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Leonardo Mariño-Ramírez, Ph.D.

spacer gif spacer gif Leonardo Mariño-Ramírez
Contact information

Staff Scientist
NCBI, NLM, NIH
Computational Biology Branch
Building 38A, Room 6S614M
8600 Rockville Pike, MSC 6075
Bethesda, MD 20894-6075

Tel: (301) 402-3708
Fax: (301) 480-2288
E-mail: marino@ncbi.nlm.nih.gov

Education

1997 – 2002
Ph.D. Biochemistry.
Texas A&M University. College Station, TX.

1988 – 1992
B.Sc. Microbiology.
Universidad de Los Andes. Bogotá, Colombia.

Reprints for personal use only

Research Articles
  1. Kim, N-K., Tharakaraman, K., Mariño-Ramírez, L. and Spouge, J. L. (2008) Finding sequence motifs with Bayesian models incorporating positional information: an application to transcription factor binding sites. BMC Bioinformatics. 9:262. [PubMed] [PDF]
  2. Polavarapu, N., Mariño-Ramírez, L., Landsman, D., McDonald, J. F. and Jordan, I. K. (2008) Evolutionary rates and patterns for human transcription factor binding sites derived from repetitive DNA. BMC Genomics. 9:226. [PubMed] [PDF] Highly accessed in BMC
  3. Tharakaraman K., Bodenreider O., Landsman D., Spouge J. L. and Mariño-Ramírez, L. (2008) The biological function of some human transcription factor binding motifs varies with position relative to the transcription start site. Nucleic Acids Research. 36:2777-2786. [PubMed] [PDF]
  4. Resch, A. M., Carmel, L., Mariño-Ramírez, L., Ogurtsov, A. Y., Shabalina, S. A., Rogozin, I. B. and Koonin, E. V. (2007) Widespread Positive Selection in Synonymous Sites of Mammalian Genes. Molecular Biology and Evolution. 24:1821-1831. [PubMed] [PDF]
  5. Piriyapongsa, J., Mariño-Ramírez, L. and Jordan, I. K. (2007) Origin and evolution of human microRNAs from transposable elements. Genetics. 176:1323-1337. [PubMed] [PDF]
    Evaluated by F1000 Biology
  6. Riz I., Akimov S. S., Eaker S. S., Baxter K. K., Lee H. J., Mariño-Ramírez, L., Landsman D., Hawley T. S. and Hawley R. G. (2007) TLX1/HOX11-induced hematopoietic differentiation blockade. Oncogene. 26:4115-4123. [PubMed] [PDF]
  7. Mariño-Ramírez, L., Jordan, I. K. and Landsman, D. (2006) Multiple independent evolutionary solutions to core histone gene regulation. Genome Biology. 7:R122. [PubMed] [PDF] Highly accessed in BMC
  8. Mariño-Ramírez, L., Bodenreider, O., Kantz, N. and Jordan, I. K. (2006) Co-evolutionary Rates of Functionally Related Yeast Genes. Evolutionary Bioinformatics. 2:295-300. [PubMed] [PDF]
  9. Tsaparas, P., Mariño-Ramírez, L., Bodenreider, O., Koonin, E. V. and Jordan, I. K. (2006) Global similarity and local divergence in human and mouse gene co-expression networks. BMC Evolutionary Biology. 6:70. [PubMed] [PDF] Highly accessed in BMC
  10. Mariño-Ramírez, L., Tharakaraman, K., Sheetlin, S. L., Landsman, D. and Spouge, J. L. (2006) Scanning sequences after Gibbs sampling to find multiple occurrences of functional elements. BMC Bioinformatics. 7:408. [PubMed] [PDF]
  11. Mariño-Ramírez, L. and Jordan, I. K. (2006) Transposable element derived DNaseI-hypersensitive sites in the human genome. Biology Direct. 1:20. [PubMed] [PDF]
    Evaluated by F1000 Biology
  12. Mariño-Ramírez, L., Hsu, B., Baxevanis, A. D. and Landsman, D. (2006) The Histone Database: a comprehensive resource for histones and histone fold-containing proteins. Proteins. 62:838-842. [PubMed] [PDF]
  13. Eriksson, P. R., Mendiratta, G., McLaughlin, N. B., Wolfsberg, T. G., Mariño-Ramírez, L., Pompa, T. A., Jainerin, M., Landsman, D., Shen, C-H. and Clark, D. J. (2005) Global regulation by the yeast Spt10 protein is mediated through chromatin structure and the histone UAS elements. Molecular and Cellular Biology. 25:9127-9137. [PubMed] [PDF]
  14. Mariño-Ramírez, L., Tharakaraman, K., Sheetlin, S., Landsman, D. and Spouge, J. L. (2005) Alignments anchored on genomic landmarks can aid in the identification of regulatory elements. Bioinformatics. 21 Suppl 1:i440-i448. [PubMed] [PDF]
  15. Jordan, I. K., Mariño-Ramírez, L. and Koonin, E. V. (2005) Evolutionary significance of gene expression divergence. Gene. 345:119-126. [PubMed] [PDF]
    Evaluated by F1000 Biology
  16. Mariño-Ramírez, L., Spouge, J. L., Kanga, G. C. and Landsman, D. (2004) Statistical analysis of over-represented words in human promoter sequences. Nucleic Acids Research. 32:949-958. [PubMed] [PDF]
  17. Jordan, I. K., Mariño-Ramírez, L., Wolf, Y. I. and Koonin, E. V. (2004) Conservation and co-evolution in the scale-free human gene co-expression network. Molecular Biology and Evolution. 21:2058-2070. [PubMed] [PDF]
  18. Mariño-Ramírez, L., Minor, J. L., Reading, N. and Hu, J. C. (2004) Identification and mapping of self-assembling protein domains encoded by the Escherichia coli K-12 genome using lambda repressor fusions. J. Bacteriol. 186:1311-1319. [PubMed] [PDF]
  19. Mariño-Ramírez, L. and Hu, J. C. (2002) Isolation and mapping of self-assembling protein domains encoded by the Saccharomyces cerevisiae genome. Yeast. 19:641-650. [PubMed] [PDF]
  20. Mariño-Ramírez, L. (1997) Clonación del gen de la cápside proteica de una cepa colombiana del virus del mosaico del pepino (CMV) para su expresión en plantas por transformación mediante Agrobacterium. Revista Corpoica 2. 58-59. [PDF]
  21. Hernández Fernández, J., Mariño-Ramírez, L., Orozco Cárdenas, M. L. y Narváez Vásquez J. (1996) Uso de la reacción en cadena de la polimerasa para la caracterización de aislamientos nativos de Bacillus thuringiensis. Revista Corpoica 2. 1-9. [PDF]
  22. Mariño-Ramírez, L., Hernández Fernández, J., Orozco Cárdenas, M. L. y Narváez Vásquez J. (1996) Caracterización Molecular de Genes cry de Bacillus thuringiensis utilizando PCR Extra-Rápida. Revista Corpoica 1. 47-47. [PDF]
  23. Reichel, H., Mariño-Ramírez, L., Kummert, J., Belalcazar, S. y Narváez, J. (1996) Caracterización del gen de la proteína de la cápside de dos aislamientos del virus del mosaico del pepino (CMV), obtenidos de plátano y banano (Musa spp.) Revista Corpoica 1. 1-5. [PDF]
Invited Review Articles
  1. Mariño-Ramírez, L., Kann, M. G., Shoemaker, B. A. and Landsman, D. (2005) Histone structure and nucleosome stability. Expert Review of Proteomics. 2:719-729. [PubMed] [PDF]
  2. Mariño-Ramírez, L., Lewis, K. C., Landsman, D. and Jordan, I. K. (2005) Transposable elements donate lineage-specific regulatory sequences to host genomes.
    3. Cytogenetic and Genome Research. 110:333-341. [PubMed] [PDF]
Invited Book Chapters
  1. Jordan, I. K. and Mariño-Ramírez, L. (2007) Evolutionary genomics of gene expression, in Structural Approaches to Sequence Evolution Molecules, Networks, Populations, (Bastolla, U.; Porto, M.; Roman, H.E.; Vendruscolo, M. ed.), Springer, New York, NY. [Springer]
  2. Mariño-Ramírez, L., Campbell, L. and Hu, J. C. (2003) Screening peptide/protein libraries fused to the lambda repressor DNA-binding Domain in E. coli cells, in Methods in Molecular Biology: E. coli Gene Expression Protocols, (Vaillancourt, P. ed.) 205:235-250, Humana Press, Totowa, NJ. [PubMed] [PDF]
  3. Mariño-Ramírez, L. and Hu, J. C. (2002) Using lambda repressor fusions to isolate and characterize self-assembling domains, in Protein-Protein Interactions: A Laboratory Manual, (Golemis, E., and Serebriiskii, I. ed.) 375-394, Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY. [CSHL Press] [PDF]

Presentations and Abstracts
  1. Mariño-Ramírez, L. (2008) Translating bioinformatics and computational biology into usable clinical knowledge. Presented at the Myeloma Institute for Research and Therapy - University of Arkansas for Medical Sciences (April 28, 2008). Little Rock, AR
  2. Mariño-Ramírez, L. (2007) Evolutionary trends of transcriptional regulation in core histone genes. Presented at the Bioinformatics Week in Odaiba (BiWO2007) - The Annual Meeting of Computational Biology Research Center (CBRC2007) (December 19 – 20, 2007). Tokyo Academic Park - Odaiba, Japan [Program] [Announcement]
  3. Mariño-Ramírez, L. (2007) Evolutionary mechanisms of core histone gene regulation. Presented at the Pontificia Universidad Javeriana (June 18 – 19, 2007). Bogotá, Colombia
  4. Mariño-Ramírez, L. (2007) Multiple evolutionary solutions to core histone gene regulation. Presented at the 2007 Experimental Biology Meeting (April 28 – May 2, 2007). Washington, DC
  5. Mariño-Ramírez, L. (2006) Multiple independent solutions to core histone gene regulation. Presented at the 2006 Georgia Tech Bioinformatics Retreat (November 4 – 5, 2006). Clarkesville, GA
  6. Mariño-Ramírez, L. (2006) Functional assignment and gene discovery using NCBI resources.
    7. Presented at CENICAFE (October 6, 2006). Chinchiná, Colombia
  7. Mariño-Ramírez, L. (2006) Using NCBI tools for the functional assignment of disease-related genes.
    8. Presented at the National Institutes of Health (INS) (October 4, 2006). Bogotá, Colombia
  8. Mariño-Ramírez, L. (2006) Functional assignment of disease-related genes in the post-genomic era.
    9. Presented at the II International Symposium Post-genomic Era: HIV-AIDS, Cancer, Advances in diagnostic and treatment (September 28 – 29, 2006). Montería, Colombia [Program]
  9. Mariño-Ramírez, L., Jordan, I. K. and Landsman, D.(2006) Multiple convergent solutions to core histone gene regulation. Presented at the Transcriptional Regulation During Cell Growth, Differentiation and Development - 2006 FASEB Summer Research Conference - (August 12 – 17, 2006). Saxtons River, VT
  10. Riz, I., Akimov, S. S., Eaker, S. S., Mariño-Ramírez, L., Landsman, D., Hawley, T. S. and Hawley R. G. (2005) TLX1/HOX11-Mediated Disruption of Hematopoietic Differentiation Programs. Presented at the American Society of Hematology (ASH) meeting 2005 (December 10 – 13, 2005). Atlanta, GA [Abstract]
  11. Mariño-Ramírez, L., Tharakaraman, K., Sheetlin, S., Landsman, D. and Spouge, J. L. (2005) Alignments anchored on genomic landmarks can aid in the identification of regulatory elements. Presented at the International Society for Computational Biology (ISMB) meeting 2005 (June 25 – 29, 2005). Detroit, MI [Abstract]
  12. Mariño-Ramírez, L. (2005) Identification of regulatory elements using alignments anchored on genomic landmarks. Presented at the Department of Biochemistry and Molecular Biology. Genomics and Proteomics Seminar Series. The George Washington University Medical Center (April 8, 2005). Washington, DC
  13. Mariño-Ramírez, L., Tharakaraman, K., Landsman, D. and Spouge, J. L. (2004) Identification of positionally clustered sequence elements in human proximal promoter regions. Presented at the 2004 Genomics Workshop on Identification of Functional Elements in Mammalian Genomes (November 11 – 13, 2004). Cold Spring Harbor Laboratory, NY
  14. Jordan, I. K., Mariño-Ramírez, L., Wolf, Y. I. and Koonin, E. V. (2004) Sequence evolution and the human gene expression network. Presented at Genomes and Evolution 2004 (June 17 – 20, 2004). The Pennsylvania State University. University Park, PA [Abstract]
  15. Mariño-Ramírez, L., Spouge, J. L. and Landsman, D. (2003) Statistical Analysis of DNA Sequences in Human Promoter Regions. Presented at the 2003 NIH Research Festival (October 14 – 17, 2003). Bethesda, MD
  16. Mariño-Ramírez, L. (2003) Genome-wide mapping of homotypic interactions encoded in microbial genomes. Presented at Molecular Genetics of Bacteria & Phages (August 5 – 10, 2003). Madison, WI
  17. Mariño-Ramírez, L., Spouge, J. L. and Landsman, D. (2003) Identification of candidate regulatory sequence elements in Homo sapiens. Presented at the LXVIII Cold Spring Harbor Symposium on Quantitative Biology (May 28 – June 2, 2003). Cold Spring Harbor Laboratory, NY
  18. Mariño-Ramírez, L. (2002) Characterization of protein homotypic interactions encoded by four microbial genomes. Presented at 2002 Lost Pines Molecular Biology Conference (October 25-27, 2002). Smithville, TX
  19. Mariño-Ramírez, L. (2002) Mycobacterium tuberculosis protein oligomerization domains identified with repressor fusions. Presented at Third TB Structural Genomics Consortium Retreat (September 8 – 10, 2002). Santa Fe, NM
  20. Mariño-Ramírez, L., Minor, J. L., Reading, N. and Hu, J. C. (2002) Genome-wide mapping of protein oligomerization domains in microorganisms. Presented at Molecular Genetics of Bacteria & Phages (August 20 – 25, 2002). Cold Spring Harbor Laboratory, NY
  21. Mariño-Ramírez, L., Minor, J. L. and Hu, J. C. (2002) Genetic approaches to study protein interactions. Presented at The Association of Biomolecular Resource Facilities meeting (March 10 – 12, 2002) Austin, TX [Abstract]
  22. Gill, C. A., Xavier, S. R., Abbey, C. A., Mariño-Ramírez, L. and Adelson, D. L. (2002) An integrated genomics database for beef cattle. Presented at Plant, Animal & Microbe Genomes X Conference (January 12 – 16, 2002) San Diego, CA [Abstract]
  23. Mariño-Ramírez, L. and Hu, J. C. (2001) Genome-wide mapping of protein oligomerization domains in Saccharomyces cerevisiae. Presented at Beyond Genome 2001. PROTEOMICS (June 21 – 22, 2001) San Francisco, CA
  24. Mariño-Ramírez, L., Simon-Marshall, S. and Hu, J. C. (2000) Lambda repressor fusions as a tool to study protein oligomerization in Saccharomyces cerevisiae. Presented at the Yeast Genetics and Molecular Biology Meeting (July 25 – 30, 2000) University of Washington, Seattle, WA [Abstract]
  25. Moon, Y. S., Clendennen, S. K., Mariño-Ramírez, L. and May, G. D. (1997) Differential gene expression during the break in potato tuber dormancy. Presented at Plant Biology ’97 (August 2 – 6, 1997) Vancouver, British Columbia, Canada. Plant Physiol., 114: 1636-1636 Suppl. S. [Abstract]
  26. Mariño-Ramírez, L., Hernández Fernández, J., Orozco Cárdenas, M. L. y Narváez Vásquez J. (1995) Aislamiento y caracterización de cepas de Bacillus thuringiensis en Colombia. Presented at XXII Congreso de la Sociedad Colombiana de Entomología SOCOLEN (July 26 – 28, 1995) Santafé de Bogotá, Colombia.
  27. Mariño-Ramírez, L., Hernández Fernández, J., Orozco Cárdenas, M. L. y Narváez Vásquez J. (1995) Molecular Characterization of Native Strains of Bacillus thuringiensis. Presented at REDBIO ’95: Second Latin-American Plant Biotechnology Meeting (June 2 – 6, 1995) Puerto Iguazú, Argentina.

Teaching Experience
  • Lecturer
    2008
    Computational Genomics - School of Biology - Georgia Institute of Technology. [Program]
    Atlanta, GA
  • Lecturer
    2007
    Curso de Bioinformática: Fundamentos para el manejo y uso de datos biológicos. [Program]
    Montería, Colombia
  • Lecturer
    2006
    Curso Internacional: Manejo de Herramientas Básicas en Bioinformática. [Program]
    Bogotá, Colombia
  • Lecturer
    2005
    Curso Internacional de Bioinformática: Manejo de las herramientas básicas. [Program]
    Bogotá, Colombia

Professional Experience
  • Staff Scientist
    2004 – Present
    Computational Biology Branch.
    National Center for Biotechnology Information.
    National Institutes of Health.
    Bethesda, MD

  • Research Fellow
    2002 – 2004
    Computational Biology Branch.
    National Center for Biotechnology Information.
    National Institutes of Health.
    Bethesda, MD

  • Research Assistant
    1997 – 2002
    Jim Hu's Laboratory.
    Department of Biochemistry and Biophysics.
    Texas A&M University.
    College Station, TX

  • Visiting Scientist
    1996
    Boyce Thompson Institute for Plant Research.
    Cornell University.
    Ithaca, NY

  • Visiting Scientist
    1995
    Institute of Biosciences and Technology.
    Texas A&M University.
    Houston, TX

  • Research Assistant
    1994 - 1997
    National Plant Biotechnology Program.
    Corporación Colombiana de Investigación Agropecuaria (CORPOICA).
    Bogotá, Colombia

  • Research Assistant
    1992 - 1994
    Immunology Institute.
    San Juan de Dios Hospital. National University of Colombia.
    Bogotá, Colombia


Honors and Awards
  • 2006
    DHHS / NIH / NLM
    Special Achievement Award. PDF
  • 2005
    GlaxoSmithKline Bioinformatics Prize.
    Best paper award 13th Annual International Conference on Intelligent Systems for Molecular Biology.
    ISMB 2005 PDF
  • 1997
    Encyclopædia Britannica Scholarship.

    Fulbright / Colciencias / IIE pre-doctoral Fellowship.

  • 1996
    Fellowship in Bioinformatics. International Centre for Genetic Engineering and Biotechnology – ICGEB.

    Short-Term Fellowship in Biotechnology. UNESCO.

  • 1995
    Cochran Fellowship Program in Biotechnology. United States Department of Agriculture – USDA.


Academic Service


Memberships in Professional Societies
  • American Society for Biochemistry and Molecular Biology - ASBMB.
  • International Society for Computational Biology - ISCB.

  • The Fulbright Association - Fulbright Association.

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Revised: June 26, 2008.