2012 Biophysics Student Publications

2012 Publications:

Ball MP, Thakuria JV, Zaranek AW, Clegg T, Rosenbaum AM, Wu X, Angrist M, Bhak J, Bobe J, Callow MJ, Cano C, Chou MF, Chung WK, Douglas SM, Estep PW, Gore A, Hulick P, Labarga A, Lee JH, Lunshof JE, Kim BC, Kim JI, Li Z, Murray MF, Nilsen GB, Peters BA, Raman AM, Rienhoff HY, Robasky K, Wheeler MT, Vandewege W, Vorhaus DB, Yang JL, Yang L, Aach J, Ashley EA, Drmanac R, Kim SJ, Li JB, Peshkin L, Seidman CE, Seo JS, Zhang K, Rehm HL, Church GM. 2012. A public resource facilitating clinical use of genomes. Proc Natl Acad Sci USA. 109(30):11920-7.

Zong C, Lu S, Chapman AR, Xie XS. 2012. Genome-wide detection of single-nucleotide and copy-number variations of a single human cell. Science. 338(6114):1622-6.

Lu S, Zong C, Fan W, Yang M, Li J, Chapman AR, Zhu P, Hu X, Xu L, Yan L, Bai F, Qiao J, Tang F, Li R, Xie XS. 2012. Probing meiotic recombination and aneuploidy of single sperm cells by whole-genome sequencing. Science. 338(6114):1627-30.

Cheng A, Lu TK. 2012. Synthetic Biology - An Emerging Engineering Discipline. Annu Rev Biomed Eng. 14:155-78.

Uppal R, Ciesienski KL, Chonde DB, Loving GS, Caravan P. 2012. Discrete bimodal probes for thrombus imaging. J Am Chem Soc. 134(26):10799-802.

Wei B, Dai M, Yin P. Complex shapes self-assembled from single-stranded DNA tiles. Nature. 2012 May 30;485(7400):623-6.

Bayraktar H, Fields AP, Kralj JM, Spudich JL, Rothschild KJ, Cohen AE. 2012. Ultrasensitive measurements of microbial rhodopsin photocycles using photochromic FRET. Photochem. & Photobiol. 88, 90-97.

Fields AP, Cohen AE. 2012. Optimal tracking of a Brownian particle. Optics Express, 20, 22585-22601.

Fudenberg G, Mirny LA. 2012. Higher-order chromatin structure: bridging physics and biology. Curr Opin Genet Dev. 22(2):115-24.

Imakaev M*, Fudenberg G*, McCord RP, Naumova N, Goloborodko A, Lajoie BR, Dekker J, Mirny LA. 2012. Iterative correction of Hi-C data reveals hallmarks of chromosome organization. Nat Methods. 9(10):999-1003. (*co-1st authors).

Gelbart MA, He B, Martin AC, Thiberge SY, Wieschaus EF, & Kaschube M. 2012. Volume conservation principle involved in cell lengthening and nucleus movement during tissue morphogenesis. Proc Natl Acad Sci USA. 109 (47) 19298-19303.

Kanapathipillai M, Mammoto A, Mammoto T, Kang JH, Jiang E, Ghosh K, Korin N, Gibbs A, Mannix R, Ingber DE. 2012. Inhibition of mammary tumor growth using lysyl oxidase-targeting nanoparticles to modify extracellular matrix. Nano Lett. 12(6):3213-7.

Rosenbloom DI, Hill AL, Rabi SA, Siliciano RF, Nowak MA. 2012. Antiretroviral dynamics determines HIV evolution and predicts therapy outcome. Nat Med. 18(9):1378-85.

Hill AL, Rosenbloom DI, Nowak MA. 2012. Evolutionary dynamics of HIV at multiple spatial and temporal scales. J Mol Med (Berl). 90(5):543-61.

Tennessen JA, Bigham AW, O'Connor TD, Fu W, Kenny EE, Gravel S, McGee S, Do R, Liu X, Jun G, Kang HM, Jordan D, Leal SM, Gabriel S, Rieder MJ, Abecasis G, Altshuler D, Nickerson DA, Boerwinkle E, Sunyaev S, Bustamante CD, Bamshad MJ, Akey JM; Broad GO; Seattle GO; NHLBI Exome Sequencing Project. 2012. Evolution and functional impact of rare coding variation from deep sequencing of human exomes. Science, Vol 337: 64-69.

Tootoonian S, Coen P, Kawai R, Murthy M. 2012. Neural representations of courtship song in the Drosophila brain. J Neurosci. 32(3):787-98.

Eroshenko N, Kosuri S, Marblestone AH, Conway N, Church GM. 2012. Gene Assembly from Chip-Synthesized Oligonucleotides. Curr Protoc Chem Biol. pii: ch110190.

Zamft BM*, Marblestone AH*, Kording K, Schmidt D, Martin-Alarcon D, Tyo K, Boyden ES, Church G. 2012.  Measuring Cation Dependent DNA Polymerase Fidelity Landscapes by Deep Sequencing. PLoS ONE 7(8): e43876. (*co-1st authors).

Wang HH*, Huang PY*, Xu G, Haas W, Marblestone A, Li J, Gygi SP, Forster AC, Jewett MC, Church GM. 2012. Multiplexed in vivo His-tagging of enzyme pathways for in vitro single-pot multi-enzyme catalysis. ACS Synth Biol. 1(2):43-52. (*co-1st authors)

Schmidt JC, Arthanari H, Boeszoermenyi A, Dashkevich NM, Wilson-Kubalek EM, Monnier N, Markus M, Oberer M, Milligan RA, Bathe M, Wagner G, Grishchuk EL, Cheeseman IM. 2012. The Kinetochore-Bound Ska1 Complex Tracks Depolymerizing Microtubules and Binds to Curved Protofilaments. Dev Cell. 23(5): 968-80. 

Guo SM, He J, Monnier N, Sun G, Wohland T, Bathe M. 2012. Bayesian approach to the analysis of fluorescence correlation spectroscopy data II: application to simulated and in vitro data. Anal Chem. 84(9):3880-8.

Monnier N, Guo SM, Mori M, He J, Lénárt P, Bathe M. 2012. Bayesian Approach to MSD-Based Analysis of Particle Motion in Live Cells. Biophys J. 2012 Aug 8; 103(3): 616–626.

Jung Y, Nichols AJ, Klein OJ, Roussakis E, Evans CL. 2012. Label-Free, Longitudinal Visualization of PDT Response In Vitro with Optical Coherence Tomography. Isr J Chem. 52(8-9):728-744.

Briggs AW, Rios X, Chari R, Yang L, Zhang F, Mali P, Church GM. 2012. Iterative capped assembly: rapid and scalable synthesis of repeat-module DNA such as TAL effectors from individual monomers. Nucleic Acids Res. 40(15):e117. 

Rios X, Briggs AW, Christodoulou D, Gorham JM, Seidman JG, Church GM. 2012.  Stable gene targeting in human cells using single-strand oligonucleotides with modified bases. PLoS One. 7(5):e36697.      

Larman HB*, Xu GJ*, Pavlova NN, Elledge SJ. 2012. Construction of a rationally designed antibody platform for sequencing-assisted selection. Proc Natl Acad Sci USA. 109(45):18523-8. (*co-1st authors).

Carr PA, Wang HH, Sterling B, Isaacs FJ, Lajoie MJ, Xu G, Church GM, Jacobson JM. 2012. Enhanced multiplex genome engineering through co-operative oligonucleotide co-selection. Nucleic Acids Res. 40(17):e132.

Rosenbluh J, Nijhawan D, Cox AG, Li X, Neal JT, Schafer EJ, Zack TI, Wang X, Tsherniak A, Schinzel AC, Shao DD, Schumacher SE, Weir BA, Vazquez F, Cowley GS, Root DE, Mesirov JP, Beroukhim R, Kuo CJ, Goessling W, Hahn WC. 2012. β-Catenin-Driven Cancers Require a YAP1 Transcriptional Complex for Survival and Tumorigenesis. Cell. 151(7):1457-73.

Carter SL, Cibulskis K, Helman E, McKenna A, Shen H, Zack T, Laird PW, Onofrio RC, Winckler W, Weir BA, Beroukhim R, Pellman D, Levine DA, Lander ES, Meyerson M, Getz G. 2012. Absolute quantification of somatic DNA alterations in human cancer. Nat Biotechnol. 30(5):413-21.

Nijhawan D, Zack TI, Ren Y, Strickland MR, Lamothe R, Schumacher SE, Tsherniak A, Besche HC, Rosenbluh J, Shehata S, Cowley GS, Weir BA, Goldberg AL, Mesirov JP, Root DE, Bhatia SN, Beroukhim R, Hahn WC. 2012. Cancer vulnerabilities unveiled by genomic loss. Cell. 150(4):842-54.