2014 Biophysics Student Publications

2014 Publications:

Wang SR, Agarwala V, Flannick J, Chiang CW, Altshuler D; GoT2D Consortium; Hirschhorn JN. 2014. Simulation of Finnish population history, guided by empirical genetic data, to assess power of rare-variant tests in Finland. Am J Hum Genet. 94(5):710-20.

Ghosh D*, Bagley AF*, Na YJ, Birrer MJ, Bhatia SN, Belcher AM. 2014. Deep, noninvasive imaging and surgical guidance of submillimeter tumors using targeted M13-stabilized single-walled carbon nanotubes. Proc Natl Acad Sci USA. 111(38):13948-53. (*co-1st authors).

Zhao B*, Barrera LA*, Ersing I, Willox B, Schmidt SC, Greenfeld H, Zhou H, Mollo SB, Shi TT, Takasaki K, Jiang S, Cahir-McFarland E, Kellis M, Bulyk ML, Kieff E, Gewurz BE. 2014. The NF-kappaB genomic landscape in lymphoblastoid B-cells. Cell Reports. 8(5):1595-606.  (*co-1st authors).

Campàs O, Mammoto T, Hasso S, Sperling RA, O'Connell D, Bischof AG, Maas R, Weitz DA, Mahadevan L, Ingber DE. 2014. Quantifying cell-generated mechanical forces within living embryonic tissues. Nat Methods. 11(2):183-9.

Zhao ZW, Roy R, Gebhardt JC, Suter DM, Chapman AR, Xie XS. 2014. Spatial organization of RNA polymerase II inside a mammalian cell nucleus revealed by reflected light-sheet superresolution microscopy. Proc Natl Acad Sci USA. 111(2):681-6.

Chen AY, Deng Z, Billings AN, Seker UO, Lu MY, Citorik RJ, Zakeri B, Lu TK. 2014. Synthesis and patterning of tunable multiscale materials with engineered cells. Nature Mater. 13(5):515-23.

Cheng AA, Ding H, Lu TK. 2014. Enhanced killing of antibiotic-resistant bacteria enabled by massively parallel combinatorial genetics. Proc Natl Acad Sci USA. 11(34):12462-7.

Zhong C, Gurry T, Cheng AA, Downey J, Deng Z, Stultz CM, Lu TK. 2014. Strong underwater adhesives made by self-assembling multi-protein nanofibres. Nat Nanotechnol. 9(10):858-66.

Izquierdo-Garcia D, Hansen AE, Förster S, Benoit D, Schachoff S, Fürst S, Chen KT, Chonde DB, Catana C. 2014. An SPM8-based approach for attenuation correction combining segmentation and nonrigid template formation: application to simultaneous PET/MR brain imaging. J Nucl Med. 55(11):1825-30.

Catana C, Chonde DB, Chen KT, Izquierdo-Garcia D, Bowen S, Hooker J, Roffman J. 2014. Combined MR-assisted motion and partial volume effects corrections - impact on PET data quantification. Eur J Nucl Med Mol Imaging. Phys. 1(Suppl 1):A38.

Akeju O, Loggia ML, Catana C, Pavone KJ, Vazquez R, Rhee J, Contreras Ramirez V, Chonde DB, Izquierdo-Garcia D, Arabasz G, Hsu S, Habeeb K, Hooker JM, Napadow V, Brown EN, Purdon PL. 2014. Disruption of thalamic functional connectivity is a neural correlate of dexmedetomidine-induced unconsciousness. Elife. 3:e04499.

Chonde DB, Izquierdo-Garcia D, Chen K, Bowen SL, Catana C. 2014. Masamune: a tool for automatic dynamic PET data processing, image reconstruction and integrated PET/MRI data analysis. Eur J Nucl Med Mol Imaging. Phys. 1(Suppl 1):A57.

Izquierdo-Garcia D, Chen KT, Hansen AE, Förster S, Benoit D, Schachoff S, Fürst S, Chonde DB, Catana C. 2014. New SPM8-based MRAC method for simultaneous PET/MR brain images: comparison with state-of-the-art non-rigid registration methods. Eur J Nucl Med Mol Imaging. Phys. 1(Suppl 1):A29.

Poynton CB, Chen KT, Chonde DB, Izquierdo-Garcia D, Gollub RL, Gerstner ER, Batchelor TT, Catana C. 2014. Probabilistic atlas-based segmentation of combined T1-weighted and DUTE MRI for calculation of head attenuation maps in integrated PET/MRI scanners. Am J Nucl Med Mol Imaging. 4(2):160-71.

Wey HY, Catana C, Hooker JM, Dougherty DD, Knudsen GM, Wang DJ, Chonde DB, Rosen BR, Gollub RL, Kong J. 2014. Simultaneous fMRI-PET of the opioidergic pain system in human brain. Neuroimage. 102 Pt 2:275-82.

Jungmann R, Avendaño MS, Woehrstein JB, Dai M, Shih WM, Yin P. Multiplexed 3D cellular super-resolution imaging with DNA-PAINT and Exchange-PAINT. Nat Methods. 2014 Mar;11(3):313-8.

Frenkel EM, Good BH, Desai MM. 2014. The Fates of Mutant Lineages and the Distribution of Fitness Effects of Beneficial Mutations in Laboratory Budding Yeast Populations. Genetics. 196(4): 1217–1226.

Doyle B, Fudenberg G, Imakaev M, Mirny LA. 2014. Chromatin loops as allosteric modulators of enhancer-promoter interactions. PLoS Comput Biol. 10(10):e1003867.

Mizuguchi T*, Fudenberg G*, Mehta S, Belton JM, Taneja N, Folco HD, FitzGerald P, Dekker J, Mirny L, Barrowman J, Grewal SIS. 2014. Cohesin-dependent globules and heterochromatin shape 3D genome architecture in S. pombe. Nature. 516(7531):432-435. (*co-1st authors).

Gelbart MA, Snoek J, Adams RP. 2014. Bayesian optimization with unknown constraints. arXiv preprint arXiv:1403.5607.

Rippel O, Gelbart M, Adams R. 2014. Learning Ordered Representations with Nested Dropout. Proceedings of the 31st International Conference on Machine Learning. PMLR 32(2):1746-1754, 2014.

Hwang WL, Deindl S, Harada BT, Zhuang X. 2014. Histone H4 tail mediates allosteric regulation of nucleosome remodelling by linker DNA. Nature. 512(7513): 213-7.

Humplik J, Hill AL, Nowak MA. 2014. Evolutionary dynamics of infectious diseases in finite populations. J Theor Biol. 360:149-162.

Hill AL, Rosenbloom DI, Fu F, Nowak MA, Siliciano RF. 2014. Predicting the outcomes of treatment to eradicate the latent reservoir for HIV-1. Proc Natl Acad Sci USA. 111(37):13475-80. Erratum in: Proc Natl Acad Sci USA. 111(43):15598.

Whitney JB, Hill AL, Sanisetty S, Penaloza-MacMaster P, Liu J, Shetty M, Parenteau L, Cabral C, Shields J, Blackmore S, Smith JY, Brinkman AL, Peter LE, Mathew SI, Smith KM, Borducchi EN, Rosenbloom DI, Lewis MG, Hattersley J, Li B, Hesselgesser J, Geleziunas R, Robb ML, Kim JH, Michael NL, Barouch DH. 2014. Rapid seeding of the viral reservoir prior to SIV viraemia in rhesus monkeys. Nature. 512(7512):74-7.

Giannakis M*, Hodis E*, Jasmine Mu X, Yamauchi M, Rosenbluh J, Cibulskis K, Saksena G, Lawrence MS, Qian ZR, Nishihara R, Van Allen EM, Hahn WC, Gabriel SB, Lander ES, Getz G, Ogino S, Fuchs CS, Garraway LA. 2014. RNF43 is frequently mutated in colorectal and endometrial cancers. Nat Genet. 46(12):1264-6. (*co-1st authors).

Kath JE, Jergic S, Heltzel JM, Jacob DT, Dixon NE, Sutton MD, Walker GC, Loparo JJ. 2014, Polymerase exchange on single DNA molecules reveals processivity clamp control of translesion synthesis. Proc. Natl. Acad. Sci. USA. 111, 7647-52. 

Liu JC, Lerou PH, Lahav G. 2014. Stem cells: balancing resistance and sensitivity to DNA damage. Trends Cell Biol. 24 (5):268-74.

Lee JH, Daugharthy ER, Scheiman J, Kalhor R, Yang JL, Ferrante TC, Terry R, Jeanty SS, Li C, Amamoto R, Peters DT, Turczyk BM, Marblestone AH, Inverso SA, Bernard A, Mali P, Rios X, Aach J, Church GM. 2014. Highly multiplexed subcellular RNA sequencing in situ. Science. 343(6177):1360-3.

Yaglom JA, McFarland C, Mirny L, Sherman MY.  2014. Oncogene-triggered suppression of DNA repair leads to DNA instability in cancer. Oncotarget. 5(18):8367-78.

McFarland CD, Mirny LA, Korolev KS.  2014. Tug-of-war between driver and passenger mutations in cancer and other adaptive processes. Proc Natl Acad Sci USA. 111(42):15138-43.

Nichols AJ, Rousakis E, Klein OJ, Evans CL. 2014. Click-assembled, oxygen sensing nanoconjugates for depth-resolved, near-infrared imaging in a 3D cancer model. Angw. Chem. Int. Ed. 53(14):3671-4.

Li Z, Roussakis E, Koolen PG, Ibrahim AM, Kim K, Rose LF, Wu J, Nichols AJ, Baek Y, Birngruber R, Apiou-Sbirlea G, Matyal R, Huang T, Chan R, Lin SJ, Evans CL. 2014. Non-invasive transdermal two-dimensional mapping of cutaneous oxygenation with a rapid-drying liquid bandage. Biomed Opt Express. 5(11):3748-64.

Dickinson BC, Packer MS, Badran, AH, Liu DR. 2014. A System For the Continuous Directed Evolution of Proteases Rapidly Reveals Drug-Resistance Mutations. Nature Comm. 5:5352.

Roquet N, Lu TK. 2014. Digital and analog gene circuits for biotechnology. Biotechnol J. 9(5):597-608.

Im H, Shao H, Park YI, Peterson VM, Castro CM, Weissleder R, Lee H. 2014. Label-free detection and molecular profiling of exosomes with a nano-plasmonic sensor. Nat Biotechnol. 32(5):490-5.

Castro CM, Ghazani AA, Chung J, Shao H, Issadore D, Yoon TJ, Weissleder R, Lee H. 2014. Miniaturized nuclear magnetic resonance platform for detection and profiling of circulating tumor cells. Lab Chip. 14(1):14-23.

Graham TGW, Wang X, Song D, Etson CM, van Oijen AM, Rudner DZ, Loparo JJ. 2014. ParB spreading requires DNA bridging. Genes Dev. 28(11): 1228-38.

Kalwa H, Sartoretto JL, Martinelli R, Romero N, Steinhorn BS, Tao M, Ozaki CK, Carman CV, Michel T.  2014. Central role for hydrogen peroxide in P2Y1 ADP receptor-mediated cellular responses in vascular endothelium. Proc Natl Acad Sci USA. 111(9): 3383–3388.

Li J, Fettiplace M, Chen SJ, Steinhorn B, Shao Z, Zhu X, Li C, Harty S, Weinberg G, Vanden Hoek TL. 2014. Lipid emulsion rapidly restores contractility in stunned mouse cardiomyocytes: a comparison with therapeutic hypothermia. Critical Care Medicine 42(12):e734-40.

Tang H, Buia C, Madhavan R, Crone NE, Madsen JR, Anderson WS, Kreiman G. 2014. Spatiotemporal dynamics underlying object completion in human ventral visual cortex. Neuron. 83(3):736-48.

Turetsky A, Kim E, Kohler RH, Miller MA, Weissleder R. 2014. Single cell imaging of Bruton's tyrosine kinase using an irreversible inhibitor. Sci Rep. 4:4782.

Cohen AE, Venkatachalam,V. 2014. Bringing bioelectricity to light. Annu Rev Biophys. 43:211-32. 

Venkatachalam V, Brinks D, Maclaurin D, Hochbaum D, Kralj J, Cohen AE. 2014. Flash memory: photochemical imprinting of neuronal action potentials onto a microbial rhodopsin. J Am Chem Soc. 136(6):2529-37.

Venkatachalam V, Cohen AE. 2014. Imaging GFP-based reporters in neurons with multiwavelength optogenetic control. Biophys J. 2014 Oct 7;107(7):1554-63. 

Hou JH, Venkatachalam V, Cohen AE. 2014. Temporal dynamics of microbial rhodopsin fluorescence reports absolute membrane voltage. Biophys J. 106(3):639-48.

Gong Y, Zack TI, Morris LG, Lin K, Hukkelhoven E, Raheja R, Tan IL, Turcan S, Veeriah S, Meng S, Viale A, Schumacher SE, Palmedo P, Beroukhim R, Chan TA. 2014. Pan-cancer genetic analysis identifies PARK2 as a master regulator of G1/S cyclins. Nat Genet. 46(6):588-94.

Hill SJ, Rolland T, Adelmant G, Xia X, Owen MS, Dricot A, Zack TI, Sahni N, Jacob Y, Hao T, McKinney KM, Clark AP, Reyon D, Tsai SQ, Joung JK, Beroukhim R, Marto JA, Vidal M, Gaudet S, Hill DE, Livingston DM. 2014. Systematic screening reveals a role for BRCA1 in the response to transcription-associated DNA damage. Genes Dev. 28(17):1957-75.