Publications
We encourage our members to use the PABI affiliation as shown below in their publications whenever possible:
"PanAmerican Bioinformatics Institute, Santa Marta, Magdalena, Colombia"
Here is a list of publications that show the PABI affiliation:
2016
Medina Rivas, M.A., Norris, E.T., Rishishwar, L., Conley, A.B., Medrano Trochez, C., Valderrama-Aguirre, A., Vannberg, F.O., Mariño-Ramírez, L., and Jordan, I.K., 2016. El Chocó Colombia: a hotspot of human biodiversity.
Rev. Biodivers. Neotrop. in press
2015
Rishishwar, L., Tellez Villa, C.E. and Jordan, I.K., 2015. Transposable element polymorphisms recapitulate human evolution.
Mob. DNA. 6: 21
Rishishwar, L., Conley, A.B., Vidakovic, B. and Jordan, I.K., 2015. A combined evidence Bayesian method for human ancestry inference applied to Afro-Colombians.
Gene. S0378-1119(15)00983-X [Epub ahead of print]
Niu, P., Smagul, A., Wang, L., Sadvakas, A., Sha, Y., Pérez, L.M., Nussupbekova, A., Amirbekov, A., Akanov, A.A., Gálvez, B.G., Jordan, I.K. and Lunyak, V., 2015. Transcriptional profiling of interleukin-2-primed human adipose derived mesenchymal stem cells revealed dramatic changes in stem cells response imposed by replicative senescence.
Oncotarget. 6: 17938-17957 [Epub ahead of print]
Wang, J., Vicente-García, C., Seruggia, D., Moltó, E., Fernandez-Miñán, A., Neto, A., Lee, E., Gómez-Skarmeta, J.L., Montoliu, L., Lunyak, V. and Jordan, I.K., 2015. MIR retotransposon sequences provide insulators to the human genome.
Proc. Natl. Acad. Sci. USA. 112: E4428-4437. [Epub ahead of print]
Rishishwar, L., Conley, A.B., Wigington, C.H., Wang, L., Valderrama-Aguirre, A. and Jordan, I.K., 2015. Ancestry, admixture and selection in Colombian genomes.
Sci. Rep. 5: 12376
2014
Gladney, L.M., Katz, L., Knipe, K.M., Rowe, L., Conley, A.B., Rishishwar, L., Mariño-Ramírez, L., Jordan, I.K., and Tarr, C.L., 2014. Genome Sequences of Vibrio navarrensis, a Potential Human Pathogen.
Genome Announcements. 2: e01188-14
Castillo, A., Wang, L., Koriyama, C., Eizuru, Y., Jordan, I.K., and Akiba, S., 2014. A systems biology analysis of the changes in gene expression via silencing of HPV-18 E1 expression in HeLa cells.
Open Biol. 4: 130119
Jjingo, D., Conley, A.B., Wang, J., Mariño-Ramírez, L., Lunyak, V.V., and Jordan, I.K., 2014. Mammalian-wide interspersed repeat (MIR)-derived enhancers and the regulation of human gene expression.
Mob DNA. 5: 14
Dunn, J., Qiu, H., Kim, S., Jjingo, D., Hoffman, R., Kim, C.W., Jang, I., Son, D.J., Kim, D., Pan, C., Fan, Y., Jordan, I.K., and Jo, H., 2014. Flow-dependent epigenetic DNA methylation regulates endothelial gene expression and atherosclerosis.
J Clin Invest. 124: 3187-3199
Hu, B., Ying, X., Wang, J., Piriyapongsa, J., Jordan, I.K., Sheng, J., Yu, F., Zhao, P., Li, Y., Wang, H., Ng, W.L., Hu, S., Wang, X., Wang, C., Zheng, X., Li, W., Curran, W.J., and Wang, Y., 2014. Identification of a tumor suppressive human specific microRNA within the FHIT tumor suppressor gene.
Cancer Res. 74: 2283-94
Rishishwar, L., Petit, R., Kraft, C.S., and Jordan, I.K., 2014. A genome sequence based discriminator for vancomycin-intermediate Staphylococcus aureus.
J Bacteriol. 196: 940-948
2013
Enciso-Rodríguez, F.E., González, C., Rodríguez, E.A., López, C.E., Landsman, D., Barrero, L.S., Mariño-Ramírez, L., 2013. Identification of Immunity Related Genes to Study the Physalis peruviana–Fusarium oxysporum Pathosystem.
PloS One. 8: e68500.
Lopes, F.R., Jjingo, D., da Silva, C.R.M., Andrade, A.C., Marraccini, P., Teixeira, J.B., Carazzolle, M.F., Pereira, G.A.G., Pereira, L.P.F., Vanzela, A.L.L., Wang, L., Jordan, I.K., and Carareto, C.M.A., 2013. Transcriptional activity, chromosomal distribution and expression effects of transposable elements in Coffea genomes.
PLoS ONE 8: e78931
Jjingo, D., Wang, J., Conley, A.B., Lunyak, V.V., and Jordan, I.K, 2013. Compound cis-regulatory elements with both boundary and enhancer sequences in the human genome.
Bioinformatics 29: 3109-3112
Zhoa, Y., Jordan, I.K. and Lunyak, V.V., 2013. Epigenetics components of aging in the central nervous system.
Neurotherapeutics 10: 647-663
Sebastian, A., Rishishwar, L., Wang, J., Bernard, K.F., Conley, A.B., McCarty, N.A. and Jordan, I.K., 2013. Origin and evolution of the cystic fibrosis transmembrane regulator protein R domain.
Gene 523: 137-146
Tobar-Tosse, F., Rodríguez, A.C., Vélez, P.E., Zambrano, M.M., Moreno, P.A., 2013. Exploration of Noncoding Sequences in Metagenomes.
PLoS ONE. 8: e59488.
Wang, J., Jordan, I.K., Lunyak, V.V., 2013. BroadPeak: a novel algorithm for identifying broad peaks in diffuse ChIP-seq datasets.
Bioinformatics. 29: 492-3
2012
Conley, A.B. and Jordan, I.K., 2012. Cell type-specific termination of transcription by transposable element sequences.
Mob DNA. 3: 15
Wang, J., Lunyak, V.V., Jordan, I.K., 2012. Chromatin signature discovery via histone modification profile alignments.
Nucleic Acids Res. 40: 10642-56
Rishishwar, L., Katz, L.S., Sharma, N.V., Rowe, L., Frace, M., Dolan Thomas,J., Harcourt, B.H., Mayer, L.W., and Jordan, I.K., 2012. Genomic Basis of a Polyagglutinating Isolate of Neisseria meningitidis.
J. Bacteriol. 194: 5649-5656
Rishishwar, L., Varghese, N., Tyagi, E., Harvey, S.C., Jordan, I.K., McCarty, N.A., 2012. Relating the Disease Mutation Spectrum to the Evolution of the Cystic Fibrosis Transmembrane Conductance Regulator (CFTR).
PLoS ONE. 7: e42336
Kostka, J.E., Green, S.J., Rishishwar, L., Prakash, O., Katz, L.S., Marino-Ramirez, L., Jordan, I.K., Watson, D.B., Brown, S.D., Palumbo, A.V., Brooks, S.C., 2012. Genome sequences for six Rhodanobacter strains isolated from soils and the terrestrial subsurface with variable denitrification capabilities.
J. Bacteriol. 194: 4461
Hansen, L., Mariño-Ramírez, L., Landsman, D., 2012. Differences in local genomic context of bound and unbound motifs. Gene. (In Press)
Jjingo, D., Conley, A.B., Yi, S.V., Lunyak, V.V., Jordan, I.K., 2012. On the presence and role of human gene-body DNA methylation.
Oncotarget. 3: 462-74
Lee, K.J., Conley, A.B., Lunyak, V.V., and I.K. Jordan, 2012. Do human transposable element small RNAs serve primarily as genome defenders or genome regulators?
Mob Genet Elements. 2: 1–7
Blackwell, B., Lopez M.F., Wang, J., Krastins, B., Sarracino, D., Tollervey, J.R., Dobke, M.,I.K. Jordan and Lunyak, V.V., 2012. Protein interactions with piALU RNA indicates putative participation of retroRNA in the cell cycle, DNA repair and chromatin assembly
Mob Genet Elements. 2: 1–10
Conley, A.B. and I.K. Jordan, 2012. Epigenetic regulation of human cis-natural antisense transcripts.
Nucleic Acids Res. 40: 1438–1445
Wang, J., Lunyak, V.V., and I.K. Jordan, 2012. Genome-wide prediction and analysis of human chromatin boundary elements.
Nucleic Acids Res. 40: 511-529
Garzón-Martínez, G.A., Zhu, I., Landsman, D., Barrero, L.S., Marino-Ramirez L., 2012. The Physalis peruviana leaf transcriptome: assembly, annotation and gene model prediction. BMC Genomics. 13:151.
2011
Hansen, L., Kim, N.K., Mariño-Ramírez, L., Landsman, D., 2011. Analysis of biological features associated with meiotic recombination hot and cold spots in Saccharomyces cerevisiae. PLoS One. 6:e29711.
Simbaqueba, J., Sánchez, P., Sanchez, E., Núñez Zarantes, V.M., Chacon, M.I., Barrero, L.S., Mariño-Ramírez, L., 2011. Development and characterization of microsatellite markers for the Cape gooseberry Physalis peruviana. PLoS One. 6:e26719
Huda, A., Tyagi, E., Mariño-Ramírez, L., Bowen, N.J., Jjingo. D. and I.K. Jordan, 2011. Prediction of transposable element derived enhancers using chromatin modification profiles.
PLoS ONE 6: e27513
Katz, L.S., Humphrey, J.C., Conley, A.B., Nelakuditi, V., Kislyuk, A.O., Agrawal, S., Jayaraman, P., Harcourt, B.H., Olsen- Rasmussen, M.A., Frace, M., Sharma, N.V., Mayer, L.W., and I.K. Jordan, 2011. Neisseria Base: a comparative genomics database for Neisseria meningitidis.
Database 2011: bar 035
González Pérez, M., Murcia, M., Landsman, D., Jordan, I. K., and L. Mariño-Ramírez, 2011. The genome sequence of Mycobacterium colombiense CECT 3035 type strain.
J Bacteriol. 193: 5866–5867
Jordan, I. K., Conley, A., Antonov, I., Arthur, R., Cook, E., Cooper, G., Jones, B., Knipe, K., Lee, K., Liu, X., Mitchell, G., Pande, P., Petit, R., Qin, S., Rajan, V., Sarda, S., Sebastian, A., Tang, S., Thapliyal, R., Varghese, N., Ye, T., Katz, L. S., Wang, X., Rowe, L., Frace, M. and L. Mayer, 2011. Genome sequences for five strains of the emerging pathogen Haemophilus haemolyticus.
J Bacteriol. 193: 5879–5880
Katz, L.S., Sharma, N.V., Harcourt, B.H., Thomas, J.D., Wang, X., Mayer L.W., I.K. Jordan, 2011. Using single-nucleotide polymorphisms to discriminate disease-associated from carried genomes of Neisseria meningitidis.
J Bacteriol. 193: 3633-3641
Jjingo, D., Huda, A., Gundapuneni, M., Mariño-Ramírez, L. and I.K. Jordan, 2011. Effect of the transposable element environment of human genes on gene length and expression.
Genome Biol. Evol. 3: 259-271