Leonardo Mariño-Ramírez

Summary

Affiliation: National Institutes of Health
Country: USA

Publications

  1. pmc Analysis of biological features associated with meiotic recombination hot and cold spots in Saccharomyces cerevisiae
    Loren Hansen
    Computational Biology Branch, National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland, United States of America
    PLoS ONE 6:e29711. 2011
  2. pmc Development and characterization of microsatellite markers for the Cape gooseberry Physalis peruviana
    Jaime Simbaqueba
    Plant Molecular Genetics Laboratory, Center of Biotechnology and Bioindustry, Colombian Corporation for Agricultural Research CORPOICA, Bogota, Colombia
    PLoS ONE 6:e26719. 2011
  3. pmc The biological function of some human transcription factor binding motifs varies with position relative to the transcription start site
    Kannan Tharakaraman
    Computational Biology Branch, National Center for Biotechnology Information and National Library of Medicine, National Institutes of Health, 8600 Rockville Pike, MSC 6075 Bethesda, MD 20894 6075, USA
    Nucleic Acids Res 36:2777-86. 2008
  4. pmc Multiple independent evolutionary solutions to core histone gene regulation
    Leonardo Mariño-Ramírez
    Computational Biology Branch, National Center for Biotechnology Information, National Institutes of Health, 8600 Rockville Pike, Bethesda, Maryland 20894 6075, USA
    Genome Biol 7:R122. 2006
  5. pmc Identification of immunity related genes to study the Physalis peruviana--Fusarium oxysporum pathosystem
    Felix E Enciso-Rodríguez
    Plant Molecular Genetics Laboratory, Center for Biotechnology and Bioindustry, Colombian Corporation for Agricultural Research, CORPOICA, Bogota, Colombia
    PLoS ONE 8:e68500. 2013
  6. pmc Epigenetic histone modifications of human transposable elements: genome defense versus exaptation
    Ahsan Huda
    School of Biology, Georgia Institute of Technology, 310 Ferst Drive, Atlanta, GA 30332, USA
    Mob DNA 1:2. 2010
  7. pmc Evolutionary rates and patterns for human transcription factor binding sites derived from repetitive DNA
    Nalini Polavarapu
    School of Biology, Georgia Institute of Technology, Atlanta, GA 30332, USA
    BMC Genomics 9:226. 2008
  8. pmc Global similarity and local divergence in human and mouse gene co-expression networks
    Panayiotis Tsaparas
    Basic Research Unit, Helsinki Institute for Information Technology, University of Helsinki, Helsinki, Finland
    BMC Evol Biol 6:70. 2006
  9. pmc Histone structure and nucleosome stability
    Leonardo Mariño-Ramírez
    Computational Biology Branch, National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
    Expert Rev Proteomics 2:719-29. 2005
  10. pmc The Histone Database: an integrated resource for histones and histone fold-containing proteins
    Leonardo Mariño-Ramírez
    Computational Biology Branch, National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, 8600 Rockville Pike, MSC 6075, Bethesda, MD 20894 6075, USA
    Database (Oxford) 2011:bar048. 2011

Collaborators

Detail Information

Publications32

  1. pmc Analysis of biological features associated with meiotic recombination hot and cold spots in Saccharomyces cerevisiae
    Loren Hansen
    Computational Biology Branch, National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland, United States of America
    PLoS ONE 6:e29711. 2011
    ..Next generation sequencing can exhibit a bias that is strong enough to lead to incorrect conclusions. Care must be taken when interpreting high throughput sequencing data where systematic biases have been documented...
  2. pmc Development and characterization of microsatellite markers for the Cape gooseberry Physalis peruviana
    Jaime Simbaqueba
    Plant Molecular Genetics Laboratory, Center of Biotechnology and Bioindustry, Colombian Corporation for Agricultural Research CORPOICA, Bogota, Colombia
    PLoS ONE 6:e26719. 2011
    ..Here we report the first P. peruviana specific microsatellite set, a valuable tool for a wide variety of applications, including functional diversity, conservation and improvement of the species...
  3. pmc The biological function of some human transcription factor binding motifs varies with position relative to the transcription start site
    Kannan Tharakaraman
    Computational Biology Branch, National Center for Biotechnology Information and National Library of Medicine, National Institutes of Health, 8600 Rockville Pike, MSC 6075 Bethesda, MD 20894 6075, USA
    Nucleic Acids Res 36:2777-86. 2008
    ..By exploiting the phenomenon of positional regulation, it uses position to differentiate the biological functions of subsets of TFBSs sharing a common sequence motif...
  4. pmc Multiple independent evolutionary solutions to core histone gene regulation
    Leonardo Mariño-Ramírez
    Computational Biology Branch, National Center for Biotechnology Information, National Institutes of Health, 8600 Rockville Pike, Bethesda, Maryland 20894 6075, USA
    Genome Biol 7:R122. 2006
    ..Core histone genes are periodically expressed along the cell cycle and peak during S phase. Core histone gene expression is deeply evolutionarily conserved from the yeast Saccharomyces cerevisiae to human...
  5. pmc Identification of immunity related genes to study the Physalis peruviana--Fusarium oxysporum pathosystem
    Felix E Enciso-Rodríguez
    Plant Molecular Genetics Laboratory, Center for Biotechnology and Bioindustry, Colombian Corporation for Agricultural Research, CORPOICA, Bogota, Colombia
    PLoS ONE 8:e68500. 2013
    ....
  6. pmc Epigenetic histone modifications of human transposable elements: genome defense versus exaptation
    Ahsan Huda
    School of Biology, Georgia Institute of Technology, 310 Ferst Drive, Atlanta, GA 30332, USA
    Mob DNA 1:2. 2010
    ..To date, all available evidence points to the genome defense hypothesis as the best explanation for the biological role of TE epigenetic modifications...
  7. pmc Evolutionary rates and patterns for human transcription factor binding sites derived from repetitive DNA
    Nalini Polavarapu
    School of Biology, Georgia Institute of Technology, Atlanta, GA 30332, USA
    BMC Genomics 9:226. 2008
    ..We also evaluated the position-specific patterns of variation among TFBS to look for signs of functional constraint on TFBS derived from repetitive and non-repetitive DNA...
  8. pmc Global similarity and local divergence in human and mouse gene co-expression networks
    Panayiotis Tsaparas
    Basic Research Unit, Helsinki Institute for Information Technology, University of Helsinki, Helsinki, Finland
    BMC Evol Biol 6:70. 2006
    ..Expression profiles were resolved into species-specific coexpression networks, and the topological properties of the networks were compared between species...
  9. pmc Histone structure and nucleosome stability
    Leonardo Mariño-Ramírez
    Computational Biology Branch, National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
    Expert Rev Proteomics 2:719-29. 2005
    ..The authors review recent findings on the structure of chromatin that confirm previous interparticle interactions observed in crystal structures...
  10. pmc The Histone Database: an integrated resource for histones and histone fold-containing proteins
    Leonardo Mariño-Ramírez
    Computational Biology Branch, National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, 8600 Rockville Pike, MSC 6075, Bethesda, MD 20894 6075, USA
    Database (Oxford) 2011:bar048. 2011
    ..The Histone Sequence Database is an inclusive resource for the analysis of chromatin structure and function focused on histones and histone fold-containing proteins...
  11. pmc Alignments anchored on genomic landmarks can aid in the identification of regulatory elements
    Kannan Tharakaraman
    Computational Biology Branch, National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health Building 38A, 8600 Rockville Pike, Bethesda, MD 20894 6075, USA
    Bioinformatics 21:i440-8. 2005
    ..However, since the positional anchors focus A-GLAM on the motif of interest, masking DNA repeats during Gibbs sampling becomes unnecessary...
  12. pmc Many sequence-specific chromatin modifying protein-binding motifs show strong positional preferences for potential regulatory regions in the Saccharomyces cerevisiae genome
    Loren Hansen
    Computational Biology Branch, National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, 8900 Rockville Pike, Bethesda, MD 20894, USA
    Nucleic Acids Res 38:1772-9. 2010
    ..Since many of these DNA-binding proteins have chromatin remodeling properties, they can alter the local nucleosome structure to a more permissive and/or restrictive state, thereby assisting in determining DNA-binding protein specificity...
  13. pmc Finding sequence motifs with Bayesian models incorporating positional information: an application to transcription factor binding sites
    Nak Kyeong Kim
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland 20894, USA
    BMC Bioinformatics 9:262. 2008
    ..Although some programs for identifying sequence motifs exploit positional information, most of them model it only implicitly and with ad hoc methods, making them unsuitable for general motif searches...
  14. pmc Identification of cis-regulatory elements in gene co-expression networks using A-GLAM
    Leonardo Mariño-Ramírez
    Computational Biology Branch, National Center for Biotechnology Information, National Institutes of Health, Bethesda, MD, USA
    Methods Mol Biol 541:1-22. 2009
    ..Using this approach, we analyze the cell-cycle co-expression network of the yeast Saccharomyces cerevisiae, showing that this approach correctly identifies cis-regulatory elements present in clusters of co-expressed genes...
  15. ncbi request reprint Conservation and coevolution in the scale-free human gene coexpression network
    I King Jordan
    National Center for Biotechnology Information, National Institutes of Health Bethesda, Maryland, USA
    Mol Biol Evol 21:2058-70. 2004
    ....
  16. pmc Global regulation by the yeast Spt10 protein is mediated through chromatin structure and the histone upstream activating sequence elements
    Peter R Eriksson
    Laboratory of Molecular Growth Regulation, National Instistute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892, USA
    Mol Cell Biol 25:9127-37. 2005
    ..No other high-affinity sites are predicted in the yeast genome. Thus, Spt10p is a sequence-specific activator of the histone genes, possessing a DNA-binding domain fused to a likely HAT domain...
  17. pmc The Histone Database: a comprehensive resource for histones and histone fold-containing proteins
    Leonardo Mariño-Ramírez
    Computational Biology Branch, National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland 20894 6075, USA
    Proteins 62:838-42. 2006
    ..The Histone Database is a comprehensive bioinformatics resource for the study of structure and function of histones and histone fold-containing proteins. The database is available at http://research.nhgri.nih.gov/histones/...
  18. pmc Differences in local genomic context of bound and unbound motifs
    Loren Hansen
    Computational Biology Branch, National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, 8900 Rockville Pike, Bethesda, MD 20894, USA
    Gene 506:125-34. 2012
    ..We concluded that there are multiple combinations of genomic features that characterize bound or unbound motifs...
  19. pmc Scanning sequences after Gibbs sampling to find multiple occurrences of functional elements
    Kannan Tharakaraman
    Computational Biology Branch, National Center for Biotechnology Information National Library of Medicine, National Institutes of Health, 8600 Rockville Pike, MSC 6075 Bethesda, MD 20894 6075, USA
    BMC Bioinformatics 7:408. 2006
    ..Many DNA regulatory elements occur as multiple instances within a target promoter. Gibbs sampling programs for finding DNA regulatory elements de novo can be prohibitively slow in locating all instances of such an element in a sequence set...
  20. pmc Statistical analysis of over-represented words in human promoter sequences
    Leonardo Mariño-Ramírez
    Computational Biology Branch, National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, 8600 Rockville Pike, MSC 6075 Bethesda, MD 20894 6075, USA
    Nucleic Acids Res 32:949-58. 2004
    ..These controls have important implications for evaluating over- and under-represented words with z-scores...
  21. pmc In silico identification and characterization of the ion transport specificity for P-type ATPases in the Mycobacterium tuberculosis complex
    Lorena Novoa-Aponte
    Chemistry Department, Faculty of Sciences, Universidad Nacional de Colombia, Bogota, Colombia, Carrera 30 45 03, Ciudad Universitaria, Bogota, Colombia
    BMC Struct Biol 12:25. 2012
    ..Currently, the distribution and function of these ion transporters in mycobacteria are poorly understood...
  22. pmc HMGN1 modulates nucleosome occupancy and DNase I hypersensitivity at the CpG island promoters of embryonic stem cells
    Tao Deng
    Protein Section, Laboratory of Metabolism, Center for Cancer Research, National Cancer Institute, Bethesda, Maryland, USA
    Mol Cell Biol 33:3377-89. 2013
    ..Thus, architectural chromatin-binding proteins affect the transcription profile and chromatin structure during embryonic stem cell differentiation. ..
  23. pmc The Physalis peruviana leaf transcriptome: assembly, annotation and gene model prediction
    Gina A Garzón-Martínez
    Plant Molecular Genetics Laboratory, Center of Biotechnology and Bioindustry CBB, Colombian Corporation for Agricultural Research CORPOICA, Bogota, Colombia
    BMC Genomics 13:151. 2012
    ..A broad range of genomic tools is available for other Solanaceae, including tomato and potato. However, limited genomic resources are currently available for Cape gooseberry...
  24. pmc Promoter analysis: gene regulatory motif identification with A-GLAM
    Leonardo Mariño-Ramírez
    Computational Biology Branch, National Center for Biotechnology Information, National Library of Medicine, NIH, Bethesda, MD, USA
    Methods Mol Biol 537:263-76. 2009
    ..Here we present a survey of recent computational methods for eukaryotic promoter analysis and describe the use of an alignment-based method implemented in the A-GLAM program...
  25. pmc Expression patterns of protein kinases correlate with gene architecture and evolutionary rates
    Aleksey Y Ogurtsov
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland, USA
    PLoS ONE 3:e3599. 2008
    ..They encode regulatory enzymes that control a vast variety of cellular processes through phosphorylation of their protein substrates. Expression of PK genes is subject to complex transcriptional regulation which is not fully understood...
  26. pmc Evolutionary significance of gene expression divergence
    I King Jordan
    National Center for Biotechnology Information, National Institutes of Health 8600 Rockville Pike, Bldg 38A Room 5N511 M, Bethesda, MD 20894, USA
    Gene 345:119-26. 2005
    ..Taken together, these results indicate that gene expression divergence is subject to the effects of purifying selective constraint and suggest that it might also be substantially influenced by positive Darwinian selection...
  27. pmc Widespread positive selection in synonymous sites of mammalian genes
    Alissa M Resch
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA
    Mol Biol Evol 24:1821-31. 2007
    ..Positive selection at synonymous sites might act through mRNA destabilization affecting mRNA levels and translation...
  28. pmc The practical evaluation of DNA barcode efficacy
    John L Spouge
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA
    Methods Mol Biol 858:365-77. 2012
    ..This chapter states explicitly how to calculate PCI, how to estimate its statistical sampling error, and how to use data on PCR failure to set limits on how much improvements in PCR technology can improve species identification...
  29. pmc Virulence and immune response induced by Mycobacterium avium complex strains in a model of progressive pulmonary tuberculosis and subcutaneous infection in BALB/c mice
    Mónica González-Pérez
    Department of Microbiology, Medicine School, National University of Colombia, Bogota, Colombia
    Infect Immun 81:4001-12. 2013
    ..Thus, MAC infection evokes different immune and inflammatory responses depending on the MAC species and affected tissue. ..
  30. ncbi request reprint Searching for repeats, as an example of using the generalised Ruzzo-Tompa algorithm to find optimal subsequences with gaps
    John L Spouge
    Computational Biology Branch, National Center for Biotechnology Information, Bethesda, MD 20894, USA
    Int J Bioinform Res Appl 10:384-408. 2014
    ..With minimal programming effort, the generalised Ruzzo-Tompa algorithm could improve the performance of many programs for finding biological subsequences of unusual composition. ..
  31. pmc Genome sequence of the Mycobacterium colombiense type strain, CECT 3035
    Mónica González-Pérez
    Departamento de Microbiologia, Facultad de Medicina, Universidad Nacional de Colombia, Bogota, Colombia
    J Bacteriol 193:5866-7. 2011
    ..Preliminary comparative analyses indicate that the M. colombiense lineage has experienced a substantial genome expansion, possibly contributing to its distinct pathogenic capacity...