Publications

The following publications, ordered chronologically, made use of computational resources and services at CCV.

2012

J. K. Weltman, “Some Implications of Mathematical Analyses of Epidemics,” Journal of Medical Microbiology & Diagnosis 1(6), 1–3, Oct. 2012. doi:10.4172/2161-0703.1000e115

C. W. Pfrang, P. Deift, and G. Menon, “How long does it take to compute the eigenvalues of a random symmetric matrix?,” arXiv:1203.4635v1

A. Uzun, S. Sharma, S. Istrail, and J. F. Padbury, “Preterm Birth: A Novel Bioinformatics and Genomics Approach,” presented at the Human Genetics & Genomics Conference, Newport, RI, USA, Jul. 2012.

P. A. Flight and D. M. Rand, “Genetic Variation in the Acorn Barnacle from Allozymes to Population Genomics,” Integrative and Comparative Biology, Jul. 2012. doi:10.1093/icb/ics099

A. J. Taggart, A. M. DeSimone, J. S. Shih, M. E. Filloux, and W. G. Fairbrother, “Large-scale mapping of branchpoints in human pre-mRNA transcripts in vivo,” Nature Structural & Molecular Biology 19(7), 719-721, Jul. 2012. doi:10.1038/nsmb.2327

M. Howison, N. A. Sinnott-Armstrong, and C. W. Dunn, “BioLite, a lightweight bioinformatics framework with automated tracking of diagnostics and provenance,” in Proceedings of the 4th USENIX Workshop on the Theory and Practice of Provenance (TaPP '12), Jun. 2012. [bib]

M. Donato, F. Cremona, W. Jin, R. I. Bahar, W. Patterson, A. Zaslavsky, J. Mundy, “A Noise-Immune Sub-Threshold Circuit Design Based on Selective use of Schmitt-Trigger Logic,” in Proceedings of the ACM Great Lakes Symposium on VLSI, 39-44, May 2012. doi:10.1145/2206781.2206792

W. A. Thompson and J. K. Weltman, “Bioinformatic Analyses of 2009-2010 Pandemic H1N1 Influenza A Hemagglutinin Subsets,” Journal of Medical Microbiology & Diagnosis 1(3), May 2012. doi:10.4172/2161-0703.1000110

E. W. Bethel and M. Howison, “Multi-core and many-core shared-memory parallel raycasting volume rendering optimization and tuning,” International Journal of High Performance Computing Applications, Apr. 2012. doi:10.1177/1094342012440466 [bib]

A. Uzun, S. Sharma, and J. F. Padbury, “A Bioinformatics Approach to Preterm Birth,” American Journal of Reproductive Immunology 67(4), 273-277, Apr. 2012. doi:10.1111/j.1600-0897.2012.01122.x

A. Uzun, B. Feenstra, M. L. Marazita, M. Melby, J. C. Murray, and J. F. Padbury, “Analysis of runs of homozygosity (ROH) mapping from GWAS data for preterm birth,” presented at the 2012 Pediatric Academic Societies’ Annual Meeting, Boston, MA, USA, Apr. 2012.

A. Uzun, A. Laliberte, J. Parker, C. Andrew, E. Winterrowd, S. Sharma, S. Istrail, and J. F. Padbury, “A knowledge based bioinformatics application for preterm birth,” presented at the 2012 Pediatric Academic Societies’ Annual Meeting, Boston, MA, USA, Apr. 2012.

A. Uzun and J. F. Padbury, “Analyzing biological pathways in genome-wide association studies (GWAS) for preterm birth,” presented at the 2012 Pediatric Academic Societies’ Annual Meeting, Boston, MA, USA, Apr. 2012.

A. Uzun, A. Laliberte, J. Parker, C. Andrew, E. Winterrowd, S. Sharma, S. Istrail, and J. F. Padbury, “dbPTB: a database for preterm birth,” Database 2012, Feb. 2012. doi:10.1093/database/bar069

P. Dupuis, K. Spiliopoulos, and H. Wang, “Importance Sampling for Multiscale Diffusions,” Multiscale Modeling & Simulation 10(1), 1-27, Jan. 2012. doi:10.1137/110842545

W. A. Thompson and J. K. Weltman, “Intergenic subset organization within a set of geographically-defined viral sequences from the 2009 H1N1 influenza A pandemic,” American Journal of Molecular Biology 2(1), 32-41, Jan. 2012. doi:10.4236/ajmb.2012.21004

2011

D. L. Miranda, J. B. Schwartz, A. C. Loomis, E. L. Brainerd, B. C. Fleming, and J. J. Crisco, “Static and Dynamic Error of a Biplanar Videoradiography System Using Marker-Based and Markerless Tracking Techniques,” Journal of Biomechanical Engineering 133(12), 121002, Dec. 2011. doi:10.1115/1.4005471

M. Cauchoix, A. Arlsan, D. Fize and T. Serre, “The neural dynamics of visual processing in monkey extrastriate cortex: A comparison between univariate and multivariate techniques,” presented at Neural Information Processing Systems – Workshop on Machine Learning and Interpretation in Neuroimaging, Dec. 2011.

S. M. Crouzet and T. Serre, “What are the visual features underlying rapid object recognition?,” Frontiers in Psychology 2(326), Nov. 2011. doi:10.3389/fpsyg.2011.00326

H. Kuehne, H. Jhuang, E. Garrote, T. Poggio, and T. Serre, “HMDB: A large video database for human motion recognition,” in Proceedings of the IEEE International Conference on Computer Vision (ICCV), 2556–2563, Nov. 2011. doi:10.1109/ICCV.2011.6126543

S. A. Smith, N. G. Wilson, F. E. Goetz, C. Feehery, S. C. S. Andrade, G. W. Rouse, G. Giribet, and C. W. Dunn, “Resolving the evolutionary relationships of molluscs with phylogenomic tools,” Nature 480, 364-367, Oct. 2011. doi:10.1038/nature10526

A. Uzun, S. Sharma, A. Laliberte, B. Buzzell, J. C. Murray, and J. F. Padbury, “Analyzing biological pathways in genome-wide association studies (GWAS) for preterm birth,” presented at the New England Conference on Perinatal Research, Chatham, MA, USA, Oct. 2011.

J. Huffman, A. S. Forsberg, A. Loomis, J. W. Head, J. L. Dickson, and C. Fassett, “Integrating advanced visualization technology into the planetary Geoscience workflow,” Planetary and Space Science 59(11-12), 1273-1279, Sep. 2011. doi:10.1016/j.pss.2010.07.015

S. Siebert, M. D. Robinson, S. C. Tintori, F. Goetz, R. R. Helm, S. A. Smith, N. Shaner, S. H. D. Haddock, and C. W. Dunn, “Differential Gene Expression in the Siphonophore Nanomia bijuga (Cnidaria) Assessed with Multiple Next-Generation Sequencing Workflows,” PLoS ONE 6(7), e22953, Jul. 2011. doi:10.1371/journal.pone.0022953

2010

J. L. Dickson, J. W. Head, D. R. Marchant, “Kilometer-scale ice accumulation and glaciation in the northern mid-latitudes of Mars: Evidence for crater-filling events in the Late Amazonian at the Phlegra Montes,” Earth and Planetary Science Letters 294(3-4), 332-342, Jun. 2010. doi:10.1016/j.epsl.2009.08.031

J. W. Head, D. R. Marchant, J. L. Dickson, A. M. Kress, and D. M. Baker, “Northern mid-latitude glaciation in the Late Amazonian period of Mars: Criteria for the recognition of debris-covered glacier and valley glacier landsystem deposits,” Earth and Planetary Science Letters 294(3-4), 306-320, Jun. 2010. doi:10.1016/j.epsl.2009.06.041

J. S. Levy, J. W. Head, J. L. Dickson, C. I. Fassett, G. A. Morgan, and S. C. Schon, “Identification of Gully Debris Flow Deposits in Protonilus Mensae, Mars: Characterization of a Water-Related, Energetic Gully-Forming Process,” Earth and Planetary Science Letters 294(3-4), 368-377, Jun. 2010. doi:10.1016/j.epsl.2009.08.002 

2009

J. L. Dickson, C. I. Fassett, and J. W. Head, “Amazonian-Aged Valley Networks in a Climatic Microenvironment on Mars: Melting of Ice Deposits on the Interior of Lyot Crater,” Geophysical Research Letters 36, L08201, 2009. doi:10.1029/2009GL037472

S. J. Kadish, N. G. Barlow, and J. W. Head, “Latitude dependence of Martian pedestal craters: Evidence for a sublimation-driven formation mechanism,” Journal of Geophysical Research 114, E10001, 2009. doi:10.1029/2008JE003318

J. S. Levy, J. W. Head and D. R. Marchant, “Concentric crater fill in Utopia Planitia: History and interaction between glacial “brain terrain” and periglacial mantle processes,” Icarus 202(2), 462-476, Aug. 2009. doi:10.1016/j.icarus.2009.02.018

2008

J. W. Head, D. R. Marchant and M. A. Kreslavsky, “Formation of gullies on Mars: Link to recent climate history and insolation microenvironments implicate surface water flow origin,” Proceedings of the National Academy of Sciences 105(36), 13258-13263, Sep. 2008. doi:10.1073/pnas.0803760105

J. W. Head, J. N. Huffman, A. S. Forsberg, D. M. Hurwitz, A. T. Basilevsky, M. A. Ivanov, J. L. Dickson and P. Senthil Kumar, “Testing geoscience data visualization systems for geological mapping and training,” in Proceedings of the European Planetary Science Congress, Münster, Germany, EPSC2008-A-00432, Sep. 2008.

D. Keefe, D. Acevedo, J. Miles, F. Drury, S. Swartz, and D. H. Laidlaw. “Scientific Sketching for Collaborative VR Visualization Design,” IEEE Transactions on Visualization and Computer Graphics 14(4), 835-847, Jul. 2008. doi:10.1109/TVCG.2008.31 [bib]

J. J. LaViola, Prabhat, A. S. Forsberg, D. H. Laidlaw, and A. van Dam. “Virtual Reality-Based Interactive Scientific Visualization Environments,” in E. Zudilova-Seinstra et al. (eds.) Trends in Interactive Visualization, 225-250, 2008. doi:10.1007/978-1-84800-269-2_10 [bib]