SELECTED ARTICLES:

Books

  1. N. Allsopp, A. Tabary, J. Follows, P. Vezolle, M. Hennecke, H. Reddy, F. Ishibashi, C. Sosa, M. Paolini, S. Prakash, D. Quintero, O. Lascu, “Unfolding IBM eServer Blue Gene Solution”, RedBook, SG24-6686-00, ISBN 0738494070Poughkeepsie, NY, September 20, 2005: http://www.redbooks.ibm.com/redbooks/pdfs/sg246686.pdf
  2. Scott Vetter, Ben Gibbs, Balaji Atyam, Frank Berres, Bruno Blanchard, Lancelot Castillo, Pedro Coelho, Nicolas Guerin, Lei Liu, Cesar Diniz Maciel, Carlos Sosa, Ravikiran Thirumalai “Advanced POWER Virtualization on IBM p5 Servers: Architecture and  Performance Considerations”, RedBook, SG24-5768-01, ISBN 0738494070, Austin, Texas, 2005. http://www.redbooks.ibm.com/Redbooks.nsf/RedbookAbstracts/sg245768.html?Open
  3. Gary Lakner, Gary Schulten-Multz, and Carlos P Sosa "IBM System Blue Gene Solution: Applications Development", RedBook, SG24-7179, ISBN 0738489395, Rochester, Minnesota, 2007. http://www.redbooks.ibm.com/abstracts/sg247179.html?Open
  4. Carlos P. Sosa "IBM System Blue Gene Solution: Blue Gene/P Application Development " First Edition, RedBook, SG24-7287, ISBN 0738488674, Rochester, Minnesota, 2008. http://www.redbooks.ibm.com/abstracts/sg247287.html?Open

Computer Science

  1. J. Ochterski. C. Sosa and J. Carpenter: “Performance of Parallel Gaussian 94 on Cray Research Vector Supercomputers:, CUG 1996 Spring Proceedings, pp. 108, (Fine Point Editorial Service, WV, 1996).
  2. C. P. Sosa, J. Ochterski, J. Carpenter, and M. J. Frisch: ”Performance of Parallel Gaussian 94 on the Cray T3E”, CUG 1997 Speing Proceedings, pp. 50, (Fine Point Editorial Service, WV, 1997).
  3. C. P. Sosa and Nicholas Carriero: ”How to Write Parallel Programs on the T3E Using Linda”, CUG 1997 Speing Proceedings, pp. 50, (Fine Point Editorial Service, WV, 1997).
  4. C. P. Sosa, J. Ochterski, J. Carpenter, and M. J. Frisch: "Ab Initio Quantum Chemistry on the Cray T3E Massively Parallel Supercomputer: II", J. Comp. Chem. 19, 1053-1063(1998).
  5. S. K. Goh, C. P. Sosa, and A. St-Amant: "A Scalable Divide-and-Conquer Algorithm Combining Coarse and Fine-Grain Parallelization", Theor. Chem. Acc. 99, 197-206(1998).
  6. C. P. Sosa, G. Scalmani, R. Gomperts, and M. J. Frisch: "Ab Initio Quantum Chemistry on a ccNUMA Architecture Using OpenMP: III", Parallel Computing 26, 843-856(2000).
  7. C. P. Sosa, T. Hewitt, M. R. Lee, and D. A. Case: "Vectorization of the Generalized Born Model for Molecular Dynamics on Shared-Memory Computers", J. Mol. Structure (Theochem) 549, 193-201(2001).
  8. C. P. Sosa, Z. J. Tu, and P. L. Fast: “Some Practical Suggestions for Performing NCBI BLAST Benchmarks on a pSeries 690 System”, IBM Form Number REDP0437, June 3, 2002, http://www.redbooks.ibm.com/abstracts/redp0437.html?Open
  9. C. P. Sosa and P. Fast: “Ab Initio Quantum Chemistry on the IBM pSeries 690: A Comparison Between Turbo 1.3 GHz and Turbo 1.1 GHz”, IBM Form Number REDP0444, April 26, 2002, http://www.redbooks.ibm.com/abstracts/redp0444.html?Open
  10. C. P. Sosa and S. Andersson: “Some Practical Suggestions for Performing Gaussian Benchmarks on a pSeries 690 System”, IBM Form Number REDP0424, April 24, 2002, http://www.redbooks.ibm.com/abstracts/redp0424.html?Open
  11. C. P. Sosa, John D. McCalpin, P. Fast, and Michael J. Frisch: “Gaussian Performance Analysis on the IBM pSeries POWER4 Systems”, Editor Elisabeth Stahl, IBM Form Number REDP3692, May 20, 2003, http://publib-b.boulder.ibm.com/Redbooks.nsf/RedpaperAbstracts/redp3692.html?Open
  12. B. Atyam, R. Panda, and C. P. Sosa: “Performance Comparison of Scientific Applications on AIX and Linux for PowerPC”, Editor Elisabeth Stahl, IBM Form Number REDP3692, May 20, 2003, http://publib-b.boulder.ibm.com/Redbooks.nsf/RedpaperAbstracts/redp3692.html?Open
  13. C. P. Sosa, M. Crowley, D. A. Case, and B. Atyam: “AMBER7 Performance Analysis on the IBM pSeries POWER4 Systems” , Editor Elisabeth Stahl,  IBM Form Number REDP3692, May 20, 2003, http://publib-b.boulder.ibm.com/Redbooks.nsf/RedpaperAbstracts/redp3692.html?Open
  14. C. P. Sosa and T. Tarquinio, "Gaussian Performance Using AIX Large Pages", IBM Form Number REDP-3761-00, 25 September 2003, http://www.redbooks.ibm.com/abstracts/redp3761.html?Open
  15. C. P. Sosa, M. Accapadi, and B. Atyam, “BLAST Throughput Benchmarks: mmap versus read ”, Editor Elisabeth Stahl,  IBM Form Number REDP3692, May 20, 2003, http://publib-b.boulder.ibm.com/Redbooks.nsf/RedpaperAbstracts/redp3692.html?Open
  16. B. V. Atyam, R. Panda, R. Panda, A. Rossi and C. P. Sosa,  “Single Processor Performance of Scientific Applications on AIX® and Linux on POWER ™ Systems”, Editor Elisabeth Stahl,  IBM Form Number REDP-3895-00, July 27, 2004, http://www.redbooks.ibm.com/abstracts/redp3895.html?Open
  17. C. P. Sosa, S. Behling, and D. Barrs, “Single Processor Tunning on the IBM POWER4 processor”, Education: pSeries, April 2004, http://www-1.ibm.com/servers/enable/site/peducation/eibp/p4_processor/index.html
  18. C. P. Sosa, B. V. Atyam, P. Heyrman, N. Nayar, and J. Hilsabeck, “Life Sciences Applications on IBM POWER5 and AIX 5L Version 5.3: Virtualization Exploitation through Micro-Partitioning Implementation”, IBM Form Number REDP-3966-00, March 2, 2005, http://www.redbooks.ibm.com/abstracts/redp3966.html
  19. C. P. Sosa, B. Atyam, and C. Strauss, “IBM Micro-Partitioning concepts, operations and programming”, pSeries Education, 2005, http://www-03.ibm.com/servers/enable/site/peducation/ibp/4c02/index.html
  20. C. P. Sosa and B. V. Atyam, “Performance Analysis of Simultaneous Multi-Threading on IBM POWER5 eserver pSeries Systems Using Gaussian03”, Proceedings of the Forum 2006 for the Frontier of Computational Science: Present and Future Led by POWER, Kyushu University, Fukuoka, Japan, Aug. 2006, p[1-2].
  21. Oystein Thorsen, Karl Jian, Amanda Peters, Brian Smith, Heshan Lin, Wu-chun Feng, Carlos P. Sosa, "Parallel Genomic Sequence-Search on a Massively Parallel System", Proceedings of the 4th international conference on Computing frontiers, Ischia, Italy, SESSION: Mapping applications on parallel platforms table of contents, Pages: 59 - 68, 2007, ISBN:978-1-59593-683-7
  22. X. Feng, K. W. Cameron, B. Smith, and C. Sosa , “Building the Tree of Life on Terascale Systems”, Proceedings of the 21st IEEE  International Parallel and Distributed Processing Symposium (IPDPS 07), March 2007.
  23. K. Jiang, O. Thorsen, A. Peters, B. Smith, and C. P. Sosa, "An Efficient Parallel Implementation of the Hidden Markov Methods for Genomic Sequence-Search on a Massively Parallel System", IEEE Transactions in Parallel Distributed Systems, 19, 15-23(2008).
  24. G. Lakner and C. P. Sosa, "Evolution of the IBM Blue Gene Solution", RedPaper, REDP-4247, Rochester, Minnesota, 2007.
  25. H. Lin, P. Balaji, R. Poole, C. P. Sosa, X. Ma and W. Feng, “Massively Parallel Genomic Sequence Search on the Blue Gene/P Architecture,” IEEE/ACM International Conference for High-Performance Computing, Networking, Storage and Analysis (SC), 2008.

Structural Biology

  1. Imre Jákli, András Perczel, Ödön Farkas, Attila G. Császár, Carlos P. Sosa, Imre G. Csizmadia, "Peptide models XXIII. Conformational model for polar side-chain containing amino acid residues: A comprehensive analysis of RHF, DFT, and MP2 properties of HCO-L-SER-NH2", J. Comp. Chem., 21, 626(2000)
  2. J. C. Vank, C. P. Sosa, A. Perczel, and I. G. Csizmadia, "Peptide Models XXVII. An Exploratory Ab Initio Study on the 21st Amino Acid Side-chain Conformations of N-formyl-L-selenocysteinamide (For-L-Sec-NH2) and N-acetyl-L-selenocysteine-N-methylamide (Ac-L-sec-NHMe) in their gammaL Backbone Conformation", Can. J. Chem., 78, 395(2000).
  3. G. I. Csonka, C. P. Sosa, and I. G. Csizmadia, "Ab Initio Study of the Lowest Energy Conformers of Lewis X (Lex) Trisaccharide", J. Phys. Chem., A 104, 3381(2000)
  4. G. I. Csonka, K. Elias, I. Kolossvary, C. P. Sosa, I. G. Csizmadia, "Theoretical Study of the Ring Puckering of a-Fucopyranose" J. Phys. Chem. A, 102, 1219(1998) .
  5. A. Peters, M. Lundberg, T. Lang, C. P. Sosa, "High Throughput Computing Validation for Drug Discovery Using the DOCK Program on a Massively Parallel System", Redpaper 4410, Poughkeepsie, NY, April, 16 2008.
  6. T-S. Lee, G. M. Giambasu, C. P. Sosa, M. Martick, W. G. Scott and D. M. York, "Threshold occupancy and specific cation binding modes in the hammerhead ribozyme active site are required for active conformation", J. Mol. Biology, 388, 195-206(2009).
  7. G. M. Giambasu, T-S. Lee, C. P. Sosa, M. P. Robertson, W. G. Scott and D. M. York, "Identification of dynamical hinge points of the L1 ligase molecular switch", RNA, 16, 769-780(2010).

Bioinformatics

  1. E. W. Klee and C. P. Sosa, Invited Review Article: “Computational classification of classically secreted proteins”, Drug Discovery Today, 12, 234-239(2007). Supplemental material.
  2. Oystein Thorsen, Karl Jiang, Amanda Peters, Brian Smith, Heshan Lin, Wu-chun Feng, Carlos P. Sosa, "Parallel Genomic Sequence-Search on a Massively Parallel System", Proceedings of the 4th international conference on Computing frontiers, Ischia, Italy, SESSION: Mapping applications on parallel platforms table of contents, Pages: 59 - 68, 2007, ISBN:978-1-59593-683-7
  3. X. Feng, K. W. Cameron, B. Smith, and C. P. Sosa , “Building the Tree of Life on Terascale Systems”, Proceedings of the 21st IEEE  International Parallel and Distributed Processing Symposium (IPDPS 07), March 2007.
  4. K. Jiang, O. Thorsen, A. Peters, B. Smith, and C. P. Sosa, "An Efficient Parallel Implementation of the Hidden Markov Methods for Genomic Sequence-Search on a Massively Parallel System", IEEE Transactions in Parallel Distributed Systems, 19, 15-23(2008).
  5. C. P. Sosa, "In Silico Classification of Secreted Proteins", Scirus Topic Page, March 2008.
  6. H. Lin, P. Balaji, R. Poole, C. Sosa, X. Ma and W. Feng, “Massively Parallel Genomic Sequence Search on the Blue Gene/P Architecture,” IEEE/ACM International Conference for High-Performance Computing, Networking, Storage and Analysis (SC), 2008.
Last modified: November 2, 2010  

 

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