Student Publications and Alumni

​Integrated Program in Cellular, Molecular, and Biomedical Studies

Selected Recent Publications

2018-2019

  • Blazejewski, T., H.I. Ho, and H.H. Wang. 2019. Synthetic sequence entanglement augments stability and containment of genetic information in cells. Science. 365:595-598.
  • Chowdhury, S., S. Castro, C. Coker, T.E. Hinchliffe, N. Arpaia, and T. Danino. 2019. Programmable bacteria induce durable tumor regression and systemic antitumor immunity. Nat Med. 25:1057-1063.
  • Chramiec, A., and G. Vunjak-Novakovic. 2019. Tissue engineered models of healthy and malignant human bone marrow. Adv Drug Deliv Rev. 140:78-92.
  • Das Sharma, S., Metz, J*, H. Li, B.D. Hobson, N. Hornstein, D. Sulzer, G. Tang, and P.A. Sims. 2019. Widespread Alterations in Translation Elongation in the Brain of Juvenile Fmr1 Knockout Mice. Cell Rep. 26:3313-3322 e3315.
  • Decker, M., J. Leslie, Q. Liu, and L. Ding. 2018. Hepatic thrombopoietin is required for bone marrow hematopoietic stem cell maintenance. Science. 360:106-110.
  • Dieck, C.L., and A. Ferrando. 2019. Genetics and mechanisms of NT5C2-driven chemotherapy resistance in relapsed ALL. Blood. 133:2263-2268.
  • Dieck, C.L., G. Tzoneva, F. Forouhar, Z. Carpenter, A. Ambesi-Impiombato, M. Sanchez-Martin, R. Kirschner-Schwabe, S. Lew, J. Seetharaman, L. Tong, and A.A. Ferrando. 2018. Structure and Mechanisms of NT5C2 Mutations Driving Thiopurine Resistance in Relapsed Lymphoblastic Leukemia. Cancer Cell. 34:136-147 e136.
  • Dionne, G., X. Qiu, M. Rapp, X. Liang, B. Zhao, G. Peng, P.S. Katsamba, G. Ahlsen, R. Rubinstein, C.S. Potter, B. Carragher, B. Honig, U. Muller, and L. Shapiro. 2018. Mechanotransduction by PCDH15 Relies on a Novel cis-Dimeric Architecture. Neuron. 99:480-492 e48.
  • Ebstein, S.Y., I. Yagudayeva*, and N.A. Shneider. 2019. Mutant TDP-43 Causes Early-Stage Dose-Dependent Motor Neuron Degeneration in a TARDBP Knockin Mouse Model of ALS. Cell Rep. 26:364-373 e364.
  • Eckels, E.C., S. Haldar, R. Tapia-Rojo, J.A. Rivas-Pardo, and J.M. Fernandez. 2019. The Mechanical Power of Titin Folding. Cell Rep. 27:1836-1847 e1834.
  • Eckels, E.C., R. Tapia-Rojo, J.A. Rivas-Pardo, and J.M. Fernandez. 2018. The Work of Titin Protein Folding as a Major Driver in Muscle Contraction. Annu Rev Physiol. 80:327-351.
  • Fu, Z., G. Indrisiunaite, S. Kaledhonkar, B. Shah, M. Sun, B. Chen, R.A. Grassucci, M. Ehrenberg, and J. Frank. 2019. The structural basis for release-factor activation during translation termination revealed by time-resolved cryogenic electron microscopy. Nat Commun. 10:2579.
  • Garcia, E.J., J.D. Vevea, and L.A. Pon. 2018. Lipid droplet autophagy during energy mobilization, lipid homeostasis and protein quality control. Front Biosci (Landmark Ed). 23:1552-1563.
  • Groopman, E., D. Goldstein, and A. Gharavi. 2019a. Diagnostic Utility of Exome Sequencing for Kidney Disease. Reply. N Engl J Med. 380:2080-2081.
  • Groopman, E.E., and A.G. Gharavi. 2019. Expanding opportunities and emerging challenges: broadening the scope of genetic testing in nephrology. Kidney Int. 95:743-746.
  • Groopman, E.E., M. Marasa, S. Cameron-Christie, S. Petrovski, V.S. Aggarwal, H. Milo-Rasouly, Y. Li, J. Zhang, J. Nestor, P. Krithivasan, W.Y. Lam, A. Mitrotti, S. Piva, B.H. Kil, D. Chatterjee, R. Reingold, D. Bradbury, M. DiVecchia, H. Snyder, X. Mu, K. Mehl, O. Balderes, D.A. Fasel, C. Weng, J. Radhakrishnan, P. Canetta, G.B. Appel, A.S. Bomback, W. Ahn, N.S. Uy, S. Alam, D.J. Cohen, R.J. Crew, G.K. Dube, M.K. Rao, S. Kamalakaran, B. Copeland, Z. Ren, J. Bridgers, C.D. Malone, C.M. Mebane, N. Dagaonkar, B.C. Fellstrom, C. Haefliger, S. Mohan, S. Sanna-Cherchi, K. Kiryluk, J. Fleckner, R. March, A. Platt, D.B. Goldstein, and A.G. Gharavi. 2019b. Diagnostic Utility of Exome Sequencing for Kidney Disease. N Engl J Med. 380:142-151.
  • Halpin-Healy, T.S., S.E. Klompe, S.H. Sternberg, and I.S. Fernandez. 2019. Structural basis of DNA targeting by a transposon-encoded CRISPR-Cas system. Nature [Epub ahead of print]. 
  • Hill, V.M., R.M. O'Connor, G.B. Sissoko, I.S. Irobunda, S. Leong, J.C. Canman, N. Stavropoulos, and M. Shirasu-Hiza. 2018. A bidirectional relationship between sleep and oxidative stress in Drosophila. PLoS biology. 16:e2005206.
  • Hobson, B.D., and P.A. Sims. 2019. Critical Analysis of Particle Detection Artifacts in Synaptosome Flow Cytometry. eNeuro. 6.
  • Jacko, M., S.M. Weyn-Vanhentenryck, J.W. Smerdon, R. Yan, H. Feng, D.J. Williams, J. Pai, K. Xu, H. Wichterle, and C. Zhang. 2018. Rbfox Splicing Factors Promote Neuronal Maturation and Axon Initial Segment Assembly. Neuron. 97:853-868 e856.
  • Johns, N.I., A.L.C. Gomes, S.S. Yim, A. Yang, T. Blazejewski, C.S. Smillie, M.B. Smith, E.J. Alm, S. Kosuri, and H.H. Wang. 2018. Metagenomic mining of regulatory elements enables programmable species-selective gene expression. Nature methods. 15:323-329.
  • Kratchmarov, R., A.M. Magun, and S.L. Reiner. 2018a. TCF1 expression marks self-renewing human CD8(+) T cells. Blood Adv. 2:1685-1690.
  • Kratchmarov, R., S. Viragova, M.J. Kim, N.J. Rothman, K. Liu, B. Reizis, and S.L. Reiner. 2018b. Metabolic control of cell fate bifurcations in a hematopoietic progenitor population. Immunol Cell Biol.
  • Kumar, B.V., Kratchmarov, R., Miron, M., Carpenter, D., Senda, T., Lerner, H., Friedman, A., Reiner, S.L. and Farber, D.L. (2018) Functional heterogeneity of human tissue resident memory T cells based on dye efflux capacities. JCI Insight. 3: 123568. doi: 10.1172/jci.insight.123568.
  • Ji, B.W., R.U. Sheth*, P.D. Dixit, Y. Huang, A. Kaufman, H.H. Wang, and D. Vitkup. 2019. Quantifying spatiotemporal variability and noise in absolute microbiota abundances using replicate sampling. Nat Methods. 16:731-736.
  • Kaledhonkar, S., Z. Fu*, K. Caban, W. Li, B. Chen, M. Sun, R.L. Gonzalez, Jr., and J. Frank. 2019. Late steps in bacterial translation initiation visualized using time-resolved cryo-EM. Nature. 570:400-404.
  • Klompe, S.E., P.L.H. Vo, T.S. Halpin-Healy, and S.H. Sternberg. 2019. Transposon-encoded CRISPR-Cas systems direct RNA-guided DNA integration. Nature. 571:219-225.
  • Kumar, B.V., T.J. Connors, and D.L. Farber. 2018. Human T Cell Development, Localization, and Function throughout Life. Immunity. 48:202-213.
  • Lee, H., S. Bao, Y. Qian, S. Geula, J. Leslie, C. Zhang, J.H. Hanna, and L. Ding. 2019. Stage-specific requirement for Mettl3-dependent m(6)A mRNA methylation during haematopoietic stem cell differentiation. Nat Cell Biol. 21:700-709.
  • Levitin, H.M., J. Yuan, and P.A. Sims. 2018. Single-Cell Transcriptomic Analysis of Tumor Heterogeneity. Trends Cancer. 4:264-268.
  • Levitin, H.M., J. Yuan, Y.L. Cheng, F.J. Ruiz, E.C. Bush, J.N. Bruce, P. Canoll, A. Iavarone, A. Lasorella, D.M. Blei, and P.A. Sims. 2019. De novo gene signature identification from single-cell RNA-seq with hierarchical Poisson factorization. Mol Syst Biol. 15:e8557.
  • Liu, B., B.W. Lee, K. Nakanishi, A. Villasante, R. Williamson, J. Metz, J. Kim, M. Kanai, L. Bi, K. Brown, G. Di Paolo, S. Homma, P.A. Sims, V.K. Topkara, and G. Vunjak-Novakovic. 2018. Cardiac recovery via extended cell-free delivery of extracellular vesicles secreted by cardiomyocytes derived from induced pluripotent stem cells. Nat Biomed Eng. 2:293-303.
  • Liu, Q., D.C. Georgieva*, D. Egli, and K. Wang. 2019. NanoMod: a computational tool to detect DNA modifications using Nanopore long-read sequencing data. BMC Genomics. 20:78.
  • Mathur, D., E. Stratikopoulos, S. Ozturk, N. Steinbach, S. Pegno, S. Schoenfeld, R. Yong, V.V. Murty, J.M. Asara, L.C. Cantley, and R. Parsons. 2017. PTEN Regulates Glutamine Flux to Pyrimidine Synthesis and Sensitivity to Dihydroorotate Dehydrogenase Inhibition. Cancer Discov. 7:380-390.
  • McGoldrick, L.L., A.K. Singh, K. Saotome, M.V. Yelshanskaya, E.C. Twomey, R.A. Grassucci, and A.I. Sobolevsky. 2018. Opening of the human epithelial calcium channel TRPV6. Nature. 553:233-237.
  • McGoldrick, L.L., A.K. Singh, L. Demirkhanyan, T.Y. Lin, R.G. Casner, E. Zakharian, and A.I. Sobolevsky. 2019. Structure of the thermo-sensitive TRP channel TRP1 from the alga Chlamydomonas reinhardtii. Nat Commun. 10:4180.
  • Park, J., and H.H. Wang. 2018. Systematic and synthetic approaches to rewire regulatory networks. Curr Opin Syst Biol. 8:90-96.
  • Sheth, R.U., M. Li, W. Jiang, P.A. Sims, K.W. Leong, and H.H. Wang. 2019. Spatial metagenomic characterization of microbial biogeography in the gut. Nat Biotechnol. 37:877-883.
  • Sheth, R.U., and H.H. Wang. 2018. DNA-based memory devices for recording cellular events. Nat Rev Genet. 19:718-732.
  • Siegmund, S.E., R. Grassucci, S.D. Carter, E. Barca, Z.J. Farino, M. Juanola-Falgarona, P. Zhang, K. Tanji, M. Hirano, E.A. Schon, J. Frank, and Z. Freyberg. 2018. Three-Dimensional Analysis of Mitochondrial Crista Ultrastructure in a Patient with Leigh Syndrome by In Situ Cryoelectron Tomography. iScience. 6:83-91.
  • Singer, R.A., L. Arnes, Yi, Cui, J. Wang, Y. Gao, M.A. Guney, K.E. Burnum-Johnsom, R. Rabadan, C. Ansong, G. Orr, and L. Sussel. 2019. The long noncoding RNA paupar modulates PAX6 regulatory activities to promote alpha cell development and function. Cell Metabolism. Doi.org/10.1016/j.cmet.2019.09.013. 
  • Singh, A.K., L.L. McGoldrick*, K. Saotome, and A.I. Sobolevsky. 2018a. X-ray crystallography of TRP channels. Channels (Austin). 12:137-152.
  • Singh, A.K., L.L. McGoldrick*, and A.I. Sobolevsky. 2018b. Structure and gating mechanism of the transient receptor potential channel TRPV3. Nat Struct Mol Biol. 25:805-813.
  • Singh, A.K., L.L. McGoldrick*, and A.I. Sobolevsky. 2019. Expression, Purification, and Crystallization of the Transient Receptor Potential Channel TRPV6. Methods Mol Biol. 1987:23-37.
  • Singh, A.K., L.L. McGoldrick*, E.C. Twomey, and A.I. Sobolevsky. 2018c. Mechanism of calmodulin inactivation of the calcium-selective TRP channel TRPV6. Sci Adv. 4:eaau6088.
  • Steinbach, N., D. Hasson, D. Mathur, E.E. Stratikopoulos, R. Sachidanandam, E. Bernstein, and R.E. Parsons. 2019. PTEN interacts with the transcription machinery on chromatin and regulates RNA polymerase II-mediated transcription. Nucleic Acids Res. 47:5573-5586.
  • Steinfeld, J.B., O. Belan, Y. Kwon, T. Terakawa, A. Al-Zain, M.J. Smith, J.B. Crickard, Z. Qi, W. Zhao, R. Rothstein, L.S. Symington, P. Sung, S.J. Boulton, and E.C. Greene. 2019. Defining the influence of Rad51 and Dmc1 lineage-specific amino acids on genetic recombination. Genes Dev.
  • Szabo, P.A.‡, Levitin, H.M.‡, Miron, M., Snyder, M.E., Senda, T., Yuan, J., Cheng, Y.L., Bush, E.C., Dogra, P., Thapa, P., Farber, D.L.*, and Sims, P.A.* (2019) Single-cell transcriptomics of human T cells reveals tissue and activation signatures in health and disease. Nat. Comm. In Press. *co-senior author, ‡co-first author
  • Szymanski, J.R., and R. Yuste. 2019. Mapping the Whole-Body Muscle Activity of Hydra vulgaris. Curr Biol. 29:1807-1817 e1803.
  • Tapia-Rojo, R., E.C. Eckels*, and J.M. Fernandez. 2019. Ephemeral states in protein folding under force captured with a magnetic tweezers design. Proc Natl Acad Sci USA. 116:7873-7878.
  • Tenen, C.C., and I. Greenwald. 2019. Cell Non-autonomous Function of daf-18/PTEN in the Somatic Gonad Coordinates Somatic Gonad and Germline Development in C. elegans Dauer Larvae. Curr Biol. 29:1064-1072 e1068.
  • Thomas, D.G., A.C. Doran, P. Fotakis, M. Westerterp, P. Antonson, H. Jiang, X.C. Jiang, J.A. Gustafsson, I. Tabas, and A.R. Tall. 2018. LXR Suppresses Inflammatory Gene Expression and Neutrophil Migration through cis-Repression and Cholesterol Efflux. Cell Rep. 25:3774-3785 e3774.
  • Van Alstyne, M., C.M. Simon, S.P. Sardi, L.S. Shihabuddin, G.Z. Mentis, and L. Pellizzoni. 2018. Dysregulation of Mdm2 and Mdm4 alternative splicing underlies motor neuron death in spinal muscular atrophy. Genes Dev. 32:1045-1059.
  • Wang, E.C.E., Z. Dai, and A.M. Christiano. 2018a. Novel therapies for alopecia areata: The era of rational drug development. The Journal of allergy and clinical immunology. 141:499-504.
  • Wang, E.C.E., Z. Dai, A.W. Ferrante, C.G. Drake, and A.M. Christiano. 2019. A Subset of TREM2(+) Dermal Macrophages Secretes Oncostatin M to Maintain Hair Follicle Stem Cell Quiescence and Inhibit Hair Growth. Cell Stem Cell. 24:654-669 e656.
  • Weyn-Vanhentenryck, S.M., H. Feng, D. Ustianenko, R. Duffie, Q. Yan, M. Jacko, J.C. Martinez, M. Goodwin, X. Zhang, U. Hengst, S. Lomvardas, M.S. Swanson, and C. Zhang. 2018. Precise temporal regulation of alternative splicing during neural development. Nature communications. 9:2189.
  • Yen, B., K.T. Fortson, N.J. Rothman, N. Arpaia, and S.L. Reiner. 2018. Clonal Bifurcation of Foxp3 Expression Visualized in Thymocytes and T Cells. Immunohorizons. 2:119-128.
  • Zhao, J., A.X. Chen*, R.D. Gartrell, A.M. Silverman, L. Aparicio, T. Chu, D. Bordbar, D. Shan, J. Samanamud, A. Mahajan, I. Filip, R. Orenbuch, M. Goetz, J.T. Yamaguchi, M. Cloney, C. Horbinski, R.V. Lukas, J. Raizer, A.I. Rae, J. Yuan, P. Canoll, J.N. Bruce, Y.M. Saenger, P. Sims, F.M. Iwamoto, A.M. Sonabend, and R. Rabadan. 2019. Immune and genomic correlates of response to anti-PD-1 immunotherapy in glioblastoma. Nat Med. 25:462-469.

2017-2018

  • Baker, Z., M. Schumer, Y. Haba, L. Bashkirova, C. Holland, G.G. Rosenthal, and M. Przeworski. 2017. Repeated losses of PRDM9-directed recombination despite the conservation of PRDM9 across vertebrates. Elife. 6.
  • Decker, M., J. Leslie, Q. Liu, and L. Ding. 2018. Hepatic thrombopoietin is required for bone marrow hematopoietic stem cell maintenance. Science. 360:106-110.
  • Decker, M., L. Martinez-Morentin, G. Wang, Y. Lee, Q. Liu, J. Leslie, and L. Ding. 2017. Leptin-receptor-expressing bone marrow stromal cells are myofibroblasts in primary myelofibrosis. Nat Cell Biol. 19:677-688.
  • Dieck, C.L., G. Tzoneva, F. Forouhar, Z. Carpenter, A. Ambesi-Impiombato, M. Sanchez-Martin, R. Kirschner-Schwabe, S. Lew, J. Seetharaman, L. Tong, and A.A. Ferrando. 2018. Structure and Mechanisms of NT5C2 Mutations Driving Thiopurine Resistance in Relapsed Lymphoblastic Leukemia. Cancer Cell. 34:136-147 e136.
  • Dionne, G., X. Qiu, M. Rapp, X. Liang, B. Zhao, G. Peng, P.S. Katsamba, G. Ahlsen, R. Rubinstein, C.S. Potter, B. Carragher, B. Honig, U. Muller, and L. Shapiro. 2018. Mechanotransduction by PCDH15 Relies on a Novel cis-Dimeric Architecture. Neuron. 99:480-492 e485.
  • Echelman, D.J., A.Q. Lee, and J.M. Fernandez. 2017. Mechanical forces regulate the reactivity of a thioester bond in a bacterial adhesin. The Journal of Biological Chemistry. 292:8988-8997.
  • Eckels, E.C., R. Tapia-Rojo, J.A. Rivas-Pardo, and J.M. Fernandez. 2018. The Work of Titin Protein Folding as a Major Driver in Muscle Contraction. Annu Rev Physiol. 80:327-351.
  • Hill, V.M., R.M. O'Connor, G.B. Sissoko, I.S. Irobunda, S. Leong, J.C. Canman, N. Stavropoulos, and M. Shirasu-Hiza. 2018. A bidirectional relationship between sleep and oxidative stress in Drosophila. PLoS Biology. 16:e2005206.
  • Jacko, M., S.M. Weyn-Vanhentenryck, J.W. Smerdon, R. Yan, H. Feng, D.J. Williams, J. Pai, K. Xu, H. Wichterle, and C. Zhang. 2018. Rbfox Splicing Factors Promote Neuronal Maturation and Axon Initial Segment Assembly. Neuron. 97:853-868 e856.
  • Johns, N.I., A.L.C. Gomes, S.S. Yim, A. Yang, T. Blazejewski, C.S. Smillie, M.B. Smith, E.J. Alm, S. Kosuri, and H.H. Wang. 2018. Metagenomic mining of regulatory elements enables programmable species-selective gene expression. Nature Methods. 15:323-329.
  • Kratchmarov, R., A.M. Magun, and S.L. Reiner. 2018a. TCF1 expression marks self-renewing human CD8(+) T cells. Blood Adv. 2:1685-1690.
  • Kratchmarov, R., S.A. Nish, W.W. Lin, W.C. Adams, Y.H. Chen, B. Yen, N.J. Rothman, U. Klein, and S.L. Reiner. 2017. IRF4 Couples Anabolic Metabolism to Th1 Cell Fate Determination. Immunohorizons. 1:156-161.
  • Kratchmarov, R., S. Viragova, M.J. Kim, N.J. Rothman, K. Liu, B. Reizis, and S.L. Reiner. 2018b. Metabolic control of cell fate bifurcations in a hematopoietic progenitor population. Immunol Cell Biol.
  • Kribelbauer, J.F., O. Laptenko, S. Chen, G.D. Martini, W.A. Freed-Pastor, C. Prives, R.S. Mann, and H.J. Bussemaker. 2017. Quantitative Analysis of the DNA Methylation Sensitivity of Transcription Factor Complexes. Cell Reports. 19:2383-2395.
  • Kumar, B.V., T.J. Connors, and D.L. Farber. 2018. Human T Cell Development, Localization, and Function throughout Life. Immunity. 48:202-213.
  • Kumar, B.V., W. Ma, M. Miron, T. Granot, R.S. Guyer, D.J. Carpenter, T. Senda, X. Sun, S.H. Ho, H. Lerner, A.L. Friedman, Y. Shen, and D.L. Farber. 2017. Human Tissue-Resident Memory T Cells Are Defined by Core Transcriptional and Functional Signatures in Lymphoid and Mucosal Sites. Cell Reports. 20:2921-2934.
  • Levitin, H.M., J. Yuan, and P.A. Sims. 2018. Single-Cell Transcriptomic Analysis of Tumor Heterogeneity. Trends Cancer. 4:264-268.
  • Ma, C.J., J.B. Steinfeld, and E.C. Greene. 2017. Single-Stranded DNA Curtains for Studying Homologous Recombination. Methods Enzymol. 582:193-219.
  • Madubata, C.J., A. Roshan-Ghias, T. Chu, S. Resnick, J. Zhao, L. Arnes, J. Wang, and R. Rabadan. 2017. Identification of potentially oncogenic alterations from tumor-only samples reveals Fanconi anemia pathway mutations in bladder carcinomas. NPJ Genom Med. 2:29.
  • Mathur, D., E. Stratikopoulos, S. Ozturk, N. Steinbach, S. Pegno, S. Schoenfeld, R. Yong, V.V. Murty, J.M. Asara, L.C. Cantley, and R. Parsons. 2017. PTEN Regulates Glutamine Flux to Pyrimidine Synthesis and Sensitivity to Dihydroorotate Dehydrogenase Inhibition. Cancer Discovery. 7:380-390.
  • McGoldrick, L.L., A.K. Singh, K. Saotome, M.V. Yelshanskaya, E.C. Twomey, R.A. Grassucci, and A.I. Sobolevsky. 2018. Opening of the human epithelial calcium channel TRPV6. Nature. 553:233-237.
  • Mountoufaris, G., W.V. Chen, Y. Hirabayashi, S. O'Keeffe, M. Chevee, C.L. Nwakeze, F. Polleux, and T. Maniatis. 2017. Multicluster Pcdh diversity is required for mouse olfactory neural circuit assembly. Science. 356:411-414.
  • O'Connor, R.M., E.F. Stone, C.R. Wayne, E.V. Marcinkevicius, M. Ulgherait, R. Delventhal, M.M. Pantalia, V.M. Hill, C.G. Zhou, S. McAllister, A. Chen, J.S. Ziegenfuss, W.B. Grueber, J.C. Canman, and M.M. Shirasu-Hiza. 2017. A Drosophila model of Fragile X syndrome exhibits defects in phagocytosis by innate immune cells. The Journal of Cell Biology. 216:595-605.
  • Schrank, B.R., T. Aparicio, Y. Li, W. Chang, B.T. Chait, G.G. Gundersen, M.E. Gottesman, and J. Gautier. 2018. Nuclear ARP2/3 drives DNA break clustering for homology-directed repair. Nature. 559:61-66.
  • Sheth, R.U., S.S. Yim, F.L. Wu, and H.H. Wang. 2017. Multiplex recording of cellular events over time on CRISPR biological tape. Science. 358:1457-1461.
  • Siegmund, S.E., H. Yang, R. Sharma, M. Javors, O. Skinner, V. Mootha, M. Hirano, and E.A. Schon. 2017. Low-dose rapamycin extends lifespan in a mouse model of mtDNA depletion syndrome. Human Molecular Genetics. 26:4588-4605.
  • Singer, R.A., and L. Sussel. 2018. Islet Long Noncoding RNAs: A Playbook for Discovery and Characterization. Diabetes. 67:1461-1470.
  • Tan, Y.Z., P.R. Baldwin, J.H. Davis, J.R. Williamson, C.S. Potter, B. Carragher, and D. Lyumkis. 2017. Addressing preferred specimen orientation in single-particle cryo-EM through tilting. Nature Methods. 14:793-796.
  • Twomey, E.C., and A.I. Sobolevsky. 2018. Structural Mechanisms of Gating in Ionotropic Glutamate Receptors. Biochemistry. 57:267-276.
  • Twomey, E.C., M.V. Yelshanskaya, A.A. Vassilevski, and A.I. Sobolevsky. 2018. Mechanisms of Channel Block in Calcium-Permeable AMPA Receptors. Neuron. 99:956-968 e954.
  • Tzoneva, G., C.L. Dieck, K. Oshima, A. Ambesi-Impiombato, M. Sanchez-Martin, C.J. Madubata, H. Khiabanian, J. Yu, E. Waanders, I. Iacobucci, M.L. Sulis, M. Kato, K. Koh, M. Paganin, G. Basso, J.M. Gastier-Foster, M.L. Loh, R. Kirschner-Schwabe, C.G. Mullighan, R. Rabadan, and A.A. Ferrando. 2018. Clonal evolution mechanisms in NT5C2 mutant-relapsed acute lymphoblastic leukaemia. Nature. 553:511-514.
  • Van Alstyne, M., C.M. Simon, S.P. Sardi, L.S. Shihabuddin, G.Z. Mentis, and L. Pellizzoni. 2018. Dysregulation of Mdm2 and Mdm4 alternative splicing underlies motor neuron death in spinal muscular atrophy. Genes Dev. 32:1045-1059.
  • Wang, E.C., Z. Dai, and A.M. Christiano. 2018a. Novel therapies for alopecia areata: The era of rational drug development. The Journal of Allergy and Clinical Immunology. 141:499-504.
  • Wang, E.H., B.N. Sallee, C.I. Tejeda, and A.M. Christiano. 2018b. JAK Inhibitors for Treatment of Alopecia Areata. The Journal of Investigative Dermatology. 138:1911-1916.
  • Wang, G.Z., and S.P. Goff. 2017. Transcriptional Silencing of Moloney Murine Leukemia Virus in Human Embryonic Carcinoma Cells. J Virol. 91.
  • Weyn-Vanhentenryck, S.M., H. Feng, D. Ustianenko, R. Duffie, Q. Yan, M. Jacko, J.C. Martinez, M. Goodwin, X. Zhang, U. Hengst, S. Lomvardas, M.S. Swanson, and C. Zhang. 2018. Precise temporal regulation of alternative splicing during neural development. Nature Communications. 9:2189.
  • Wynne, C.L., and R.B. Vallee. 2018. Cdk1 phosphorylation of the dynein adapter Nde1 controls cargo binding from G2 to anaphase. J Cell Biol. 212:3019-3029. 
  • Yen, B., K.T. Fortson, N.J. Rothman, N. Arpaia, and S.L. Reiner. 2018. Clonal Bifurcation of Foxp3 Expression Visualized in Thymocytes and T Cells. Immunohorizons. 2:119-128.

Graduate Program Alumni

Defense
 

Name
 

Current Position
 

Mentor
 

2018

Eberle-Singh, Jaime

Medical Student, Sidney Kimmel Medical College at Thomas Jefferson University

Kenneth Olive

2018

Kribelbauer, Judith

Post-Doctoral Scientist, Columbia University Irving Medical Center

Harmen Bussemaker & Richard Mann

2018

Hill, Vanessa

Biology Teacher at Saddle River Day School, New York

Mimi Shirasu-Hiza

2018

Ladewig, Erik

Post-Doctoral Sceintist, Memorial Sloan Kettering Cancer Center

Raul Rabadan

2018

Lee, Annie

Medical Associate at the Scienomics Group, Stamford, CT

Frank Polleux

2018

Mahadevia, Darshini

Associate Consultant at McKinsey & Company, NYC

Mark Ansorge

2018

Szymanski, John

Post-Doctoral Scientist, Columbia University Irving Medical Center

Rafael Yuste

2018

Twomey, Edward

Post-Doctoral Scientist, Harvard Medical School

Alexander Sobolevsky & Joachim Frank

2017

Avrutsky, Maria

Post-Doctoral Scientist, Columbia University Irving Medical Center

Carol Troy

2017

Broyde, Joshua

Research Statistician/Digital Innovator, Roivant Sciences, NY

Barry Honig

2017

Chen, Jun Kui

Data Analyst/Big Data Engineer Fellow, Zero One Consulting, LLC

Donna Farber

2017

Closser, Michael

Post-Doctoral Scientist, Columbia University Irving Medical Center

Hynek Wichterle

2017

Fong, Wendy

Post-Doctoral Scientist, Stanford University

Ai Yamamoto

2017

Jacunski, Alexandra

Consultant, the Boston Consulting Group (BCG)

Nickalas Tatonetti

2017

Palmer, Cameron

IRTA Postdoctoral Fellow, Laboratory of Cellular & Development Biology, NIDDK/NIH

Itsik Pe'er

2017

Steinbach, Nicole

Post-Doctoral Scientist, Mt. Sinai Icahn School of Medicine

Ramon Parsons

2017

Walker, Chandler

Post-Doctoral Scientist, Astra Zeneca

Ulrich Hengst

2017

Wang, Etienne

Consultant in Dermatology, National Skin Center, Singapore

Angela Christiano

2017

Weyn, Sebastien

Bioinformatics Scientist, Stoke Therapeutics, Boston

Chaolin Zhang

2017

Zhu, Ruijun

Post-Doctoral Scientis, UCSF

Gregg Gundersen

2016

Allen, Victoria

Medical Technologist, Catalyst Lab, Florida

Mimi Shirasu-Hiza

2016

Churchill, Michael

Senior Scientist, SEngine Precision Medicine

Siddhartha Mukherjee

2016

Wynne-Lazar, Caitlin

Currently on maternity leave

Richard Vallee

2016

Liu, Chenshu

Post-Doctoral Scientist, UC Berkeley

Yinghui Mao

2016

Marshall, Kara

Post-Doctoral Scientist, UCSD

Ellen Lumpkin

2016

Mathur, Deepti

Post-Doctoral Scientist, Memorial Sloan Kettering Cancer Center

Ramon Parsons

2016

Mountoufaris, George

Post-Doctoral Scientist, CIT

Tom Maniatis

2016

Taveras, Carmen

Post-Doctoral Scientist, Australia

Yinghui Mao

2016

Xie, Angela (Yaying)

Post-Doctoral Scientist, AmGen

Rando Allikmets

2015

DeLeo, Annina

Post-Doctoral Scientist, Boston University Medical School

Fiona Doetsch

2015

Gordon, Patricia

Research Associate, MRC, King's College, London

Oliver Hobert

2015

Jilishitz, Irina

Post-Doctoral Scientist, Cornell University Medical School

Jan Kitajewski

2015

Lau, Colleen

Post-Doctoral Scientist, Memorial Sloan Kettering Cancer Center

Boris Reizis

2015

Leclerc, Kevin

Post-Doctoral Scientist, New York University

Frank Costantini

2015

Nader, Guilherme

Post-Doctoral Scientist, Marie Curie Institute, Paris

Gregg Gundersen

2015

Tisdale, Sara

Post-Doctoral Scientist, Memorial Sloan Kettering Cancer Center

Livio Pellizzoni

2015

Zhou, Zhou

Software Engineer, Google

Fred Chang

2014

Alessi-Wolken, Dana

Post-Doctoral Scientist, Regeneron

Liza Pon

2014

Driver, Ian

Scientist, AmGen

Ben Ohlstein

2014

Miller, Edward

Associate Principal Scientist, Schroedinger

Richar Friesner

2014

Seeley, John

Research Administration Fellow, Columbia University Irving Medical Center

Sankar Ghosh

2014

Torres, Ciara

Adjunct Assistant Professor, Psychology, Columbia University

David Sulzer

2013

Amir, El-ad

CEO and Co-Founder, Astrolabe Diagnostics, New York

Dana Pe'er

2013

Bylund, Joseph

Data Scientist, Moat

Richard Friesner

2013

Goss, Lindsie

Senior Technology Manager, Fred Hutchison Cancer Center

Jonathan Dworkin

2013

Hopkins, Ben

Post-Doctoral Scientist, Cornell University Medical School

Ramon Parsons

2013

Kofler, Natalie

Founder, Editing Nature, Yale University

Jan Kitajewski

2013

Lei, Ya-Ting

Senior Market Development Manager, Illumina, Singapore

Steven Siegelbaum

2013

Palmer, Colin

Post-Doctoral Scientist, Harvard Medical School

Boris Reizis

2013

Plata, German

Associate Research Scientist, Columbia University Irving Medical Center

Dennis Vitkup

2013

Stafford, Kate

Senior Scientist, Atomwise, San Francisco

Arthur Palmer

2012

Bastien, Jason

Clinical Laboratory Technologist, Mt. Sinai Health System

Gilbert Di Paolo

2012

Bhansali, Punita

Assistant Professor, CUNY Queensborough College

Carol Mason

2012

Gupta, Amithaba

Scientific Communications Coordinator, Fred Hutchison Cancer Center

Rodney Rothstein

2012

Hsu, Pei-Ken

Scientist, Synthego Cororation, San Francisco

Joseph Gogos

2012

Ostten, Jeremiah

Research Scientist II, Vertex Pharmaceuticals, San Diego

Rober Kass

2012

Scanfeld, Dan

Software Engineer, Google

David Fidock

2012

Siddiqi, Sara

Director, New Product Planning, Jazz Pharmaceuticals

Igor Matushansky

2012

Ziskind, Avi

Computer Scientist, SRI International

Kenneth Miller

2011

Englander, Michael

Senior Manager, regeneron Pharmaceuticals

Virginia Cornish

2011

Jabado, Omar

Senior Research Investigator, Bristol-Myers-Squibb

Ian Lipkin

2011

Lefort, Roger

Assistant Professor, Columbia University Irving Medical Center

Michael Shelanski

2011

Mandelbaum, Jonathan

Principal, Accelerator Corporation

Riccardo Dalla-Favera

2011

McKellar, Heather

Senior Manager of Education and Outreach, NYU Langone

Joseph Gogos

2011

Orozco, Ian

Post-Doctoral Scientist, Max Delbrueck Center Molecular Medicine

Ottavio Arancio

2011

Ravussin, Yann

Post-Doctoral Scientist, Columbia University Irving Medical Center

Rudolph Leibel

2011

Scobie, Kimberly

Scientific Associate, Simons Foundation

Rene Hen

2011

Tung, Jennifer

Senior Cell Biologist, Finless Foods, Oakland

Jan Kitajewski

2010

Basu, Roshni

Senior Analyst, Inthought Research LLC, Houston

Fred Chang

2010

Chang, Belle

Staff Scientist II, Yumanity Therapeutics

Gilbert Di Paolo

2010

Dufraine, Joseph

Director of R&D, Biophi, LIC, Washington, DC

Jan Kitajewski

2010

Luca, Edlira

Post-Doctoral Scientis, University of Zurich

Lorna Role

2010

Tepper, Ron

Deceased

Harmen Bussemaker

2009

Colonna, Lucrecia

Instructor, University of Washington

Raphael Clynes

2009

Flowers, Eileen

Licensing Manager, Memorial Sloan Kettering Cancer Center

Oliver Hobert

2009

Halasz, Gabor

Staff Scientist, Regeneron Pharmaceuticals

Harmen Bussemaker

2009

Kalinovsky, Anna

Assistant Research Scientist, Indiana University

Peter Scheiffele

2009

Kim, Connie

Principal, Prescient Healthcare

William Dauer

2009

Reeves, Claire Vech

Independent Editor & Consultant, Bioscience

Jan Kitajewski

2009

Neisa, Roberto

Anesthesiologist, Rochester, NY

Yinghui Mao

2009

Wrzeszczynski, Kaz

Assistant Director, Clinical Oncology Informatics, NY Genome Center

Burkhard Rost

2009

Yonetani, Ann

Adjunct Professor, The New School

Fred Chang

2008

Boysen, Jacob

Staff Scientist, Regeneron Pharmaceutical

Aaron Mitchell

2008

Fung, Cindy

Director, Medical Communications, Wave Life Science, Cambridge

Lorraine Symington

2008

Galan, Jose

Managing Director, ClearView Healthcare Partners, NY

Boris Reizis

2008

Harel, Sivan

Associate Manager, Regeneron Pharmaceuticals

Boris Reizis

2008

Kruse, Jan-Philip

Alliance Director, Cardiovascular Research Hub, Bayer

Wei Gu

2008

Lewandowski, Nicole

MSL Associate Director, US Clinical Development & Medical Affairs, Novartis

Scott Small

2008

Peng, Wayne

Medical Communications Lead, Bristol-Myers-Squibb

Richard Mann

2008

Posy, Soshana

Senior Research Investigator, Bristol-Myers-Squibb

Barry Honig

2008

Shafer, Beth

Director, Global Business Development and Licensing, Novartis

Jane Dodd

2008

Tang, Chris

Pricipal Data Scientist, Bombfell

Barry Honig

2008

Tsai, Jin-Wu

Associate Professor, National Taiwan University

Richard Vallee

2007

Desouza, Nikhil

Key Account Director, Komodo Health, New York

Andrew Marks

2007

Ho, Chu Kwen (Ron)

Director of STEM, Weymouth Public Schools

Lorraine Symington

2007

Lieberman, Michael

Senior VP Medical Strategy Director, Area 23

Lorna Role

2007

McKay, Daniel

Assistant Professor, University of North Carolina, Chapel Hill

Richard Mann

2007

Okada, Hirokazu

Senior Scientist, ETH Zurich

Tae-Wan Kim

2007

Padte, Neil

Director of Product Development, Aaron Diamond AIDS Research Center

Fred Chang

2007

Suwwan, Karim

Research Analyst and Portfolio Manager, Fidelity Investments

Howard Shuman

2006

Assee, Andrew

Software Developer, Intersystems

Ning Qian

2006

Bergtold, Amy

Looking for position, currently raising her kids

Raphael Clynes

2006

Chen, Albert

Assistant Professor, Nanyang Technology University

Thomas Jessell

2006

Eng, Christina

Senior Scientist, Pfizer Inc.

Gregg Gundersen

2006

Hamill, Stephanie

Associate Research Scientist, Yale University

Anna Pyle

2006

Hancock, Melissa

Engineer, Active Learning Labs, Harvard SEAS

Lorna Role

2006

Hodakoski, Cindy

Post-Doctoral Scientist, Cornell Unviersity Medical Center

Ramon Parsons

2005

Auerbach, Marcy

Senior Research Associate, Genentech, San Francisco

Ila Singh

2005

DeSouza, Katia

Medical Communication Leader, Novartis

Brett Lauring

2005

Greenwood, Jessica

Principal Scientific Officer, Francis Crick Institute, London

Jean Gautier

2005

Kawate, Toshimitsu

Assistant Professor, Cornell University

J. Eric Gouaux

2005

Langston, Lance

Research Associate, Rockefeller University, New York

Lorraine Symington

2005

Leung, Juliana

Director, Strategic Alliance at the Broad Institute

Stephen Goff

2005

Limnander, Andre

Staff Scientist, Regeneron Pharmaceuticals, Tarrytown, NY

Paul Rothman

2005

Phan, Ryan

Associate Professor, VA Greater Los Angeles

Riccardo Dalla-Favera

2005

Saxe, Michael

Senior Investigator II/Head of in vivo Pharmacology, Novartis

Rene Hen

2005

Shendelman, Shoshana

Chief Executive Officer, Applied Therapeutic, Inc. NY

Asa Abeliovich

2005

Stallings, Christina

Assistant Professor of Microbiology, Washington University School of Medicine

Saul Silverstein

2005

Yoo, Andrew

Assistant Professor of Developmental Biology, Washington University St. Louis

Iva Greenwald

2005

Zimmerman, Sabina

Regulatory Affairs, Genentech, San Francisco

Fred Chang

2004

Bruno, Vincent

Assistant Professor, University of Maryland School of Medicine

Aaron Mitchell

2004

Brutsaert, Siska

Dean of Studies, Bard High School Early College

Christian Schindler

2004

Chen, Ning

Diagnostic Product Development Scientist, Nanostring Technologies, Inc. Seattle

Iva Greenwald

2004

Gurer, Cagan

Associate Director, Regeneron Pharmaceuticals, Tarrytown, NY

Jeremy Luban

2004

Kukekov, Nikolay

Healthcare Investment Banking at Highline Research Advisors, New York

Lloyd Greene

2004

O'Donnell, Sean

Principal at Ballast IP Capital Group LLC

Richard Axel

2004

Rohani, Christy

Medical Education Consultant, Geneva, Switzerland

Richard Axel

2004

Schechter, David

Associate Professor of Biochemistry, Albert Einstein College of Medicine

Jean Gautier

2004

Schwartz, Jennifer

Director at Profectus BioScineces, Inc. Baltimore

Saul Silverstein

2004

Shakya, Reena

Research Scientist, the Ohio State University

Frank Costantini

2004

Siddique, Azeems

Staff Scientist, Scripps Research Institute and iGenomX Inc.

David Figurski

2004

Siggers, Keri

Regulatory and Development Team, Halloran Consulting Group

Arthur Palmer

2004

Trott, Oleg

Staff Scientist in the Molecular Graphics Lab, Scripps Research Institute 

Arthur Palmer

2004

Vyas, Valmik

Research Scientist, Whitehead Institute for Biomedical Research, MIT

Marian Carlson

2004

Xu, Wenjie

Technical Service Scientist, NanoString Technologies, Inc. Seattle

Aaron Mitchell

2004

Ying, Carol

Associate Research Scientist, Columbia University, Currently on maternity leave

Jean Gautier

2003

Adler, Naiche

Research Scientist/Lab Director, University of Illinois at Chicago

Virginia Papaioannou

2003

Chen, Brenden

Senior Scientist, AbbVie, Lake Bluff, IL

Riccardo Dalla-Favera

2003

Evans, Matthew

Associate Professor of Microbiology, Icahn Shcool of Medicine at Mt. Sinai

Stephen Goff

2003

Pelham, Robert

Director, Biomarkers and Companion Diagnostics at BeiGene

Fred Chang

2002

Goryunov, Dmitri

Staff Scientist, Sequenom, San Diego, CA

Ronald Liem

2001

Chang, David

Research Scientist, Center for Cancer Research and Genomic Medicine, Paramus, NJ

Kathryn Calame

2001

Chang, Winston

Anesthesiologist, Stanislaus Surgical Hospital, Portland, OR

J. Chloe Bulinski

2001

Chen, I-Hwei Amy

Associate Professor of Neurology, Medical University of South Carolina

Eric Kandel

2001

Jerome, Loydie

Associate Professor of Pediatrics, Faculty of Medicine, McGill University

Virginia Papaioannou

2001

Koticha, Darshan

Associate Director at Dr. Reddys Biologics, Bachupally, Hyderabad, India

Guilia Baldini

2001

Livstone, Michael

Senior Scientific Data Curator at Celgene

Timothy Bestor

2001

Ofek, Gilad

Assistant Professor, Institute for Bioscience and Biotechnology Research, University of Maryland

Dimitris Thanos

2001

Wang, Lei

Assistant Professor, Georgia Health Science University, Augusta, GA

Eric Kandel

2001

Williams, Daniel

Associate Professor and Chair of Basic and Applied Science, Mt. Ida College

Myles Akabas