Dennis Shasha

Silver Professor; Professor of Computer Science

1983 …2019
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Research Output 1983 2019

2019

Deferred runtime pipelining for contentious multicore software transactions

Mu, S., Angel, S. & Shasha, D., Mar 25 2019, Proceedings of the 14th EuroSys Conference 2019. Association for Computing Machinery, Inc, 3303966. (Proceedings of the 14th EuroSys Conference 2019).

Research output: Chapter in Book/Report/Conference proceedingConference contribution

Throughput
Concurrency control
Data storage equipment
Opacity
Network protocols

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

Randomized anti-counterfeiting

Shasha, D., Jan 1 2019, In : Communications of the ACM. 62, 1

Research output: Contribution to journalShort survey

Simple pattern-only heuristics lead to fast subgraph matching strategies on very large networks

Aparo, A., Bonnici, V., Micale, G., Ferro, A., Shasha, D., Pulvirenti, A. & Giugno, R., Jan 1 2019, Practical Applications of Computational Biology and Bioinformatics, 12th International Conference. Rocha, M., Mohamad, M. S., De Paz, J. F., Fdez-Riverola, F. & Gonzalez, P. (eds.). Springer-Verlag, p. 131-138 8 p. (Advances in Intelligent Systems and Computing; vol. 803).

Research output: Chapter in Book/Report/Conference proceedingConference contribution

Computational complexity

Upstart puzzles fighting for lava

Shasha, D., Apr 1 2019, In : Communications of the ACM. 62, 4

Research output: Contribution to journalComment/debate

Upstart puzzles opioid games

Shasha, D., Jul 1 2019, In : Communications of the ACM. 62, 7, p. 95-96 2 p.

Research output: Contribution to journalShort survey

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

Finding October

Shasha, D., Apr 1 2018, In : Communications of the ACM. 61, 4

Research output: Contribution to journalShort survey

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

Point pattern search in big data

Porto, F., Krone-Martins, A., Rittmeyer, J. N., Valduriez, P., Ogasawara, E. & Shasha, D., Jul 9 2018, Scientific and Statistical Database Management - 30th International Conference, SSDBM 2018, Proceedings. Bohlen, M., Gamper, J., Kroger, P. & Sacharidis, D. (eds.). Association for Computing Machinery

Research output: Chapter in Book/Report/Conference proceedingConference contribution

Parallel algorithms
Big data

RadiusSketch: Massively distributed indexing of time series

Yagoubi, D. E., Akbarinia, R., Masseglia, F. & Shasha, D., Jan 16 2018, Proceedings - 2017 International Conference on Data Science and Advanced Analytics, DSAA 2017. Institute of Electrical and Electronics Engineers Inc., Vol. 2018-January. p. 262-271 10 p.

Research output: Chapter in Book/Report/Conference proceedingConference contribution

Indexing
Time series
Response Time
Query
Random Projection

Scientific data analysis using data-intensive scalable computing: The SciDISC project

Valduriez, P., Mattoso, M., Akbarinia, R., Borges, H., Camata, J., Coutinho, A., Gaspar, D., Lemus, N., Liu, J., Lustosa, H., Masseglia, F., Silva, F. N. D., Silva, V., Souza, R., Ocaña, K., Ogasawara, E., Oliveira, D. D., Pacitti, E., Porto, F. & Shasha, D., Jan 1 2018, In : CEUR Workshop Proceedings. 2170, p. 1-8 8 p.

Research output: Contribution to journalConference article

Electric sparks

Spark-Parsketch: A massively distributed indexing of time series datasets

Levchenko, O., Yagoubi, D. E., Akbarinia, R., Masseglia, F., Kolev, B. & Shasha, D., Oct 17 2018, CIKM 2018 - Proceedings of the 27th ACM International Conference on Information and Knowledge Management. Paton, N., Candan, S., Wang, H., Allan, J., Agrawal, R., Labrinidis, A., Cuzzocrea, A., Zaki, M., Srivastava, D., Broder, A. & Schuster, A. (eds.). Association for Computing Machinery, p. 1951-1954 4 p.

Research output: Chapter in Book/Report/Conference proceedingConference contribution

Indexing
Finance
Similarity search
Single machine
Time trade-off

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

Upstart puzzles polychromatic choreography

Shasha, D., Jan 1 2018, In : Communications of the ACM. 61, 1, 1 p.

Research output: Contribution to journalComment/debate

Upstart puzzles string wars

Shasha, D., Jul 1 2018, In : Communications of the ACM. 61, 7, 1 p.

Research output: Contribution to journalComment/debate

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

Improving tourism prediction models using climate and social media data: A fine-grained approach

Khatibi, A., Belem, F., Silva, A. P., Shasha, D., Almeida, J. M. & Gonçalves, M. A., Jan 1 2017, 12th International AAAI Conference on Web and Social Media, ICWSM 2018. AAAI press, p. 636-639 4 p.

Research output: Chapter in Book/Report/Conference proceedingConference contribution

Climate models
Linear regression
Websites
Profitability
Planning

Pre-processing and indexing techniques for constellation queries in big data

Khatibi, A., Porto, F., Rittmeyer, J. G., Ogasawara, E., Valduriez, P. & Shasha, D., 2017, Big Data Analytics and Knowledge Discovery - 19th International Conference, DaWaK 2017, Proceedings. Springer Verlag, Vol. 10440 LNCS. p. 164-172 9 p. (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); vol. 10440 LNCS).

Research output: Chapter in Book/Report/Conference proceedingConference contribution

Indexing
Preprocessing
Query
Astronomy
Processing

Ruby risks

Shasha, D., Jul 1 2017, In : Communications of the ACM. 60, 7, p. 104 1 p.

Research output: Contribution to journalComment/debate

Ruby

Upstart puzzles: Partitioned peace

Shasha, D., Oct 1 2017, In : Communications of the ACM. 60, 10

Research output: Contribution to journalComment/debate

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

A course on programming and problem solving

Sheth, S., Murphy, C., Ross, K. A. & Shasha, D., Feb 17 2016, SIGCSE 2016 - Proceedings of the 47th ACM Technical Symposium on Computing Science Education. Association for Computing Machinery, Inc, p. 323-328 6 p.

Research output: Chapter in Book/Report/Conference proceedingConference contribution

Computer programming
programming
Students
Robot programming
Technical presentations

Alphacodes: Usable, secure transactions with untrusted providers using human computable puzzles

Sharma, A., Chandrasekaran, V., Amjad, F., Shasha, D. & Subramanian, L., Nov 18 2016, Proceedings of the 7th Annual Symposium on Computing for Development, ACM DEV-7 2016. Association for Computing Machinery, Inc, a5

Research output: Chapter in Book/Report/Conference proceedingConference contribution

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

Conjugate conformal prediction for online binary classification

Kocak, M. A., Erkip, E. & Shasha, D., 2016, 32nd Conference on Uncertainty in Artificial Intelligence 2016, UAI 2016. Association For Uncertainty in Artificial Intelligence (AUAI), p. 347-356 10 p.

Research output: Chapter in Book/Report/Conference proceedingConference contribution

Learning systems
Rain
Experiments

Positive-Unlabeled Learning in the Face of Labeling Bias

Youngs, N., Shasha, D. & Bonneau, R., Jan 29 2016, Proceedings - 15th IEEE International Conference on Data Mining Workshop, ICDMW 2015. Institute of Electrical and Electronics Engineers Inc., p. 639-645 7 p. 7395727

Research output: Chapter in Book/Report/Conference proceedingConference contribution

Labeling
Labels
Supervised learning
Learning algorithms
Costs

ReproZip: Computational reproducibility with ease

Chirigati, F., Rampin, R., Shasha, D. & Freire, J., Jun 26 2016, SIGMOD 2016 - Proceedings of the 2016 International Conference on Management of Data. Association for Computing Machinery, Vol. 26-June-2016. p. 2085-2088 4 p.

Research output: Chapter in Book/Report/Conference proceedingConference contribution

Experiments
Computer operating systems
Packaging
Linux

ThePlantGame: Actively training human annotators for domain-specific crowdsourcing

Servajean, M., Joly, A., Shasha, D., Champ, J. & Pacitti, E., Oct 1 2016, MM 2016 - Proceedings of the 2016 ACM Multimedia Conference. Association for Computing Machinery, Inc, p. 720-721 2 p.

Research output: Chapter in Book/Report/Conference proceedingConference contribution

Labels

Upstart puzzles: Find me quickly

Shasha, D., Oct 1 2016, In : Communications of the ACM. 59, 10, p. 96 1 p.

Research output: Contribution to journalComment/debate

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

Upstart puzzles chair games

Shasha, D., Jul 1 2016, In : Communications of the ACM. 59, 7, p. 128 1 p.

Research output: Contribution to journalComment/debate

2015

Brighten up

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

Research output: Contribution to journalShort survey

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

Quiet: Faster belief propagation for images and related applications

Fujiwara, Y. & Shasha, D., 2015, IJCAI 2015 - Proceedings of the 24th International Joint Conference on Artificial Intelligence. International Joint Conferences on Artificial Intelligence, Vol. 2015-January. p. 3497-3503 7 p.

Research output: Chapter in Book/Report/Conference proceedingConference contribution

Costs
Experiments

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