No photo of Dennis Shasha

Dennis Shasha

Silver Professor; Professor of Computer Science

    1983 …2020

    Research output per year

    If you made any changes in Pure these will be visible here soon.

    Research Output

    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

    Upstart puzzles: Stopping tyranny

    Shasha, D., Feb 24 2020, In : Communications of the ACM. 63, 3, p. 104+103

    Research output: Contribution to journalComment/debate

    Upstart puzzles feedback for foxes

    Shasha, D., Jan 2020, In : Communications of the ACM. 63, 1, 1 p.

    Research output: Contribution to journalEditorial

    2019

    Debugging machine learning pipelines

    Lourenço, R., Freire, J. & Shasha, D., Jun 30 2019, Proceedings of the 3rd Workshop on Data Management for End-To-End Machine Learning, DEEM 2019 - In conjunction with the 2019 ACM SIGMOD/PODS Conference. Association for Computing Machinery, 3329489. (Proceedings of the ACM SIGMOD International Conference on Management of Data).

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

    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

    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

    Randomized anti-counterfeiting

    Shasha, D., Jan 2019, In : Communications of the ACM. 62, 1, p. 120+119

    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

    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

    Upstart puzzles dust wars considering will ful approache stoag old enop portunity

    Shasha, D., Oct 2019, In : Communications of the ACM. 62, 10, p. 103-104 2 p.

    Research output: Contribution to journalComment/debate

    Upstart puzzles fighting for lava

    Shasha, D., Apr 2019, In : Communications of the ACM. 62, 4, p. 144+143

    Research output: Contribution to journalComment/debate

    Upstart puzzles opioid games

    Shasha, D., Jul 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

    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

    Finding October

    Shasha, D., Apr 2018, In : Communications of the ACM. 61, 4, p. 96+95

    Research output: Contribution to journalShort survey

    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 2018, 12th International AAAI Conference on Web and Social Media, ICWSM 2018. AAAI press, p. 636-639 4 p. (12th International AAAI Conference on Web and Social Media, ICWSM 2018).

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

    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

    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, (ACM International Conference Proceeding Series).

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

    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

    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. (International Conference on Information and Knowledge Management, Proceedings).

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

    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

    Upstart puzzles polychromatic choreography

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

    Research output: Contribution to journalComment/debate

    Upstart puzzles string wars

    Shasha, D., Jul 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 2017, In : IEEE Transactions on Multimedia. 19, 6, p. 1376-1391 16 p., 7819540.

    Research output: Contribution to journalArticle

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

    Khatibi, A., Porto, F., Rittmeyer, J. G., Ogasawara, E., Valduriez, P. & Shasha, D., Jan 1 2017, Big Data Analytics and Knowledge Discovery - 19th International Conference, DaWaK 2017, Proceedings. Bellatreche, L. & Chakravarthy, S. (eds.). Springer Verlag, 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

    RadiusSketch: Massively distributed indexing of time series

    Yagoubi, D. E., Akbarinia, R., Masseglia, F. & Shasha, D., Jul 2 2017, Proceedings - 2017 International Conference on Data Science and Advanced Analytics, DSAA 2017. Institute of Electrical and Electronics Engineers Inc., p. 262-271 10 p. (Proceedings - 2017 International Conference on Data Science and Advanced Analytics, DSAA 2017; vol. 2018-January).

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

    Ruby risks

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

    Research output: Contribution to journalComment/debate

    Upstart puzzles: Partitioned peace

    Shasha, D., Oct 2017, In : Communications of the ACM. 60, 10, p. 112 and 111

    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 journalEditorial

    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. (SIGCSE 2016 - Proceedings of the 47th ACM Technical Symposium on Computing Science Education).

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

    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. (Proceedings of the 7th Annual Symposium on Computing for Development, ACM DEV-7 2016).

    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

    Conjugate conformal prediction for online binary classification

    Kocak, M. A., Erkip, E. & Shasha, D. E., Jan 1 2016, 32nd Conference on Uncertainty in Artificial Intelligence 2016, UAI 2016. Janzing, D. & Ihler, A. (eds.). Association For Uncertainty in Artificial Intelligence (AUAI), p. 347-356 10 p. (32nd Conference on Uncertainty in Artificial Intelligence 2016, UAI 2016).

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

    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. Wu, X., Tuzhilin, A., Xiong, H., Dy, J. G., Aggarwal, C., Zhou, Z-H. & Cui, P. (eds.). Institute of Electrical and Electronics Engineers Inc., p. 639-645 7 p. 7395727. (Proceedings - 15th IEEE International Conference on Data Mining Workshop, ICDMW 2015).

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

    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, p. 2085-2088 4 p. (Proceedings of the ACM SIGMOD International Conference on Management of Data; vol. 26-June-2016).

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

    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. (MM 2016 - Proceedings of the 2016 ACM Multimedia Conference).

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

    Upstart puzzles: Ice trap

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

    Research output: Contribution to journalComment/debate

    Upstart puzzles: Find me quickly

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

    Research output: Contribution to journalComment/debate

    Upstart puzzles: Sleep no more

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

    Research output: Contribution to journalComment/debate

    Upstart puzzles chair games

    Shasha, D., Jul 2016, In : Communications of the ACM. 59, 7, 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., Jan 1 2015, In : F1000Research. 4, 479.

    Research output: Contribution to journalArticle

    Quiet: Faster belief propagation for images and related applications

    Fujiwara, Y. & Shasha, D., Jan 1 2015, IJCAI 2015 - Proceedings of the 24th International Joint Conference on Artificial Intelligence. Wooldridge, M. & Yang, Q. (eds.). International Joint Conferences on Artificial Intelligence, p. 3497-3503 7 p. (IJCAI International Joint Conference on Artificial Intelligence; vol. 2015-January).

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

    Take your seats

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

    Research output: Contribution to journalComment/debate

    Upstart puzzles: Auction triplets

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

    Research output: Contribution to journalComment/debate