I finished my B.S.E. in Chemical Engineering at Princeton University, with minors in Quantitative & Computational Biology, and Engineering Biology. While at Princeton, I studied in David Botstein’s Integrated Science Curriculum; this course sequence motivated me to pursue research in quantitative molecular biology.
After finishing my undergraduate degree in 2012, I spent a year as a Research Intern / Computational Biologist working in the Bay Area at Sangamo BioSciences (now Sangamo Therapeutics). There, I worked closely with Jeff Miller and Ed Rebar to develop high-throughput sequencing assays to map potential off-target genomic sites for de novo engineered zinc finger and TALE nucleases. I then moved to Seattle, where I completed my Ph.D. in Genome Sciences in Jay Shendure’s lab at the University of Washington. In Jay’s lab, I developed new molecular technologies to study biomolecular phenomena at scale. I first developed RNA Proximity Ligation, a high-throughput method to resolve RNA structures transcriptome-wide using proximity ligation and sequencing. I then worked with Andrew Adey, Junyue Cao, Darren Cusanovich, Zhijun Duan, and a bunch of other incredibly talented scientists in our lab and at Illumina to co-develop single-cell combinatorial indexing (“sci” sequencing), a methodological approach for molecularly characterizing thousands of single-cells without ever resorting to single-cell isolation. As a graduate student I also developed an interest in chromatin structure and transcriptional regulation; I worked closely with Christine Disteche’s lab to apply novel bulk- and single-cell sequencing technologies to dissect the dynamics underlying mammalian X chromosome inactivation, wherein one entire X chromosome is heterochromatinized during early female mammalian development.
I began my own independent research group as a Sandler Faculty Fellow in the Fall of 2018. Broadly, our overarching goal is to continue developing novel molecular methods to study gene regulatory phenomena across the central dogma.
Aidan Keith, BS
Junior Research Specialist
aidan.keith (at) ucsf.edu
I recently finished my B.S. degree in Biology at the University of Washington. In February 2017 I began working as an undergraduate research assistant in Jay Shendure’s lab in the UW department of Genome Sciences. In Jay’s lab I worked closely with Jason Klein to research regulatory DNA in the context of evolution and disease. To do so, we used “Massively Parallel Reporter Assays” (MPRAs), a variation of traditional reporter assays that can test thousands of sequences for regulatory activity en masse by using Next Generation Sequencing (NGS) as a readout. Notably, we applied MPRAs to study the evolution of enhancers in primates, as well as to functionally characterize and prioritize GWAS SNPs that may be involved in osteoarthritis pathogenesis. Since MPRAs often rely on testing short array-synthesized sequences, I also helped develop a protocol to assemble thousands of array oligos into longer sequences that are closer to the size of most predicted enhancers.
I am very excited to be joining the Ramani lab, where I will get to continue studying gene regulation by implementing and developing new -omics techniques.
Nour Abdulhay, BA
Graduate Student (BMS)
nour.abdulhay (at) ucsf.edu
I graduated from Wellesley College in 2014 where I studied Biology. Afterwards, I worked for several years in Vijay Sankaran’s lab at Boston Children’s Hospital / The Broad Institute, which studies hematopoiesis and how genetic variation alters blood cell production. I did research to understand mechanisms that lead to rare blood disorders, specifically using human pluripotent stem cells for disease modeling and investigated aberrant splicing mutations from patients with hematological disorders. In my main project, I explored how noncoding mutations disrupt the spliceosome and may lead to dyserythropoietic anemia. I am currently a 2nd-year PhD graduate student in the Biomedical Sciences program at UCSF. I rotated in the Ramani lab in Spring 2019, where I worked on methods for generating single-molecule and genome-wide maps of epigenetic modification. I look forward to starting my thesis research here, where I will develop high-throughput technologies to investigate how applied metabolic and genetic perturbations affect protein-DNA interactions and overall cellular-state changes.
Colin McNally, PhD
colin.p.mcnally (at) gmail.com
I graduated with my A.B. in Molecular Biology from Princeton in 2013. For my senior thesis I worked in the lab of Leonid Kruglyak and studied the genetic architecture of heat and salt shock survival in yeast. I then earned my Ph.D. in the department of Genome Sciences at the University of Washington, where I worked with Elhanan Borenstein. In my graduate research I studied bacterial coevolution using metabolic models of microbial growth. In my first project I simulated two species evolving together over a long time scale and in tight isolation, analogous to the evolution of insect symbionts. I found frequent emergence of cooperation and investigated the metabolic phenotypes and genetic causes. In my second project I simulated the growth of many E. coli reaction knockouts in the context of various mixed communities of other species. I used this data to study how the adaptive landscape of a focal species changes as a function of the ecological context.
I am excited to be joining the Ramani Lab and applying my skills to study gene regulation datasets generated from cutting-edge methodologies.
Siva Kasinathan, MD, PhD
Understudy to the Lab Mascot / Resident Physician
skas (at) stanford.edu
After studying Pharmaceutical Sciences, Molecular Biology, and Mathematics at Drake University in Iowa, I headed west to join the Medical Scientist Training Program at the University of Washington in 2010. I did my PhD in Molecular and Cell Biology with Steve Henikoff at the Fred Hutchinson Cancer Research Center, where I contributed to the development of a number of molecular tools for high-resolution chromatin profiling including techniques for purifying cell type-specific nuclei from whole animals (INTACT), mapping transcription factor binding sites on native chromatin (ORGANIC), and mapping genomic binding of DNA-binding proteins using targeted endogenous cleavage (ChEC-seq). We applied these approaches to better characterize transcription factor binding and understand targeting of Polycomb-mediated repression (with Guillaume Orsi and Kami Ahmad). I also worked with Jeetu Thakur and Paul Talbert to define recently evolved functional alpha satellite dimers at human centromeres and investigate short repeats at Drosophila centromeres. Our analysis of centromeric satellites from a variety of species also suggested a role for non-B-form DNA structures in templating centromere identity.
In 2019, I joined the Pediatrics Residency Program at Stanford University / Lucile Packard Children’s Hospital. As a physician and basic scientist, I hope to work with the Ramani lab to dissect gene dysregulation in human disease through novel molecular technologies.
We are hiring!
Research Technician / Graduate Student / Postdoctoral Fellow
your.e-mail (at) ucsf.edu
Interested postdoctoral fellows should e-mail me at vijay.ramani (at) ucsf.edu with a summary of their research thus far, a brief description of the types of projects they would like to work on, and 2-3 references. We are also always looking for motivated undergraduates and graduate students!
|Name||Graduate Program / Quarter / Year||Thesis Lab|
|Derek Bogdanoff||Tetrad / Winter / 18-19||Nowakowski Lab|
|Wei Gordon||Tetrad / Spring / 18-19||Ahituv Lab|
|Tianna Grant||iPQB / Summer / 19-20||TBD|
|Laurel Estes||iPQB / Fall / 19-20||TBD|