2019 Biophysics Student Publications

2019 Publications:

Kosuri P*, Altheimer BD*, Dai M, Yin P, Zhuang X. 2019. Rotation tracking of genome-processing enzymes using DNA origami rotors. Nature. 572(7767):136-140. (*co-1st authors).

Finn EH, Pegoraro G, Brandão HB, Valton AL, Oomen ME, Dekker J, Mirny L, Misteli T. Extensive Heterogeneity and Intrinsic Variation in Spatial Genome Organization. Cell. 2019 Mar 7;176(6):1502-1515.e10.

Brandão HB, Paul P, van den Berg AA, Rudner DZ, Wang X, Mirny LA. RNA polymerases as moving barriers to condensin loop extrusion. Proc Natl Acad Sci USA. 2019 Oct 8;116(41):20489-20499.

Catipovic MA, Bauer BW, Loparo JJ, Rapoport TA. 2019. Protein translocation by the SecA ATPase occurs by a power-stroke mechanism. EMBO J. 38(9):e101140.

Ma C, Wu X, Sun D, Park E, Catipovic MA, Rapoport TA, Gao N, Li L. 2019. Structure of the substrate-engaged SecA-SecY protein translocation machine. Nat Commun. 10(1):2872.

Watanabe A, McCarthy KR, Kuraoka M, Schmidt AG, Adachi Y, Onodera T, Tonouchi K, Caradonna TM, Bajic G, Song S, McGee CE, Sempowski GD, Feng F, Urick P, Kepler TB, Takahashi Y, Harrison SC, Kelsoe G.  2019. Antibodies to a Conserved Influenza Head Interface Epitope Protect by an IgG Subtype-Dependent Mechanism. Cell. 177(5):1124-1135.e16.

Wang C, Lu T, Emanuel G, Babcock HP, Zhuang X. 2019. Imaging-based pooled CRISPR screening reveals regulators of lncRNA localization. Proc Natl Acad Sci USA. 116(22):10842-10851.

Xia C, Fan J, Emanuel G, Hao J, Zhuang X. 2019. Spatial transcriptome profiling by MERFISH reveals subcellular RNA compartmentalization and cell cycle-dependent gene expression. Proc Natl Acad Sci USA. 116(39):19490-19499.

Guo Y, Vucelja M, Amir A. 2019. Stochastic tunneling across fitness valleys can give rise to a logarithmic long-term fitness trajectory. Sci Adv. 5(7):eaav3842.

Lee JB, Yonar A, Hallacy T, Shen CH, Milloz J, Srinivasan J, Kocabas A, Ramanathan S. 2019. A compressed sensing framework for efficient dissection of neural circuits. Nat Methods. 16(1):126-133.

Maruvka YE, Haradhvala NJ, Getz G. 2019. Analyzing Frequently Mutated Genes and the Association With Tumor Mutation Load. JAMA Oncol.;5(4):577.

Hess JM, Bernards A, Kim J, Miller M, Taylor-Weiner A, Haradhvala NJ, Lawrence MS, Getz G. 2019. Passenger Hotspot Mutations in Cancer. Cancer Cell. 36(3):288-301.e14.

Yizhak K, Aguet F, Kim J, Hess JM, Kübler K, Grimsby J, Frazer R, Zhang H, Haradhvala NJ, Rosebrock D, Livitz D, Li X, Arich-Landkof E, Shoresh N, Stewart C, Segrè AV, Branton PA, Polak P, Ardlie KG, Getz G. 2019. RNA sequence analysis reveals macroscopic somatic clonal expansion across normal tissues. Science. 364(6444). pii: eaaw0726.

Taylor-Weiner A, Aguet F, Haradhvala NJ, Gosai S, Anand S, Kim J, Ardlie K, Van Allen EM, Getz G. 2019. Scaling computational genomics to millions of individuals with GPUs. Genome Biol. 20(1):228.

Haskell MW, Cauley SF, Bilgic B, Hossbach J, Splitthoff DN, Pfeuffer J, Setsompop K, Wald LL. 2019. Network Accelerated Motion Estimation and Reduction (NAMER): Convolutional neural network guided retrospective motion correction using a separable motion model. Magnetic resonance in medicine. 82(4):1452-1461.

Vokes NI, Liu D, Ricciuti B, Jimenez-Aguilar E, Rizvi H, Dietlein F, He MX, Margolis CA, Elmarakeby HA, Girshman J, Adeni A, Sanchez-Vega F, Schultz N, Dahlberg S, Zehir A, Jänne PA, Nishino M, Umeton R, Sholl LM, Van Allen EM, Hellmann MD, Awad MM. 2019. Harmonization of Tumor Mutational Burden Quantification and Association With Response to Immune Checkpoint Blockade in Non-Small-Cell Lung Cancer. JCO Precis Oncol. 2019;3:PO.19.00171.

Liu D, Schilling B, Liu D, Sucker A, Livingstone E, Jerby-Arnon L, Zimmer L, Gutzmer R, Satzger I, Loquai C, Grabbe S, Vokes N, Margolis CA, Conway J, He MX, Elmarakeby H, Dietlein F, Miao D, Tracy A, Gogas H, Goldinger SM, Utikal J, Blank CU, Rauschenberg R, von Bubnoff D, Krackhardt A, Weide B, Haferkamp S, Kiecker F, Izar B, Garraway L, Regev A, Flaherty K, Paschen A, Van Allen EM, Schadendorf D. 2019. Integrative molecular and clinical modeling of clinical outcomes to PD1 blockade in patients with metastatic melanoma. Nat Med. 25(12):1916-1927. (Erratum in: Nat Med. 2020 26(7):1147)

Kotliar D, Veres A, Nagy MA, Tabrizi S, Hodis E, Melton DA, Sabeti PC. 2019. Identifying gene expression programs of cell-type identity and cellular activity with single-cell RNA-Seq. Elife. 8:e43803.

Kalluri AS, Vellarikkal SK, Edelman ER, Nguyen L, Subramanian A, Ellinor PT, Regev A, Kathiresan S, Gupta RM. 2019. Single-Cell Analysis of the Normal Mouse Aorta Reveals Functionally Distinct Endothelial Cell Populations. Circulation. 140(2):147-163.

Chang S, Naiman K, Thrall ES, Kath JE, Jergic S, Dixon NE, Fuchs RP, Loparo JJ. 2019. A gatekeeping function of the replicative polymerase controls pathway choice in the resolution of lesion-stalled replisomes. Proc Natl Acad Sci USA 116(51):25591-25601.

Kimchi O, Cragnolini T, Brenner MP, Colwell LJ. 2019. A Polymer Physics Framework for the Entropy of Arbitrary Pseudoknots. Biophys J. 117(3):520-532.

Chen H, Liu S, Padula S, Lesman D, Griswold K, Lin A, Zhao T, Marshall JL, Chen F. 2019. Efficient, continuous mutagenesis in human cells using a pseudo-random DNA editor. Nat Biotechnol. 38(2):165-168.

Lo WCY, Uribe-Patarroyo N, Hoebel K, Beaudette K, Villiger M, Nishioka NS, Vakoc BJ, Bouma BE. 2019. Balloon catheter-based radiofrequency ablation monitoring in porcine esophagus using optical coherence tomography. Biomed Opt Express. 10(4):2067-2089.

Howard TP, Arnoff TE, Song MR, Giacomelli AO, Wang X, Hong AL, Dharia NV, Wang S, Vazquez F, Pham MT, Morgan AM, Wachter F, Bird GH, Kugener G, Oberlick EM, Rees MG, Tiv HL, Hwang JH, Walsh KH, Cook A, Krill-Burger JM, Tsherniak A, Gokhale PC, Park PJ, Stegmaier K, Walensky LD, Hahn WC, Roberts CWM. 2019. MDM2 and MDM4 Are Therapeutic Vulnerabilities in Malignant Rhabdoid Tumors. Cancer Res. 79(9):2404-2414.

Adam Y, Kim JJ, Lou S, Zhao Y, Xie ME, Brinks D, Wu H, Mostajo-Radji MA, Kheifets S, Parot V, Chettih S, Williams KJ, Gmeiner B, Farhi SL, Madisen L, Buchanan EK, Kinsella I, Zhou D, Paninski L, Harvey CD, Zeng H, Arlotta P, Campbell RE, Cohen AE. 2019. Voltage imaging and optogenetics reveal behaviour-dependent changes in hippocampal dynamics. Nature. 569(7756):413-417.

Farhi SL, Parot VJ, Grama A, Yamagata M, Abdelfattah AS, Adam Y, Lou S, Kim JJ, Campbell RE, Cox DD, Cohen AE. 2019. Wide-Area All-Optical Neurophysiology in Acute Brain Slices. J Neurosci. 39(25):4889-4908.

Petkova MD, Tkačik G, Bialek W, Wieschaus EF, Gregor T. 2019. Optimal Decoding of Cellular Identities in a Genetic Network. Cell. 176(4):844-855.e15.

Piatt SC, Loparo JJ, Price AC. 2019. The Role of Noncognate Sites in the 1D Search Mechanism of EcoRI. Biophys J. 116(12):2367-2377. 

Riglar DT, Richmond DL, Potvin-Trottier L, Verdegaal AA, Naydich AD, Bakshi S, Leoncini E, Lyon LG, Paulsson J, Silver PA. 2019. Bacterial variability in the mammalian gut captured by a single-cell synthetic oscillator. Nat Commun. 10(1):4665. Erratum in: Nat Commun. 12(1):1818.

Rogers JM, Waters CT, Seegar TCM, Jarrett SM, Hallworth AN, Blacklow SC, Bulyk ML. 2019. Bispecific Forkhead Transcription Factor FoxN3 Recognizes Two Distinct Motifs with Different DNA Shapes. Mol Cell. 2074(2):245-253.e6.

Loynachan CN, Soleimany AP, Dudani JS, Lin Y, Najer A, Bekdemir A, Chen Q, Bhatia SN, Stevens MM. 2019. Renal clearable catalytic gold nanoclusters for in vivo disease monitoring. Nat Nanotechnol. 14(9):883-890.

Schuerle S, Soleimany AP, Yeh T, Anand GM, Häberli M, Fleming HE, Mirkhani N, Qiu F, Hauert S, Wang X, Nelson BJ, Bhatia SN. 2019. Synthetic and living micropropellers for convection-enhanced nanoparticle transport. Sci Adv. 5(4):eaav4803.

Sorrentino A, Steinhorn B, Troncone L, Saravi SSS, Badole S, Eroglu E, Kijewski MF, Divakaran S, Di Carli M, Michel T. 2019. Reversal of heart failure in a chemogenetic model of persistent cardiac redox stress. Am J Physiol Heart Circ Physiol. 317(3):H617-H626.

Mao AS, Özkale B, Shah NJ, Vining KH, Descombes T, Zhang L, Tringides CM, Wong SW, Shin JW, Scadden DT, Weitz DA, Mooney DJ. 2019. Programmable microencapsulation for enhanced mesenchymal stem cell persistence and immunomodulation. Proc Natl Acad Sci USA. 116(31):15392-15397.

Du Z, Lin JR, Rashid R, Maliga Z, Wang S, Aster JC, Izar B, Sorger PK, Santagata S. 2019. Qualifying antibodies for image-based immune profiling and multiplexed tissue imaging. Nat Protoc. 14(10):2900-2930.

Wang S, Lin JR, Sontag ED, Sorger PK. 2019. Inferring reaction network structure from single-cell, multiplex data, using toric systems theory. PLoS Comput Biol. 15(12):e1007311.

Monnahan P, Kolář F, Baduel P, Sailer C, Koch J, Horvath R, Laenen B, Schmickl R, Paajanen P, Šrámková G, Bohutínská M, Arnold B, Weisman CM, Marhold K, Slotte T, Bomblies K, Yant L.  2019. Pervasive population genomic consequences of genome duplication in Arabidopsis arenosa. Nat Ecol Evol. 3(3):457-468.

Ma L, Dichwalkar T, Chang JYH, Cossette B, Garafola D, Zhang AQ, Fichter M, Wang C, Liang S, Silva M, Kumari S, Mehta NK, Abraham W, Thai N, Li N, Wittrup KD, Irvine DJ.  2019.  Enhanced CAR-T cell activity against solid tumors by vaccine boosting through the chimeric receptor. Science. 365(6449):162-168.