2019

Doctoral Thesis Title: Evolutionary and structural signatures of protein-coding function; synonymous acceleration, read-through, and structural impact of mutations Publications while at MIT:  1. Evidence for secondary-variant genetic burden and non-random distribution across biological modules in a recessive ciliopathy. Kousi M, Söylemez O, Ozanturk A, Mourtzi N, Akle S, Jungreis I, Muller J, Cassa CA, Brand H, Mokry…

Doctoral Thesis Title: Understanding neurodegenerative disease-relevant molecular effects of perturbagens using a multi-omics approach Publications while at MIT: 1 .A Multi-Omics Interpretable Machine Learning Model Reveals Modes of Action of Small Molecules. Patel-Murray NL, Adam M, Huynh N, Wassie BT, Milani P, Fraenkel E.Sci Rep. 2020 Jan 22;10(1):954. doi: 10.1038/s41598-020-57691-7.PMID: 31969612 Free PMC article. 2. Cell freezing protocol suitable…

Cleary Lab Website The Cleary Lab studies tissue physiology, cellular pathways, and human genetics using a combination of algorithmic insights, new experimental methods, and advanced computational tools. Doctoral Thesis Title: Leveraging latent patterns in the study of living systems Publications while at MIT:  1. Optimal-Transport Analysis of Single-Cell Gene Expression Identifies Developmental Trajectories in Reprogramming. Schiebinger G,…

Doctoral Thesis Title: Understanding the selective permeability of biological hydrogels  Publications while at MIT: 1. Molecular Characterization of Mucus Binding. Witten J, Samad T, Ribbeck K. Biomacromolecules. 2019 Apr 8;20(4):1505-1513. doi: 10.1021/acs.biomac.8b01467. Epub 2019 Mar 12. PMID:30779551 2. Selective permeability of mucus barriers. Witten J, Samad T, Ribbeck K. Curr Opin Biotechnol. 2018 Aug;52:124-133. doi: 10.1016/j.copbio.2018.03.010. Epub…

Doctoral Thesis Title: Regulation by RNA-binding proteins: sequence determinants and evolutionary dynamics Publications while at MIT: 1. Acidification of Tumor at Stromal Boundaries Drives Transcriptome Alterations Associated with Aggressive Phenotypes. Rohani N, Hao L, Alexis MS, Joughin BA, Krismer K, Moufarrej MN, Soltis AR, Lauffenburger DA, Yaffe MB, Burge CB, Bhatia SN, Gertler FB. Cancer Res. 2019…

Doctoral Thesis Title: Statistically Inferring the Mechanisms of Phage-Host Interactions Publications while at MIT: 1. Natural bacterial communities serve as quantitative geochemical biosensors. Smith MB, Rocha AM, Smillie CS, Olesen SW, Paradis C, Wu L, Campbell JH, Fortney JL, Mehlhorn TL, Lowe KA, Earles JE, Phillips J, Techtmann SM, Joyner DC, Elias DA, Bailey KL, Hurt RA Jr, Preheim SP, Sanders MC, Yang J,…

Doctoral Thesis Title: Dynamics of DNA methylation and genomic imprinting in Arabidopsis Publications while at MIT: 1.Identification and Comparison of Imprinted Genes Across Plant Species. Picard CL, Gehring M.Methods Mol Biol. 2020;2093:173-201. doi: 10.1007/978-1-0716-0179-2_13.PMID: 32088897 2. Proximal methylation features associated with nonrandom changes in gene body methylation. Picard CL, Gehring M.Genome Biol. 2017 Apr 26;18(1):73. doi: 10.1186/s13059-017-1206-2.PMID: 28446217 Free…