Biochemistry and Molecular Biophysics Graduate Group

BMB Home » Students » Student Publications

Student Publications


retreat picture 2010

Publications of Current Students
Publications of Former Students


PUBLICATIONS OF CURRENT STUDENTS (Names of students are in bold)

Hilaire MR*, Ahmed IA*, Lin CW, Jo H, DeGrado WF, Gai F. Blue fluorescent amino acid for biological spectroscopy and microscopy. Proc Natl Acad Sci U S A. 2017 Jun 6;114(23):6005-6009.

Anderson JL, Armstrong CT, Kodali G, Lichtenstein BR, Watkins DW, Mancini JA, Boyle AL, Farid TA, Crump MP, Moser CC, Dutton PL (2014) Constructing a man-made c-type cytochrome maquette in vivo: electron transfer, oxygen transport and conversion to a photoactive light harvesting maquette. Chem Sci. 5(2):507-514.

Baud M.G.J., Lin-Shiao E., Zengerle M., Tallant C. and Ciulli A. (2015) New Synthetic Routes to Triazolo-Benzodiazepine Analogues: Expanding the Scope of the Bump-and-Hole Approach for Selective BET Bromodomain Inhibition. Journal of Medicinal Chemistry Sep 14. [Epub ahead of print]

Bassett, EA., J. DeNizio, MC. Barnhart-Dailey, T. Panchenko, N. Sekulic, DJ. Rogers, DR. Foltz, BE. Black (2012) HJURP uses distinct CENP-A surfaces to recognize and to stabilize CENP-A/histone H4 for centromere assembly. Dev. Cell. 22(4):749-62.

Bassett EA, Wood S, Salimian KJ, Ajith S, Foltz DR, Black BE (2010) Epigenetic centromere specification directs aurora B accumulation but is insufficient to efficiently correct mitotic errors. J Cell Biol. 190(2):177-85

Baud MGJ*, Lin-Shiao E*, Cardote T*, Tallant C, Pschibul A, Chan KH, Zengerle M, Garcia JR, Kwan TTL, Ferguson FM and Ciulli A (2014) ‘A Bump-and-Hole Approach to Engineer Controlled Selectivity of BET Bromodomain Chemical Probes. Science, 16 October 2014 (10.1126/science.1249830).
* These authors contributed equally to this work

Bessman, N.J., Bagchi, A., Ferguson, K.M. and Lemmon, M.A. (2014) Complex relationship between ligand binding and dimerization in the Epidermal Growth Factor Receptor. Cell Reports. 9:1-12.

Castro, C, F Kilcherr, Do-Nyun Kim, E Lin Shiao, T Wauer, P Wortmann, M Bathe and K Dietz (2011) A primer to scaffolded DNA origami. Nature Methods; 8(3):221-9.

Carey, J.N., Mettert, E.L., Roggiani, M., Myers, K.S., Kiley, P.J., and Goulian, M. (2018). Regulated stochasticity in a bacterial signaling network permits tolerance to a rapid environmental change. Cell. In press.

Yadavalli SS, Carey J.N., Leibman RS, Chen AI, Stern AM, Roggiani M, Lippa AM, and Goulian M (2016) Antimicrobial peptides trigger a division block in Escherichia coli through stimulation of a signalling system. Nat Commun 7:12340

Choi DW, Semrau JD, Antholine WE, Hartsel SC, Anderson RC, Carey JN, Dreis AM, Kenseth EM, Renstrom JM, Scardino LL, Van Gorden GS, Volkert AA, Wingad AD, Yanzer PJ, McEllistrem MT, de la Mora AM, and DiSpirito AA (2008) Oxidase, superoxide dismutase, and hydrogen peroxide reductase activities of methanobactin from types I and II methanotrophs. J Inorg Biochem 102:1571-1580

Courtis, A ., SA Santos, Y Guan, JA Hendricks,B Ghos M Szantai-Kis, S A. Reis, J V. Shah and R Mazitschek (2014) Monoalkoxy BODIPYs—A Fluorophore Class for Bioimaging, Bioconjugate Chem. 25(6):1043-51.

DeNizio, J.E., S.J. Elsässer SJ and B.E. Black (2014) DAXX co-folds with H3.3/H4 using high local stability conferred by the H3.3 variant recognition residues. Nucl. Acids Res. Feb 3. [Epub ahead of print]

Dodevski I, Nucci NV, Valentine KG, Sidhu GK, O'Brien ES, Pardi A and AJ Wand. (2014) Optimized reverse micelle surfactant system for high-resolution NMR spectroscopy of encapsulated proteins and nucleic acids dissolved in low viscosity fluids. J Am Chem Soc 136(9), 3465-74

Falk SJ*, Guo LY*, Sekulic N*, Smoak EM*, Mani T, Logsdon GA, Gupta K, Jansen LE, Van Duyne GD, Vinogradov SA, Lampson MA, Black BE (2015). CENP-C reshapes and stabilizes CENP-A nucleosomes at the centromere. Science. 2015 May 8 (10.1126/science.1259308).
* These authors contributed equally to this work

Farid TA, Kodali G, Solomon LA, Lichtenstein BR, Sheehan MM, Fry BA, Bialas C, Ennist NM, Siedlecki JA, Zhao Z, Stetz MA, Valentine KG, Anderson JL, Wand AJ, Discher BM, Moser CC and Dutton PL. (2013) Elementary tetrahelical protein design for diverse oxidoreductase functions. Nat Chem Biol. 9(12):826-33.

Fachinetti D*, Logsdon GA*, Abdullah A, Selzer EB, Cleveland D, Black BE. CENP-A modifications on Ser68 and Lys124 are dispensable for establishment, maintenance, and long-term function of human centromeres. Dev. Cell 2017;40(1):104-113. *Contributed equally to the work.

Fields, PA., Cox, .M. and Karch, KR. (2012) Latitudinal variation in protein expression after heat stress in the salt marsh mussel Geukensia demissa. Integr. Comp. Biol. 52, 636–647.

Ganetzky R, Finn E, Bagchi A, Zollo O, Conlin L, Deardorff M, Harr M, Simpson MA, McGrath JA, Zackai E, Lemmon MA, Sondheimer N. EGFR mutations cause a lethal syndrome of epithelial dysfunction with progeroid features. Mol Genet Genomic Med. 2015 Sep;3(5):452-8. doi: 10.1002/mgg3.156. Epub 2015 Jun 4.

Guo, LY, Alekseev O, Li Y, Song Y, Dunaief JL (2014). Iron increases APP translation and amyloid-beta production in the retina (2014). Exp Eye Res. 2014 Dec;129:31-7.

Harpole KW, O'Brien ES, Clark MA, McKnight CJ, Vugmeyster L, Wand AJ. The unusual internal motion of the villin headpiece subdomain. Protein Sci. 2016 Feb;25(2):423-32. doi: 10.1002/pro.2831

Ikotun OF, Higbee EM, Ouellette W and Doyle RP. Pyrophosphate-bridged complexes with picomolar toxicity. J Inorg Biochem. 2009, 103, 1254-1264.

Ikotun OF, Higbee EM, Ouellette W, Lloret F, Julve M, and Doyle R (2008). Synthesis, Structural, Magnetic and Thermal Characterization of {[Cu(bipy)]2(μ-HP2O7)(μ-Cl)}·H2O. Eur J Inorg Chem. 2008:5281-5286.

Karch KR., JE. DeNizio, BE. Black and BA. Garcia. (2013) Identification and interrogation of combinatorial histone modifications. Front. Genet. 4:264.

Karch, KR., Zee, BM. and Garcia, BA. (2014). High resolution is not a strict requirement for characterization and quantification of histone post-translational modifications. J. Proteome Res. 13, 6152-6259.

Ko GJ, Linfert D, Jang HR, Higbee E, Watkins T, Cheadle C, Liu M, Racusen L, Grigoryev and Rabb H. (2012) Transcriptional analysis of infiltrating T cells in kidney ischemia/reperfusion injury reveals a pathophysiologic role for CCR5. Am J Physiol Renal Physiol. 302, F762-73.

Ko GJ, Jang HR, Huang Y, Womer KL, Liu M, Higbee E, Xiao Z, Yagita H, Racusen L, Hamad AR and Rabb H .(2011) Blocking Fas ligand on leukocytes attenuates kidney ischemia-reperfusion injury. J Am Soc Nephrol. 22:732-42.

Kramer, M.C., D. Liang, D.C. Tatomer, B. Gold, Z.M. March, S. Cherry, and J.E. Wilusz. (2015). Combinatorial control of Drosophila circular RNA expression by intronic repeats, hnRNPs, and SR proteins. Genes and Dev. dos: 10.1101/gad.270421.115

Lichtenstein, BR., TA. Farid, G Kodali, L A. Solomon, J.L. Anderson, MM. Sheehan, N M. Ennist, B A. Fry, S E. Chobot, C Bialas, JA. Mancini, T. Armstrong, Z Zhao, Tatiana V. Esipova, D Snell, SA. Vinogradov, B M. Discher, C C. Moser and P. L Dutton (2012) Engineering oxidoreductases: maquette proteins designed from scratch. Biochemical Society Transactions. 40 (2):561-566.

Liu M, Reddy N, Higbee E, Potetti H, Racusen L, Kensler T, Sporn M, Reddy and Rabb H.(2014) Nrf2 activator triterpenoid CDDO-imidazolide protects kidneys from ischemia reperfusion injury in mice. Kidney Int. 85:134-41.

Logsdon, GA, Barrey, EJ., Bassett, EA., DeNizio, JE., Guo, LY., Panchenko, T., Dawicki-McKenna, JM., Heun, P., and Black, BE. (2015). Both tails and the centromere targeting domain of CENP-A are required for centromere establishment. J Cell Biol jcb.201412011.

Mack KL, Shorter J. (2016). Engineering and evolution of molecular chaperones and protein disaggregases with enhanced activity. Front. Mol. Biosci. 3:8.

Mack KL, Moroz OV, Moroz YS, Olsen AB, McLaughlin J ,and Korendovych IV (2013) Reprogramming EF-hands for design of catalytically amplified lanthanide sensors. J. Biol. Inorg. Chem. 4:411-8.

Mallory MJ, Allon SJ, Qiu J, Gazzara MR, Tapescu I, Martinez NM, Fu XD, Lynch KW. Induced transcription and stability of CELF2 mRNA drives widespread alternative splicing during T-cell signaling. Proc Natl Acad Sci U S A. 2015 Apr 28;112(17):E2139-48. doi: 10.1073/pnas.1423695112. Epub 2015 Apr 13.

Marques, Bryan S.; Nucci, Nathaniel V.; Dodevski, Igor; Wang, Kristina W. C.; Athanasoula, Evangelia A.; Jorge, Christine; Wan and A. Joshua (2014) Measurement and control of pH in the aqueous interior of reverse micelles. J. Phys. Chem. B. 118: 2020-31.

Martinez NM, Agosto L, Qiu J, Mallory MJ, Gazzara MR, Barash Y, Fu XD, Lynch KW Widespread JNK-dependent alternative splicing induces a positive feedback loop through CELF2-mediated regulation of MKK7 during T-cell activation.
.Genes Dev. 2015 Oct 1;29(19):2054-66. doi: 10.1101/gad.267245.115.

Martinez NM, Lynch KW. Control of alternative splicing in immune responses: many regulators, many predictions, much still to learn. Immunol Rev. 2013 May;253(1):216-36

Martinez, NM., Pan, Q., Cole, BS., Yarosh, CA., Babcock, GA., Heyd, F., Ajith, S., Zhu, W., Blencowe, BJ., and KW. Lynch (2012) Alternative splicing networks regulated by signaling in human T cells. RNA 18: 1029-1040.

Mayne L, Kan ZY, Chetty PS, Ricciuti A, Walters BT, Englander SW. (2011) Many overlapping peptides for protein hydrogen exchange experiments by the fragment separation-mass spectrometry method. J Am Soc Mass Spectrom.22(11):1898-905

Moroz YS, Dunston TT, Makhlynets OV, Moroz OV, Wu Y, Yoon JH, Olsen AB, McLaughlin JM, Mack KL, Gosavi PM, van Nuland NA, Korendovych IV (2015) New Tricks for Old Proteins: Single Mutations in a Nonenzymatic Protein Give Rise to Various Enzymatic Activities. J. Am. Chem. Soc. 137:14905-11.

Moroz OV, Moroz YS, Wu Y, Olsen AB, Cheng H, Mack KL, McLaughlin JM, Raymond EA, Zhezherya K, Roder H, Korendovych IV. (2013) A single mutation in a regulatory protein produces evolvable allosterically regulated catalyst of nonnatural reaction. Angew. Chem. Int. Ed. Engl. 24:6246-9.

Morozova, O.A., Z.M. March, A.S. Robinson and D.W. Colby (2013) (2013). Conformational features of tau fibrils from Alzheimer's disease brain are faithfully propagated by unmodified recombinant protein. Biochemistry. 52(40): 6960-6967

Mutter; A C., J A Norman; M T Tiederrmna Singh; Sha Sha; Sara Morsi; Ismail Ahmed; Martin J Stillman; Ronald L Koder (2014) Rational Design of a Zinc Phthalocyanine Binding Protein. Journal of Structural Biology, 185:178-185.

O'Brien ES, Nucci NV, Fuglestad B, Tommos C, Wand AJ. Defining the Apoptotic Trigger: The Interaction of Cytochrome c and Cardiolipin. J Biol Chem. 2015 Dec 25;290(52):30879-87. doi: 10.1074/jbc.M115.689406

Raymond EA, Mack KL, Yoon JH, Moroz OV, Moroz YS, Korendovych IV (2014). Design of an allosterically regulated retroaldolase. Protein Sci. Dec 16. [Epub ahead of print]

Rogers JM, Lippert LG, Gai F. (2010) Non-natural amino acid fluorophores for one- and two-step fluorescence resonance energy transfer applications. Anal Biochem. 399(2):182-9.

Salimian, K.J., Ballister, E.R., Smoak, E.M., Wood, S., Panchenko, T., Lampson, M.A, and Black, B.E. (2011) Feedback control in sensing chromosome biorientation by the aurora B kinase. Current Biology, 21(13), 1158–65. doi:10.1016/j.cub.2011.06.015

Schmitz, K.R., Bagchi, A., Roovers, R.C., van Bergen en Henegouwen, P.M.P. and Ferguson, K.M. (2013) Structural evaluation of EGFR inhibition mechanisms for nanobodies/VHH domains. Structure 21: 1214-1224.

Shah PP, Zheng X, Epshtein A, Carey JN, Bishop DK and Klein HL (2010) Swi2/Snf2-related translocases prevent accumulation of toxic Rad51 complexes during mitotic growth. Mol Cell 39:862-872

Sharp KA, O'Brien E, Kasinath V, Wand AJ.On the relationship between NMR-derived amide order parameters and protein backbone entropy changes. Proteins. 2015 May;83(5):922-30. doi: 10.1002/prot.24789

Sidoli, S., Lin, S., Xiong, L., Bhanu, N.V., Karch, K.R., Johansen, E., Hunter, C., Mollah, S., and Garcia, B.A. (2015). SWATH analysis for characterization and quantification of histone post-translational modifications. Mol. Cell. Proteomics mcp.O114.046102.

Sidoli, S., Yuan, Z.-F., Lin, S., Karch, K., Wang, X., Bhanu, N., Arnaudo, A.M., Britton, L.-M., Cao, X.-J., Gonzales-Cope, M., Han, Y., Liu, S., Molden, R.C., Wein, S., Afjehi-Sadat, L., Garcia, B.A. (2015). Drawbacks in the use of unconventional hydrophobic anhydrides for histone derivatization in bottom-up proteomics PTM analysis. Proteomics. 10.1002/pmic.201400483

Sidoli, S., Lin, S., Karch, KR., Garcia, BA (2015). Bottom-up and middle-down proteomics have comparable accuracies in defining histone PTM relative abundance and stoichiometry. Anal. Chem. ac-2015-00072w.R1

Soufi, A., M. Fernandez Garcia, A. Jaroszewicz, N. Osman, M. Pellegrini and K. Zaret (2015) Pioneer transcription factors target partial DNA motifs on nucleosomesto initiate reprogramming. Cell 161: 1–14

Turegun B, Kast D, Dominguez R (2013) Subunit Rtt102 controls the conformation of the Arp7/9 heterodimer and its interactions with nucleotide and the catalytic subunit of SWI/SNF remodelers. J Biol Chem 288:35758-35768

Walters BT, Ricciuti A, Mayne L, Englander SW. (2012) Minimizing back exchange in the hydrogen exchange-mass spectrometry experiment. J Am Soc Mass Spectrom. 23(12):2132-9

Wand AJ, Moorman VR, Harpole KW. (2013) A surprising role for conformational entropy in protein function. Top Curr Chem. 2013;337:69-94.

Woody, M.S., Lewis, J.H., Greenberg, M.J., Goldman, Y.E., and Ostap, E.M. (2016). MEMLET: An Easy-to-Use Tool for Data Fitting and Model Comparison Using Maximum-Likelihood Estimation. Biophysical Journal 111, 273–282.

Yarosh, C. A., Iacona, J. R., Lutz, C. S. & Lynch, K. W. (2015) PSF: nuclear busy-body or nuclear facilitator? Wiley Interdisciplinary Reviews: RNA 6, 351-367.

Yarosh, C. A., Tapescu, I., Thompson, M. G., Qiu, J., Mallory, M. J., Fu, X. & Lynch, K. W. (2015). TRAP150 interacts with the RNA-binding domain of PSF and antagonizes splicing of numerous PSF-target genes in T cells. Nucleic Acids Res. 43 (18), 9006–9016.

Yokom AL, SN Gates, ME Jackrel, KL Mack, M Su, J Shorter, and DR Southworth. (2016). Spiral architecture of the Hsp104 disaggregase reveals the basis for polypeptide translocation. Nat. Struct. Mol. Biol. 23(9):830-7.

Yoon S, Carey JN, and Semrau JD (2009) Feasibility of atmospheric methane removal using methanotrophic biotrickling filters. Appl Microbiol Biot 83:949-956

Zhang, L, Anderson, J L; Ahmed, I; Norman, J; Negron, C; Mutter, A; Dutton PL; Koder R (2011), Manipulating cofactor binding thermodynamics in an artificial oxygen transport protein. Biochemistry 5:10254-61.

PUBLICATIONS OF FORMER STUDENTS (past 5 years) (Names of former students are in bold)

Artim SC, Mendrola JM, Lemmon MA. (2012) Assessing the range of kinase autoinhibition mechanisms in the insulin receptor family. Biochem J. 448(2):213-20.

Abdulghani J, Allen JE, Dicker DT, Liu YY, Goldenberg D, Smith CD, Humphreys R, El-Deiry WS (2013) Sorafenib sensitizes solid tumors to Apo2L/TRAIL and Apo2L/TRAIL receptor agonist antibodies by the Jak2-Stat3-Mcl1 axis. PLoS One. 8(9):e75414

Acharya R, Carnevale V, Fiorin G, Levine BG, Polishchuk AL, Balannik V, Samish I, Lamb RA, Pinto LH, DeGrado WF, Klein ML.(2010) Structure and mechanism of proton transport through the transmembrane tetrameric M2 protein bundle of the influenza A viru. Proc Natl Acad Sci U S A. 107(34):15075-80.

Allen JE, El-Deiry WS. (2011) Oxaliplatin uses JNK to restore TRAIL sensitivity in cancer cells through Bcl-xL inactivation. Gastroenterology. 141(2):430-4.

Allen JE, Ferrini R, Dicker DT, Batzer G, Chen E, Oltean DI, Lin B, Renshaw MW, Kretz-Rommel A, El-Deiry WS. (2012) Targeting TRAIL death receptor 4 with trivalent DR4 Atrimer complexes. Mol Cancer Ther. (10):2087-95

Allen JE, Gallant JN, Dicker DT, Amin S, Irby RB, Sharma AK, El-Deiry WS.(2013)Correction: The Akt Inhibitor ISC-4 Synergizes with Cetuximab in 5-FU-Resistant Colon Cancer. PLoS One. 8(11).

Allen JE, El-Deiry WS. (2013) Calcein-effluxing human colon cancer cells are enriched for self-renewal capacity and depend on β-catenin. Oncotarget. 4(2):184-91

Allen, Joshua E, Gabriel Krigsfeld, Patrick A. Mayes, Luv Patel, David T. Dicker, Akshal S. Patel, Nathan G. Dolloff,, Evangelos Messaris, Kimberly A. Scata, Wenge Wang, Jun-Ying Zhou, Gen Sheng W6 and Wafik S. El-Deiry (2013) Dual inactivation of Akt and ERK by TIC10 signals Foxo3a nuclear translocation, TRAIL gene induction, and potent antitumor effects. Transl Med 5: p. 171ra17

Allen JE, El-Deiry WS. (2012) Regulation of the human TRAIL gene. Cancer Biol Ther 13(12):1143-51

Allen JE, Gallant JN, Dicker DT, Amin S, Irby RB, Sharma AK, El-Deiry WS. (2013 )The Akt inhibitor ISC-4 synergizes with cetuximab in 5-FU-resistant colon cancer. PLoS One. 8(3):e59380.

Allen JE, Krigsfeld G, Mayes PA, Patel L, Dicker DT, Patel AS, Dolloff NG, Messaris E, Scata KA, Wang W, Zhou JY, Wu GS, El-Deiry WS. (2013) Dual inactivation of Akt and ERK by TIC10 signals Foxo3a nuclear translocation, TRAIL gene induction, and potent antitumor effects. Sci Transl Med. 5(171):171ra17.

Allen JE, El-Deiry WS. (2010) Circulating Tumor Cells and Colorectal Cancer. Curr Colorectal Cancer Rep. 6(4):212-220.

Allen JE, Hart LS, Dicker DT, Wang W, El-Deiry WS. (2009) Visualization and enrichment of live putative cancer stem cell populations following p53 inactivation or Bax deletion using non-toxic fluorescent dyes. Cancer Biol Ther. 8(22):2194-205

Allen JE, Patel A, Prabhu VV, Dicker DT, Sheehan JM, Glantz M, El-Deiry WS. COX-2 drives metastatic breast cells from brain lesions into the cerebrospinal fluid and systemic circulation. Cancer Res. 2014 Mar 10. [Epub ahead of print

Allen JE, Saroya BS, Kunkel M, Dicker DT, Das A, Peters KL, Joudeh J, Zhu J, El-Deiry WS. Apoptotic circulating tumor cells (CTCs) in the peripheral blood of metastatic colorectal cancer patients are associated with liver metastasis but not CTCs. Oncotarget. 2013 Oct 17. [Epub ahead of print]

Alvarado D, Klein DE, Lemmon MA. Structural basis for negative cooperativity in growth factor binding to an EGF receptor. Cell. 2010 Aug 20;142(4):568-79

Alvarado D, Klein DE, Lemmon MA. ErbB2 resembles an autoinhibited invertebrate epidermal growth factor receptor. Nature. 2009 Sep 10;461(7261):287-91

Barnhart MC, Kuich PH, Stellfox ME, Ward JA, Bassett EA, Black BE, Foltz DR. (2011) HJURP is a CENP-A chromatin assembly factor sufficient to form a functional de novo kinetochore. J Cell Biol. 194(2):229-43.

Ballister ER, Riegman M, Lampson MA (2014) Recruitment of Mad1 to metaphase kinetochores is sufficient to reactivate the mitotic checkpoint. J Cell Biol. 204(6):901-908.

Berger BW, Kulp DW, Span LM, DeGrado JL, Billings PC, Senes A, Bennett JS, DeGrado WF. (2010) Consensus motif for integrin transmembrane helix association. Proc Natl Acad Sci U S A. 107(2):703-8.

Bessman NJ, Lemmon MA. Finding the missing links in EGFR. Nat Struct Mol Biol. 2012 Jan 5;19(1):1-3.

Bethoney KA, King MC, Hinshaw JE, Ostap EM, Lemmon MA. A possible effector role for the pleckstrin homology (PH) domain of dynamin. Proc Natl Acad Sci U SA. 2009 Aug 11:106(32):13359-64

Bresler SC, Wood AC, Haglund EA, Courtright J, Belcastro LT, Plegaria JS, Cole K, Toporovskaya Y, Zhao H, Carpenter EL, Christensen JG, Maris JM, Lemmon MA, Mossé YP .(2011) Differential inhibitor sensitivity of anaplastic lymphoma kinase variants found in neuroblastoma. Sci Transl Med. 3(108):108ra114.

Carpenter EL, Haglund EA, Mace EM, Deng D, Martinez D, Wood AC, Chow AK, Weiser DA, Belcastro LT, Winter C, Bresler SC, Vigny M, Mazot P, Asgharzadeh S, Seeger RC, Zhao H, Guo R, Christensen JG, Orange JS, Pawel BR, Lemmon MA, Mossé YP. (2012) Antibody targeting of anaplastic lymphoma kinase induces cytotoxicity of human neuroblastoma.Oncogene. 31(46):4859-67.

Cheng H, Hong B, Zhou L, Allen JE, Tai G, Humphreys R, Dicker DT, Liu YY, El-Deiry WS. (2012) Mitomycin C potentiates TRAIL-induced apoptosis through p53-independent upregulation of death receptors: evidence for the role of c-Jun N-terminal kinase activation. Cell Cycle.11(17):3312-23.

Coelho M, Dereli A, Haese A, Kühn S, Malinovska L, DeSantis ME, Shorter J, Alberti S, Gross T, Toicl-Nørrelykke IM (2013) Fission yeast does not age under favorable conditions, but does so after stress. Curr Biol. 23(19):1844-52.

Culik RM, Annavarapu S, Nanda V, Gai F. (2013) Using D-amino acids to delineate the mechanism of protein folding: application to Trp-cage.Chem Phys. 422:131-134

Culik RM, Jo H, DeGrado WF, Gai F. (2012) Using thioamides to site-specifically interrogate the dynamics of hydrogen bond formation in β-sheet folding. J Am Chem Soc. 134(19):8026-9.

Culik RM, Serrano AL, Bunagan MR, Gai F (2011) Achieving secondary structural resolution in kinetic measurements of protein folding: a case study of the folding mechanism of Trp-cage. Angew Chem Int Ed Engl. 50(46):10884-7.

Daber R, Sochor MA, Lewis M. (2011) Thermodynamic analysis of mutant lac repressors. J Mol Biol. 409:76-87.

Dersh D, Jones SM, Eletto D, Christianson JC, Argon Y. (2014) OS-9 facilitates turnover of nonnative GRP94 marked by hyperglycosylation. Mol Biol Cell. 25(15):2220-34

DeSantis ME, Shorter J. (2012) Hsp104 drives "protein-only" positive selection of Sup35 prion strains encoding strong [PSI(+)]. Chem Biol. 19:1400-10.

DeSantis ME, Dersh D. (2010) Preventing Parkinson's pathology. Dis Model Mech. 3: 399-400.

DeSantis, M.E., Leung, E.H., Sweeny, E.A., Jackrel, M., Cushman-Nick, M., Neuhaus-Follini, A., Vashist, S., Sochor, M.A, Knight, M.N, and Shorter, J. (2012) Operational Plasticity Enables Hsp104 to Disaggregate Diverse Amyloid and Nonamyloid Clients. Cell 151:778-793.

DeSantis, M.E., Sweeny, E.A., Snead, D., Leung, E.H., Go, M.S., Gupta, K, Wendler, P., and Shorter, J. (2013) Conserved distal loop residues in the Hsp104 and ClpB middle domain contact nucleotide-binding domain 2 and enable Hsp70-dependent protein disaggregation. J. Biol. Chem. 289:848-67.

Dolloff NG, Allen JE, Dicker DT, Aqui N, Vogl D, Malysz J, Talamo G, El-Deiry WS (2012) Sangivamycin-like molecule 6 exhibits potent anti-multiple myeloma activity through inhibition of cyclin-dependent kinase-9. Mol Cancer Ther. 11:2321-30

Donald JE, Kulp DW, DeGrado WF. (2011) Salt bridges: geometrically specific, designable interactions. Proteins. 79:898-915.

Doulias PT, Tenopoulou M, Greene JL, Raju K, Ischiropoulos H. (2013) Nitric oxide regulates mitochondrial fatty acid metabolism through reversible protein S-nitrosylation. Sci Signal. 2013 6(256):rs1.

Doulias PT, Raju K, Greene JL, Tenopoulou M, Ischiropoulos H. (2013) Mass spectrometry-based identification of S-nitrosocysteine in vivo using organic mercury assisted enrichment. Methods. 62(2):165-70.

Doulias PT, Greene JL, Greco TM, Tenopoulou M, Seeholzer SH, Dunbrack RL, Ischiropoulos H. (2010)Structural profiling of endogenous S-nitrosocysteine residues reveals unique features that accommodate diverse mechanisms for protein S-nitrosylation. Proc Natl Acad Sci U S A.107(39):16958-63.

Eletto D, Dersh D, Argon Y. (2010) GRP94 in ER quality control and stress responses. Semin Cell Dev Biol. 21(5):479-85

Eletto D, Maganty A, Eletto D, Dersh D, Makarewich C, Biswas C, Paton JC, Paton AW, Doroudgar S, Glembotski CC, Argon Y. (2012) Limitation of individual folding resources in the ER leads to outcomes distinct from the unfolded protein response. J Cell Sci. 125(Pt 20): 4865-75.

Eletto D, Eletto D, Dersh D, Gidalevitz T, Argon Y. (2014) Protein disulfideiIsomerase A6 controls the decay of IRE1 signaling via disulfide-dependen-association. Mol Cell. 53(4): 562-76.

Faltas B, Zeidan A, Peters K, Das A, Joudeh J, Navaraj A, Dolloff NG, Harvey HA, Jiang Y, Allen JE, Dicker DT, El Deiry WS.(2011) Identifying circulating tumor stem cells that matter: the key to prognostication and therapeutic targeting. J Clin Oncol. 29(21):2946-7

Foltz DR, Jansen LE, Bailey AO, Yates JR 3rd, Bassett EA, Wood S, Black BE, Cleveland DW (2009 .Centromere-specific assembly of CENP-a nucleosomes is mediated by HJURP. Cell. 137(3):472-84.

Fu Y, Kasinath V, Moorman VR, Nucci NV, Hilser VJ and Wand AJ (2012) Coupled motion in proteins revealed by pressure perturbation. J Am Chem Soc. 134(20):8543-50

Gallant JN, Allen JE, Smith CD, Dicker DT, Wang W, Dolloff NG, Navaraj A, El-Deiry WS.(2011) Quinacrine synergizes with 5-fluorouracil and other therapies in colorectal cancer.
Cancer Biol Ther. 12(3):239-51.

Gibb B, Gupta K, Ghosh K, Sharp R, Chen J, Van Duyne GD. (2010) Requirements for catalysis in the Cre recombinase active site. Nucleic Acids Res. 38(17):5817-32.

Gledhill JM Jr, Walters BT, Wand AJ (2009) AMORE-HX: a multidimensional optimization of radial enhanced NMR-sampled hydrogen exchange. J Biomol NMR. 45(1-2):233-9

Gledhill JM Jr, Kasinath V and Wand AJ. (2011) Optimized linear prediction for radial sampled multidimensional NMR experiments. J Magn Reson. Sep;212(1):240-4. doi: 10.1016/j.jmr.2011.06.019. Epub 2011 Jun 28.

Goldberg, J.M.; Chen, X., Meinhardt, N.; Greenbaum, D.C.; Petersson, E.J. (2014) Thioamide-Based Fluorescent Protease Sensors. J. Am. Chem. Soc. 136(5), 2086-2093.

Gonzalez, Gabriel, Brett Hannigan and William F. DeGrado (2014) A Real-Time All-Atom Structural Search Engine for Protein. PLOS Computational Biology DOI: 10.1371/journal.pcbi.1003750

Grigoryan G, Moore DT, DeGrado WF (2011) Transmembrane communication: general principles and lessons from the structure and function of the M2 proton channel, K? channels, and integrin receptors. Annu Rev Biochem. 80:211-37.

Hasson D, Panchenko T, Salimian KJ, Salman MU, Sekulic N, Alonso A, Warburton PE, Black BE .(2013) The octamer is the major form of CENP-A nucleosomes at human centromeres. Nat Struct Mol Biol. 20(6):687-95

Hernandez, Dulce Alonso, Wei Liu, Gabriel Rosenblum, Tomoyasu Mani, Yale Goldman, Barry Cooperman (2013) Tb3+-tRNA for LRET studies of Protein Synthesis, Bioconjugate Chemistry, 24, 1186-1190.

Hu W, Walters BT, Kan ZY, Mayne L, Rosen LE, Marqusee S, Englander SW (2013)Stepwise protein folding at near amino acid resolution by hydrogen exchange and mass spectrometry.
Proc Natl Acad Sci U S A. 110(19):7684-9.

Jackrel ME, DeSantis ME, Martinez BA, Castellano LM, Stewart RM, Caldwell KA, Caldwell GA, Shorter J. (2014) Potentiated Hsp104 variants antagonize diverse proteotoxic misfolding events. Cell. 156(1-2):170-82.

Janmey PA, Slochower DR, Wang YH, Wen Q, Cebers A. (2014) Polyelectrolyte properties of filamentous biopolymers and their consequences in biological fluids. Soft Matter 10(10):1439-49.

Jian C, Xiao J, Gong L, Skipwith CG, Jin SY, Kwaan HC, Zheng XL (2012) Gain-of-function ADAMTS13 variants that are resistant to autoantibodies against ADAMTS13 in patients with acquired thrombotic thrombocytopenic purpura. Blood. 119(16):3836-43

Jin SY, Skipwith CG, Shang D, Zheng XL. (2009) von Willebrand factor cleaved from endothelial cells by ADAMTS13 remains ultralarge in size.J Thromb Haemost. 7(10):1749-52.

Jin SY, Skipwith CG, Zheng XL. (2010) Amino acid residues Arg(659), Arg(660), and Tyr(661) in the spacer domain of ADAMTS13 are critical for cleavage of von Willebrand factor. Blood. 115(11):2300-10.

Jo, H*.; Meinhardt, N*.; Wu, Y.; Kulkarni, S.; Hu, X.; Low, K. E.; Davies, P.L.; DeGrado, W. F., Greenbaum, D. C (2012) .Development of α-Helical Calpain Probes by Mimicking a Natural Protein-Protein Interaction. J. Am. Chem. Soc. 134(42), 17704-17713
(*Co-first author)

Jo, H, Culik RM, Korendovych IV, DeGrado WF, Gai F. (2010) Selective incorporation of nitrile-based infrared probes into proteins via cysteine alkylation. Biochemistry. 49(49):10354-6.

Joudeh J, Allen JE, Das A, Prabhu V, Farbaniec M, Adler J, El-Deiry WS. (2013)Novel antineoplastics targeting genetic changes in colorectal cancer. Adv Exp Med Biol. 779:1-34

Kan ZY, Walters BT, Mayne L, Englander SW. (2013) Protein hydrogen exchange at residue resolution by proteolytic fragmentation mass spectrometry analysis. Proc Natl Acad Sci U S A. 110(41):16438-43

Kasinath V, Valentine KG and Wand AJ (2013).A 13C labeling strategy reveals a range of aromatic side chain motion in calmodulin. J Am Chem Soc. 135(26):9560-3.

Kasinath V, Sharp KA, Wand AJ. (2013) Microscopic insights into the NMR relaxation-based protein conformational entropy meter. J Am Chem Soc. Oct 9;135(40):15092-100.

Korendovych IV, Kulp DW, Wu Y, Cheng H, Roder H, DeGrado W .(2011)Design of a switchable eliminase. Proc Natl Acad Sci U S A. 108(17):6823-7.

Lichtenstein BR, Cerda JF, Koder RL, Dutton PL. (2009) Reversible proton coupled electron transfer in a peptide-incorporated naphthoquinone amino acid. Chem Commun (Camb). (2):168-70.

Lichtenstein BR, Moorman VR, Cerda JF, Wand AJ, Dutton PL .(2012) Electrochemical and structural coupling of the naphthoquinone amino acid. Chem Commun (Camb). 48(14):1997-9.

Lin CW, Culik RM, Gai F. (2013) Using VIPT-jump to distinguish between different folding mechanisms: application to BBL and a Trpzip. J Am Chem Soc. 135(20):7668-73.

Lin CC, Huoh YS, Schmitz KR, Jensen LE, Ferguson KM. (2008) Pellino proteins contain a cryptic FHA domain that mediates interaction with phosphorylated IRAK1. Structure. 16(12):1806-16.

Ma C, Polishchuk AL, Ohigashi Y, Stouffer AL, Schön A, Magavern E, Jing X, Lear JD, Freire E, Lamb RA, DeGrado WF, Pinto LH. (2009) Identification of the functional core of the influenza A virus A/M2 proton-selective ion channel. Proc Natl Acad Sci U S A. 106(30):12283-8.

Mani, Tomoyasu, Ana Christina L. Opina, Piyu Zhao, Mary Evbuomwan, Nate Milburn, Gyula Tircso, Cemile Kumas, and A. Dean Sherr (2014) . The stereochemistry of amide side-chains containing carboxyl groups influences water exchange rates in EuDOTA-tetraamide complexes, Journal of Biological Inorganic Chemistry 19:161-171.

Mani, Tomoyasu, Dariusz M. Niedzwiedzik, and Sergei A. Vinogradov (2012) Generation of phosphorescent triplet states via photoinduced electron transfer: energy and electron transfer dynamics in Pt porphyrin-Rhodamine B dyads. Journal of Physical Chemistry A, 116:3598–3610

Mani, Tomoyasu, Mana Tanabe, Seigo Yamauchi, Nikolai V. Tkachenko, Sergei A. Vinogrado (2012), Modulation of Visible Room Temperature Phosphorescence by Weak Magnetic Fields, Journal of Physical Chemistry Letters, 3:3115-3119.

Mani, Tomoyasu,, Gyula Tircso, Piyu Zhao, A. Dean Sherry, and Mark Woods (2009. The Effect of the Regiochemistry of Butyl Amide Substituents on the Solution-State Structures of Lanthanide(III) DOTA-tetraamide complexes, Inorganic Chemistry, 48:10338-10345.

Mani, Tomoyasu, Gyula Tircso, Osamu Togao, Piyu Zhao, Todd Soesbe, Masaya Takahashi, and A. Dean Sheryr (2009) Modulation of Water Exchange in Ln(III) DOTA-tetraamide Complexes: Considerations for CEST Imaging, Contrast Media and Molecular Imaging, 4:183-191.

Martin R, Gupta K, Ninan NS, Perry K, Van Duyne GD. (2012) The survival motor neuron protein forms soluble glycine zipper oligomers. Structure. 20(11):1929-39.

Mani, Tomoyasu and Sergei A. Vinogrado (2013) . Magnetic Field Effects on Upconverted Emission in Solutions Sensitized by Triplet-Triplet Annihilation, Journal of Physical Chemistry Letters, 4, 2799-2804.

Markiewicz BN, Jo H, Culik RM, DeGrado WF, Gai F. (2013) Assessment of local friction in protein folding dynamics using a helix cross-linker. J Phys Chem B. 2 117(47):14688-96.

Markiewicz BN, Yang L, Culik RM, Gao YQ, Gai F. (2014) How Quickly Can a β-Hairpin Fold from Its Transition State? J Phys Chem B. 118(12):3317-25.

Mayes PA, Dolloff NG, Daniel CJ, Liu JJ, Hart LS, Kuribayashi K, Allen JE, Jee DI, Dorsey JF, Liu YY, Dicker DT, Brown JM, Furth EE, Klein PS, Sears RC, El-Deiry WS.(2011)Overcoming hypoxia-induced apoptotic resistance through combinatorial inhibition of GSK-3β and CDK1. Cancer Res. 71(15):5265-75.

Mellon EA, Pilkinton DT, Clark CM, Elliott MA, Witschey WR 2nd, Borthakur A, Reddy R. (2009) Sodium MR imaging detection of mild Alzheimer disease: preliminary study
Am J Neuroradiol. 30(5):978-84.

Mendrola JM, Shi F, Park JH, Lemmon MA. Receptor tyrosine kinases with intracellular pseudokinase domains. Biochem Soc Trans. 2013 Aug;41(4):1029-36

Metcalf DG, Kulp DW, Bennett JS, DeGrado WF. (2009) Multiple approaches converge on the structure of the integrin alphaIIb/beta3 transmembrane heterodimer. J Mol Biol. 392(4):1087-101.

Metcalf DG, Moore DT, Wu Y, Kielec JM, Molnar K, Valentine KG, Wand AJ, Bennett JS, DeGrado WF.(2010 )NMR analysis of the alphaIIb beta3 cytoplasmic interaction suggests a mechanism for integrin regulation. Proc Natl Acad Sci U S A. 107(52):22481-6.

Milk L, Daber R, Lewis M. (2010)Functional rules for lac repressor-operator associations and implications for protein-DNA interactions. Protein Sci. 19(6):1162-72.

Miller MW, Basra S, Kulp DW, Billings PC, Choi S, Beavers MP, McCarty OJ, Zou Z, Kahn ML, Bennett JS, DeGrado WF. (2009) Small-molecule inhibitors of integrin alpha2beta1 that prevent pathological thrombus formation via an allosteric mechanism. Proc Natl Acad Sci U S A. 106(3):719-24

Montalvo GL, Gai F, Roder H, DeGrado WF. (2014) Slow folding-unfolding kinetics of an octameric β-peptide bundle. ACS Chem Biol. 9(1):276-81

Moore DT, Nygren P, Jo H, Boesze-Battaglia K, Bennett JS, DeGrado WF (2012) Affinity of talin-1 for the β3-integrin cytosolic domain is modulated by its phospholipid bilayer environment.
Proc Natl Acad Sci U S A. 109(3):793-8.

Moorman VR, Valentine KG, Wand AJ .(2012) The dynamical response of hen egg white lysozyme to the binding of a carbohydrate ligand. Protein Sci. 21(7):1066-73.

Moravcevic K, Oxley CL, Lemmon MA. (2012)Conditional peripheral membrane proteins: facing up to limited specificity. Structure. 20(1):15-27.

Moravcevic K, Mendrola JM, Schmitz KR, Wang YH, Slochower D, Janmey PA, Lemmon MA (2010) Kinase associated-1 domains drive MARK/PAR1 kinases to membrane targets by binding acidic phospholipids. Cell 143(6):966-77.

Moronetti Mazzeo LE, Dersh D, Boccitto M, Kalb RG and Lamitina T. (2012) Stress and aging induce distinct polyQ protein aggregation states. Proc Natl Acad Sci. 109(26):10587-92.

Niiya M, Endo M, Shang D, Zoltick PW, Muvarak NE, Cao W, Jin SY, Skipwith CG, Motto DG, Flake AW, Zheng XL.(2009)Correction of ADAMTS13 deficiency by in utero gene transfer of lentiviral vector encoding ADAMTS13 genes. Mol Ther. 17(1):34-41.

Nishihama R, Schreiter JH, Onishi M, Vallen EA, Hanna J, Moravcevic K, Lippincott MF, Han H, Lemmon MA, Pringle JR, Bi E. (2009) Role of Inn1 and its interactions with Hof1 and Cyk3 in promoting cleavage furrow and septum formation in S. cerevisiae. J Cell Biol. 185(6):995-1012.

Nucci NV, Marques BS, Bédard S, Dogan J, Gledhill JM Jr, Moorman VR, Peterson RW, Valentine KG, Wand AL, Wand AJ .(2011) Optimization of NMR spectroscopy of encapsulated proteins dissolved in low viscosity fluids.J Biomol NMR. 50(4):421-30.

Patel AS, Allen JE, Dicker DT, Peters KL, Sheehan JM, Glantz MJ, El-Deiry WS. (2011) Identification and enumeration of circulating tumor cells in the cerebrospinal fluid of breast cancer patients with central nervous system metastases. Oncotarget. 2011 2(10):752-60.

Park JH, Lemmon MA. Occupy EGFR. Cancer Discov. 2012 May;2(5):398-400.

Park JH, Liu Y, Lemmon MA, Radhakrishnan R. Erlotinib binds both inactive and active conformations of the EGFR tyrosine kinase domain. Biochem J. 2012 Dec 15;448(3):417-23.

Pilkinton DT, Hiraki T, Detre JA, Greenberg JH, Reddy R. (2012) Absolute cerebral blood flow quantification with pulsed arterial spin labeling during hyperoxia corrected with the simultaneous measurement of the longitudinal relaxation time of arterial blood. Magn Reson Med. 67(6):1556-65.

Pilkinton DT, Gaddam SR, Reddy R. (2011) Characterization of paramagnetic effects of molecular oxygen on blood oxygenation level-dependent-modulated hyperoxic contrast studies of the human brain. Magn Reson Med. 66(3):794-801.

Polishchuk AL, Cristian L, Pinto LH, Lear JD, DeGrado WF. (2014) Mechanistic insights from functional characterization of an unnatural His37 mutant of the influenza A/M2 protein. Biochim Biophys Acta. 1838(4):1082-7.
Polishchuk AL, Lear JD, Ma C, Lamb RA, Pinto LH, Degrado WF. (2010) A pH-dependent conformational ensemble mediates proton transport through the influenza A/M2 protein Biochemistry. 49(47):10061-71.

Prabhu VV, Allen JE, Hong B, Zhang S, Cheng H, El-Deiry (2012) Therapeutic targeting of the p53 pathway in cancer stem cells. Expert Opin Ther Target 16(12):1161-74

Raju K, Doulias PT, Tenopoulou M, Greene JL, Ischiropoulos H. (2012) Strategies and tools to explore protein S-nitrosylation. Biochim Biophys Acta. 1820(6):684-8.

Red Brewer M, Choi SH, Alvarado D, Moravcevic K, Pozzi A, Lemmon MA, Carpenter G. (2009) The juxtamembrane region of the EGF receptor functions as an activation domain. Mol Cell. 3R4(6):641-51.

Reig AJ, Pires MM, Snyder RA, Wu Y, Jo H, Kulp DW, Butch SE, Calhoun JR, Szyperski T, Solomon EI, DeGrado WF. (2012) Alteration of the oxygen-dependent reactivity of de novo Due Ferri proteins. Nat Chem. 4(11):900-6.

Rivera-Santiago, RF., S. Harper, S. Zhou, S. Sriswasdi, S. Feinstein, A. Fisher and DW Speicher (2015) Solution structure of the reduced form of human peroxiredoxin-6 elucidated using zero-length chemical cross-linking and homology modeling. Biochem. J. Mar 6 [Epub ahead of print]

Rivera-Santiago RF, Sriswasdi S, Harper SL, Speicher DW. (2015) Probing structures of large protein complexes using zero-length cross-linking. Methods. 2015 May 1. pii: S1046-2023(15)00178-4. doi: 10.1016/j.ymeth.2015.04.031. [Epub ahead of print]

Roberts B.E, Duennwald, M.L., Wang, H., Chung, C., Lopreiato, N.P., Sweeny, E.A., Knight, N.M., and Shorter, J. (2009) A Synergistic Small-Molecule Combination Directly Eradicates Diverse Prion Strain Structures. Nat. Chem. Biol. 5(12):936-946.

Rogers JM, Polishchuk AL, Guo L, Wang J, DeGrado WF, Gai F. (2011 )Photoinduced electron transfer and fluorophore motion as a probe of the conformational dynamics of membrane proteins: application to the influenza a M2 proton channel. Langmuir. 27(7):3815-21.

Sarachan KL, Valentine KG, Gupta K, Moorman VR, Gledhill JM Jr, Bernens M, Tommos C, Wand AJ, Van Duyne GD. (2012) Solution structure of the core SMN-Gemin2 complex. Biochem J. 445(3):361-70.

Schramm CA, Hannigan BT, Donald JE, Keasar C, Saven JG, DeGrado WF, Samish I. (2012) Knowledge-based potential for positioning membrane-associated structures and assessing residue-specific energetic contributions. Structure. 20(5):924-35.

Schmitz KR, Ferguson KM. (2009) Interaction of antibodies with ErbB receptor extracellular regions. Exp Cell Res. 315(4):659-70.

Schroeder HW 3rd, Hendricks AG, Ikeda K, Shuman H, Rodionov V, Ikebe M, Goldman YE, Holzbaur EL.(2012) Force-dependent detachment of kinesin-2 biases track switching at cytoskeletal filament intersections. Biophys J. 103(1):48-58.

Schroeder HW 3rd, Mitchell C, Shuman H, Holzbaur EL, Goldman YE.(2010)Motor number controls cargo switching at actin-microtubule intersections in vitro. Curr Biol. 20(8):687-96.

Scott JN, Vanderkooi JM. (2011) Evidence of a structural defect in Ice VII and the side-chain-dependent response of small model peptides to increased pressure. Appl Spectrosc. 65(7):756-64.

Sekulic N, Bassett EA, Rogers DJ, Black BE. (2010) The structure of (CENP-A-H4)(2) reveals physical features that mark centromeres. Nature. 467(7313):347-51.

Shandler SJ, Korendovych IV, Moore DT, Smith-Dupont KB, Streu CN, Litvinov RI, Billings PC, Gai F, Bennett JS, DeGrado WF. (2011) Computational design of a β-peptide that targets transmembrane helices. J Am Chem Soc. 133(32):12378-81.

Sharp KA, Kasinath V and Wand AJ. Banding of NMR-derived methyl order parameters: Implications for protein dynamics. Proteins. 2014 Sep;82(9):2106-17.doi: 10.1002/prot.24566.Epub 2014 Apr 18.

Shi F, Lemmon MA. Biochemistry. KSR plays CRAF-ty. Science. 2011 May 27;332(6033):1043-4

Shi F, Telesco SE, Liu Y, Radhakrishnan R, Lemmon MA. ErbB3/HER3 intracellular domain is competent to bind ATP and catalyze autophosphorylation. Proc Natl Acad Sci U S A. 2010 Apr 27;107(17):7692-7

Shih AJ, Telesco SE, Choi SH, Lemmon MA, Radhakrishnan R. Molecular dynamics analysis of conserved hydrophobic and hydrophilic bond-interaction networks in ErbB family kinases. Biochem J. 2011 Jun 1;436(2):241-51

Skinner JJ, Lim WK, Bédard S, Black BE, Englander SW. (2012) Protein hydrogen exchange: testing current models.
Protein Sci. 21(7):987-95.

Skinner JJ, Lim WK, Bédard S, Black BE, Englander SW.(2012) Protein dynamics viewed by hydrogen exchange.
Protein Sci. 21(7):996-1005.

Skipwith CG, Cao W, Zheng XL. (2010) Factor VIII and platelets synergistically accelerate cleavage of von Willebrand factor by ADAMTS13 under fluid shear stress. J Biol Chem. 285(37):28596-603.

Skipwith CG, Haberichter SL, Gehrand A, Zheng XL. (2013)Compromised shear-dependent cleavage of type 2N von Willebrand factor variants by ADAMTS13 in the presence of factor VIII. Thromb Haemost. 110(1):202-4.

Slochower DR, Wang YH, Tourdot RW, Radhakrishnan R, Janmey PA.(2014) Counterion-mediated pattern formation in membranes containing anionic lipids. Adv Colloid Interface Sci. Jan 30. pii: S0001-8686(14)00028-1.

Slochower DR, Huwe PJ, Radhakrishnan R, Janmey PA (2013) Quantum and all-atom molecular dynamics simulations of protonation and divalent ion binding to phosphatidylinositol 4,5-bisphosphate (PIP2). J Phys Chem B. 117(28):8322-9.

Wang YH, Slochower DR, Janmey PA. (2014) Counterion-mediated cluster formation by polyphosphoinositides. Chem Phys Lipids. Jan 15. pii: S0009-3084(14)00002-4. doi: 10.1016/j.chemphyslip.2014.01.001.

Smith, MH., TF. Miles, M Sheehan, KN. Alfieri, B Kokona, and R Fairman (2009) Polyglutamine protofibrils are formed using a simple designed beta-hairpin model. Proteins. 78 (8): 1971-1979.

Sun Y, Schroeder HW 3rd, Beausang JF, Homma K, Ikebe M, Goldman YE.(2010) Myosin VI lever arm rotation: fixed or variable? Proc Natl Acad Sci U S A. 107(16):E63

Sweeny, E.A., DeSantis, M.E. and Shorter, J. (2011) Purification of Hsp104, a Protein Disaggregase. Journal of Visual Experiments (55): 3190.

Sweeny, E.A. and J. Shorter. (2008) Prion proteostasis: Hsp104 meets its supporting cast. Prion 2(4): 135-40.

Vorobyev DY, Kuo CH, Kuroda DG, Scott JN, Vanderkooi JM, Hochstrasser RM. (2010) Water-induced relaxation of a degenerate vibration of guanidinium using 2D IR echo spectroscopy. J Phys Chem B. 114(8):2944-53.

Vorobyev DY, Kuo CH, Chen JX, Kuroda DG, Scott JN, Vanderkooi JM, Hochstrasser RM. (2009) Ultrafast vibrational spectroscopy of a degenerate mode of guanidinium chloride. J Phys Chem B. 113(46):15382-91.

Waegele MM, Culik RM, Gai F. (2011) Site-specific spectroscopic reporters of the local electric field, hydration, structure, and dynamics of biomolecules. J Phys Chem Lett. 2:2598-2609.

Walters BT, Mayne L, Hinshaw JR, Sosnick TR, Englander SW. (2013) Folding of a large protein at high structural resolution. Proc Natl Acad Sci U S A. 110(47):18898-903.

Wang, E., Ballister, E.R. and Lampson, M. A. (2011). Aurora B dynamics at centromeres create a diffusion-based phosphorylation gradient. J Cell Biol. 194(4), 539–49.

Wang W, Gallant JN, Katz SI, Dolloff NG, Smith CD, Abdulghani J, Allen JE, Dicker DT, Hong B, Navaraj A, El-Deiry WS.(2011) Quinacrine sensitizes hepatocellular carcinoma cells to TRAIL and chemotherapeutic agents. Cancer Biol Ther. 12(3):229-38.

Stalker TJ, Welsh JD, Tomaiuolo M, et al. (2014) A systems approach to hemostasis: 3. Thrombus consolidation regulates intrathrombus solute transport and local thrombin activity. Blood. DOI:

Tomaiuolo M, Stalker TJ, Welsh JD, Diamond SL, Sinno T, Brass LF .(2014) A systems approach to hemostasis: 2. Computational analysis of molecular transport in the thrombus microenvironment. Blood. DOI:

Welsh JD, Stalker TJ, Voronov R, et al (2014) A systems approach to hemostasis: 1. The interdependence of thrombus architecture and agonist movements in the gaps between platelets. Blood. DOI:

Witschey WR, Borthakur A, Elliott MA, Fenty M, Sochor MA, Wang C, Reddy R (2008) T1rho-prepared balanced gradient echo for rapid 3D T1rho MRI. J Magn Reson Imaging 28(3):744-54.

Wood CS, Hung CS, Huoh YS, Mousley CJ, Stefan CJ, Bankaitis V, Ferguson KM, Burd CG. (2012) Local control of phosphatidylinositol 4-phosphate signaling in the Golgi apparatus by Vps74 and Sac1 phosphoinositide phosphatase. Mol Biol Cell. 23(13):2527-36.

Wood CS, Schmitz KR, Bessman NJ, Setty TG, Ferguson KM, Burd CG. (2009) PtdIns4P recognition by Vps74/GOLPH3 links PtdIns 4-kinase signaling to retrograde Golgi trafficking. J Cell Biol. 187(7):967-75

Zhang L, Ren X, Cheng Y, Liu X, Allen JE, Zhang Y, Yuan Y, Huang SY, Yang W, Berg A, Webb BS, Connor J, Liu CG, Lu Z, El-Deiry WS, Yang JM The NFκB inhibitor, SN50, induces differentiation of glioma stem cells and suppresses their oncogenic phenotype. Cancer Biol Ther. 2014 Feb 20;15(5). [Epub ahead of print]

Zheng XL, Wu HM, Shang D, Falls E, Skipwith CG, Cataland SR, Bennett CL, Kwaan HC. (2010) Multiple domains of ADAMTS13 are targeted by autoantibodies against ADAMTS13 in patients with acquired idiopathic thrombotic thrombocytopenic purpura. Haematologica. 95(9):1555-62.

Zhang Y, Kulp DW, Lear JD, DeGrado WF. (2009) Experimental and computational evaluation of forces directing the association of transmembrane helices. J Am Chem Soc. 131(32):11341-3