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 |
2019 |
Baker, Zachary |
Post-Doctoral Scientist, Columbia University Irving Medical Center |
Molly Przeworski |
2019 |
Brandt, Margot |
Post-Doctoral Scientist, Columbia University Irving Medical Center |
Tuuli Lappalainen |
2019 |
Fu, Ziao |
Post-Doctoral Scientist, Rockefeller University |
Joachim Frank |
2019 |
Georgieva, Daniela |
Post-Doctoral Scientist, Columbia University Irving Medical Center |
Dieter Egli |
2019 |
Kahiapo, Jerome |
Post-Doctoral Scientist, Columbia University Irving Medical Center |
Stavros Lomvardas |
2019 |
Lee, Seoeun |
Consultant, Boston Consulting Group (BCG) |
Lori Zeltser |
2019 |
McCurdy, Ethan |
Program Coordinator, NYU Langone's Neuroscience Inst. |
Ulrich Hengst |
2019 |
McGoldrick, Luke |
Post-Doctoral Fellow, Yale University |
Alexander Sobolevsky |
2019 |
Sheth, Ravi |
Co-Founder, New Co (Microbiome and Synthetic Biology) |
Harris Wang |
2019 |
Tan, Yong Zi |
Post-Doctoral Fellow, The Hospital for Sick Children Research Institute, Toronto, Canada |
Bridget Carragher |
2019 |
van Alstyne, Meaghav |
Post-Doctoral Scientist, Columbia University Irving Medical Center |
Livio Pellizzioni |
2018 |
Eberle-Singh, Jaime |
Medical Student, Sidney Kimmel Medical College at Thomas Jefferson University |
Kenneth Olive |
2019 |
Szymanski, John |
Post-Doctoral Scientist, Columbia University Irving Medical Center |
Rafael Yuste |
2018 |
Kribelbauer, Judith |
Post-Doctoral Scientist, Columbia University Irving Medical Center |
Harmen Bussemaker & Richard Mann |
2018 |
Hill, Vanessa |
Biology Teacher, 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, the Scienomics Group, Stamford, CT |
Frank Polleux |
2018 |
Mahadevia, Darshini |
Associate Consultant, 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 |
Grinshpun, Boris |
Post-Doctoral Fellow, EMD Serono, Inc. |
Michael Shen |
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 |
Assistant Professor, Mt. Sinai Icahn School of Medicine |
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 |
Senior 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 |
Executive Director, Neuroscience Institute, NYU Langone |
Joseph Gogos |
2011 |
Orozco, Ian |
Senor Research Scientist, Van Andel Institute |
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 |
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