2018 Biophysics Student Publications

2018 Publications:

Okumus B*, Baker CJ*, Arias-Castro JC, Lai GC, Leoncini E, Bakshi S, Luro S, Landgraf D, Paulsson J. 2018. Single-cell microscopy of suspension cultures using a microfluidics-assisted cell screening platform. Nat Protoc. 13(1):170-194. (*co-1st authors).

Harris NC, Born DA, Cai W, Huang Y, Martin J, Khalaf R, Drennan CL, Zhang W. 2018. Isonitrile Formation by a Non-Heme Iron(II)-Dependent Oxidase/Decarboxylase. Angew Chem Int Ed Engl. 57(31):9707-9710.

Wang X, Hughes AC, Brandão HB, Walker B, Lierz C, Cochran JC, Oakley MG, Kruse AC, Rudner DZ. In Vivo Evidence for ATPase-Dependent DNA Translocation by the Bacillus subtilis SMC Condensin Complex. Mol Cell. 2018 Sep 6;71(5):841-847.e5.

Chen KT, Salcedo S, Chonde DB, Izquierdo-Garcia D, Levine MA, Price JC, Dickerson BC, Catana C. 2018. MR-assisted PET motion correction in simultaneous PET/MRI studies of dementia subjects. J Magn Reson Imaging. 48(5):1288-1296.

Guo Y, Tikhonov M, Brenner MP. 2018. Local growth rules can maintain metabolically efficient spatial structure throughout growth. Proc Natl Acad Sci USA. 115(14):3593-3598.

Brody Y, Kimmerling RJ, Maruvka YE, Benjamin D, Elacqua JJ, Haradhvala NJ, Kim J, Mouw KW, Frangaj K, Koren A, Getz G, Manalis SR, Blainey PC. 2018. Quantification of somatic mutation flow across individual cell division events by lineage sequencing. Genome Res. 28(12): 1901-1918.

Cooley CZ, Haskell MW, Cauley SF, Sappo C, Lapierre CD, Ha CG, Stockmann JP, Wald LL. 2018. Design of sparse Halbach magnet arrays for portable MRI using a genetic  algorithm. IEEE Trans Magn. 54(1). pii: 5100112. 

Wang F, Bilgic B, Dong Z, Manhard MK, Ohringer N, Zhao B, Haskell M, Cauley SF, Fan Q, Witzel T, Adalsteinsson E, Wald LL, Setsompop K. 2018. Motion-robust sub-millimeter isotropic diffusion imaging through motion corrected generalized slice dithered enhanced resolution (MC-gSlider) acquisition. Magn Reson Med. 80(5):1891-1906.

Haskell MW, Cauley SF, Wald LL. 2018. TArgeted Motion Estimation and Reduction (TAMER): Data Consistency Based Motion Mitigation for MRI Using a Reduced Model Joint Optimization. IEEE Trans Med Imaging. 37(5):1253-1265. 

Jenkins, R.W., Aref, A.R., Lizotte, P.H., Ivanova, E., Stinson, S., Zhou, C.W., Bowden, M., Deng, J., Liu, H., Miao, D., He. M.X., et al. 2018. Ex Vivo Profiling of PD-1 Blockade Using Organotypic Tumor Spheroids. Cancer Discov. 8(2):196-215.

Smart AC, Margolis CA, Pimentel H, He MX, Miao D, Adeegbe D, Fugmann T, Wong KK, Van Allen EM. 2018. Intron retention is a source of neoepitopes in cancer. Nat Biotechnol. 36(11):1056-1058.

Kwan TT, Bardia A, Spring LM, Giobbie-Hurder A, Kalinich M, Dubash T, Sundaresan T, Hong X, LiCausi JA, Ho U, Silva EJ, Wittner BS, Sequist LV, Kapur R, Miyamoto DT, Toner M, Haber DA, Maheswaran S. 2018. A Digital RNA Signature of Circulating Tumor Cells Predicting Early Therapeutic Response in Localized and Metastatic Breast Cancer. Cancer Discov. 8(10):1286-1299.

Miyamoto DT, Lee RJ, Kalinich M, LiCausi J, Zheng Y, Chen T, Milner JD, Emmons E, Ho U, Broderick K, Silva E, Javaid S, Kwan TT, Hong X, Dahl DM, McGovern FJ, Efstathiou JA, Smith MR, Sequist LV, Kapur R, Wu CL, Stott SL, Ting DT, Giobbie-Hurder A, Toner M, Maheswaran S, Haber DA. 2018. An RNA-based digital circulating tumor cell signature is predictive of drug response and early dissemination in prostate cancer. Cancer Discov. 8(3):288-303.

Kalinich M, Haber DA. 2018. Cancer detection: Seeking signals in blood. Science. 359(6378):866-867.

Bhan I, Mosesso K, Goyal L, Philipp J, Kalinich M, Franses JW, Choz M, Oklu R, Toner M, Maheswaran S, Haber DA, Zhu AX, Chung RT, Aryee M, Ting DT. 2018. Detection and Analysis of Circulating Epithelial Cells in Liquid Biopsies From Patients With Liver Disease. Gastroenterology. 155(6):2016-2018.e11.

Hong X, Sullivan RJ, Kalinich M, Kwan TT, Giobbie-Hurder A, Pan S, LiCausi JA, Milner JD, Nieman LT, Wittner BS, Ho U, Chen T, Kapur R, Lawrence DP, Flaherty KT, Sequist LV, Ramaswamy S, Miyamoto DT, Lawrence M, Toner M, Isselbacher KJ, Maheswaran S, Haber DA. 2018. Molecular signatures of circulating melanoma cells for monitoring early response to immune checkpoint therapy. Proc Natl Acad Sci USA.  115(10):2467-2472.

Bintu B, Mateo LJ, Su JH, Sinnott-Armstrong NA, Parker M, Kinrot S, Yamaya K, Boettiger AN, Zhuang X. 2018. Super-resolution chromatin tracing reveals domains and cooperative interactions in single cells. Science. 362(6413):eaau1783.

Tang H, Schrimpf M, Lotter W, Moerman C, Paredes A, Ortega Caro J, Hardesty W, Cox D, Kreiman G. 2018. Recurrent computations for visual pattern completion. Proc Natl Acad Sci USA. 115(35):8835-8840.

Isik L*, Lotter W*, Crone NE, Cox D, Kanwisher N, Anderson WS, Kreiman G. 2017. Task dependent modulation before, during and after visually evoked responses in human intracranial recordings. Society for Neuroscience Annual Meeting. Washington, DC. (*co-1^st authors).

Escudero S, Zaganjor E, Lee S, Mill CP, Morgan AM, Crawford EB, Chen J, Wales TE, Mourtada R, Luccarelli J, Bird GH, Steidl U, Engen JR, Haigis MC, Opferman JT, Walensky LD. 2018. Dynamic Regulation of Long-Chain Fatty Acid Oxidation by a Noncanonical Interaction between the MCL-1 BH3 Helix and VLCAD. Mol Cell. 69(5):729-743.e7.

Stolte B, Iniguez AB, Dharia NV, Robichaud AL, Conway AS, Morgan AM, Alexe G, Schauer NJ, Liu X, Bird GH, Tsherniak A, Vazquez F, Buhrlage SJ, Walensky LD, Stegmaier K. 2018. Genome-scale CRISPR-Cas9 screen identifies druggable dependencies in TP53 wild-type Ewing sarcoma. J Exp Med. (8):2137-2155.

Potvin-Trottier L, Luro S, Paulsson J. 2018. Microfluidics and single-cell microscopy to study stochastic processes in bacteria. Curr Opin Microbiol. 43:186-192.

Wang S, Powers RE, Gold VA, Rapoport TA. 2018. The ER morphology-regulating lunapark protein induces the formation of stacked bilayer discs. Life Sci Alliance. 1(1):e201700014.

Liu Q, Onal P, Datta RR, Rogers JM, Schmidt-Ott U, Bulyk ML, Small S, Thornton JW. 2018. Ancient mechanisms for the evolution of the bicoid homeodomain's function in fly development. Elife. 7. pii: e34594.

Liu N, Hargreaves VV, Zhu Q, Kurland JV, Hong J, Kim W, Sher F, Macias-Trevino C, Rogers JM, Kurita R, Nakamura Y, Yuan GC, Bauer DE, Xu J, Bulyk ML, Orkin SH. 2018. Direct Promoter Repression by BCL11A Controls the Fetal to Adult Hemoglobin Switch. Cell. 173(2):430-442.e17.

Rogers JM, Bulyk ML. 2018. Diversification of transcription factor-DNA interactions and the evolution of gene regulatory networks. Wiley Interdiscip Rev Syst Biol Med. 25:e1423.

Steinhorn B, Sorrentino A, Badole S, Bogdanova Y, Belousov V, Michel T. 2018. Chemogenetic generation of hydrogen peroxide in the heart induces severe cardiac dysfunction. Nat Commun. 9(1):4044.

Lin JR, Izar B, Wang S, Yapp C, Mei S, Shah PM, Santagata S, Sorger PK. 2018. Highly multiplexed immunofluorescence imaging of human tissues and tumors using t-CyCIF and conventional optical microscopes. Elife. 7:e31657.

Jerby-Arnon L, Shah P, Cuoco MS, Rodman C, Su MJ, Melms JC, Leeson R, Kanodia A, Mei S, Lin JR, Wang S, Rabasha B, Liu D, Zhang G, Margolais C, Ashenberg O, Ott PA, Buchbinder EI, Haq R, Hodi FS, Boland GM, Sullivan RJ, Frederick DT, Miao B, Moll T, Flaherty KT, Herlyn M, Jenkins RW, Thummalapalli R, Kowalczyk MS, Cañadas I, Schilling B, Cartwright ANR, Luoma AM, Malu S, Hwu P, Bernatchez C, Forget MA, Barbie DA, Shalek AK, Tirosh I, Sorger PK, Wucherpfennig K, Van Allen EM, Schadendorf D, Johnson BE, Rotem A, Rozenblatt-Rosen O, Garraway LA, Yoon CH, Izar B, Regev A. 2018. A Cancer Cell Program Promotes T Cell Exclusion and Resistance to Checkpoint Blockade. Cell. 175(4):984-997.e24.

Moynihan KD, Holden RL, Mehta NK, Wang C, Karver MR, Dinter J, Liang S, Abraham W, Melo MB, Zhang AQ, Li N, Le Gall S, Pentelute B, Irvine DJ. 2018. Enhancement of peptide vaccine immunogenicity by increasing lymphatic drainage and boosting serum stability. Cancer Immunology Research. 6(9):1025-1038.

Douam F, Ziegler CGK, Hrebikova G, Fant B, Leach R, Parsons L, Wang W, Gaska JM, Winer BY, Heller B, Shalek AK, Ploss A. 2018. Selective expansion of myeloid and NK cells in humanized mice yields human-like vaccine responses. Nat Commun. 9(1):5031.