2022

Zhong Lab Website Doctoral Thesis Title:  Machine Learning for Reconstructing Dynamic Protein Structures from Cryo-EM Images Publications while at MIT: Conformational landscape of the yeast SAGA complex as revealed by cryo-EM. Vasyliuk D, Felt J, Zhong ED, Berger B, Davis JH, Yip CK.Sci Rep. 2022 Jul 19;12(1):12306. doi: 10.1038/s41598-022-16391-0.PMID: 35853968 Free PMC article. Cryo-EM structure of the plant 26S…

Doctoral Thesis Title: Bayesian Linear Modeling in High Dimensions: Advances in Hierarchical Modeling, Inference, and Evaluation Publications while at MIT: Diffusion probabilistic modeling of protein backbones in 3D for the motif-scaffolding problem BL Trippe, J Yim, D Tischer, T Broderick, D Baker, R Barzilay, T Jaakkola arXiv preprint arXiv:2206.04119 Many processors, little time: MCMC for partitions…

Doctoral Thesis Title: Transcriptome-wide pseudouridine profiling reveals modification of critical E. coli mRNAs Publications while at MIT: Transcriptome-wide mapping reveals a diverse dihydrouridine landscape including mRNA. Draycott AS, Schaening-Burgos C, Rojas-Duran MF, Wilson L, Schärfen L, Neugebauer KM, Nachtergaele S, Gilbert WV.PLoS Biol. 2022 May 24;20(5):e3001622. doi: 10.1371/journal.pbio.3001622. eCollection 2022 May.PMID: 35609439 Free PMC article. Pseudouridine synthases modify human…

Doctoral Thesis Title:  Differential analysis of ScRNA-Seq dara to characterize epithelial cells in health and disease Publications while at MIT:  HIV specific CD8+ TRM-like cells in tonsils express exhaustive signatures in the absence of natural HIV control. Fardoos R, Nyquist SK, Asowata OE, Kazer SW, Singh A, Ngoepe A, Giandhari J, Mthabela N, Ramjit D, Singh S,…

Doctoral Thesis Title: Systems Biology Approaches for Elucidating Early ALS Disease Processes Publications while at MIT:  A multi-omic analysis of MCF10A cells provides a resource for integrative assessment of ligand-mediated molecular and phenotypic responses. Gross SM, Dane MA, Smith RL, Devlin KL, McLean IC, Derrick DS, Mills CE, Subramanian K, London AB, Torre D, Evangelista…

Doctoral Thesis Title: Gene-regulatory circuitry of disease risk and progression Publications while at MIT: Neurons burdened by DNA double-strand breaks incite microglia activation through antiviral-like signaling in neurodegeneration. Welch GM, Boix CA, Schmauch E, Davila-Velderrain J, Victor MB, Dileep V, Bozzelli PL, Su Q, Cheng JD, Lee A, Leary NS, Pfenning AR, Kellis M, Tsai LH.Sci…

Doctoral Thesis Title: High throughput measurement and perturbation of tissues and tissue-derived cellular models Publications while at MIT:  Single-cell profiling of environmental enteropathy reveals signatures of epithelial remodeling and immune activation. Kummerlowe C, Mwakamui S, Hughes TK, Mulugeta N, Mudenda V, Besa E, Zyambo K, Shay JES, Fleming I, Vukovic M, Doran BA, Aicher TP,…

Doctoral Thesis Title:  Machine Learning Applications for Neurological Diseases Publications while at MIT:  Aberrant Development Corrected in Adult-Onset Huntington’s Disease iPSC-Derived Neuronal Cultures via WNT Signaling Modulation. Smith-Geater C, Hernandez SJ, Lim RG, Adam M, Wu J, Stocksdale JT, Wassie BT, Gold MP, Wang KQ, Miramontes R, Kopan L, Orellana I, Joy S, Kemp PJ, Allen…