Andrew Sundstrom

Andrew Sundstrom

Background

I'm a Senior Research Scientist at the Courant Institute of Mathematical Sciences.

My training is in computer science (B.A. from Cornell University in 1993, and M.S. from the Courant Institute of Mathematical Sciences in 2008) and computational biology (Ph.D. from the Courant Institute of Mathematical Sciences in 2013), and over the past 25 years, I've cultivated interests in a number of problems in the nexus of computation and biology.

Research Interests

Computation brings mechanism, scale, and rigor to the task of understanding biological phenomena. Living systems necessarily involve high degrees of heterogeneity, and span several discrete spatiotemporal scales. In this way, computation can be seen as a scientific instrument that can help render visible and measurable the salient features contained within biological complexity. As a computational biologist, I seek to discover principles that drive that complexity. As an accomplished software developer, I seek to build computational instruments that are broad enough to implement general principles, yet adaptive enough to fit to specific biological hypotheses under investigation.

My dissertation research focused on how hypoxia arises in heterogeneous and spatially complex tumor cell populations. It is a combination of simulation, histological image characterization, formal verification, and adaptive high-dimensional space exploration. My aim here was to provide a computational framework able to model and test several aspects of this phenomenon in silico, and solve the inverse problem: under what initial conditions and model parameter values do local regions of tumor cell hypoxia arise with high probability? Taken together, my system components formulate a novel approach to the inverse problem, and constitute a design for a tool that can be placed into the hands of experimentalists, for testing hypotheses based upon known parameter values or ones the tool might discover. In principle, this design can be generalized to other biological phenomena involving large heterogeneous populations of interacting cells.

I am currently a Senior Research Scientist at the Courant Institute of Mathematical Sciences, affiliated with the RiskEcon® Decision Metrics Lab, extending aspects of my dissertation research, investigating the emergence of cancer cell metabolic heterogeneity as an economic phenomenon, and developing methods for distinguishing people's stated vs. revealed preferences in a social network setting.

More broadly, I am interested in using the theory and methods of computer science to develop computational approaches for modeling abiogenesis, cell populations, and social phenomena across spatiotemporal scales.

Questions That Keep Me Up at Night

How can computation shed light on abiogenesis, how chemistry becomes biology? On the major transitions in evolution, like the advent of multicellularity? On the deep interplay of conservation and novelty in the evolution of biological systems? On epigenesis? The exquisite process of embryogenesis places me in a state of awe. How much of what we can observe is algorithmic in character? How do the horizons of computability give rise to observable constraints in developing biological systems? Are engineering or design principles, like modularity, at work in what's unfolding, and if so, then how can these be expressed algorithmically? How does an embryo generate its own complexity? Can you compute an organism? How do physical and informatic processes interact, often in widely distinct scales of space and time, to give rise to biotic systems?

Refereed Journal Papers

Justin Jee, Andrew Sundstrom, Steven E. Massey, Bud Mishra. "What can information-asymmetric games tell us about the context of Crick's 'frozen accident'?" Published in Journal of the Royal Society Interface, 10(88):20130614, 6 Nov 2013. Published online before print 28 Aug 2013. [doi: 10.1098/rsif.2013.0614] [pmid: 23985735] [article: pdf] [supplementary material #1: pdf], [supplementary material #2: pdf], [supplementary material #3: pdf], [supplementary material #4: pdf], [supplementary material #5: pdf]

Andrew Sundstrom, Silvio Cirrone, Salvatore Paxia, Carlin Hsueh, Rachel Kjolby, James K. Gimzewski, Jason Reed, Bud Mishra. "Image analysis and length estimation of biomolecules using AFM". Published in IEEE Transactions on Information Technology in Biomedicine, 16(6):1200-1207, Nov 2012. Published online before print 29 Jun 2012. [doi: 10.1109/titb.2012.2206819] [pmid: 22759526] [article: pdf] [supplementary material: pdf]

Jason Reed, Carlin Hsueh, Miu-Ling Lam, Rachel Kjolby, Andrew Sundstrom, Bud Mishra, and James K. Gimzewski. "Identifying individual DNA species in a complex mixture by precisely measuring the spacing between nicking restriction enzymes with atomic force microscope". Published in Journal of the Royal Society Interface, 9(74):2341-2350, 7 Sep 2012. Published online before print 28 March 2012. [doi: 10.1098/rsif.2012.0024] [pmid: 22456455] [article: pdf] [supplementary material: doc]

Hao Wu, Kevin J. Kim, Kshama Mehta, Salvatore Paxia, Andrew Sundstrom, Thomas Anantharaman, Ali I. Kuraishy, Tri Doan, Jayati Ghosh, April D. Pyle, Amander Clark, William Lowry, Guoping Fan, Tim Baxter, Bud Mishra, Yi Sun, Michael A. Teitell. "Copy number variant analysis of human embryonic stem cells". Published in Stem Cells, 26(6):1484-1489, Jun 2008. Published online before print 27 Mar 2008. [doi: 10.1634/stemcells.2007-0993] [pmid: 18369100] [article: pdf] [supplementary material #1: pdf] [supplementary material #2: pdf]

Ph.D. Dissertation

"Toward a computational solution to the inverse problem of how hypoxia arises in metabolically heterogeneous cancer cell populations". Accepted 23 Sep 2013 (readers: Profs. Bud Mishra, Dafna Bar-Sagi, and Leslie Greengard; auditors: Profs. Ravi Iyengar and Ernest Davis).

Masters Thesis

"Measuring biomolecules: an image processing and length estimation pipeline using atomic force microscopy to measure DNA and RNA with high precision". Accepted 22 Sep 2008 (readers: Profs. Bud Mishra and Davi Geiger). [pdf]

Patents

Methods and Systems for Measuring a Property of a Macromolecule. Filed 28 Jul 2010 (U.S. Application Pending: 12/817,004) with Jason Reed and Bud Mishra

Referee

Molecular Cancer Therapeutics, since 2009
Journal of Nanoparticle Research, since 2013

Technical Reviewer

Perl Best Practices, by Damian Conway. O'Reilly Media, 2005.

Honors & Awards

NYU Henry M. MacCracken Fellowship (2008-2013)
NSF IGERT Fellowship (2008-2011)

Academic & Professional Habitats

New York University (2004-present)
Cold Spring Harbor Laboratory (2009)
Morgan Stanley (1998-2007)
IBM Thomas J. Watson Research Center (1996-1998)
Nortel Networks (1994-1996)
Prime Factors, Inc. (1992)
Cornell University (1989-1993)

Geographic Habitats

New York, New York (1996-present)
Dallas, Texas (1993-1996)
Ithaca, New York (1989-1993)
Eugene, Oregon (1977-1989)
Salem, Oregon (1970-1977)

Academic & Professional Activities

I manage the Courant Institute Linked-In group, and here is my Linked-In page.
I am a member of the ACM (since 1997), IEEE (since 1997), AAAS (since 1999), and NYAS (since 2008).
Here are my pages for Zotero, Mendeley, and Academia.edu.
Here is my Google Scholar profile.

Artistic Activities

I am a lapsed student of Ed Young in the Cheng Man-ch'ing school of t'ai chi ch'uan, and of Nicki Orbach at the Art Students League of New York, though my involvement with the Tiffany Mills Company has proven integral since its inception in 1995.

Obligatory Trivia

My Erdos number is 4...

  1. Janos Pach, Harold Shapiro, Donald Newman
  2. Jacob Schwartz
  3. Bud Mishra
  4. Andrew Sundstrom

...which is almost a Colbert number; now, if my brother-in-law can score me a credited role in a film with him, then my Bacon number will plummet from Infinity to 2...

  1. Sean Patrick Reilly
  2. Andrew Sundstrom

...and then my Erdos-Bacon number will drop from Infinity to 6, placing me into direct rivalry with Natalie Portman.

Mwuhahaha!

Contact

[the last three letters of the plural form of the word that means "ice cream served with a topping"] at
[an acronym for {cherry, mango, apple} arranged alphabetically] dot
[rhymes with the first syllable of the surname of America's finest actor, Ernest Borgnine]