CIS Computing & Information Services

Publications, Papers, and Theses

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

2015 2014 2013 2012 2011 2010 2009 2008


Daniel Kim, Clark Bowman, Jackson T. Del Bonis-O’Donnell, Anastasios Matzavinos, and Derek Stein, Giant Acceleration of DNA Diffusion in an Array of Entropic Barriers, Phys. Rev. Lett. 118, 048002. DOI:10.1103/PhysRevLett.118.048002

Lee, J.-E., A. Shen, B. Fox-Kemper, and Y. Ming (2017), Hemispheric sea ice distribution sets the glacial tempo, Geophys. Res. Lett., 44, DOI:10.1002/2016GL071307

D. Kapush, S. V. Ushakov, A. Navrotsky, Q.-J. Hong, H. Liu, and A. van de Walle. A combined experimental and theoretical study of enthalpy of phase transition and fusion of yttria above 2000 °C using 'drop-n-catch' calorimetry and first-principles calculations. Acta Materialia, 124:204, 2017. DOI:10.1016/j.actamat.2016.11.003


Joel K. Weltman. Sets and Subsets of Mutating Amino Acids in Zika Virus Polyprotein. J Med Microb Diagn 2016, 5:4. DOI:10.4172/2161-0703.1000247

Wenyu Bai, Gerald J. Diebold, Charles M. Wynn, Robert W. Haupt, and John H. Doherty. A numerical study of shock waves generated through laser ablation of explosives. Journal of Applied Physics 120, 194903 (2016). DOI:10.1063/1.4967825

X. Cheng, Y. Zhang, E. Jonssón, H. Jonssón and P. M. Weber, “Charge localization in a diamine cation provides a test of energy functionals and self-interaction correction” Nat. Commun. 2016, 7, 11013.

X. Cheng, Y. Gao, F. Rudakov and P. M. Weber, “Charge transfer and ultrafast nuclear motions: the complex structural dynamics of an electronically excited triamine”, Chem. Sci. 2016, 7, 619.

B. Sevilmis and B. B. Kimia. Shape-based image correspondence: In British Machine Vision Conference (BMVC), 2016.

S. Eberhardt, J. Cader & T. Serre. How deep is the feature analysis underlying rapid visual categorization? In: Proc. Neural Information Processing Systems (NIPS), 2016.

E. C. Y. Ho and Wilson Truccolo. Interaction between synaptic inhibition and glial-potassium dynamics leads to diverse seizure transition modes in biophysical models of human focal seizures. J Comput Neurosci. 2016; 41(2): 225–244. DOI:10.1007/s10827-016-0615-7

H. Y. Chang, X. J. Li, H. Li, and G. E. Karniadakis. MD/DPD multiscale framework for predicting morphology and stresses of red blood cells in health and disease. PLOS Comput. Biol. 2016, 12, e1005173. DOI:10.1371/journal.pcbi.1005173

X. J. Li, E. Du, H. Lei, Y.-H. Tang, M. Dao, S. Suresh, and G. E. Karniadakis. Patient-specific modeling and predicting blood viscosity in sickle-cell anemia. Interface Focus 2016, 6, 20150065.DOI:10.1098/rsfs.2015.0065

Mély, David A., Kim, Junkyung, McGill, Mason, Guo, Yuliang, Serre, Thomas. A systematic comparison between visual cues for boundary detection Vision research. 2016; 120 : 93-107. DOI:10.1016/j.visres.2015.11.007

Cauchoix, Maxime, Crouzet, Sébastien M., Fize, Denis, Serre, Thomas. Fast ventral stream neural activity enables rapid visual categorization NeuroImage. 2016; 125 : 280-290. DOI:10.1016/j.neuroimage.2015.10.012

LUX Collaboration (incl. R. J. Gaitskell, W. C. Taylor, J. R. Verbus, et al.), "Results on the Spin-Dependent Scattering of Weakly Interacting Massive Particles on Nucleons from the Run 3 Data of the LUX Experiment", Phys. Rev. Lett, 116:161302, April 2016. DOI: 10.1103/PhysRevLett.116.161302, arXiv:1602.03489

LUX Collaboration (incl. R. J. Gaitskell, W. C. Taylor, J. R. Verbus, et al.), Signal yields, energy resolution, and recombination fluctuations in liquid xenon. arXiv:1610.02076 [physics.ins-det]

Benjamin J. Knörlein, David B. Baier, Stephen M. Gatesy, J. D. Laurence-Chasen, Elizabeth L. Brainerd, Validation of XMALab software for marker-based XROMM. Journal of Experimental Biology 2016. DOI:10.1242/jeb.145383

Xin Bian, Mingge Deng, Yu-Hang Tang, and George Em Karniadakis, Analysis of hydrodynamic fluctuations in heterogeneous adjacent multidomains in shear flow. Phys. Rev. E 93, 033312. DOI:10.1103/PhysRevE.93.033312

LUX Collaboration (incl. R. J. Gaitskell, W. C. Taylor, J. R. Verbus, et al.), Results from a search for dark matter in LUX with 332 live days of exposure. arXiv:1608.07648 [astro-ph.CO]

R. Sun and A. van de Walle, Automating impurity-enhanced antiphase boundary energy calculations from ab initio Monte Carlo. Calphad Volume 53, June 2016, Pages 20–24. DOI:10.1016/j.calphad.2016.02.005

Andrew A. Peterson, Acceleration of saddle-point searches with machine learning. J. Chem. Phys. 145, 074106 (2016). DOI:10.1063/1.4960708

Alireza Khorshidi, Andrew A. Peterson, Amp: A modular approach to machine learning in atomistic simulations. Computer Physics Communications. DOI:10.1016/j.cpc.2016.05.010

Yan, K; Adit Maark, T; Khorshidi, A; Sethuraman, VA; Peterson, AA; Guduru, PR. The influence of elastic strain on catalytic activity in the hydrogen evolution reaction. Angewandte Chemie International Edition 55:6175--6181, 2016. DOI:10.1002/anie.201508613

Kim, SK; Zhang, Y; Bergstrom, H; Michalsky, R; Peterson, A. Understanding the low-overpotential production of CH4 from CO2 on Mo2C catalysts. ACS Catalysis 6:2003-2013, 2016. DOI:10.1021/acscatal.5b02424

James R. Verbus, An Absolute Calibration of Sub-1 keV Nuclear Recoils in Liquid Xenon Using D-D Neutron Scattering Kinematics in the LUX Detector. Ph.D. Thesis, Department of Physics. Brown Digital Repository PDF

LUX Collaboration (incl. R. J. Gaitskell, W. C. Taylor, J. R. Verbus, et al.), Low-energy (0.7-74 keV) nuclear recoil calibration of the LUX dark matter experiment using D-D neutron scattering kinematics. arXiv:1608.05381 [physics.ins-det]

J. R. Verbus, C. A. Rhyne, D. C. Malling, M. Genecov, S. Ghosh, A. G. Moskowitz, S. Chan, J. J. Chapman, L. de Viveiros, C. H. Faham, S. Fiorucci, D. Q. Huang, M. Pangilinan, W. C. Taylor, R. J. Gaitskell, Proposed low-energy absolute calibration of nuclear recoils in a dual-phase noble element TPC using D-D neutron scattering kinematics. arXiv:1608.05309 [physics.ins-det]

McDowell, I.C., T.H. Modak, C. E. Lane, M. Gomez-Chiarri 2016. Multi-species protein similarity clustering reveals novel expanded immune gene families in the eastern oyster Crassostrea virginica. Fish and Shellfish Immunology. 53:13-23. DOI:10.1016/j.fsi.2016.03.157

Alison C. Cleary and Edward G. Durbin, Unexpected prevalence of parasite 18S rDNA sequences in winter among Antarctic marine protists. Journal of Plankton Research. February 2016. DOI: 10.1093/plankt/fbw005

Peter Wilf, Shengping Zhang, Sharat Chikkerur, Stefan A. Little, Scott L. Wing, and Thomas Serre. Computer vision cracks the leaf code. Proceedings of the National Academy of Sciences. March 2016. DOI:10.1073/pnas.1524473113

Qi-Jun Hong and Axel van de Walle. A user guide for SLUSCHI: Solid and Liquid in Ultra Small Coexistence with Hovering Interfaces. Calphad Volume 52, March 2016, Pages 88–97. DOI:10.1016/j.calphad.2015.12.003


Stephen M. Doris, Deborah R. Smith, Julia N. Beamesderfer, Benjamin J. Raphael, Judith A. Nathanson and Susan A. Gerbi, Universal and domain-specific sequences in 23S–28S ribosomal RNA identified by computational phylogenetics. DOI:10.1261/rna.051144.115

Michael S. Foulk John M. Urban, Cinzia Casella, and Susan A. Gerbi, Characterizing and controlling intrinsic biases of lambda exonuclease in nascent strand sequencing reveals phasing between nucleosomes and G-quadruplex motifs around a subset of human replication origins. Genome Res 25(5):725–735. DOI:10.1101/gr.183848.114

Misner, I., Blouin, N., Leonard, G., Richards, T. A., & Lane, C. E. (2015). The secreted proteins of Achlya hypogyna and Thraustotheca clavata identify the ancestral oomycete secretome and reveal gene acquisitions by horizontal gene transfer. Genome Biol Evol. 2014 Dec 18;7(1):120-35. DOI: 10.1093/gbe/evu276

McCleary, J., dell'Antonio, I., & Huwe, P., Mass Substructure in Abell 3128, 2015, Astrophysical Journal, 805, 40. DOI: 10.1088/0004-637X/805/1/40

Ashley M. Behrman-Lay, Christina Usher, Thomas E. Conturo, Stephen Correia, David H. Laidlaw, Elizabeth M. Lane, Jacob Bolzenius, Jodi M. Heaps, Lauren E. Salminen, Laurie M. Baker, Ryan Cabeen, Erbil Akbudak, Xi Luo, Peisi Yan, Robert H. Paul. Fiber bundle length and cognition: a length-based tractography MRI study. Brain Imaging and Behavior. December 2015, Volume 9, Issue 4, pp 765-775.

Felipe Zapata , Freya E. Goetz, Stephen A. Smith, Mark Howison, Stefan Siebert, Samuel H. Church, Steven M. Sanders, Cheryl Lewis Ames, Catherine S. McFadden, Scott C. France, Marymegan Daly, Allen G. Collins, Steven H. D. Haddock, Casey W. Dunn, Paulyn Cartwright. Phylogenomic Analyses Support Traditional Relationships within Cnidaria. October 14, 2015. DOI: 10.1371/journal.pone.0139068.

Zhang, Y; Peterson, AA. Oxygen-induced changes to selectivity-determining steps in electrocatalytic CO2 reduction. Physical Chemistry Chemical Physics 17:4505--4515, 2015.

Li, H; Lausche, AC; Peterson, AA; Hansen, HA; Studt, F; Bligaard*, T. Using microkinetic analysis to search for novel anhydrous formaldehyde production catalysts. Surface Science 641:105 - 111, 2015.

Andrew A. Peterson. (Invited) Optimizing Electrocatalyst Selectivity for CO2 Reduction over H2 Evolution. doi: 10.1149/06603.0041ecst ECS Trans. 2015 volume 66, issue 3, 41-52.

R. Michalsky, A. M. Avram, B. A. Peterson, P. H. Pfromm and A. A. Peterson. Chemical looping of metal nitride catalysts: low- pressure ammonia synthesis for energy storage. Chem. Sci., 2015, 6, 3965.

S.M. Parker & T. Serre. Unsupervised invariance learning of transformation sequences in a model of object recognition yields selectivity for non-accidental properties. Frontiers in Computational Neuroscience, Special Issue on Integrating computational and neural findings in visual object perception, 2015

I. Sofer, S. Crouzet & T. Serre. Explaining the timing of natural scene understanding with a computational model of perceptual categorization. PLOS Computational Biology, 2015

J.W. Hofmann, X. Zhao, M. De Cecco, A.L. Peterson, L. Pagliaroli, J. Manivannan, G.B. Hubbard, Y. Ikeno, Y. Zhang, B. Feng, T. Serre, W. Qi, H. Van Remmen, R.A. Miller, K.G. Bath, R. de Cabo, H. Xu, N. Neretti & John M. Sedivy. Reduced expression of the proto-oncogene Myc increases mouse longevity and enhances healthspan. Cell, 2015

A. van de Walle, Q. Hong, S. Kadkhodaei, and R. Sun. The free energy of mechanically unstable phases. Nature Commun., 6:7559, 2015.

Q.-J. Hong and A. van de Walle. Prediction of the material with highest known melting point from ab initio molecular dynamics calculations. Phys. Rev. B Rapid Communications, 92:020104(R), 2015.

James Verbus. "Measurement of Ultra-low Energy Nuclear Recoils in the LUX Detector Using a D-D Neutron Generator" (Sept. 23, 2015)

Dongqing Huang. "Ultra-low energy calibration of LUX using 127-Xe"

Adrian Reich, Casey Dunn, Koji Akasaka, and Gary Wessel, "Phylogenomic Analyses of Echinodermata Support the Sister Groups of Asterozoa and Echinozoa," PLoS ONE 03/2015; 10(3):e0119627. DOI:10.1371/journal.pone.0119627

Xinxin Cheng, Yao Zhang, Yan Gao, Hannes Jónsson, and Peter M. Weber, "Ultrafast structural pathway of charge transfer in n,n,n',n'-tetramethylethylenediamine," J. Phys. Chem. A 119, 2813-2818 (2015). doi:10.1021/acs.jpca.5b01797

Goudge, T. A., J. F. Mustard, J. W. Head, C. I. Fassett, and S. M. Wiseman (2015), Assessing the mineralogy of the watershed and fan deposits of the Jezero crater paleolake system, Mars, J. Geophys. Res., 120, 775–808, DOI: 10.1002/2014JE004782

Goudge, T. A., J. F. Mustard, J. W. Head, M. R. Salvatore, and S. M. Wiseman (2015), Integrating CRISM and TES hyperspectral data to characterize a halloysite-bearing deposit in Kashira crater, Mars, Icarus, 250, 165–187, DOI: 10.1016/j.icarus.2014.11.034.

Weltman, JK, Identification of Invariant Peptide Domains within Ebola Virus Glycoprotein GP1, 2. J Med Microb Diagn 4:176. doi:10.4172/2161-0703.10001762


Qi-Jun Honga, Sergey V. Ushakov, Alexandra Navrotsky, Axel van de Walle, Combined computational and experimental investigation of the refractory properties of La2Zr2O7. Acta Mater., 84:275-282, 2015. DOI:10.1016/j.actamat.2014.10.026

Talia R. Seider, Xi Luo, Assawin Gongvatana, Kathryn N. Devlin, Suzanne M. de la Monte, Jesse D. Chasman, Peisi Yan, Karen T. Tashima, Bradford Navia & Ronald A. Cohen. Verbal memory declines more rapidly with age in HIV infected versus uninfected adults. Journal of Clinical and Experimental Neuropsychology. Volume 36, Issue 4, 2014, pages 356-367. DOI:10.1080/13803395.2014.892061

Zhang, Y; Sethuraman, V; Michalsky, R; Peterson, AA. Competition between CO2 reduction and H2 evolution on transition-metal electrocatalysts. ACS Catalysis 4:3742-3748, 2014.

Y. Zhang, S. Zhang, Q. Huang & T. Serre. Learning sparse prototypes for crowd perception via ensemble coding mechanisms. In: Proc. 5th International Workshop on Human Behavior Understanding, 2014

D. Reichert & T. Serre. Neuronal synchrony in complex-valued deep networks. International Conference on Learning Representations, 2014

J. Chapman, "First WIMP Search Results from the LUX Dark Matter Experiment," Ph.D. thesis, Brown University (2014).

D. Malling, "Measurement and Analysis of WIMP Detection Backgrounds, and Characterization and Performance of the Large Underground Xenon Dark Matter Search Experiment," Ph.D. thesis, Brown University (2014).

C. Faham, "Prototype, Surface Commissioning and Photomultiplier Tube Characterization for the Large Underground Xenon (LUX) Direct Dark Matter Search Experiment," Ph.D. thesis, Brown University (2014).

C. Chan, J.J. Chapman, R.J. Gaitskell, D.Q. Huang, D.C. Malling, M. Pangilinan, J.R. Verbus, et al., "First results from the LUX dark matter experiment at SURF," Phys. Rev. Lett. 112, 091303 arXiv:1310.8214

Cheng X, Zhang Y, Deb S, Minitti MP, Gao Y, Jonsson H, Weber PM, "Ultrafast structural dynamics in Rydberg excited N,N,N',N'-tetramethylethylenediamine: conformation dependent electron lone pair interaction and charge delocalization," Chem. Sci. 5, 4394-4403 (2014). doi:10.1039/C4SC01646G

Zapata F, Wilson NG, Howison M, Andrade SCS, Jörger KM, Schrödl M, Goetz FE, Giribet G, Dunn CW, "Phylogenomic analyses of deep gastropod relationships reject Orthogastropoda," Proc R Soc B 281, 20141739, Sep 2014. doi:10.1098/rspb.2014.1739 [EPSCoR]

McDowell IC, Nikapitiya C, Aguiar D, Lane CE, Istrail S, Gomez-Chiarri M, "Transcriptome of American oysters, Crassostrea virginica, in response to bacterial challenge: Insights into potential mechanisms of disease resistance," PLoS ONE 9(8), e105097, Aug 2014. doi:10.1371/journal.pone.0105097 [EPSCoR]

Oulhen N, Xu D, Wessel GM, "Conservation of sequence and function in fertilization of the cortical granule serine protease in echinoderms," Biochemical and Biophysical Research Communications 450(3), 1135-1141, Aug 2014. doi:10.1016/j.bbrc.2014.05.098

Weltman JK, "MERS-Cov and Immunobioinformatics," J Med Microb Diagn 3(3), e126, Jul 2014. doi:10.4172/2161-0703.1000e126

Weltman JK, "An Immunobioinformatic Comparison of Influenza A Subtype Hemagglutinins," J Med Microb Diagn 3(135), Jul 2014. doi:10.4172/2161-0703.1000135

Zazueta-Novoa V, Wessel GM, "Protein degradation machinery is present broadly during early development in the sea urchin," Gene Expression Patterns 15(2), 135-141, Jul 2014. doi:10.1016/j.gep.2014.06.002

Christin P-A, Arakaki M, Osborne CP, Bräutigam A, Sage RF, Hibberd JM, Kelly S, Covshoff S, Wong GK-S, Hancock L, Edwards EJ, "Shared origins of a key enzyme during the evolution of C4 and CAM metabolism," J Exp Bot 65(13), 3609-3621, Jul 2014. doi:10.1093/jxb/eru087

Hancock L, Edwards EJ, "Phylogeny and the inference of evolutionary trajectories," J Exp Bot 65(13), 3491-3498, Jul 2014. doi:10.1093/jxb/eru118

Howison M, Bethel EW, "GPU-accelerated denoising of 3D magnetic resonance images," Journal of Real-Time Image Processing, Jun 2014. doi:10.1007/s11554-014-0436-8

Howison M, Zapata F, Edwards EJ, Dunn CW, "Bayesian Genome Assembly and Assessment by Markov Chain Monte Carlo Sampling," PLoS ONE 9(6), e99497, Jun 2014. doi:10.1371/journal.pone.0099497

Clement WL, Arakaki M, Sweeney PW, Edwards EJ, Donoghue MJ, "A chloroplast tree for Viburnum (Adoxaceae) and its implications for phylogenetic classification and character evolution," Am J Bot 101(6), 1029-1049, Jun 2014. doi:10.3732/ajb.1400015

R Michalsky, Y-J Zhang, AJ Medford, AA Peterson, "Departures from the Adsorption Energy Scaling Relations for Metal Carbide Catalysts," J. Phys. Chem. C, Jun 2014. doi:10.1021/jp503756g

M Tamaki, JW Bang, T Watanabe, Y Sasaki, "The first-night effect suppresses the strength of slow-wave activity originating in the visual areas during sleep," Vision Research 99, 154-161, Jun 2014. doi:10.1016/j.visres.2013.10.023

H Kuehne, A Arlsan, T Serre, "The Language of Actions: Recovering the Syntax and Semantics of Goal-Directed Human Activities," in Proceedings of the 2014 IEEE Computer Society Conference on Computer Vision and Pattern Recognition (CVPR), Jun 2014.

Pombert J-F, Blouin NA, Lane C, Boucias D, Keeling PJ, "A Lack of Parasitic Reduction in the Obligate Parasitic Green Alga Helicosporidium," PLoS Genet 10(5), e1004355. doi:10.1371/journal.pgen.1004355

Oulhen N, Onorato T, Ramos I, Wessel GM, "Dysferlin is essential for endocytosis in the sea star oocyte," Developmental Biology 388(1), 94-102, Apr 2014. doi:10.1016/j.ydbio.2013.12.018

Fresques T, Zazueta-Novoa V, Reich A, Wessel GM, "Selective accumulation of germ-line associated gene products in early development of the sea star and distinct differences from germ-line development in the sea urchin," Dev Dyn. 243(4), 568-587, Apr 2014. doi:10.1002/dvdy.24038

H Xu, "Comparing Spatial and Multilevel Regression Models for Binary Outcomes in Neighborhood Studies," Sociological Methodology 0081175013490188, Apr 2014. doi:10.1177/0081175013490188

A Kenyon, J van Rosendale, S Fulcomer, DH Laidlaw, "The Design of a Retinal Resolution Fully Immersive VR Display," in Proceedings of the 2014 IEEE Virtual Reality Conference, 89-90, Mar 2014. doi:10.1109/VR.2014.6802065

Yajima M, Gustafson EA, Song JL, Wessel GM, "Piwi regulates Vasa accumulation during embryogenesis in the sea urchin," Developmental Dynamics 243(3), 451-458, Mar 2014. doi:10.1002/dvdy.24096

R Michalsky, Y-J Zhang, AA Peterson, "Trends in the Hydrogen Evolution Activity of Metal Carbide Catalysts," ACS Catal. 4(5), 1274-1278, Mar 2014. doi:10.1021/cs500056u

BDL Marshall, SR Friedman, JFG Monteiro, M Paczkowski, B Tempalski, ER Pouget, MN Lurie, S Galea, "Prevention And Treatment Produced Large Decreases In HIV Incidence In A Model Of People Who Inject Drugs," Health Affairs 33(3), 401-409, Mar 2014. doi:10.1377/hlthaff.2013.0824

Y Zhang, Stefan M. Sievert, "Pan-genome analyses identify lineage- and niche-specific markers of evolution and adaptation in Epsilonproteobacteria," Front Microbiol. 5, 110, Mar 2014. doi:10.3389/fmicb.2014.00110

AP Sergeeva, IA Popov, ZA Piazza, W-L Li, C Romanescu, L-S Wang, AI Boldyrev, "Understanding Boron through Size-Selected Clusters: Structure, Chemical Bonding, and Fluxionality," Acc. Chem. Res. 47(4), 1349-1358, Mar 2014. doi:10.1021/ar400310g

AA Peterson, "Global Optimization of Adsorbate–Surface Structures While Preserving Molecular Identity," Topics in Catalysis 57(1-4), 40-53, Feb 2014. doi:10.1007/s11244-013-0161-8

P Chen, H Ghassemi-Armaki, S Kumar, A Bower, S Bhat, S Sadagopan, "Microscale-calibrated modeling of the deformation response of dual-phase steels," Acta Materialia 65(10), 133-149, Feb 2014. doi:10.1016/j.actamat.2013.11.036

TA Maark, AA Peterson, "Understanding Strain and Ligand Effects in Hydrogen Evolution over Pd(111) Surfaces," J. Phys. Chem. C 118(8), 4275-4281, Jan 2014. doi:10.1021/jp4121035

ZA Piazza, H-S Hu, W-L Li, Y-F Zhao, J Li, L-S Wang, "Planar hexagonal B36 as a potential basis for extended single-atom layer boron sheets," Nature Communications 5, 3113, Jan 2014. doi:10.1038/ncomms4113

M Cauchoix, G Barragan-Jason, T Serre, EJ Barbeau, "The neural dynamics of face detection in the wild revealed by MVPA," J. Neurosci. 34(3), 856-854, Jan 2014. doi:10.1523/JNEUROSCI.3030-13.2014

Juliano CE, Reich A, Liu N, Götzfried J, Zhong M, Uman S, Reenan RA, Wessel GM, Steele RE, Lin H, "PIWI proteins and PIWI-interacting RNAs function in Hydra somatic stem cells," PNAS 111(1), 337-342, Jan 2014. doi:10.1073/pnas.1320965111


Rick Gaitskell. "First Science Results from the LUX Dark Matter Experiment"

Brayboy LM, Oulhen N, Witmyer J, Robins J, Carson S, Wessel GM, "Multidrug Resistant Transport Activity Protects Oocytes From Chemotherapeutic Agents And Changes During Oocyte Maturation," Fertility and Sterility 100(5), 1428-1435, Nov 2013. doi:10.1016/j.fertnstert.2013.07.002

Dunn CW, Howison M, Zapata F, "Agalma: an automated phylogenomics workflow," BMC Bioinformatics 14, 330, Nov 2013. doi:10.1186/1471-2105-14-330

W Zhu, R Michalsky, Ö Metin, H Lv, S Guo, CJ Wright, X Sun, AA Peterson, S Sun, "Monodisperse Au Nanoparticles for Selective Electrocatalytic Reduction of CO2 to CO," J. Am. Chem. Soc. 135(45), 16833-16836, Oct 2013. doi:10.1021/ja409445p

IA Popov, ZA Piazza, W-L Li, L-S Wang, AI Boldyrev, "A combined photoelectron spectroscopy and ab initio study of the quasi-planar B24 cluster," J. Chem. Phys. 139(14), 144307, Oct 2013. doi:10.1063/1.4824156

F Chen and J Shen, "A GPU parallelized spectral method for elliptic equations in rectangular domains," Journal of Computational Physics 250, 555-564, Oct 2013. doi:10.1016/

Misner I, Bicep C, Lopez P, Halary S, Bapteste E, Lane CE, "Sequence Comparative Analysis using Networks (SCAN): software for evaluating de novo transcript assembly from next generation sequencing," Molecular Biology and Evolution 30(8), Aug 2013. doi:10.1093/molbev/mst087 [EPSCoR]

M Zayernouri, S-W Park, DM Tartakovsky, GE Karniadakis, "Stochastic smoothed profile method for modeling random roughness in flow problems", Computer Methods in Applied Mechanics and Engineering 263, 99-112, Aug 2013. doi:101016/jcma201305007

M Tamaki, T-R Huang, Y Yotsumoto, M Hämäläinen, F-H Lin, JE Náñez Sr, T Watanabe, Y Sasaki, "Enhanced Spontaneous Oscillations in the Supplementary Motor Area Are Associated with Sleep-Dependent Offline Learning of Finger-Tapping Motor-Sequence Task," J. Neurosci. 33(34), 13894-13902, Aug 2013. doi:10.1523/JNEUROSCI.1198-13.2013

Wiecki TV, Sofer I, Frank MJ, "HDDM: Hierarchical Bayesian estimation of the Drift-Diffusion Model in Python," Frontiers of Neuroinformatics 7(14), Jul 2013. doi:10.3389/fninf.2013.00014

Y Yang, I Roy, C-W Shu, L-Z Fang, "The Angular Distribution of Lyα Resonant Photons Emerging from an Optically Thick Medium," The Astrophysical Journal 772(1), Jun 2013. doi:10.1088/0004-637X/772/1/3

H Ghassemi-Armaki, P Chen, S Bhat, S Sadagopan, S Kumar, A Bower, "Microscale-calibrated modeling of the deformation response of low-carbon martensite," Acta Materialia 61(10), 3640-3652, Jun 2013. doi:10.1016/j.actamat.2013.02.051

DS Akerib, X Bai, E Bernard, et al., "Technical results from the surface run of the LUX dark matter experiment," Astroparticle Physics 45, 34-43, May 2013. doi:10.1016/j.astropartphys.2013.02.001

K Yeo and MR Maxey, "Dynamics and rheology of concentrated, finite-Reynolds-number suspensions in a homogeneous shear flow," Physics of Fluids 25, 053303, May 2013. doi:10.1063/1.4802844

Oulhen N, Yoshida T, Yajima M, Song JL, Sakuma T, Sakamoto N, Yamamoto T, Wessel GM, "The 3'UTR of nanos2 directs enrichment in the germ cell lineage of the sea urchin," Developmental Biology 377(1), 275-283, May 2013. doi:10.1016/j.ydbio.2013.01.019

CW Pfrang, P Deift, G Menon, "How long does it take to compute the eigenvalues of a random symmetric matrix?,", May 2013. arXiv:1203.4635v2

RR Helm, S Siebert, S Tulin, J Smith, CW Dunn, "Characterization of differential transcript abundance through time during Nematostella vectensis development," BMC Genomics 14(1), 266, Apr 2013. doi:10.1186/1471-2164-14-266 [EPSCoR]

Wiecki TV and Frank MJ, "A computational model of inhibitory control in frontal cortex and basal ganglia," Psychological Review 120(2), 329-355, Apr 2013. doi:10.1037/a0031542

A Uzun, AT Dewan, S Istrail, JF Padbury, "Pathway-based genetic analysis of preterm birth," Genomics 101(3), 163-170, Mar 2013. doi:10.1016/j.ygeno.2012.12.005

M Howison, "High-Throughput Compression of FASTQ Data with SeqDB," IEEE/ACM Transactions on Computational Biology and Bioinformatics 10(1), 213-218, Feb 2013. pdf doi:10.1109/TCBB.2012.160

Yajima M, Suglia E, Gustafson EA, Wessel GM, "Meiotic gene expression initiates during larval development in the sea urchin," Developmental Dynamics 242(2), 155-63, Feb 2013. doi:10.1002/dvdy.23904

Oulhen N, Reich A, Wong J, Wessel GM, "Diversity in the fertilization envelope of echinoderms," Evolution and Development 15(1), 28-40, Jan 2013. doi: 10.1111/ede.12012](


EW 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 26(4), 399-412, Nov 2012. doi:10.1177/1094342012440466

AP Sergeeva, ZA Piazza, C Romanescu, W-L Li, AI Boldyrev, L-S Wang, "B22– and B23–: All-Boron Analogues of Anthracene and Phenanthrene," J. Am. Chem. Soc 134(43), 18065–18073, Oct 2012. doi:10.1021/ja307605t

J Zhang, Y Barhomi, T Serre, "A New Biologically Inspired Color Image Descriptor," in Proceedings of the 12th European Conference on Computer Vision (ECCV '12), Oct 2012. doi:10.1007/978-3-642-33715-4_23

M Narayanan and B Kimia, "Bottom-Up Perceptual Organization of Images into Object Part Hypotheses," in Proceedings of the 12th European Conference on Computer Vision (ECCV '12), Oct 2012. doi:10.1007/978-3-642-33718-5_19

Song JL and Wessel GM, "The forkhead transcription factor FoxY regulates Nanos," Molecular Reproduction and Development 79(10), 680–688, Oct 2012. doi:10.1002/mrd.22073

Yajima M, Fairbrother WG, Wessel GM, "ISWI contributes to ArsI insulator function in development of the sea urchin," Development 139(19), 3613-3622, Oct 2012. doi:10.1242/dev.081828

JK 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

Reich A, Neretti N, Freiman R, Wessel GM, "Transcriptome variance in single oocytes within, and between, genotypes," Molecular Reproduction and Development 79(8), 502, Aug 2012. doi:10.1002/mrd.22061

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

PA Flight and DM Rand, "Genetic Variation in the Acorn Barnacle from Allozymes to Population Genomics," Integrative and Comparative Biology 52(3), 418-429, Jul 2012. doi:10.1093/icb/ics099

AJ Taggart, AM DeSimone, JS Shih, ME Filloux, WG 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, NA Sinnott-Armstrong, CW 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.

M Donato, F Cremona, W Jin, RI 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

WA Thompson and JK Weltman, "Bioinformatic Analyses of 2009-2010 Pandemic H1N1 Influenza A Hemagglutinin Subsets," Journal of Medical Microbiology & Diagnosis 1:110, May 2012. doi:10.4172/2161-0703.1000110

A Uzun, S Sharma, JF 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, ML Marazita, M Melby, JC Murray, JF 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, JF 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 JF 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, JF Padbury, "dbPTB: a database for preterm birth," Database 2012, Feb 2012. doi:10.1093/database/bar069

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

WA Thompson and JK 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


DL Miranda, JB Schwartz, AC Loomis, EL Brainerd, BC Fleming, JJ 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, 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.

SM 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, 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

SA Smith, NG Wilson, FE Goetz, C Feehery, SCS Andrade, GW Rouse, G Giribet, CW 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, JC Murray, JF 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, AS Forsberg, A Loomis, JW Head, JL Dickson, 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

Cavanagh JF, Wiecki TV, Cohen MX, Figueroa CM, Samanta J, Sherman SJ, Frank MJ, "Subthalamic nucleus stimulation reverses mediofrontal influence over decision threshold," Nature Neuroscience 14(11),1462-1467, Sep 2011. doi:10.1038/nn.2925

S Siebert, MD Robinson, SC Tintori, F Goetz, RR Helm, SA Smith, N Shaner, SHD Haddock, CW 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


JL Dickson, JW Head, DR 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

JW Head, DR Marchant, JL Dickson, AM Kress, DM 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

JS Levy, JW Head, JL Dickson, CI Fassett, GA Morgan, SC 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 


JL Dickson, CI Fassett, JW 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

SJ Kadish, NG Barlow, JW 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

JS Levy, JW Head, DR 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


JW Head, DR Marchant, MA 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

JW Head, JN Huffman, AS Forsberg, DM Hurwitz, AT Basilevsky, MA Ivanov, JL 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, DH 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

JJ LaViola, Prabhat, AS Forsberg, DH Laidlaw, 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