Lenore J. Cowen

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. You can see a current CV Here

Check out the article about corals project that appeared in Tufts Now in October 2020!!

I also work on:

Computational Structural Biology , and Remote Sequence Homology: pre the protein language model era, my research group was probably best known for its work on recognizing beta-structural motifs, and for the Matt multiple structure alignment program. We also provided the Mattbench benchmark of protein structural alignments as a service to the community for testing your favorite protein sequence aligner. More recently, we are working on lightweight pre-trained protein language models for protein-protein interaction and drug-target interaction prediction.

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), Nicholas Rabb (Tufts/2024: co-advised with Prof. JP de Ruiter) Plus I co-advised Guangtao Ge's doctorate in 2009 and was on the committee for Sarah Hladikova's interdisciplinary Ph.D. doctorate in 2024.

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

Teaching

I was on sabbatical for academic year 2023-2024. In Spring 2025, I will be teaching 2 classes: CS 142 Network Science and CS 260 Advanced Algorithms.

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).

Publications

Selected Publications in Computational Biology (for Full list, see CV or Google Scholar)
New! K. Devkota, A. Blumer, X. Hu and L. Cowen Approximate IsoRank for Scalable and Meaningful Cross-Species Alignments of Protein Interaction Networks, Journal of Computational Biology, 2024. Preliminary version appeared at Recomb 2024.
New! S. Sledzieski, K. Devkota, R. Singh, L. Cowen and B. Berger TT3D: Leveraging precomputer protein 3D sequence models to predict protein-protein interactions. Bioinformatics, Vol 39 (2023), btad663.
New! R. Singh, S. Sledzieski, B. Bryson, L. Cowen and B. Berger, Contrastive learning in protein language space predicts interactions between drugs and targets, PNAS, Volume 120 (2023), e2220778120.
L. J. Cowen and H. M. Putnam, Bioinformatics of Corals: Investigating Heterogeneous Omics Data from Coral Holobionts for Insight Into Reef Health and Resilience Annual Reviews of Biomedical Data Science, Vol 5 (2022), 205-231
K. Devkota, H. Schmidt, M. Werenski, J.M. Murphy, M. Erden, V. Arsenscu and L. Cowen, GLIDER: Function Prediction from GLIDE-based Neighborhoods Bioinformatics, Vol 38 (2022), 3395-3406.
S. Sledzieski, R. Singh, L. Cowen and B. Berger D-SCRIPT translates genome to phenome with sequence-based, structure-aware, genome-scale predictions of protein-protein interactions Cell Systems, Vol 12 (2021), 969-982.e6
V. Arsenescu, K. Devkota, M. Erden, P. Shpilker, M. Werenski and L. Cowen, MUNDO: Protein function prediction embedded in a multispecies world Bioinformatics Advances, Vol 2 (2022), vbab025.
K. Devkota, J. M. Murphy, L.J. Cowen, GLIDE: combining local methods and diffusion state embeddings to predict missing interactions in biological networks Bioinformatics, Vol 36 (2020), i464-i473.
J.P. Baskaran, A. Weldy, J. Guarin, G. Munoz, P. Shpilker, M. Kotlik, N. Subbiah, A. Wishart, Y. Peng, M. Miller, L.J. Cowen, M. J. Oudin, Cell shape, and not 2D migration, predicts extracellular matrix-driven 3D cell invasion in breast cancer, APL Bioengineering, Vol 4(2) (2020), 026105.
S. Choobdar, M. E. Ahsen, J. Crawford, M. Tomasoni, T. Fang, D. Lamparter, J. Lin, B. Hescott, X. Hu, J. Mercer, T. Natoli, R. Narayan, The DREAM Module Identification Challenge Consortium, A. Subramanian, J. D. Zhang, G. Stolovitzky, Z. Kutalik, K. Lage, D. K. Slonim, J. Saez-Rodriguez, L. J. Cowen, S. Bergmann and D. Marbach, Assessment of Network Module Identification Across Complex Diseases Nature Methods, Vol 16 (2019), 843-852.
J. Lazarsfeld, J. Rodriguez, M. Erden, Y. Liu and L. Cowen, Majority Vote Cascading: A Semi-Supervised Framework for Improving Protein Function Prediction, IEEE/ACM Transactions on Computational Biology and Bioinformatics, 2021 Special issue, Best Papers in ACM BCB 2019
Update: we found a bug shortly after publishing: S. Hall-Swan, J. Crawford, R. Newman and L. Cowen, "Detangling PPI Networks to Uncover Functionally Meaningful Clusters," BMC Systems Biology, 12(Suppl 3) (2018): and have withdrawn the paper. Here is a link to our retraction note The journal is looking to publish a correction, and it's in progress, but here's a Preprint of our corrected manuscript
L. Cowen, T. Ideker, B. Raphael and R. Sharan, Network propagation: a universal amplifier of genetic associations Nature Reviews Genetics, Vol 18 (2017), pages 551-562.
M. Cao and L.J. Cowen When should we NOT transfer functional annotation between sequence paralogs? Proceedings of the Pacific Symposium on Biocomputing, 2017, pages 15-26.
N. Daniels, A. Gallant, N. Ramsey and L.J. Cowen, MRFy: Remote homology detection for beta-structural proteins using Markov random fields and stochastic search IEEE/ACM Transactions on Computational Biology and Bioinformatics, Vol 12, no. 1 (2015) pp. 4-16. (Conference version won best student paper at ACM BCB 2013).
M. Cao, C. M. Pietras, X. Feng, K.J. Doroschak, T. Schaffner, J. Park, H. Zhang, L. J. Cowen and B. Hescott, New directions for diffusion-based network prediction of protein function: incorporating pathways with confidence Bioinformatics, Volume 30, ISMB 2014 Proceedings, i219-i227, 2014.
M. Cao, H. Zhang, J. Park, N. Daniels, M. E. Crovella, L. J. Cowen and B. Hescott, Going the Distance for Protein Function Prediction: A New Distance Metric for Protein Interaction Networks PLOS ONE, Volume 8, e76339, 2013.
N. Daniels, A. Gallant, J. Peng, L.J. Cowen, M. Baym and B. Berger, Compressive genomics for protein databases Bioinformatics, Volume 29(13), 2013, i283-i290.
A. Gallant, M.D. Leiserson, M. Kachalov, L. J. Cowen and B. J. Hescott Genecentric: a package to uncover graph-theoretic structure in high-throughput epistasis data. BMC bioinformatics, Volume 14(1), 2013, 23.
N. Daniels, S. Nadimaplli and L. Cowen, Formatt: Correcting protein multiple structural alignments by incorporating sequence alignment, BMC Bioinformatics, Volume 13, 2012, 259.
S. Su, C. Gramazio, D. Extrum-Fernandez, C. Crumm, L. Cowen, M. Menke and M. Strait, Molli: Interactive Visualization for Exploratory Protein Analysis, IEEE Computer Graphics and Applications, Volume 32, Number 5, 2012, 62-69.
N. Daniels, R. Hosur, B. Berger and L. Cowen, SMURFLite: combining simplified Markov random fields with simulated evolution improves protein remote homology detection into the twilight zone Bioinformatics 28(9): 1216--1222, 2012.
N. Daniels, A. Kumar, L. Cowen and M. Menke, Touring Protein Space with Matt IEEE/ACM Transactions on Computational Biology, Vol 9, Issue 1, January 2012. doi: 10.1109/TCBB.2011.70.
A. W. Bryan Jr, C. W. O'Donnell, M. Menke, L. Cowen, S. Lindquist and B. Berger, STITCHER: Dynamic assembly of likely amyloid and prion beta-structures from secondary structure predicitons, Proteins: Structure, Function and Bioinformatics, Vol 80, Issue 2, February 2012, pp. 410420.
A. Kumar and L. Cowen, Recognition of beta-structural motifs using hidden Markov models trained with simulated evolution Bioinformatics 2010 26: ISMB 2010: i287-i293; doi:10.1093/bioinformatics/btq199
M. Menke, B. Berger and L. Cowen, Markov random fields reveal an N-terminal double beta-propeller motif as part of a bacterial hybrid two-component sensor system, PNAS, March 2, 2010 107(9), 4069-4074.
A. Kumar and L. Cowen, Augmented training of Hidden Markov Models to recognize remote homologs via simulated evolution Bioinformatics 25(13), 2009, pp. 1602--1608.
B. Hescott, M. Leiserson, L. Cowen and D. Slonim, "Evaluating Between-Pathway Models with Expression Data", RECOMB 2009, ppp. 372-386, and Journal version in Journal of Computational Biology, 17(3), Match 2010: pp. 443-457.
A. Brady, K. Maxwell, N. Daniels and L. Cowen, Fault Tolerance in Protein Interaction Networks: Stable Bipartite Subgraphs and Redundant Pathways PLoS One 4(4): e5364. doi:10.1371/journal.pone.0005364 2009.
A. Bryan, M. Menke, L. Cowen, S. Lindquist, B. Berger, BETASCAN: Probable beta-amyloids identified by pairwise probabilities PLoS Computational Biology 5(3): e1000333. doi:10.1371/journal.pcbi.1000333 2009.
M. Menke, B. Berger, and L. Cowen, "Matt: Local Flexibility Aids Protein Multiple Structure Alignment" PLoS Computational Biology, Volume 4, No. 1, 2008.
A. McDonnell, M. Menke, N. Palmer, J. King, L. Cowen and B. Berger, "Fold Recognition and Accurate Alignment of Sequences Directing Beta Sheet Folding by Profile Wrapping" Proteins: Structure, Function and Bioinformatics , Volume 63, 976-985, 2006
M. Menke, J. King, B. Berger and L. Cowen, "Wrap-and-Pack: A New Paradigm for Beta Structural Motif Recognition with Application to Recognizing Beta Trefoils" Journal of Computational Biology , Volume 12, 6, 777-795, 2005
L. Cowen, P. Bradley, M. Menke, J. King and B. Berger, "Predicting the Beta-Helix Fold from Protein Sequence Data," Journal of Computational Biology, Vol 9, No 2, 2002, pp. 261-276.
Algorithms
L. Cowen, K. Devkota, X. Hu, JM. Murphy, K. Wu "Diffusion State Distances: Multitemporal Analysis, Fast Algorithms, and Applications to Biological Networks," SIAM Journal on Mathematics of Data Science, 3(1), 142-170.
J. Lin, L. Cowen, B. Hescott and X. Hu, "Computing the diffusion state distance on graphs via algebraic multigrid and random projections," Numer Linear Algebra Appl., Vol 25, 2018, e2156.
L. Cowen, Packet Routing in Networks, Encyclopedia of Algorithms Invited Article, 2008.
M. Arias, L. Cowen and K. Laing, Compact Roundtrip Routing with Topology Independent Node Names, Journal Comput. Syst. Sci. 74(5): 775-795, 2008.
A. Brady and L. Cowen, Exact Distance Labeling Yield Additive Stretch Compact Routing Schemes , DISC 2006.
A. Brady and L. Cowen, Compact Routing on Power Law Graphs with Additive Stretch , 119-128, ALENEX 2006.
M. Arias, L. Cowen, K. Laing, R. Rajaraman, and O. Taka, Compact Routing with Name Independence STo appear in SIAM Journal on Discrete Mathematics . Preliminary version in SPAA 2003.
L. Cowen and C. Wagner, Compact Roundtrip Routing in Directed Networks, Journal of Algorithms, 50(1): 79-95, 2004. Preliminary version in PODC 2000.
M. Arias, L. Cowen, K. Laing Compact Roundtrip Routing with Topology-Independent Node Names Names PODC 2003.
L. Cowen, Compact Routing with Minimum Stretch SODA 99. Invited for special issue, Best Papers in SODA 99, Journal of Algorithms.
B. Awerbuch, B. Berger, L. Cowen and D. Peleg, Near-Linear Cost Sequential and Distributed Constructions of Sparse Neighborhood Covers SIAM Journal of Computing. 28:1: 263-277, 1999. (preliminary version in FOCS).
B. Awerbuch, B. Berger, L. Cowen and D. Peleg Fast Distributed Network Decompositions and Covers. Journal of Parallel and Distributed Computing, 39:2: 105-114. 1996. (Preliminary version in PODC).
L. Cowen and R. Mathar The Offset Problem. Combinatorics, Probability and Compting 6: 159-164, 1997.
B. Berger and L. Cowen, Scheduling with Concurrency-Based Constraints. Journal of Algorithms 18, 1995, 98-123. (preliminary version in SODA).
B. Awerbuch, B. Berger, L. Cowen and D. Peleg, Low-Diameter Graph Decomposition is in NC . Random Structures and Algorithms, 5(3), 1994, 441-452.
B. Awerbuch, L. Cowen and M. Smith Efficient Asynchronous Distributed Symmetry-Breaking STOC 1994. We never made a journal version of this paper, but the full proofs are in the final chapter of my PhD thesis.
L. Cowen, A Linear Time Algorithm for Network Decomposition DIMACS TR-94-56. 1994.
Graph Theory and Combinatorics
L. Cowen, R. Cowen and A. Steinberg, Totally Greedy Coinsets and Greedy Obstructions Electronic Journal of Combinatorics, Vol 15 (R90), 2008.
A. Brady and L. Cowen, Exact Distance Labeling Yield Additive Stretch Compact Routing Schemes , DISC 2006.
B. Bogstad and L. Cowen, "The Distinguishing Number of the Hypercube," Discrete Mathematics, Vol 283: 1-3, 39-35, 2004.
C. Cheng and L. Cowen, On the Local Distinguishing Number of Cycles Discrete Mathematics, Vol 196: 1-3, 97-108, 1999.
L. Cowen, W. Goddard and E. Jesurum, Coloring with Defect . SODA 1997. Journal version entitled "Defective Coloring Revisited" in Journal of Graph Theory 24:3: 205-219, 1997.
L. Cowen, D. Kleitman, F. Lasaga and D. Sussman, Enumeration of Full Graphs: Onset of the Asymptotic Region . Studies in Applied Mathematics 36:339-350. 1996.
D. Kleitman, F. Lasaga, and L. Cowen, Asymptotic Enumeration of Full Graphs . Journal of Graph Theory 20: 59-69, 1995.
L. Cowen, R. Cowen, and D. Woodall, Defective Colorings of Graphs on Surfaces: Partitions into Subgraphs of Bounded Valency. Journal of Graph Theory 10: 187-195, 1986.
High-Dimesional Data Analysis
A. Cannon and L. Cowen Approximation Algorithms for the Class Cover Problem Annals of Mathematics and Artificial Intelligence, 40(3-4), 2004: 215-224. (Special issue, best papers AMAI 2000).
F. Crimins, R. Dimitri, T. Klein, N. Palmer and L. Cowen "Higher Dimensional Approach for Classification of Lung Cancer Microarray Data" Proceedings of the 2003 Critical Assesment of Microarray Data Analysis (CAMDA) conference.
W. Zhou, W. Wu, N. Palmer, E. Mower, L. Cowen and A. Blumer Microarray Data Analysis of Survival Times of Patients with Lung Adenocarcinomas Using ADC and K-Medians Clustering, in Proceedings of the 2003 Critical Assesment of Microarray Data Analysis (CAMDA) conference.
S. Stitzel, L. Cowen, K. Albert, and D. Walt, ``Array-to-Array Transfer of an Artificial Nose Classifier,'' Annalytical Chemistry 73(21), 2001: 5266--5271.
L.J. Cowen and C.E. Priebe, Randomized non-linear projections uncover high-dimensional structure. Advances in Applied Math 19:319-331, 1997.
A. Cannon, L. Cowen and C.E. Priebe, Approximate Distance Classification, Proceedings of the 1998 Symposium on the Interface between Computer Science and Statistics.
C. E. Priebe and L.J. Cowen, Mine Detection Via Generalized Wilcoxon-Mann-Whitney Classification. Proceedings of the SPIE 3392: 906-917, 1998.
Structures
L. Cowen, J. Feigenbaum and S. Kannan, A Formal Framework for Evaluating Heuristic Programs Annals of Mathematics and Artificial Intelligence Vol 22, no. 3-4 (1998), pp. 193-206. (Preliminary version at ICALP 96)

Talks

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. I was on the organizing committee for the 2017 SIAM Annual Meeting.

I was program committee chair for Recomb 2019

I was co-conference chair for ACM-BCB 2017, SIAM ACDA 2023, and Recomb 2024.

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 , Co-chair of General Computational Biology Track of ISMB/ECCB 2023, Recomb 2020-2025.

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

Current graduate students at Tufts:

Polina Shpilker
Blessing Kolawole (Primary advisor: Valencia Koomson)
Mert Erden
Faith Ocitti
Weiwei Lou
Christopher Ratigan (in the Mathematics department)
Jocelyn Garcia

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

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) (Old homepage: now at Amazon )
Monsurat Olaosebikan (Tufts/2023) (co-advised by Orit Shaer)
Kapil Devkota (Tufts/2023)
Nicholas Rabb (Tufts/2024) (co-advised by JP deRuiter)

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, and Sarah Hladikova (Tufts/2024) got her Ph.D. in AI and Ethics through the Tufts Interdisciplinary Doctoral Program, advised by Peter Levine, and co-supervised by myself, and John Shattuck.

Useful Links

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.