US Mail: Email: cowen at cs.tufts.edu OR firstname.lastname at tufts.edu OR firstname.lastname at gmail.com CS Department Tufts University Phone: +1-617-627-5134 161 College Avenue Medford, MA 02155 Fax: +1-617-627-2227 U.S.A.
I am interested in graphs, networks and algorithms. Lately, I have been applying my expertise in these areas to Computational Molecular Biology: we live in a golden age of exponential growth in the amount of sequence, structure, expression, network, and other types of high-throughput data that is becoming available for the study of genes, proteins and human diseases. I am interested in designing better algorithms to make functional inferences integrated across these heterogeneous data sets. More specifically, I work on:
1) Computational Structural Biology , and Remote Sequence Homology: in this area, my research group is probably best known for its work on recognizing beta-structural motifs, and for the Matt multiple structure alignment program. We also provide the Mattbench benchmark of protein structural alignments as a service to the community for testing your favorite protein sequence aligner.
2) Biological Networks Here my training in graph theory and graph algorithms has led to new diffusion metrics for "detangling" PPI network hairballs , work on redundant pathways and dense bipartite structure, and also for methods to incorporate known pathways into random walk-based predictions of protein function. All network science work is a collaboration with my colleagues Ben Hescott and Donna Slonim ; together we jointly run the Tufts BCB group and welcome interested students to email one of us for an invitation to visit our weekly group meetings during the semester.
My research in computational biology was funded by NIH grant 1R01GM080330-01A1 from 2008-2013. . A long time ago, a grant from NSF (grant CCR0208629) funded work on approximate routing, and portions of my computational biology research were previously funded by an NSF Large ITR grant with me as the Tufts PI and Simon Kasif of BU as the main PI.
My Ph.D. advisor was Daniel J. Kleitman ; my graduated Ph.D. students to date are Christine Cheng (JHU/1999), 1/2 Christopher Wagner (JHU/1999), Adam Cannon (JHU/2000), Arthur Brady (Tufts/2008), Anoop Kumar (Tufts/2010) and Noah Daniels, (Tufts/2013), and Mengfei Cao (Tufts/2016) . Plus I co-advised Guangtao Ge's doctorate in 2009.
(My Erdos number is 2 (but so is everyone else's)).
Fall 2017 I am going to be teaching Computation Theory
Spring 2017 I am teaching Discrete Mathematics which I also taught in Fall 2008, Fall 2009, Spring 2010, Spring 2012, Fall 2012, Spring 2013, Spring 2016 and Fall 2016.
Fall 2016 I experimented with trying to teach an elective course which was an introduction to Computational Biology from the perspective of Big Data. More details coming soon.
Spring 2015, I taught Advanced Algorithms which I last taught in Spring 2011 and in Spring 2009.
Some older classes: Comp 167-- Computational Biology (Fall 2011), Protein Bioinformatics Topics (Fall 2010), , and one of my favorite classes to teach: Graph Theory (Fall 2007).
L. Cowen, Packet Routing in Networks, Encyclopedia of Algorithms Invited Article, 2008.
PAPERS IN GRAPH THEORY AND COMBINATORICS
HIGH DIMENSIONAL DATA
Check out video of my invited talk at the Simons Institute on:
Some older talk slides:
I serve on the editorial board of the IEEE/ACM Transaction on Computational Biology and Bioinformatics (TCBB)
I was Vice-Chair of SIAM's SIAG on Discrete Mathematics from 2013-2015.
Editorial Board member, SIAM Journal on Discrete Mathematics, 2003-2011
Editorial Board member, SIAM Review, 2008-2013
Conference co-chair, SIAM 2008 Annual Meeting, and in charge of the "Discrete Math" track at the SIAM 2009 Annual Meeting where we had a BANQUET FOR DANNY KLEITMAN'S 75th BIRTHDAY! I was Conference chair for the SIAM 2012 Discrete Mathematics conference. Most recently, I am on the organizing committee for the 2017 SIAM Annual Meeting.
PC Committees: SODA 2008, , ICALP 2008 ,
RECOMB 2010 , WABI 2010 , RECOMB 2011 , WABI 2011 , SIAM DM 2012 (chair) , RECOMB 2012 , ISMB 2012 (area co-chair: protein structure and function) , WABI 2012, ACM-BCB 2012 (area co-chair: protein and RNA structure), ISMB/ECCB 2013 (area co-chair: protein structure and function), WABI 2013, ACM-BCB 2013 (area co-chair: protein and RNA structure). RECOMB 2014, ISMB 2014 (area co-chair: applied bioinformatics) ACM-BCB 2014 , WABI 2014 , ACM-BCB-2015, RECOMB 2015, ISMB/ECCB 2015 (late-breaking research track), APBC 2016, RECOMB 2016 , ISMB 2016 (area co-chair: protein structure and function), APBC 2017, Recomb 2017, ISMB/ECCB 2017
I am also co-conference chair of ACM-BCB 2017 which is taking place right here in the Boston area in August!
In 2013 I hosted summer DREU undergraduate student Katie Doroschak
In 2010 I was the Freshman faculty advisor for the NSF funded Tufts CSEMS program. and hosted two CRA-W summer DREU undergraduate students (co-advising with Sara Su): Caitlin Crumm and Dani Extrum-Fernandez
Current students at Tufts:
Undergraduate Research Advisees, Past and Present: Alana Fu, Sam Haney, Maxim Kachalov, Max Leiserson , Dan Malmer , Kyle Maxwell, Emily Mower , Shilpa Nadimpalli , Greg Pallotta, Nathan Palmer , Ali Qadri, Patrick Schmid , Daniel Wolchonok.
Current Masters student:
For a list of past Masters students click here.
Graduated Ph.D. students:
Christine Cheng (JHU/1999)
Christopher Wagner (JHU/1999) (co-advised with Mike Goodrich)
Adam Cannon (JHU/2000).
Arthur Brady (Tufts/2008)
Anoop Kumar (Tufts/2010)
Noah Daniels (Tufts/2013)
Mengfei Cao (Tufts/2016)
High School Math Camps
The American Mathematics Society is now giving out grants to high school math camps!! They are currently raising endowment to support it, they are having real mathematicians judging the programs, they are charging 0 overhead to administer the program, and basically, I can't think of a better "bang" for your buck than supporting this, so check out their application process and give them money!!
As part of their effort, they are also (orthogonal to this) providing a central website where you can read about all the math camps (whether they applied for an AMS grant or not) -- so if you know a bright high school student, point them at this Information about High School Math Camps Site (I myself an alum of the Hampshire College Summer Studies in Math program, and I recommend it very highly!!)
Here's a Page I wrote about recommended places to pursue a graduate CS degree in Computational Biology (with suggested faculty advisors).
Important note! If I ever die or become permanently disabled or go anywhere where I can't take this content with me and put it up publically, it is a strong wish of mine that a static archive at the time of my death
of everything web accessible under the ~cowen hierarchy be stored in a public archive at