lab members

Vijay Ramani, PhD
Principal Investigator
vijay.ramani (at) gladstone.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 and transitioned to an Assistant Professor position at the Gladstone Institute for Data Science & Biotechnology / UCSF Department of Biochemistry & Biophysics in 2021. Broadly, our overarching goal is to continue developing novel molecular methods to study gene regulatory phenomena across the central dogma.

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 Ketavarapu
Undergraduate Volunteer

I am currently an undergraduate student at UC Santa Barbara pursuing a B.S in Biochemistry and Molecular Biology with a minor in Statistical Sciences. I am expected to graduate with my B.S. in June 2023, after which I plan to attend graduate school studying computational biology. I am excited to be working remotely with the Ramani Lab as an introduction into research in the field of systems biology. I look forward to analyzing sequencing data and implementing neural networks in order to study gene regulatory mechanisms.

Camille Moore, BA
Graduate Student joint w/ Narlikar Lab (Tetrad)
camille.moore (at) ucsf.edu

I graduated from UC Berkeley in 2020 with a B.A in Molecular and Cell Biology and a minor in English. At Berkeley, I studied chromatin remodelers via Cryo-EM under Dr. Eva Nogales. My thesis project focused on the architecture of RSC and its mechanism of nucleosome remodeling. As a 2018 Amgen scholar, I investigated the mammalian heat stress response at Kyoto University with Dr. Fuyuki Ishikawa.

I’m currently a first year student in the Tetrad program, jointly advised by the Ramani and Narlikar labs. I look forward to developing minimal molecular systems in order to study chromatin structure and genome organization.

Megan Ostrowski, BA
Research Associate
megan.ostrowski (at) ucsf.edu

I graduated in 2020 from Princeton University with a Bachelor’s degree in Molecular Biology. While at Princeton, I worked in Bonnie Bassler’s lab studying the quorum sensing response of V. cholerae. Part of my work in the Bassler lab concentrated on increasing the experimental space in which we could study quorum sensing behaviors and the other part of my work focused on optimizing fluorescent fusions to work towards the rationale design of fluorescently tagged proteins.

In the future, I hope to continue on to grad school with a focus on computational approaches to biomedical science. I am excited to be a part of the Ramani lab and increase my skills in computation and biological research while applying novel approaches to study gene regulation in response to various perturbations.

Ke (Coco) Wu, BS
Research Associate
ke.wu (at) ucsf.edu

I recently graduated from UCLA, with a B.S in Biochemistry and a minor in Statistics. Ever since my first year in college, I started working in the lab of Chong Liu on the development of a photocatalytic inorganic-biological hybrid system to achieve nitrogen reduction using Cadmium Telluride quantum dots and X. Autotrophicus nitrogen-fixing bacteria. My research project specifically tested the nitrogen reduction efficiency under various experimental conditions given different types of electron donors. Ultimately, I presented the result of this project at 2020 Undergraduate Research Week to complete my Undergraduate Research Fellowship Program at UCLA. In addition, I have led multiple data science projects in the field of statistical modeling, including natural language processing, linear/logistic regression, cluster analysis, and principal component analysis.

I am currently a research specialist in Ramani Lab to help with the development of high-throughput sequencing technologies to study the mechanism of gene regulation in chromatin remodeling and epigenetics. I am excited to start this position and accumulate experience in both experimental skillsets and computational analysis.

Sean Wang, BS
Research Associate
sean.wang (at) gladstone.ucsf.edu

I graduated from Carnegie Mellon University in 2022 with a B.S. in Biology and Psychology and a minor in Human-Computer Interaction. While at CMU, I worked in Dr. Rule’s lab characterizing the Ca-loop of C. albicans thymidylate kinase. I’m excited to join the Ramani Lab to expand and develop my skills in both experimental and computational approaches towards studying gene and transcriptional regulation through novel methodologies. In the future, I hope to continue on to grad school and study genome and transcription in biomedical contexts.

Marty Yang, PhD
Postdoctoral Fellow
marty.yang (at) gladstone.ucsf.edu
@MartyYang

I graduated from Duke University in 2015 with a B.S. in Neuroscience and minors in Chemistry and Romance Studies. At Duke, I conducted my senior thesis in Anne West’s lab combining CRISPR/Cas9 technology with single-cell readouts of gene expression to study the function of neuronal activity-dependent enhancers. After graduation, I moved to Boston and worked as a tech in Mike Greenberg’s lab at Harvard Medical School. There, I studied how sequence changes at transcription factor binding motifs contribute to species-specific patterns of gene transcription in the human retina and developing brain. I joined the Program in Neuroscience (PiN) in 2017 and I continued as a Ph.D. student in Mike’s lab. My graduate work focused on using a genetic approach to explore the determinants of enhancer function, focusing on the role of Ras/MAPK signaling and AP-1 TFs in establishing cell type-specific gene regulatory landscapes. More specifically, I leveraged naturally occurring genetic variation between inbred mouse strains to perform a large-scale mutagenesis screen of enhancer sequences in their native chromatin state. I started as a postdoc in the Ramani lab in 2022, where I am interested in employing single-molecule methods to study the interplay between transcription factors and chromatin remodelers in defining genome organization. In particular, I am looking to study how nucleosome structure is established in endoderm development, with an emphasis on understanding how these processes go awry in disease

Hannah J Richter, PhD
Postdoctoral Fellow
hannah.richter (at) gladstone.ucsf.edu
@MdmPalindrome

I graduated in 2015 with a B.S. in Biochemistry and Philosophy from Beloit College, a small liberal arts college in southern Wisconsin. My undergraduate research experience focused on the physiological underpinnings of memory and Alzheimer’s disease in mouse model systems. From there, I joined the Biochemistry and Molecular Biophysics graduate group at the University of Pennsylvania and began my PhD in the lab of Dr. Mitch Lazar. My work there interrogated the interplay between transcription and physiology by studying the role of the histone deacetylase corepressors NCoR1/2 in brown adipose tissue thermogenesis. I uncovered a surprising function for these corepressors in mediating inflammation using genetic mouse models, RNA-sequencing, and ChIP-sequencing methods. I joined the Ramani lab in 2022 and aim to combine my knowledge of physiology and nuclear receptor biology with cutting-edge methods of sequencing and chromatin mapping to understand the basic molecular biology behind tissue development and function. I’m looking forward to expanding my skills in computational biology and biochemistry to complement this work. I’m also passionate about teaching and mentoring and am excited to continue to develop those interests during my time at Gladstone.

Siva Kasinathan, MD, PhD
Clinical Fellow
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.

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

woof woof woof! =)

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!