Lenore J. Cowen

Dr. Lenore J. Cowen is a Professor in the Computer Science Department at Tufts University She also has a courtesy appointment in the Tufts Mathematics Department. She received a BA in Mathematics from Yale and a Ph.D. in Mathematics from MIT. After finishing her Ph.D. in 1993, she was an NSF Postdoctoral Fellow and then joined the faculty of the Mathematical Sciences Department (now the Applied Mathematics and Statistics department) at Johns Hopkins University where she was promoted to the rank of Associate Professor in 2000. Dr. Cowen was named an ONR Young Investigator and a fellow of the Radcliffe Institute for Advanced Study. Lured by the Boston area, and the prospect of making an impact in a growing young department, she joined Tufts in September, 2001. She was named both a SIAM fellow and a fellow of the International Society for Computational Biology (ISCB) in 2023.

Dr. Cowen's research interests span three areas: Discrete Mathematics (since high school), Algorithms (since 1991 in graduate school) and most recently Computational Molecular Biology, where she focuses on predicting protein function from structural and biological network information. She led a team that won the DREAM Disease Module Identification challenge in 2016. She is on the Editorial Board of the IEEE/ACM Transactions of Computational Biology and Bioinformatics (TCBB) and an Associate Editor of the journal Bioinformatics(from Oxford University press). In 2020, she was awarded both the CRA-E Undergraduate Research Faculty Mentoring Award from the Computing Research Association, and the NCWIT Undergraduate Research Mentoring Award from the National Center for Women and Information Technology.

On a more personal note, she notes that she is proudly married to a computer geek, but she is still trying to get used to the fact that she is now the mother of college students!

US Mail:
CS Department
Tufts University
161 College Avenue
Medford, MA 02155
Email: cowen at cs.tufts.edu OR firstname.lastname at tufts.edu OR firstname.lastname at gmail.com

Phone: +1-617-627-5134
(answered when I am at my desk; please don't leave a message: either send me email or call the main CS department office).


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. You can see a current CV Here

Check out the article about corals project that appeared in Tufts Now in October!!

I also work on:

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.

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. Together with my colleague Donna Slonim 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.

I recently led the Tufts effort in 2 grants that were part of the National Science Foundation's "Harnessing the Data Revolution" big idea:

1) T-Tripods @ Tufts Read about our NSF-funded institute for transdisciplinary research for Foundations of Data Science at Tufts

2) Synthetic Coral project I am working on the bioinformatics behind trying to understand and model Coral Reefs as a "living 3D printer" in the laboratory with an exciting interdisciplinary team of researchers.

Prior to this research in biological networks was funded by NSF DMS-1812503, in a project joint with my math department colleague Xiaozhe Hu. 10 years ago, my research in computational structural biology was funded by NIH grant 1R01GM080330-01A1 (from 2008-2013). Even longer ago, a grant from NSF (grant CCR0208629) funded work on approximate routing, and portions of my computational biology research first funded by an NSF Large ITR grant (with PI Simon Kasif of BU).

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), Noah Daniels, (Tufts/2013), Mengfei Cao (Tufts/2016) , Monsurat Olaosebikan (Tufts/2023: co-advised with Prof Orit Shaer from Wellesley College) Kapil Devkota (Tufts/2023), Plus I co-advised Guangtao Ge's doctorate in 2009.

(My Erdos number is 2 (but so is everyone else's)).


I am on sabbatical for academic year 2023-2024 and not teaching.

Spring 2023, I taught Advanced Algorithms which I last taught in Fall 2021.

Fall 2022 I again taught Network Science . This is a course I created and taught for the first two times in Fall 2019 and Fall 2020; it now has moved from a Special Topics course number to its dedicated course number CS 142.

Summer 2022 I taught Discrete Mathematics

Spring 2022: I taught Comp 170, Theory of Computation, which I last taught in Spring 2021 and before that in Fall 2017. The information and the course website is mostly on the University Canvas site, which (sorry!) only those enrolled in the class have access to (the zoom integration was just too attractive, so I went with the centralized university solution--) Some limited information about the course is publicly accessible here: Comp 170

Fall 2018, I taught Comp 167-- Computational Biology which I last taught in Fall 2011.

Spring 2017 I taught 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 also experimented with trying to teach an elective course which was an introduction to Computational Biology from the perspective of Big Data.

In the past, I have also taught Protein Bioinformatics Topics (Fall 2010), , and one of my favorite classes to teach: Graph Theory (Fall 2007).



I gave an invited talk at SIAM ACDA in July 2021 and at Recomb in May 2022. In 2023, I spoke at the NCI Summer School for Algorithmic Cancer Biology, and at the DAiSB workshop at the CIRM in France.

Editorial and Service

I serve as an associate editor for the journal Bioinformatics published by Oxford University press.

I serve on the editorial board of the IEEE/ACM Transaction on Computational Biology and Bioinformatics (TCBB)

I was again Vice-Chair of SIAM's SIAG on Discrete Mathematics in 2021-2022. I was also Vice-Chair from 2013-2015, and one time before that so long ago that I forget the exact year....

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.

I was program committee chair for Recomb 2019

I am co-area chair for the General Computational Biology track for ISMB/ECCB in 2023.

Past 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, Recomb 2018, ISMB 2018, ACM-BCB 2018 (Highlights Co-Chair), APBC 2019, Macromolecular Sequence, Structure and Function Track of ISMB/ECCB 2019, Recomb 2020-2024.

I was also co-conference chair of ACM-BCB 2017 which took place right here in the Boston area in August 2017!


New! So honored to have been co-awarded two awards for mentoring undergraduate research in 2020; the CRA-E Undergraduate Research Faculty Mentoring Award and the NCWIT Mentoring Award for Undergraduate Research

Current graduate students at Tufts:

Kapil Devkota (Graduating August, 2023)
Polina Shpilker
Blessing Kolawole (Primary advisor: Valencia Koomson)
Mert Erden
Nicholas Rabb (co-advised by JP deRuiter) (Graduating May 2024) Faith Ocitti
Weiwei Lou

Recent Masters students: Jake Crawford, John Lazarsfeld, Yuelin Liu, Matt Werenski, Megan Gelement, Andrew delMastro, Blessing Kolawole, Grigorii Sterin

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)
Monsurat Olaosebikan (Tufts/2023) (co-advised by Orit Shaer)

In addition, Guangtao Ge (Tufts/2009) got his Ph.D. in Bioinformatics through the Tufts Interdisciplinary Doctoral Program, co-supervised by Giovanni Widmer, Susan Ernst, and myself.

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!!)

New! This page was recently brought to my attention, and also lists options for students younger than high school. Including a link to the summer camp offered at the National Museum of Mathematics! Interesting and Fun Links
Long Now
Take Jim Propp's Self-Referential Aptitute Test!
User Friendly
Ladle Rat Rotten Hut

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 www.archive-it.org and an endowment be set up to pay the subscription fees.