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2020

Better together: Elements of successful scientific software development in a distributed collaborative community

RosettaCommons Consortium, May 1 2020, In : PLoS computational biology. 16, 5, e1007507.

Research output: Contribution to journalReview article

Open Access

Big Data Analytics and the Struggle for Equity in Health Care: The Promise and Perils

Ibrahim, S. A., Charlson, M. E. & Neill, D. B., Apr 1 2020, In : Health Equity. 4, 1, p. 99-101 3 p.

Research output: Contribution to journalReview article

Open Access

Macromolecular modeling and design in Rosetta: recent methods and frameworks

Leman, J. K., Weitzner, B. D., Lewis, S. M., Adolf-Bryfogle, J., Alam, N., Alford, R. F., Aprahamian, M., Baker, D., Barlow, K. A., Barth, P., Basanta, B., Bender, B. J., Blacklock, K., Bonet, J., Boyken, S. E., Bradley, P., Bystroff, C., Conway, P., Cooper, S., Correia, B. E. & 88 others, Coventry, B., Das, R., De Jong, R. M., DiMaio, F., Dsilva, L., Dunbrack, R., Ford, A. S., Frenz, B., Fu, D. Y., Geniesse, C., Goldschmidt, L., Gowthaman, R., Gray, J. J., Gront, D., Guffy, S., Horowitz, S., Huang, P. S., Huber, T., Jacobs, T. M., Jeliazkov, J. R., Johnson, D. K., Kappel, K., Karanicolas, J., Khakzad, H., Khar, K. R., Khare, S. D., Khatib, F., Khramushin, A., King, I. C., Kleffner, R., Koepnick, B., Kortemme, T., Kuenze, G., Kuhlman, B., Kuroda, D., Labonte, J. W., Lai, J. K., Lapidoth, G., Leaver-Fay, A., Lindert, S., Linsky, T., London, N., Lubin, J. H., Lyskov, S., Maguire, J., Malmström, L., Marcos, E., Marcu, O., Marze, N. A., Meiler, J., Moretti, R., Mulligan, V. K., Nerli, S., Norn, C., Ó’Conchúir, S., Ollikainen, N., Ovchinnikov, S., Pacella, M. S., Pan, X., Park, H., Pavlovicz, R. E., Pethe, M., Pierce, B. G., Pilla, K. B., Raveh, B., Renfrew, P. D., Burman, S. S. R., Rubenstein, A., Sauer, M. F., Scheck, A., Schief, W., Schueler-Furman, O., Sedan, Y., Sevy, A. M., Sgourakis, N. G., Shi, L., Siegel, J. B., Silva, D. A., Smith, S., Song, Y., Stein, A., Szegedy, M., Teets, F. D., Thyme, S. B., Wang, R. Y. R., Watkins, A., Zimmerman, L. & Bonneau, R., Jul 1 2020, In : Nature methods. 17, 7, p. 665-680 16 p.

Research output: Contribution to journalReview article

2019

Deception, identity, and security: The game theory of sybil attacks

Casey, W., Kellner, A., Memarmoshrefi, P., Morales, J. A. & Mishra, B., Jan 2019, In : Communications of the ACM. 62, 1, p. 85-93 9 p.

Research output: Contribution to journalReview article

Keeping Score: Predictive Analytics in Policing

Fitzpatrick, D. J., Gorr, W. L. & Neill, D. B., Jan 13 2019, In : Annual Review of Criminology. 2, p. 473-491 19 p.

Research output: Contribution to journalReview article

Twenty-five years of information extraction

Grishman, R., Nov 1 2019, In : Natural Language Engineering. 25, 6, p. 677-692 16 p.

Research output: Contribution to journalReview article

2018

A probabilistic approach to discovering dynamic full-brain functional connectivity patterns

Manning, J. R., Zhu, X., Willke, T. L., Ranganath, R., Stachenfeld, K., Hasson, U., Blei, D. M. & Norman, K. A., Oct 15 2018, In : NeuroImage. 180, p. 243-252 10 p.

Research output: Contribution to journalReview article

Control Mechanisms of Static and Dynamic Balance in Adults With and Without Vestibular Dysfunction in Oculus Virtual Environments

Lubetzky, A. V., Hujsak, B. D., Kelly, J. L., Fu, G. & Perlin, K., Nov 2018, In : PM and R. 10, 11, p. 1223-1236.e2

Research output: Contribution to journalReview article

Why are there hotspot mutations in the TP53 gene in human cancers?

Baugh, E. H., Ke, H., Levine, A. J., Bonneau, R. A. & Chan, C. S., 2018, In : Cell Death and Differentiation. 25, 1, p. 154-160 7 p.

Research output: Contribution to journalReview article

2017

Biophysically motivated regulatory network inference: Progress and prospects

Äijö, T. & Bonneau, R., Jan 1 2017, In : Human Heredity. 81, 2, p. 62-77 16 p.

Research output: Contribution to journalReview article

Geometric Deep Learning: Going beyond Euclidean data

Bronstein, M. M., Bruna, J., Lecun, Y., Szlam, A. & Vandergheynst, P., Jul 2017, In : IEEE Signal Processing Magazine. 34, 4, p. 18-42 25 p., 7974879.

Research output: Contribution to journalReview article

Logical formalizations of commonsense reasoning: A survey

Davis, E., May 2017, In : Journal of Artificial Intelligence Research. 59, p. 651-723 73 p.

Research output: Contribution to journalReview article

Open Access

Lousy advice to the lovelorn

Davis, E., Dec 2017, In : Communications of the ACM. 60, 12, p. 33-35 3 p.

Research output: Contribution to journalReview article

Overview of Millimeter Wave Communications for Fifth-Generation (5G) Wireless Networks-With a Focus on Propagation Models

Rappaport, T. S., Xing, Y., MacCartney, G. R., Molisch, A. F., Mellios, E. & Zhang, J., Dec 2017, In : IEEE Transactions on Antennas and Propagation. 65, 12, p. 6213-6230 18 p., 7999294.

Research output: Contribution to journalReview article

2016

The scope and limits of simulation in automated reasoning

Davis, E. & Marcus, G., Apr 2016, In : Artificial Intelligence. 233, p. 60-72 13 p.

Research output: Contribution to journalReview article

2015

Commonsense reasoning and commonsense knowledge in artificial intelligence

Davis, E. & Marcus, G., Sep 1 2015, In : Communications of the ACM. 58, 9, p. 92-103 12 p.

Research output: Contribution to journalReview article

Deep learning

Lecun, Y., Bengio, Y. & Hinton, G., May 27 2015, In : Nature. 521, 7553, p. 436-444 9 p.

Research output: Contribution to journalReview article

Demystifying Quadrilateral Remeshing

Panozzo, D., Mar 1 2015, In : IEEE Computer Graphics and Applications. 35, 2, p. 88-95 8 p., 7064658.

Research output: Contribution to journalReview article

Quantum XOR games

Regev, O. & Vidick, T., Aug 1 2015, In : ACM Transactions on Computation Theory. 7, 4, 15.

Research output: Contribution to journalReview article

2014

A catalog of stream processing optimizations

Hirzel, M., Soulé, R., Schneider, S., Gedik, B. & Grimm, R., Apr 2014, In : ACM Computing Surveys. 46, 4, 46.

Research output: Contribution to journalReview article

2013

Quad-mesh generation and processing: A survey

Bommes, D., Lévy, B., Pietroni, N., Puppo, E., Silva, C., Tarini, M. & Zorin, D., Sep 2013, In : Computer Graphics Forum. 32, 6, p. 51-76 26 p.

Research output: Contribution to journalReview article

Social media and political communication: A survey of twitter users during the 2013 Italian general election

Vaccari, C., Valeriani, A., Barberá, P., Bonneau, R., Jost, J. T., Nagler, J. & Tucker, J., Dec 2013, In : Italian Political Science Review. 43, 3, p. 381-410 30 p.

Research output: Contribution to journalReview article

2012

Information and communication technologies for development [Guest editors' introduction]

Cáceres, R., Belding, E., Parikh, T. & Subramanian, L., 2012, In : IEEE Pervasive Computing. 11, 3, p. 12-14 3 p., 6228596.

Research output: Contribution to journalReview article

2011

Technical perspective concerto for violin and markov model

Bello, J., LeCun, Y. & Rowe, R., Mar 2011, In : Communications of the ACM. 54, 3, 1 p.

Research output: Contribution to journalReview article

2010

Dynamics of stochastic neuronal networks and the connections to random graph theory

Lee DeVille, R. E., Peskin, C. S. & Spencer, J. H., Jan 2010, In : Mathematical Modelling of Natural Phenomena. 5, 2, p. 26-66 41 p.

Research output: Contribution to journalReview article

2009

Learning global models of transcriptional regulatory networks from data.

Madar, A. & Bonneau, R., 2009, In : Methods in molecular biology (Clifton, N.J.). 541, 1 p.

Research output: Contribution to journalReview article

2008

Adiabatic quantum computation is equivalent to standard quantum computation

Aharonov, D., Van Dam, W., Kempe, J., Landau, Z., Lloyd, S. & Regev, O., 2008, In : SIAM Review. 50, 4, p. 755-787 33 p.

Research output: Contribution to journalReview article

Learning biological networks: From modules to dynamics

Bonneau, R., Nov 2008, In : Nature Chemical Biology. 4, 11, p. 658-664 7 p.

Research output: Contribution to journalReview article

2007

From bytes to bedside: Data integration and computational biology for translational cancer research

Mathew, J. P., Taylor, B. S., Bader, G. D., Pyarajan, S., Antoniotti, M., Chinnaiyan, A. M., Sander, C., Burakoff, S. J. & Mishra, B., Feb 2007, In : PLoS computational biology. 3, 2, p. 153-163 11 p.

Research output: Contribution to journalReview article

2005

Making snapshot isolation serializable

Fekete, A., Liarokapis, D., O'Neil, E., O'Neil, P. & Shasha, D., Jun 2005, In : ACM Transactions on Database Systems. 30, 2, p. 492-528 37 p.

Research output: Contribution to journalReview article

Systems biology for the virtual plant

Gutiérrez, R. A., Shasha, D. E. & Coruzzi, G. M., 2005, In : Plant physiology. 138, 2, p. 550-554 5 p.

Research output: Contribution to journalReview article

2004

One.world: Experiences with a pervasive computing architecture

Grimm, R., Jul 2004, In : IEEE Pervasive Computing. 3, 3, p. 22-30 9 p.

Research output: Contribution to journalReview article

Systems biology experimental design - Considerations for building predictive gene regulatory network models for prokaryotic systems

Facciotti, M. T., Bonneau, R., Hood, L. & Baliga, N. S., Nov 2004, In : Current Genomics. 5, 7, p. 527-544 18 p.

Research output: Contribution to journalReview article

Verifying Your Circuits

Shasha, D. E., Jan 2004, In : Scientific American. 290, 1, 1 p.

Research output: Contribution to journalReview article

2003

Ab initio methods.

Chivian, D., Robertson, T., Bonneau, R. & Baker, D., 2003, In : Methods of biochemical analysis. 44, p. 547-557 11 p.

Research output: Contribution to journalReview article

BSML: A binding schema markup language for data interchange in problem solving environments

Verstak, A., Ramakrishnan, N., Watson, L. T., He, J., Shaffer, C. A., Bae, K. K., Jiang, J., Tranter, W. H. & Rappaport, T. S., 2003, In : Scientific Programming. 11, 3, p. 199-224 26 p.

Research output: Contribution to journalReview article

Open Access

High spies

Shasha, D. E., Jul 2003, In : Scientific American. 289, 1, 1 p.

Research output: Contribution to journalReview article

Liquid Switchboard

Shasha, D. E., Nov 2003, In : Scientific American. 289, 5, 1 p.

Research output: Contribution to journalReview article

Prime squares

Shasha, D. E., Jun 2003, In : Scientific American. 288, 6, 1 p.

Research output: Contribution to journalReview article

Protein chime

Shasha, D. E., Jan 2003, In : Scientific American. 288, 1, 1 p.

Research output: Contribution to journalReview article

Safecracking

Shasha, D. E., Mar 2003, In : Scientific American. 288, 3, 1 p.

Research output: Contribution to journalReview article

Short taps

Shasha, D. E., Aug 2003, In : Scientific American. 289, 2, 1 p.

Research output: Contribution to journalReview article

The graph of life

Shasha, D. E., Apr 2003, In : Scientific American. 288, 4, 1 p.

Research output: Contribution to journalReview article

2002

Plumbers

Shasha, D. E., Dec 2002, In : Scientific American. 287, 6, 1 p.

Research output: Contribution to journalReview article

2001

Ab initio protein structure prediction: Progress and prospects

Bonneau, R. & Baker, D., 2001, In : Annual Review of Biophysics and Biomolecular Structure. 30, p. 173-189 17 p.

Research output: Contribution to journalReview article

1999

Fintime - A financial time series benchmark

Jacob, K. J. & Shasha, D., Dec 1999, In : SIGMOD Record (ACM Special Interest Group on Management of Data). 28, 4, p. 42-47 6 p.

Research output: Contribution to journalReview article

Optical mapping and its potential for large-scale sequencing projects

Aston, C., Mishra, B. & Schwartz, D. C., Jul 1 1999, In : Trends in Biotechnology. 17, 7, p. 297-302 6 p.

Research output: Contribution to journalReview article

1998

Overview of spatial channel models for antenna array communication systems

Ertel, R. B., Cardieri, P., Sowerby, K. W., Rappaport, T. S. & Reed, J. H., Feb 1998, In : IEEE Personal Communications. 5, 1, p. 10-22 13 p.

Research output: Contribution to journalReview article

1989

Constrained nonlinear programming

Gill, P. E., Murray, W., Saunders, M. A. & Wright, M. H., Jan 1 1989, In : Handbooks in Operations Research and Management Science. 1, C, p. 171-210 40 p.

Research output: Contribution to journalReview article