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Lenore Cowen - Publications

Affiliations: 
Johns Hopkins University, Baltimore, MD 
Area:
Mathematics
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25 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2023 Sledzieski S, Devkota K, Singh R, Cowen L, Berger B. TT3D: Leveraging Pre-Computed Protein 3D Sequence Models to Predict Protein-Protein Interactions. Bioinformatics (Oxford, England). PMID 37897686 DOI: 10.1093/bioinformatics/btad663  0.526
2023 Singh R, Sledzieski S, Bryson B, Cowen L, Berger B. Contrastive learning in protein language space predicts interactions between drugs and protein targets. Proceedings of the National Academy of Sciences of the United States of America. 120: e2220778120. PMID 37289807 DOI: 10.1073/pnas.2220778120  0.48
2023 Kumar L, Brenner N, Sledzieski S, Olaosebikan M, Roger LM, Lynn-Goin M, Klein-Seetharaman R, Berger B, Putnam H, Yang J, Lewinski NA, Singh R, Daniels NM, Cowen L, Klein-Seetharaman J. Transfer of knowledge from model organisms to evolutionarily distant non-model organisms: The coral Pocillopora damicornis membrane signaling receptome. Plos One. 18: e0270965. PMID 36735673 DOI: 10.1371/journal.pone.0270965  0.488
2022 Singh R, Devkota K, Sledzieski S, Berger B, Cowen L. Topsy-Turvy: integrating a global view into sequence-based PPI prediction. Bioinformatics (Oxford, England). 38: i264-i272. PMID 35758793 DOI: 10.1093/bioinformatics/btac258  0.514
2021 Sledzieski S, Singh R, Cowen L, Berger B. D-SCRIPT translates genome to phenome with sequence-based, structure-aware, genome-scale predictions of protein-protein interactions. Cell Systems. PMID 34536380 DOI: 10.1016/j.cels.2021.08.010  0.515
2015 Daniels NM, Gallant A, Ramsey N, Cowen LJ. MRFy: Remote Homology Detection for Beta-Structural Proteins Using Markov Random Fields and Stochastic Search. Ieee/Acm Transactions On Computational Biology and Bioinformatics / Ieee, Acm. 12: 4-16. PMID 26357074 DOI: 10.1109/Tcbb.2014.2344682  0.322
2013 Daniels NM, Gallant A, Peng J, Cowen LJ, Baym M, Berger B. Compressive genomics for protein databases. Bioinformatics (Oxford, England). 29: i283-90. PMID 23812995 DOI: 10.1093/Bioinformatics/Btt214  0.506
2012 Daniels NM, Hosur R, Berger B, Cowen LJ. SMURFLite: Combining simplified Markov random fields with simulated evolution improves remote homology detection for beta-structural proteins into the twilight zone Bioinformatics. 28: 1216-1222. PMID 22408192 DOI: 10.1093/Bioinformatics/Bts110  0.553
2012 Bryan AW, O'Donnell CW, Menke M, Cowen LJ, Lindquist S, Berger B. STITCHER: Dynamic assembly of likely amyloid and prion β-structures from secondary structure predictions. Proteins. 80: 410-20. PMID 22095906 DOI: 10.1002/Prot.23203  0.496
2012 Daniels NM, Kumar A, Cowen LJ, Menke M. Touring protein space with Matt. Ieee/Acm Transactions On Computational Biology and Bioinformatics / Ieee, Acm. 9: 286-93. PMID 21464511 DOI: 10.1109/Tcbb.2011.70  0.324
2010 Kumar A, Cowen L. Recognition of beta-structural motifs using hidden Markov models trained with simulated evolution Bioinformatics. 26. PMID 20529918 DOI: 10.1093/Bioinformatics/Btq199  0.337
2010 Menke M, Berger B, Cowen L. Markov random fields reveal an N-terminal double beta-propeller motif as part of a bacterial hybrid two-component sensor system. Proceedings of the National Academy of Sciences of the United States of America. 107: 4069-74. PMID 20147619 DOI: 10.1073/Pnas.0909950107  0.598
2009 Kumar A, Cowen L. Augmented training of hidden Markov models to recognize remote homologs via simulated evolution Bioinformatics. 25: 1602-1608. PMID 19389731 DOI: 10.1093/Bioinformatics/Btp265  0.306
2009 Bryan AW, Menke M, Cowen LJ, Lindquist SL, Berger B. BETASCAN: probable beta-amyloids identified by pairwise probabilistic analysis. Plos Computational Biology. 5: e1000333. PMID 19325876 DOI: 10.1371/Journal.Pcbi.1000333  0.546
2008 Ge G, Cowen L, Feng X, Widmer G. Protein coding gene nucleotide substitution pattern in the apicomplexan protozoa Cryptosporidium parvum and Cryptosporidium hominis. Comparative and Functional Genomics. 879023. PMID 18551181 DOI: 10.1155/2008/879023  0.615
2008 Menke M, Berger B, Cowen L. Matt: local flexibility aids protein multiple structure alignment. Plos Computational Biology. 4: e10. PMID 18193941 DOI: 10.1371/Journal.Pcbi.0040010  0.576
2006 McDonnell AV, Menke M, Palmer N, King J, Cowen L, Berger B. Fold recognition and accurate sequence-structure alignment of sequences directing beta-sheet proteins. Proteins. 63: 976-85. PMID 16547930 DOI: 10.1002/Prot.20942  0.599
2005 Menke M, King J, Berger B, Cowen L. Wrap-and-Pack: a new paradigm for beta structural motif recognition with application to recognizing beta trefoils. Journal of Computational Biology : a Journal of Computational Molecular Cell Biology. 12: 777-95. PMID 16108716 DOI: 10.1089/Cmb.2005.12.777  0.583
2002 Cowen L, Bradley P, Menke M, King J, Berger B. Predicting the beta-helix fold from protein sequence data. Journal of Computational Biology : a Journal of Computational Molecular Cell Biology. 9: 261-76. PMID 12015881 DOI: 10.1089/10665270252935458  0.599
2001 Bradley P, Cowen L, Menke M, King J, Berger B. BETAWRAP: successful prediction of parallel beta -helices from primary sequence reveals an association with many microbial pathogens. Proceedings of the National Academy of Sciences of the United States of America. 98: 14819-24. PMID 11752429 DOI: 10.1073/Pnas.251267298  0.602
1998 Awerbuch B, Berger B, Cowen L, Peleg D. Near-Linear Time Construction of Sparse Neighborhood Covers Siam Journal On Computing. 28: 263-277. DOI: 10.1137/S0097539794271898  0.503
1997 Cowen L, Goddard W, Jesurum CE. Defective Coloring Revisited Journal of Graph Theory. 24: 205-219. DOI: 10.1002/(Sici)1097-0118(199703)24:3<205::Aid-Jgt2>3.0.Co;2-T  0.556
1996 Awerbuch B, Berger B, Cowen L, Peleg D. Fast distributed network decompositions and covers Journal of Parallel and Distributed Computing. 39: 105-114. DOI: 10.1006/Jpdc.1996.0159  0.48
1995 Berger B, Cowen L. Scheduling with Concurrency-Based Constraints Journal of Algorithms. 18: 98-123. DOI: 10.1006/Jagm.1995.1003  0.49
1994 Awerbuch B, Berger B, Cowen L, Peleg D. Low-diameter graph decomposition is in NC Random Structures and Algorithms. 5: 441-452. DOI: 10.1002/Rsa.3240050305  0.488
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