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.

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 teenagers!


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

Phone: +1-617-627-5134
Fax: +1-617-627-2227

Research


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.

New! Now funded with 2 new grants as part of the National Science Foundation's "Harnessing the Data Revolution" big idea:

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

Here is the Schedule for the Tripods Launch Event on Friday, January 31

(Here is a Temporary Link for Slides )

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. Read more here (still under construction)

Check out the new 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. My research in biological networks is funded by NSF DMS-1812503. The co-PI is my colleague in the math dept, Xiaozhe Hu.

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 coPI 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), 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)).

Teaching


Fall 2020 I am again teaching Network Science, a course I piloted and taught for the first time in Fall 2019.

Spring 2020, I am teaching Advanced Algorithms which I last taught in Spring 2019.

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

Fall 2017 I taught Computation Theory

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).


Publications




Talks


New! Check out video of my invited talk at the Simons Institute on: Diffusion-Based Metrics for Biological Network Analysis

Some older talk slides:

Talk on SMURF at 3DSIG (Requires these two video files and video files to play the movie inside the talk.)

Genecentric talk

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 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.

I am program chair for Recomb 2019

I am co-area chair for the Macromolecular Sequence, Structure and Function Track of ISMB/ECCB 2019

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, ISMB 2019 (area co-chair; macromolecular structure and function), Recomb 2020.

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

Students


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

In 2020, I am supervising three undergraduates, two funded through my NSF grants, and one through the Tufts GRAP program.

In 2018 and 2019, I supervised undergraduate student Jonathan Rodriguez through the Tufts Laidlaw Scholars program.

In 2017 I hosted summer DREU undergraduate student Indrani Ray.

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:

Monsurat Olaosebikan (co-advised by Dr. Orit Shaer)
Kapil Devkota
Matt Werenski
Polina Shpilker
Blessing Kolawole
Mert Erden
Nicholas Rabb

Undergraduate Research Advisees: For current and most recent undergraduate students, please see the BCB group page. Other past undergraduate students included Maxim Kachalov, Max Leiserson , Dan Malmer, Kyle Maxwell, Emily Mower , Shilpa Nadimpalli, nathan Palmer, Patrick Schmid, Sarah Hall-Swan, Daniel Wolchonok.

Recent Masters students: Jake Crawford, John Lazarsfeld, Yuelin Liu.

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)

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.

I am the faculty advisor for the Tufts Student Chapter of ACM-W and for Tufts WiCS.


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!

Computational Biology
Here's a Page I wrote about recommended places to pursue a graduate CS degree in Computational Biology (with suggested faculty advisors).

Interesting and Fun Links
Long Now
Take Jim Propp's Self-Referential Aptitute Test!
User Friendly
Ladle Rat Rotten Hut

templink for slides

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.