2016 Biophysics Student Publications

2016 Publications:

Healey D, Axelrod K, Gore J. 2016. Negative frequency-dependent interactions can underlie phenotypic heterogeneity in a clonal microbial population. Mol Syst Biol. 12(8):877.

Hoek TA, Axelrod K, Biancalani T, Yurtsev EA, Liu J, Gore J. 2016. Resource Availability Modulates the Cooperative and Competitive Nature of a Microbial Cross-Feeding Mutualism. PLoS Biol. 14(8):e1002540. Erratum in: PLoS Biol. 2017 15(6):e1002606.

Barrera LA, Vedenko A, Kurland JV, Rogers JM, Gisselbrecht SS, Rossin EJ, Woodard J, Mariani L, Kock KH, Inukai S, Siggers T, Shokri L, Gordân R, Sahni N, Cotsapas C, Hao T, Yi S, Kellis M, Daly MJ, Vidal M, Hill DE, Bulyk ML. 2016. Survey of variation in human transcription factors reveals prevalent DNA binding changes. Science. 351(6280):1450-1454.

Dai M, Jungmann R, Yin P. Optical imaging of individual biomolecules in densely packed clusters. Nat Nanotechnol. 2016 Sep;11(9):798-807.

Jungmann R, Avendaño MS, Dai M, Woehrstein JB, Agasti SS, Feiger Z, Rodal A, Yin P. Quantitative super-resolution imaging with qPAINT. Nat Methods. 2016 May;13(5):439-42.

Fudenberg G, Imakaev M, Lu C, Goloborodko A, Abdennur N, Mirny LA. 2016. Formation of Chromosomal Domains by Loop Extrusion. Cell Rep. 15(9):2038-49.

Khrameeva EE, Fudenberg G, Gelfand MS, Mirny LA. 2016. History of chromosome rearrangements reflects the spatial organization of yeast chromosomes. J Bioinform Comput Biol. 14(2):1641002.

Boettiger AN, Bintu B, Moffitt JR, Wang S, Beliveau BJ, Fudenberg G, Imakaev M, Mirny LA, Wu CT, Zhuang X. 2016. Super-resolution imaging reveals distinct chromatin folding for different epigenetic states. Nature. 529(7586):418-22.

Hern JM, Gelbart MA, Adams RP, Hoffman MW, Ghahramani Z.  2016. A General Framework for Constrained Bayesian Optimization using Information-based Search. Journal of Machine Learning Research. 17(160): 1-53.

Hernández-Lobato JM, Gelbart MA, Reagen B, Adolf R, Hernández-Lobato D, Whatmough PN, Brooks D, Wei G-Y, Adams RP. 2016. Designing neural network hardware accelerators with decoupled objective evaluations. Proceedings of the NIPS workshop on Bayesian Optimization. Vol. 10.

Harada BT, Hwang WL, Deindl S, Chatterjee N, Bartholomew B, Zhuang X. 2016. Stepwise nucleosome translocation by RSC remodeling complexes. Elife. 5:e10051.

ibson WJ, Hoivik EA, Halle MK, Taylor-Weiner A, Cherniack AD, Berg A, Holst F, Zack TI, Werner HM, Staby KM, Rosenberg M, Stefansson IM, Kusonmano K, Chevalier A, Mauland KK, Trovik J, Krakstad C, Giannakis M, Hodis E, Woie K, Bjorge L, Vintermyr OK, Wala JA, Lawrence MS, Getz G, Carter SL, Beroukhim R, Salvesen HB. 2016. The genomic landscape and evolution of endometrial carcinoma progression and abdominopelvic metastasis. Nat Genet. 48(8):848-55.

Lenz TL, Spirin V, Jordan DM, Sunyaev SR. 2016. Excess of Deleterious Mutations around HLA Genes Reveals Evolutionary Cost of Balancing Selection. Mol Biol Evol. 33(10):2555-64.

Kath JE, Chang S, Scotland MK, Wilbertz JH, Jergic S, Dixon NE, Sutton MD, Loparo JJ. 2016. Exchange between Escherichia coli polymerases II and III on a processivity clamp. Nucleic Acids Res. 44(4):1681-90.

Ostrov N*, Landon M*, Guell M*, Kuznetsov G*, Teramoto J, Cervantes N, Zhou M, Singh K, Napolitano MG, Moosburner M, Shrock E, Pruitt BW, Conway N, Goodman DB, Gardner CL, Tyree G, Gonzales A, Wanner BL, Norville JE, Lajoie MJ, Church GM. 2016. Design, synthesis, and testing toward a 57-codon genome. Science, 353(6301), 819-822. (*co-1st authors).

Napolitano MG, Landon M, Gregg CJ, Lajoie MJ, Govindarajan L, Mosberg JA, Kuznetsov G, Goodman DB, Vargas-Rodriguez O, Isaacs FJ, Söll D, Church GM. 2016. Emergent rules for codon choice elucidated by editing rare arginine codons in Escherichia coli. PNAS, 113(38), E5588-E5597.

Prentice-Mott HV, Meroz Y, Carlson A, Levine MA, Davidson MW, Irimia D, Charras GT, Mahadevan L, Shah JV. 2016. Directional memory arises from long-lived cytoskeletal asymmetries in polarized chemotactic cells. PNAS USA, 113 (5): 1267-72. 

Bowen SL, Fuin N, Levine MA, Catana C. 2016. Transmission imaging for integrated PET-MR systems. Phys Med Biol. 61(15):5547-68.

Paek AL, Liu JC, Loewer A, Forrester WC, Lahav G. 2016. Cell-to-Cell Variation in p53 Dynamics Leads to Fractional Killing. Cell. 165(3):631-42.

Lo WCY, Villiger M, Golberg A, Broelsch GF, Khan S, Lian CG, Austen WG Jr, Yarmush M, Bouma BE. 2016. Longitudinal, 3D Imaging of Collagen Remodeling in Murine Hypertrophic Scars In Vivo Using Polarization-Sensitive Optical Frequency Domain Imaging. J Invest Dermatol. 136(1):84-92.

Golberg A, Villiger M, Khan S, Quinn KP, Lo WCY, Bouma BE, Mihm MC Jr, Austen WG Jr, Yarmush ML. 2016. Preventing Scars after Injury with Partial Irreversible Electroporation. J Invest Dermatol. 136(11):2297-2304.

Lotter W, Kreiman G, Cox D. 2016. Unsupervised representation learning using predictive generative works. International Conference on Machine Learning Representations, Puerto Rico. (Peer-Reviewed Abstract)

Nelms BD, Waldron L, Barrera LA, Weflen AW, Goettel JA, Guo G, Montgomery RK, Neutra MR, Breault DT, Snapper SB, Orkin SH, Bulyk ML, Huttenhower C, Lencer WI. 2016. CellMapper: rapid and accurate inference of gene expression in difficult-to-isolate cell types. Genome Biol. 17(1):201.

Wang, H, Osseiran, S, Igras, V, Nichols, AJ, Roider, EM, Prussner, J, Tsao H, Fisher, DF, Evans, CL. 2016.  In vivo coherent Raman imaging of the melanomagenesis-associated pigment pheomelanin. Scientific Reports. 6, 37986.

Komor AC, Kim YB, Packer MS, Zuris JA, Liu DR. 2016. Programmable Editing of a Target Base in Genomic DNA Without Double-Stranded DNA Cleavage. Nature. 533(7603):420-4.

Lou S, Adam Y, Weinstein EN, Williams E, Williams K, Parot V, Kavokine N, Liberles S, Madisen L, Zeng H, Cohen AE. 2016. Genetically Targeted All-Optical Electrophysiology with a Transgenic Cre-Dependent Optopatch Mouse. J Neurosci. 36(43):11059-11073.

Uphoff S, Lord ND, Okumus B, Potvin-Trottier L, Sherratt DJ, Paulsson J. 2016. Stochastic activation of a DNA damage response causes cell-to-cell mutation rate variation. Science. 351(6277):1094-7.

Potvin-Trottier L, Lord ND, Vinnicombe G, Paulsson J. 2016. Synchronous long-term oscillations in a synthetic gene circuit. Nature. 538(7626):514-517.

Roquet N, Soleimany AP, Ferris AC, Aaronson S, Lu TK. 2016. Synthetic recombinase-based state machines in living cells. Science. 353(6297): aad8559.

Zhao B, Sedlak JC, Srinivas R, Creixell P, Pritchard JR, Tidor B, Lauffenburger DA, Hemann MT. 2016.  Exploiting Temporal Collateral Sensitivity in Tumor Clonal Evolution. Cell. 165(1):234-246.

Song D, Graham TGW, Loparo JJ. 2016. A general approach to visualize protein binding and DNA conformation without protein labeling. Nat. Commun. 7: 10976.

Su MY, Fisher DE. 2016. Immunotherapy in the Precision Medicine Era: Melanoma and Beyond. PLoS Med. 13(12): e1002196. (Review)

Tang H, Yu HY, Chou CC, Crone NE, Madsen JR, Anderson WS, Kreiman G. 2016. Cascade of neural processing orchestrates cognitive control in human frontal cortex. Elife. Feb 18;5. Pii: e12352.

Tang H, Singer J, Ison MJ, Pivazyan G, Romaine M, Frias R, Meller E, Boulin A, Carroll J, Perron V, Dowcett S, Arellano M, Kreiman G. 2016. Predicting episodic memory formation for movie events. Sci Rep. 6:30175.

Woodard JC, Dunatunga S, Shakhnovich EI. 2016. A Simple Model of Protein Domain Swapping in Crowded Cellular Environments. Biophysical journal. 110(11):2367-76.

Serebryany E, Woodard JC, Adkar BV, Shabab M, King JA, Shakhnovich EI. 2016. An Internal Disulfide Locks a Misfolded Aggregation-prone Intermediate in Cataract-linked Mutants of Human γD-Crystallin. The Journal of biological chemistry. 291(36):19172-83.

Xu GJ*, Shah AA*, Li MZ, Xu Q, Rosen A, Casciola-Rosen L, Elledge SJ. 2016. Systematic autoantigen analysis identifies a distinct subtype of scleroderma with coincident cancer. Proc Natl Acad Sci USA. 113(47):E7526-E7534. (*co-1st authors).

Nelson CE, Hakim CH, Ousterout DG, Thakore PI, Moreb EA, Castellanos Rivera RM, Madhavan S, Pan X, Ran FA, Yan WX, Asokan A, Zhang F, Duan D, Gersbach CA. 2016. In vivo genome editing improves muscle function in a mouse model of Duchenne muscular dystrophy. Science. 351(6271): 403–407. 

Tabebordbar, M., Zhu, K., Cheng, J.K.W., Chew, W.L., Widrick, J.J., Yan, W.X., Maesner, C., Wu, E.Y., Xiao, R., Ran, F.A., Cong, L., Zhang, F., Vandenberghe, L.H., Church, G.M., and Wagers, A.J.  2016.  In vivo gene editing in dystrophic mouse muscle and muscle stem cells.  Science. 351(6271): 407–411.

Slaymaker IM, Gao L, Zetsche B, Scott DA, Yan WX, Zhang F. 2016. Rationally engineered Cas9 nucleases with improved specificity. Science. 351(6268): 84–88.

Zhao ZW, Xie XS, Ge H. 2016. Nonequilibrium Relaxation of Conformational Dynamics Facilitates Catalytic Reaction in an Elastic Network Model of T7 DNA Polymerase. J Phys Chem B. 120(11):2869-77.

Tirosh I, Izar B, Prakadan SM, Wadsworth MH 2nd, Treacy D, Trombetta JJ, Rotem A, Rodman C, Lian C, Murphy G, Fallahi-Sichani M, Dutton-Regester K, Lin JR, Cohen O, Shah P, Lu D, Genshaft AS, Hughes TK, Ziegler CG, Kazer SW, Gaillard A, Kolb KE, Villani AC, Johannessen CM, Andreev AY, Van Allen EM, Bertagnolli M, Sorger PK, Sullivan RJ, Flaherty KT, Frederick DT, Jané-Valbuena J, Yoon CH, Rozenblatt-Rosen O, Shalek AK, Regev A, Garraway LA. 2016. Dissecting the multicellular ecosystem of metastatic melanoma by single-cell RNA-seq. Science. 2016 352(6282): 189–196.