Lenore J. Cowen

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    Brief Bio

    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. 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 has been named an ONR Young Investigator and a fellow of the Radcliffe Institute for Advanced Study. Her 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).

    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!

    Contact Information

    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


    What I work on

    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. 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.

    New! My research in biological networks is now 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) 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)).


    Spring 2019, I am teaching Advanced Algorithms which I last taught in Spring 2018.

    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).


    Selected Preprints