2017
Taking Word Clouds Apart: An Empirical Investigation of the Design Space for Keyword Summaries.
Cristian Felix, Steven Franconeri, Enrico Bertini.
IEEE Transactions on Visualization and Computer Graphics (Proc. of InfoVis), 2017.[GitHub Page]
A Workflow for Visual Diagnostics of Binary Classifiers using Instance-Level Explanations.
Josua Krause, Aritra Dasgupta, Jordan Swartz, Yindalon Aphinyanaphongs, Enrico Bertini.
Proc. of IEEE Conference and Visual Analytics Science and Technology (VAST), 2017.[GitHub Page]
Interpreting Black-Box Classifiers Using Instance-Level Visual Explanations.
Paolo Tamagnini, Josua Krause, Aritra Dasgupta, Enrico Bertini.
Proc. of SIGMOD Workshop on Human-In-the-Loop Data Analytics (HILDA), 2017.
Showing People Behind Data: Does Anthropomorphizing Visualizations Elicit More Empathy for Human Rights Data?
Jeremy Boy, Margaret Satterthwaite, Anshul Vikram Pandey, Oded Nov, John Emerson, Enrico Bertini
Proc. of ACM CHI Conference on Human Factors in Computing Systems (CHI), 2017.
*** Best Paper Award: Honorable Mention ***
High-resolution Temporal Representations of Alcohol and Tobacco Behaviors from Social Media Data
T. Huang, A. Elghafari, K. Relia, R. Chunara
Proceedings of the ACM: Human Computer Interaction (PACM), CSCW 2018 Online First.
Using Sparse Digital Traces to Fill in Individual Level Mobility Timelines
N.A. Rehman, K. Relia, R. Chunara
pre-print
Assessing Behavioral Stages From Social Media Data
Liu, E.R. Weitzman, R. Chunara.
ACM Conference on Computer-Supported Cooperative Work and Social Computing. 2017
ARIES: Enabling Visual Exploration and Organization of Art Image Collections
L Crissaff, LW Ruby, S Deutch, RL DuBois, JD Fekete, J Freire, C Silva
IEEE Computer Graphics and Applications. 2017
A collaborative approach to computational reproducibility
F Chirigati, R Capone, D Shasha, R Rampin, J Freire
arXiv preprint arXiv:1709.01154
noWorkflow: a tool for collecting, analyzing, and managing provenance from python scripts
JF Pimentel, L Murta, V Braganholo, J Freire
Proceedings of the VLDB Endowment 10 (12), 1841-1844
STaRS: Simulating Taxi Ride Sharing at Scale
M Ota, H Vo, C Silva, J Freire
IEEE Transactions on Big Data
Querying and Exploring Polygamous Relationships in Urban Spatio-Temporal Data Sets
YY Chan, F Chirigati, H Doraiswamy, CT Silva, J Freire
Proceedings of the 2017 ACM International Conference on Management of Data
2016
Network Inference from Multimodal data: A Review of Approaches from Infectious Disease Transmission
Ray, E. Ghedin, R. Chunara.
Journal of Biomedical Informatics. 2016
Using Propensity Score Matching to Understand the Relationship Between Online Health Information Sources and Vaccination Sentiment.
Rehman NA, Liu J, Chunara R.
Association for the advancement of Artificial Intelligence Spring Symposium. Stanford University Palo Alto, CA, USA. 2016
TextTile: An Interactive Visualization Tool for Seamless Exploratory Analysis of Structured Data and Unstructured Text.
Cristian Felix, Anshul Vikram Pandey, and Enrico Bertini.
Institute of Electrical and Electronics Engineers, Transactions on Visualization and Computer Graphics (Proc. of VAST), 2016 [pre-print].
Using Visual Analytics to Interpret Predictive Machine Learning Models.
Josua Krause, Adam Perer, Enrico Bertini. ICML Workshop on Human Interpretability in Machine Learning (WHI), 2016.[arXiv]
Data Visualization for Human Rights Advocacy
Katharina Rall, Margaret L. Satterthwaite, Anshul Vikram Pandey, John Emerson, Jeremy Boy, Oded Nov, Enrico Bertini.
Journal of Human Rights Practice, 8, 2016, 171–197
Towards Understanding Human Similarity Perception in the Analysis of Large Sets of Scatter Plots.
Anshul Vikram Pandey, Josua Krause, Cristian Felix, Jeremy Boy, Enrico Bertini.
Proc. of Association for Computing Machinery CHI Conference on Human Factors in Computing Systems (CHI), 2016.
[Best Paper Award: Honorable Mention]
Longitudinal Modeling of Appearance and Shape and its Potential for Clinical Use, Medical Image Analysis,
Gerig, G. and Fishbaugh, J. and Sadeghi, N., Elsevier
In press (link), 2016
Hyperspectral Autofluorescence Imaging of Drusen and Retinal Pigment Epithelium in Donor
Yuehong Tong, PhD; Tal Ben Ami, MD; Sungmin Hong, MSc; Rainer Heintzmann, PhD; Guido Gerig, PhD; Zsolt Ablonczy, PhD; Christine A. Curcio, PhD; Thomas Ach, MD; R. Theodore Smith, MD, PhD. RETINA The Journal of Retinal and Vitreous Diseases, in print, 2016
The IBIS Network, Development of Cortical Shape in the Human Brain from 6 to 24 Months of Age via a Novel Measure of Shape Complexity
Sun Hyung Kim; Ilwoo Lyu; Vladimir S Fonov; Clement Vachet; Heather C Hazlett; Rachel G Smith; Joseph Piven; Stephen R Dager; Robert C McKinstry; John R Pruett Jr; Alan C Evans; Louis D Collins; Kelly N Botteron; Robert T Schultz; Guido Gerig; Martin A Styner;
Neuroimage, In print
Modeling 4D Pathological Changes by Leveraging Normative Models, Computer Vision and Image Understanding
Bo Wang, Marcel Prastawa, Andrei Irimia, Avishek Saha, Wei Liu, S.Y. Matthew Goh, Paul M Vespa, John D Van Horn, Guido
CVIU-15-121R1, in print
Itk-snap: An Interactive Tool for Semi-Automatic Segmentation of Multi-Modality Biomedical Images
Paul A. Yushkevich, Yang Gao, and Guido Gerig.
In Proceedings of Institute of Electrical and Electronics Engineers EMBS, 2016. in print.
Compressive Sensing based Q-space Resampling for handling fast bulk motion in HARDI acquisitions
Shireen Elhabian, Clement Vachet, Joseph Piven, Martin Styner and Guido Gerig,
Institute of Electrical and Electronics Engineers ISBI 2016, April 2016
Image Registration And Segmentation In Longitudinal MRI Using Temporal Appearance Modeling
Yang Gao, Miaomiao Zhang, P. Thomas Fletcher and Guido Gerig,
Institute of Electrical and Electronics EngineersISBI 2016, April 2016
Bayesian Covariate Selection in Mixed-Effects Models For Longitudinal Shape Analysis Prasanna Muralidharan, James Fishbaugh, Eun Young Kim, Jane Paulsen, Hans Johnson, Guido Gerig and P. Thomas Fletcher,
Institute of Electrical and Electronics EngineersISBI 2016, April 2016
Reproducibility of Data-Oriented Experiments in e-Science (Dagstuhl Seminar 16041). Juliana Freire, Norbert Fuhr and Andreas Rauber.
Dagstuhl Reports 6(1):108–159, 2016.
Exploring What not to Clean in Urban Data: A Study Using New York City Taxi Trips. Freire, A. Bessa, F. Chirigati, H. Vo, and K. Zhao.
Institute of Electrical and Electronics EngineersData Engineering Bulletin, 39(2):63-77, 2016.
A collaborative approach to computational reproducibility.
Fernando Chirigati, Rebecca Capone, Rmi Rampin, Juliana Freire, Dennis Shasha
Information Systems, Volume 59 (C): 95-97, 2016.
Finding seeds to bootstrap focused crawlers.
Karane Vieira, Luciano Barbosa, Altigran Soares da Silva, Juliana Freire, Edleno Moura. World Wide Web 19(3): 449-474, 2016.
Visually Exploring Transportation Schedules.
Cesar Palomo, Zhan Guo, Claudio T. Silva, and Juliana Freire.
Institute of Electrical and Electronics Engineers Transactions on Visualization and Computer Graphics (TVCG) 22(1): 170-179, 2016.
Anonymizing NYC Taxi Data: Does It Matter?
Marie Douriez, Harish Doraiswamy, Claudio Silva, and Juliana Freire.
In Institute of Electrical and Electronics Engineers International Conference on Data Science and Advanced Analytics (DSAA), 2016 (to appear).
A Unified Index for Spatio-Temporal Keyword Queries.
Hoang-Vu, H. Vo, and J. Freire.
In Association of Computing Machinery CIKM, 2016 (to appear).
Interactive Exploration for Domain Discovery on the Web.
Krishnamurthy, K. Pham, A. Santos, and J. Freire.
In Association of Computing Machinery KDD Workshop on Interactive Data Exploration and Analytics (IDEA), pp. 64-71, 2016.
Understanding Website Behavior based on User Agent.
Kien Pham, Acio S. R. Santos, and Juliana Freire.
In Association of Computing Machinery SIGIR, pp. 1053-1056, 2016.
Data Polygamy: The Many-Many Relationships among Urban Spatio-Temporal Data Sets.
Chirigati, H. Doraiswamy, T. Damoulas, and J Freire.
In Association of Computing Machinery SIGMOD, pp. 1011-1025, 2016.
ReproZip: Computational Reproducibility With Ease.
Chirigati, R. Rampin, D. Shasha, and J. Freire.
In Association of Computing Machinery SIGMOD, pp. 2085-2088, 2016.
The Exception that Improves the Rule.
Freire, B. Glavic, O. Kennedy, and H Mueller.
In Association of Computing Machinery SIGMOD Workshop on Human-In-the-Loop Data Analytics (HILDA), 2016.
A GPU-Based Index to Support Interactive Spatio-Temporal Queries over Historical Data.
Harish Doraiswamy, Huy T. Vo, Claudio Silva, and Juliana Freire.
In Proceedings of Institute of Electrical and Electronics Engineers International Conference on Data Engineering (ICDE), pp. 1086-1097, 2016.
Virtual Lightweight Snapshots for Consistent Analytics in NoSQL Stores,
Fernando Chirigati, Jerome Simeon, Martin Hirzel, and Juliana Freire.
In Proceedings of Institute of Electrical and Electronics Engineers International Conference on Data Engineering (ICDE), pp. 1310-1321, 2016.
A First Study on Temporal Dynamics of Topics on the Web,
Ae ́cio Santos, Bruno Pasini and Juliana Freire.
In Proceedings of World Wide Web Workshop on Temporal Web Analytics, pp. 849-854, 2016.
Prov Viewer: a graph-based visualization tool for interactive exploration of provenance data.
Troy Kohwalter, Thiago Oliveira, Juliana Freire, Esteban Clua, and Leonardo Murta.
In Proceedings of the International Provenance and Annotation Workshop (IPAW), pp. 71-82, 2016.
Tracking and Analyzing the Evolution of Provenance from Scripts.
Joa ̃o F. N. Pimentel, Juliana Freire, Vanessa Braganholo, and Leonardo Murta.
In Proceedings of the International Provenance and Annotation Workshop (IPAW), pp. 16-28, 2016.
Fine-Grained Provenance Collection over Scripts Through Program Slicing.
Joa ̃o F. N. Pimentel, Juliana Freire, Vanessa Braganholo, and Leonardo Murta.
In Proceedings of the International Provenance and Annotation Workshop (IPAW), pp. 199-203, 2016
Bijective Maps from Simplicial Foliations,
Campen, C. Silva, and D. Zorin,
Association of Computing Machinery Transactions on Graphics (SIGGRAPH 2016), to appear.
Statcast Dashboard: Exploration of Spatiotemporal Baseball Data,
Lage J. Piazentin Ono, D. Cervone, J. Chiang, C. Dietrich, and C. Silva,
Institute of Electrical and Electronics Engineers Computer Graphics and Applications, accepted.
VisFlow – Web-based Visualization Framework for Tabular Data with a Subset Flow Model,
Yu and C. Silva,
Institute of Electrical and Electronics Engineers Transactions on Visualization and Computer Graphics (VAST 2016), to appear.
Urban Pulse: Capturing the Rhythm of Cities,
Miranda, H. Doraiswamy, M. Lage, K. Zhao, B. Gonc ̧alves, L. Wilson, M. Hsieh, and C. Silva,
Institute of Electrical and Electronics Engineers Transactions on Visualization and Computer Graphics (SCIVIS 2016), to appear.
Visual Analysis of Bike-Sharing Systems,
Oliveira, J. Sotomayor, R. Torchelsen, C. Silva, and J. Comba,
Computers & Graphics, accepted.
State of the Art in Surface Reconstruction from Point Clouds,
Berger, A. Tagliasacchi, L. Seversky, P. Alliez, G. Guennebaud, J. Levine, A. Sharf and C. Silva,
Computer Graphics Forum, to appear.
Reducing the Analytical Bottleneck for Domain Scientists: Lessons from a Climate Data Visualization Case Study,
Dasgupta, J. Poco, E. Bertini, and C. Silva Cludio T. Silva,
Computing in Science and Engineering, 18(1): 92–100, 2016.
2015
Estimating influenza attack rates in the United States using a participatory cohort.
Chunara, R., Goldstein, E., Patterson-Lomba, O., & Brownstein, J. S.
Scientific reports, 5. (2015 Impact factor: 5.228)
Surveillance of Acute Respiratory Infections Using Community-Submitted Symptoms and Specimens for Molecular Diagnostic Testing.
, Rowe A, Brownstein JS, Chunara R
PLoS currents7 (2015). (2015 Impact factor: 4.05)
Characterizing sleep issues using Twitter.
McIver DJ, Hawkins JB, Chunara R, Chatterjee AK, Bhandari A, Fitzgerald TP and Brownstein, JS (2015).
Journal of medical Internet research, 17(6). (2015 Impact factor: 3.428)
Flu Near You: Crowdsourced Symptom Reporting Spanning 2 Influenza Seasons.
Smolinski, MS, Crawley AW, Baltrusaitis K, Chunara R, Olsen JM, Wójcik O, Santillana M, Nguyen A, and Brownstein JS.
American Journal of Public Health 0 (2015): e1-e7. (2015 Impact factor: 4.552)
Integrating Genomic Data in a Community-based Multi-modal Viral Transmission Model for Network Inference.
Ray B and Chunara R.
NIPS Workshop on ML for Healthcare, Montreal Canada, 2015.
Social Capital Deserts: Obesity Surveillance using a Location-Based Social Bai H, Chunara R and Varshney LR.
Proceedings of the Data for Good Exchange (D4GX), New York, New York, 28 September 2015.
[NYC Media Lab – Bloomberg Data for Good Exchange Paper Award]
RevEx: Visual Investigative Journalism with A Million Healthcare Reviews.
Cristian Felix Da Silva, Anshul Vikram Pandey, and Enrico Bertini.
In Proc. of Computation + Journalism Symposium (CJ), 2015.
Bridging Theory with Practice: An Exploratory Study of Visualization Use and Design for Climate Model Comparison.
Dasgupta, J. Poco, Y. Wei, R. Cook, E. Bertini, C. Silva.
Institute of Electrical and Electronics Engineers Transactions on Visualization and Computer Graphics, 2015.
How Deceptive are Deceptive Visualizations?: An Empirical Analysis of Common Distortion Techniques.
V. Pandey, K. Rall, M. Satterthwaite, O. Nov, E. Bertini.
Proc. of ACM CHI Conference on Human Factors in Computing Systems (CHI), 2015.
Splenium Development and Early Spoken Language in Human Infants.
Meghan R. Swanson, Jason J. Wolff, Jed T. Elison, Hongbin Gu, Heather C. Hazlett, Kelly Botteron, Martin Styner, Sarah Paterson, Guido Gerig, John Constantino, Steve Dager, Annette Estes, Clement Vachet, and Joseph Piven.
Dev Sci. 2015 Oct 21. doi: 10.1111/desc.12360. PMID: 26490257
Performance of an efficient image-registration algorithm in processing MR renography data.
Conlin CC, Zhang JL, Rousset F, Vachet C, Zhao Y, Morton KA, Carlston K, Gerig G, Lee VS.,
J Magn Reson Imaging. 2015 Jul 14. doi: 10.1002/jmri.25000. [Epub ahead of print], PMID: 26174884
The DTI Challenge: Towards Standardized Evaluation of Diffusion Tensor Imaging Tractography for Neurosurgery,
Sonia Marie Aurore Pujol , William Wells , Carlo Pierpaoli , Caroline Brun , James Gee , Guang Cheng , Baba Vemuri , Olivier Commowick , Sylvain Prima , Aymeric Stamm , Maged Goubran , Ali Khan , Peter Neher , Klaus Maier-Hein , Yundi Shi , Antonio Tristan-Vega , Carl-Fredrik Westin, Gopalkrishna Veni, Ross Whitaker , Martin Styner , Sylvain Gouttard , Isaiah Norton a, Laurent Chauvin , Hatsuho Mamata , Guido Gerig , Arya Nabavi, Alexandra Golby and Ron Kikinis
J Neuroimaging. 2015 Nov;25(6):875-82. doi: 10.1111/jon.12283. Epub 2015 Aug 11.
Violence: Heightened brain attentional network response is selectively muted in down syndrome
Jeffrey S Anderson, Scott M Treiman, Michael A Fergusonand Jared A Nielsen, Jamie O Edgin, Li Dai, Guido Gerig, and Julie R Korenberg
J Neurodev Disord. 2015;7(1):15. doi: 10.1186/s11689-015-9112-y. Epub 2015 Jun 3. PMCID: PMC4486123
Investigating maternal brain structure and its relationship to substance use and motivational systems
Helena J.V. Rutherford, Guido Gerig, Sylvain Gouttard, Marc N. Potenza and Linda C. Mayes, , Yale J Biol Med. 2015 Sep 3;88(3):211-7. eCollection 2015 Sep. PMID: 26339203, PMCID: PMC4553640
YesWorkflow: A User-Oriented, Language-Independent Tool for Recovering Workflow Information from Scripts.
Timothy McPhillips, Tianhong Song, Tyler Kolisnik, Steve Aulenbach, Khalid Belhaj- jame, R. Kyle Bocinsky, Yang Cao, James Cheney, Fernando Chirigati, Saumen Dey, Juliana Freire, Christopher Jones, James Hanken, Keith W. Kintigh, Timothy A. Kohler, David Koop, James A. Mack- lin, Paolo Missier, Mark Schildhauer, Christopher Schwalm, Yaxing Wei, Mark Bieda, Bertram Lud- scher.
International Journal of Digital Curation, 10(1):298-313, 2015.
Exploring Traffic Dynamics in Urban Environments Using Vector-Valued Functions. Jorge Poco, Harish Doraiswamy, Huy. T. Vo, Joa ̃o L. D. Comba, Juliana Freire and Claudio T. Silva.
Computer Graphics Forum, 34 (3): 161-170, 2015.
A Scalable Approach for Data – Driven Taxi Ride-Sharing Simulation.
Masayo Ota, Huy Vo, Claudio T. Silva, and Juliana Freire.
In Proceedings of Institute of Electrical and Electronics Engineers International Conference on Big Data, pp. 888-897, 2015.
Visualizing the Evolution of Module Workflows.
Marcel Hlawatsch, Michael Burch, Fabian Beck, Juliana Freire, Claudio T. Silva, and Daniel Weiskopf.
In Proceedings of the Institute of Electrical and Electronics Engineers, International Conference on Information Visualization, pp. 40-49, 2015.
RioBusData: Outlier Detection in Bus Routes of Rio de Janeiro.
Aline Bessa, Fernando de Mesentier Silva, Rodrigo Frassetto Nogueira, Enrico Bertini, and Juliana Freire.
Proceedings of Symposium on Visualization in Data Science (VDS), 2015.
Collecting and Analyzing Provenance on Interactive Notebooks: when IPython meets noWorkflow.
Joa ̃o Felipe Nicolaci Pimentel, Vanessa Braganholo, Leonardo Murta, Juliana Freire.
In Proceedings of the USENIX Workshop on the Theory and Practice of Provenance (TaPP), 2015.
Reproducibility Made Easy.
Freire. In Proceedings of EuroRV3:
EuroVis Workshop on Reproducibility, Verification, and Validation in Visualization, 2015.
An Urban Data Profiler.
Ribeiro, H. Vo, J. Freire and C. Silva.
In Proceedings of the 24th Presented at the World Wide Web Workshop on Data Science and Smart Cities. International Conference on World Wide Web Companion, pp. 1389-1394, 2015.
Managing and Reusing Provenance as a Critical Capability for (Data) Scientists.
Freire.
In Proceedings of the AAAS Annual Meeting, 2015.
Topology-based Catalogue Exploration Framework for Identifying View-Enhanced Tower Designs,
Doraiswamy, N. Ferreira, M. Lage, H. Vo, L. Wilson, H. Werner, M. Park, and C. Silva,
ASSOCIATION OF COMPUTING MACHINERY Transactions on Graphics, 34(6):230, 2015.
2014
The Influence of Contour on Similarity Perception of Star Glyphs.
Fuchs, P. Isenberg, A. Bezerianos, F. Fischer, and E. Bertini.
Institute of Electrical and Electronics Engineers Transactions on Visualization and Computer Graphics (Proc. of InfoVis), vol. 20, no. 12, pp. 2251 – 2260, 2014.
SimilarityExplorer: A Visual Inter-Comparison Tool for Multifaceted Climate Data.
Poco, A. Dasgupta, Y. Wei, W. Hargrove, C. Schwalm, R. Cook, E. Bertini, and C. Silva. Eurographics/Institute of Electrical and Electronics Engineers, Computer Graphics Forum (Proc. of EuroVis), vol. 33, no. 3, pp. 341 – 350, 2014. VIDEO
The Persuasive Power of Data Visualization.
V. Pandey, O. Nov, A. Manivannan, M. Satterthwaite, and E. Bertini.
Institute of Electrical and Electronics Engineers, Transactions on Visualization and Computer Graphics (Proc. of InfoVis), vol. 20, no. 12, pp. 2211 – 2220, 2014.
A Principled Way of Assessing Visualization Literacy.
Boy, R. Rensink, E. Bertini, and J. Fekete.
Institute of Electrical and Electronics Engineers Transactions on Visualization and Computer Graphics (Proc. of InfoVis), vol. 20, no. 12, pp. 1963 – 1972, 2014.
INFUSE: Interactive Feature Selection for Predictive Modeling of High Dimensional Data.
Krause, A. Perer, and E. Bertini.
Institute of Electrical and Electronics Engineers, Transaction on Visualization and Computer Graphics (Proc. of VAST), vol. 20, no. 12, pp. 1614 – 1623, 2014.
Riding from Urban Data to Insight Using New York City Taxis.
Freire, C. Silva, H. Vo, H. Doraiswamy, N. Ferreira, and J. Poco.
Institute of Electrical and Electronics Engineers, Data Engineering Bulletin, 37(4):43-55, 2014.
Structured Open Urban Data: Understanding the Landscape.
Barbosa, K. Pham, C. Silva, M. Vieira, and J. Freire.
Big Data Journal, 2(3): 144-154, 2014.
Using Topological Analysis to Support Event-Guided Exploration in Urban Data.
Doraiswamy, N. Ferreira, T. Damoulas, J. Freire, and C. Silva.
Institute of Electrical and Electronics Engineers, Transactions on Visualization and Computer Graphics (TVCG), 20(12): 2634-2643, 2014.
Should we all be teaching “intro to data science” instead of “intro to databases”?
Howe, M. J. Franklin, J. Freire, J. Frew, T. Kraska, R. Ramakrishnan.
In Proceedings of Association of Computing Machinery, SIGMOD, pp. 917-918, 2014.
A model project for reproducible papers: critical temperature for the Ising model on a square lattice.
Dolfi, J. Gukelberger, A. Hehn, J. Imriska, K. Pakrouski, T. F. Rnnow, M. Troyer, I. Zintchenko, F. Chirigati, J. Freire, and D. Shasha.
CoRR abs/1401.2000, 2014.
Bridging Vocabularies to Link Tweets and News.
Hoang-Vu, A. Bessa, L. Barbosa, and J. Freire.
In Proceedings of WebDB, 2014.
Towards Understanding Real-Estate Ownership in New York City: Opportunities and Challenges.
Hoang-Vu, V. Been, I. Gould Ellen, M, Weselcouch, and J. Freire.
In Proceedings of Data Science for Macro-Modeling with Financial and Economic Datasets (DSMM), 2014.
noWorkflow: Capturing and Analyzing Provenance of Scripts.
Murta, V. Braganholo, F. Chirigati, D. Koop, and J. Freire.
In Proceedings of the International Provenance and Annotation Workshop (IPAW), pp. 71-83, 2014.
Reorganizing workflow evolution provenance.
Koop and J. Freire.
In USENIX Workshop on the Theory and Practice of Provenance (TaPP), 2014.
Using Physically Based Rendering to Benchmark SL Scanners,
Medeiros, H. Doraiswamy, M. Berger, and C. Silva,
Computer Graphics Forum (Proceedings of Pacific Graphics 2014), 33(7):71– 80, 2014.
Genotet: An Interactive Web-based Visual Exploration Framework to Support Validation of Gene Regulatory Networks,
Yu, H. Doraiswamy, X. Chen, E. Miraldi, M. Arrieta-Ortiz, C. Hafemeister, A. Madar, R. Bonneau, and C. Silva,
Institute of Electrical and Electronics Engineers Transactions on Visualization and Computer Graphics, 20(12):1903–1912, 2014.
A Weighted Delaunay Triangulation Framework for Merging Triangulations in a Connectivity Oblivious,
F. Silva, L.F. Scheidegger, T. Etiene, J. Comba, L. Nonato, and C. Silva,
Computer Graphics Forum, 33(6):18–30, 2014.
Fast Adaptive Blue Noise on Polygonal Surfaces,
Esdras medeiros, Lis Ingrid, Sinesio Pesco, and Claudio Silva,
Graphical Models, 76(1):17–29, 2014.
Verifying Volume Rendering Using Discretization Error Analysis,
Tiago Etiene, D. Jonsson, T. Ropin- ski, C. Scheidegger, J. Comba, L. G. Nonato, R. M. Kirby, A. Ynnerman, and C. T. Silva,
Institute of Electrical and Electronics Engineers Transactions on Visualization and Computer Graphics, 20(1):140–154, 2014.
2013
Evaluation of Alternative Glyph Designs for Time Series Data in a Small Multiple Setting.
Fuchs, F. Fischer, F. Mansmann, E. Bertini, and P. Isenberg.
Proc. of Association of Computing Machinery Conference on Human Factors in Computing Systems (CHI), 2013. [Best Paper Award: Honorable Mention]
A computational reproducibility benchmark.
Chirigati, M. Troyer, D. Shasha, and J. Freire.
Institute of Electrical and Electronics Engineers Data Engineering Bulletin, 36(4):54-59, 2013.
Visual Exploration of Big Spatio-Temporal Urban Data: A Study of New York City Taxi Trips.
Ferreira, J. Poco, H. Vo, J. Freire, and C. Silva.
Institute of Electrical and Electronics Engineers Transactions on Visualization and Computer Graphics (Proceedings of VAST) 19(12): 2149-58, 2013.
ReproZip: Using Provenance to Support Computational Reproducibility.
Chirigati, D. Shasha, and J. Freire. In USENIX Workshop on the Theory and Practice of Provenance (TaPP), 2013.
Packing Experiments for Sharing and Publication
Chirigati, D. Shasha, and J. Freire.
In Association of Computing Machinery SIGMOD, 2013.
Visual Summaries for Graph Collections.
Koop, J. Freire, C. Silva.
In Proceedings of the Institute of Electrical and Electronics Engineers Pacific Visualization Symposium (PacificVis), pp. 57-64, 2013.
VisTrails provenance traces for benchmarking.
Chirigati, J., D. Koop, C. T. Silva.
Extending Database Technology/International Conference on Extending Database Technology (EDBT/ICDT) Workshops 2013: 323-324.
Practical considerations on Marching Cubes 33 topological correctness,
Lis Custodio, Tiago Etiene, Sinesio Pesco, Claudio T. Silva,
Computers & Graphics 37(7):840–850, 2013.
Vector Field k-Means: Clustering Trajectories by Fitting Multiple Vector Fields,
Ferreira, J.T. Klosowski, C. Scheidegger, and C. Silva,
Computer Graphics Forum (Proceedings of EuroVis 2013).[Best paper honourable mention award]
UltrascaleVisualizationofClimateData,
Williams,T.Bremer,C.Doutriaux,J.Patchett,S.Williams, G. Shipman, R. Miller, D. Pugmire, B. Smith, C. Steed, E. Wes Bethel, H. Childs, H. Krishnan, P. Prab- hat, M. Wehner, C. Silva, E. Santos, D. Koop, T. Ellqvist, J. Poco, B. Geveci, A. Chaudhary, A. Bauer, A. Pletzer, D. Kindig, G. Potter, and T. Maxwell,
Institute of Electrical and Electronics Engineers Computer, 46(9): 68-76, 2013.
UV-CDAT: Analyzing Climate Datasets from a User’s Perspective,
Santos, J. Poco, Y. Wei, S. Liu, B. Cook, D. Williams and C. Silva,
Computing in Science & Engineering, 15(1):94–103, 2013.
VisTrailsSAHM:visualizationandworkflowmanagementforspecieshabitatmodeling,
T.Morisette, C.S. Jarnevich, T.R. Holcombe, C.B. Talbert, D. Ignizio, M.K. Talbert, C. Silva, D. Koop, A. Swanson, and N.E. Young,
Ecography, 36(2):129-135, 2013.
A Benchmark for Surface Reconstruction,
Berger, J. Levine, L. G. Nonato, G. Taubin, and C. Silva,
Association of Computing Machinery Transactions on Graphics, 32(2):20, 2013.
Quad-Mesh Generation and Processing: a survey,
Bommes, B. Le ́vy, N. Pietroni, E. Puppo, C. Silva, M. Tarini, and D. Zorin,
Computer Graphics Forum (Proceedings of Eurographics 2012), 32(6):51-76, 2013.
2012
StreamSqueeze: A Dynamic Stream Visualization for Monitoring of Event Data.
Mansmann, M. Krstajic, F. Fischer, and E. Bertini.
Proc. of Conference on Visualization and Data Analysis (VDA), 2012.
HiTSEE: A Visualization Tool for Hit Selection and Analysis in High-Throughput Screening Experiments for KNIME Platform.
Bertini, H. Strobelt, J. Braun, O. Deussen, U. Groth, T. U. Mayer, and D. Merhof.
BMC Bioinformatics, vol. 13, no. 8, p. S4, 2012.
Empirical Studies in Information Visualization: Seven Scenarios.
Lam, E. Bertini, P. Isenberg, C. Plaisant, and S. Carpendale.
Institute of Electrical and Electronics Engineers Transactions on Visualization and Computer Graphics, vol. 18, no. 9, pp. 1520–1536,
2012
A Qualitative Study on the Exploration of Temporal Changes in Flow Maps with Animation and Small-Multiples.
Boyandin, E. Bertini, and D. Lalanne. Eurographics/Institute of Electrical and Electronics Engineers Computer Graphics Forum (Proc. of EuroVis), vol. 31, no. 3, pp. 1005–1014, 2012.
Subspace Search and Visualization to Make Sense of Alternative Clusterings in High-Dimensional Data.
Tatu, F. Maas, I. Farber, E. Bertini, T. Schreck, T. Seidl, and D. Keim. Proc. of Institute of Electrical and Electronics Engineers Conference on Visual Analytics Science and Technology (VAST), 2012.
Making Computations and Publications Reproducible with VisTrails.
Freire and Claudio Silva.
Computing in Science and Engineering 14(4): 18-25, 2012.
Clustering Wikipedia Infoboxes to Discover their Types.
Nguyen, H. Nguyen , V. Moreira and J. Freire.
In Proceedings of CIKM, pp. 2134-2138, 2012.
Computational reproducibility: state-of-the-art, challenges, and database research opportunities.
Freire, P. Bonnet, D. Shasha.
In Proceedings of SIGMOD, pp. 593-596, 2012.
Towards Integrating Workflow and Database Provenance: A Practical Approach.
Chirigati and J. Freire.
In Proceedings of the International Provenance and Annotation Workshop (IPAW), pp. 11-23, 2012.
Designing a Provenance-Based Climate Data Analysis Application.
Santos, D. Koop, T. Maxwell, C. Doutriaux, T. Ellqvist, G. Potter, J. Freire, D. Williams and C. Silva.
In Proceedings of the International Provenance and Annotation Workshop (IPAW), pp. 214-219, 2012.
Nonrigid Matching of Undersampled Shapes via Medial Diffusion,
Berger and C. Silva.
Computer Graphics Forum (Proceedings of Symposium on Geometry Processing 2012), 31(5):1587–1596, 2012.
Making Computations and Publications Reproducible with Vis Trails,
Freire and C. Silva,
Computing in Science and Engineering, 14(4):18–25, 2012.
Medial Kernels,
Berger and C. Silva.
Computer Graphics Forum (Proceedings of Eurographics 2012), 31(2):795–804, 2012.
ISP: An Optimal Out-Of-Core Image-Set Processing Streaming Architecture for Parallel Heteroge- neous Systems,
Ha, J. Krueger, J. Comba, C. Silva, and S. Joshi,
Institute of Electrical and Electronics Engineers Transactions on Visualization and Computer Graphics), 18(6):838–851, 2012.
Simple and Efficient Mesh Layout with Space-filling Curves,
Vo, L. Scheidegger, V. Pascucci, and C. Silva, Journal of Graphics Tools, GPU, and Game Tools, 16(1):25–39, 2012.
Interactive Quadrangulation with Reeb Atlases and Connectivity Textures,
Tierny, J. Daniels II, L. G. Nonato, V. Pascucci and C. Silva,
Institute of Electrical and Electronics Engineers Transactions on Visualization and Computer Graphics), 18(10):1650–1663, 2012.
HyperFlow and ITK v4 Integration: Exploring the use of a modern parallel dataflow architecture in ITK,
Vo, L. Lins, and C. Silva,
The Insight Journal, 04-2012.
Managing Data for Visual Analytics: Opportunities and Challenges,
-D. Fekete and C. Silva,
Institute of Electrical and Electronics Engineers Data Eng. Bull. 35(3): 27-36, 2012.
Topology Verification for Isosurface Extraction,
Etiene, L. Nonato, C. Scheidegger, J. Tierny, T. Peters, V. Pascucci, R. M. Kirby, and C. Silva,
Institute of Electrical and Electronics Engineers Transactions on Visualization and Computer Graphics, 18(6):952–965, 2012.[Spotlight paper]
2011
CloudLines: Compact Display of Event Episodes in Multiple Time-Series.
Krstajić, E. Bertini, and D. Keim.
Institute of Electrical and Electronics Engineers Transaction on Visualization and Computer Graphics (Proc. of InfoVis), vol. 17, no. 12, pp. 2432–2439, 2011.
HiTSEE: A Visualization Tool for Hit Selection and Analysis in High-Throughput Screening Experiments. Bertini, H. Strobelt, J. Braun, O. Deussen, U. Groth, T. U. Mayer, and D. Merhof.
In Proc. of Institute of Electrical and Electronics Engineers Symposium on Biological Data Visualization (BioVis), 2011, vol. [Best Paper Award: Honorable Mention]
Flowstrates: An Approach for Visual Exploration of Temporal Origin-Destination Data.
Boyandin, E. Bertini, P. Bak, and D. Lalanne.
Eurographics/Institute of Electrical and Electronics Engineers Computer Graphics Forum (Proc. of EuroVis), vol. 30, no. 3, pp. 971–980, 2011.
Quality Metrics in High-Dimensional Data Visualization: An Overview and Systematization.
Bertini, A. Tatu, and D. Keim.
Institute of Electrical and Electronics Engineers Transaction on Visualization and Computer Graphics (Proc. of InfoVis), vol. 17, no. 12, pp. 2203–2212, 2011.
BirdVis: Visualizing and Understanding Bird Populations.
Ferreira, L. Lins, D. Fink, S. Kelling, C. Wood, J. Freire, and C. Silva.
Institute of Electrical and Electronics Engineers Transactions on Visualization and Computer Graphics (TVCG) 17(12): 2374-2383, 2011.
Multilingual Schema Matching for Wikipedia Infoboxes.
Nguyen, V. Moreira, H. Nguyen, H. Nguyen, and J. Freire.
In Proceedings of the VLDB Endowment (PVLDB), 5(2): 133-144, 2011.
XML Management for Bioinformatics Applications.
Lena Stro ̈mba ̈ck and J. Freire.
Computing in Science and Engineering 13(5): 12-23, 2011.
Guest Editors’ Introduction: Provenance in Web Applications.
Geetika T. Lakshmanan, Francisco Curbera, J. Freire, and Amit P. Sheth.
Institute of Electrical and Electronics Engineers Internet Computing 15(1): 17-21, 2011.
Repeatability and Workability Evaluation of SIGMOD 2011,
Philippe Bonnet, Stefan Manegold, Ma- tias Bjorling, Wei Cao, Javier Gonzales, Joel Granados, Nancy Hall, Stratos Idreos, Milena Ivanova, Ryan Johnson, David Koop, Tim Kraska, Ren Mller, Dan Olteanu, Paolo Papotti, Christine Reilly, Dimitris Tsirogiannis, Cong Yu, Juliana Freire and Dennis Shasha.
In SIGMOD Record, vol. 40, no. 2, pp. 45-48, 2011.
Exploring the Coming Repositories of Repeatable Experiments: Challenges and Opportunities,
Freire, P. Bonnet, and D. Shasha.
In Proceedings of the VLDB Endowment (PVLDB), vol. 4, no. 12, pp. 1494-1497, 2011.
Synthesizing Products for Online Catalogs,
Nguyen, A. Fuxman, S. Paparizos, J.Freire, R. Agrawal.
In Proceedings of the VLDB Endowment (PVLDB), vol. 4, no. 7, pp. 409-418, 2011.
The ALPS project release 2.0: Open source software for strongly correlated systems.
Bauer, L. D. Carr, H.G. Evertz, A. Feiguin, J. Freire, S. Fuchs, L. Gamper, J. Gukelberger, E. Gull, S. Guertler, A. Hehn, R. Igarashi, S.V. Isakov, D. Koop, P.N. Ma, P. Mates, H. Matsuo, O. Parcollet, G. Pawlowski, J.D. Picon, L. Pollet, E. Santos, V.W. Scarola, U. Schollwck, C. Silva, B. Surer, S. Todo, S. Trebst, M. Troyer, M.L. Wall, P. Werner, S. Wessel.
Journal of Statistical Mechanics: Theory and Experiment (JSTAT), 2011(05), 2011.
The Open Provenance Model – Core Specification (v1.1), Moreau, B. Clifford, J. Freire, Y. Gil, P. Groth, J. Futrelle, N. Kwasnikowska, S. Miles, P. Missier, J. Myers, Y. Simmhan, E. Stephan, and J. Van den Bussche.
Future Generation Computer Systems, 27(6), 743-756, 2011.
Using VisTrails and Provenance for Teaching Scientific Visualization.
Silva, E. Anderson, E. Santos, and J. Freire.
Computer Graphics Forum, 30(1), pp. 75-84, 2011.[Best Paper Award]
Parallel Visualization on Large Clusters Using MapReduce.
Vo, J. Bronson, B. Summa, J. Comba, J. Freire, B. Howe, V. Pascucci and C. Silva.
In Large Scale Data Analysis and Visualization Symposium (LDAV), pp. 81-88, 2011.
VisCareTrails: Visualizing Trails in the Electronic Health Record with Timed Word Trees, a Pancreas Cancer Use Case.
Lins, M. Heilbrun, J. Freire, and C. Silva.
Workshop on Visual Analytics in Healthcare (VAHC), 2011.
crowdLabs: Social Analysis and Visualization for the Sciences.
Mates, E. Santos, J. Freire, and C. Silva.
In Proceedings of the 23rd International Conference on Scientific and Statistical Database Management (SSDBM), pp. 555-564, 2011.
A Provenance-Based Infrastructure to Support the Life Cycle of Executable Papers.
Koop, E. Santos, P. Mates, H. Vo, P. Bonnet, B. Bauer, B. Surer, M. Troyer, D. Williams, J. Tohline, J. Freire and C. Silva.
In Proceedings of the International Conference on Computational Science. Procedia Computer Science, vol. 4, pp. 648-657, 2011.
Inspired Quadrangulation,
Tierny, J. Daniels II, L. G. Nonato, V. Pascucci and C. Silva,
Computer- Aided Design (Proceedings of SIAM Conference on Geometric and Physical Modeling), 43(11):1516– 1526, 2011.
Efficient Probabilistic and Geometric Anatomical Mapping using Particle Mesh Approximation on GPUs,
Ha, M. Prastawa, G. Gerig, J. Gilmore, C. Silva and S. Joshi,
International Journal of Biomedical Imaging, 2011.
Template –Based Quadrilateral Mesh Generation from Imaging Data,
Lizier, M. Siqueira, J. Daniels II, C. Silva and L. Nonato,
The Visual Computer, 27(10):887–903, 2011.
Streaming-Enabled Parallel Data Flow Framework in the Visualization ToolKit,
Vo, J. Comba, B. Geveci, and C. Silva,
Computing in Science and Engineering, 13(3):72-83, 2011.
A User Study of Visualization Effectiveness Using EEG and Cognitive Load,
Anderson, K. Potter, L. Matzen, J. Shepherd, G. Preston, and C. Silva,
Computer Graphics Forum (Proceedings of EuroVis 2011).[Best paper award – 2nd prize.
]
Template-based Quadrilateral Meshing,
Daniels II, M. Lizier, M. Siqueira, C. Silva and L.G. Nonato,
Computers and Graphics (Proceedings of Shape Modeling International 2011), 35(3), 2011.
2010
Using VisTrails and Provenance for Teaching Scientific Visualization,
Silva, E. Anderson, E. Santos, and J. Freire,
Computer Graphics Forum, 30(1):75–84, 2011. (Presented at EUROGRAPHICS 2010 Educator Program, 2010).