Dennis Shasha

Silver Professor; Professor of Computer Science

1983 …2019
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Research Output 1983 2019

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2019

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

Heuristic algorithms
Experiments
Heuristics

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., Dec 1 2019, In : Nature Communications. 10, 1, 1569.

Research output: Contribution to journalArticle

Open Access
walking
genome
charts
Walking
Transcription Factors

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

Application programs
Virtual reality
Linux
2018

An adaptive geometric search algorithm for macromolecular scaffold selection

Jiang, T., Renfrew, P. D., Drew, K., Youngs, N., Butterfoss, G., Bonneau, R. & Shasha, D., Sep 1 2018, In : Protein engineering, design & selection : PEDS. 31, 9, p. 345-354 10 p.

Research output: Contribution to journalArticle

Open Access
Scaffolds (biology)
Scaffolds
Proteins
Peptidomimetics
Catalytic Domain

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

Time series
Telecommunication networks
Fusion reactions
Monitoring
Sensors

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

Protein Interaction Maps
Food Chain
Proteins
Labels
Disjoint

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., 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

Nitrogen
Gene Regulatory Networks
Transcription Factors
Genes
Genome
2017

Crowdsourcing Thousands of Specialized Labels: A Bayesian Active Training Approach

Servajean, M., Joly, A., Shasha, D., Champ, J. & Pacitti, E., Jun 1 2017, In : IEEE Transactions on Multimedia. 19, 6, p. 1376-1391 16 p., 7819540.

Research output: Contribution to journalArticle

Labels
Labeling
Computer vision
Learning systems

Fast analytical methods for finding significant labeled graph motifs

Micale, G., Giugno, R., Ferro, A., Mongiovì, M., Shasha, D. & Pulvirenti, A., Nov 2 2017, (Accepted/In press) In : Data Mining and Knowledge Discovery. p. 1-28 28 p.

Research output: Contribution to journalArticle

Labels
Analytical models
2016

A collaborative approach to computational reproducibility

Chirigati, F., Capone, R., Rampin, R., Freire, J. & Shasha, D., Jul 1 2016, In : Information Systems. 59, p. 95-97 3 p.

Research output: Contribution to journalArticle

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

protein
prediction
Proteins
proteins
methodology
Sleep
Sleep

Upstart puzzles: Sleep no more

Shasha, D., Apr 1 2016, In : Communications of the ACM. 59, 4, p. 96 1 p.

Research output: Contribution to journalArticle

Sleep

Upstart puzzles: Ice trap

Shasha, D., Jan 1 2016, In : Communications of the ACM. 59, 1, p. 136 1 p.

Research output: Contribution to journalArticle

Ice
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., 2015, In : F1000Research. 4, 479.

Research output: Contribution to journalArticle

Application programs

Take your seats

Shasha, D., Jan 28 2015, In : Communications of the ACM. 58, 2, p. 104 1 p.

Research output: Contribution to journalArticle

Seats

Upstart puzzles: Strategic friendship

Shasha, D., May 1 2015, In : Communications of the ACM. 58, 5, p. 88 1 p.

Research output: Contribution to journalArticle

Upstart puzzles: Auction triplets

Shasha, D., Nov 1 2015, In : Communications of the ACM. 58, 11, p. 136 1 p.

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

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., 2014, In : Database. 2009, bap008.

Research output: Contribution to journalArticle

Knowledge Bases
MicroRNAs
microRNA
phenotype
Databases

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., 2014, In : Nucleic Acids Research. 42, 9, p. 5416-5425 10 p.

Research output: Contribution to journalArticle

MicroRNAs
RNA Interference
Genes
Gene Expression Regulation
Epidermal Growth Factor Receptor

Negative Example Selection for Protein Function Prediction: The NoGO Database

Youngs, N., Penfold-Brown, D., Bonneau, R. & Shasha, D., 2014, In : PLoS Computational Biology. 10, 6, e1003644.

Research output: Contribution to journalArticle

Genes
Databases
Proteins
Protein
protein

Proving without teaching/ teaching without proving

Shasha, D., Nov 1 2014, In : Communications of the ACM. 57, 11, p. 120 1 p.

Research output: Contribution to journalArticle

Teaching

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

Subgraph
Isomorphism
Graph in graph theory
C++
Biological Networks

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

Krouk, G., Lingeman, J., Marshall Colon, A., Coruzzi, G. & Shasha, D., Jun 27 2013, (Accepted/In press) In : Genome Biology. p. 123 1 p.

Research output: Contribution to journalArticle

Systems Biology
Gene Regulatory Networks
Causality
learning
perturbation

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

Software
Databases
Protein Interaction Maps
Proteins
Chemical compounds

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 : Bioinformatics. 29, 9, p. 1190-1198 9 p.

Research output: Contribution to journalArticle

Proteins
Protein
Prediction
Proteome
Yeasts
2012

Fast elastic peak detection for mass spectrometry data mining

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

Research output: Contribution to journalArticle

Liquid chromatography
Mass spectrometry
Data mining
Data structures
Time series

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 2012, In : Bioinformatics. 28, 23, p. 3166-3168 3 p.

Research output: Contribution to journalArticle

MicroRNA
Binding sites
MicroRNAs
Databases
Target
2011
Cytokinins
Nitrates
Nitrogen
Economics
Transcriptome

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

Alleles
alleles
Temperature
prediction
mutation

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 2011, In : SIGMOD Record (ACM Special Interest Group on Management of Data). 40, 2, p. 45-48 4 p.

Research output: Contribution to journalArticle

Experiments
Linux

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 2011, In : Genome Research. 21, 11, p. 1981-1994 14 p.

Research output: Contribution to journalArticle

Proteome
Gene Ontology
Human Genome
Arabidopsis
Diptera
2010

An interview with Michael Rabin

Shasha, D., Feb 1 2010, In : Communications of the ACM. 53, 2, p. 37-42 6 p.

Research output: Contribution to journalArticle

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., 2010, In : BMC Evolutionary Biology. 10, 1, 357.

Research output: Contribution to journalArticle

artificial intelligence
genome
gene
genes
gene duplication

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

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

Research output: Contribution to journalArticle

Transcriptome
transcriptome
Nitrates
nitrates
nitrate

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

Subgraph
Databases
Graph in graph theory
Image understanding
Chemical compounds

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., Coruzzi, G. & Gutiérrez, R. A., Feb 2010, In : Plant Physiology. 152, 2, p. 500-515 16 p.

Research output: Contribution to journalArticle

support systems
Systems Biology
Gene Regulatory Networks
Arabidopsis
Software
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 2009, In : PLoS Computational Biology. 5, 3

Research output: Contribution to journalArticle

Arabidopsis
Systems Analysis
Gene expression
Cues
Genome

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

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 (ACM Special Interest Group on Management of Data). 38, 3, p. 40-43 4 p.

Research output: Contribution to journalArticle

Feedback
Experiments

Revelation on demand

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

Research output: Contribution to journalArticle

Data warehouses
Marketing
Sales
Health
Statistics
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

Arabidopsis
Gene Networks
Signaling Pathways
Gene Regulatory Networks
Systems Analysis