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1

HistoneDB 2.0: a histone database with variants—an integrated resource to explore histones and their variants

Draizen, Eli J., Shaytan, Alexey K., Mariño-Ramírez, Leonardo, Talbert, Paul B., Landsman, David, Panchenko, Anna R.

Journal:

Year:

2016

Language:

english

File:

PDF, 1015 KB

english, 2016

2

Epigenetic histone modifications of human transposable elements: genome defense versus exaptation

Ahsan Huda, Leonardo Mariño-Ramírez, I King Jordan

Journal:

Year:

2010

Language:

english

File:

PDF, 929 KB

english, 2010

3

The histone database: A comprehensive resource for histones and histone fold-containing proteins

Leonardo Mariño-Ramírez, Benjamin Hsu, Andreas D. Baxevanis, David Landsman

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

2006

Language:

english

File:

PDF, 415 KB

english, 2006

4

Isolation and mapping of self-assembling protein domains encoded by the Saccharomyces cerevisiae genome using λ repressor fusions

Leonardo Mariño-Ramírez, James C. Hu

Journal:

Year:

2002

Language:

english

File:

PDF, 181 KB

english, 2002

5

Scanning sequences after Gibbs sampling to find multiple occurrences of functional elements

Kannan Tharakaraman, Leonardo Mariño-Ramírez, Sergey L Sheetlin, David Landsman, John L Spouge

Journal:

BMC Bioinformatics

Year:

2006

Language:

english

File:

PDF, 559 KB

english, 2006

6

Finding sequence motifs with Bayesian models incorporating positional information: an application to transcription factor binding sites

Nak-Kyeong Kim, Kannan Tharakaraman, Leonardo Mariño-Ramírez, John L Spouge

Journal:

BMC Bioinformatics

Year:

2008

Language:

english

File:

PDF, 344 KB

english, 2008

7

Global similarity and local divergence in human and mouse gene co-expression networks

Panayiotis Tsaparas, Leonardo Mariño-Ramírez, Olivier Bodenreider, Eugene V Koonin, I King Jordan

Journal:

BMC Evolutionary Biology

Year:

2006

Language:

english

File:

PDF, 1.56 MB

english, 2006

8

Evolutionary rates and patterns for human transcription factor binding sites derived from repetitive DNA

Nalini Polavarapu, Leonardo Mariño-Ramírez, David Landsman, John F McDonald, I King Jordan

Journal:

Year:

2008

Language:

english

File:

PDF, 547 KB

english, 2008

9

Evolutionary significance of gene expression divergence

I. King Jordan, Leonardo Mariño-Ramírez, Eugene V. Koonin

Journal:

Year:

2005

Language:

english

File:

PDF, 428 KB

english, 2005

10

Repetitive DNA elements, nucleosome binding and human gene expression

Ahsan Huda, Leonardo Mariño-Ramírez, David Landsman, I. King Jordan

Journal:

Year:

2009

Language:

english

File:

PDF, 1.28 MB

english, 2009

11

Differences in local genomic context of bound and unbound motifs

Loren Hansen, Leonardo Mariño-Ramírez, David Landsman

Journal:

Year:

2012

Language:

english

File:

PDF, 1.02 MB

english, 2012

12

ThePhysalis peruvianaleaf transcriptome: assembly, annotation and gene model prediction

Garzón-Martínez, Gina A, Zhu, Z, Landsman, David, Barrero, Luz S, Mariño-Ramírez, Leonardo

Journal:

Year:

2012

Language:

english

File:

PDF, 630 KB

english, 2012

13

Transposable element derived DNaseI-hypersensitive sites in the human genome

Leonardo Mariño-Ramírez, I King Jordan

Journal:

Year:

2006

Language:

english

File:

PDF, 727 KB

english, 2006

14

Multiple independent evolutionary solutions to core histone gene regulation

Leonardo Mariño-Ramírez, I King Jordan, David Landsman

Journal:

Year:

2006

Language:

english

File:

PDF, 2.85 MB

english, 2006

15

Mammalian-wide interspersed repeat (MIR)-derived enhancers and the regulation of human gene expression

Jjingo, Daudi, Conley, Andrew B, Wang, Jianrong, Mariño-Ramírez, Leonardo, Lunyak, Victoria V, Jordan, I

Journal:

Year:

2014

Language:

english

File:

PDF, 679 KB

english, 2014

16

[IEEE 2012 IEEE 2nd International Conference on Computational Advances in Bio and Medical Sciences (ICCABS) - Las Vegas, NV, USA (2012.02.23-2012.02.25)] 2012 IEEE 2nd International Conference on Computational Advances in Bio and medical Sciences (ICCABS) - The ruzzo-tompa algorithm can find the maximal paths in weighted, directed graphs on a one-dimensional lattice

Spouge, John L., Marino-Ramirez, Leonardo, Sheetlin, Sergey L.

Year:

2012

Language:

english

File:

PDF, 380 KB

english, 2012

17

A c-Myc regulatory subnetwork from human transposable element sequences

Wang, Jianrong, Bowen, Nathan J., Mariño-Ramírez, Leonardo, Jordan, I. King

Journal:

Molecular BioSystems

Year:

2009

Language:

english

File:

PDF, 2.19 MB

english, 2009

18

Histone structure and nucleosome stability

Mariño-Ramírez, Leonardo, Kann, Maricel G, Shoemaker, Benjamin A, Landsman, David

Journal:

Expert Review of Proteomics

Year:

2005

Language:

english

File:

PDF, 217 KB

english, 2005

19

CisMiner: Genome-Wide In-Silico Cis-Regulatory Module Prediction by Fuzzy Itemset Mining

Navarro, Carmen, Lopez, Francisco J., Cano, Carlos, Garcia-Alcalde, Fernando, Blanco, Armando, Mariño-Ramírez, Leonardo

Journal:

Year:

2014

Language:

english

File:

PDF, 802 KB

english, 2014

20

Identification and Comparative Analysis of ncRNAs in Human, Mouse and Zebrafish Indicate a Conserved Role in Regulation of Genes Expressed in Brain

Qu, Zhipeng, Adelson, David L., Mariño-Ramírez, Leonardo

Journal:

Year:

2012

Language:

english

File:

PDF, 850 KB

english, 2012

21

Genome Sequences of Multidrug-Resistant Salmonella enterica Serovar Paratyphi B (dT+) and Heidelberg Strains from the Colombian Poultry Chain: TABLE 1

Donado-Godoy, Pilar, Bernal, Johan F., Rodríguez, Fernando, Gomez, Yolanda, Agarwala, Richa, Landsman, David, Mariño-Ramírez, Leonardo

Journal:

Genome Announcements

Year:

2015

Language:

english

File:

PDF, 172 KB

english, 2015

22

Genome Sequence of the Banana Plant Growth-Promoting Rhizobacterium Bacillus amyloliquefaciens BS006

Gamez, Rocío M., Rodríguez, Fernando, Bernal, Johan F., Agarwala, Richa, Landsman, David, Mariño-Ramírez, Leonardo

Journal:

Genome Announcements

Year:

2015

Language:

english

File:

PDF, 167 KB

english, 2015

23

Genetic diversity and population structure in Physalis peruviana and related taxa based on InDels and SNPs derived from COSII and IRG markers

Garzón-Martínez, Gina A., Osorio-Guarín, Jaime A., Delgadillo-Durán, Paola, Mayorga, Franklin, Enciso-Rodríguez, Felix E., Landsman, David, Mariño-Ramírez, Leonardo, Barrero, Luz Stella

Journal:

Year:

2015

Language:

english

File:

PDF, 861 KB

english, 2015

24

Whole-Genome Sequences of Two Campylobacter coli Isolates from the Antimicrobial Resistance Monitoring Program in Colombia: TABLE 1

Bernal, Johan F., Donado-Godoy, Pilar, Valencia, María Fernanda, León, Maribel, Gómez, Yolanda, Rodríguez, Fernando, Agarwala, Richa, Landsman, David, Mariño-Ramírez, Leonardo

Journal:

Genome Announcements

Year:

2016

Language:

english

File:

PDF, 166 KB

english, 2016

25

Genome Sequence of the Banana Plant Growth-Promoting Rhizobacterium Pseudomonas fluorescens PS006

Gamez, Rocío M., Rodríguez, Fernando, Ramírez, Sandra, Gómez, Yolanda, Agarwala, Richa, Landsman, David, Mariño-Ramírez, Leonardo

Journal:

Genome Announcements

Year:

2016

Language:

english

File:

PDF, 156 KB

english, 2016

26

Benchmarking computational tools for polymorphic transposable element detection

Rishishwar, Lavanya, Mariño-Ramírez, Leonardo, Jordan, I. King

Journal:

Briefings in Bioinformatics

Year:

2016

Language:

english

File:

PDF, 844 KB

english, 2016

27

Whole-Genome Sequences of 26 Vibrio cholerae Isolates

Watve, Samit S., Chande, Aroon T., Rishishwar, Lavanya, Mariño-Ramírez, Leonardo, Jordan, I. King, Hammer, Brian K.

Journal:

Genome Announcements

Year:

2016

Language:

english

File:

PDF, 168 KB

english, 2016

28

Human population-specific gene expression and transcriptional network modification with polymorphic transposable elements

Wang, Lu, Rishishwar, Lavanya, Mariño-Ramírez, Leonardo, Jordan, I. King

Journal:

Nucleic Acids Research

Year:

2016

Language:

english

File:

PDF, 5.56 MB

english, 2016

29

Population and clinical genetics of human transposable elements in the (post) genomic era

Rishishwar, Lavanya, Wang, Lu, Clayton, Evan A., Mariño-Ramírez, Leonardo, McDonald, John F., Jordan, I. King

Journal:

Mobile Genetic Elements

Year:

2017

Language:

english

File:

PDF, 1.01 MB

english, 2017

30

Complete mitochondrial genome of the nesting Colombian Caribbean Hawksbill Turtle

Hernández-Fernández, Javier, Beltrán-Torres, Gerson, Mariño-Ramírez, Leonardo

Journal:

Mitochondrial DNA Part B

Year:

2017

Language:

english

File:

PDF, 860 KB

english, 2017

31

De novo transcriptome assembly of loggerhead sea turtle nesting of the Colombian Caribbean

Hernández-Fernández, Javier, Pinzón, Andrés, Mariño-Ramírez, Leonardo

Journal:

Year:

2017

Language:

english

File:

PDF, 157 KB

english, 2017

32

Most of the tight positional conservation of transcription factor binding sites near the transcription start site reflects their co-localization within regulatory modules

Natalia Acevedo-Luna,Leonardo Mariño-Ramírez,Armand Halbert…

Journal:

BMC Bioinformatics

Year:

2016

Language:

english

File:

PDF, 1.29 MB

english, 2016

33

Workflow and web application for annotating NCBI BioProject transcriptome data

Vera Alvarez, Roberto, Medeiros Vidal, Newton, Garzón-Martínez, Gina A., Barrero, Luz S., Landsman, David, Mariño-Ramírez, Leonardo

Journal:

Year:

2017

Language:

english

File:

PDF, 1.46 MB

english, 2017

34

A Comparative Analysis of Genetic Ancestry and Admixture in the Colombian Populations of Chocó and Medellín

Conley, Andrew B., Rishishwar, Lavanya, Norris, Emily T., Valderrama-Aguirre, Augusto, Mariño-Ramírez, Leonardo, Medina-Rivas, Miguel A., Jordan, I. King

Journal:

G3 Genes|Genome|Genetics

Year:

2017

Language:

english

File:

PDF, 3.42 MB

english, 2017

35

Co-Evolutionary Rates of Functionally Related Yeast Genes

Mariño-Ramírez, Leonardo, Bodenreider, Olivier, Kantz, Natalie, Jordan, I. King

Journal:

Evolutionary Bioinformatics

Year:

2006

Language:

english

File:

PDF, 430 KB

english, 2006

36

Genome Sequences of 15 Klebsiella sp. Isolates from Sugarcane Fields in Colombia’s Cauca Valley

Medina-Cordoba, Luz K., Chande, Aroon T., Rishishwar, Lavanya, Mayer, Leonard W., Mariño-Ramírez, Leonardo, Valderrama-Aguirre, Lina C., Valderrama-Aguirre, Augusto, Kostka, Joel E., Jordan, I. King

Journal:

Genome Announcements

Year:

2018

Language:

english

File:

PDF, 143 KB

english, 2018

37

Spatial Proximity and Similarity of the Epigenetic State of Genome Domains

Khrameeva, Ekaterina E., Mironov, Andrey A., Fedonin, Gennady G., Khaitovich, Philipp, Gelfand, Mikhail S., Mariño-Ramírez, Leonardo

Journal:

Year:

2012

Language:

english

File:

PDF, 681 KB

english, 2012

38

Expression Patterns of Protein Kinases Correlate with Gene Architecture and Evolutionary Rates

Ogurtsov, Aleksey Y., Mariño-Ramírez, Leonardo, Johnson, Gibbes R., Landsman, David, Shabalina, Svetlana A., Spiridonov, Nikolay A., Hannenhalli, Sridhar

Journal:

Year:

2008

Language:

english

File:

PDF, 843 KB

english, 2008

39

Genomic Organization of H2Av Containing Nucleosomes in Drosophila Heterochromatin

Zhang, Zhenhai, Pugh, B. Franklin, Mariño-Ramírez, Leonardo

Journal:

Year:

2011

Language:

english

File:

PDF, 813 KB

english, 2011

40

Prediction of Transposable Element Derived Enhancers Using Chromatin Modification Profiles

Huda, Ahsan, Tyagi, Eishita, Mariño-Ramírez, Leonardo, Bowen, Nathan J., Jjingo, Daudi, Jordan, I. King, Dalal, Yamini

Journal:

Year:

2011

Language:

english

File:

PDF, 1.91 MB

english, 2011

41

Improving Transmission Efficiency of Large Sequence Alignment/Map (SAM) Files

Sakib, Muhammad Nazmus, Tang, Jijun, Zheng, W. Jim, Huang, Chin-Tser, Mariño-Ramírez, Leonardo

Journal:

Year:

2011

Language:

english

File:

PDF, 207 KB

english, 2011

42

Gentle Masking of Low-Complexity Sequences Improves Homology Search

Frith, Martin C., Mariño-Ramírez, Leonardo

Journal:

Year:

2011

Language:

english

File:

PDF, 701 KB

english, 2011

43

Transcriptional Regulation of N-Acetylglutamate Synthase

Heibel, Sandra Kirsch, Lopez, Giselle Yvette, Panglao, Maria, Sodha, Sonal, Mariño-Ramírez, Leonardo, Tuchman, Mendel, Caldovic, Ljubica, Cheriyath, Venugopalan

Journal:

Year:

2012

Language:

english

File:

PDF, 1.89 MB

english, 2012

44

Analysis of Biological Features Associated with Meiotic Recombination Hot and Cold Spots in Saccharomyces cerevisiae

Hansen, Loren, Kim, Nak-Kyeong, Mariño-Ramírez, Leonardo, Landsman, David, Jordan, I. King

Journal:

Year:

2011

Language:

english

File:

PDF, 746 KB

english, 2011

45

Reduced Polymorphism in Domains Involved in Protein-Protein Interactions

Itzhaki, Zohar, Margalit, Hanah, Mariño-Ramírez, Leonardo

Journal:

Year:

2012

Language:

english

File:

PDF, 453 KB

english, 2012

46

Bivalent-Like Chromatin Markers Are Predictive for Transcription Start Site Distribution in Human

Zhang, Zhihua, Ma, Xiaotu, Zhang, Michael Q., Mariño-Ramírez, Leonardo

Journal:

Year:

2012

Language:

english

File:

PDF, 440 KB

english, 2012

47

A Global Genome Segmentation Method for Exploration of Epigenetic Patterns

Steiner, Lydia, Hopp, Lydia, Wirth, Henry, Galle, Jörg, Binder, Hans, Prohaska, Sonja J., Rohlf, Thimo, Mariño-Ramírez, Leonardo

Journal:

Year:

2012

Language:

english

File:

PDF, 1003 KB

english, 2012

48

Next Generation Sequencing Based Transcriptome Analysis of Septic-Injury Responsive Genes in the Beetle Tribolium castaneum

Altincicek, Boran, Elashry, Abdelnaser, Guz, Nurper, Grundler, Florian M. W., Vilcinskas, Andreas, Dehne, Heinz-Wilhelm, Mariño-Ramírez, Leonardo

Journal:

Year:

2013

Language:

english

File:

PDF, 360 KB

english, 2013

49

Chromatin Accessibility Data Sets Show Bias Due to Sequence Specificity of the DNase I Enzyme

Koohy, Hashem, Down, Thomas A., Hubbard, Tim J., Mariño-Ramírez, Leonardo

Journal:

Year:

2013

Language:

english

File:

PDF, 1.06 MB

english, 2013

50

Unique and Conserved MicroRNAs in Wheat Chromosome 5D Revealed by Next-Generation Sequencing

Kurtoglu, Kuaybe Yucebilgili, Kantar, Melda, Lucas, Stuart J., Budak, Hikmet, Mariño-Ramírez, Leonardo

Journal:

Year:

2013

Language:

english

File:

PDF, 1.08 MB

english, 2013

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