#  2013 Biophysics Student Publications 

 



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 **2013 Publications:**

 Flannick J, Beer NL, Bick AG, **Agarwala V,** Molnes J, Gupta N, Burtt NP, Florez JC, Meigs JB, Taylor H, Lyssenko V, Irgens H, Fox E, Burslem F, Johansson S, Brosnan MJ, Trimmer JK, Newton-Cheh C, Tuomi T, Molven A, Wilson JG, O'Donnell CJ, Kathiresan S, Hirschhorn JN, Njølstad PR, Rolph T, Seidman JG, Gabriel S, Cox DR, Seidman CE, Groop L, Altshuler D. 2013. Assessing the phenotypic effects in the general population of rare variants in genes for a dominant Mendelian form of diabetes. Nat Genet. 45(11):1380-5.

 **Agarwala V**, Flannick J, Sunyaev S; GoT2D Consortium; Altshuler D. 2013. Evaluating empirical bounds on complex disease genetic architecture. Nat Genet. 45(12):1418-27.

 **Bagley AF,** Hill S, Rogers GS, Bhatia SN. 2013. Plasmonic photothermal heating of intraperitoneal tumors through the use of an implanted near-infrared source. ACS Nano. 7(9):8089-97.

 Gisselbrecht SS, **Barrera LA,** Porsch M, Aboukhalil A, Estep PW 3rd, Vedenko A, Palagi A, Kim Y, Zhu X, Busser BW, Gamble CE, Iagovitina A, Singhania A, Michelson AM, Bulyk ML. 2013. Highly parallel assays of tissue-specific enhancers in whole Drosophila embryos. Nat Methods. 10(8):774-80.

 Werfel J, Krause S, **Bischof AG,** Mannix RJ, Tobin H, Bar-Yam Y, Bellin RM, Ingber DE. 2013. How Changes in Extracellular Matrix Mechanics and Gene Expression Variability Might Combine to Drive Cancer Progression. PLoS One. 8(10): e76122.

 **Bischof AG,** Yüksel D, Mammoto T, Mammoto A, Krause S, Ingber DE. 2013. Breast cancer normalization induced by embryonic mesenchyme is mediated by extracellular matrix biglycan. Integr Biol (Camb). 5(8):1045-56.

 Ni X, Zhuo M, Su Z, Duan J, Gao Y, Wang Z, Zong C, Bai H, **Chapman AR,** Zhao J, Xu L, An T, Ma Q, Wang Y, Wu M, Sun Y, Wang S, Li Z, Yang X, Yong J, Su XD, Lu Y, Bai F, Xie XS, Wang J. 2013. Reproducible copy number variation patterns among single circulating tumor cells of lung cancer patients. Proc Natl Acad Sci USA. 110(52):21083-8.

 Gebhardt JC, Suter DM, Roy R, Zhao ZW, **Chapman AR,** Basu S, Maniatis T, Xie XS. 2013. Single-molecule imaging of transcription factor binding to DNA in live mammalian cells. Nat Methods. 10(5):421-6.

 **Chonde DB,** Abolmaali N, Arabasz G, Guimaraes AR, Catana C. 2013. Effect of MRI acoustic noise on cerebral fludeoxyglucose uptake in simultaneous MR-PET imaging. Invest Radiol. 48 (5):302-12.

 Schroeder FA, **Chonde DB,** Riley MM, Moseley CK, Granda ML, Wilson CM, Wagner FF, Zhang YL, Gale J, Holson EB, Haggarty SJ, Hooker JM. 2013. FDG-PET imaging reveals local brain glucose utilization is altered by class I histone deacetylase inhibitors. Neurosci Lett. 550:119-24.

 Ciesienski KL, Yang Y, Ay I, **Chonde DB,** Loving GS, Rietz TA, Catana C, Caravan P. 2013. Fibrin-targeted PET probes for the detection of thrombi. Mol Pharm. 10(3):1100-10.

 Bowen SL, Byars LG, Michel CJ, **Chonde DB,** Catana C. 2013. Influence of the partial volume correction method on (18)F-fluorodeoxyglucose brain kinetic modelling from dynamic PET images reconstructed with resolution model based OSEM. Phys Med Biol. 58(20):7081-106.

 Wei B, **Dai M,** Myhrvold C, Ke Y, Jungmann R, Yin P. Design space for complex DNA structures. J Am Chem Soc. 2013 Dec 4;135(48):18080-8.

 Myhrvold C, **Dai M,** Silver PA, Yin P. Isothermal self-assembly of complex DNA structures under diverse and biocompatible conditions. Nano Lett. 2013 Sep 11;13(9):4242-8.

 **Fields AP,** Meyer E, Cohen AE. 2013. Euler buckling and nonlinear kinking of double-stranded DNA. Nucl. Acids Res. 41, 9881-9890.

 Naumova N, Imakaev M, **Fudenberg G,** Zhan Y, Lajoie BR, Mirny LA, Dekker J. 2013. Organization of the mitotic chromosome. Science. 342(6161):948-53.

 **Hansen CH,** van Oudenaarden A. 2013. Allele-specific detection of single mRNA molecules in situ. Nat Methods. 10(9):869-71.

 Seim I, Fang X, Xiong Z, Lobanov AV, Huang Z, Ma S, Feng Y, Turanov AA, Zhu Y, Lenz TL, Gerashchenko MV, Fan D, Hee Yim S, Yao X, **Jordan D,** Xiong Y, Ma Y, Lyapunov AN, Chen G, Kulakova OI, Sun Y, Lee SG, Bronson RT, Moskalev AA, Sunyaev SR, Zhang G, Krogh A, Wang J, Gladyshev VN. 2013. Genome analysis reveals insights into physiology and longevity of the Brandt's bat Myotis brandtii. Nat Commun. 2013;4:2212.

 Adzhubei I, **Jordan DM.**, Sunyaev SR. 2013. Predicting functional effect of human missense mutations using PolyPhen-2. Curr Protoc Hum Genet. Jan; Chapter 7:Unit7.20.

 Poddar R, **Kawai R,** Ölveczky BP. 2013. A fully automated high-throughput training system for rodents. PLoS One. 8(12):e83171.

 **Kueh HY**, Niethammer P, Mitchison TJ. 2013. Maintenance of mitochondrial oxygen homeostasis by cosubstrate compensation. Biophys J. 104(6):1338-48.

 **Liu JC,** Guan X, Ryan JA, Rivera AG, Mock C, Agrawal V, Letai A, Lerou PH, Lahav G. 2013. High mitochondrial priming sensitizes hESCs to DNA-damage-induced apoptosis. Cell Stem Cell. 13(4):483-91.

 Payne AC, Andregg M, Kemmish K, Hamalainen M, Bowell C, Bleloch A, Klejwa N, Lehrach W, Schatz K, Stark H, **Marblestone A,** Church G, Own CS, Andregg W. 2013. Molecular threading: mechanical extraction, stretching and placement of DNA molecules from a liquid-air interface. PLoS One. 8(7):e69058.

 **Marblestone AH\*,** Zamft BM\*, Maguire YG, Shapiro MG, Cybulski TR, Glaser JI, Amodei D, Stranges PB, Kalhor R, Dalrymple DA, Seo D, Alon E, Maharbiz MM, Carmena JM, Rabaey JM, Boyden ES, Church GM, Kording KP. 2013. Physical principles for scalable neural recording. Front Comput Neurosci. 7:137. (\*co-1st authors).

 Glaser JI\*, Zamft BM\*, **Marblestone AH\*,** Moffitt JR, Tyo K, Boyden ES, Church G, Kording KP. 2013. Statistical analysis of molecular signal recording. PLoS Comput Biol. 9(7):e1003145. (\*co-1st authors).

 **McFarland CD**, Korolev KS, Kryukov GV, Sunyaev SR, Mirny LA. 2013. Impact of deleterious passenger mutations on cancer progression. Proc Natl Acad Sci USA. 110(8):2910-5.

 Yang L, Guell M, Byrne S, Yang JL, De Los Angeles A, Mali P, Aach J, Kim-Kiselak C, Briggs AW, **Rios X,** Huang PY, Daley G, Church G. 2013. Optimization of scarless human stem cell genome editing. Nucleic Acids Res. 41(19):9049-61.

 DiCarlo JE, Norville JE, Mali P, **Rios X,** Aach J, Church GM. 2013. Genome engineering in Saccharomyces cerevisiae using CRISPR-Cas systems. Nucleic Acids Res. 41(7):4336-43.

 Nakagawa S\*, Gisselbrecht SS\*, **Rogers JM\*,** Hartl DL, Bulyk ML. 2013. DNA-binding specificity changes in the evolution of forkhead transcription factors. Proc Natl Acad Sci USA. 110(30):12349-54. (\*co-1st authors)

 Toms AV, Deshpande A, McNally R, Jeong Y, **Rogers JM,** Kim CU, Gruner SM, Ficarro SB, Marto JA, Sattler M, Griffin JD, Eck MJ. 2013. Structure of a pseudokinase-domain switch that controls oncogenic activation of Jak kinases. Nat Struct Mol Biol. 20(10):1221-3.

 **Tan RZ**, Ji N, Mentink RA, Korswagen HC, van Oudenaarden A. 2013. Deconvolving the roles of Wnt ligands and receptors in sensing and amplification. Mol Syst Biol. 9:631.

 Maclaurin D\*, **Venkatachalam V\*,** Lee H, Cohen AE. 2013. Mechanism of voltage-sensitive fluorescence in a microbial rhodopsin. Proc Natl Acad Sci USA. 110(15):5939-44. (\*co-1st authors)

 Park J, Werley CA, **Venkatachalam V,** Kralj JM, Dib-Hajj SD, Waxman SG, Cohen AE. 2013. Screening fluorescent voltage indicators with spontaneously spiking HEK cells. PLoS One. 8(12):e85221.

 Larman HB, Laserson U, Querol L, Verhaeghen K, Solimini NL, **Xu GJ,** Klarenbeek PL, Church GM, Hafler DA, Plenge RM, Nigrovic PA, De Jager PL, Weets I, Martens GA, O'Connor KC, Elledge SJ. 2013. PhIP-Seq characterization of autoantibodies from patients with multiple sclerosis, type 1 diabetes and rheumatoid arthritis. J Autoimmun. 43:1-9.

 Shao DD, Tsherniak A, Gopal S, Weir BA, Tamayo P, Stransky N, Schumacher SE, **Zack TI,** Beroukhim R, Garraway LA, Margolin AA, Root DE, Hahn WC, Mesirov JP. 2013. ATARiS: Computational quantification of gene suppression phenotypes from multi-sample RNAi screens. Genome Res. 23(4):665-78.

 **Zack TI,** Schumacher SE, Carter SL, Cherniack AD, Saksena G, Tabak B, Lawrence MS, Zhsng CZ, Wala J, Mermel CH, Sougnez C, Gabriel SB, Hernandez B, Shen H, Laird PW, Getz G, Meyerson M, Beroukhim R. 2013. Pan-cancer patterns of somatic copy number alteration. Nat Genet. 45(10):1134-1140.

 Gebhardt JC, Suter DM, Roy R, **Zhao ZW,** Chapman AR, Basu S, Maniatis T, Xie XS. 2013. Single-molecule imaging of transcription factor binding to DNA in live mammalian cells. Nat Methods. 10(5):421-6.