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Dennis Shasha

Silver Professor; Professor of Computer Science

    1983 …2020

    Research output per year

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    Research Output

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    2020

    OutPredict: multiple datasets can improve prediction of expression and inference of causality

    Cirrone, J., Brooks, M. D., Bonneau, R., Coruzzi, G. M. & Shasha, D. E., Dec 1 2020, In : Scientific reports. 10, 1, 6804.

    Research output: Contribution to journalArticle

    Open Access
    2019

    Fast methods for finding significant motifs on labelled multi-relational networks

    Micale, G., Pulvirenti, A., Ferro, A., Giugno, R. & Shasha, D., Apr 15 2019, In : Journal of Complex Networks. 7, 6, p. 817-837 21 p.

    Research output: Contribution to journalArticle

    Fast Subgraph Matching Strategies Based on Pattern-Only Heuristics

    Aparo, A., Bonnici, V., Micale, G., Ferro, A., Shasha, D., Pulvirenti, A. & Giugno, R., Mar 1 2019, In : Interdisciplinary Sciences: Computational Life Sciences. 11, 1, p. 21-32 12 p.

    Research output: Contribution to journalArticle

    Network Walking charts transcriptional dynamics of nitrogen signaling by integrating validated and predicted genome-wide interactions

    Brooks, M. D., Cirrone, J., Pasquino, A. V., Alvarez, J. M., Swift, J., Mittal, S., Juang, C. L., Varala, K., Gutiérrez, R. A., Krouk, G., Shasha, D. & Coruzzi, G. M., Dec 1 2019, In : Nature communications. 10, 1, 1569.

    Research output: Contribution to journalArticle

    Open Access

    TACITuS: Transcriptomic data collector, integrator, and selector on big data platform

    Alaimo, S., Di Maria, A., Shasha, D., Ferro, A. & Pulvirenti, A., Nov 22 2019, In : BMC bioinformatics. 20, 366.

    Research output: Contribution to journalArticle

    Open Access

    VersionClimber: Version Upgrades without Tears

    Pradal, C., Cohen-Boulakia, S., Valduriez, P. & Shasha, D., Sep 1 2019, In : Computing in Science and Engineering. 21, 5, p. 87-93 7 p., 8798946.

    Research output: Contribution to journalArticle

    2018

    An adaptive geometric search algorithm for macromolecular scaffold selection

    Jiang, T., Renfrew, P. D., Drew, K., Youngs, N., Butterfoss, G. L., Bonneau, R. & Shasha, D. N., Sep 1 2018, In : Protein Engineering, Design and Selection. 31, 9, p. 345-354 10 p.

    Research output: Contribution to journalArticle

    Open Access

    Fast analytical methods for finding significant labeled graph motifs

    Micale, G., Giugno, R., Ferro, A., Mongiovì, M., Shasha, D. & Pulvirenti, A., Mar 1 2018, In : Data Mining and Knowledge Discovery. 32, 2, p. 504-531 28 p.

    Research output: Contribution to journalArticle

    ParCorr: efficient parallel methods to identify similar time series pairs across sliding windows

    Yagoubi, D. E., Akbarinia, R., Kolev, B., Levchenko, O., Masseglia, F., Valduriez, P. & Shasha, D., Sep 1 2018, In : Data Mining and Knowledge Discovery. 32, 5, p. 1481-1507 27 p.

    Research output: Contribution to journalArticle

    SuperNoder: a tool to discover over-represented modular structures in networks

    Dessì, D., Cirrone, J., Recupero, D. R. & Shasha, D., Sep 10 2018, In : BMC bioinformatics. 19, 1, 1 p.

    Research output: Contribution to journalArticle

    Temporal transcriptional logic of dynamic regulatory networks underlying nitrogen signaling and use in plants

    Varala, K., Marshall-Colón, A., Cirrone, J., Brooks, M. D., Pasquino, A. V., Léran, S., Mittal, S., Rock, T. M., Edwards, M. B., Kim, G. J., Ruffel, S., Richard McCombie, W., Shasha, D. & Coruzzi, G. M., Jun 19 2018, In : Proceedings of the National Academy of Sciences of the United States of America. 115, 25, p. 6494-6499 6 p.

    Research output: Contribution to journalArticle

    2017

    Crowdsourcing Thousands of Specialized Labels: A Bayesian Active Training Approach

    Servajean, M., Joly, A., Shasha, D., Champ, J. & Pacitti, E., Jun 2017, In : IEEE Transactions on Multimedia. 19, 6, p. 1376-1391 16 p., 7819540.

    Research output: Contribution to journalArticle

    2016

    An expanded evaluation of protein function prediction methods shows an improvement in accuracy

    Jiang, Y., Oron, T. R., Clark, W. T., Bankapur, A. R., D'Andrea, D., Lepore, R., Funk, C. S., Kahanda, I., Verspoor, K. M., Ben-Hur, A., Koo, D. C. E., Penfold-Brown, D., Shasha, D., Youngs, N., Bonneau, R., Lin, A., Sahraeian, S. M. E., Martelli, P. L., Profiti, G., Casadio, R. & 127 others, Cao, R., Zhong, Z., Cheng, J., Altenhoff, A., Skunca, N., Dessimoz, C., Dogan, T., Hakala, K., Kaewphan, S., Mehryary, F., Salakoski, T., Ginter, F., Fang, H., Smithers, B., Oates, M., Gough, J., Törönen, P., Koskinen, P., Holm, L., Chen, C. T., Hsu, W. L., Bryson, K., Cozzetto, D., Minneci, F., Jones, D. T., Chapman, S., Bkc, D., Khan, I. K., Kihara, D., Ofer, D., Rappoport, N., Stern, A., Cibrian-Uhalte, E., Denny, P., Foulger, R. E., Hieta, R., Legge, D., Lovering, R. C., Magrane, M., Melidoni, A. N., Mutowo-Meullenet, P., Pichler, K., Shypitsyna, A., Li, B., Zakeri, P., ElShal, S., Tranchevent, L. C., Das, S., Dawson, N. L., Lee, D., Lees, J. G., Sillitoe, I., Bhat, P., Nepusz, T., Romero, A. E., Sasidharan, R., Yang, H., Paccanaro, A., Gillis, J., Sedeño-Cortés, A. E., Pavlidis, P., Feng, S., Cejuela, J. M., Goldberg, T., Hamp, T., Richter, L., Salamov, A., Gabaldon, T., Marcet-Houben, M., Supek, F., Gong, Q., Ning, W., Zhou, Y., Tian, W., Falda, M., Fontana, P., Lavezzo, E., Toppo, S., Ferrari, C., Giollo, M., Piovesan, D., Tosatto, S. C. E., del Pozo, A., Fernández, J. M., Maietta, P., Valencia, A., Tress, M. L., Benso, A., Di Carlo, S., Politano, G., Savino, A., Rehman, H. U., Re, M., Mesiti, M., Valentini, G., Bargsten, J. W., van Dijk, A. D. J., Gemovic, B., Glisic, S., Perovic, V., Veljkovic, V., Veljkovic, N., Almeida-e-Silva, D. C., Vencio, R. Z. N., Sharan, M., Vogel, J., Kansakar, L., Zhang, S., Vucetic, S., Wang, Z., Sternberg, M. J. E., Wass, M. N., Huntley, R. P., Martin, M. J., O'Donovan, C., Robinson, P. N., Moreau, Y., Tramontano, A., Babbitt, P. C., Brenner, S. E., Linial, M., Orengo, C. A., Rost, B., Greene, C. S., Mooney, S. D., Friedberg, I. & Radivojac, P., Sep 7 2016, In : Genome biology. 17, 1, 184.

    Research output: Contribution to journalArticle

    2015

    DNA sequence classification via an expectation maximazation algorithm and neural networks: A case study

    Ma, Q., Wang, J. T. L., Shasha, D. & Wu, C. H., 2015, (Submitted) In : IEEE Transactions on Broadcasting. Special Issue on Knowledge Management, To appear.

    Research output: Contribution to journalArticle

    Netmatchstar: An enhanced Cytoscape network querying app [version 2; referees: 2 approved]

    Rinnone, F., Micale, G., Bonnici, V., Bader, G. D., Shasha, D., Ferro, A., Pulvirenti, A. & Giugno, R., Jan 1 2015, In : F1000Research. 4, 479.

    Research output: Contribution to journalArticle

    Upstart puzzles brighten up

    Shasha, D., Aug 1 2015, In : Communications of the ACM. 58, 8, p. 96 1 p.

    Research output: Contribution to journalArticle

    2014

    Dearly beloved: The five rules to help your parents die a peaceful death

    Shasha, D., Mar 27 2014, Quartz Online magazine.

    Research output: Contribution to specialist publicationArticle

    MiR-Synth: A computational resource for the design of multi-site multi-target synthetic miRNAs

    Laganà, A., Acunzo, M., Romano, G., Pulvirenti, A., Veneziano, D., Cascione, L., Giugno, R., Gasparini, P., Shasha, D., Ferro, A. & Croce, C. M., May 2014, In : Nucleic acids research. 42, 9, p. 5416-5425 10 p.

    Research output: Contribution to journalArticle

    Negative Example Selection for Protein Function Prediction: The NoGO Database

    Youngs, N., Penfold-Brown, D., Bonneau, R. & Shasha, D., Jun 2014, In : PLoS computational biology. 10, 6, e1003644.

    Research output: Contribution to journalArticle

    Synthetic RNAs for gene regulation: deign principles and computational tools

    Laganà, A., Shasha, D. & Croce, C. M., Dec 2014, In : Frontiers in Bioengineering and Biotechnology.

    Research output: Contribution to journalArticle

    2013

    A computational reproducibility benchmark

    Chirigati, F., Troyer, M., Shasha, D. & Freire, J., 2013, In : IEEE Data Engineering Bulletin. 36, 4, p. 54-59

    Research output: Contribution to journalArticle

    A subgraph isomorphism algorithm and its application to biochemical data

    Bonnici, V., Giugno, R., Pulvirenti, A., Shasha, D. & Ferro, A., Apr 22 2013, In : BMC bioinformatics. 14, SUPPL7, S13.

    Research output: Contribution to journalArticle

    Gene regulatory networks in plants: Learning causality from time and perturbation

    Krouk, G., Lingeman, J., Colon, A. M., Coruzzi, G. & Shasha, D., Jun 27 2013, In : Genome biology. 14, 6, 123.

    Research output: Contribution to journalArticle

    GRAPES: A Software for Parallel Searching on Biological Graphs Targeting Multi-Core Architectures

    Giugno, R., Bonnici, V., Bombieri, N., Pulvirenti, A., Ferro, A. & Shasha, D., Oct 22 2013, In : PloS one. 8, 10, e76911.

    Research output: Contribution to journalArticle

    Parametric Bayesian priors and better choice of negative examples improve protein function prediction.

    Youngs, N., Penfold-Brown, D., Drew, K., Shasha, D. & Bonneau, R., May 1 2013, In : Unknown Journal. 29, 9, p. 1190-1198 9 p.

    Research output: Contribution to journalArticle

    2012

    Fast elastic peak detection for mass spectrometry data mining

    Zhang, X., Shasha, D. E., Song, Y. & Wang, J. T. L., Mar 7 2012, In : IEEE Transactions on Knowledge and Data Engineering. 24, 4, p. 634-648 15 p., 5645627.

    Research output: Contribution to journalArticle

    MiR-EdiTar: A database of predicted A-to-I edited miRNA target sites

    Laganà, A., Paone, A., Veneziano, D., Cascione, L., Gasparini, P., Carasi, S., Russo, F., Nigita, G., MacCa, V., Giugno, R., Pulvirenti, A., Shasha, D., Ferro, A. & Croce, C. M., Dec 1 2012, In : Bioinformatics. 28, 23, p. 3166-3168 3 p.

    Research output: Contribution to journalArticle

    2011

    Rational design of temperature-sensitive alleles using computational structure prediction

    Poultney, C. S., Butterfoss, G. L., Gutwein, M. R., Drew, K., Gresham, D., Gunsalus, K. C., Shasha, D. E. & Bonneau, R., Sep 2 2011, In : PloS one. 6, 9, e23947.

    Research output: Contribution to journalArticle

    Repeatability and workability evaluation of SIGMOD 2011

    Bonnet, P., Manegold, S., Bjørling, M., Cao, W., Gonzalez, J., Granados, J., Hall, N., Idreos, S., Ivanova, M., Johnson, R., Koop, D., Kraska, T., Müller, R., Olteanu, D., Papotti, P., Reilly, C., Tsirogiannis, D., Yu, C., Freire, J. & Shasha, D., Jun 1 2011, In : SIGMOD Record. 40, 2, p. 45-48 4 p.

    Research output: Contribution to journalArticle

    The Proteome Folding Project: Proteome-scale prediction of structure and function

    Drew, K., Winters, P., Butterfoss, G. L., Berstis, V., Uplinger, K., Armstrong, J., Riffle, M., Schweighofer, E., Bovermann, B., Goodlett, D. R., Davis, T. N., Shasha, D., Malmström, L. & Bonneau, R., Nov 1 2011, In : Genome Research. 21, 11, p. 1981-1994 14 p.

    Research output: Contribution to journalArticle

    2010

    Estimation of genome-wide redundancy in Arabidopsis thaliana

    Chen, H-W., Bandyopadhyay, S., Shasha, D. & Birnbaum, K., 2010, In : BMC Evolutionary Biology. 10, p. 357

    Research output: Contribution to journalArticle

    Predicting genome-wide redundancy using machine learning

    Chen, H. W., Bandyopadhyay, S., Shasha, D. E. & Birnbaum, K. D., Nov 22 2010, In : BMC Evolutionary Biology. 10, 1, 357.

    Research output: Contribution to journalArticle

    Predictive network modeling of the high-resolution dynamic plant transcriptome in response to nitrate

    Krouk, G., Mirowski, P., LeCun, Y., Shasha, D. E. & Coruzzi, G. M., Dec 23 2010, In : Genome biology. 11, 12, R123.

    Research output: Contribution to journalArticle

    SING: Subgraph search In Non-homogeneous Graphs

    Di Natale, R., Ferro, A., Giugno, R., Mongiovì, M., Pulvirenti, A. & Shasha, D., Feb 19 2010, In : BMC bioinformatics. 11, 96.

    Research output: Contribution to journalArticle

    VirtualPlant: A software platform to support systems biology research

    Katari, M. S., Nowicki, S. D., Aceituno, F. F., Nero, D., Kelfer, J., Thompson, L. P., Cabello, J. M., Davidson, R. S., Goldberg, A. P., Shasha, D. E., Coruzzi, G. M. & Gutiérrez, R. A., Feb 1 2010, In : Plant physiology. 152, 2, p. 500-515 16 p.

    Research output: Contribution to journalArticle

    2009

    A systems approach uncovers restrictions for signal interactions regulating genome-wide responses to nutritional cues in Arabidopsis

    Krouk, G., Tranchina, D., Lejay, L., Cruikshank, A. A., Shasha, D., Coruzzi, G. M. & Gutiérrez, R. A., Mar 1 2009, In : PLoS computational biology. 5, 3

    Research output: Contribution to journalArticle

    DNA hash pooling and its application

    Shasha, D. & Amos, M., 2009, In : International Journal of Nanotechnology and Molecular Computation. 1, 1, p. 18-32 arXiv: 0705.3597.

    Research output: Contribution to journalArticle

    miRo: A miRNA knowledge base

    Laganà, A., Forte, S., Giudice, A., Arena, M. R., Puglisi, P. L., Giugno, R., Pulvirenti, A., Shasha, D. & Ferro, A., 2009, In : Journal of Biological Databases and Curation, Oxford University Press.

    Research output: Contribution to journalArticle

    MiRò: A miRNA knowledge base

    Laganà, A., Forte, S., Giudice, A., Arena, M. R., Puglisi, P. L., Giugno, R., Pulvirenti, A., Shasha, D. & Ferro, A., 2009, In : Database. 2009, bap008.

    Research output: Contribution to journalArticle

    Repeatability & Workability Evaluation of SIGMOD 2009

    Manegold, S., Manolescu, I., Afanasiev, L., Feng, J., Gou, G., Hadjieleftheriou, M., Harizopoulos, S., Kalnis, P., Karanasos, K., Laurent, D., Lupu, M., Onose, N., Ré, C., Sans, V., Senellart, P., Wu, T. & Shasha, D., Sep 2009, In : SIGMOD Record. 38, 3, p. 40-43 4 p.

    Research output: Contribution to journalArticle

    Revelation on demand

    Anciaux, N., Benzine, M., Bouganim, L., Pucheral, P. & Shasha, D., Apr 1 2009, In : Distributed and Parallel Databases. 25, 1-2, p. 5-28 24 p.

    Research output: Contribution to journalArticle

    2008

    An integrated genetic, genomic and systems approach defines gene networks regulated by the interaction of light and carbon signaling pathways in Arabidopsis

    Thum, K. E., Shin, M. J., Gutiérrez, R. A., Mukherjee, I., Katari, M. S., Nero, D., Shasha, D. & Coruzzi, G. M., Apr 4 2008, In : BMC Systems Biology. 2, 31.

    Research output: Contribution to journalArticle

    GraphClust: A method for clustering database of graphs

    Reforgiato, D., Gutierrez, R. & Shasha, D., Dec 1 2008, In : Journal of Information and Knowledge Management. 7, 4, p. 231-241 11 p.

    Research output: Contribution to journalArticle

    GraphFind: Enhancing graph searching by low support data mining techniques

    Ferro, A., Giugno, R., Mongiovì, M., Pulvirenti, A., Skripin, D. & Shasha, D., Apr 25 2008, In : BMC bioinformatics. 9, SUPPL. 4, S10.

    Research output: Contribution to journalArticle

    The repeatability experiment of SIGMOD 2008

    Manolesc, I., Afanasiev, L., Arion, A., Dittrich, J., Manegold, S., Polyzotis, N., Schnaitter, K., Senellart, P., Zoupanos, S. & Shasha, D., Mar 2008, In : SIGMOD Record. 37, 1, p. 39-45 7 p.

    Research output: Contribution to journalArticle

    2007

    Homology search for genes

    Cui, X., Vinař, T., Brejová, B., Shasha, D. & Li, M., Jul 1 2007, In : Bioinformatics. 23, 13, p. i97-i103

    Research output: Contribution to journalArticle

    Insights into the genomic nitrate response using genetics and the Sungear Software System

    Gutiérrez, R. A., Gifford, M. L., Poultney, C., Wang, R., Shasha, D. E., Coruzzi, G. M. & Crawford, N. M., Jul 1 2007, In : Journal of Experimental Botany. 58, 9, p. 2359-2367 9 p.

    Research output: Contribution to journalArticle

    NetMatch: A Cytoscape plugin for searching biological networks

    Ferro, A., Giugno, R., Pigola, G., Pulvirenti, A., Skripin, D., Bader, G. D. & Shasha, D., Apr 1 2007, In : Bioinformatics. 23, 7, p. 910-912 3 p.

    Research output: Contribution to journalArticle

    Qualitative network models and genome-wide expression data define carbon/ nitrogen-responsive molecular machines in Arabidopsis

    Gutiérrez, R. A., Lejay, L. V., Dean, A., Chiaromonte, F., Shasha, D. E. & Coruzzi, G. M., Jan 11 2007, In : Genome biology. 8, 1, R7.

    Research output: Contribution to journalArticle