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Dennis Shasha - Publications

Affiliations: 
New York University, New York, NY, United States 
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35 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 Shen B, Coruzzi G, Shasha D. EnsInfer: a simple ensemble approach to network inference outperforms any single method. Bmc Bioinformatics. 24: 114. PMID 36964499 DOI: 10.1186/s12859-023-05231-1  0.524
2020 Cirrone J, Brooks MD, Bonneau R, Coruzzi GM, Shasha DE. Author Correction: OutPredict: multiple datasets can improve prediction of expression and inference of causality. Scientific Reports. 10: 14141. PMID 32811842 DOI: 10.1038/S41598-020-69883-2  0.641
2020 Cirrone J, Brooks MD, Bonneau R, Coruzzi GM, Shasha DE. OutPredict: multiple datasets can improve prediction of expression and inference of causality. Scientific Reports. 10: 6804. PMID 32321967 DOI: 10.1038/S41598-020-63347-3  0.676
2019 Brooks MD, Cirrone J, Pasquino AV, Alvarez JM, Swift J, Mittal S, Juang CL, Varala K, Gutiérrez RA, Krouk G, Shasha D, Coruzzi GM. Network Walking charts transcriptional dynamics of nitrogen signaling by integrating validated and predicted genome-wide interactions. Nature Communications. 10: 1569. PMID 30952851 DOI: 10.1038/S41467-019-09522-1  0.568
2018 Varala K, Marshall-Colón A, Cirrone J, Brooks MD, Pasquino AV, Léran S, Mittal S, Rock TM, Edwards MB, Kim GJ, Ruffel S, McCombie WR, Shasha D, Coruzzi GM. Temporal transcriptional logic of dynamic regulatory networks underlying nitrogen signaling and use in plants. Proceedings of the National Academy of Sciences of the United States of America. PMID 29769331 DOI: 10.1073/Pnas.1721487115  0.593
2017 Servajean M, Joly A, Shasha D, Champ J, Pacitti E. Crowdsourcing Thousands of Specialized Labels: A Bayesian Active Training Approach Ieee Transactions On Multimedia. 19: 1376-1391. DOI: 10.1109/Tmm.2017.2653763  0.316
2017 Micale G, Giugno R, Ferro A, Mongiovì M, Shasha D, Pulvirenti A. Fast analytical methods for finding significant labeled graph motifs Data Mining and Knowledge Discovery. 32: 504-531. DOI: 10.1007/S10618-017-0544-8  0.306
2016 Jiang Y, Oron TR, Clark WT, Bankapur AR, D'Andrea D, Lepore R, Funk CS, Kahanda I, Verspoor KM, Ben-Hur A, Koo da CE, Penfold-Brown D, Shasha D, Youngs N, Bonneau R, et al. An expanded evaluation of protein function prediction methods shows an improvement in accuracy. Genome Biology. 17: 184. PMID 27604469 DOI: 10.1186/S13059-016-1037-6  0.752
2016 Youngs N, Shasha D, Bonneau R. Positive-Unlabeled Learning in the Face of Labeling Bias Proceedings - 15th Ieee International Conference On Data Mining Workshop, Icdmw 2015. 639-645. DOI: 10.1109/ICDMW.2015.207  0.743
2014 Youngs N, Penfold-Brown D, Bonneau R, Shasha D. Negative example selection for protein function prediction: the NoGO database. Plos Computational Biology. 10: e1003644. PMID 24922051 DOI: 10.1371/Journal.Pcbi.1003644  0.78
2013 Krouk G, Lingeman J, Colon AM, Coruzzi G, Shasha D. Gene regulatory networks in plants: learning causality from time and perturbation. Genome Biology. 14: 123. PMID 23805876 DOI: 10.1186/Gb-2013-14-6-123  0.601
2013 Youngs N, Penfold-Brown D, Drew K, Shasha D, Bonneau R. Parametric Bayesian priors and better choice of negative examples improve protein function prediction. Bioinformatics (Oxford, England). 29: 1190-8. PMID 23511543 DOI: 10.1093/Bioinformatics/Btt110  0.767
2012 Bonnici V, Giugno R, Pulvirenti A, Shasha D, Ferro A. Core algorithms to search in biological structured data Embnet.Journal. 18: 65-66. DOI: 10.14806/Ej.18.A.416  0.323
2011 Ruffel S, Krouk G, Ristova D, Shasha D, Birnbaum KD, Coruzzi GM. Nitrogen economics of root foraging: transitive closure of the nitrate-cytokinin relay and distinct systemic signaling for N supply vs. demand. Proceedings of the National Academy of Sciences of the United States of America. 108: 18524-9. PMID 22025711 DOI: 10.1073/Pnas.1108684108  0.558
2011 Poultney CS, Butterfoss GL, Gutwein MR, Drew K, Gresham D, Gunsalus KC, Shasha DE, Bonneau R. Rational design of temperature-sensitive alleles using computational structure prediction. Plos One. 6: e23947. PMID 21912654 DOI: 10.1371/Journal.Pone.0023947  0.74
2011 Drew K, Winters P, Butterfoss GL, Berstis V, Uplinger K, Armstrong J, Riffle M, Schweighofer E, Bovermann B, Goodlett DR, Davis TN, Shasha D, Malmström L, Bonneau R. The Proteome Folding Project: proteome-scale prediction of structure and function. Genome Research. 21: 1981-94. PMID 21824995 DOI: 10.1101/Gr.121475.111  0.572
2010 Krouk G, Mirowski P, LeCun Y, Shasha DE, Coruzzi GM. Predictive network modeling of the high-resolution dynamic plant transcriptome in response to nitrate. Genome Biology. 11: R123. PMID 21182762 DOI: 10.1186/Gb-2010-11-12-R123  0.578
2010 Chen HW, Bandyopadhyay S, Shasha DE, Birnbaum KD. Predicting genome-wide redundancy using machine learning. Bmc Evolutionary Biology. 10: 357. PMID 21087504 DOI: 10.1186/1471-2148-10-357  0.53
2010 Katari MS, Nowicki SD, Aceituno FF, Nero D, Kelfer J, Thompson LP, Cabello JM, Davidson RS, Goldberg AP, Shasha DE, Coruzzi GM, Gutiérrez RA. VirtualPlant: a software platform to support systems biology research. Plant Physiology. 152: 500-15. PMID 20007449 DOI: 10.1104/Pp.109.147025  0.577
2009 Krouk G, Tranchina D, Lejay L, Cruikshank AA, Shasha D, Coruzzi GM, Gutiérrez RA. A systems approach uncovers restrictions for signal interactions regulating genome-wide responses to nutritional cues in Arabidopsis. Plos Computational Biology. 5: e1000326. PMID 19300494 DOI: 10.1371/Journal.Pcbi.1000326  0.533
2008 Thum KE, Shin MJ, Gutiérrez RA, Mukherjee I, Katari MS, Nero D, Shasha D, Coruzzi GM. An integrated genetic, genomic and systems approach defines gene networks regulated by the interaction of light and carbon signaling pathways in Arabidopsis. Bmc Systems Biology. 2: 31. PMID 18387196 DOI: 10.1186/1752-0509-2-31  0.532
2007 Gutiérrez RA, Gifford ML, Poultney C, Wang R, Shasha DE, Coruzzi GM, Crawford NM. Insights into the genomic nitrate response using genetics and the Sungear Software System. Journal of Experimental Botany. 58: 2359-67. PMID 17470441 DOI: 10.1093/Jxb/Erm079  0.751
2007 Gutiérrez RA, Lejay LV, Dean A, Chiaromonte F, Shasha DE, Coruzzi GM. Qualitative network models and genome-wide expression data define carbon/nitrogen-responsive molecular machines in Arabidopsis. Genome Biology. 8: R7. PMID 17217541 DOI: 10.1186/Gb-2007-8-1-R7  0.534
2007 Poultney CS, Gutiérrez RA, Katari MS, Gifford ML, Paley WB, Coruzzi GM, Shasha DE. Sungear: interactive visualization and functional analysis of genomic datasets. Bioinformatics (Oxford, England). 23: 259-61. PMID 17018536 DOI: 10.1093/Bioinformatics/Btl496  0.753
2005 Gutiérrez RA, Shasha DE, Coruzzi GM. Systems biology for the virtual plant. Plant Physiology. 138: 550-4. PMID 15955912 DOI: 10.1104/Pp.104.900150  0.474
2005 Zhao X, Zhang X, Neylon T, Shasha D. Incremental methods for simple problems in time series: Algorithms and experiments Proceedings of the International Database Engineering and Applications Symposium, Ideas. 2005: 3-14. DOI: 10.1109/IDEAS.2005.35  0.737
2004 Lejay LV, Shasha DE, Palenchar PM, Kouranov AY, Cruikshank AA, Chou MF, Coruzzi GM. Adaptive combinatorial design to explore large experimental spaces: approach and validation. Systems Biology. 1: 206-12. PMID 17051692 DOI: 10.1049/sb:20045020  0.529
2003 Thum KE, Shasha DE, Lejay LV, Coruzzi GM. Light- and carbon-signaling pathways. Modeling circuits of interactions. Plant Physiology. 132: 440-52. PMID 12805577 DOI: 10.1104/Pp.103.022780  0.483
2003 Levesque M, Shasha D, Kim W, Surette MG, Benfey PN. Trait-to-gene: a computational method for predicting the function of uncharacterized genes. Current Biology : Cb. 13: 129-33. PMID 12546786 DOI: 10.1016/S0960-9822(03)00009-5  0.381
2001 Shasha DE, Kouranov AY, Lejay LV, Chou MF, Coruzzi GM. Using combinatorial design to study regulation by multiple input signals. A tool for parsimony in the post-genomics era. Plant Physiology. 127: 1590-4. PMID 11743103 DOI: 10.1104/Pp.010683  0.534
2001 Wang JTL, Ma Q, Shasha D, Wu CH. New techniques for extracting features from protein sequences Ibm Systems Journal. 40: 426-441. DOI: 10.1147/Sj.402.0426  0.319
2001 Cochinwala M, Kurien V, Lalk G, Shasha D. Efficient data reconciliation Information Sciences. 137: 1-15. DOI: 10.1016/S0020-0255(00)00070-0  0.343
1999 Wang JT, Rozen S, Shapiro BA, Shasha D, Wang Z, Yin M. New techniques for DNA sequence classification. Journal of Computational Biology : a Journal of Computational Molecular Cell Biology. 6: 209-18. PMID 10421523  0.338
1996 Wang JT, Marr TG, Shasha D, Shapiro BA, Chirn GW, Lee TY. Complementary classification approaches for protein sequences. Protein Engineering. 9: 381-6. PMID 8795038 DOI: 10.1093/Protein/9.5.381  0.309
1994 Wang JT, Marr TG, Shasha D, Shapiro BA, Chirn GW. Discovering active motifs in sets of related protein sequences and using them for classification. Nucleic Acids Research. 22: 2769-75. PMID 8052532 DOI: 10.1093/Nar/22.14.2769  0.343
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