#  2015 Biophysics Student Publications 

 



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 **2015 Publications:**

 Moutsianas L, **Agarwala V,** Fuchsberger C, Flannick J, Rivas MA, Gaulton KJ, Albers PK; GoT2D Consortium; McVean G, Boehnke M, Altshuler D, McCarthy MI. 2015. The power of gene-based rare variant methods to detect disease-associated variation and test hypotheses about complex disease. PLoS Genet. 11(4):e1005165.

 **Axelrod K,** Sanchez A, Gore J. 2015. Phenotypic states become increasingly sensitive to perturbations near a bifurcation in a synthetic gene network. Elife. 4:e07935.

 **Bagley AF,** Scherz-Shouval R, Galie PA, Zhang AQ, Wyckoff J, Whitesell L, Chen CS, Lindquist S, Bhatia SN. 2015. Endothelial Thermotolerance Impairs Nanoparticle Transport in Tumors. Cancer Res. 75(16):3255-67.

 Hume MA, **Barrera LA**, Gisselbrecht SS, Bulyk ML. 2015. UniPROBE, update 2015: new tools and content for the online database of protein-binding microarray data on protein-DNA interactions. Nucleic Acids Research 43(Database issue): D117-122.

 Jost M, **Born DA,** Cracan V, Banerjee R, Drennan CL. 2015. Structural Basis for Substrate Specificity in Adenosylcobalamin-Dependent Isobutyryl-CoA Mutase and Related Acyl-CoA Mutases. Journal of Biological Chemistry. 290(45): 26882-98.

 **Chapman AR,** He Z, Lu S, Yong J, Tan L, Tang F, Xie XS. 2015. Single cell transcriptome amplification with MALBAC. PLoS One. 10(3):e0120889.

 Huang L, Ma F, **Chapman A,** Lu S, Xie XS. 2015. Single-Cell Whole-Genome Amplification and Sequencing: Methodology and Applications. Annu Rev Genomics Hum Genet. 16:79-102.

 **Chen AY,** Zhong C, Lu TK. 2015. Engineering living functional materials. ACS Synth Biol. 4(1):8-11.

 Wong AS, Choi GC, **Cheng AA,** Purcell O, Lu TK. 2015. Massively parallel high-order combinatorial genetics in human cells. Nat Biotechnol*.* 33(9):952-61.

 Sander CY, Keil B, Chonde DB, Rosen BR, Catana C, Wald LL. 2015. A 31-channel MR brain array coil compatible with positron emission tomography. Magn Reson Med. 73(6):2363-75.

 Loggia ML, **Chonde DB,** Akeju O, Arabasz G, Catana C, Edwards RR, Hill E, Hsu S, Izquierdo-Garcia D, Ji RR, Riley M, Wasan AD, Zürcher NR, Albrecht DS, Vangel MG, Rosen BR, Napadow V, Hooker JM. 2015. Evidence for brain glial activation in chronic pain patients. Brain. 138(Pt 3):604-15.

 Zürcher NR, Loggia ML, Lawson R, **Chonde DB,** Izquierdo-Garcia D, Yasek JE, Akeju O, Catana C, Rosen BR, Cudkowicz ME, Hooker JM, Atassi N. 2015. Increased in vivo glial activation in patients with amyotrophic lateral sclerosis: assessed with \[(11)C\]-PBR28. Neuroimage Clin. 7:409-14.

 **Frenkel EM,** McDonald MJ, Van Dyken JD, Kosheleva K, Lang GI, Desai MM. 2015. Crowded growth leads to the spontaneous evolution of semistable coexistence in laboratory yeast populations. Proc Natl Acad Sci USA. 112(36): 11306–11311.

 Kind J, Pagie L, de Vries SS, Nahidiazar L, Dey SS, Bienko M, Zhan Y, Lajoie B, de Graaf CA, Amendola M, **Fudenberg G,** Imakaev M, Mirny LA, Jalink K, Dekker J, van Oudenaarden A, van Steensel B. 2015. Genome-wide maps of nuclear lamina interactions in single human cells. Cell. 163(1):134-47.

 Imakaev MV, **Fudenberg G,** Mirny LA. 2015. Modeling chromosomes: Beyond pretty pictures. FEBS Lett. Oct 7; 589(20 Pt A):3031-6.

 Hernandez-Lobato JM, **Gelbart M,** Hoffman M, Adams R, Ghahramani Z. 2015. Predictive Entropy Search for Bayesian Optimization with Unknown Constraints. Proceedings of the 32nd International Conference on Machine Learning. PMLR 37:1699-1707.

 Leventhal GE, **Hill AL,** Nowak MA, Bonhoeffer S. 2015. Evolution and emergence of infectious diseases in theoretical and real-world networks. Nat Commun. 6:6101.

 Moreno-Gamez S, **Hill AL**, Rosenbloom DI, Petrov DA, Nowak MA, Pennings PS. 2015. Imperfect drug penetration leads to spatial monotherapy and rapid evolution of multidrug resistance. Proc Natl Acad Sci USA. 112(22):E2874-83.

 **(Hodis E)** Cancer Genome Atlas Network. 2015. Genomic Classification of Cutaneous Melanoma. Cell. 161(7):1681-96.

 **Jordan DM,** Frangakis SG, Golzio C, Cassa CA, Kurtzberg J; Task Force for Neonatal Genomics; Davis EE, Sunyaev SR, Katsanis N. 2015. Identification of cis-suppression of human disease mutations by comparative genomics. Nature. 524(7564):225-9.

 Akle S, Chun S, **Jordan DM**, Cassa CA. 2015. Mitigating false-positive associations in rare disease gene discovery. Hum Mutat. 36(10):998-1003.

 Sahni N, Yi S, Taipale M, Fuxman Bass JI, Coulombe-Huntington J, Yang F, Peng J, Weile J, Karras GI, Wang Y, Kovács IA, Kamburov A, Krykbaeva I, Lam MH, Tucker G, Khurana V, Sharma A, Liu YY, Yachie N, Zhong Q, Shen Y, Palagi A, San-Miguel A, Fan C, Balcha D, Dricot A, **Jordan DM,** Walsh JM, Shah AA, Yang X, Stoyanova AK, Leighton A, Calderwood MA, Jacob Y, Cusick ME, Salehi-Ashtiani K, Whitesell LJ, Sunyaev S, Berger B, Barabási AL, Charloteaux B, Hill DE, Hao T, Roth FP, Xia Y, Walhout AJM, Lindquist S, Vidal M. Widespread macromolecular interaction perturbations in human genetic disorders. 2015. Widespread macromolecular interaction perturbations in human genetic disorders. Cell. 161(3):647-60.

 Scotland MK, Heltzel JM, **Kath JE,** Choi JS, Berdis AJ, Loparo JJ, Sutton MD. 2015. A Genetic Selection for dinB Mutants Reveals an Interaction between DNA Polymerase IV and the Replicative Polymerase That Is Required for Translesion Synthesis. PLoS Genet. 11(9):e1005507.

 Otchy TM, Wolff SB, Rhee JY, Pehlevan C, **Kawai R,** Kempf A, Gobes SM, Ölveczky BP. 2015. Acute off-target effects of neural circuit manipulations. Nature. 528(7582):358-63.

 **Kawai R**, Markman T, Poddar R, Ko R, Fantana AL, Dhawale AK, Kampff AR, Olveczky BP. 2015. Motor cortex is required for learning but not for executing a motor skill. Neuron. 86(3):800-12.

 Mandell DJ, Lajoie MJ, Mee MT, Takeuchi R, **Kuznetsov G,** Norville JE, Gregg CJ, Stoddard BL, Church GM. 2015. Biocontainment of genetically modified organisms by synthetic protein design. Nature, 518(7537), 55-60.

 Cybulski TR, Glaser JI, **Marblestone AH,** Zamft BM, Boyden ES, Church GM, Kording KP. 2015. Spatial information in large-scale neural recordings. Front Comput Neurosci*.* 8:172.

 **Monnier N\*,** Barry Z\*, Park HY, Su KC, Katz Z, English BP, Dey A, Pan K, Cheeseman IM, Singer RH, Bathe M. 2015. Inferring transient particle transport dynamics in live cells. Nat Methods. 12(9): 838–840. (\*co-1st authors).

 Rao M, **Nelms BD,** Dong L, Salinas-Rios V, Rutlin M, Gershon MD, Corfas G. 2015. Enteric glia express proteolipid protein 1 and are a transcriptionally unique population of glia in the mammalian nervous system. Glia. 63(11):2040-2057.

 Roussakis E, Li Z, Nowell NH, **Nichols AJ,** Evans CL. 2015. Bright, “Clickable” Porphyrins for the Visualization of Oxygenation under Ambient Light. Angew Chem Int Ed Engl. 54(49):14728-31.

 Roussakis E, Li Z, **Nichols AJ,** Evans CL. 2015. Oxygen-Sensing Methods in Biomedicine from the Macroscale to the Microscale. Angew Chem Int Ed Engl. 54(29):8340-62. Review.

 **Packer MS**, Liu DR. 2015. Methods for the Directed Evolution of Proteins. Reviews Genetics 16(7):379-94.

 **Rogers JM\*,** Barrera LA\*, Reyon D, Sander JD, Kellis M, Joung JK, Bulyk ML. 2015. Context influences on TALE-DNA binding revealed by quantitative profiling. Nature Communications. 6:7440. (\*co-1st authors).

 Lee K, **Shao H,** Weissleder R, Lee H. 2015. Acoustic purification of extracellular microvesicles. ACS Nano. 9(3):2321-7.

 **Shao H,** Chung J, Lee K, Balaj L, Min C, Carter BS, Hochberg FH, Breakefield XO, Lee H, Weissleder R. 2015. Chip-based analysis of exosomal mRNA mediating drug resistance in glioblastoma. Nat Commun. 6:6999.

 Im H, Castro CM, **Shao H,** Liong M, Song J, Pathania D, Fexon L, Min C, Avila-Wallace M, Zurkiya O, Rho J, Magaoay B, Tambouret RH, Pivovarov M, Weissleder R, Lee H. 2015. Digital diffraction analysis enables low-cost molecular diagnostics on a smartphone. Proc Natl Acad Sci USA. 112(18):5613-8.

 Im H, **Shao H,** Weissleder R, Castro CM, Lee H. 2015. Nano-plasmonic exosome diagnostics. Expert Rev Mol Diagn. 15(6):725-33.

 **Song D**, Mousley B, Gambino S, Helou E, Loparo JJ, Price AC. 2015. Tethered particle motion with single DNA molecules. Am. J. Phys*.* 83: 418-426.

 **Song D,** Loparo JJ. 2015. Building bridges within the bacterial chromosome. Trends Genet 31: 164-173.

 Price AC, Pilkiewicz KR, Graham TGW, **Song D,** Eaves JD, Loparo JJ. 2015. DNA motion capture reveals the mechanical properties of DNA at the mesoscale. Biophys J 108(10): 2532-2540.

 **Steinhorn BS**, Loscalzo J, Michel T. 2015. Nitroglycerine and nitric oxide—a Rondo of Themes in Cardiovascular Therapeutics. New England Journal of Medicine 373(3):277-80.

 Madhavan R, Millman D, **Tang H,** Crone NE, Lenz FA, Tierney TS, Madsen JR, Kreiman G, Anderson WS. 2015. Decrease in gamma-band activity tracks sequence learning. Front Syst Neurosci. 8:222.

 **Turetsky A**, Lee K, Song J, Giedt RJ, Kim E, Kovach AE, Hochberg EP, Castro CM, Lee H, Weissleder R. 2015. On chip analysis of CNS lymphoma in cerebrospinal fluid. Theranostics. 5(8):796-804.

 Tian J\*, Woodard JC\*, Whitney A, Shakhnovich EI. 2015. Thermal stabilization of dihydrofolate reductase using monte carlo unfolding simulations and its functional consequences. PLoS Comput Biol. 11(4):e1004207. (\*co-1st authors).

 **Xu GJ\*,** Kula T\*, Xu Q, Li MZ, Vernon SD, Ndung'u T, Ruxrungtham K, Sanchez J, Brander C, Chung RT, O'Connor KC, Walker B, Larman HB, Elledge SJ. 2015. Viral immunology. Comprehensive serological profiling of human populations using a synthetic human virome. Science. 348(6239):aaa0698. (\*co-1st authors).

 Nishimasu H, Le Cong L, **Yan WX,** Ran FA, Zetsche B, Li Y, Kurabayashi A, Ishitani R, Zhang F, Nureki O. 2015. Crystal structure of Staphylococcus aureus Cas9. Cell. 162(5): 1113-26.

 Ran FA\*, Cong L\*, **Yan WX\*,** Scott DA, Gootenberg JS, Kriz AJ, Zetsche B, Shalem O, Wu X, Makarova KS, Koonin EV, Sharp PA, Zhang F. 2015. *In vivo* genome editing using Staphylococcus aureus Cas9. Nature 520(7546):186-91. (\*co-1st authors).