Staff Publications

Article Index

Staff Publications (within the last 10 years)

Adams, Andrew

V. Hazlewood, K. Benninger, G. Peterson, J. Charcalla, B. Sparks, J. Hanley, A. Adams, B. Learn, R. Budden, D. Simmel, J. Lappa, J. Yanovich. Developing Applications with Networking Capabilities via End-to-End SDN (DANCES). XSEDE16, Miami, FL, July 17-21, 2016

Andrew K. Adams and Adam J. Lee, Combining Social Authentication and Untrusted Clouds for Private Location Sharing, in Proceedings of the 18th ACM Symposium on Access Control Models and Technologies (SACMAT), June 2013

A. Adams, A. J. Lee, and D. Mosse, Receipt-Mode Trust Negotiation: Efficient Authorization Through Outsourced Interactionsin Proceedings of the Sixth ACM Symposium on Information, Computer, and Communication Security (ASIACCS 2011), March 2010.

V. Paxson, A. Adams, M. Mathis, Experiences with NIMI, Passive and Active Measurement Workshop 2000, Proceedings, April 2000.

Peisert, Sean; Welch, Von; Adams, Andrew; Bevier, RuthAnne; Dopheide, Michael; LeDuc, Rich; Meunier, Pascal; Schwab, Steve; Stocks, Karen. Open Science Cyber Risk Profile (OSCRP)., 2017.


Begandy, Cheryl

Preparing Teachers to Infuse Computational Science into their Classroom Instruction. Susan Ragan, Charlotte M. Trout, Cheryl Begandy, Nancy R. Bunt, and Scott A. Sinex Journal of Computational Science Education,  Volume 2, Issue 1, pp. 9–14. Dec. 2011.


Blood, Phil

Seetharam A, Gomez A, Purcell C, Hyde J, Blood P, et al. NCBI-BLAST programs optimization on XSEDE resources for sustainable aquaculture. Proceedings of the 2015 XSEDE Conference: Scientific Advancements Enabled by Enhanced Cyberinfrastructure. ACM. 2015. DOI: 10.1145/2792745.2792749

Ghaffari N, Sanchez-Flores A, Doan R, Garcia-Orozco KD, Chen PL, Ochoa-Leyva A, Lopez-Zavala AA, Carrasco JS, Hong C, Brieba LG, Rudiño-Piñera E, Blood PD, Sawyer JE, Johnson CD, Dindot SV, Sotelo-Mundo RR, Criscitiello MF. Novel transcriptome assembly and improved annotation of the whiteleg shrimp (Litopenaeus vannamei), a dominant crustacean in global seafood mariculture. Sci Rep. 2014 Nov 25;4:7081. doi: 10.1038/srep07081. PubMed PMID: 25420880; PubMed Central PMCID: PMC4243063

Blood PD, Marcus S, Schatz MC. Large-scale Sequencing and Assembly of Cereal Genomes Using Blacklight. Proceedings of the 2014 Annual Conference on Extreme Science and Engineering Discovery Environment. ACM. 2014. DOI: 10.1145/2616498.2616502

LeDuc R, Vaughn M, Fonner JM, Sullivan M, Williams JG, Blood PD, Taylor J, Barnett W. Leveraging the national cyberinfrastructure for biomedical research. J Am Med Inform Assoc. 2014 Mar-Apr;21(2):195-9. doi: 10.1136/amiajnl-2013-002059. Epub 2013 Aug 20. PubMed PMID: 23964072; PubMed Central PMCID: PMC3932465

Couger MB, Pipes L, Squina F, Prade R, Siepel A, Palermo R, Katze MG, Mason CE, Blood PD. Enabling large-scale next-generation sequence assembly with Blacklight. Concurr Comput. 2014 Sep 10;26(13):2157-2166. PubMed PMID: 25294974; PubMed Central PMCID: PMC4185199

Haas BJ, Papanicolaou A, Yassour M, Grabherr M, Blood PD, Bowden J, Couger MB, Eccles D, Li B, Lieber M, Macmanes MD, Ott M, Orvis J, Pochet N, Strozzi F, Weeks N, Westerman R, William T, Dewey CN, Henschel R, Leduc RD, Friedman N, Regev A. De novo transcript sequence reconstruction from RNA-seq using the Trinity platform for reference generation and analysis. Nat Protoc. 2013 Aug;8(8):1494-512. doi: 10.1038/nprot.2013.084. Epub 2013 Jul 11. PubMed PMID: 23845962; PubMed Central PMCID: PMC3875132

Pipes L, Li S, Bozinoski M, Palermo R, Peng X, Blood P, Kelly S, Weiss JM, Thierry-Mieg J, Thierry-Mieg D, Zumbo P, Chen R, Schroth GP, Mason CE, Katze MG. The non-human primate reference transcriptome resource (NHPRTR) for comparative functional genomics. Nucleic Acids Res. 2013 Jan;41(Database issue):D906-14. doi: 10.1093/nar/gks1268. Epub 2012 Nov 29. PubMed PMID: 23203872; PubMed Central PMCID: PMC3531109

Nystrom N, Welling J, Blood P. Contemporary High Performance Computing: From Petascale Toward Exascale. Vetter JS, editor. Boca Raton, FL: CRC Press; 2013. Blacklight: Coherent Shared Memory for Enabling Science; p.421-439

Peng Y, Knight C, Blood P, Crosby L, Voth GA. Extending parallel scalability of LAMMPS and multiscale reactive molecular simulations. Proceedings of the 1st Conference of the Extreme Science and Engineering Discovery Environment, ACM. 2012. DOI: 10.1145/2335755.2335833

Blood PD, Swenson RD, Voth GA. Factors influencing local membrane curvature induction by N-BAR domains as revealed by molecular dynamics simulations. Biophys J. 2008 Aug;95(4):1866-76. doi: 10.1529/biophysj.107.121160. Epub 2008 May 9. PubMed PMID: 18469070; PubMed Central PMCID: PMC2483763

Ayton GS, Blood PD, Voth GA. Membrane remodeling from N-BAR domain interactions: insights from multi-scale simulation. Biophys J. 2007 May 15;92(10):3595-602. Epub 2007 Feb 26. PubMed PMID: 17325001; PubMed Central PMCID: PMC1853153


Brown, Shawn

Lee BY, Haidari LA, Prosser W, Connor DL, Bechtel R, Dipuve A, Kassim H, Khanlawia B, Brown ST. (2016) Re-designing the Mozambique vaccine supply chain to improve access to vaccines. Vaccine, 34(41): 4998-5004

Haidari LA, Brown ST, Constenla D, Zenkov E, Ferguson M, de Broucker G, Ozawa S, Clark S, Lee BY. (2016) The economic value of increasing geospatial access to tetanus toxoid immunization in Mozambique. Vaccine, 34(35): 4161-5

Haidari LA, Brown ST, Ferguson M, Bancroft E, Spiker M, Wilcox A, Ambikapathi R, Sampath V, Connor DL, Lee BY. (2016) The economic and operational value of using drones to transport vaccines. Vaccine, 34(34): 4062-7

Mueller LE, Haidari LA, Wateska AR, Phillips RJ, Schmitz MM, Connor DL, Norman BA, Brown ST, Welling JS, Lee BY. (2016) The impact of implementing a demand forecasting system into a low-income country’s supply chain. Vaccine, 34(32):3663-9

Lee BY, Connor DL, Wateska AR, Norman BA, Rajgopal J, Cakouros BE, Chen S, Claypool EG, Haidari LA, Karir V, Leonard J, Mueller LE, Paul P, Schmitz MM, Welling JS, Weng Y, Brown ST. (2015) Landscaping the structures of GAVI country vaccine supply chains and testing the effects of radical redesign. Vaccine, 33(36):4451-8

Norman BA, Rajgopal J, Lim J, Gorham K, Haidari LA, Brown ST, Lee BY. (2015) Modular vaccine packaging increases packing efficiency. Vaccine, 33(27):3135-41.

Lee BY, Schreiber B, Wateska AR, Connor DL, Dicko HM, Jaillard P, Mvundura M, Levin C, Avella M, Haidari LA, Brown ST. (2015) The Benin experience: How computational modeling can assist major vaccine policy changes in low and middle income countries. Vaccine, 33(25):2858-61

Haidari LA, Wahl B, Brown ST, Privor-Dumm L, Wallman-Stokes C, Gorham K, Connor DL, Wateska AR, Schriber B, Dicko H, Jaillard P, Avella M, Lee BY. (2015) One size does not fit all: The impact of primary vaccine container size on vaccine distribution and delivery. Vaccine, 33(28):3242-7

Portnoy A, Ozawa S, Grewal S, Norman BA, Rajgopal J, Gorham KM, Haidari LA, Brown ST, Lee BY. (2015) Costs of vaccine programs across 94 low- and middle-income countries. Vaccine, 33(S1):A99-108

Brown ST, Schreiber B, Cakouros BE, Wateska AR, Dicko HM, Connor DL, Jaillard P, Mvundura M, Norman BA, Levin C, Rajgopal J, Avella M, Lebrun C, Claypool E, Paul P, Lee BY. (2014) The benefits of redesigning Benin's vaccine supply chain. Vaccine, 32(32):4097-103

Brown ST, Lee BY. (2014) Unless changes are made in Benin, multiple storage and transport bottlenecks may prevent vaccines from reaching the population. Vaccine, 32(21): 2518-9.

Norman BA, Nourollahi S, Chen S, Brown ST, Claypool EG, Connor DL, Schmitz MM, Rajgopal J, Wateska AR, Lee BY. (2013) A passive cold storage device economic model to evaluate selected immunization location scenarios. Vaccine, 31(45):5232-8

Haidari LA, Connor DL, Wateska AR, Brown ST, Mueller LE, Norman BA, Schmitz MM, Paul P, Rajgopal J, Welling JS, Leonard J, Chen S, Lee BY. (2013) Augmenting transport versus increasing cold storage to improve vaccine supply chains. Plos One, 8(5):e64303

Assi TM, Brown ST, Kone S, Norman BA, Djibo A, Connor DL, Wateska AR, Rajgopal J, Slayton RB, Lee BY. (2013)  Removing the regional level from the Niger vaccine supply chain. Vaccine, 31(26):2828-34

Haidari LA, Connor DL, Wateska AR, Brown ST, Mueller LE, Norman BA, Schmitz MM, Paul P, Rajgopal J, Welling JS, Leonard J, Claypool EG, Weng Y, Chen S, Lee BY. (2013) Only adding stationary storage to vaccine supply chains may create and worsen transport bottlenecks. Journal of Public Health Management and Practice, 19(S2):S65-7

***Link to full listing of Shawn Brown's publications here:


Budden, Bob

R. Budden & D. Simmel. DMOVER: Scheduled Data Transfer for HPC Grid Workflows. HPC 2008 - High Performance Computing and Grids - Cetraro, Italy

J. Taylor, R. Budden, A. Nekrutenko, N. Coraor, P. Blood, A. J. Ropelewski, Z. Zhang, J. Palencia, S. Sanielevici, and J. Yanovich. A sustainable national gateway for biological computation - XSEDE Conference, 2013, ACM: doi>10.1145/2484762.2484817

R. Budden & D. Simmel. DMOVER: Scheduled Data Transfer for Distributed Computational Workflows. Paper & Presentation at Teragrid 2008 - Las Vegas, NV

R. Budden & R. Scott. Using OpenStack to Manage a Data Analytics HPC Cluster at PSC - Intel HPC Developer Conference Austin, TX 2015

R. Budden & M. Lowe. Deploying OpenStack for The National Science Foundation's Newest Supercomputers Presentation at OpenStack Summit - Austin, TX 2016

R. Budden, M. Lowe, K. Keahey, J. Mills, B. Bethwaite, S. Teller, P. Calleja. HPC/Research Computing: Leveraging The Architectures, Flexibilities, and Tools Emerging from the Members of the OpenStack Scientific Community Panel Presentation at Supercomputing Conference 2016

R. Budden, J. Fischer, M. Lowe. Image is Everything: Dynamic HPC VM Repositories using Murano Presentation/Video at OpenStack Summit - Barcelona, Spain 2016

V. Hazlewood, K. Benninger, G Peterson., J. Charcalla, B. Sparks, J. Hanley, A. Adams, B. Learn, R. Budden, D. Simmel, J. Lappa, J. Yanovich. Developing Applications with Networking Capabilities via End-to-End SDN (DANCES) at XSEDE, 2016

J. Taylor, A. Nekrutenko, N. Coraor, P. Blood, A. Ropelewski, Z. Zhang, J. Palencia, S. Sanielevici, J. Yanovich, R. Budden. A sustainable national gateway for biological computation at XSEDE, 2013 - ACM DOI=10.1145/2484762.2484817

V. Hazlewood, K. Benninger, G. Peterson, J. Charcalla, B. Sparks, J. Hanley, A. Adams, B. Learn, R. Budden, D. Simmel, J. Lappa, J. Yanovich, Developing Applications with Networking Capabilities via End-to-End SDN (DANCES), XSEDE16, Miami, FL, July 17-21, 2016.


Chiacchia, Ken

Deriving Effective Sweep Width for Air-scent Dog Teams. Chiacchia KB, Houlahan HE, Hostetter RS.Wilderness Environ Med. 2015 Jun;26(2):142-9. doi: 10.1016/j.wem.2014.10.004. PMID: 25754903

Use of the visual range of detection to estimate effective sweep width for land search and rescue based on 10 detection experiments in North America. Koester RJ, Chiacchia KB, Twardy CR, Cooper DC, Frost JR, Robe RQ. Wilderness Environ Med. 2014 Jun;25(2):132-42. doi: 10.1016/j.wem.2013.09.016

Effectors of visual search efficacy on the Allegheny Plateau. Chiacchia KB, Houlahan HE. Wilderness Environ Med. 2010 Sep;21(3):188-201. doi: 10.1016/j.wem.2010.06.002. Erratum in: Wilderness Environ Med. 2010 Dec;21(4):386


DePasse, Jay


Smith KJ, Nowalk MP, Wateska A, Brown ST, DePasse JV, Raviotta JM, Shim E, Zimmerman RK. Potential Consequences of Not Using Live Attenuated Influenza Vaccine. Am J Prev Med. 2017 Oct;53(4):500-503. doi: 10.1016/j.amepre.2017.02.019. Epub 2017 Apr 18. PubMed PMID: 28431811; PubMed Central PMCID: PMC5610050.

Raviotta JM, Smith KJ, DePasse J, Brown ST, Shim E, Nowalk MP, Zimmerman RK. Reply to: Estimating the Full Value of High-Dose Influenza Vaccine. J Am Geriatr Soc. 2017 Sep;65(9):2111-2112. doi: 10.1111/jgs.14976. Epub 2017 Jun 6. PubMed PMID: 28586104; PubMed Central PMCID: PMC5603375.

DePasse JV, Nowalk MP, Smith KJ, Raviotta JM, Shim E, Zimmerman RK, Brown ST. Does cost-effectiveness of influenza vaccine choice vary across the U.S.? An agent-based modeling study. Vaccine. 2017 Jul 13;35(32):3974-3981. doi: 10.1016/j.vaccine.2017.05.093. Epub 2017 Jun 9. PubMed PMID: 28606814.

Lee BY, Bartsch SM, Stone NTB, Zhang S, Brown ST, Chatterjee C, DePasse JV, Zenkov E, Briët OJT, Mendis C, Viisainen K, Candrinho B, Colborn J. The Economic Value of Long-Lasting Insecticidal Nets and Indoor Residual Spraying Implementation in Mozambique. Am J Trop Med Hyg. 2017 Jun;96(6):1430-1440. doi: 10.4269/ajtmh.16-0744. PubMed PMID: 28719286; PubMed Central PMCID: PMC5462583.

DePasse JV, Smith KJ, Raviotta JM, Shim E, Nowalk MP, Zimmerman RK, Brown ST. Does Choice of Influenza Vaccine Type Change Disease Burden and Cost-Effectiveness in the United States? An Agent-Based Modeling Study. Am J Epidemiol. 2017 May 1;185(9):822-831. doi: 10.1093/aje/kww229. PubMed PMID: 28402385; PubMed Central PMCID: PMC5411677.

Raviotta JM, Smith KJ, DePasse J, Brown ST, Shim E, Nowalk MP, Zimmerman RK. Cost-Effectiveness and Public Health Effect of Influenza Vaccine Strategies for U.S. Elderly Adults. J Am Geriatr Soc. 2016 Oct;64(10):2126-2131. doi: 10.1111/jgs.14323. Epub 2016 Oct 6. PubMed PMID: 27709600; PubMed Central PMCID: PMC5302117.

Shim E, Brown ST, DePasse J, Nowalk MP, Raviotta JM, Smith KJ, Zimmerman RK. Cost Effectiveness of Influenza Vaccine for U.S. Children: Live Attenuated and Inactivated Influenza Vaccine. Am J Prev Med. 2016 Sep;51(3):309-17. doi: 10.1016/j.amepre.2016.02.027. Epub 2016 Apr 11. PubMed PMID: 27079638; PubMed Central PMCID: PMC5384696.

Hogan WR, Wagner MM, Brochhausen M, Levander J, Brown ST, Millett N, DePasse J, Hanna J. The Apollo Structured Vocabulary: an OWL2 ontology of phenomena in infectious disease epidemiology and population biology for use in epidemic simulation. J Biomed Semantics. 2016 Aug 18;7:50. doi: 10.1186/s13326-016-0092-y. PubMed PMID: 27538448; PubMed Central PMCID: PMC4989460.

Smith KJ, Raviotta JM, DePasse JV, Brown ST, Shim E, Patricia Nowalk M, Zimmerman RK. Cost Effectiveness of Influenza Vaccine Choices in Children Aged 2-8 Years in the U.S. Am J Prev Med. 2016 May;50(5):600-608. doi: 10.1016/j.amepre.2015.12.010. Epub 2016 Feb 8. PubMed PMID: 26868283; PubMed Central PMCID: PMC4841730.

Poon LL, Song T, Rosenfeld R, Lin X, Rogers MB, Zhou B, Sebra R, Halpin RA, Guan Y, Twaddle A, DePasse JV, Stockwell TB, Wentworth DE, Holmes EC, Greenbaum B, Peiris JS, Cowling BJ, Ghedin E. Quantifying influenza virus diversity and transmission in humans. Nat Genet. 2016 Feb;48(2):195-200. doi: 10.1038/ng.3479. Epub 2016 Jan 4. PubMed PMID: 26727660; PubMed Central PMCID: PMC4731279.

Taft AS, Ozawa M, Fitch A, Depasse JV, Halfmann PJ, Hill-Batorski L, Hatta M, Friedrich TC, Lopes TJ, Maher EA, Ghedin E, Macken CA, Neumann G, Kawaoka Y. Identification of mammalian-adapting mutations in the polymerase complex of an avian H5N1 influenza virus. Nat Commun. 2015 Jun 17;6:7491. doi: 10.1038/ncomms8491. PubMed PMID: 26082035; PubMed Central PMCID: PMC4557292.

Lukens S, DePasse J, Rosenfeld R, Ghedin E, Mochan E, Brown ST, Grefenstette J, Burke DS, Swigon D, Clermont G. A large-scale immuno-epidemiological simulation of influenza A epidemics. BMC Public Health. 2014 Sep 29;14:1019. doi: 10.1186/1471-2458-14-1019. PubMed PMID: 25266818; PubMed Central PMCID: PMC4194421.

Kerr PJ, Rogers MB, Fitch A, Depasse JV, Cattadori IM, Twaddle AC, Hudson PJ, Tscharke DC, Read AF, Holmes EC, Ghedin E. Genome scale evolution of myxoma virus reveals host-pathogen adaptation and rapid geographic spread. J Virol. 2013 Dec;87(23):12900-15. doi: 10.1128/JVI.02060-13. Epub 2013 Sep 25. PubMed PMID: 24067966; PubMed Central PMCID: PMC3838154.

Kerr PJ, Rogers MB, Fitch A, Depasse JV, Cattadori IM, Hudson PJ, Tscharke DC, Holmes EC, Ghedin E. Comparative analysis of the complete genome sequence of the California MSW strain of myxoma virus reveals potential host adaptations. J Virol. 2013 Nov;87(22):12080-9. doi: 10.1128/JVI.01923-13. Epub 2013 Aug 28. PubMed PMID: 23986601; PubMed Central PMCID: PMC3807925.

Grefenstette JJ, Brown ST, Rosenfeld R, DePasse J, Stone NT, Cooley PC, Wheaton WD, Fyshe A, Galloway DD, Sriram A, Guclu H, Abraham T, Burke DS. FRED (a Framework for Reconstructing Epidemic Dynamics): an open-source software system for modeling infectious diseases and control strategies using census-based populations. BMC Public Health. 2013 Oct 8;13:940. doi: 10.1186/1471-2458-13-940. PubMed PMID: 24103508; PubMed Central PMCID: PMC3852955.

Min JY, Santos C, Fitch A, Twaddle A, Toyoda Y, DePasse JV, Ghedin E, Subbarao K. Mammalian adaptation in the PB2 gene of avian H5N1 influenza virus. J Virol. 2013 Oct;87(19):10884-8. doi: 10.1128/JVI.01016-13. Epub 2013 Jul 17. PubMed PMID: 23864613; PubMed Central PMCID: PMC3807384.

Saira K, Lin X, DePasse JV, Halpin R, Twaddle A, Stockwell T, Angus B, Cozzi-Lepri A, Delfino M, Dugan V, Dwyer DE, Freiberg M, Horban A, Losso M, Lynfield R, Wentworth DN, Holmes EC, Davey R, Wentworth DE, Ghedin E; INSIGHT FLU002 Study Group.; INSIGHT FLU003 Study Group.. Sequence analysis of in vivo defective interfering-like RNA of influenza A H1N1 pandemic virus. J Virol. 2013 Jul;87(14):8064-74. doi: 10.1128/JVI.00240-13. Epub 2013 May 15. PubMed PMID: 23678180; PubMed Central PMCID: PMC3700204.

Ghedin E, Holmes EC, DePasse JV, Pinilla LT, Fitch A, Hamelin ME, Papenburg J, Boivin G. Presence of oseltamivir-resistant pandemic A/H1N1 minor variants before drug therapy with subsequent selection and transmission. J Infect Dis. 2012 Nov 15;206(10):1504-11. doi: 10.1093/infdis/jis571. Epub 2012 Sep 10. PubMed PMID: 22966122; PubMed Central PMCID: PMC3475640.

Kerr PJ, Ghedin E, DePasse JV, Fitch A, Cattadori IM, Hudson PJ, Tscharke DC, Read AF, Holmes EC. Evolutionary history and attenuation of myxoma virus on two continents. PLoS Pathog. 2012;8(10):e1002950. doi: 10.1371/journal.ppat.1002950. Epub 2012 Oct 4. PubMed PMID: 23055928; PubMed Central PMCID: PMC3464225.

Ghedin E, Laplante J, DePasse J, Wentworth DE, Santos RP, Lepow ML, Porter J, Stellrecht K, Lin X, Operario D, Griesemer S, Fitch A, Halpin RA, Stockwell TB, Spiro DJ, Holmes EC, St George K. Deep sequencing reveals mixed infection with 2009 pandemic influenza A (H1N1) virus strains and the emergence of oseltamivir resistance. J Infect Dis. 2011 Jan 15;203(2):168-74. doi: 10.1093/infdis/jiq040. PubMed PMID: 21288815; PubMed Central PMCID: PMC3071067.

Ghedin E, Wentworth DE, Halpin RA, Lin X, Bera J, DePasse J, Fitch A, Griesemer S, Hine E, Katzel DA, Overton L, Proudfoot K, Sitz J, Szczypinski B, StGeorge K, Spiro DJ, Holmes EC. Unseasonal transmission of H3N2 influenza A virus during the swine-origin H1N1 pandemic. J Virol. 2010 Jun;84(11):5715-8. doi: 10.1128/JVI.00018-10. Epub 2010 Mar 17. PubMed PMID: 20237080; PubMed Central PMCID: PMC2876599.

Ghedin E, Hailemariam T, DePasse JV, Zhang X, Oksov Y, Unnasch TR, Lustigman S. Brugia malayi gene expression in response to the targeting of the Wolbachia endosymbiont by tetracycline treatment. PLoS Negl Trop Dis. 2009 Oct 6;3(10):e525. doi: 10.1371/journal.pntd.0000525. PubMed PMID: 19806204; PubMed Central PMCID: PMC2754610.

Ghedin E, Fitch A, Boyne A, Griesemer S, DePasse J, Bera J, Zhang X, Halpin RA, Smit M, Jennings L, St George K, Holmes EC, Spiro DJ. Mixed infection and the genesis of influenza virus diversity. J Virol. 2009 Sep;83(17):8832-41. doi: 10.1128/JVI.00773-09. Epub 2009 Jun 24. PubMed PMID: 19553313; PubMed Central PMCID: PMC2738154.

Click here for Jay's ncbi bibliography:


Gomez, Roberto

A framework for large-scale relativistic simulations in the characteristic approach. Roberto Gomez, Willians Barreto and Simonetta Frittelli Phys. Rev. D 76, 124029 (2007), DOI:, arXiv:0711.0564

Initial-boundary-value problem of the self-gravitating scalar field in the Bondi-Sachs gauge. Simonetta Frittelli and Roberto Gomez  Phys. Rev. D 75, 044021 (2007), DOI:

On Boundary Conditions for the Einstein Equations. Simonetta Frittelli and Roberto Gomez. Lecture Notes in Physics, Vol. 692, pp. 205-222, (2006) Editors: Joerg Frauendiener, Domenico J.W. Giulini, Volker Perlick, Springer Berlin/Heidelberg (2006), ISBN: 3-540-31027-4


Hood, Greg

Lee WC, Bonin V, Reed M, Graham BJ, Hood G, Glattfelder K, Reid RC. Anatomy and function of an excitatory network in the visual cortex. Nature. 2016; 532(7599):370-4. NIHMSID: NIHMS757168 PubMed [journal] PMID: 27018655, PMCID: PMC4844839

Glaubius RL, Hood G, Penrose KJ, Parikh UM, Mellors JW, Bendavid E, Abbas UL. Cost-effectiveness of Injectable Preexposure Prophylaxis for HIV Prevention in South Africa. Clinical infectious diseases : an official publication of the Infectious Diseases Society of America. 2016; 63(4):539-47. PubMed [journal] PMID: 27193745, PMCID: PMC4967601

Abbas UL, Glaubius R, Hood G, Mellors JW. Antiretroviral treatment, preexposure prophylaxis, and drug resistance in sub-Saharan Africa: a consensus among mathematical models. The Journal of infectious diseases. 2014; 209(1):164-6. PubMed [journal] PMID: 24133186

Abbas UL, Glaubius R, Mubayi  A, Hood G, Mellors JW. Antiretroviral therapy and pre-exposure prophylaxis: combined impact on HIV transmission and drug resistance in South Africa. The Journal of infectious diseases. 2013; 208(2):224-34. PubMed [journal] PMID: 23570850, PMCID: PMC3895950

Zhang X, Badea C, Hood G, Wetzel A, Qi Y, Stiles J, Johnson GA. High-resolution reconstruction of fluorescent inclusions in mouse thorax using anatomically guided sampling and parallel Monte Carlo computing. Biomedical optics express. 2011; 2(9):2449-60. PubMed [journal] PMID: 21991539, PMCID: PMC3184855

Abbas UL, Hood G, Wetzel AW, Mellors JW. Factors influencing the emergence and spread of HIV drug resistance arising from rollout of antiretroviral pre-exposure prophylaxis (PrEP). PloS one. 2011; 6(4):e18165. PubMed [journal] PMID: 21525976,PMCID: PMC3078109

Bock DD, Lee WC, Kerlin AM, Andermann ML, Hood G, Wetzel AW, Yurgenson S, Soucy ER, Kim HS, Reid RC. Network anatomy and in vivo physiology of visual cortical neurons. Nature. 2011; 471(7337):177-82. NIHMSID: NIHMS263529 PubMed [journal] PMID: 21390124, PMCID: PMC3095821

Zhang X, Badea CT, Hood G, Wetzel AW, Stiles JR, Johnson GA. Free-space fluorescence tomography with adaptive sampling based on anatomical information from microCT. Proceedings of SPIE--the International Society for Optical Engineering. 2010; 7757(775706). NIHMSID: NIHMS304986 PubMed [journal] PMID: 21743784, PMCID: PMC3132136


Laghaei, Rozita

Water and Ion Permeability of a Claudin Model: A Computational Study, Rozita Laghaei, Alan S. L Yu and Rob D. Coalson, PROTEINS: Structure, Function, and Bioinformatics 2016, 84, 305-315

Early Oligomerization Stages for the Non-Amyloid Component of Alpha-Synuclein Amyloid. Cindie Eugène, Rozita Laghaei and Normand Mousseau, J. Chem. Phys. 2014; 141,135103

Calculation of Iron Transport through Human H-chain Ferritin.  Rozita Laghaei, William Kowallis, Deborah G. Evans and Rob D. Coalson J. Phys. Chem. A. 2014; 118, 7442−7453

Metal Binding Sites of Human H-chain Ferritin and Iron Transport Mechanism to the Ferroxidase Sites: A Molecular Dynamics Simulation Study Rozita Laghaei, Deborah G. Evans and Rob D. Coalson, Proteins: Structure, Function, and Bioinformatics, 2013; 81, 1042–1050

Langevin Dynamics Simulation of 3D Colloidal Crystal Vacancies and Phase Transitions. Rozita Laghaei,  Sanford A. Asher and Rob D. Coalson, J. Phys. Chem. B, 2013, 117, 5271–5279

Distinct Dimerization for Various Alloforms of the Amyloid-Beta Protein: Aβ1-40, Aβ1-42 and Aβ1-40(D23N), Sébastien Côté, Rozita Laghaei, Philippe Derreumaux and Normand Mousseau, J. Phys. Chem. B, 2012; 116, 4043-4055

Structure and Thermodynamics of Amylin Dimer Studied by Hamiltonian- Temperature Replica Exchange Molecular Dynamics Simulations, Rozita Laghaei,  Normand Mousseau and Guanghong Wei, J. Phys. Chem. B, 2011; 115, 3146–3154

Effect of the Disulfide Bond on the Monomeric Structure of Human Amylin Studied by Combined Hamiltonian and Temperature Replica Exchange Molecular  Dynamics Simulations. Rozita Laghaei,  Normand Mousseau and Guanghong Wei, J. Phys. Chem. B, 2010; 114 , 7071-7077

Spontaneous formation of polyglutamine nanotubes with molecular dynamics simulations. Rozita Laghaei and Normand Mousseau, J. Chem. Phys. 2010; 132, 165102

Replica Exchange Molecular Dynamics Simulations of Coarse-grained Proteins in Implicit Solvent. Yassmine Chebaro, Xiao Dong, Rozita Laghaei, Philippe Derreumaux and Normand MousseauJ. Phys. Chem. B, 2009; 113, 267–274

Computational studies on thermodynamic properties, effective diameters, and free volume of argon using an ab initio potential. Afshin Eskandari Nasrabad and Rozita Laghaei, J. Chem. Phys 2006; 125, 084510