Selected Staff Publications

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.


Buitrago, Paola A.

Buitrago, P. A. and Nystrom, N. A. (2020). Strengthening the Adoption of AI in Research and Cyberinfrastructure. In Proceedings of the NSF Workshop on Smart Cyberinfrastructure (Smart CI 2020). Forthcoming.

Buitrago, P. A., Nystrom, N. A., Gupta, R., & Saltz, J. (2020). Delivering Scalable Deep Learning to Research with Bridges-AI. In High Performance Computing: 6th Latin American Conference, CARLA 2019, Turrialba, Costa Rica, September 25–27, 2019 (Vol. 1087, pp. 200–214). Gewerbestrasse, Switzerland: Springer Nature. doi: 10.1007/978-3-030-41005-6_14.

Huang, H., Webster, K., Nystrom, N. A., and Buitrago, P. A. (Eds.). (2019). AIDR ’19: Proceedings of the Conference on Artificial Intelligence for Data Discovery and Reuse. Pittsburgh, Pennsylvania: Association for Computing Machinery, New York, NY, May 2019.

Nicholas A. Nystrom, Paola A. Buitrago, and Philip D. Blood. (2019) Bridges: Converging HPC, AI, and Big Data for Enabling Discovery. In Contemporary High-Performance Computing: From Petascale toward Exascale, Volume Three (ed. Vetter, J. S.) (CRC Press, 2019).

Buitrago, P. A. and Nystrom, Nicholas A. (2019). Open Compass: Accelerating the Adoption of AI in Open Research. In Proceedings of the Practice and Experience in Advanced Research Computing on Rise of the Machines (Learning) (pp. 72:1–72:9). New York, NY, USA: ACM.

Toropov, E., Buitrago, P. A., & Moura, J. M. F. (2019). Shuffler: A Large Scale Data Management Tool for Machine Learning in Computer Vision. In Proceedings of the Practice and Experience in Advanced Research Computing on Rise of the Machines (Learning) (pp. 23:1–23:8). New York, NY, USA: ACM. Received PEARC 2019 Best Student Paper Award in the “Advanced Research Computing Software and Application” Track.


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


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


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


Lambert, Michael

Wimberly, F, M Lambert, N Nystrom, A Ropelewski and W Young. Porting Third-Party Applications Packages to the Cray T3D: Programming Issues and Scalability Results. Parallel Computing 22(1996) 1073–1089.

Lambert, MH, ed. A Model for Common Operational Statistics. Request for Comments 1857, Internet Engineering Task Force (1995).

Wimberly, F, S Chitre, C Gonzalez, M Lambert, N Nystrom, A Ropelewski and W Young. Porting Third-Party Applications Packages to the Cray MPP: Experiences at the Pittsburgh Supercomputing Center, In: Thirty-Third Semi-Annual Cray User Group Meeting, San Diego, California, March 1994, 39–43.

Gonzalez, C, A Ropelewski, S Chitre, M Lambert, N Nystrom, D Deerfield, H Nicholas, F Wimberly and A Pai. Use of the Cray T3D Emulator in Implementing Scientific Applications, In: Thirty-First Semi-Annual Cray User Group Meeting, Montreux, Switzerland, March/April 1993, 39–42.

Lambert, MH and TR Chay. Cardiac arrhythmias modelled by Cai-inactivated Ca2+ channels. Biological Cybernetics 61(1989) 21–28.