Ambrose J. Carr

Ph.D. Candidate at Columbia University |


I am a Ph.D. Candidate at Columbia University using machine learning and statistics to personalize cancer treatment. I am accomplishing this by improving analytical methods for single-cell sequencing technologies and using them to extract meaningful data from large numbers of individual cells in patients' tumors. We are applying these methods to identify the drug resistance properties of cells subjected to immunological therapies in ongoing cancer trials.

In my spare time, I volunteer at InSITE, connecting innovative New York start-ups with teams of graduate students, and am an avid rock climber, runner and cyclist.


Columbia University
Biological Sciences and Center for Computational Biology & Bioinformatics
Doctor of Philosophy - EXPECTED FALL, 2017
Master of Philosophy - JUNE, 2014
Master of Arts - OCTOBER, 2013

Princeton University
Molecular Biology
Bachelor of Arts - JUNE, 2009
Certificate in Neuroscience - JUNE, 2009


Ph.D. Candidate
Pe'er Laboratory of Computational Systems Biology
Columbia University

My goal is to personalize cancer treatment. To accomplish this, I collaborated with several groups including the Sims and Mazutis labs to develop RNA sequencing technologies that can characterize tens of thousands of individual tumor and immune cells before and after they are treated with cancer drugs. Using this data, we can identify which tumors and cell types are resistant to each drug.

However, each cell's RNA must be amplified before it can be sequenced, producing technological variation, which complicates data analysis. I work extensively with statistical and machine learning methods to characterize this noise and extract biologically informative results. We are piloting these methods on a breast cancer trial, where we are determining the influence of the tumor microenvironment on tissue resident immune cells by comparing tumor infiltrating immune cell phenotypes to immune cells in healthy breast tissue in the same patient. When this technology is mature, it will enable physicians to better understand which patients are good candidates for immunotherapy.


Research Assistant
Leibowitz Lab of Behavioral Neurobiology
Rockefeller University

In the Leibowitz lab, I endeavored to answer two questions. First, how do low doses of nicotine snowball into full-blown addiction? To answer this question, I created a model of nicotine self-administration. Rats trained on this model were tested for modified neurotransmitter production using qRT-PCR and immunofluorescence, which identified changes in hypothalamic and arcuate neurotransmitter production as the level of addiction grew stronger.

Second, dietary fat is well known to influence neurological cognates of hunger and food seeking behaviors, but no one had asked how different types of fats exert these effects. By both creating modified diets and directly injecting different fatty acids into the brain, I discovered that long, saturated fatty acids decreased the relative production of orexin in the hypothalamus, a response associated with satiety. This suggests that longer-chain fats may be more filling, relative to their caloric value.

JUNE 2009 - AUGUST 2011

Undergraduate Research Assistant
Hoebel Lab of Behavioral Neurobiology
Princeton University

In the Hoebel lab I focused on characterizing the neurological systems required to initiate and perpetuate alcoholism. To accomplish this, I investigated the roles of several neuronal systems known to act in other addictive disorders. I first identified that opioid-expressing neurons in the hypothalamus stimulate ethanol intake. Second, I determined that they do so through a positive feedback loop with dopamine neurons in the striatum. Finally, I determined that the baseline expression of these neuropeptides can be used to predict an animal's likelihood to develop alcohol addiction, and that the levels of these peptides correlate with the average amount of alcohol consumption. Together, these discoveries illuminate a neurological system that facilitates alcohol addiction, which might be useful in the future to identify a person's susceptibility to alcoholism.

JUNE 2007 - JUNE 2009


Vice President, Science
Through half-year partnerships, InSITE matches teams of graduate students with early stage start-up companies to assist with marketing and brand development, product development, consumer research, and pricing strategy, among many other services. If you're the founder of a New York based start-up with a focus on health, medicine, or biological science and you think you'd be interested in working with us, please get in touch.


I leveraged broad experience in biology and technology development to carry out a market analyses of the DNA sequencing space for a large, multinational diagnostics company

JUNE 2014 - JUNE 2015


HHMI International Pre-doctoral Fellow
Howard Hughes Medical Institute
Awarded to pursue computational approaches based on single-cell sequencing to improve cancer diagnosis and treatment


Columbia Faculty Fellow
Columbia University Biological Sciences
Highest entrance award for Columbia Ph.D. students, confers full funding for 5 years of graduate study


Dataminr Prize for Best Poster
New York Academy of Sciences 10th Annual Machine Learning Symposium
For "Dirichlet Process Mixture Model for Correcting Technical Variation in Single-Cell Gene Expression Data"

MARCH 2016

Thomas Hunt Morgan Prize for Best Poster
Columbia University Biological Sciences Biannual Symposium
For "A highly scalable platform for single-cell RNA-seq"


Best Poster
Columbia MAGNet symposium
For "A highly scalable platform for single-cell RNA-seq"

JULY 2014

HHMI Princeton Undergraduate Research Grant Recipient
Howard Hughes Medical Institute
Grant to pursue neurobiological research on alchol addiction

JULY 2008

Mellon Foundation Summer Research Grant Recipient
Princeton University & The Mellon Foundation
Grant to pursue neurobiological research on audio-visual stimulus responses

JULY 2006


Measuring Signaling and RNA-Seq in the Same Cell Links Gene Expression to Dynamic Patterns of NF-κB Activation
Lane K, Van Valen D, DeFelice MM, Macklin DN, Kudo T, Jaimovich A, Carr A, Meyer T, Pe'er D, Boutet SC, Covert MW
Cell Syst. 26;4(4):458-469

Tensor Decomposition for Single-cell RNA-seq Data
Choi, K*, Carr AJ*, Prabhakaran, S, Pe'er D
30th Conference on Neural Information Processing Systems (NIPS), 2016, Workshop on Practical Bayesian Nonparametrics

Dirichlet Process Mixture Model for Correcting Technical Variation in Single-Cell Gene Expression Data
Prabhakaran S*, Azizi E*, Carr AJ, Pe'er D
Journal of Machine Learning Research, W&CP (ICML). 48, 2016

Scalable microfluidics for single-cell RNA printing and sequencing.
Bose S, Wan Z, Carr A, Rizvi AH, Vieira G, Pe'er D, Sims PA.
Genome Biol. 2015 Jun 6;16:120

Broadening horizons: holistic viewpoints from the Biology of Genomes.
Carr AJ, Pe'er D
GENOME BIOL. 2014 JUL 25;15(7):416

Predictors of ethanol consumption in adult Sprague-Dawley rats: relation to hypothalamic peptides that stimulate ethanol intake.
Karatayev O, Barson JR, Carr AJ, Baylan J, Chen YW, Leibowitz SF
ALCOHOL. 2010 JUN;44(4):323-34

Opioids in the hypothalamic paraventricular nucleus stimulate ethanol intake.
Barson JR, Carr AJ, Soun JE, Sobhani NC, Rada P, Leibowitz SF, Hoebel BG
ALCOHOL CLIN EXP RES. 2010 Feb;34(2):214-22

Opioids in the nucleus accumbens stimulate ethanol intake.
Barson JR, Carr AJ, Soun JE, Sobhani NC, Leibowitz SF, Hoebel BG
PHYSIOL BEHAV. 2009 Oct 19;98(4):453-9


Machine Learning

Python & R

Photoshop & Illustrator


Distributed/Cloud Computing

HTML, CSS & Javascript



1212 Amsterdam Avenue,
New York, NY, USA


Copyright © Ambrose J. Carr 2014