lab members


Vijay Ramani, PhD
Vijay Ramani, PhD
Principal Investigator
vijay.ramani (at) ucsf.edu
Scholar Citations
@vram142

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.


Nour Abdulhay, BA
Nour Abdulhay, BA
Graduate Student (BMS)
nour.abdulhay (at) ucsf.edu
@nourabdulhay

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 McNally, PhD
Postdoctoral Fellow
colin.p.mcnally (at) gmail.com
@cpmcnally

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.


Laurel Estes, BA
Laurel Estes, BA
Graduate Student joint w/ Goodarzi Lab (iPQB)
laurel.estes (at) ucsf.edu

I graduated from Pomona College in 2015 with a major in Molecular Biology and a minor in Computer Science. As an undergraduate, I worked for two summers in the lab of Dr. Tejal Desai at UCSF, where I constructed and tested biocompatible membrane devices for the controlled release of large and small molecules in vivo. Ultimately, I presented the results of this project in a talk at the 2013 Biomedical Engineering Society conference in Seattle. At Pomona, for my senior thesis, I worked in the lab of Professor Jane Liu on an ongoing project characterizing and engineering riboswitches in V. cholerae. After graduation I worked at Ginkgo Bioworks in Boston for two years, helping set up and operate high-throughput pipelines in their foundry for various fundamental procedures in synthetic biology. The summer before starting at UCSF, I worked at Teselagen Biotechnology and helped them design their LIMS system in collaboration with their clients’ lab managers.

I am currently a second-year PhD student in the Integrated Program in Quantitative Biology, Bioinformatics track. In my rotation with the Ramani Lab, I worked on applying the neural network architecture Basenji to ATAC-Seq data from The Cancer Genome Atlas, with the goal of using the correlations between sequence and chromatin accessibility encapsulated by the trained model to search for cis-regulatory elements of tRNA genes. I am very excited to be joining the Ramani Lab, and I am looking forward to continuing my previous project and developing my thesis work in the intersections of machine learning and regulatory logic in biological systems.


Dan Xu, BS
Dan Xu, BS
Junior Research Specialist
daniel.xu (at) ucsf.edu

I graduated from Georgia Institute of Technology in the year of 2018 with B.S.degree in Biochemistry. Prior to my graduation, I participated in both biomedical engineering and organic chemistry laboratory settings. With the objective to study the proteolytic network between cathepsin proteases and extracellular matrix in malignant tumors, my role in the bioengineering laboratory was to optimize and execute experimental methods from literature reviews, to purify and activate precursor-cathepsins from transfected HEK 293T cells. Secondly, for my initial undergraduate project, I synthesized HDAC inhibitors to determine their optimal antiproliferative activity on breast cancer cell lines. Afterwards, I joined the University of California, San Francisco and facilitated a study that focused on whether cellular matrix dimensionality intrinsically affects cell behaviors that predispose to cell dormancy.

Having committed in different research settings and conferences at both Georgia Institute of Technology and the University of California, San Francisco, I have found that I take inspiration in understanding of human diseases in a genomic level through experimental and computational methods. I am very much excited to join the Ramani Lab, where I can contribute through applying my experimental knowledge and enhance my background on genetics and bioinformatics.


Scott Nanda, BA, MSc
Scott Nanda, BA, MSc
Graduate Student joint w/ Goodarzi Lab (BMI)
scott.nanda (at) ucsf.edu

I graduated from Pomona College in 2017, with a B.A in Molecular Biology and a minor in mathematics. As a Beckman Scholar, I worked with Matt Sazinsky on engineering novel proteins capable of hydroxylating straight-chain and cyclic carbon compounds. I spent my junior year as a research associate working in the lab of David Lomas at University College London, which inspired me to pursue graduate study in the UK. I subsequently completed a masters in Computational Biology at the University of Cambridge in 2018, working with Serena Nik-Zainal to study tumorigenesis through the lens of mutational signatures. While there, I helped develop new statistical models for understanding how DNA damage and repair can shape the tumor genome - which led to a strong interest in how cancer evades and co-opts cellular machinery to survive.

I’m currently a 2nd year student in the Biological and Medical Informatics program, jointly advised between the Ramani Lab and the Goodarzi Lab. As I begin my thesis research, I’m excited to leverage both experimental and computational approaches towards mapping the genomic and epigenomic drivers of cancer metastasis.


Mythili Kethavarapu
Mythili Kethavarapu
Undergraduate Volunteer

I recently finished my first year as an undergraduate student at UC Santa Barbara. I am currently pursuing a B.S. in Biochemistry and Molecular Biology with a minor in Statistical Science. In the future, I hope to go to grad school to study Bioinformatics and Computational Biology. I am very excited to be working with the Ramani Lab this summer as an introduction to research in the field of systems biology. In my time at the lab I will be focusing on their research about the regulation of tRNA genes, while gaining an exposure to machine learning and DNA sequencing.


Bertie Woof, PhD
Bertie Woof, PhD
Lab Mascot / Resident Treat Eater
just give me treats plz.

woof woof woof! =)


Siva Kasinathan, MD, PhD
Siva Kasinathan, MD, PhD
Understudy to the Lab Mascot / Resident Physician
skas (at) stanford.edu
Scholar Citations
@SivaKasinathan

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!
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!


Rotation 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 Ye Lab
Jasmine Sims Tetrad / Spring / 19-20 TBD

Lab Alumni:

Name Previous Position / Years Currently
Aidan Keith Research Specialist / 2018 - 2020 PhD Program @ UW Genome Sciences