Download PDF | Last updated: March 1, 2022
Education
New York University
Ph.D. Biology - August 2015-May 2021
Advisor: Rahul Satija
University of Texas at Austin
B.S. Biology Honors - August 2011-May 2015
Research Experience
Single-cell virology - September 2021 - Current
Advisor: Jesse Bloom
- Conducting research applying and developing single-cell genomic methodologies to address questions regarding heterogeneity in viral infections.
Single-cell genomics - May 2016 - August 2021
Advisor: Rahul Satija
- Conducted research on methods development for single-cell RNA-seq analsysis. Topics of interest included cell type identification through supervised and unsupervised analyses and methods for data integration. Also contributed as one of the lead developers to Seurat, the open source R package developed and maintained by the Satija lab.
Computational Biology - Summer 2013 - Spring 2015
Advisor: Claus Wilke
- Conducted research focused on improving multiple protein sequence alignment. Hidden markov models were used as the basis of these alignment algorithms in order to incorporate relevant biochemical/biophysical information into the alignments. Also contributed to a collaborative project aiming to better characterize bacterial metabolism. Worked primarily with RNA-Seq data to understand tRNA gene levels
Virtual Drug Screening - Freshman Research Initiative - Summer 2012 - Spring 2013
Advisor: Josh Beckham
- Conducted preliminary drug discovery research. A combination of wet lab techniques and virtual high throughput screening methods were used in an attempt to find inhibitors for a protein target of interest. Worked primarily on a protein critical to viability in Plasmodium falciparum.
Publications
“geneBasis: an iterative approach for unsupervised selection of targeted gene
panels from scRNA-seq.”
Alsu Missarova,
Jaison Jain,
Andrew Butler,
Shila Ghazanfar,
Tim Stuart,
Maigan Brusko,
Clive Wasserfall,
Harry Nick,
Todd Brusko,
Mark Atkinson,
Rahul Satija,
John Marioni.
Genome Biology . December 2021.
“Characterizing the molecular regulation of inhibitory immune checkpoints with
multi-modal single-cell screens.”
Efthymia Papalexi,
Eleni Mimitou,
Andrew Butler,
Samantha Foster,
Bernadette Bracken,
William Mauck,
Hans-Hermann Wessels,
Yuhan Hao,
Bertrand Yeung,
Peter Smibert,
Rahul Satija.
Nature Genetics . March 2021.
“Integrated analysis of multimodal single-cell
data.”
Yuhan Hao*,
Stephanie Hao*,
Erica Andersen-Nissen,
William M. Mauck,
Shiwei Zheng,
Andrew Butler,
Maddie Jane Lee,
Aaron J. Wilk,
Charlotte Darby,
Michael Zagar,
Paul Hoffman,
Marlon Stoeckius,
Efthymia Papalexi,
Eleni P. Mimitou,
Jaison Jain,
Avi Srivastava,
Tim Stuart,
Lamar B. Fleming,
Bertrand Yeung,
Angela J. Rogers,
Juliana M. McElrath,
Catherine A. Blish,
Raphael Gottardo,
Peter Smibert,
Rahul Satija.
Cell . October 2021.
“Toward a Common Coordinate Framework for the Human
Body.”
Jennifer E. Rood,
Tim Stuart*,
Shila Ghazanfar*,
Tommaso Biancalani*,
Eyal Fisher,
Andrew Butler,
Anna Hupalowska,
Leslie Gaffney,
William Mauck,
Gokcen Eraslan,
John C.Marioni,
Aviv Regev,
Rahul Satija.
Cell . December 2019.
“Comprehensive Integration of Single-Cell
Data.”
Tim Stuart*,
Andrew Butler*,
Paul Hoffman,
Christoph Hafemeister,
Efthymia Papalexi,
William M Mauck III,
Yuhan Hao,
Marlon Stoeckius,
Peter Smibert,
Rahul Satija.
Cell . June 2019.
“Integrated analysis of single cell transcriptomic data across conditions,
technologies, and species.”
Andrew Butler,
Paul Hoffman,
Peter Smibert,
Efthymia Papalexi,
Rahul Satija.
Nature Biotechnology . April 2018.
“Molecular transitions in early progenitors during human cord blood
hematopoiesis.”
Shiwei Zheng,
Efthymia Papalexi,
Andrew Butler,
William Stephenson,
Rahul Satija.
Molecular Systems Biology . March 2018.
“Developmental diversification of cortical inhibitory
interneurons.”
Christian Mayer*,
Christoph Hafemeister*,
Rachel C. Bandler*,
Robert Machold,
Renata Batista Brito,
Xavier Jaglin,
Kathryn Allaway,
Andrew Butler,
Gord Fishell,
Rahul Satija.
Nature . March 2018.
“Single-Cell RNA-Seq Of Rheumatoid Arthritis Synovial Tissue Using Low Cost
Microfluidic
Instrumentation.”
William Stephenson*,
Laura T Donlin*,
Andrew Butler*,
Cristina Rozo,
Ali Rashidfarrokhi,
Susan M Goodman,
Lionel B Ivashkiv,
Vivian P Bykerk,
Dana E Orange,
Robert B Darnell,
Harold P Swerdlow,
Rahul Satija.
Nature Comunications . February 2018.
“Single-cell RNA-seq reveals new types of human blood dendritic cells,
monocytes, and
progenitors.”
Alexandra-Chloe Villani*,
Rahul Satija*,
Gary Reynolds,
Siranush Sarkizova,
Karthik Shekhar,
James Fletcher,
Morgane Griesbeck,
Andrew Butler,
Shiwei Zheng,
Suzan Lazo,
Laura Jardine,
David Dixon,
Emily Stephenson,
Emil Nilsson,
Ida Grundberg,
David McDonald,
Andrew Filby,
Weibo Li,
Philip L De Jager,
Orit Rozenblatt-Rosen,
Andrew A Lane,
Muzlifah Haniffa,
Aviv Regev,
Nir Hacohen.
Science . April 2017.
“Seq-Well: portable, low-cost RNA sequencing of single cells at high
throughput.”
Todd M Gierahn,
Marc H Wadsworth II,
Travis K Hughes,
Bryan D Bryson,
Andrew Butler,
Rahul Satija,
Sarah Fortune,
J Christopher Love,
Alex K Shalek.
Nature Methods . February 2017.
Teaching Experience
New York University - Recitation Leader - Statistical learning from large- scale biological data - Fall 2017, Fall 2019
- Led a recitation help section for 10-15 graduate students. Taught introductory statistics, machine learning, and programming concepts and graded assignments.
New York University - Recitation Leader - Biostatistics - Fall 2016, Spring 2017, Fall 2018
- Led recitation sections for the undergraduate biostatistics course. Taught introductory statistics concepts and the programming language R. Graded assignments and tests for 40+ students.
University of Texas at Austin - Peer Mentor - Freshman Research Initiative
-
Spring 2013 - Fall 2013
- Worked as a peer mentor for the Freshman Research Initiative Program. Helped teach proper laboratory techniques and provided assistance and guidance to freshman students interested in research. Supervised by Dr. Josh Beckham.
University of Texas at Austin - Undergraduate Teaching Assistant - Biostatistics - Fall 2012
- Worked as an undergraduate teaching assistant for Dr. Bindu Viswanathan’s “Biostatistics” course. Graded lab and homework assignments for 20+ students. Provided assistance to students during lab time and with in-class assignments.
Selected Presentations
Stockholm, Sweden - Single Cell Genomics - September 2019
- Presented a poster on recent improvements and developments with respect to my work on integration methods for scRNA-seq data
Keystone Symposium - Single Cell Biology - January 2019
- Presented a workshop talk and poster on integration methods for scRNA-seq data.
New York University - NYU Biology Department Annual Retreat - September 2017
- Presented a summary of my research on integration methods for scRNA-seq data.
University of Texas at Austin - Undergraduate Research Forum - April 2015
- Presented a poster summarizing my undergraduate honors thesis research on RNA-seq read coverage variability in tRNA reads.
Michigan State University - BEACON Congress - August 2013
- Presented a summary of my research related to Hidden Markov Model multiple protein sequence alignment in a short oral talk.
University of Wisconsin - La Crosse - National Conference on Undergraduate Research - April 2013
- Presented a poster demonstrating the research done towards discovering novel inhibitors for a protein target in Plasmodium falciparum.
Selected Honors
Awards
- Harold M. Weintraub Graduate Student Award 2020
- New York Genome Center Outstanding Contribution (PhD student) 2017
Graduate Fellowships
- NSF Graduate Research Fellowship 2017
- MacCracken Fellowship 2015
Undergraduate Awards and Scholarships
- College Scholar 2013, 2014, 2015
- President’s Achievement Scholarship 2012, 2013, 2014, 2015
- Phi Beta Kappa 2015
- College of Natural Sciences Undergraduate Research Fellowship 2012