Dennis Shasha

2024

ArcMatch: high-performance subgraph matching for labeled graphs by exploiting edge domains

Bonnici, V., Grasso, R., Micale, G., Maria, A. D., Shasha, D., Pulvirenti, A. & Giugno, R., Nov 2024, In: Data Mining and Knowledge Discovery. 38, 6, p. 3868-3921

Research output: Contribution to journal › Article › peer-review

Open Access

AutoTag: automated metadata tagging for film post-production

Sandoval-Castañeda, M., Copti, S. & Shasha, D., Jan 2024, In: Multimedia Tools and Applications. 83, 3, p. 6731-6753 23 p.

Research output: Contribution to journal › Article › peer-review

Open Access

Bankruptcy prediction with low-quality financial information

da Silva Mattos, E. & Shasha, D., Mar 1 2024, In: Expert Systems with Applications. 237, 121418.

Research output: Contribution to journal › Article › peer-review

Bipartite networks represent causality better than simple networks: evidence, algorithms, and applications

Shen, B., Curozzi, G. & Shasha, D., May 2024, In: Frontiers in Genetics. 15, 1371607.

Research output: Contribution to journal › Article › peer-review

Open Access

Machine Learning-Enhanced Pairs Trading

Hadad, E., Hodarkar, S., Lemeneh, B. & Shasha, D., Jun 2024, In: Forecasting. 6, 2, p. 434-455 22 p.

Research output: Contribution to journal › Article › peer-review

Open Access

Phylogenetically diverse wild plant species use common biochemical strategies to thrive in the Atacama Desert

Dussarrat, T., Nilo-Poyanco, R., Moyano, T. C., Prigent, S., Jeffers, T. L., Díaz, F. P., Decros, G., Audi, L., Sondervan, V. M., Shen, B., Araus, V., Rolin, D., Shasha, D., Coruzzi, G. M., Gibon, Y., Latorre, C., Pétriacq, P. & Gutiérrez, R. A., Jun 7 2024, In: Journal of Experimental Botany. 75, 11, p. 3596-3611 16 p.

Research output: Contribution to journal › Article › peer-review

2023

BugDoc: Iterative debugging and explanation of pipeline

Lourenço, R., Freire, J., Simon, E., Weber, G. & Shasha, D., Jan 2023, In: VLDB Journal. 32, 1, p. 75-101 27 p.

Research output: Contribution to journal › Article › peer-review

Cooperation in the Commons

Shasha, D., Mar 23 2023, In: Communications of the ACM. 66, 4, p. 104 and 103

Research output: Contribution to journal › Article › peer-review

Data Structures for Data-Intensive Applications: Tradeoffs and Design Guidelines

Athanassoulis, M., Idreos, S. & Shasha, D., Jul 31 2023, In: Foundations and Trends in Databases. 13, 1-2, p. 1-168 168 p.

Research output: Contribution to journal › Article › peer-review

EnsInfer: a simple ensemble approach to network inference outperforms any single method

Shen, B., Coruzzi, G. & Shasha, D., Dec 2023, In: BMC bioinformatics. 24, 1, 114.

Research output: Contribution to journal › Article › peer-review

Open Access

Forgetful Forests: Data Structures for Machine Learning on Streaming Data under Concept Drift

Yuan, Z., Sun, Y. & Shasha, D., Jun 2023, In: Algorithms. 16, 6, 278.

Research output: Contribution to journal › Article › peer-review

Open Access

Seesaw Gold

Shasha, D., Dec 21 2023, In: Communications of the ACM. 67, 1, p. 136 and 135

Research output: Contribution to journal › Article › peer-review

Open Access

2022

Exclusivity probes

Shasha, D., Jul 2022, In: Communications of the ACM. 65, 7, p. 96+95

Research output: Contribution to journal › Article › peer-review

Orbit design

Shasha, D., Jan 2022, In: Communications of the ACM. 65, 1, p. 120 1 p.

Research output: Contribution to journal › Article › peer-review

2021

BestNeighbor: efficient evaluation of kNN queries on large time series databases

Levchenko, O., Kolev, B., Yagoubi, D. E., Akbarinia, R., Masseglia, F., Palpanas, T., Shasha, D. & Valduriez, P., Feb 2021, In: Knowledge and Information Systems. 63, 2, p. 349-378 30 p.

Research output: Contribution to journal › Article › peer-review

Open Access

Cell-by-cell dissection of phloem development links a maturation gradient to cell specialization

Roszak, P., Heo, J. O., Blob, B., Toyokura, K., Sugiyama, Y., de Luis Balaguer, M. A., Lau, W. W. Y., Hamey, F., Cirrone, J., Madej, E., Bouatta, A. M., Wang, X., Guichard, M., Ursache, R., Tavares, H., Verstaen, K., Wendrich, J., Melnyk, C. W., Oda, Y. & Shasha, D. & 12 others, Ahnert, S. E., Saeys, Y., De Rybel, B., Heidstra, R., Scheres, B., Grossmann, G., Mähönen, A. P., Denninger, P., Göttgens, B., Sozzani, R., Birnbaum, K. D. & Helariutta, Y., Dec 24 2021, In: Science. 374, 6575, eaba5531.

Research output: Contribution to journal › Article › peer-review

Open Access

Pheniqs 2.0: accurate, high-performance Bayesian decoding and confidence estimation for combinatorial barcode indexing

Galanti, L., Shasha, D. & Gunsalus, K. C., Dec 2021, In: BMC bioinformatics. 22, 1, 359.

Research output: Contribution to journal › Article › peer-review

Open Access

SafePredict: A Meta-Algorithm for Machine Learning That Uses Refusals to Guarantee Correctness

Kocak, M. A., Ramirez, D., Erkip, E. & Shasha, D. E., Feb 1 2021, In: IEEE Transactions on Pattern Analysis and Machine Intelligence. 43, 2, p. 663-678 16 p., 8784215.

Research output: Contribution to journal › Article › peer-review

Open Access

Verifying concurrent multicopy search structures

Patel, N., Krishna, S., Shasha, D. & Wies, T., Oct 2021, In: Proceedings of the ACM on Programming Languages. 5, OOPSLA, 113.

Research output: Contribution to journal › Article › peer-review

Open Access

2020

Inexpensive, non-invasive biomarkers predict Alzheimer transition using machine learning analysis of the Alzheimer’s Disease Neuroimaging (ADNI) database

for the Alzheimer's Disease Neuroimaging Initiative, Jul 2020, In: PloS one. 15, 7, e0235663.

Research output: Contribution to journal › Article › peer-review

Open Access

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 journal › Article › peer-review

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 journal › Article › peer-review

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 journal › Article › peer-review

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 journal › Article › peer-review

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 journal › Article › peer-review

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 journal › Article › peer-review

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 journal › Article › peer-review

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 journal › Article › peer-review

Go with the flow: Compositional abstractions for concurrent data structures

Krishna, S., Shasha, D. & Wies, T., Jan 2018, In: Proceedings of the ACM on Programming Languages. 2, POPL, 37.

Research output: Contribution to journal › Article › peer-review

Open Access

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 journal › Article › peer-review

Open Access

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, p. 318 1 p., 318.

Research output: Contribution to journal › Article › peer-review

Open Access

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 journal › Article › peer-review

Open Access

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 journal › Article › peer-review

Open Access

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 journal › Article › peer-review

Open Access

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 journal › Article › peer-review

Netmatchstar: An enhanced Cytoscape network querying app

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 journal › Article › peer-review

Open Access

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 publication › Article

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 journal › Article › peer-review

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 journal › Article › peer-review

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 journal › Article › peer-review

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 journal › Article › peer-review

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 journal › Article › peer-review

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 journal › Article › peer-review

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 journal › Article › peer-review

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 journal › Article › peer-review

Open Access

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 journal › Article › peer-review

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 journal › Article › peer-review

2011

Nitrogen economics of root foraging: Transitive closure of the nitrate-cytokinin relay and distinct systemic signaling for N supply vs. demand

Ruffel, S., Krouk, G., Ristova, D., Shasha, D., Birnbaum, K. D. & Coruzzi, G. M., Nov 8 2011, In: Proceedings of the National Academy of Sciences of the United States of America. 108, 45, p. 18524-18529 6 p.

Research output: Contribution to journal › Article › peer-review

Open Access

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 journal › Article › peer-review

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. 40, 2, p. 45-48 4 p.

Research output: Contribution to journal › Article › peer-review

Open Access

Dennis Shasha

Research output

Search results