Curriculum Vitae

Humberto Ortiz-Zuazaga

Department of Computer Science
Rio Piedras Campus
University of Puerto Rico
17 Ave Universidad Ste 1701
San Juan PR 00925-2537
Tel (787) 764-0000 x88363
humberto.ortiz@upr.edu

and

High Performance Computing facility
University of Puerto Rico
PO Box 23334
San Juan, PR 00931-3334
humberto@hpcf.upr.edu

and

https://plus.codes/77CMCX33+RF

Degrees

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

Additional Education

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

Experience

Interim Chairperson
Department of Computer Science, Rio Piedras Campus, University of Puerto Rico, September 1, 2020 to December 31, 2021.
Professor
Department of Computer Science, Rio Piedras Campus, University of Puerto Rico, since August 25, 2020.
Associate Professor
Department of Computer Science, Rio Piedras Campus, University of Puerto Rico, July 1, 2015 to August 25, 2020.
Assistant Professor
Department of Computer Science, Rio Piedras Campus, University of Puerto Rico, January 21, 2010 to June 30, 2015.
Adjunct Professor
Deanship for Academic Affairs, Medical Sciences Campus, University of Puerto Rico, January 21, 2010 to December 31, 2010.
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).
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
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.
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 visualization and analysis 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.
Consultant
Datacom Caribe Inc., 1998. System administration tasks on BSDI UNIX computers. Developed CGI applications.
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.
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.
Technical staff assistant
University of Texas at San Antonio, 1995. Developed neural networks to classify features in fetal heart rate recordings.
Teaching assistant
University of Texas at San Antonio, 1995. Lectured in two microcomputer applications courses.
Systems administrator
Silicon Graphics Inc., 1995. Technical support and system administration for SGI Employees.
Research Associate
University of Cincinnati, 1994-1995. Worked porting GRACE to UNIX, integrating GRACE with GRASS, the US Army Corps of Engineers geographical information system.
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 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.
Research assistant
Department of Physiology and Biophysics, University of Cincinnati, 1989-1993. Developed and studied computer simulations of action potential propagation across cell membranes.
Consultant
Medical Sciences Campus, University of Puerto Rico, 1989. Taught introductory and intermediate BITNET usage.
Consultant
Phaedrus Computer Consultants, San Juan, Puerto Rico, 1988. Taught microcomputer applications.
Research assistant
Institute of Neurobiology, University of Puerto Rico, 1988-1989. Data acquisition and analysis of electrophysiological experiments.
Undergraduate research student
Department of Pharmacology, University of Puerto Rico, 1986-1987. Characterized the biochemical properties of potential anti-cancer agents.

Honors

University of Cincinnati, William McIntire Memorial Scholarship, 1993.

Memberships

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

Patents

United States Patent 8868349 (pdf)
Methods, systems, and products for quantitatively measuring the degree of concordance between or among microarray probe level data sets. Cheung; Philip; (San Diego, CA) ; Tully; Timothy P.; (Solana Beach, CA) ; Ortiz-Zuazaga; Humberto; (San Juan, PR) ; Moreno; Oscar; (Rio Piedras, PR). October 21, 2014.

Publications

Book Chapters

  1. Ordóñez Franco P., Pérez Hernández M.E., Ortiz-Zuazaga H., García Arrarás J. (2020) Building a Data Science Program Through Hackathons and Informal Training in Puerto Rico. In: Celi L., Majumder M., Ordóñez P., Osorio J., Paik K., Somai M. (eds) Leveraging Data Science for Global Health. Springer, Cham. https://doi.org/10.1007/978-3-030-47994-7_29

Journal Articles

  1. Auger, N.A.; Medina-Feliciano, J.G.; Quispe-Parra, D.J.; Colón-Marrero, S.; Ortiz-Zuazaga, H.; García-Arrarás, J.E. Characterization and Expression of Holothurian Wnt Signaling Genes during Adult Intestinal Organogenesis. Genes 2023, 14, 309. https://doi.org/10.3390/genes14020309

  2. Cruz-González, S.; Quesada-Díaz, E.; Miranda-Negrón, Y.; García-Rosario, R.; Ortiz-Zuazaga, H.; García-Arrarás, J.E. The Stress Response of the Holothurian Central Nervous System: A Transcriptomic Analysis. Int. J. Mol. Sci. 2022, 23, 13393. https://doi.org/10.3390/ijms232113393

  3. Quispe-Parra, D. J., Medina-Feliciano, J. G., Cruz-González, S., Ortiz-Zuazaga, H., & García-Arrarás, J. E. (2021). Transcriptomic analysis of early stages of intestinal regeneration in Holothuria glaberrima. Scientific Reports, 11(1), 1-14. https://doi.org/10.1038/s41598-020-79436-2

  4. Pedraza-Marrón, Carmen; Silva, Raimundo; Deeds, Johnathan ; Van Belleghem, Steven; Mastretta-Yanes, Alicia; Dominguez-Dominguez, Omar; Rivero-Vega, Rafael; Lutackas, Loretta; Murie, Debra; Parkyn, Daryl; Bullock, Lew; Foss, Kristin; Ortiz-Zuazaga, Humberto; Narváez-Barandica, Juan; Acero, Arturo; Gomes, Grazielle; Betancur-R, Ricardo. Genomics overrules mitochondrial DNA, siding with morphology on a controversial case of species delimitation. Published online 3 April 2019 in Proceedings of the Royal Society B. https://doi.org/10.1098/rspb.2018.2924

  5. Ingrid Forestier-Román, Andrés López-Rivas, María Sánchez-Vázquez, Krizia Rohena-Rivera, Gretchen Nieves-Burgos, Humberto Ortiz-Zuazaga, Carlos Torres-Ramos, and Magaly Martinez-Ferrer. Andrographolide Induces DNA Damage in Prostate Cancer Cells. Oncotarget 10: 1085-1101 (2019). https://doi.org/10.18632/oncotarget.26628

  6. Jessica Morales, Victoria Deal, Fiorella Reyes, Geronimo Maldonado, Nahomy Lesdesma, Franklin Staback, Cheyanne Croft, Amanda Pacheco, Humberto Ortiz-Zuazaga, Christian Yost, Jesse Rowley, Bismark Madera, Alex St. John, Junmei Chen, Jose Lopez, Matthew Rondina, Robert Hunter, Angela Gibson, and A Valance Washington. TLT-1 is a Prognostic Indicator in ALI/ARDS and Prevents Tissue Damage in the Lungs in a Mouse model. Blood: the Journal of the American Society of Hematology, December 6, 2018. 132(23):2495-2505. https://doi.org/10.1182/blood-2018-03-841593

  7. Velda J Gonzalez, Leorey N Saligan, Brooke L Fridley, Humberto Ortiz-Zuazaga, Lauren S Aaronson, "Gene Expression, and Fatigue in Puerto Rican Men during Radiotherapy for Prostate Cancer: an Exploratory Study", Puerto Rico health sciences journal, Vol 36, No 4 (2017). http://prhsj.rcm.upr.edu/index.php/prhsj/article/view/1534

  8. Van Belleghem, Steven; Papa, Riccardo; Ortiz-Zuazaga, Humberto; Hendrickx, Frederik; Jiggins, Chris; McMillan, W.; Counterman, Brian. patternize: An R package for quantifying color pattern variation. Methods in Ecology and Evolution. 3 August 2017. doi:10.1111/2041-210X.12853

  9. Eric Gamess, Humberto Ortiz-Zuazaga, "Low Level Performance Evaluation of InfiniBand with Benchmarking Tools", International Journal of Computer Network and Information Security(IJCNIS), Vol. 8, No. 10, pp. 12-22, 2016. https://dx.doi.org/10.5815/ijcnis.2016.10.02

  10. Eric Gamess and Humberto Ortiz-Zuazaga, “Analytical Performance Evaluation of Ipv6 and Ipv4 Over 10 Gigabit Ethernet and Infiniband using Ipoib”. International Journal of Advanced Computer Science and Applications(IJACSA), 7(8), 2016. https://dx.doi.org/10.14569/IJACSA.2016.070829

  11. Edgardo Castro-Pérez, Emilio Soto-Soto, Marizabeth Pérez-Carambot, Dawling Dionisio-Santos, Kristian Saied-Santago, Humberto Ortiz Zuazaga and Sandra Peña de Ortiz. Identification and Characterization of the V(D)J Recombination Activating Gene 1 in Long-Term Memory of Context Fear Conditioning. Neural Plasticity, vol. 2016, Article ID 1752176, 19 pages, 2016. https://dx.doi.org/10.1155/2016/1752176

  12. Humberto Ortiz-Zuazaga, Roberto Arce-Corretjer, Juan M. Solá-Sloan, José G. Conde. SalHUD – A Graphical Interface to Public Health Data in Puerto Rico. International Journal of Environmental Research and Public Health. Vol 13, No 1, 18, 2015. doi:10.3390/ijerph13010018

  13. Crusoe MR, Alameldin HF, Awad S et al. The khmer software package: enabling efficient nucleotide sequence analysis [version 1; referees: 2 approved, 1 approved with reservations] F1000Research 2015, 4:900 (doi: 10.12688/f1000research.6924.1)

  14. Mónica Rivera-Díaz, Miguel A Miranda-Román, Daniel Soto, Mario Quintero-Aguilo, Humberto Ortiz-Zuazaga, María J Marcos-Martinez, Pablo E Vivas-Mejía. MicroRNA-27a distinguishes glioblastoma multiforme from diffuse and anaplastic astrocytomas and has prognostic value. American Journal of Cancer Research. 2014 December 15, 5(1), 201–218. PMCID: PMC4300691

  15. Nadeau N, Ruiz M, Salazar P, Counterman B, Medina JA, Ortiz-Zuazaga H, Morrison A, McMillan WO, Jiggins CD, Papa R. Population genomics of parallel hybrid zones in the mimetic butterflies, H. melpomene and H. erato. Genome Res. 2014 May 13. pii: gr.169292.113. doi:10.1101/gr.169292.113

  16. Leah J. Campbell, Edna C. Suárez-Castillo, Humberto Ortiz-Zuazaga, Dunja Knapp, Elly M. Tanaka, Craig M. Crews. Gene Expression Profile of the Regeneration Epithelium during Axolotl Limb Regeneration. Developmental Dynamics, 240(7):1826-1840. July 2011. doi:10.1002/dvdy.22669

  17. 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

  18. 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

  19. 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

  20. 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

  21. 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

  22. 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

  23. J. Ge, N. Sperelakis, H. Ortiz-Zuazaga. Simulation of action potential propagation with electronic circuits. Innov. et Tech. en Biol. et Med., 14(4):404-420, 1993.

  24. 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. doi:10.1016/0895-7177(93)90097-I

  25. 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. doi:10.1016/0895-7177(92)90109-X

  26. 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.

Refereed Proceedings

  1. P. Ordóñez, H. Ortiz-Zuazaga and J. S. Ramírez-Lugo, "Broadening Participation in Computing through a Biology Summer Research Experience for Undergraduates," 2020 Research on Equity and Sustained Participation in Engineering, Computing, and Technology (RESPECT), Portland, OR, USA, 2020, pp. 1-2, doi: https://dx.doi.org/10.1109/RESPECT49803.2020.9272417.

  2. Patricia Ordóñez Franco, María-Eglée Pérez Hernández, Humberto Ortiz Zuazaga. Estimulando la Innovación en Ciencia de Datos Interdisciplinaria a Través de "Hackathons". 16th LACCEI International Multi-Conference for Engineering, Education, and Technology, July 18-20 2018, Lima Peru. https://dx.doi.org/10.18687/LACCEI2018.1.1.345

  3. Eric Gamess, Humberto Ortiz-Zuazaga. Evaluation of Point-to-Point Network Performance of HPC Clusters at the Level of UDP, TCP, and MPI. Proceedings of Simposio Científico y Tecnológico en Computación (SCTC 2016) Escuela de Computación de la Universidad Central de Venezuela, del 9 al 11 de mayo de 2016. Pages 116-122. PDF

  4. J Ortiz-Ubarri, H Ortiz-Zuazaga, A Maldonado, E Santos, J Grullón. Toa: A Web Based Network Flow Data Monitoring System at Scale. 2015 IEEE International Congress on Big Data, 438-443. https://doi.org/10.1109/BigDataCongress.2015.71

  5. Edusmildo Orozco, Rafael Arce-Nazario, José Ortiz-Ubarri, and Humberto Ortiz-Zuazaga. A Curricular Experience With Parallel Computational Thinking: A Four Years Journey. The Workshop on Parallel, Distributed, and High-Performance Computing in Undergraduate Curricula (EduPDHPC) 2013. November 18, 2013, Denver Colorado, USA. PDF

  6. Humberto Ortiz-Zuazaga, Roberto Arce-Corretjer. Majority logic decoding: a discrete method for detecting differential expression in RNA-Seq data. Proceedings of BIOCOMP'13: The 14th International Conference on Bioinformatics and Computational Biology. July 22-25, 2013, Las Vegas, Nevada, USA. http://ccom.uprrp.edu/~humberto/research/biocomp-hoz-rnaseq.pdf

  7. 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. https://dx.doi.org/10.6084/m9.figshare.2056644.v1

  8. 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. https://dx.doi.org/10.6084/m9.figshare.2056614.v1

  9. Edna C. Suárez-Castillo, Humberto Ortiz-Zuazaga, Josué Hernández-Pasos, José E. García-Arrarás. Microarray analysis of the sea cucumber intestinal regeneration process. Developmental Biology, Volume 306, Issue 1, 1 June 2007, Pages 379-380. doi:10.1016/j.ydbio.2007.03.351

  10. 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.

  11. 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.

  12. 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.

  13. 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.

  14. 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.

  15. 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.

  16. 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.

  17. 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.

  18. 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.

Preprints

  1. Cruz-González, S.; Quesada-Díaz, E.; Miranda-Negrón, Y.; García-Rosario, R.; Ortiz-Zuazaga, H.; García-Arrarás, J.E. Molecular Characterization of the Stress Response of the Holothurian Central Nervous System. Preprints 2022, 2022100087 (doi: 10.20944/preprints202210.0087.v1).

Conferences

  1. Dharsy D. Rodriguez-Velazquez, Humberto G. Ortiz-Zuazaga. A new horizon for differential expression using binarization as a tool for scRNA-seq. Poster presented at the 2024 NHGRI Training Meeting. April 7-10, 2024, Seattle, Washington, USA.

  2. Dharsy D. Rodriguez-Velazquez, Humberto G. Ortiz-Zuazaga. A new horizon for differential expression using binarization as a tool for scRNA-seq. Poster presented at the 2024 SACNAS Local Conference UPRRP. March 9, 2024, UPRRP, Rio Piedras, PR.

  3. Juan F. Hernandez José, Humberto Ortiz-Zuazaga. Binarizing scRNA-seq Data with Alevin Fry Method: Assessing Efficiency in Diabetes and COVID-19 Models. Presented at 39th Seminario Interuniversitario de Investigación en Ciencias Matemáticas (SIDIM), UPR Humacao. March 1-2, 2024.

  4. Patricia Ordóñez Franco, Juan S. Ramírez-Lugo, Humberto Ortiz Zuazaga, Maria-Eglée Pérez Hernández, Luis Raul Pericchi and José E. García Arrarás Enhancing Undergraduate Education and Curriculum through an Interdisciplinary and Quantitative Initiative to Broaden Participation in Big Data. Virtual presentation at LACCEI 2020: 18TH LACCEI INTERNATIONAL MULTI-CONFERENCE FOR ENGINEERING, EDUCATION, AND TECHNOLOGY. July 28, 2020.

  5. David Quispe, Sebastián Cruz, Joshua Medina, Humberto Ortiz-Zuazaga and José García-Arrarás. Differential Gene Expression during Early Stages of Regeneration in Holothuria glaberrima. Accepted for presentation at RECOMB 2020 (The 24th International Conference on Research in Computational Molecular Biology). Padova, Italy. 2020.

  6. Sebastian Cruz-Gonzalez, Eduardo Quesada-Diaz, Humberto Ortiz-Zuazaga and Jose Garcia-Arraras. Identification and characterization of genes of the Central Nervous System of the sea cucumber Holothuria glaberrima. Accepted for presentation at RECOMB 2020 (The 24th International Conference on Research in Computational Molecular Biology). Padova, Italy. 2020.

  7. Briknie Báez Rodríguez; Luis F. Mieses Gómez; Humberto Ortiz-Zuazaga. Diffhash, a More Efficient Way of Finding Differentially Expressed Genes. XXXV Seminario Interuniversitario de Investigación en Ciencias Matemáticas. University of Puerto Rico, Cayey, Puerto Rico. March 6-7, 2020.

  8. Miguel A. Hernández-Betancourt, Juan F. Hernández-José, Roberto C. Lopéz-Rivera, Humberto G. Ortiz-Zuazaga. Autoencoders vs LASSO: Applications To Breast Cancer Research. XXXV Seminario Interuniversitario de Investigación en Ciencias Matemáticas. University of Puerto Rico, Cayey, Puerto Rico. March 6-7, 2020.

  9. Sebastian Cruz-Gonzalez, David Quispe-Parra, Humberto Ortiz-Zuazaga and Jose E. Garcia-Arraras. “Gene set enrichment analysis of early intestinal regeneration in the sea cucumber Holothuria glaberrima." 2019 Junior Technical Meeting (JTM) and 39th Puerto Rico Interdisciplinary Scientific Meeting (PRISM), Mayaguez, PR, May 4, 2019.

  10. Anatoliy Chornyy, Nataliya Chorna, Humberto Ortiz-Zuazaga. Gene Activity Quantification In Real Time RT-PCR. NIGMS 7th Bienial National IDeA Symposium of Biomedical Research Excellence (NISBRE) conference, Washington DC, June 23-27, 2018.

  11. Ingrid Samari Forestier-Roman, María Sánchez, Krizia Rohena, Humberto Ortiz-Zuazaga, and Magaly Martínez-Ferrer. Microarray and Pathway Analysis of Prostate Cancer Tumors Treated with Andrographolide. FASEB J. April 2017 31:766.12.

  12. Jimenez-Ruiz, Ivan; Ortiz-Zuazaga, Humberto; Gonzalez-Mendez, Ricardo; Ropelewski, Alexander; Agosto Rivera, Jose. Comparing Reference-Based and De Novo Assemblies Using Drosophila melanogaster data. Annual Biomedical Research Conference for Minority Students (ABRCMS), November 9-12, 2016, Tampa, Florida.

  13. Grace M. Rodríguez Gómez, Humberto Ortiz-Zuazaga. Techniques for Anomaly Detection in IPv6 Network Flows. ACM Richard Tapia Celebration of Diversity in Computing, September 14-17, 2016. Austin, TX

  14. José Ortiz-Ubarri, Albert Maldonado, Eric Santos and Humberto Ortiz-Zuazaga. Toa: an open source web based NetFlow data network monitoring system. Accepted for oral presentation at FlowCon 2015, January 12 - 15, 2015. Portland, Oregon, USA.

  15. Ortiz-Zuazaga, Humberto; Arce-Corretjer, Roberto; Solá-Sloan, Juan M.; Conde, José G. (2014): SalHUD - A Graphical Interface to Public Health Data. Poster presented at the 2014 International Symposium on Minority Health and Health Disparities. December 1 – 3, 2014 National Harbor, Maryland, USA. figshare. doi:10.6084/m9.figshare.1248894 Retrieved 23:55, Nov 23, 2014 (GMT)

  16. J Morris-Pastrana, BG Nieves, CB Torres-Nieves, A Lora-Gálvez, RA Kirken, K Johnson, E Fernández-Repollet, HG Ortiz-Zuazaga, and JG Conde. An electronic system for documenting instrument use in core facilities. Poster presented at the 2014 International Symposium on Minority Health and Health Disparities. December 1 – 3, 2014 National Harbor, Maryland, USA.

  17. Jorge F. Ortiz-Carpena; Amneris Hernández-Figueroa; Charlton Díaz; Norma Rodríguez; Guillermo Delgado; Francheska Merced; Beatriz Cardona; José Luis Agosto-Alicea; Sandra Peña de Ortiz; Adrinel Vázquez-Montes; and Humberto Ortiz-Zuazaga. Microarray Gene Expression Analysis of Lead (Pb2+)-exposed Drosophila melanogaster during Development. Accepted to the 2013 Annual Biomedical Research Conference for Minority Students (ABRCMS).

  18. Roberto Arce Corretjer and Humberto Ortiz-Zuazaga. Comparing empirical Bayes and majority logic decoding methods for detecting differential expression in public RNA-Seq data from Drosophila melanogaster. XXVIII Inter University Seminar on Mathematical Sciences Research (SIDIM). Universidad Metropolitana, San Juan, Puerto Rico, March 1-2, 2013.

  19. J Morris-Pastrana, BG Nieves, CB Torres-Nieves, E Fernández-Repollet, H Ortiz-Zuazaga, and JG Conde. An e-Ticket System for Tracking Research Support Services. 13th RCMI International Research Symposium in San Juan, Puerto Rico, December 10-13, 2012.

  20. Jorge Felipe Ortiz-Carpena, Adrinel Vázquez-Montes, Amneris Hernández, Daniel Vélez- Costas, Eduardo Galindez-Cintrón, Sandra Peña de Ortiz, Humberto Ortiz-Zuazaga. Developmental Exposure to Lead (Pb2+) Results in Social Interaction Deficits in D. melanogaster. 21st PR Neuroscience Conference UPR-Rio Piedras Campus December 1st, 2012.

  21. León Ricardo B., Planas S., Ortiz H., Papa R. "Using Next Generation 454 Pyrosequencing Technology To Understand Potential Molecular Relations Between Butterfly And Human Eye Development". ABRCMS or Annual Biomedical Research Conference for Minority Students San Jose, California (USA). November 7-10, 2012. Poster.

  22. Medina, Jose & Ruiz, Mayt & Papa, Riccardo & Ortiz-Zuazaga, Humberto. (2012). Challenges and improvements in bioinformatics analysis of Next Generation Sequencing applied to natural population. Presented at 2012 Society for Advancement of Hispanics/Chicanos and Native Americans in Science National Conference (SACNAS). October 2012.

  23. Daniel Velez Costas, Eduardo Galindez Cintron, Jorge Ortiz-Carpena, Amneris Hernandez Figueroa, Adrinel Vazquez Montes, Humberto Ortiz-Zuazaga, Sandra Peña de Ortiz. High throughput video tracking of Drosophila melanogaster behaviour. 7th Transdisciplinary Research Conference. San Juan, Puerto Rico, May 3-4, 2012.

  24. Roberto Arce, Humberto Ortiz-Zuazaga. Detecting differential expression in public RNASeq data from Drosophila melanogaster. 7th Transdisciplinary Research Conference. San Juan, Puerto Rico, May 3-4, 2012.

  25. A.P. Chornyy and H.G. Ortiz Zuazaga. Program of Real Time PCR: DeltaDeltaCT_v02. Southeast Regional IDeA Meeting. New Orleans, LA, September 22-24, 2011.

  26. Vázquez-Montes, A., Rivera K., Ortiz-Carpena J., Peña de Ortiz, S., and Ortiz-Zuazaga, H. G. Developmental exposure to lead (Pb+2) results in social interaction deficits in D. melanogaster. Southeast Regional IDeA Meeting. New Orleans, LA, September 22-24, 2011.

  27. Ruiz Goyco, A., Falcón Dvorsky, E. and Ortiz-Zuazaga, H. Assembly of next-generation sequences from sea cucumber. Southeast Regional IDeA Meeting. New Orleans, LA, September 22-24, 2011.

  28. Medina-Cruz, J.A., Ortiz Ubarri, J. and Ortiz-Zuazaga, H. Automated creation of virtual clusters on a single server for parallel programming education. 5th Computing alliance of hispanic-serving institutions (CAHSI) annual meeting. San Juan, Puerto Rico, March 27-29, 2011.

  29. Ruiz Goyco, A., Falcón Dvorsky, E. and Ortiz-Zuazaga, H. Assembly of Second Generation Sequencing Data. 31st Puerto Rico Interdisciplinary Meeting (PRISM). Bayamon, Puerto Rico, March 12, 2011.

  30. Medina-Cruz, J.A., Ortiz Ubarri, J. and Ortiz-Zuazaga, H. Automated creation of virtual network topology and virtual cluster nodes for parallel programming on a single server. XXVI Inter University Seminar on Mathematical Sciences Research (SIDIM). University of Puerto Rico at Humacao and Palmas del Mar, Puerto Rico, February 25-26, 2011.

  31. Ruiz Goyco, A., Falcón Dvorsky, E., and Ortiz-Zuazaga, H. Ensamblando secuencias nucleicas de segunda generación. XXVI Inter University Seminar on Mathematical Sciences Research (SIDIM). University of Puerto Rico at Humacao and Palmas del Mar, Puerto Rico, February 25-26, 2011.

  32. 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.

  33. 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.

  34. 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.

  35. 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.

  36. 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

  37. 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.

  38. 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.

  39. 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.

  40. 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.

  41. 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

  42. 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.

  43. 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.

  44. 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.

  45. 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.

  46. 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.

  47. 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.

  48. 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.

  49. 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.

  50. 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.

  51. 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.

  52. 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.

Educational Modules

  1. Greg Wilson, Christina Koch, Rayna Michelle Harris, Karen Word, Maneesha Sane, Raniere Silva, … trk. (2019, June 16). carpentries/instructor-training: The Carpentries Instructor Training June 2019 (Version v2019.06.1). Zenodo. http://doi.org/10.5281/zenodo.3246985

Invited Talks

  1. Airined Montes Mercado, Carlos Morales Rivera, Diego Rosado Tristani, Humberto Ortiz Zuazaga, Angelica Rosado Quinones, Juan Ramirez Lugo, Noah A Auger (2022) IDGeNe Data Carpentry Genomics Workshop. San Juan, Puerto Rico, June 27 - July 1. https://idi-bd2k.github.io/2022-06-27-uprrp-genomics/

  2. Rosado-Quinones, Angelica, Ortiz-Zuazaga, Humberto, Ramirez-Lugo, Juan S. (2022) IQBio/IDGeNe Software Carpentry in Python Workshop. San Juan, Puerto Rico, June 9-15. https://idi-bd2k.github.io/2022-06-09-uprrp-python/

  3. Airined Montes Mercado, Carlos Morales Rivera, Diego Rosado Tristani, Juan Ramirez Lugo, Noah A Auger, Humberto Ortiz-Zuazaga (2022) IQBio/IDGeNe Software Carpentry in R Workshop. San Juan, Puerto Rico, June 9-15. https://idi-bd2k.github.io/2022-06-09-uprrp-r/

  4. Patricia Ordóñez, Wilson Lozano Rolón, Humberto Ortiz Zuazaga, Diego Rosado, Laura Ospina Gomez, Carlos Morales Rivera, Airined Montes Mercado, David Quispe (2021) IQ-Bio-REU Introduction to Programming Workshop. Online, May 31 - June 4. https://idi-bd2k.github.io/2021-05-31-iqbio/

  5. Ortiz-Zuazaga, Humberto (2020): Detection of Anomalies in Network Traffic. Online seminar for Women in Cybersecurity, University of Puerto Rico, Bayamon Campus. Puerto Rico, September 17, 2020.

  6. Humberto Ortiz-Zuazaga, Patricia Ordoñez, Sofia Melendez, Wilson Lozano. Helpers: Sebastian Cruz Gonzalez, Joshua Medina Feliciano, Laura Ospina, David Quispe, Dayanlee de Leon-Cordero, José Constantino Sánchez Curet, Christopher L. Ayala-Griffin. IQ-BIO-REU Software Carpentry Workshop. Offered online June 1-5 and 8-9, 2020. https://idi-bd2k.github.io/2020-06-01-puerto-rico/

  7. Ortiz-Zuazaga, Humberto (2019): A short introduction to LaTeX. Workshop (based on material by Andre Geldenhuis) offered to undergraduate political science students in the America Political Science Association- Minority Graduate Placement Program (APSA-MIGAP). San Juan, Puerto Rico, July 17 and 18, 2019.

  8. Humberto Ortiz-Zuazaga, Sofía Meléndez. Helpers: Briknie Baez, Israel Dilán, Marc De Jesus Ellsworth. (2019): Software Carpentry Introduction to Programming in R. Offered to undergraduate and graduate students as part of the IQ-Bio-REU summer internship. San Juan, Puerto Rico, June 3-7, 2019. https://idi-bd2k.github.io/2019-06-03-puerto_rico-R/

  9. Humberto Ortiz-Zuazaga, Sofía Meléndez. Helpers: Jeffrey Chan, Heriberto Camacho, Israel Dilán, Louis Gil, Briknie Báez. Software Carpentry Introduction to Programming in R. Offered to graduate and undergraduate students as part of the IDI-BD2K program. San Juan, Puerto Rico, January 11-12, 2019. https://idi-bd2k.github.io/2019-01-11-puerto_rico-R/

  10. Nelly Selem, Humberto Ortiz-Zuazaga. Helpers: Eveliz Peguero, Sebastian Cruz, Israel Dilán, Kevin Legarreta Gonzalez. Data Carpentry Genomics workshop. Offered to graduate and undergraduate students and faculty. San Juan, Puerto Rico, August 17-18, 2018. https://idi-bd2k.github.io/2018-08-17-puertorico-genomics/

  11. Ortiz-Zuazaga, Humberto (2017): The Escambron mRNAseq Protocol. A workshop for sequence analysis on local computing resources. San Juan, Puerto Rico, August 29-30, 2017. http://escambron-protocols.readthedocs.io/en/latest/mrnaseq/index.html

  12. Ortiz-Zuazaga, Humberto (2015): Computational Problems in Genetics and Genomics. figshare. https://dx.doi.org/10.6084/m9.figshare.1570959 Retrieved 15:18, Oct 09, 2015 (GMT)

  13. Ortiz-Zuazaga, Humberto (2015): UPR workshop: Processing TCGA mRNA expression data. figshare. https://dx.doi.org/10.6084/m9.figshare.1385358 Retrieved 12:49, Apr 21, 2015 (GMT)

  14. Ortiz-Zuazaga, Humberto (2014): Microarray Analysis With Bioconductor Workshop. figshare. https://dx.doi.org/10.6084/m9.figshare.1251183 Retrieved 13:33, Nov 25, 2014 (GMT)

  15. Using limma for microarray and RNA-Seq analysis. A workshop for the Research Design, Biostatistics and Clinical Research Ethics (DBE) key function of the PRCTRC, San Juan, PR, March 7, 2013. (Handout)

  16. Introduction to Python (course page), an AECC workshop on the python programming language, San Juan, PR, March 17, 24 and 31, and again in October 2012.

  17. Introduction to nanocomputation (20 contact hours). In Workshops for Science Teachers in the K-12 Level, Mayaguez, PR, November 12-13, 2011.

  18. Microarray analysis of oral cancer samples (slides, handout). Presented at An Introduction to Microarray Data Analysis workshop, Puerto Rico Comprehensive Cancer Center, San Juan, Puerto Rico, April 27, 2011. (Sweave sources: slides, manual)

  19. Research Networking in Puerto Rico. Presented at the Caribbean Telecommunications Union Caribbean Information Communication Technology Roadshow, San Juan, Puerto Rico, April 15, 2011.

  20. Bioinformatics: Principles and Applications, workshop held Thursday, May 27, 2010 at the Centro de Educacion Virtual in the Encarnacion Valdez Library of the Pontificial Catholic University of Puerto Rico.

  21. Network Tuning for Rapid Transmission of Multispectral Images for Relief Efforts in Haiti Presented at the Caribbean Regional Interest Group, Internet2 Member Meeting, Arlington, Virginia, April 29, 2010.

  22. Network Tuning at the UPR for Transmission of Multispectral Images in Support of Relief Efforts in Haiti, Presented at the Internet2 Member Meeting, Arlington, Virginia, April 27, 2010.

  23. Clustering and reverse engineering: from genes to the metabolome. given September 18, 2009 for Dr. Nataliya Chorna's Metabolomics class in UPR-RP. The slides were supposed to update and combine my clustering and reverse engineering talks on microarrays, but I didn't quite succeed (latex source).

  24. Two talks given as part of my interview for a position in the computer science department at UPR-RP "Bioinformatics and Computational Biology" for the undergraduate student seminar on August 18, and "Analysis Techniques for Probe-level Microarray Data" for the faculty on August 20, 2009. Latex here and here.

  25. Linux at the HPCf: given Monday, June 9, 2003 at the Desarollo de Linux en Puerto Rico conference, San Juan Marriott Hotel. The above link is the PDF of the slides, here is the latex source to the slides.

  26. A Survey of Bioinformatics: a look at some problems in bioinformatics I find intereseting (835 KB PDF file, updated from the 1997 talk). Given as part of Dr. Janwa's Introduction to Information Theory and Bioinformatics course, February 18, 2003, UPR-RP. Many of the source files for the illustrations were lost, Maria Mergal was kind enough to scan some old transparencies, and those are included in the PDF file. The latex source for the talk.

  27. Genes for Geeks: an introduction to molecular biology for computer scientists (138 KB PDF file). Given as part of Dr. Janwa's Introduction to Information Theory and Bioinformatics course, February 11, 2003, UPR-RP. Revised September 7, 2005 for Dr. Oscar Moreno's Bioinformatics course UPR-RP. The latex source for the talk.

  28. Finite Fields and Microarrays. (175 KB PDF file) Presented January 29, 2003 at the HPCf and UPR-RUM, in fulfillment of the doctoral seminar. The latex source for the talk.

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

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

  31. 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.

  32. Bootstrapping into Bioinformatics: the outline of a 5 week crash course on bioinformatics being developed for Dr. Fernando Gonzalez, UPR-RP.

  33. 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 .

  34. 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.

  35. 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.

  36. 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.

  37. 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.

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

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

  40. 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.

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

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

Research support

Current research support

  1. Landsliding and rhizobiota link the short- and long-term carbon cycles: A “multi-omic” approach
    Puerto Rico Science Trust: Catalyzer Research Grant Program
    PI: Carla Restrepo
    Co-PI: Humberto Ortiz-Zuazaga
    Start date: January 1, 2023
    End date: December 31, 2024
    Funds: $69,476
    Role on project: Co-PI, mentor graduate and undergraduate students in metagenomic analysis of samples on local and remote HPC resources, develop methods and procedures to analize and plot data and results.

  2. Increasing diversity in genomics for the next generation.
    NIH-NHGRI 1R25HG012702-01
    PI: Jose Garcia Arraras
    Start date: September 9, 2022
    End date: July 31, 2027 Funds: $1,373,000
    Role on project: Train undergraduate students in genomics and bioinformatics, provide resources for computational research.
    https://reporter.nih.gov/project-details/10533583

  3. Collaborative Research: Microbiota Role in Intestinal Regeneration.
    NSF IOS 2100494
    PI: Jose Garcia-Arraras
    Start Date: September 15, 2021
    End Date: June 30, 2024
    Funds: $661,175
    Role on project: Collaborator, consult and collaborate on metagenomic data analysis. Provide computational resources for genomics.
    https://www.nsf.gov/awardsearch/showAward?AWD_ID=2100494

  4. RII Track-2 FEC: Genomic Logic Underlying Adaptive Morphological Divergence.
    NSF OIA 1736026
    PI: Riccardo Papa
    Start Date: August 1, 2017
    End Date: July 31, 2021
    Funds: $2,000,000
    Role on project: Senior personnel, establish a repository of genotypes and phenotypes for data analysis, collaborate on the analysis of sequence and morphometric data.
    https://www.nsf.gov/awardsearch/showAward?AWD_ID=1736026

  5. ADVANCING COMPETITIVE BIOMEDICAL RESEARCH IN PUERTO RICO
    NIH NIGMS P20GM103475
    PI: Jose Rodriguez Medina
    Start Date: September 1, 2015
    End Date: May 31, 2020
    Funds: $20,369,321
    Role on Project: Director, Bioinformatics Core. Will provide, in conjunction with the bioinfomatics core personnel, bioinformatics support for INBRE researchers.
    https://projectreporter.nih.gov/project_info_description.cfm?aid=9282454&icde=35427079

  6. UPR/MDACC Partnership for Excellence in Cancer Research
    NIH National Cancer Institute U54CA096297
    PI: Brad R. Weiner, Reynold Lopez-Enriquez, Ana Patricia Ortiz, Elizabeth L. Travis
    Role on Project: Bioinformatics director, Data and Omics Science Core.
    Funds: $13M
    https://projectreporter.nih.gov/project_info_description.cfm?aid=9848093&icde=4757569

Completed Research Support

  1. Increasing Diversity in Interdisiplinary Big Data to Knowledge
    NIH NIMHD R25 MD010399
    PI: José E. García-Arrarás
    Other PI: Patricia Ordonez, María-Egleé Pérez Hernández
    Start Date: September 25, 2015
    End Date: June 30, 2020
    Funds: $1,067,600
    Role on project: Support undergraduate training in biomedical big data analysis, research mentoring of undergraduates, coordinate seminars and workshops in biomedical big data.
    https://projectreporter.nih.gov/project_info_description.cfm?aid=9303202&icde=35426999

  2. UPR/MDACC Partnership for Excellence in Cancer Research
    NIH National Cancer Institute U54CA096297
    PI: Marcia Cruz-Correa, Gabriel Lopez-Berestein, Reynold Lopez-Enriquez, José F. Cordero, Brad R. Weiner, Elizabeth L. Travis, David W. Wetter, and Michelle Barton
    Role on Project: Bioinformatics director, Biostatistics, Epidemiology and Bioinformatics Core (BEBiC).
    Funds: $5,364,836
    https://projectreporter.nih.gov/project_info_description.cfm?aid=9131639&icde=35427169

  3. Academics and Training for the Advancement of Cybersecurity Knowledge in Puerto Rico (ATACK PR)
    NSF DUE-1438838
    PI: Jose Ortiz-Ubarri
    Co-PI: Patricia Ordonez, Humberto Ortiz-Zuazaga, Rafael Arce Nazario
    Project Goals: Boost the education and training in cybersecurity in the undergraduate CS curriculum through the development of easy-to-adopt and transferable educational activities in cybersecurity for the core courses of the CS curriculum and the design and offering of new courses in cybersecurity to develop a security aware workforce.
    $299,982, Start date September 1, 2014.
    https://www.nsf.gov/awardsearch/showAward?AWD_ID=1438838

  4. CC-NIE Networking Infrastructure: Perimeter Network to Expedite the Transmission of Science Project (PR NETS)
    NSF ACI 1340959
    PI: Jose Ortiz-Ubarri
    Co-PI: Humberto Ortiz-Zuazaga, Rafael Arce Nazario
    Project goals: Facilitate scientific research on the Rio Piedras campus of the University of Puerto Rico by constructing a ScienceDMZ. This specialized research network will allow researchers in diverse fields including psychology, biology, chemistry, physics and computer and environmental sciences to transmit large data sets to collaborators.
    Funds: $499,667
    https://www.nsf.gov/awardsearch/showAward?AWD_ID=1340959

  5. EPSCoR Research Infrastructure Improvement Track 1 Nanotechnology from Basic Science to Emerging Applications: Institute for Functional Nanomaterials (IFN)
    NSF EPSCoR 1002410
    PI: Brad Weiner
    CoPI: Arturo Hernandez
    Role on project: Director of the computational nanoscience resource center (CNaRC). Will provide cyberinfrastructure for computational nanoscience research to IFN. The grant is for $20 M for 5 years support. https://www.nsf.gov/awardsearch/showAward?AWD_ID=1002410

  6. Advancing Competitive Biomedical Research in Puerto Rico
    NIH NIGMS P20GM103475
    PI: José Rodriguez Medina
    Start date: August 1, 2009
    End Date July 31, 2014
    Funds: USD 18,050,756
    Role on project: Director of the Bioinformatics Resource Center (BiRC), providing bioinformatics hardware, software and consulting support to all INBRE researchers in Puerto Rico, at all INBRE institutions on the island. This grant was awarded in 2001 with USD 4M in NCRR funding, and was successfully renewed in 2004 for 5 years and USD 10M. A third cycle has been awarded in 2009 for an additional 5 years at USD 18M.

  7. EPSCoR Research Infrastructure Improvement Track 1
    NSF Award # EPS-0701525
    PI: Brad Weiner
    Co-PI: Manuel Gomez
    Role on project: Director of the Computational Nanoscience Resource Center (CNaRC), providing hardware, software, consulting and training support to nanoscience researchers in the Institute for Functional Nanomaterials. This grant was awarded in 2007, for $9M over 3 years.
    https://www.nsf.gov/awardsearch/showAward?AWD_ID=0701525

  8. Networking research resources across America,
    NIH NCRR U24RR029822
    PI: Emma Fernandez Repollet
    Start date: September 25, 2009
    End date: August 31, 2011
    Funds: $7,499,857
    Role on Project: informatics lead, advised PI on informatics issues related to the identification and sharing of unique research resources in UPR system.
    https://projectreporter.nih.gov/project_info_description.cfm?aid=7940935&icde=35427532

  9. MRI–R2: Acquisition of genomic and bioinformatic technology to promote research at the University of Puerto Rico
    NSF Award No. DBI-0959864
    PI: Tomas Hrbek
    Role: Co-PI (Co-Principal Investigator)
    Start date: July 1, 2010
    End date: June 30, 2013
    Funds: $637,739
    Role on project: Manage data storage and analysis for next-generation sequencing efforts at the Sequencing and Genotyping Facility. Collaborate with researchers on the analysis of high-throughput sequence data.
    https://www.nsf.gov/awardsearch/showAward?AWD_ID=0959864

  10. Puerto Rico Clinical and Translational Research Consortium
    NIH NCRR U54RR026139
    PI: Frontera, Walter R.
    Start date: 17-SEP-2010
    End date: 30-JUN-2013
    Funds $16,398,579
    Role on project: Biomedical informatics key function leader. Direct staff responsible for biomedical informatics infrastructure, coordinate training in biomedical informatics, establish research collaborations in biomedical informatics in support of clinical and translational research within the consortium.
    https://projectreporter.nih.gov/project_info_description.cfm?aid=8144269&icde=35427598

  11. EPSCoR Research Infrastructure Improvement Track 2 Collaborative Research: Cyberinfrastructure-enabled Computational Nanoscience for Energy Technologies
    NSF Proposal #1010094
    PI: Manuel Gomez
    Co-PI: Julian Velev, Humberto Ortiz Zuazaga, Peter M. Musial
    Role on project: Director of the CNaRC, and Co-PI of the overall grant, a collaboration with the Nebraska jurisdiction. The grant will provide additional computational resources and support for researchers in computational nanoscience. The grant is for $2.7 M for 3 years support.
    https://www.nsf.gov/awardsearch/showAward?AWD_ID=1010094