Selected Publications

N. Daniels, A. Gallant, N. Ramsey and L. Cowen, MRFy: Remote homology detection for beta-structural proteins using Markov random fields and stochastic search , IEEE/ACM Transactions on Computational Biology and Bioinformatics, Volume 12(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 Bioinfo rmatics, 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, 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, pp. 372-386. and Journal version in Journal of Computational Biology , 17(3): 477-487, 2010.
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, 26-37, 2008
M. Menke, B. Berger and L. Cowen, "Matt: Local Flexibility Aids Protein Multiple Structure Alignment," PLoS Computational Biology, Vol. 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) , 298-307.
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.
The protein folding work is a collaboration with the Berger Lab and the King Lab at MIT.
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.
The artificial nose work is a project of the Walt Lab in the Tufts Chemistry Department.
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.