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 renamed 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)
Molecular Biology (since 2000).
I am on sabbatical for academic year 2014-2015.
However, I will still be reading and responding to email.
Please give me a little extra time to get back to you. Thanks!
US Mail: Email: cowen at cs.tufts.edu
Tufts University Phone: +1-617-627-5134
161 College Avenue
Medford, MA 02155 Fax: +1-617-627-2227
New 12/13/06: confirmation that some email is getting eaten by CS department spam filters. While this is being worked on, if you didn't hear back from me, PLEASE try my alternate email address.
You can also reach me at firstname.lastname at gmail.com
Cowen research group page
Fall 2013, I am teaching Discrete Mathematics which I also taught in Fall 2008, Fall 2009, Spring 2010, and Spring 2012 , Fall 2012 and Spring 2013.
Spring 2013 I am also taught an advanced graduate seminar in
Computational Biology, focused on PPI networks, and protein structure
Fall 2011, I taught Comp 167-- Computational Biology--
Spring 2011, I taught Advanced Algorithms which I last taught in Spring 2009.
Fall 2010, I taught Protein Bioinformatics Topics
Please note that the course links below point to the course web
page for the *current* semester at Tufts, i.e. if it's a previous year,
and I wasn't the last to teach it, you are going to be looking at
the homepage for someone else's version of the class.
Spring 2008 I taught Algorithms.
Fall 2007 I taught one of my favorite courses:
In Fall 2006, I taught Algorithms and an advanced topics seminar in Computational Biology.
In Spring 2006 I taught an introductory course in Cryptography
In Fall 2005 I taught Combinatorial Optimization
In Fall 2004 I taught
(I also co-taught this class in Fall of 2002. )
Spring 2004 and Spring 2002 I taught an Advanced Algorithms class.
Here's a little blurb.
Spring 2003 and Spring 2005 I taught and co-taught
Theory of Computing
Fall 2002 I taught:
Cryptography and Security and
Fall 2001 I taught COMP 15: Data Structures in C++.
Here are the classnotes for two of the graduate courses I taught at Hopkins:
Approximation Algorithms and
The Probabilistic Method.
What I work on
I would say that my research interests are
probably far too broad for my
own good. I have inherited my advisor's love of good
problems, wherever they be found.
Exploiting locality and approximate distance have been persistent themes,
even across catagories, for example they have been used in our approach both
to routing and to classification and clustering problems. Now I am finding that my work on networks and graph algorithms may have some interesting synergies with computational biology and functional genomics. Research interests include:
My research in computational structural bioinformatics is funded
by NIH grant 1R01GM080330-01A1 . Previous recent grants
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 Ph.D. students to
date were 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). My current Ph.D. students are Mengfei Cao , Andrew Gallant and Hao Zhang.
(My Erdos number
is 2 (but so is everyone else's)).
The following papers are available in postscript (.ps)  or pdf format; If you would like a copy of one of the other
papers on my publication list, please send email
to cowen at cs.tufts.edu.
- Papers in Algorithms
- Papers in Graph Theory
- Papers on High-Dimesional Data Analysis
- Papers in Computational Biology
PAPERS IN ALGORITHMS
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
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
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
We never made a journal version of this paper, but
the full proofs are in the final chapter of my
- L. Cowen,
A Linear Time Algorithm for Network Decomposition
DIMACS TR-94-56. 1994.
PAPERS IN 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 DIMENSIONAL DATA
- 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
- 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.
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)
- 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, N. Ramsey and L. Cowen, MRFy: Remote
homology detection for beta-structural proteins using Markov random
fields and stochastic search, Proceedings of ACM-BCB 2013. Full version to appear in IEEE-ACM Transactions on Computational Biology and Bioinformatics, special issue, best papers in ACM-BCB 2013, in press.
- 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.
- M. Leiserson, D. Tatar, L. Cowen and B. Hescott, Inferring mechanisms of Compensation from E-MAP and SGA Data Using Local Search Algorithms for Max Cut," Proceedings of RECOMB 2011, pp. 154-167. and Journal of Computational Biology 18(11), 2011.
- 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.
- G. Widmer, L. Cowen, G. Ge and X. Feng,
"Protein coding gene nucleotide substitution pattern in the apicomplexan protozoa Cryptosporidium parvum and Cryptosporidium hominis" Comparative and Functional Genomics , 2008.
- X. Wei, L. Cowen, C. Brodley, A. Brady, D. Sculley, D. Slonim, "A Distance-Based Method for Detecting Horizontal Gene Transfer in Whole Genomes," Proceedings of the 4th International Symposium on Bioinformatics Research and Applications (ISBRA 2008) , Springer Lecture Notes in Computer Science, 23-37, 2008.
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
M. Menke, E. Scanlon, J. King, B. Berger and L. Cowen, "Wrap-and-Pack: A New Paradigm for Beta Structural Motif Recognition with
Application to Recognizing Beta Trefoils" Proceedings of the Eighth International Conference on Computational
Molecular Biology (RECOMB 2004) ,
- P. Bradley, L. Cowen, M. Menke, J. King and B. Berger, "Predicting
the Beta Helix Fold From Protein Sequence Data (Extended Abstract),
Proceedings of the
Fifth International Conference on Computational Molecular Biology
(RECOMB 2001) , 58--66.
- P. Bradley, L. Cowen, M. Menke, J. King and B. Berger, "``BETAWRAP: Successful prediction of parallel $\beta$-helices
from primary sequence reveals an association with many microbial
pathogens'' Proceedings of the National Academy of Sciences (PNAS)
98(26), 2001: 14819-14824.
- 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.
A Few Recent Talks
Talk on SMURF at 3DSIG (Requires these two video files and video files to play the movie inside the talk.)
Full Curriculum Vitae
I am currently Vice-Chair of SIAM's SIAG on Discrete Mathematics; I also served in this same role from 2006-2008.
Editorial Board member, SIAM Journal on Discrete Mathematics, 2003-2011
Editorial Board member, SIAM Review, 2008-2013
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! Most recently, I was
Conference chair for the
SIAM 2012 Discrete Mathematics conference.
From 2000-2008 I was on the Steering Committee for the ACM-SIAM Symposium for Discrete Algorithms (SODA).
Special Issue of the journal Discrete Mathematics in honor of Daniel
J. Kleitman's 65th Birthday.
JCSS, Special Issue of "Best Papers in STOC 1999 ."
PC Committees: STOC 1999 , Latin 2002 , ALICE 2003 (chair) , SODA 2004, , DISC 2005, 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 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
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:
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 PhD students:
For a list of past Masters students
For prospective graduate students: Tufts Computer Science admits to the department as a whole, not to an individual faculty member's research group. However, I am always interested in strong students who wish to work in computational biology. If you are interested in my research group, please say so in your application, so I will be sure to get to see it.
Graduated Ph.D. students:
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)
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.
Professional Links/Useful Links/Fun 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!!)
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
Take Jim Propp's Self-Referential Aptitute Test!
Ladle Rat Rotten Hut
More fun links on my personal home page
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.