2017 Biophysics Student Publications

2017 Publications:

Rogers KW, Lord ND, Gagnon JA, Pauli A, Zimmerman S, Aksel DC, Reyon D, Tsai SQ, Joung JK, Schier AF. 2017. Nodal patterning without Lefty inhibitory feedback is functional but fragile. Elife. 6. pii: e28785.

Mariani L, Weinand K, Vedenko A, Barrera LA, Bulyk ML. 2017. Identification of Human Lineage-Specific Transcriptional Coregulators Enabled by a Glossary of Binding Modules and Tunable Genomic Backgrounds. Cell Syst. 5(3):187-201.

Born DA*, Ulrich EC*, Ju KS, Peck SC, van der Donk WA, Drennan CL. 2017. Structural basis for methylphosphonate biosynthesis. Science 358(6368):1336-1339. (*co-1st authors).

Gassler J, Brandão HB, Imakaev M, Flyamer IM, Ladstätter S, Bickmore WA, Peters JM, Mirny LA, Tachibana K. A mechanism of cohesin-dependent loop extrusion organizes zygotic genome architecture. EMBO J. 2017 Dec 15;36(24):3600-3618.

Flyamer IM, Gassler J, Imakaev M, Brandão HB, Ulianov SV, Abdennur N, Razin SV, Mirny LA, Tachibana-Konwalski K. Single-nucleus Hi-C reveals unique chromatin reorganization at oocyte-to-zygote transition. Nature. 2017 Apr 6;544(7648):110-114.

Liu Y, Pan J, Jenni S, Raymond DD, Caradonna T, Do KT, Schmidt AG, Harrison SC, Grigorieff N. 2017.  CryoEM Structure of an Influenza Virus Receptor-Binding Site Antibody-Antigen Interface. J Mol Biol. 429(12):1829-1839. 

Landry MP, Ando H, Chen AY, Cao J, Kottadiel VI, Chio L, Yang D, Dong J, Lu TK, Strano MS. 2017. Single-molecule detection of protein efflux from microorganisms using fluorescent single-walled carbon nanotube sensor arrays. Nat Nanotechnol. 12(4):368-377. 

Seker UO, Chen AY, Citorik RJ, Lu TK. 2017. Synthetic Biogenesis of Bacterial Amyloid Nanomaterials with Tunable Inorganic-Organic Interfaces and Electrical Conductivity. ACS Synth Biol. 6(2):266-275.

Chen KT, Izquierdo-Garcia D, Poynton CB, Chonde DB, Catana C. 2017. On the accuracy and reproducibility of a novel probabilistic atlas-based generation for calculation of head attenuation maps on integrated PET/MR scanners. Eur J Nucl Med Mol Imaging. 44(3):398-407.

Dai M. DNA-PAINT Super-Resolution Imaging for Nucleic Acid Nanostructures. Methods Mol Biol. 2017; 1500:185-202.

Zhan P, Dutta PK, Wang P, Song G, Dai M, Zhao SX, Wang ZG, Yin P, Zhang W, Ding B, Ke Y. Reconfigurable Three-Dimensional Gold Nanorod Plasmonic Nanostructures Organized on DNA Origami Tripod. ACS Nano. 2017 Feb 28;11(2):1172-1179.

Han D, Qi X, Myhrvold C, Wang B, Dai M, Jiang S, Bates M, Liu Y, An B, Zhang F, Yan H, Yin P. Single-stranded DNA and RNA origami. Science. 2017 Dec 15;358(6369):eaao2648.

Emanuel G, Moffitt JR, Zhuang X. 2017. High-throughput, image-based screening of pooled genetic-variant libraries. Nat Methods. 14(12):1159-1162.

Yao Z, Mich JK, Ku S, Menon V, Krostag AR, Martinez RA, Furchtgott L, Mulholland H, Bort S, Fuqua MA, Gregor BW, Hodge RD, Jayabalu A, May RC, Melton S, Nelson AM, Ngo NK, Shapovalova NV, Shehata SI, Smith MW, Tait LJ, Thompson CL, Thomsen ER, Ye C, Glass IA, Kaykas A, Yao S, Phillips JW, Grimley JS, Levi BP, Wang Y, Ramanathan S. 2017. A Single-Cell Roadmap of Lineage Bifurcation in Human ESC Models of Embryonic Brain Development. Cell Stem Cell. 20(1):120-134.

Furchtgott LA, Melton S, Menon V, Ramanathan S. 2017. Discovering sparse transcription factor codes for cell states and state transitions during development. Elife. 6. Pii: e20488.

Jang S, Choubey S, Furchtgott L, Zou LN, Doyle A, Menon V, Loew EB, Krostag AR, Martinez RA, Madisen L, Levi BP, Ramanathan S. 2017. Dynamics of embryonic stem cell differentiation inferred from single-cell transcriptomics show a series of transitions through discrete cell states. Elife. 6. Pii: e20487.

Reagen B, Hernández-Lobato JM, Adolf R, Gelbart M, Whatmough P, Wei GY, Brooks D. 2017. A case for efficient accelerator design space exploration via Bayesian optimization. IEEE/ACM International Symposium on Low Power Electronics and Design (ISLPED). pp. 1-6.

Bendesky A, Kwon YM, Lassance JM, Lewarch CL, Yao S, Peterson BK, He MX, Dulac C, Hoekstra HE. 2017. The genetic basis of parental care evolution in monogamous mice. Nature. 544(7651):434-439.

Johnson CP, Kim IK, Esmaeli B, Amin-Mansour A, Treacy DJ, Carter SL, Hodis E, Wagle N, Seepo S, Yu X, Lane AM, Gragoudas ES, Vazquez F, Nickerson E, Cibulskis K, McKenna A, Gabriel SB, Getz G, Van Allen EM, 't Hoen PAC, Garraway LA, Woodman SE. 2017. Systematic genomic and translational efficiency studies of uveal melanoma. PLoS One. 12(6):e0178189.

DeSantis ME, Cianfrocco MA, Htet ZM, Tran PT, Reck-Peterson SL, Leschziner AE. 2017. Lis1 Has Two Opposing Modes of Regulating Cytoplasmic Dynein. Cell. 170(6):1197-1208.e12. (*co-1st authors).

Redwine WB, DeSantis ME, Hollyer I, Htet ZM, Tran PT, Swanson SK, Florens L, Washburn MP, Reck-Peterson SL. 2017. The human cytoplasmic dynein interactome reveals novel activators of motility. Elife. 6. pii: e28257.   

Cassa CA, Weghorn D, Balick DJ, Jordan DM, Nusinow D, Samocha KE, O'Donnell-Luria A, MacArthur DG, Daly MJ, Beier DR, Sunyaev SR. 2017. Estimating the selective effects of heterozygous protein-truncating variants from human exome data. Nat Genet. 49(5):806-810.

Kalinich M*, Bhan I*, Kwan TT, Miyamoto DT, Javaid S, LiCausi JA, Milner JD, Hong X, Goyal L, Sil S, Choz M, Ho U, Kapur R, Muzikansky A, Zhang H, Weitz DA, Sequist LV, Ryan DP, Chung RT, Zhu AX, Isselbacher KJ, Ting DT, Toner M, Maheswaran S, Haber DA. 2017. An RNA-based signature enables high specificity detection of circulating tumor cells in hepatocellular carcinoma. Proc Natl Acad Sci USA 114(5):1123-1128. (*co-1st authors).

Thrall ES, Kath JE, Chang S, Loparo JJ. Single-molecule imaging reveals multiple pathways for the recruitment of translesion polymerases after DNA damage. Nat Commun. 2017 Dec 18;8(1):2170. doi: 10.1038/s41467-017-02333-2. PMID: 29255195; PMCID: PMC5735139.

Krieger B, Qiao M, Rousso DL, Sanes JR, Meister M. 2017. Four alpha ganglion cell types in mouse retina: Function, structure, and molecular signatures. PLoS One. 12(7):e0180091.

Goodman DB*, Kuznetsov G*, Lajoie MJ, Ahern BW, Napolitano MG, Chen KY, Chen C, Church GM. 2017. Millstone: software for multiplex microbial genome analysis and engineering. Genome Biology, 18(1), 101. (*co-1st authors).

Kuznetsov G*, Goodman DB*, Filsinger GT*, Landon M, Rohland N, Aach J, Lajoie MJ, Church GM 2017. Optimizing complex phenotypes through model-guided multiplex genome engineering. Genome Biology, 18(1), 100. (*co-1st authors).

Lo WC, Uribe-Patarroyo N, Nam AS, Villiger M, Vakoc BJ, Bouma BE. 2017. Laser thermal therapy monitoring using complex differential variance in optical coherence tomography. J Biophotonics. 10(1):84-91.

Lotter WE, Kreiman G, Cox D. 2017. Deep Predictive Coding Networks for Video Prediction and Unsupervised Learning. International Conference on Machine Learning Representations, Toulon, France. (Peer-Reviewed Abstract)

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. (Peer-Reviewed Abstract). (*co-1^st authors).

McFarland CD, Yaglom JA, Wojtkowiak JW, Scott JG, Morse DL, Sherman MY, Mirny LA. 2017. The Damaging Effect of Passenger Mutations on Cancer Progression. Cancer Res. 77(18):4763-4772.

Wachter F, Morgan AM, Godes M, Mourtada R, Bird GH, Walensky LD. 2017. Mechanistic validation of a clinical lead stapled peptide that reactivates p53 by dual HDM2 and HDMX targeting. Oncogene. 36(15):2184-2190.

Nelms B, Dalomba NF, Lencer W. 2017. A targeted RNAi screen identifies factors affecting diverse stages of receptor-mediated transcytosis. J Cell Biol. 216(2):511-525.

Kim YB, Komor AC, Levy JM, Packer MS, Zhao KT, Liu DR. 2017. Increasing the Genome-Targeting Scope and Precision of Base Editing With Engineered Cas9-Cytidine Deaminase Fusions. Nature Biotechnol. 35(4):371-376.

Komor AC, Zhao KT, Packer MS, Gaudelli NM, Waterbury AL, Koblan LW, Kim YB, Badran AH, Liu DR. 2017. Improved Base Excision Repair Inhibition and Bacteriophage Mu Gam Protein Yields C:G-to-T:A Base Editors With Higher Efficiency and Product Purity. Science Advances. 3(8):eaao4774.

Packer MS, Rees HA, Liu DR. 2017. Phage-Assisted Continuous Evolution of Proteases with Altered Substrate Specificity. Nature Communications. 8(1):956.

Gaudelli NM, Komor AC, Rees HA, Packer MS, Badran AH, Bryson, DI, Liu DR. 2017. Programmable Base Editing of A*T to G*C in Genomic DNA Without DNA Cleavage. Nature. 551(7681):464-471.

Powers RE, Gaudet R, Sotomayor M. 2017. A Partial Calcium-Free Linker Confers Flexibility to Inner-Ear Protocadherin-15. Structure. 25(3):482-495.

Powers RE, Wang S, Liu TY, Rapoport TA. 2017. Reconstitution of the tubular endoplasmic reticulum network with purified components. Nature. 543(7644):257-260.

Song D, Rodrigues K, Graham TGW, Loparo JJ. 2017. A network of cis and trans interactions is required for ParB spreading. Nucleic Acids Res 45(12): 7106-7117.

Steinhorn B, Sartoretto JL, Sorrentino A, Romero N, Kalwa H, Abel ED, Michel T. 2017. Insulin-dependent metabolic and inotropic responses in the heart are modulated by hydrogen peroxide from NADPH-oxidase isoforms NOX2 and NOX4. Free Radic Biol Med. 113:16-25.

Tang H, Kreiman G. 2017. Recognition of occluded objects. In: Zhao Q. (eds) Computational and Cognitive Neuroscience of Vision. Cognitive Science and Technology. Springer, Singapore. Pp 41-58.

Weisman CM, Eddy, S.R. 2017. Gene Evolution: Getting Something from Nothing. Curr Biol. 27(13):R661-R663.

Shah AA, Xu G, Rosen A, Hummers LK, Wigley FM, Elledge SJ, Casciola-Rosen L. 2017. Brief Report: Anti-RNPC-3 Antibodies As a Marker of Cancer-Associated Scleroderma. Arthritis Rheumatol. 69(6):1306-1312.

Abadi S, Yan WX, Amar D, Mayrose I. 2017. A machine learning approach for predicting CRISPR-Cas9 cleavage efficiencies and patterns underlying its mechanism of action. PLoS Comput Biol. 13(10): e1005807. 

Yan WX*, Mirzazadeh R*, Garnerone S, Scott D, Schneider MW, Kallas T, Custodio J, Wernersson E, Li Y, Gao L, Federova Y, Zetsche B, Zhang F, Bienko M, Crosetto N. 2017. BLISS is a versatile and quantitative method for genome-wide profiling of DNA double-strand breaks. Nat Commun. 8:15058. (*co-1st authors).

Jain A, Zode G, Kasetti RB, Ran FA, Yan W, Sharma TP, Bugge K, Searby CC, Fingert JH, Zhang F, Clark AF, Sheffield VC. 2017. CRISPR-Cas9–based treatment of myocilin-associated glaucoma. Proc Natl Acad Sci USA. 114(42): 11199–11204. 

Shmakov S, Smargon A, Scott D, Cox D, Pyzocha N, Yan W, Abudayyeh OO, Gootenberg JS, Makarova KS, Wolf YI, Severinov K, Zhang F, Koonin EV.  2017. Diversity and evolution of class 2 CRISPR-Cas systems. Nat Rev Microbiol. 15(3):169-182.

Gao L, Cox DBT, Yan WX, Manteiga JC, Schneider MW, Yamano T, Nishimasu H, Nureki O, Crosetto N, Zhang F. 2017. Engineered Cpf1 variants with altered PAM specificities increase genome targeting range. Nat Biotechnol. 35(8): 789–792.