidence for a role of the exocyst in insulin-stimulated Glut4 trafficking in 3T3-L1 adipocytes. J. Biol. Chem. 280(5), 3812–6.
Sano H, Kane S, Sano E, Lienhard GE (2005) Synip phosphorylation does not regulate insulin-stimulated GLUT4 translocation. Biochem. Biophys. Res. Commun. 332(3), 880–4.
Karlsson HK, Zierath JR, Kane S, Krook A, Lienhard GE, Wallberg-Henriksson H (2005) Insulin-stimulated phosphorylation of the Akt substrate AS160 is impaired in skeletal muscle of type 2 diabetic subjects. Diabetes 54(6), 1692–7.
Mîinea CP, Sano H, Kane S, Sano E, Fukuda M, Peränen J, Lane WS, Lienhard GE (2005) AS160, the Akt substrate regulating GLUT4 translocation, has a functional Rab GTPase-activating protein domain. Biochem. J. 391(Pt 1), 87–93.
Kane S, Lienhard GE (2005) Calmodulin binds to the Rab GTPase activating protein required for insulin-stimulated GLUT4 translocation. Biochem. Biophys. Res. Commun. 335(1), 175–80.
Eguez L, Lee A, Chavez JA, Miinea CP, Kane S, Lienhard GE, McGraw TE (2005) Full intracellular retention of GLUT4 requires AS160 Rab GTPase activating protein. Cell Metab. 2(4), 263–72.
Wood AW, Schlueter PJ, Duan C (2005) Targeted knockdown of insulin-like growth factor binding protein-2 disrupts cardiovascular development in zebrafish embryos. Mol. Endocrinol. 19(4), 1024–34.
Wood AW, Duan C, Bern HA (2005) Insulin-like growth factor signaling in fish. Int. Rev. Cytol. 243, 215–85.
Rush J, Moritz A, Lee KA, Guo A, Goss VL, Spek EJ, Zhang H, Zha XM, Polakiewicz RD, Comb MJ (2005) Immunoaffinity profiling of tyrosine phosphorylation in cancer cells. Nat. Biotechnol. 23(1), 94-101.
Faure S, Cau J, de Santa Barbara P, Bigou S, Ge Q, Delsert C, Morin N (2005) Xenopus p21-activated kinase 5 regulates blastomeres' adhesive properties during convergent extension movements. Dev. Biol. 277(2), 472-92.
Pan S, Zhang H, Rush J, Eng J, Zhang N, Patterson D, Comb MJ, Aebersold R (2005) High throughput proteome screening for biomarker detection. Mol. Cell Proteomics 4(2), 182-90.
Koon HB, Bubley GJ, Pantanowitz L, Masiello D, Smith B, Crosby K, Proper J, Weeden W, Miller TE, Chatis P, Egorin MJ, Tahan SR, Dezube BJ (2005) Imatinib-induced regression of AIDS-related Kaposi's sarcoma. J. Clin. Oncol. 23(5), 982-9.
Park SS, Kim JS, Tessarollo L, Owens JD, Peng L, Han SS, Tae Chung S, Torrey TA, Cheung WC, Polakiewicz RD, McNeil N, Ried T, Mushinski JF, Morse HC, Janz S (2005) Insertion of c-Myc into Igh induces B-cell and plasma-cell neoplasms in mice. Cancer Res. 65(4), 1306-15.
Morrison MD, Reiley W, Zhang M, Sun SC (2005) An atypical tumor necrosis factor (TNF) receptor-associated factor-binding motif of B cell-activating factor belonging to the TNF family (BAFF) receptor mediates induction of the noncanonical NF-kappaB signaling pathway. J. Biol. Chem. 280(11), 10018-24.
Westfall MD, Joyner AS, Barbieri CE, Livingstone M, Pietenpol JA (2005) Ultraviolet radiation induces phosphorylation and ubiquitin-mediated degradation of DeltaNp63alpha. Cell Cycle 4(5), 710-6.
Zhang R, Luo D, Miao R, Bai L, Ge Q, Sessa WC, Min W (2005) Hsp90-Akt phosphorylates ASK1 and inhibits ASK1-mediated apoptosis. Oncogene 24(24), 3954-63.
Zhang Y, Wolf-Yadlin A, Ross PL, Pappin DJ, Rush J, Lauffenburger DA, White FM (2005) Time-resolved mass spectrometry of tyrosine phosphorylation sites in the epidermal growth factor receptor signaling network reveals dynamic modules. Mol. Cell Proteomics 4(9), 1240-50.
Wetzel R, Goss VL, Norris B, Popova L, Melnick M, Smith BL (2005) Evaluation of CML model cell lines and imatinib mesylate response: determinants of signaling profiles. J. Immunol. Methods 305(1), 59-66.

2004 Publications

Wu C, Okar DA, Stoeckman AK, Peng LJ, Herrera AH, Herrera JE, Towle HC, Lange AJ (2004) A potential role for fructose-2,6-bisphosphate in the stimulation of hepatic glucokinase gene expression. Endocrinology 145(2), 650–8.
Polzin RG, Benlhabib H, Trepel J, Herrera JE (2004) E2F sites in the Op18 promoter are required for high level of expression in the human prostate carcinoma cell line PC-3-M. Gene 341, 209–18.
Wood AW, Matsumoto J, Van Der Kraak G (2004) Thyroglobulin type-1 domain protease inhibitors exhibit specific expression in the cortical ooplasm of vitellogenic rainbow trout oocytes. Mol. Reprod. Dev. 69(2), 205–14.
Rozenfeld R, Muller L, El Messari S, Llorens-Cortes C (2004) The C-terminal domain of aminopeptidase A is an intramolecular chaperone required for the correct folding, cell surface expression, and activity of this monozinc aminopeptidase. J. Biol. Chem. 279(41), 43285–95.
Ziegler RJ, Lonning SM, Armentano D, Li C, Souza DW, Cherry M, Ford C, Barbon CM, Desnick RJ, Gao G, Wilson JM, Peluso R, Godwin S, Carter BJ, Gregory RJ, Wadsworth SC, Cheng SH (2004) AAV2 vector harboring a liver-restricted promoter facilitates sustained expression of therapeutic levels of alpha-galactosidase A and the induction of immune tolerance in Fabry mice. Mol. Ther. 9(2), 231–40.
Scholl D, Kieleczawa J, Kemp P, Rush J, Richardson CC, Merril C, Adhya S, Molineux IJ (2004) Genomic analysis of bacteriophages SP6 and K1-5, an estranged subgroup of the T7 supergroup. J. Mol. Biol. 335(5), 1151-71.
Schrantz N, da Silva Correia J, Fowler B, Ge Q, Sun Z, Bokoch GM (2004) Mechanism of p21-activated kinase 6-mediated inhibition of androgen receptor signaling. J. Biol. Chem. 279(3), 1922-31.
Papa S, Zazzeroni F, Bubici C, Jayawardena S, Alvarez K, Matsuda S, Nguyen DU, Pham CG, Nelsbach AH, Melis T, De Smaele E, Tang WJ, D'Adamio L, Franzoso G (2004) Gadd45 beta mediates the NF-kappa B suppression of JNK signalling by targeting MKK7/JNKK2. Nat. Cell Biol. 6(2), 146-53.
Clark LB, Viswanathan P, Quigley G, Chiang YC, McMahon JS, Yao G, Chen J, Nelsbach A, Denis CL (2004) Systematic mutagenesis of the leucine-rich repeat (LRR) domain of CCR4 reveals specific sites for binding to CAF1 and a separate critical role for the LRR in CCR4 deadenylase activity. J. Biol. Chem. 279(14), 13616-23.
Thompson PR, Wang D, Wang L, Fulco M, Pediconi N, Zhang D, An W, Ge Q, Roeder RG, Wong J, Levrero M, Sartorelli V, Cotter RJ, Cole PA (2004) Regulation of the p300 HAT domain via a novel activation loop. Nat. Struct. Mol. Biol. 11(4), 308-15.
Pende M, Um SH, Mieulet V, Sticker M, Goss VL, Mestan J, Mueller M, Fumagalli S, Kozma SC, Thomas G (2004) S6K1(-/-)/S6K2(-/-) mice exhibit perinatal lethality and rapamycin-sensitive 5'-terminal oligopyrimidine mRNA translation and reveal a mitogen-activated protein kinase-dependent S6 kinase pathway. Mol. Cell. Biol. 24(8), 3112-24.
Raught B, Peiretti F, Gingras AC, Livingstone M, Shahbazian D, Mayeur GL, Polakiewicz RD, Sonenberg N, Hershey JW (2004) Phosphorylation of eucaryotic translation initiation factor 4B Ser422 is modulated by S6 kinases. EMBO J. 23(8), 1761-9.
Russello SV (2004) Assessing cellular protein phosphorylation: high throughput drug discovery technologies. Assay Drug Dev Technol 2(2), 225-35.
Cheung WC, Kim JS, Linden M, Peng L, Van Ness B, Polakiewicz RD, Janz S (2004) Novel targeted deregulation of c-Myc cooperates with Bcl-X(L) to cause plasma cell neoplasms in mice. J. Clin. Invest. 113(12), 1763-73.
Hornbeck PV, Chabra I, Kornhauser JM, Skrzypek E, Zhang B (2004) PhosphoSite: A bioinformatics resource dedicated to physiological protein phosphorylation. Proteomics 4(6), 1551-61.
Ohira T, Bannenberg G, Arita M, Takahashi M, Ge Q, Van Dyke TE, Stahl GL, Serhan CN, Badwey JA (2004) A stable aspirin-triggered lipoxin A4 analog blocks phosphorylation of leukocyte-specific protein 1 in human neutrophils. J. Immunol. 173(3), 2091-8.
Smith BL, Chin D, Maltzman W, Crosby K, Hortobagyi GN, Bacus SS (2004) The efficacy of Herceptin therapies is influenced by the expression of other erbB receptors, their ligands and the activation of downstream signalling proteins. Br. J. Cancer 91(6), 1190-4.
Sun L, Rush J, Ghosh I, Maunus JR, Xu MQ (2004) Producing peptide arrays for epitope mapping by intein-mediated protein ligation. BioTechniques 37(3), 430-6, 438, 440 passim.
Li Y, Soos TJ, Li X, Wu J, Degennaro M, Sun X, Littman DR, Birnbaum MJ, Polakiewicz RD (2004) Protein kinase C Theta inhibits insulin signaling by phosphorylating IRS1 at Ser(1101). J. Biol. Chem. 279(44), 45304-7.
Maleri S, Ge Q, Hackett EA, Wang Y, Dohlman HG, Errede B (2004) Persistent activation by constitutive Ste7 promotes Kss1-mediated invasive growth but fails to support Fus3-dependent mating in yeast. Mol. Cell. Biol. 24(20), 9221-38.
Mattioli I, Dittrich-Breiholz O, Livingstone M, Kracht M, Schmitz ML (2004) Comparative analysis of T-cell costimulation and CD43 activation reveals novel signaling pathways and target genes. Blood 104(10), 3302-4.
Pasqualucci L, Guglielmino R, Houldsworth J, Mohr J, Aoufouchi S, Polakiewicz R, Chaganti RS, Dalla-Favera R (2004) Expression of the AID protein in normal and neoplastic B cells. Blood 104(10), 3318-25.
Buss H, Dörrie A, Schmitz ML, Frank R, Livingstone M, Resch K, Kracht M (2004) Phosphorylation of serine 468 by GSK-3beta negatively regulates basal p65 NF-kappaB activity. J. Biol. Chem. 279(48), 49571-4.
Thomas GV, Horvath S, Smith BL, Crosby K, Lebel LA, Schrage M, Said J, De Kernion J, Reiter RE, Sawyers CL (2004) Antibody-based profiling of the phosphoinositide 3-kinase pathway in clinical prostate cancer. Clin. Cancer Res. 10(24), 8351-6.

2003 Publications

Wood AW, Van Der Kraak G (2003) Yolk proteolysis in rainbow trout oocytes after serum-free culture: evidence for a novel biochemical mechanism of atresia in oviparous vertebrates. Mol. Reprod. Dev. 65(2), 219–27.
Rozenfeld R, Reaux A, Iturrioz X, Fassot C, Fournie-Zaluski MC, David C, Maigret B, Roques BP, Corvol P, Llorens-Cortes C (2003) Aminopeptidase A, generating one of the main effector peptides of the brain renin-angiotensin system, angiotensin III, plays a key role in central control of blood pressure. Proc. West. Pharmacol. Soc. 46, 39–44.
Rozenfeld R, Iturrioz X, Okada M, Maigret B, Llorens-Cortes C (2003) Contribution of molecular modeling and site-directed mutagenesis to the identification of a new residue, glutamate 215, involved in the exopeptidase specificity of aminopeptidase A. Biochemistry 42(50), 14785–93.
Dolled-Filhart M, Camp RL, Kowalski DP, Smith BL, Rimm DL (2003) Tissue microarray analysis of signal transducers and activators of transcription 3 (Stat3) and phospho-Stat3 (Tyr705) in node-negative breast cancer shows nuclear localization is associated with a better prognosis. Clin. Cancer Res. 9(2), 594-600.
Kielhorn E, Provost E, Olsen D, D'Aquila TG, Smith BL, Camp RL, Rimm DL (2003) Tissue microarray-based analysis shows phospho-beta-catenin expression in malignant melanoma is associated with poor outcome. Int. J. Cancer 103(5), 652-6.
Yang H, Cooley D, Legakis JE, Ge Q, Andrade R, Mattingly RR (2003) Phosphorylation of the Ras-GRF1 exchange factor at Ser916/898 reveals activation of Ras signaling in the cerebral cortex. J. Biol. Chem. 278(15), 13278-85.
Kovarova H, Hajduch M, Livingstone M, Dzubak P, Lefkovits I (2003) Analysis of state-specific phosphorylation of proteins by two-dimensional gel electrophoresis approach. J. Chromatogr. B Analyt. Technol. Biomed. Life Sci. 787(1), 53-61.
Wang Y, Ge Q, Houston D, Thorner J, Errede B, Dohlman HG (2003) Regulation of Ste7 ubiquitination by Ste11 phosphorylation and the Skp1-Cullin-F-box complex. J. Biol. Chem. 278(25), 22284-9.
Solan JL, Fry MD, TenBroek EM, Lampe PD (2003) Connexin43 phosphorylation at S368 is acute during S and G2/M and in response to protein kinase C activation. J. Cell. Sci. 116(Pt 11), 2203-11.
Gerber SA, Rush J, Stemman O, Kirschner MW, Gygi SP (2003) Absolute quantification of proteins and phosphoproteins from cell lysates by tandem MS. Proc. Natl. Acad. Sci. U.S.A. 100(12), 6940-5.
Choe G, Horvath S, Cloughesy TF, Crosby K, Seligson D, Palotie A, Inge L, Smith BL, Sawyers CL, Mischel PS (2003) Analysis of the phosphatidylinositol 3'-kinase signaling pathway in glioblastoma patients in vivo. Cancer Res. 63(11), 2742-6.
Jacobberger JW, Sramkoski RM, Frisa PS, Ye PP, Gottlieb MA, Hedley DW, Shankey TV, Smith BL, Paniagua M, Goolsby CL (2003) Immunoreactivity of Stat5 phosphorylated on tyrosine as a cell-based measure of Bcr/Abl kinase activity. Cytometry A 54(2), 75-88.
Li Y, Eitan S, Wu J, Evans CJ, Kieffer B, Sun X, Polakiewicz RD (2003) Morphine induces desensitization of insulin receptor signaling. Mol. Cell. Biol. 23(17), 6255-66.
Eitan S, Bryant CD, Saliminejad N, Yang YC, Vojdani E, Keith D, Polakiewicz R, Evans CJ (2003) Brain region-specific mechanisms for acute morphine-induced mitogen-activated protein kinase modulation and distinct patterns of activation during analgesic tolerance and locomotor sensitization. J. Neurosci. 23(23), 8360-9.
Zhan Q, Ge Q, Ohira T, Van Dyke T, Badwey JA (2003) p21-activated kinase 2 in neutrophils can be regulated by phosphorylation at multiple sites and by a variety of protein phosphatases. J. Immunol. 171(7), 3785-93.
Ohira T, Zhan Q, Ge Q, VanDyke T, Badwey JA (2003) Protein phosphorylation in neutrophils monitored with phosphospecific antibodies. J. Immunol. Methods 281(1-2), 79-94.

2002 Publications

Kane S, Sano H, Liu SC, Asara JM, Lane WS, Garner CC, Lienhard GE (2002) A method to identify serine kinase substrates. Akt phosphorylates a novel adipocyte protein with a Rab GTPase-activating protein (GAP) domain. J. Biol. Chem. 277(25), 22115–8.
Wood AW, van der Kraak G (2002) Inhibition of apoptosis in vitellogenic ovarian follicles of rainbow trout (Oncorhynchus mykiss) by salmon gonadotropin, epidermal growth factor, and 17beta-estradiol. Mol. Reprod. Dev. 61(4), 511–8.
Rozenfeld R, Iturrioz X, Maigret B, Llorens-Cortes C (2002) Contribution of molecular modeling and site-directed mutagenesis to the identification of two structural residues, Arg-220 and Asp-227, in aminopeptidase A. J. Biol. Chem. 277(32), 29242–52.
Zhande R, Mitchell JJ, Wu J, Sun XJ (2002) Molecular mechanism of insulin-induced degradation of insulin receptor substrate 1. Mol. Cell. Biol. 22(4), 1016-26.
Kohn EA, Ruth ND, Brown MK, Livingstone M, Eastman A (2002) Abrogation of the S phase DNA damage checkpoint results in S phase progression or premature mitosis depending on the concentration of 7-hydroxystaurosporine and the kinetics of Cdc25C activation. J. Biol. Chem. 277(29), 26553-64.
Kim GD, Ni J, Kelesoglu N, Roberts RJ, Pradhan S (2002) Co-operation and communication between the human maintenance and de novo DNA (cytosine-5) methyltransferases. EMBO J. 21(15), 4183-95.
Zhang H, Zha X, Tan Y, Hornbeck PV, Mastrangelo AJ, Alessi DR, Polakiewicz RD, Comb MJ (2002) Phosphoprotein analysis using antibodies broadly reactive against phosphorylated motifs. J. Biol. Chem. 277(42), 39379-87.
Eastman A, Kohn EA, Brown MK, Rathman J, Livingstone M, Blank DH, Gribble GW (2002) A novel indolocarbazole, ICP-1, abrogates DNA damage-induced cell cycle arrest and enhances cytotoxicity: similarities and differences to the cell cycle checkpoint abrogator UCN-01. Mol. Cancer Ther. 1(12), 1067-78.
Kue PF, Taub JS, Harrington LB, Polakiewicz RD, Ullrich A, Daaka Y (2002) Lysophosphatidic acid-regulated mitogenic ERK signaling in androgen-insensitive prostate cancer PC-3 cells. Int. J. Cancer 102(6), 572-9.

2001 Publications

Hornbeck P (2001) Enzyme-linked immunosorbent assays. Curr Protoc Immunol Chapter 2, Unit 2.1.
Hornbeck P, Fleisher TA, Papadopoulos NM (2001) Isotype determination of antibodies. Curr Protoc Mol Biol Chapter 11, Unit11.3.
Hornbeck P (2001) Double-immunodiffusion assay for detecting specific antibodies. Curr Protoc Immunol Chapter 2, Unit 2.3.
Chamberlain LH, Graham ME, Kane S, Jackson JL, Maier VH, Burgoyne RD, Gould GW (2001) The synaptic vesicle protein, cysteine-string protein, is associated with the plasma membrane in 3T3-L1 adipocytes and interacts with syntaxin 4. J. Cell. Sci. 114(Pt 2), 445–55.
Prymakowska-Bosak M, Misteli T, Herrera JE, Shirakawa H, Birger Y, Garfield S, Bustin M (2001) Mitotic phosphorylation prevents the binding of HMGN proteins to chromatin. Mol. Cell. Biol. 21(15), 5169–78.
Wood AW, Van Der Kraak GJ (2001) Apoptosis and ovarian function: novel perspectives from the teleosts. Biol. Reprod. 64(1), 264–71.
Foreyt WJ, Besser TE, Lonning SM (2001) Mortality in captive elk from salmonellosis. J. Wildl. Dis. 37(2), 399–402.
Hornbeck P, Fleisher TA, Papadopoulos NM (2001) Isotype determination of antibodies. Curr Protoc Immunol Chapter 2, Unit 2.2.
Kansra V, Groves C, Gutierrez-Ramos JC, Polakiewicz RD (2001) Phosphatidylinositol 3-kinase-dependent extracellular calcium influx is essential for CX(3)CR1-mediated activation of the mitogen-activated protein kinase cascade. J. Biol. Chem. 276(34), 31831-8.
Davids MS, Crawford E, Weremowicz S, Morton CC, Copeland NG, Gilbert DJ, Jenkins NA, Phelan MC, Comb MJ, Melnick MB (2001) STK25 is a candidate gene for pseudopseudohypoparathyroidism. Genomics 77(1-2), 2-4.
Gingras AC, Raught B, Gygi SP, Niedzwiecka A, Miron M, Burley SK, Polakiewicz RD, Wyslouch-Cieszynska A, Aebersold R, Sonenberg N (2001) Hierarchical phosphorylation of the translation inhibitor 4E-BP1. Genes Dev. 15(21), 2852-64.
Tang H, Hornstein E, Stolovich M, Levy G, Livingstone M, Templeton D, Avruch J, Meyuhas O (2001) Amino acid-induced translation of TOP mRNAs is fully dependent on phosphatidylinositol 3-kinase-mediated signaling, is partially inhibited by rapamycin, and is independent of S6K1 and rpS6 phosphorylation. Mol. Cell. Biol. 21(24), 8671-83.
Rao N, Ghosh AK, Ota S, Zhou P, Reddi AL, Hakezi K, Druker BK, Wu J, Band H (2001) The non-receptor tyrosine kinase Syk is a target of Cbl-mediated ubiquitylation upon B-cell receptor stimulation. EMBO J. 20(24), 7085-95.
Chung GG, Provost E, Kielhorn EP, Charette LA, Smith BL, Rimm DL (2001) Tissue microarray analysis of beta-catenin in colorectal cancer shows nuclear phospho-beta-catenin is associated with a better prognosis. Clin. Cancer Res. 7(12), 4013-20.

2000 Publications

Herrera JE, West KL, Schiltz RL, Nakatani Y, Bustin M (2000) Histone H1 is a specific repressor of core histone acetylation in chromatin. Mol. Cell. Biol. 20(2), 523–9.
Herrera JE, Schiltz RL, Bustin M (2000) The accessibility of histone H3 tails in chromatin modulates their acetylation by P300/CBP-associated factor. J. Biol. Chem. 275(17), 12994–9.
Shirakawa H, Herrera JE, Bustin M, Postnikov Y (2000) Targeting of high mobility group-14/-17 proteins in chromatin is independent of DNA sequence. J. Biol. Chem. 275(48), 37937–44.
Bergel M, Herrera JE, Thatcher BJ, Prymakowska-Bosak M, Vassilev A, Nakatani Y, Martin B, Bustin M (2000) Acetylation of novel sites in the nucleosomal binding domain of chromosomal protein HMG-14 by p300 alters its interaction with nucleosomes. J. Biol. Chem. 275(15), 11514–20.
McGuire TC, Leib SR, Lonning SM, Zhang W, Byrne KM, Mealey RH (2000) Equine infectious anaemia virus proteins with epitopes most frequently recognized by cytotoxic T lymphocytes from infected horses. J. Gen. Virol. 81(Pt 11), 2735–9.
Nunamaker RA, Peréz De León AA, Campbell CL, Lonning SM (2000) Oral infection of Culicoides sonorensis (Diptera: Ceratopogonidae) by vesicular stomatitis virus. J. Med. Entomol. 37(5), 784–6.

1999 Publications

Lemkin PF, Myrick JM, Lakshmanan Y, Shue MJ, Patrick JL, Hornbeck PV, Thornwal GC, Partin AW (1999) Exploratory data analysis groupware for qualitative and quantitative electrophoretic gel analysis over the Internet-WebGel. Electrophoresis 20(18), 3492–507.
Herrera JE, Sakaguchi K, Bergel M, Trieschmann L, Nakatani Y, Bustin M (1999) Specific acetylation of chromosomal protein HMG-17 by PCAF alters its interaction with nucleosomes. Mol. Cell. Biol. 19(5), 3466–73.
Iturrioz X, Rozenfeld R, Michaud A, Corvol P, Llorens-Cortes C (2001) Study of asparagine 353 in aminopeptidase A: characterization of a novel motif (GXMEN) implicated in exopeptidase specificity of monozinc aminopeptidases. Biochemistry 40(48), 14440–8.
Lonning SM, Zhang W, Leib SR, McGuire TC (1999) Detection and induction of equine infectious anemia virus-specific cytotoxic T-lymphocyte responses by use of recombinant retroviral vectors. J. Virol. 73(4), 2762–9.
Lonning SM, Zhang W, McGuire TC (1999) Gag protein epitopes recognized by CD4(+) T-helper lymphocytes from equine infectious anemia virus-infected carrier horses. J. Virol. 73(5), 4257–65.
Gingras AC, Gygi SP, Raught B, Polakiewicz RD, Abraham RT, Hoekstra MF, Aebersold R, Sonenberg N (1999) Regulation of 4E-BP1 phosphorylation: a novel two-step mechanism. Genes Dev. 13(11), 1422-37.
Carroll RS, Zhang J, Bello L, Melnick MB, Maruyama T, McL Black P (1999) KDR activation in astrocytic neoplasms. Cancer 86(7), 1335-41.

1995 Publications

Szebeni A, Herrera JE, Olson MO (1995) Interaction of nucleolar protein B23 with peptides related to nuclear localization signals. Biochemistry 34(25), 8037–42.
Herrera JE, Savkur R, Olson MO (1995) The ribonuclease activity of nucleolar protein B23. Nucleic Acids Res. 23(19), 3974–9.

1994 Publications

Herrera JE, Chaires JB (1994) Characterization of preferred deoxyribonuclease I cleavage sites. J. Mol. Biol. 236(2), 405–11.

1990 Publications

Chaires JB, Herrera JE, Waring MJ (1990) Preferential binding of daunomycin to 5'ATCG and 5'ATGC sequences revealed by footprinting titration experiments. Biochemistry 29(26), 6145–53.

1989 Publications

Herrera JE, Chaires JB (1989) A premelting conformational transition in poly(dA)-Poly(dT) coupled to daunomycin binding. Biochemistry 28(5), 1993–2000.

1987 Publications

Chaires JB, Fox KR, Herrera JE, Britt M, Waring MJ (1987) Site and sequence specificity of the daunomycin-DNA interaction. Biochemistry 26(25), 8227–36.

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