Humberto Ortiz Zuazaga

High Performance Computing facility
University of Puerto Rico
PO Box 23334
San Juan, PR 00931-3334
Tel: +1-787-753-1653
humberto -at- hpcf.upr.edu

Degrees

PhD, Computer Science and Engineering, 2008, University of Puerto Rico.
BS (computer science) with honors 1994, University of Cincinnati.

Additional Education

University of Puerto Rico, Rio Piedras campus
undergraduate work in chemistry, 1983-1987.
University of California , Berkeley
graduate and undergraduate work in computer science, 1995.
University of Texas at San Antonio
graduate work towards a Master's degree in computer science, 1995-1996.

Experience

Undergraduate research student
Department of Pharmacology, University of Puerto Rico, 1986-1987. Characterized the biochemical properties of potential anti-cancer agents.
Research assistant
Institute of Neurobiology, University of Puerto Rico, 1988-1989. Data acquisition and analysis of electrophysiological experiments.
Consultant
Phaedrus Computer Consultants, San Juan, Puerto Rico, 1988. Taught microcomputer applications.
Consultant
Medical Sciences Campus, University of Puerto Rico, 1989. Taught introductory and intermediate BITNET usage.
Research assistant
Department of Physiology and Biophysics, University of Cincinnati, 1989-1993. Developed and studied computer simulations of action potential propagation across cell membranes.
Research assistant
Department of Computer Science, University of Cincinnati, 1993. Developed and implemented distributed algorithms to solve conjunctive normal form instances of satisfiability as part of a DIMACS implementation challenge.
Undergraduate research student
Center for GeoEnvironmental Science and Technology, College of Engineering, University of Cincinnati, 1993. Preliminary work integrating GRACE, a program for visualization of groundwater contamination, with ARC/Info, a geographical information system.
Research Associate
University of Cincinnati, 1994-1995. Worked porting GRACE to UNIX, integrating GRACE with GRASS, the US Army Core of Engineers geographical information system.
Systems administrator
Silicon Graphics Inc., 1995. Technical support and system administration for SGI Employees.
Teaching assistant
University of Texas at San Antonio, 1995. Lectured in two microcomputer applications courses.
Technical staff assistant
University of Texas at San Antonio, 1995. Developed neural networks to classify features in fetal heart rate recordings.
Programmer analyst
University of Texas Health Science Center at San Antonio, 1995-1998. Develop and implement algorithms for constructing genetic maps and radiation hybrid maps from hybridization data.
Consultant
University of Puerto Rico, Rio Piedras Campus, 1998. Developed WWW based sequence analysis tools, established Internet sequence analysis server, and taught workshops on Internet use and sequence analysis.
Consultant
Datacom Caribe Inc., 1998. System administration tasks on BSDI UNIX computers. Developed CGI applications.
Bioinformatics Specialist
University of Puerto Rico, Medical Sciences Campus, Institute of Neurobiology, March 1998 to December 1999. Install and maintain TCP/IP based LAN and network servers for researchers. Assist researchers in computer analysis of results.
Visualization Specialist
University of Puerto Rico, High Performance Computing facility, January 2000 to July 2006. TCP/IP based LAN and network server administration. Programming data vizualization and analysis applications.
Director
Bioinformatics Resource Center, University of Puerto Rico, since August 2006. Manage and direct the operations of the Bioinformatics Resource Center (BiRC) at the UPR High Performance Computing facility.
Acting Director
High Performance Computing facility, University of Puerto Rico, November 2006 to May 2008. Direct operations and manage staff at the UPR HPCf, including the Internet2 GigaPOP, the BiRC, and the Center for Numerical Supercomputing.
Director
High Performance Computing facility, University of Puerto Rico, since May 2008. Direct operations and manage staff at the UPR HPCf, including the Internet2 GigaPOP, the BiRC, and the Center for Numerical Supercomputing and Computational Nanoscience Resource Center (CNaRC).

Honors

University of Cincinnati, William McIntire Memorial Scholarship, 1993.

Memberships

University of Cincinnati student chapter of the Association for Computing Machinery, secretary, 1993.

Publications

  1. N. Sperelakis, H. Ortiz-Zuazaga, and J. B. Picone. Fast conduction in the electric field model for propagation in cardiac muscle. Innov. et Tech. en Biol. et Med., 12(4):404-414, 1991.

  2. N. Sperelakis, H. Ortiz-Zuazaga, J. E. Mann, Jr. Voltage interaction between sarcolemma and junctional SR membrane. Mathl. Comput. Modelling, 16(11):101-115, 1992.

  3. G. Sfyris, N. Sperelakis, H. Ortiz-Zuazaga, J. B. Picone, and E. Stepp. Length constant as a function of intercellular coupling of a cardiac muscle strand analog with applied longitudinal current. Mathl. Comput. Modelling, 17(1):131-139, 1993.

  4. Y. Robles, P. E. Vivas, H. G. Ortiz-Zuazaga, Y. Felix, S. Peña de Ortiz. Hippocampal gene expression profiling in spatial learning. Neurobiology of Learning and Memory. 2003 Jul;80(1):80-95. doi:10.1016/S1074-7427(03)00025-X

  5. Rojas-Cartagena C, Ortiz-Pineda PA, Ramirez-Gomez F, Suarez-Castillo EC, Matos-Cruz V, Rodriguez C, Ortiz-Zuazaga H, Garcia-Arraras JE. Distinct profiles of expressed sequence tags (ESTs) during intestinal regeneration in the sea cucumber Holothuria glaberrima. Physiol Genomics. 2007 Jul 3; doi:10.1152/physiolgenomics.00228.2006

  6. Filipa Godoy-Vitorino, Ruth E. Ley, Zhan Gao, Zhiheng Pei, Humberto Ortiz-Zuazaga, Luis R. Pericchi, Maria A. Garcia-Amado, Fabian Michelangeli, Martin J. Blaser, Jeffrey I. Gordon, Maria G. Dominguez-Bello. Bacterial Community in the Crop of the Hoatzin, a Neotropical Folivorous Flying Bird. Applied and Environmental Microbiology, October 2008, p. 5905-5912, Vol. 74, No. 19. doi:10.1128/AEM.00574-08

  7. Nancy Arroyo Gonzalez , Adrinel Vázquez , Humberto G. Ortiz Zuazaga, Arup Sen , Hugo Luna Olvera , Sandra Peña de Ortiz and N. S. Govind. Genome-wide expression profiling of the osmoadaptation response of Debaryomyces hansenii. Yeast 2009. 26:111-124. doi:10.1002/yea.1656

  8. Lorena Saavedra-Rodríguez, Humberto Ortiz-Zuazaga, Lissette Andrés, Karen Rodríguez, Fernando Ramírez, Adrinel Vázquez, and Sandra Peña de Ortiz. Identification of flap-structure specific endonuclease 1 as a factor involved in long-term memory formation of aversive learning. Journal of Neuroscience, May 2009. 29(18):5726-5737 doi: 10.1523/JNEUROSCI.4033-08.2009

  9. Pablo A Ortiz-Pineda, Francisco J Ramírez-Gómez, Judit Pérez-Ortiz, Sebastián González-Díaz, Francisco Santiago-De Jesús, Josue Hernández-Pasos, Carmencita Rojas-Cartagena, Edna C Suárez-Castillo, Karen Tossas-Robles, Ana T Méndez-Merced, José L Roig-López, Cristina Del Valle-Avila, Humberto Ortiz-Zuazaga and José E García-Arrarás. Gene expression profiling of intestinal regeneration in the sea cucumber. BMC Genomics 10:262, 8 June 2009. doi:10.1186/1471-2164-10-262

Refereed Proceedings

  1. F. S. Annexstein, J. V. Franco, H. Ortiz-Zuazaga, and R. P. Swaminathan. Distributed implementations of algorithms for satisfiability problems. Ohio Aerospace Institute / Ohio Supercomputer Center / NASA, Proceedings of Symposium on Application of Parallel and Distributed Computing, April 18-19, 1994.

  2. H. Ortiz-Zuazaga and R. Plaetke. TkMap: a bioTk program for drawing genetic or radiation hybrid maps. Abstract presented at American Society for Human Genetics 46th Annual Meeting. October 1996.

  3. R. Plaetke, B.E. Reus, R. Linn, R. Rodriguez, H. Ortiz-Zuazaga, D. Buley, P. O'Connell, S.L. Naylor, and R.J. Leach. A radiation hybrid map of human chromosome 3 consisting of 153 markers. Abstract presented at American Society for Human Genetics 46th Annual Meeting. October 1996.

  4. G. Schachtel, H. Ortiz-Zuazaga, and R. Plaetke. BPE: an environment for meiotic breakpoint mapping. Abstract presented at American Society for Human Genetics 46th Annual Meeting. October 1996.

  5. H. Ortiz-Zuazaga, and R. Plaetke. Screening genetic markers with the maximum weighted clique method. Abstract presented at the First International Conference on Computational Molecular Biology. Albuquerque, NM, January 1997.

  6. H. Ortiz-Zuazaga, and R. Plaetke. Screening genetic markers with the maximum weighted clique method. Abstract presented at Genome Mapping and Sequencing. Cold Spring Harbor, May 1997.

  7. S.L. Naylor, R. Plaetke, H. Ortiz-Zuazaga, P. O'Connell, B. Reus, X. He, R. Linn, S. Wood, and R.J. Leach. Construction of Framework and Radiation Hybrid Maps of Chromosomes 3 and 8. Abstract presented at Genome Mapping and Sequencing. Cold Spring Harbor, NY, May 1997.

  8. H.G. Ortiz-Zuazaga, Y. Robles, R. Chiesa, S. Peña de Ortiz. Analysis of Learning-Related Changes in Gene Expression Using Nylon Membrane cDNA Microarrays. Abstract presented at the Fifth Annual International Conference on Computational Molecular Biology (RECOMB 2001). Montreal, Quebec, Canada. April 2001.

  9. Ortiz-Zuazaga, H., Aviño-Diaz, M. A., Laubenbacher, R., Moreno O. Finite fields are better Booleans. Refereed abstract, presented at the Seventh Annual Conference on Computational Molecular Biology (RECOMB 2003), April 10-13, 2003, Germany.

  10. Humberto Ortiz-Zuazaga, Sandra Peña de Ortiz, Oscar Moreno de Ayala. Error Correction and Clustering Gene Expression Data Using Majority Logic Decoding. Proceedings of The 2007 International Conference on Bioinformatics and Computational Biology (BIOCOMP'07), Las Vegas, Nevada, June 25-28, 2007.

  11. Humberto Ortiz Zuazaga, Tim Tully, Oscar Moreno. Majority logic decoding for probe-level microarray data. Proceedings of BIOCOMP'08 - The 2008 International Conference on Bioinformatics & Computational Biology, Las Vegas, Nevada, July 13-17, 2008.

Conferences

  1. F. S. Annexstein, J. V. Franco, H. Ortiz-Zuazaga, and R. P. Swaminathan. Distributed implementations of algorithms for satisfiability problems. Poster presentation at Second DIMACS Challenge: Cliques, Coloring and Satisfiability, October 1993.

  2. H. Ortiz-Zuazaga, B. Rosen, T. Bylander, D. Soriano, and B. Schrifrin. Training a Neural Network to Recognize Artifacts and Decelerations in Cardiotocograms. Extended Abstract presented at AAAI AIM-96. March 1996.

  3. Y. Robles, Y.Carrasquillo, S.I. Vázquez, H.G. Ortiz- Zuazaga and Sandra Peña de Ortiz. Profiling of hippocampal gene expression in spatial learning with cDNA microarrays. Abstract presented at the Society for Neuroscience annual meeting. New Orleans, LA, November 2000.

  4. I. Chevere, S. Joselyn, S. Kida Y. Robles, H.G. Ortiz-Zuazaga, A.J. Silva, and S. Peña de Ortiz. Establishment of a CREB-Dependent Gene Expression Profile for Emotional Memory. Abstract presented at the Society for Neuroscience annual meeting. New Orleans, LA, November 2000.

  5. R. Chiesa, H. Ge, J. Wehner, H.G. Ortiz-Zuazaga, and S. Peña de Ortiz. Analysis of Gene Expression in Emotional Learning. Abstract presented at the Society for Neuroscience annual meeting. New Orleans, LA, November 2000.

  6. R. Chiesa, H.G. Ortiz-Zuazaga, H. Ge, and S. Peña de Ortiz. Gene Expression Profiling in Emotional learning with cDNA Microarrays. Abstract presented at the 40th meeting of the American Society for Cell Biology. San Francisco, California. December 2000.

  7. Ortiz-Zuazaga HG, Robles Y, Chiesa, R, and Peña de Ortiz S. Analysis of Learning-Related Changes in Gene Expression Using Nylon Membrane {cDNA} Microarrays. International Meeting of the Society for Neurochemistry, Buenos Aires Argentina, 2001.

  8. Al-Banchaabouchi M, Colón WI, Ge H, Ortiz-Zuazaga HG, Menéndes R, Maldonado-Vlaar CS, Peña de Ortiz S. Expression and function of the hzf-3 gene in neurocognitive processes in the rat brain. Federation of European Neuroscience Forum Abstract, 041.7, 2002.

  9. Vázquez A, Araneda S., Ortiz-Zuazaga HG, and Peña de Ortiz S. Molecular mechanisms of lead (Pb+2)-mediated long-term memory (LTM) impairment in the adult rat brain. Federation of European Neuroscience Forum Abstract, 041.34, 2002.

  10. Julio García, Humberto Ortiz Zuazaga, Ricardo Chiesa, and Sandra Peña de Ortiz. Cluster analysis of cDNA microarrays. Poster presented at the BRIN-PR 1st Annual Symposium: Biotechnology and Modern Medicine, October 11, 2002 San Juan Puerto Rico.

  11. Oscar Moreno (UPR-Río Piedras) Maria Alicia Aviñó (UPR-Cayey) Dorothy Bollman (UPR-Mayaguez) Humberto Ortiz-Zuazaga (UPR HPCf). The Reverse Engineering Problem in Genetic Networks. Invited talk, presented at the BRIN-PR 1st Annual Symposium: Biotechnology and Modern Medicine, October 11, 2002 San Juan Puerto Rico.

  12. Weaving the Research Web in a Minority Institution. Conde JG, Fernández-Repollet E, Agostini M, Nieves BG, Cormier G, Ortiz-Zuazaga H, Cabán-Babilonia W, Vélez E and Spann ML. Eighth RCMI International Symposium on Health Disparities, December 8 - 11, 2002, Sheraton Waikiki Hotel, Honolulu, Hawaii

  13. L. Saavedra, H. G. Ortiz-Zuazaga, F. Ramírez, & S. Peña de Ortiz. Molecular Profiling of Memory Consolidation in Condition Taste Aversion. Keystone Symposia 2005, Session X3: Proteomics and Bioinformatics. Keystone, Colorado, April 8-13, 2005.

  14. L. Saavedra, H.G. Ortiz-Zuazaga, F. Ramírez, S. Peña de Ortiz. Molecular Profiling of Memory Consolidation of Conditioned Taste Aversion (CTA): DNA recombination pathways. Program No. 69.3. 2005 Abstract Viewer/Itinerary Planner. Washington, DC: Society for Neuroscience, 2005. Online.

  15. A. Vazquez, M. Sepulveda, J. Wang, L. Saavedra, H.G. Ortiz-Zuazaga, G. Quirk, S. Peña de Ortiz. Gene expression profiling of auditory fear extinction in the rat medial prefrontal cortex. Program No. 316.14. 2005 Abstract Viewer/Itinerary Planner. Washington, DC: Society for Neuroscience, 2005. Online.

  16. Godoy-Vitorino, Filipa, Gao, Z., Pei Z., Zhou M., Pericchi, L.R., Torres, D., Ortiz, H., Ayala,D., Blaser, M.J, Domínguez-Bello, M.G., Phylogenetic Analysis of Crop Bacteria in the Hoatzin (Opisthocomus hoazin). Poster presented and abstract published at the 105th General Meeting of the American Society for Microbiology (ASM), Georgia World Congress Center, Atlanta, GA, USA, 2005.

  17. Godoy-Vitorino, Filipa, Gao, Z, Pei, Z., Blaser, M., Pericchi, L., Ortiz, H., Ley, R., Gordon, J., Garcia-Amado,M., Michelangeli, F., Domínguez-Bello, M., Molecular Diversity of Bacteria and Fungi in the Foregut of a South-American Leaf-Eating bird: The Hoatzin (Opisthocomus hoazin), Poster presented at the first External Scientific Advisory Committee (ESAC) of CREST- Center for Applied Tropical Ecology and Conservation (CATEC), University of Puerto Rico, College of Natural Sciences, San Juan, Puerto Rico, 2006

  18. A.Vazquez; M.Sepulveda; E. Acevedo, G. Huguet; L.Saavedra; H.Ortiz-Zuazaga; G.Quirk; S.Pena de Ortiz, Identification of DNA recombination-related genes in the rat medial prefrontal cortex following auditory fear conditioning, poster presented at the 15th Annual Puerto Rico Neuroscience Conference, December 2, 2006, Interamerican University, Bayamon, Puerto Rico.

  19. J. Y. Laguna-Torres, E. A. Castro, M. Colón-Cesario, I. J. Santos, J.R. Fernández, H.Ortiz-Zuazaga and S. Peña de Ortiz, The role of gene rearrangement processes on hippocampal synaptic plasticity and on remote memory, poster presented at the 15th Annual Puerto Rico Neuroscience Conference, December 2, 2006, Interamerican University, Bayamon, Puerto Rico.

  20. Suárez-Castillo, E.C., Ortiz-Zuazaga, H., Hernández-Pasos, J., García-Arrarás, J.E. Microarray analysis of the Sea cucumber intestinal regeneration process. Gordon Research Conference on Tissue Repair & Regeneration. Colby-Sawyer College, New London, NH, June 17-22/ 2007.

  21. Suárez-Castillo, E.C., Ortiz-Zuazaga, H., Hernández-Pasos, J., García-Arrarás, J.E. Microarray analysis of the Sea cucumber intestinal regeneration process. First Pan American Congress in Developmental Biology. Grand Melia Hotel in Cancun, Mexico, June 16-20/ 2007.

Invited Talks

A Survey of Bioinformatics. University of Puerto Rico School of Medicine RCMI lecture series. May 1997.

``Good'' Markers and ``True'' Maps: Combinatorial Algorithms for Genetic and Radiation Hybrid Mapping. University of Puerto Rico, Biology Department regular seminar series. August 1997.

sambatalk: How to get linux to act as a file and print server to Windows and Macs. Given September 15, 1997 to Dr Isidore Brodsky's Operating Systems class at the UPR.

linux: a brief introduction to the linux way of doing things. Given to the UPR Computer Science undergraduate students on September 8, 2000.

Python: my favorite programming language. Presented at the first Linux-PR Installfest, September 17, 2000.

Bioinformatics at the HPCf an introduction to the bioinformatics services at the HPCf, and our plans for the future. Presented January 31, 2001, at the Institute of Neurobiology, and again at the UPR-RCM for Dr. Carmen Cadilla's genetics course.

Clustering Microarray Expression Data: a survey, with some examples, of clustering techniques for microarray expression data. Presented March 15, 2001, at the UPR-RRP for Dr. Sandra Peña's Functional Genomics course.

Inferring Gene Regulation Networks From Microarray Expression Data: a survey of gene regulatory network inference techniques for microarray expression data. Presented March 29, 2001, at UPR-RRP for Dr. Sandra Peña's Functional Genomics course.

Ethical issues in bioinformatics: a list of recent cases that illustrate the ethical issues confronting bioinformatics. These cases are taken from the bioinformatics.org news items. Presented May 8, 2001 as part of the UPR-RCM bioethics course held by Dr. Emma Fernandez.

Sequence analysis using seqweb at the HPCf: a workshop on the GCG web interface seqweb. Presented November 1, 2001 at the HPCf, and again November 15, 2001 at UPR-RUM .

Sequence Analysis Using SeqWeb at the High Performance Computing Facility a seminar illustrating the use of seqweb and GCG to perform simple sequence analysis tasks. Presented Tuesday, March 21, 2002 at the UPR-RCM, sponsored by the RCMI program.

Probe-level microarray analysis. Presented November 12, 2008, at the UPR-RRP Biology Department regular seminar.

Troglodita approved!

Humberto Ortiz Zuazaga
humberto -at- hpcf.upr.edu

Most recent change: 2009/6/12 at 11:37
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