Resume

Also available as an abridged PDF.

Diya Das

diyadas@alumni.princeton.edu | diyadas.github.io

Education

University of California, Berkeley, 2012 - 2018
PhD in Molecular & Cell Biology
Princeton University, 2008 - 2012
AB in Molecular Biology
Certificate in Neuroscience (Quantitative & Computational Neuroscience honors track)

Skills

single-cell RNA-sequencing analysis
assay for transposase-accessible chromatin sequencing (ATAC-seq)
assorted molecular biology lab techniques (FACS, PCR, IHC, etc.)

Tools

High performance computing
R/RStudio
Python
Bash

Experience

Development Sciences Informatics, Genentech
Senior Informatics Analyst (July 2021 - Present)
Informatics Analyst III (May 2021 – June 2021)
Informatics Analyst II (June 2019 – April 2021)
Lab of John Ngai, UC Berkeley
Postdoctoral Researcher (June 2018 – May 2019)
Graduate Student Researcher (May 2013 – May 2018)
Participant, CDIPS Data Science Workshop, UC Berkeley (July 2016)

Developed topic ontology for English Wikipedia articles and classifier for new articles.

Code available at github.com/diyadas/Topic-Ontology

Undergraduate Researcher, Lab of Sam Wang, Princeton University (June 2009 – June 2012)

Awarded John Brinster, Class of 1943, Prize (2012) for best senior thesis in Neuroscience: A Quantitative Analysis of Temperament and Connections to Neuroanatomy in the Domestic Dog (Canis familiaris).

Fellowships

Moore-Sloan Data Science Fellow, Berkeley Institute for Data Science (August 2017 – May 2019)
California Institute for Regenerative Medicine (CIRM) Predoctoral Fellow (January 2015 - December 2015)
Elizabeth Einstein Roboz Fellow (January 2015 - May 2015)

Publications & Preprints

Asterisk indicates co-first authorship.

Implementation of The FAIR Data Principles for Exploratory Biomarker Data from Clinical Trials

Alexander Arefolov, Laura Adam, Shoshana Brown, Yelena Budovskaya, Cong Chen, Diya Das, Chen Farhy, Rebecca Ferguson, Hongmei Huang, Kimberly Kanigel, Christina Lu, Oksana Polesskaya, Tracy Staton, Rajeev Tajhya, Maryann Whitley, Jee-Yeon Wong, Xiangpei Zeng, Mark McCreary. (2021). Implementation of The FAIR Data Principles for Exploratory Biomarker Data from Clinical Trials. Data Intelligence 1-25.

This paper describes our use of the FAIR data principles to manage clinical trial data. Read more

Non-neuronal expression of SARS-CoV-2 entry genes in the olfactory system suggests mechanisms underlying COVID-19-associated anosmia

David H. Brann, Tatsuya Tsukahara, Caleb Weinreb, Marcela Lipovsek, Koen Van den Berge, Boying Gong, Rebecca Chance, Iain C. Macaulay, Hsin-Jung Chou, Russell B. Fletcher, Diya Das, Kelly Street, Hector Roux De Bezieux, Yoon-Gi Choi, Davide Risso, Sandrine Dudoit, Elizabeth Purdom, Jonathan Mill, Ralph Abi Hachem, Hiroaki Matsunami, Darren W. Logan, Bradley J. Goldstein, Matthew S. Grubb, John Ngai and Sandeep Robert Datta. (2020). Non-neuronal expression of SARS-CoV-2 entry genes in the olfactory system suggests mechanisms underlying COVID-19-associated anosmia. Science Advances 6:eabc5801.

This paper addresses how SARS-CoV2 infection may lead to anosmia in COVID-19 patients. Read more

Cellular mechanisms of epithelial stem cell self‐renewal and differentiation during homeostasis and repair

Diya Das, Russell B. Fletcher and John Ngai. (2019). Cellular mechanisms of epithelial stem cell self‐renewal and differentiation during homeostasis and repair. WIREs Developmental Biology 9:e361.

Epithelia in adult mammals exhibit remarkable regenerative capacities owing to the presence of adult stem cells. Signaling pathways such as WNT, bone morphogenetic protein, and Sonic Hedgehog play critical roles in stem cell maintenance and cell fate decisions across diverse epithelia and conditions, suggesting that conserved mechanisms underlie the regenerative capacity of adult epithelial structures. Read more

Best Practices for Managing Turnover in Data Science Groups, Teams, and Labs

Dan Sholler*, Diya Das*, Fernando Hoces de la Guardia*, Chris Hoffman, Francois Lanusse, Nelle Varoquaux, Rolando Garcia, R. Stuart Geiger, Shana McDevitt, Scott Peterson and Sara Stoudt. (2019). Best Practices for Managing Turnover in Data Science Groups, Teams, and Labs. SocArXiv.

We discuss the challenges of personnel turnover and some potential practices for helping manage it, particularly for computational- and data-intensive research teams and projects. Read more

Best Practices for Fostering Diversity and Inclusion in Data Science: Report from the BIDS Best Practices in Data Science Series

R. Stuart Geiger, Orianna DeMasi, Aaron Culich, Andreas Zoglauer, Diya Das, Fernando Hoces de la Guardia, Kellie Ottoboni, Marsha Fenner, Nelle Varoquaux, Rebecca Barter, Richard Barnes, Sara Stoudt, Stacey Dorton and Stéfan van der Walt. (2019). Best Practices for Fostering Diversity and Inclusion in Data Science: Report from the BIDS Best Practices in Data Science Series. SocArXiv.

We discuss concrete actions that we can take to foster diverse and inclusive workplaces in fields around data science. Read more

clusterExperiment and RSEC: A Bioconductor package and framework for clustering of single-cell and other large gene expression datasets

Davide Risso, Liam Purvis, Russell Fletcher, Diya Das, John Ngai, Sandrine Dudoit, and Elizabeth Purdom. (2018). clusterExperiment and RSEC: A Bioconductor package and framework for clustering of single-cell and other large gene expression datasets. PLOS Computational Biology 14(9): e1006378.

With the increasing popularity of single-cell transcriptome sequencing, many experiments are creating large gene expression datasets with the goal of detecting previously unknown heterogeneity within cells. We introduce a Bioconductor R package, clusterExperiment, that implements a general and flexible clustering strategy we entitle Resampling-based Sequential Ensemble Clustering (RSEC). Read more

Creating Lineage Trajectory Maps Via Integration of Single-Cell RNA-Sequencing and Lineage Tracing

Russell B. Fletcher, Diya Das and John Ngai. (2018). Creating Lineage Trajectory Maps Via Integration of Single-Cell RNA-Sequencing and Lineage Tracing. BioEssays 40: 1800056.

Integrating transgenic lineage tracing and single‐cell RNA‐sequencing is a robust approach for mapping developmental lineage trajectories and cell fate changes. Read more

Slingshot: Cell lineage and pseudotime inference for single-cell transcriptomics

Kelly Street, Davide Risso, Russell B. Fletcher, Diya Das, John Ngai, Nir Yosef, Elizabeth Purdom and Sandrine Dudoit. (2018). Slingshot: Cell lineage and pseudotime inference for single-cell transcriptomics. BMC Genomics 19, 477.

Stable and accurate inference of branching trajectories is an important problem in single-cell genomics. We provide a quantitative comparison of existing methods and introduce a more modular novel method, Slingshot. Read more

Career Paths and Prospects in Academic Data Science: Report of the Moore-Sloan Data Science Environments Survey

R. Stuart Geiger, Charlotte Mazel-Cabasse, Chihoko Cullens, Laura Norén, Brittany Fiore-Gartland, Diya Das and Henry Brady. (2018). Career Paths and Prospects in Academic Data Science: Report of the Moore-Sloan Data Science Environments Survey. SocArXiv.

We take an in-depth look at career prospects in academic data science through a survey of members and affiliates at three institutes dedicated to data science at major U.S. universities. Read more

Injury Activates Transient Olfactory Stem Cell States With Diverse Lineage Capacities

Levi Gadye*, Diya Das*, Michael A. Sanchez*, Kelly Street, Davide Risso, Ariane Baudhuin, Michael B. Cole, Allon Wagner, Yoon Gi Choi, Elizabeth Purdom, Sandrine Dudoit, Nir Yosef, John Ngai and Russell B. Fletcher. (2017). Injury Activates Transient Olfactory Stem Cell States With Diverse Lineage Capacities. Cell Stem Cell 21, 775-790.e9.

We use multiple single-cell techniques to identify the cell state transitions underlying the stem cell self-renewal and differentiation during injury-induced regeneration of the olfactory epithelium. Olfactory stem cells shift en masse to a transient cell state unique to regeneration in which diverse fates are specified. Read more

Deconstructing Olfactory Stem Cell Trajectories at Single Cell Resolution

Russell B. Fletcher*, Diya Das*, Levi Gadye, Kelly N. Street, Ariane Baudhuin, Allon Wagner, Michael B. Cole, Quetzal Flores, Yoon Gi Choi, Nir Yosef, Elizabeth Purdom, Sandrine Dudoit, Davide Risso and John Ngai. (2017). Deconstructing Olfactory Stem Cell Trajectories at Single Cell Resolution. Cell Stem Cell 20, 817-830.e8.

The olfactory epithelium is a site of active neurogenesis. We combine single-cell transcriptomics and clonal lineage analysis to trace cell fates from the multipotent olfactory stem cell and identify multiple mechanisms controlling cell fate, including direct conversion of quiescent stem cells into support cells without cell division. Read more

Leadership

BIDS Career Paths and Alternative Metrics Working Group
Fellow Lead (October 2017 - May 2019)

The Career Paths and Alternative Metrics Working Group is a working group at the Berkeley Institute for Data Science that assesses career-related needs for data scientists in academia. Read more

BIDS Best Practices and Meta-Research Working Group
Member (October 2018 - May 2019)

The Best Practices and Meta-Research Working Group is a cross-disciplinary working group at the Berkeley Institute for Data Science that discusses technical and social aspects of how data scientists work. Read more

Beyond Academia
Co-Director & Development Lead (January 2017 - January 2018)
Development Committee (January 2017 - January 2018)
Logistics and Speakers Committees (May 2016 - March 2017)

Beyond Academia is an organization of approximately 15 graduate student and postdocs at UC Berkeley whose mission is to provide opportunities for our peers to explore careers outside of the tenure track. Our flagship event is a two-day conference featuring dozens of professionals with PhDs who have successfully transitioned to careers outside the tenure track, though we also program other events throughout the year. Read more

CDIPS Data Science Workshop
Co-Director (January 2017 - August 2017)

The CDIPS Data Science Workshop was a three-week student-run workshop that pairs small teams of grad students and postdocs with industry mentors to work on data science projects. Read more

MCB Graduate Student & Alumni Association
Co-President (June 2015 - May 2017)

The MCB Graduate Student & Alumni Association is a graduate student-led organization to promote relationships between current graduate students, alumni, and the Department of Molecular & Cell Biology at UC Berkeley. Read more

DataRescue SF Bay
Organizer (January 2017 - February 2017)

DataRescue SF Bay was an event held at the Berkeley Institute for Data Science to archive environmental data from federal websites. Read more

Student Health Advisory Committee
Graduate Student Representative (September 2012 - April 2016)

The Student Health Advisory Committee is an advisory committee to University Health Services, comprised of representatives of Berkeley student communities. Read more

MCB Graduate Student Organization
Secretary (June 2014 – June 2016)

The MCB Graduate Student Organization serves as a liaison between the Graduate Assembly, the department, and our fellow students. Read more

Graduate Affairs Committee, Dept. of Molecular & Cell Biology
Student Representative (August 2013 - May 2015)

The Graduate Affairs Committee is a committee of MCB faculty, administration, and two student representatives that meet monthly during the academic year to discuss the direction of our graduate program. Read more

Expanding Your Horizons at Berkeley
Finance & Fundraising Committee (September 2012 - April 2015)
GA/ASUC Finance Agent (March 2013 - May 2015)
Signatory (January 2014 - May 2015)

Expanding Your Horizons at Berkeley is a graduate student organization at UC Berkeley that plans an annual day of hands-on workshops for 300-500 middle school girls to encourage their pursuits in STEM fields. Read more