Rotations

Here is a list of faculty who are looking for rotation students in 2017. You should have received this in an email earlier, and you should refer back for more detail on potential rotation projects. Since most faculty here are in several programs they may have listed projects for a variety of research interests. Please take a look at lab websites as well for more information on research here. Feel free to contact faculty directly and don’t be put off is you don’t see someone you are interested in on this list, these are just the people who replied to Julia's email.

Fred Chang
Cell size control: how do cells sense their own size?

Lauren Weiss (bioinformatics)
Estimating the proportion of autism heritability

Jill Hollenbach
Mapping and identification of regulatory elements in noncoding regions in the killer immunoglobulin-like receptor (KIR) complex

Orion Weiner
Self-organizing signaling networks that underlie complex cell behaviors such as polarity and motility. We are interested in the intersection between biochemistry, the actin cytoskeleton, physical forces, and cell geometry.

Martin Kampmann
BP: Understanding molecular mechanisms of protein aggregation in neurodegenerative diseases; systematic dissection of selective vulnerability of neuronal cell types using CRISPRi and CRISPRa
BI: Computational analysis of high-content phenotypes of CRISPRi / CRISPRa based genetic screens

Noah Zaitlen
Discovering the genetic basis of differences in disease prevalence between human populations in a clinical medical record system.

Oren Rosenberg
Project 1: Mechanistic dissection of virulence in the most deadly human pathogen, M. tuberculosis
Project 2: Using novel genetic tools to combat antibiotic resistant bacteria

Brian Shoichet
CCB & BP: Development and experimental testing of ultra-large library docking, involving structure-based screens of >200 million diverse small molecules and their testing against beta-lactamase
BP, BI, & CCB: Structure-based discovery of ligands for understudied G Protein Coupled Receptors
CCB, BI, & BP: Novel ligand discovery and with new biology for overstudied GPCR drug targets (e.g., kappa opioid receptor, dopamine and serotonin receptors)

Ryan Hernandez
Evolutionary modeling of biomedical data (genome, expression, and/or immune).

Dan Minor
Structural and functional studies of novel ion channel chemical biology probes

Rob Edwards
Whole endosome recording to study neurotransmitter transporters to determine the function (and presumably the substrate) of SV2A and other family members.

Hani Goodarzi
Project ideas range from precision medicine to multi-omic integration, depending on the interest of the students.

Mark Segal
Reconstructing 3D genome architecture from Hi-C and related assays and downstream applications thereof

Peter Turnbaugh
Computational prediction of drug metabolism genes in the human gut microbiome

Andrej Sali
Integrative structural biology

Sophie Dumont
Self-organization and mechanics of the mitotic spindle: Rewiring them using light"

Danica Fujimori
Chemical biology of post-translational and post-transcriptional regulation

Lei Wang
Project 1: Evolving new synthetases to genetically encode bioactive unnatural amino acids
Project 2: Chemical crosslinking in cells to identify weak and transient protein interactions

Katie Pollard
Machine learning and bioinformatics applied to large genomics data sets to study the human microbiome, gene regulation in the 3D genome, or non-coding variants in mental disorders

Sourav Bandyopadhyay
Mapping therapeutic liabilities based on tumor heterogeneity through single cell RNA-seq analysis.

Nadav Ahituv
Generating and analyzing genomic datasets such as whole-genome sequences, RNA-seq, ChIP-seq, ATAC-seq and massively parallel reporter assays.

Yifan Cheng
Single particle cryo-EM of macromolecules, including membrane proteins and chromatin remodeling complexes

John Witte
Quantitative analysis of the shared genomic basis underlying different cancers, which will allow for using similar treatments against different cancers.

Jimmie Ye
My lab is interested in building quantitative, mechanistic, and predictive models of gene regulation by perturbing the genome (using CRISPR/Cas9) and measuring genome function (using ATAC-seq, bulk and single-cell RNA-seq)

Stephen Floor
Regulation of translation and RNA granule dynamics by RNA chaperones

Alejandro Sweet-Cordero
Project 1: Studying the role of structural alterations and mutations in gene promotors and enhancers in driving expression of oncogenes
Project 2: We are interested in using WGS and RNA-seq as well as single cell RNA-seq to study evolution of intratumor heterogeneity in response to both chemotherapy and targeted therapy

Steve Altschuler/Lani Wu
Project 1: Mapping feedback control and crosstalk of proteostasis networks in neurodegeneration
Project 2: Connecting metabolic pathways with the evolution of cancer drug resistance

James Fraser
BI: How are human disease mutations structurally compensated for in proteins from other species?
BP: Directed evolution and structural analysis of mammalian chitinases to create a new enyzme therapy for lung disease

Bo Huang
We have a wide range of rotation projects from super-resolution microscopy and single-molecule tracking to the study of subcellular compartmentalization of GPCR signaling and nuclear organization