Publications

Research outputs from the Jordan Lab

PubMed Google Scholar

2026

Pathways, outputs and impact of NIH-supported bioinformatics and genomics graduate trainees in Africa.
Jjingo D, Walakira A, Hashim S, Cheickna C, Galiwango R, Kibet C, Kivunike FN, Mboowa G, Kakembo FE, Ayodele B, Entfellner JD, de Villiers S, Wambui K, Fatumo S, Chikowore T, Mukisa J, Ssekagiri A, Bbosa N, Mulindwa J, Kyobe S, Nsubuga M, Kebirungi G, Katagirya E, Mwesigwa S, Lujumba I, Kamulegeya R, Kirimunda S, Kanyerezi S, Kiyaga S, Sserwadda I, Kiberu D, Bagaya BS, Okwir J, Nabisubi P, Nabakooza G, Atwine MT, Sserunjogi R, Julius R, Quiñones M, McCarthy M, Cruz P, Noble K, Whalen CJ, Hurt D, Giovanni MY, Tartakovsky M, Ssemwanga D, Kitayimbwa JM, Reynolds SJ, Whalen CC, Kambugu A, Hanchard NA, Jian L, Amoako-Yirenkyi P, Mardon G, Jordan IK, Salifu SP, Wele M, Adebiyi E, Shaffer JG, Doumbia S, Kateete DP, Skelton M, Mulder N, Kayondo JK, Masiga D; H3Africa Consortium. 2026
Brief Bioinform. 27(1):bbag046
[PubMed] [Google Scholar]
Sex differences in molecular pathways underlying cardiovascular health in Black Americans.
Blankson HN, Delmer C, Verma R, Guven E, Rooney K, Pearson A, Baltrus P, Quyumi AA, Pemu P, Jordan IK, Herman T, Meller R, Searles CD. 2026
Res Sq [Preprint]. rs.3.rs-8391154
[PubMed] [Google Scholar]

2025

Comparative Genomic and Microenvironmental Profiles of Hereditary and Sporadic TNBC in Colombian Women.
Zambrano-Ordoñez YT, Mejía-Garcia A, Ramírez-Mejía JM, Tsao HM, Morales-Suárez PD, Rey-Vargas L, Montero-Ovalle WJ, Huertas-Caro CA, Lopez-Correa P, Riaño-Moreno JC, Rodriguez JL, Sanabria-Salas MC, Carvajal-Carmona LG, Jordan IK, Serrano-Gomez SJ, Lopez-Kleine L, Orozco CA. 2025
Biology (Basel). 14(12):1706
[PubMed] [Google Scholar]
Pastrami: a fast and efficient algorithm for fine-scale genetic ancestry inference.
Conley AB, Rishishwar L, Sharma S, Norris ET, Jordan IK, Mariño-Ramírez L. 2025
NAR Genom Bioinform. 7(4):lqaf184
[PubMed] [Google Scholar]
The Consortium for Genomic Diversity, Ancestry, and Health in Colombia (CÓDIGO): building local capacity in genomics and bioinformatics.
Mariño-Ramírez L, Sharma S, Hamilton JM, Nguyen TL, Gupta S, Natarajan AV, Nagar SD, Menuey JL, Chen WA, Sánchez-Gómez A, Satizábal-Soto JM, Martínez B, Marrugo J, Medina-Rivas MA, Gallo JE, Jordan IK, Valderrama-Aguirre A. 2025
Commun Biol. 8(1):1062
[PubMed] [Google Scholar]
African ancestry-enriched variants in the GATM gene are associated with elevated serum creatinine levels.
Sharma S, Astore CA, Mariño-Ramírez L, Jordan IK. 2025
medRxiv [Preprint]. 2025.03.07.25323581
[PubMed] [Google Scholar]
Genetic ancestry and population structure in the All of Us Research Program cohort.
Sharma S, Nagar SD, Pemu P, Zuchner S; SEEC Consortium; Mariño-Ramírez L, Meller R, Jordan IK. 2025
Nat Commun. 16(1):4123
[PubMed] [Google Scholar]
Associations of perceived discrimination with health outcomes and health disparities in the All of Us cohort.
Lam V, Gupta S, Jordan IK, Mariño-Ramírez L. 2025
J Am Med Inform Assoc. 32(5):823-834
[PubMed] [Google Scholar]
Explainable machine learning for health disparities: type 2 diabetes in the All of Us research program.
Kambara MS, Chukka O, Choi KJ, Tsenum J, Gupta S, English NJ, Jordan IK, Mariño-Ramírez L. 2025
bioRxiv [Preprint]. 2025.02.18.638789
[PubMed] [Google Scholar]

2024

Inference of genetic ancestry from a multi-gene cancer panel in Colombian women with cancer.
Zambrano-O, Y. T., Mejía-Garcia, A., Morales, P. D., Tsao, H. M., Rey-Vargas, L., Montero-Ovalle, W., Huertas-Caro, C. A., Sanabria-Salas, M. C., Riaño-Moreno, J., Rodriguez, J. L., Orozco, C. A., Lopez-Kleine, L., Jordan, I. K., & Serrano-G, S. J. 2024
Breast Cancer Res Treat
[PubMed] [Google Scholar]
Ancestral origins of TYR and OCA2 gene mutations in oculocutaneous albinism from two admixed populations in Colombia.
Cárdenas, W. A., Conley, A. B., Nagar, S. D., Núñez-Ríos, D. L., Jordan, I. K., & Lattig, M. C. 2024
PLoS One 19:e0313777
[PubMed] [Google Scholar]
Unveiling ancestral threads: Exploring CCR5 ∆32 mutation frequencies in Colombian populations for HIV/AIDS therapeutics.
Barrios-Navas, A., Nguyen, T. L., Gallo, J. E., Mariño-Ramírez, L., Soto, J. M. S., Sánchez, A., Jordan, I. K., & Valderrama-Aguirre, A. 2024
Infect Genet Evol 125:105680
[PubMed] [Google Scholar]
Landscape of racial and ethnic health disparities in the All of Us Research Program.
Lam, V., Sharma, S., Spouge, J. L., Jordan, I. K., & Mariño-Ramírez, L. 2024
Database (Oxford) 2024:baae082
[PubMed] [Google Scholar]
Genomic data in the All of Us Research Program Nature 627:340-346.
All of Us Research Program Genomics Investigators. 2024
[PubMed] [Google Scholar]
HIVseqDB: a portable resource for NGS and sample metadata integration for HIV-1 drug resistance analysis.
Ssekagiri, A., Jjingo, D., Bbosa, N., Bugembe, D. L., Kateete, D. P., Jordan, I. K., Kaleebu, P., & Ssemwanga, D. 2024
Bioinform Adv 4:vbae008
[PubMed] [Google Scholar]
Increasing Representativeness in the All of Us Cohort Using Inverse Probability Weighting.
Kambara, M. S., Sharma, S., Spouge, J. L., Jordan, I. K., & Mariño-Ramírez, L. 2024
medRxiv 10 02 24314774
[Google Scholar]
A composite socioeconomic deprivation index from All of Us survey data: associations with health outcomes and disparities medRxiv.
Gupta, S., Lam, V., Jordan, I. K., & Mariño-Ramírez, L. 2024
10 04 24314904
[Google Scholar]

2023

Sick individuals, sick populations revisited: a test of the Rose hypothesis for type 2 diabetes disparities.
Gupta, S., Jordan, I. K., Mariño-Ramírez, L. 2024
BMJ Public Health 1:e000655
[PubMed] [Google Scholar]
The role of admixture in the rare variant contribution to inflammatory bowel disease.
Astore, C., Sharma, S., Nagpal, S., Cutler, D. J., Rioux, J. D., Cho, J. H., McGovern, D. P. B., Brant, S. R., Kugathasan, S., Jordan, I. K., Gibson, G., Niddk Ibd Genetics Consortium. 2023
Genome Medicine 15:97
[PubMed] [Google Scholar]
Ancestry-attenuated effects of socioeconomic deprivation on type 2 diabetes disparities in the All of Us cohort.
Lam, V., Sharma, S., Gupta, S., Spouge, J. L., Jordan, I. K., Mariño-Ramírez, L. 2023
BMC Glob Public Health 1:22
[PubMed] [Google Scholar]
Population Pharmacogenomics for Health Equity.
Jordan, I. K., Sharma, S., Mariño-Ramírez, L. 2023
Genes 14:1840
[PubMed] [Google Scholar]
Genomic analysis of Chlamydia psittaci from a multistate zoonotic outbreak in two chicken processing plants.
Wolff, B. J., Waller, J. L., Benitez, A. J., Gaines, A., Conley, A. B., Rishishwar, L., Chande, A. T., Morrison, S. S., Jordan, I. K., Diaz, M. H., Winchell, J. M. 2023
J Genomics 11:40-44
[PubMed] [Google Scholar]
Race, ethnicity, and pharmacogenomic variation in the United States and the United Kingdom.
Sharma, S., Mariño-Ramírez, L., Jordan, I. K. 2023
Pharmaceutics 15:1923
[PubMed] [Google Scholar]
The landscape of health disparities in the UK Biobank.
Nagar, S. D., Jordan, I. K., Mariño-Ramírez, L. 2023
Database (Oxford) 2023: baad026
[PubMed] [Google Scholar]
Transcriptome analysis identifies tumor immune microenvironment signaling networks supporting metastatic castration-resistant prostate cancer.
McKinney, L. P., Singh, R., Jordan, I. K., Varambally, S., Dammer, E. B., Lillard, J. W. Jr. 2023
Onco 3: 81-95
[Google Scholar]
Ethnic disparities in mortality and group-specific risk factors in the UK Biobank.
Lee, K. K., Norris, E. T., Rishishwar, L., Conley, A. B., Mariño-Ramírez, L., McDonald, J. F., Jordan, I. K. 2023
PLoS Glob Public Health 3: e0001560
[PubMed] [Google Scholar]
Rye: genetic ancestry inference at biobank scale.
Conley, A. B., Rishishwar, L., Ahmad, M., Sharma, S., Norris, E. T., Jordan, I. K., Mariño-Ramírez, L. 2023
Nucleic Acids Res 51: e44
[PubMed] [Google Scholar]
Honour genetic diversity to realize health equity.
Mariño-Ramírez, L., Pérez-Stable, E. J., Jordan, I. K. 2023
Nature 613: 243
[PubMed] [Google Scholar]

2022

Comparison of US Firearm-Related Deaths Among Children and Adolescents by Race and Ethnicity, 1999-2020.
Mariño-Ramírez L., Jordan I. K., Nápoles A. M., Pérez-Stable E. J. 2022
JAMA 328: 2359-2360
[PubMed] [Google Scholar]
QuasiFlow: a Nextflow pipeline for analysis of NGS-based HIV-1 drug resistance data.
Ssekagiri, A., Jjingo, D., Lujumba, I., Bbosa, N., Bugembe, D. L., Kateete, D. P., Jordan, I. K., Kaleebu, P., Ssemwanga, D. 2022
Bioinform Adv 2: vbac089
[PubMed] [Google Scholar]
Investigation of hypertension and type 2 diabetes as risk factors for dementia in the All of Us cohort.
Nagar, S. D., Pemu, P., Qian, J., Boerwinkle, E., Cicek, M., Clark, C. R., Cohn, E., Gebo, K., Loperena, R., Mayo, K., Mockrin, S., Ohno-Machado, L., Ramirez, A. H., Schully, S., Able, A., Green, A., Zuchner, S., SEEC Consortium, Jordan, I. K., Meller, R. 2022
Sci Rep 12: 19797
[PubMed] [Google Scholar]
The apportionment of pharmacogenomic variation: race, ethnicity, and adverse drug reactions.
Jordan, I. K., Sharma, S., Nagar, S. D., Mariño-Ramírez, L. 2022
Med Res Arch 10: 10 18103/mra v10i9 2986
[PubMed] [Google Scholar]
Genetic ancestry inference for pharmacogenomics.
Jordan, I. K., Sharma, S., Nagar, S. D., Valderrama-Aguirre, A., Mariño-Ramírez, L. 2022
Methods Mol Biol 2547: 595–609
[PubMed] [Google Scholar]
Comorbidities and ethnic health disparities in the UK biobank.
Teagle, W.L., Norris, E.T., Rishishwar, L., Nagar S.D., Jordan, I.K., Mariño-Ramírez, L. 2022
JAMIA Open 5: ooac057
[PubMed] [Google Scholar]
Mutations in SORL1 and MTHFDL1 possibly contribute to the development of Alzheimer's disease in a multigenerational Colombian Family.
Tejada Moreno, J.A., Villegas Lanau, A., Madrigal Zapata, L., Baena Pineda, A.Y., Velez Hernandez, J., Campo Nieto, O., Soto Ospina, A., Araque Marín, P., Rishishwar, L., Norris, E.T., Chande, A.T., Jordan, I.K., Bedoya Berrio, G. 2022
PLoS One 17: e0269955
[PubMed] [Google Scholar]
Effects of genetic ancestry and socioeconomic deprivation on ethnic differences in serum creatinine.
Mariño-Ramírez, L., Sharma, S., Rishishwar, L., Conley, A.B., Nagar, S.D., Jordan, I.K. 2022
Gene 837: 146709
[PubMed] [Google Scholar]
Epigenetics and cancer disparities: when nature might be nurture.
Jordan, I.K., Lee, K.K., McDonald, J.F., Mariño-Ramírez, L. 2022
Oncoscience 9: 23-24
[PubMed] [Google Scholar]
Association of genetic ancestry and molecular signatures with cancer survival disparities: a pan-cancer analysis.
Lee, K. K., Rishishwar, L., Ban, D., Nagar, S. D., Mariño-Ramírez, L., McDonald, J. F., Jordan, I. K. 2022
Cancer Res 82: 1222-1233
[PubMed] [Google Scholar]

2021

Comparing genetic and socioenvironmental contributions to ethnic differences in C-reactive protein.
Nagar, S. D., Conley, A. B., Sharma, S., Rishishwar, L., Jordan, I. K., Mariño-Ramírez, L. 2021
Front Genet 12: 738485
[PubMed] [Google Scholar]
Vitamin D and socioeconomic deprivation mediate COVID-19 ethnic health disparities.
Mariño-Ramírez, L., Ahmad, M., Rishishwar, L., Nagar, S. D., Lee, K. K., Norris, E. T., Jordan, I. K. 2021
medRxiv 2021 09 20 21263865
[PubMed] [Google Scholar]
Im, S.B., Gupta, S., Jain, M., Chande, A.T., Carleton, H.A., Jordan, I.K., Rishishwar, L. Genome-enabled molecular subtyping and serotyping for Shiga toxin- producing Escherichia coli. Front Sustain Food Syst. 5: 752873.
[Google Scholar]
The impact of ethnicity and genetic ancestry on disease prevalence and risk in Colombia.
Chande, A.T., Nagar, S.D., Rishishwar, L., Mariño-Ramírez, L., Medina-Rivas, M.A., Valderrama-Aguirre, A.E., Jordan, I.K., Gallo, J.E. 2021
Front Genet 12: 690366
[PubMed] [Google Scholar]
Genetic ancestry and ethnic identity in Ecuador.
Nagar, S.D., Conley, A.B., Chande, A.T., Rishishwar, L., Sharma, S., Mariño-Ramírez, L., Aguinaga-Romero, G., González-Andrade, F., Jordan, I.K. 2021
HGG Adv 2: 100050
[PubMed] [Google Scholar]
Genomic Diversity of Azole Resistant Aspergillus fumigatus in the USA.
Etienne, K.A., Berkow, E.L., Gade, L., Nunnally, N., Lockhart, S.R., Beer, K., Jordan, I.K., Rishishwar, L., Litvintseva, A.P. 2021
mBio 12: e0180321
[PubMed] [Google Scholar]
Adaptive introgression for rapid human evolution in the Americas.
Norris, E.T., Rishishwar, L., Jordan, I.K. 2021
In: Muñoz-Moreno, M L , Crawford, M H (Eds ), Human Migration: Biocultural Perspectives (pp 123-138) Oxford University Press
[Link] [Google Scholar]
Socioeconomic deprivation and genetic ancestry interact to modify type 2 diabetes ethnic disparities in the United Kingdom.
Nagar, S.D., Nápoles, A.M., Jordan, I.K., Marinño-Ramírez, L. 2021
EClinicalMedicine 37: 100960
[PubMed] [Google Scholar]
New histoplasma diagnostic assays designed via whole genome comparisons.
Gallo, J.E., Torres, I., Gómez, O.M., Rishishwar, L., Vannberg, F., Jordan, I.K., McEwen, J.G., Clay, O.K. 2021
J Fungi 7: 544
[PubMed] [Google Scholar]
Genomic characterization and computational phenotyping of nitrogen-fixing bacteria isolated from Colombian sugarcane fields.
Medina-Cordoba, L.K., Chande, A.T., Rishishwar, L., Mayer, L.W., Valderrama-Aguirre, L.C., Valderrama-Aguirre, A., Gaby, J.C., Kostka, J.E., Jordan, I.K. 2021
Sci Rep 11: 9187
[PubMed] [Google Scholar]
Colistin heteroresistance is largely undetected among carbapenem-resistant Enterobacterales in the United States.
Band, V.I., Satola, S.W., Smith, R.D., Hufnagel, D.A., Bower, C., Conley, A.B., Rishishwar, L., Dale, S.E., Hardy, D.J., Vargas, R.L., Dumyati, G., Kainer, M.A., Phipps, E.C., Pierce, R., Wilson, L.E., Sorensen, M., Nilsson, E., Jordan, I.K., Burd, E.M., Farley, M.M., Jacob, J.T., Ernst, R.K., Weiss, D.S. 2021
mBio 12: e02881-20
[PubMed] [Google Scholar]
Deconvolving human evolutionary history: using network-based approaches to better understand our past.
Nagar, S.D., Conley, A.B, Jordan, I.K. 2021
In: Wolkenhauer O (Ed), Systems Medicine: Integrative, Qualitative and Computational Approaches (Vol 3, pp 105-110) Elsevier
[Google Scholar]

2020

Absence of mgrB alleviates negative growth effects of colistin resistance in enterobacter cloacae.
Wozniak, J.E, Chande, A.T., Burd, E.M., Band, V.I., Satola, S.W., Farley, M.M., Jacob, J.T., Jordan, I.K., Weiss, D.S. 2020
Antiobiotics 9: 825
[PubMed] [Google Scholar]
Population structure and pharmacogenomic risk stratification in the United States.
Nagar, S.D., Conley, A.B., Jordan, I.K. 2020
BMC Biol 18: 140
[PubMed] [Google Scholar]
The phenotypic and functional consequences of genetic divergence between admixed Latin American populations: Antioquia and Chocó, Colombia.
Chande, A.T., Rishishwar, L., Ban, D., Nagar, S.D., Conley, A.B., Rowell, J., Valderrama-Aguirre, A., Medina-Rivas, M.A., Jordan, I.K. 2020
Genome Biol Evol 12: 1516-1527
[PubMed] [Google Scholar]
STing: accurate and ultrafast genomic profiling with exact sequence matches.
Espitia-Navarro, H.F., Chande, A.T., Nagar, S.D., Smith, H., Jordan, I.K. Rishishwar, L. 2020
Nucleic Acids Res 48: 7681-7689
[PubMed] [Google Scholar]
Ancestry effects on type 2 diabetes genetic risk inference in Hispanic/Latino populations.
Chande, A.T., Rishishwar, L., Conley, A.B., Valderrama-Aguirre, A., Medina-Rivas, M.A., Jordan, I.K. 2020
BMC Med Genet 21: 132
[PubMed] [Google Scholar]
Online COVID-19 Dashboard Calculates How Risky Reopenings and Gatherings Can Be.
Weitz, J.S., Harris, M., Chande, A.T., Gussler, J.W., Rishishwar, L. Jordan, I.K. 2020
Sci Am
An atlas of transposable element derived alternative splicing in cancer.
Clayton, E.A., Rishishwar, L., Huang, T-C., Gulati, S., Ban, D., McDonald, J.F., Jordan, I.K. 2020
Philos Trans R Soc Lond B Biol Sci 375: 20190342
[PubMed] [Google Scholar]
Admixture-enabled selection for adaptive evolution in the Americas.
Norris, E.T., Rishishwar, L., Chande, A.T., Conley, A.B., Ye, K., Valderrama-Aguirre, A., Jordan, I.K. 2020
Genome Biol 21: 29
[PubMed] [Google Scholar]
Tumor suppressor genes and allele-specific expression: mechanisms and significance.
Clayton, E.A., Khalid, S., Ban, D., Wang, L., Jordan, I.K., McDonald, J.F. 2020
Oncotarget 11: 462-479
[PubMed] [Google Scholar]
Bioinformatics: rapid bacterial typing in the post-genomic era.
Espitia-Navarro, H.F., Rishishwar, L., Mayer, L.W., Jordan, I.K. 2020
In: Budowle, B , Schutzer, S , and Morse, S (Eds ), Microbial Forensics (3rd ed , pp 267-282) Elsevier
[Google Scholar]

2019

Native American admixture recapitulates population-specific migration and settlement of the continental United States.
Jordan, I.K., Rishishwar, L., Conley, A.B. 2019
PLoS Genet 15: e1008225
[PubMed] [Google Scholar]
Analysis of Vibrio cholerae genomes identifies new Type VI Secretion System gene clusters.
Crisan, C.V., Chande, A.T., Williams, K., Raghuram, V., Rishishwar, L., Steinbach, G., Watve, S.S., Yunker, P., Jordan, I.K. and Hammer, B.K. 2019
Genome Biol 20: 163
[PubMed] [Google Scholar]
Development of anthracycline-induced dilated cardiomyopathy due to mutation on LMNA gene in a breast cancer patient: a case report.
Kuruc, J.C., Durant-Archibold, A.A., Motta, J., Rao, K.S., Trachtenberg, B., Ramos, C., Wang, H., Gorenstein, D., Vannberg, F., Jordan, I.K. 2019
BMC Cardiovasc Disord 19: 169
[PubMed] [Google Scholar]
Assortative mating on ancestry-variant traits in admixed Latin American populations.
Norris, E.T, Rishishwar, L., Wang, L., Conley, A.B., Chande, A.T., Dabrowski, A.M., Valderrama-Aguirre, A., Jordan, I.K. 2019
Front Genet 10: 359
[PubMed] [Google Scholar]
A Nationwide Screen of carbapenem-resistant Klebsiella pneumoniae reveals an isolate with enhanced virulence and clinically undetected colistin-heteroresistance.
Wozniak, J.E., Band, V.I., Conley, A.B., Rishishwar, L., Burd, E.M., Satola, S.W., Hardy, D, Tsay, R., Farley, M.M., Jacob, J., Dumyati, G., Jordan, I.K., Weiss, D.S. 2019
Antimicrob Agents Chemother 63: e00107-19
[PubMed] [Google Scholar]
Population pharmacogenomics for precision public health in Colombia.
Nagar, S.D., Moreno, A.M., Norris, E.T., Rishishwar, L., Conley, A.B., O'Neal, K.L., Vélez-Gómez, S., Montes-Rodríguez, C., Jaraba-Álvarez, W.V., Torres, I., Medina-Rivas, M.A., Valderrama-Aguirre, A.E., Jordan, I.K., Gallo, J.E. 2019
Front Genet 10: 241
[PubMed] [Google Scholar]
Whole Genome Sequence of Staphylococcus aureus Isolates from Cystic Fibrosis Lung Infections.
Bernardy, E.E., Petit, R., Moller, A., Blumenthal, J., McAdam, A., Priebe, G., Chande, A.T., Rishishwar, L., Jordan, I.K., Read, T., Goldberg, J. 2019
Microbiol Resour Announc 8: e01564-18
[PubMed] [Google Scholar]

2018

Genetic ancestry, admixture and health determinants in Latin America.
Norris, E.T., Wang, L., Conley, A.B., Rishishwar, L., Mariño-Ramírez, L., Valderrama-Aguirre, A., Jordan, I.K., 2018
BMC Genomics 19: 861
[PubMed] [Google Scholar]
Evidence for positive selection on recent human transposable element insertions Gene.
Rishishwar, L., Wang, L., Wang, J., Yi, S.V., Lachance, J., Jordan, I.K., 2018
675: 69-79
[PubMed] [Google Scholar]
GlobAl Distribution of GEnetic Traits (GADGET) web server: polygenic trait scores worldwide.
Chande, A.T., Wang, L., Rishishwar, L., Conley, A.B., Norris, E.T., Valderrama-Aguirre, A., Jordan, I.K., 2018
Nucleic Acids Res 46: W121–W126
[PubMed] [Google Scholar]
Genome sequences of 15 Klebsiella spp.
Medina-Cordoba, L.K., Chande, A.T, Rishishwar, L., Mayer, L.W., Mariño-Ramírez, L., Valderrama-Aguirre, L., Valderrama-Aguirre, A., Kostka, J.E, Jordan, I.K., 2018
isolates from sugarcane fields in Colombia’s Cauca Valley Genome Announc 6: e00104-18
[PubMed] [Google Scholar]
Transposable element activity, genome regulation and human health.
Wang, L., Jordan, I.K., 2018
Curr Opin Genet Dev 49: 25–33
[PubMed] [Google Scholar]
Diazotroph community characterization via a high-throughput nifH amplicon sequencing and analysis pipeline.
Gaby, J.C., Rishishwar, L., Valderrama-Aguirre, L., Green, S.J., Valderrama-Aguirre, A., Jordan, I.K., Kostka , J.E., 2018
Appl Environ Microbiol 84: e01512-17
[PubMed] [Google Scholar]

2017

Influence of genetic ancestry and socioeconomic status on type 2 diabetes in the diverse Colombian populations of Chocó and Antioquia.
Chande, A.T., Rowell, J., Rishishwar, L., Conley, A.B., Norris, E.T., Valderrama-Aguirre, A., Medina-Rivas, M., Jordan, I.K., 2017
Sci Rep 7: 17127
[PubMed] [Supplement]
Benchmarking computational tools for polymorphic transposable element detection.
Rishishwar, L., Mariño-Ramírez, L., and Jordan, I.K., 2017
Brief Bioinform 18: 908–918
[PubMed] [Supplement] [Google Scholar]
Genome-wide map of Apn1 binding sites under oxidative stress in Saccharomyces cerevisiae.
Morris, L.P., Conley, A.B., Degtyareva, N., Jordan, I.K., Doetsch, P.W., 2017
Yeast 34: 447–458
[PubMed] [Google Scholar]
A comparative analysis of genetic ancestry and admixture in the Colombian populations of Chocó and Medellín.
Conley, A.B., Rishishwar, L., Norris, E.T., Valderrama-Aguirre, A., Mariño-Ramírez, L., Medina-Rivas, M., Jordan, I.K., 2017
G3: Genes, Genomes, Genetics 7: 3435-3447
[PubMed] [Supplement] [Google Scholar]
Acute genotoxic stress-induced senescence in human mesenchymal cells drives a unique composition of senescence messaging secretome (SMS).
Gaur, M., Wang, L., Amaro-Ortiz, A., Dobke, M., Jordan, I.K., Lunyak, V.V., 2017
Journal of Stem Cell Research & Therapy 7: 396
[Google Scholar]
Human retrotransposon insertion polymorphisms are associated with health and disease via gene regulatory phenotypes.
Wang, L., Norris, E.T., Jordan, I.K., 2017
Front Microbiol 8: 1418
[PubMed] [Google Scholar]
A decade of viral mutations and associated drug resistance in a population of HIV-1+ Puerto Ricans: 2002–2011 PLoS One.
Sepúlveda-Torres, L.d.C., Rishishwar L., Rogers, M.L., Ríos-Olivares, E., Boukli, N., Jordan, I.K., Cubano, L.A., 2017
12: e0177452
[PubMed] [Google Scholar]
Opposing activities of oncogenic MIR17HG and tumor suppressive MIR100HG clusters and their gene targets regulate replicative senescence in human adult stem cells.
Lopez, M.F., Niu, P., Wang, L., Vogelsang, M., Gaur, M., Krastins, B., Zhao, Y., Smagul, A., Nussupbekova, A., Akanov, A.A., Jordan, I.K., and Lunyak, V.V., 2017
NPJ Aging Mech Dis 3: 7
[PubMed] [Google Scholar]
Human population-specific gene expression and transcriptional network modification with polymorphic transposable elements.
Wang, L., Rishishwar, L., Mariño-Ramírez, L. and Jordan I.K., 2017
Nuc Acids Res 45: 2318–2328
[PubMed] [Google Scholar]
Implications of human evolution and admixture for mitochondrial replacement therapy.
Rishishwar, L. and Jordan, I.K., 2017
BMC Genomics 18: 140
[PubMed] [Google Scholar]
Population and clinical genetics of human transposable elements in the (post) genomic era.
Rishishwar, L., Wang, L., Clayton, E.A., Mariño-Ramírez, L., McDonald, J.F. and Jordan I.K., 2017
Mob Genet Elements 7: 1-20
[PubMed] [Google Scholar]
stringMLST: a fast k-mer based tool for multi locus sequence typing.
Gupta, A., Jordan, I.K., Rishishwar, L., 2017
Bioinformatics 33: 119-121
[PubMed] [Supplement] [Google Scholar]
RampDB: a web application and database for the exploration and prediction of receptor activity modifying protein interactions.
Topaz, N., Mojib, N., Chande, A.T., Kubanek, J., Jordan, I.K., 2017
Database 2017: bax067
[PubMed] [Google Scholar]

2016

Patterns of transposable element expression and insertion in cancer.
Clayton, E.A., Wang, L., Rishishwar, L., Wang, J., McDonald, J.F. and Jordan I.K., 2016
Front Mol Biosci 3: 76
[PubMed] [Supplement] [Google Scholar]
Whole genome sequence of 26 environmental Vibrio cholerae isolates.
Watve, S., Chande, A.T., Rishishwar, L., Bernardy, E.E., Mariño-Ramírez, L., Jordan, I.K., Hammer, B.K., 2016
Genome Announc 4: e01396-16
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Comparative genomic analysis of Haemophilus haemolyticus and non-typeable Haemophilus influenzae and a new testing scheme for their discrimination.
Hu, F., Rishishwar, L., Sivadas, A., Mitchell, G.J., Jordan, I.K., Murphy, T.F., Gilsdorf, J.R., Mayer, L.W., and Wang, X., 2016
J Clin Micro 54: 3010-3017
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Characterization of clinical and environmental isolates of Vibrio cidicii sp.
Orata, F.D., Xu, Y., Gladney, L.M., Rishishwar, L., Case, R.J., Boucher, Y., Jordan, I.K., Tarr, C.L., 2016
nov , a close relative of Vibrio navarrensis Int J Syst Evol Microbiol 66: 4148-4155
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Population genomics of reduced vancomycin susceptibility in Staphylococcus aureus.
Rishishwar, L., Kraft, C.S., Jordan, I.K., 2016
mSphere 1: e00094-16
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The Columbian Exchange as a source of adaptive introgression in human populations.
Jordan, I.K., 2016
Biol Direct 11: 17
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Lateral gene transfer in a heavy metal-contaminated groundwater microbial community.
Hemme, C.L., Green, S.J., Rishishwar, L., Prakash, O., Pettenato, A., Chakraborty, R., Deutchbauer, A.M., Van Nostrand, J.D., Wu, L., He, L., Jordan, I.K., Hazen, T.C., Arkin, A.P., Kostka, J.E. and Zhou, J., 2016
mBio 7: e02234-15
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El Chocó Colombia: a hotspot of human biodiversity.
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
Rev Biodivers Neotrop 6: 45-54
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2015

Transposable element polymorphisms recapitulate human evolution.
Rishishwar, L., Tellez Villa, C.E. and Jordan, I.K., 2015
Mob DNA 6: 21
[PubMed] [Supplement] [Google Scholar]
A combined evidence Bayesian method for human ancestry inference applied to Afro-Colombians.
Rishishwar, L., Conley, A.B., Vidakovic, B. and Jordan, I.K., 2015
Gene 574: 345-351
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A phylogenetic perspective on molecular epidemiology.
Wang, X., Jordan, I.K., Mayer, L.W., 2015
Molecular Medical Microbiology (Second Edition) 1: 517-536
[Google Scholar]
Transcriptional profiling of interleukin-2-primed human adipose derived mesenchymal stem cells revealed dramatic changes in stem cells response imposed by replicative senescence.
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
Oncotarget 6: 17938-57
[PubMed] [Supplement] [Google Scholar]
MIR retotransposon sequences provide insulators to the human genome.
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
Proc Natl Acad Sci USA 112: E4428-4437
[PubMed] [Supplement] [Google Scholar]
Ancestry, admixture and fitness in Colombian genomes.
Rishishwar, L., Conley, A.B., Wigington, C.H., Wang, L., Valderrama-Aguirre, A. and Jordan, I.K., 2015
Sci Rep 5: 12376
[PubMed] [Supplement] [Google Scholar]

2014

Genome Sequences of Vibrio navarrensis, a Potential Human Pathogen.
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 Announc 2: e01188-14
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A systems biology analysis of the changes in gene expression via silencing of HPV-18 E1 expression in HeLa cells.
Castillo, A., Wang, L., Koriyama, C., Eizuru, Y., Jordan, I.K., and Akiba, S., 2014
Open Biol 4: 130119
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Mammalian-wide interspersed repeat (MIR)-derived enhancers and the regulation of human gene expression.
Jjingo, D., Conley, A.B., Wang, J., Mariño-Ramírez, L., Lunyak, V.V., and Jordan, I.K., 2014
Mob DNA 5: 14
[PubMed] [Supplement] [Google Scholar]
Flow-dependent epigenetic DNA methylation regulates endothelial gene expression and atherosclerosis.
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
J Clin Invest 124: 3187-3199
[PubMed] [Supplement] [Google Scholar]
Identification of a tumor suppressive human specific microRNA within the FHIT tumor suppressor gene.
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
Cancer Res 74: 2283-94
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A genome sequence based discriminator for vancomycin-intermediate Staphylococcus aureus.
Rishishwar, L., Petit, R., Kraft, C.S., and Jordan, I.K., 2014
J Bacteriol 196: 940-948
[PubMed] [Supplement] [Google Scholar]

2013

Transcriptional activity, chromosomal distribution and expression effects of transposable elements in Coffea genomes.
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
PLoS ONE 8: e78931
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Compound cis-regulatory elements with both boundary and enhancer sequences in the human genome.
Jjingo, D., Wang, J., Conley, A.B., Lunyak, V.V., and Jordan, I.K, 2013
Bioinformatics 29: 3109-3112
[PubMed] [Supplement] [Google Scholar]
Epigenetics components of aging in the central nervous system.
Zhoa, Y., Jordan, I.K. and Lunyak, V.V., 2013
Neurotherapeutics 10: 647-663
[PubMed] [Google Scholar]
Insights into environmental microbial denitrification from integrated metagenomic, cultivation and genomic analyses.
Green, S., Rishishwar, L., Prakash, O., Jordan, I.K. and Kostka, J., 2013
In: Encyclopedia of Metagenomics, (Nelson, K ed ) Springer, Berlin
Origin and evolution of the cystic fibrosis transmembrane regulator protein R domain.
Sebastian, A., Rishishwar, L., Wang, J., Bernard, K.F., Conley, A.B., McCarty, N.A. and Jordan, I.K., 2013
Gene 523: 137-146
[PubMed] [Supplement] [Google Scholar]
BroadPeak: a novel algorithm for identifying broad peaks in diffuse ChIP-seq datasets.
Wang, J., Lunyak, V.V. and Jordan, I.K., 2013
Bioinformatics 29: 492-493
[PubMed] [Supplement] [Google Scholar]

2012

Depletion of nuclear histone H2A variants is associated with chronic DNA damage signaling upon drug-evoked senescence of human somatic cells.
Lopez, M.F., Tollervey, J., Krastins, B., Garces, A., Sarracino, D., Prakash, A., Vogelsang, M., Geesman, G., Valderrama, A., Jordan, I.K. and Lunyak, V.V., 2012
Aging 4: 823-842
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Cell type-specific termination of transcription by transposable element sequences.
Conley, A.B. and Jordan, I.K., 2012
Mob DNA 3: 15
[PubMed] [Supplement] [Google Scholar]
Chromatin signature discovery via histone modification profile alignments.
Wang, J., Lunyak, V.V. and Jordan, I.K., 2012
Nucleic Acids Res 40: 10642-10656
[PubMed] [Supplement] [Google Scholar]
Genomic basis of a polyagglutinating isolate of Neisseria meningitidis.
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
J Bacteriol 194: 5649-5656
[PubMed] [Google Scholar]
Relating the disease mutation spectrum to the evolution of the Cystic Fibrosis Transmembrane Conductance Regulator (CFTR).
Rishishwar, L., Varghese, N., Tyagi, E., Harvey, S.C., Jordan, I.K. and McCarty, N.A., 2012
PLoS ONE 7: e42336
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Genome sequences for six Rhodanobacter strains isolated from soils and the terrestrial subsurface with variable denitrification capabilities.
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. and Brooks, S.C., 2012
J Bacteriol 194: 4461
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On the presence and role of human gene-body DNA methylation.
Jjingo, D., Conley, A.B., Yi, S.V., Lunyak, V.V. and Jordan, I.K., 2012
Oncotarget 3: 462-474
[PubMed] [Supplement] [Google Scholar]
Do human transposable element small RNAs serve primarily as genome defenders or genome regulators? Mob Genet Elements.
Lee, K.J., Conley, A.B., Lunyak, V.V. and Jordan, I.K., 2012
2: 1–7
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Protein interactions with piALU RNA indicates putative participation of retroRNA in the cell cycle, DNA repair and chromatin assembly Mob Genet Elements.
Blackwell, B., Lopez M.F., Wang, J., Krastins, B., Sarracino, D., Tollervey, J.R., Dobke, M.,Jordan, I.K. and Lunyak, V.V., 2012
2: 1–10
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Epigenetic regulation of human cis-natural antisense transcripts.
Conley, A.B. and Jordan, I.K., 2012
Nucleic Acids Res 40: 1438–1445
[PubMed] [Supplement] [Google Scholar]
Genome-wide prediction and analysis of human chromatin boundary elements.
Wang, J., Lunyak, V.V., and Jordan, I.K., 2012
Nucleic Acids Res 40: 511-529
[PubMed] [Supplement] [Google Scholar]

2011

Transcription factor binding sites are highly enriched within microRNA precursor sequences.
Piriyapongsa, J., Jordan, I.K., Conley, A.B., Ronan, T. and N.R. Smalheiser, 2011
Biol Direct 6: 61
[PubMed] [Supplement] [Google Scholar]
Prediction of transposable element derived enhancers using chromatin modification profiles.
Huda, A., Tyagi, E., Mariño-Ramírez, L., Bowen, N.J., Jjingo, D. and Jordan, I.K., 2011
PLoS ONE 6: e27513
[PubMed] [Supplement] [Google Scholar]
Neisseria Base: a comparative genomics database for Neisseria meningitidis.
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 Jordan, I.K., 2011
Database 2011: bar035
[PubMed] [Supplement] [Google Scholar]
The genome sequence of Mycobacterium colombiense CECT 3035 type strain.
González Pérez, M., Murcia, M., Landsman, D., Jordan, I.K. and Mariño-Ramírez, L., 2011
J Bacteriol 193: 5866–5867
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Genome sequences for five strains of the emerging pathogen Haemophilus haemolyticus.
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 Mayer, L., 2011
J Bacteriol 193: 5879–5880
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Inhibition of activated pericentromeric SINE/Alu repeat transcription in senescent human adult stem cells reinstates self-renewal.
Wang, J., Geesman, G.J., Hostikka, S.L., Atallah, M., Blackwell, B., Lee, E., Cook, P.J., Pasaniuc, B., Shariat, G., Halperin, E., Dobke, M., Rosenfeld, M.G., Jordan, I.K. and Lunyak, V.V., 2011
Cell Cycle 10: 3016-3030
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Using single-nucleotide polymorphisms to discriminate disease-associated from carried genomes of Neisseria meningitidis.
Katz, L.S., Sharma, N.V., Harcourt, B.H., Thomas, J.D., Wang, X., Mayer L.W. and Jordan, I.K., 2011
J Bacteriol 193: 3633-3641
[PubMed] [Supplement] [Google Scholar]
Computational approaches for the transcriptomics, proteomics and epigenetic analysis in adult stem cells.
Jordan, K., 2011
Cell Cycle 10: 4187
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A method for visualization of "omic" datasets for sphingolipid metabolism to predict potentially interesting differences.
Momin, A.A., Park, H., Portz, B.J., Haynes, C.A., Shaner, R.L., Kelly, S.L., Jordan, I.K. and Merrill Jr., A.H., 2011
J Lipid Res 52: 1073-1083
[PubMed] [Supplement] [Google Scholar]
Effect of the transposable element environment of human genes on gene length and expression.
Jjingo, D., Huda, A., Gundapuneni, M., Mariño-Ramírez, L. and Jordan, I.K., 2011
Genome Biol Evol 3: 259-271
[PubMed] [Supplement] [Google Scholar]
Epigenetic regulation of transposable element derived human gene promoters.
Huda, A., Bowen, N.J., Conley, A.B. and Jordan, I.K., 2011
Gene 475: 39-48
[PubMed] [Google Scholar]

2010

A Gibbs sampling strategy applied to the mapping of ambiguous short-sequence tags.
Wang, J., Huda, A., Lunyak, V.V. and Jordan, I.K., 2010
Bioinformatics 26: 2501-2508
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Identification of transcription factor binding sites derived from transposable element sequences using ChIP-seq.
Conley, A.B. and Jordan, I.K., 2010
Methods Mol Biol 674: 225-240
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A computational genomics pipeline for prokaryotic sequencing projects.
Kislyuk, A.O., Katz, L.S., Agrawal, S., Hagen, M.S., Conley, A.B., Jayaraman, P., Nelakuditi V., Humphrey, J.C., Sammons, S.A., Govil, D., Mair, R.D., Tatti, K.M., Tondella, M.L., Harcourt, B.H., Mayer, L.W. and Jordan, I.K., 2010
Bioinformatics 26: 1819-1826
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Epigenetic histone modifications of human transposable elements: genome defense versus exaptation.
Huda, A., Mariño-Ramírez, L. and Jordan, I.K., 2010
Mob DNA 1: 2
[PubMed] [Google Scholar]

2009

A c-Myc regulatory subnetwork from human transposable element sequences.
Wang, J., Bowen, N.J., Mariño-Ramírez, L. and Jordan, I.K., 2009
Mol Biosyst 5: 1831-1839
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Epigenetic regulation of mammalian genomes by transposable elements.
Huda, A. and Jordan, I.K., 2009
Ann NY Acad Sci 1178: 276-284
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Meningococcus Genome Informatics Platform: a system for analyzing multilocus sequence typing data.
Katz, L.S., Bolen, C.R., Harcourt B.H., Schmink S., Wang X., Kislyuk, A., Taylor, R.T., Mayer, L.W. and Jordan, I.K., 2009
Nucleic Acids Res 37: W606-W611
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Repetitive DNA elements, nucleosome binding and human gene expression.
Huda, A., Mariño-Ramírez, L., Landsman, D. and Jordan, I.K., 2009
Gene 436: 12-22
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Analysis of transposable element sequences using CENSOR and RepeatMasker.
Huda, A. and Jordan, I.K., 2009
Methods Mol Biol 537: 323-336
[PubMed] [Google Scholar]

2008

Evolutionary and functional divergence between the cystic fibrosis transmembrane conductance regulator and related ATP-binding cassette transporters.
Jordan, I.K., Kota, K.C., Cui, G., Thompson, C.H. and McCarty, N.A., 2008
Proc Natl Acad Sci USA 105: 18865-18870
[PubMed] [Supplement] [Google Scholar]
Natural selection governs local, but not global, evolutionary gene coexpression networks in Caenorhabditis elegans.
Jordan, I.K., Katz, L.S., Denver, D.R. and J.T. Streelman, 2008
BMC Syst Biol 2: 96
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Genome defense against transposable elements and the origins of regulatory RNA.
Jordan, I.K. and Miller, W.M., 2008
In: Genome Dynamics and Stability, (Lankenau, D H and S Scharz eds ) Springer, Berlin
[Link]
Comparative human genomics.
Jordan, I.K. and Koonin, E.V., 2008
In: Handbook of Human Molecular Evolution, (Cooper, D N and H Kehrer-Sawatzki eds ) John Wiley and Sons, London
[Google Scholar]
Retroviral promoters in the human genome.
Conley, A.B., Piriyapongsa, J. and Jordan, I.K., 2008
Bioinformatics 24: 1563-1567
[Link] [Supplement] [Google Scholar]
Evolutionary rates and patterns for human transcription factor binding sites derived from repetitive DNA.
Polavarapu, N., Mariño-Ramírez, L., Landsman, D., McDonald, J.F. and Jordan, I.K., 2008
BMC Genomics 9: 226
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Highly conserved regimes of neighbor-base-dependent mutation generated the background primary-structural heterogeneities along vertebrate chromosomes.
Antezana, M. and Jordan, I.K., 2008
PLoS ONE 3: e2145
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Dual coding of siRNAs and miRNAs by plant transposable elements.
Piriyapongsa, J. and Jordan, I.K., 2008
RNA 14: 814-821
[Link] [Supplement] [Google Scholar]
Endogenous retroviruses of the chicken genome.
Huda, A., Polavarapu, N., Jordan, I.K. and McDonald, J.F., 2008
Biol Direct 3: 9
[Link] [Google Scholar]
Human cis natural antisense transcripts initiated by transposable elements.
Conley, A.B., Miller, W.J. and Jordan, I.K., 2008
Trends Genet 24: 53-56
[Link] [Supplement] [Google Scholar]

2007

Evaluating the protein coding potential of exonized transposable element sequences.
Piriyapongsa, J., Rutledge, M.T., Patel, S., Borodovsky, M. and Jordan, I.K., 2007
Biol Direct 2: 31
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Exaptation of protein coding sequences from transposable elements.
Bowen, N.J. and Jordan, I.K., 2007
Genome Dynamics 3: 131-146
[Link] [Google Scholar]
Evolutionary genomics of gene expression.
Jordan, I.K. and L. Mariño-Ramírez, 2007
In: Structural approaches to sequence evolution: Molecules, networks, populations, (Bastolla, U , Porto, M , Roman, H E and M Vendruscolo eds ), Springer, New York
[Link]
Origin and evolution of human microRNAs from transposable elements.
Piriyapongsa, J., Mariño-Ramírez, L. and Jordan, I.K., 2007
Genetics 176: 1323-1337
[Link] [Supplement] [Google Scholar]
A family of human microRNA genes from miniature-inverted repeat transposable elements.
Piriyapongsa, J. and Jordan, I.K., 2007
PLoS ONE 2: e203
[Link] [Supplement] [Google Scholar]

2006

Multiple independent evolutionary solutions to core histone gene regulation.
Mariño-Ramírez, L., Jordan, I.K. and Landsman, D., 2006
Genome Biol 7: R122
[Link] [Supplement] [Google Scholar]
Co-evolutionary rates of functionally related yeast genes.
Mariño-Ramírez, L., Bodenreider, O., Kantz, N. and Jordan, I.K., 2006
Evol Bioinform Online 2: 295-300
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Global similarity and local divergence in human and mouse gene co-expression networks.
Tsaparas, P., Mariño-Ramírez, L., Bodenreider, O., Koonin, E.V. and Jordan, I.K., 2006
BMC Evol Biol 6: 70
[Link] [Supplement] [Google Scholar]
Protein evolution: Causes of trends in amino-acid gain and loss (Reply).
Jordan, I.K., Kondrashov, F.A., Adzhubei, I.A., Wolf, Y.I., Koonin, E.V., Kondrashov, A.S. and Sunyaev, S., 2006
Nature 442: E12
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Transposable element derived DNaseI-hypersensitive sites in the human genome.
Mariño-Ramírez, L. and Jordan, I.K., 2006
Biol Direct 1:20
[Link] [Google Scholar]
Evolutionary tinkering with transposable elements.
Jordan, I.K., 2006
Proc Natl Acad Sci USA 96: 12621-12625
[Link] [Google Scholar]

2005

Transposable elements donate lineage-specific regulatory elements to host genomes.
Mariño-Ramírez, L., Lewis, K.C., Landsman, D. and Jordan, I.K., 2005
Cytogenet Genome Res 110: 333-341
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APOBEC4, a new member of the AID/APOBEC family of polynucleotide (deoxy)cytidine deaminases predicted by computational analysis.
Rogozin, I.B., Basu, M.K., Jordan, I.K., Pavlov, Y.I. and Koonin, E.V., 2005
Cell Cycle 4: 1281-1285
[Link] [Google Scholar]
Evolutionary significance of gene expression divergence.
Jordan, I.K., Mariño-Ramírez, L. and Koonin, E.V., 2005
Gene 345: 119-126
[Link] [Google Scholar]
A universal trend of amino acid gain and loss in protein evolution.
Jordan, I.K., Kondrashov, F.A., Adzhubei, I.A., Wolf, Y.I., Koonin, E.V., Kondrashov, A.S. and Sunyaev, S., 2005
Nature 433: 633-638
[Link] [Supplement] [Google Scholar]

2004

Conservation and co-evolution in the scale-free human gene co-expression network.
Jordan, I.K., Mariño-Ramírez, L., Wolf, Y.I. and Koonin, E.V., 2004
Mol Biol Evol 21: 2058-2070
[Link] [Google Scholar]
Duplicated genes evolve slower than singletons despite the initial rate increase.
Jordan, I.K., Wolf, Y.I. and Koonin, E.V., 2004
BMC Evol Biol 4: 22
[Link] [Google Scholar]
Horizontal transfer and prokaryotic genome evolution.
Jordan, I.K. and Koonin, E.V., 2004
Microbial Evolution: Gene Establishment, Survival and Exchange (Day, M and B Miller eds ), ASM Press, Washington, DC
[Link] [Google Scholar]
Computational analysis of transposable element sequences.
Jordan, I.K. and Bowen, N.J., 2004
Methods Mol Biol 260: 59-71
[Link] [Google Scholar]

2003

Retrotransposons and their recognition of pol II promoters: A comprehensive survey of the transposable elements derived from the complete genome sequence of Schizosaccharomyces pombe.
Bowen, N.J., Jordan, I.K., Epstein, J.A., Wood, V. and Levin, H.L., 2003
Genome Res 13: 1984-1997
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Comparative genomics.
Jordan, I.K. and Koonin, E.V., 2003
Encyclopedia of the Human Genome 1: 897-903 (Cooper, D N and M Calais eds ), Nature Publishing, London, UK
[Link]
Phylogenomic analysis of the Giardia intestinalis transcarboxylase reveals multiple instances of domain fusion and fission in the evolution of biotin-dependent enzymes.
Jordan, I.K., Henze, K., Fedorova, N.D., Koonin, E.V. and Galperin, M.Y., 2003
J Mol Microbiol Biotechnol 5: 172-189
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Origin of a substantial fraction of human regulatory sequences from transposable elements.
Jordan, I.K., Rogozin I.B., Glazko G.V. and Koonin, E.V., 2003
Trends Genet 19: 68-72
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No simple dependence between protein evolutionary rate and the number of protein-protein interactions: only the most prolific interactors tend to evolve slowly.
Jordan, I.K., Wolf, Y.I. and Koonin, E.V., 2003
BMC Evolutionary Biology 3: 1
[Link] [Google Scholar]

2002

Dasheng and RIRE2: a non-autonomous LTR element and its putative autonomous partner in the rice genome.
Jiang, N., Jordan, I.K. and Wessler, S.R., 2002
Plant Physiol 130: 1697-1705
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Transposable elements and the evolution of eukaryotic complexity.
Bowen, N.J. and Jordan, I.K., 2002
Curr Issues Mol Biol 4: 65-76
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A biologically active family of human endogeneous retroviruses (HERVs) evolved from an ancient inactive lineage.
Jordan, I.K. and McDonald, J.F., 2002
Genome Lett 1: 105-109
[Link] [Google Scholar]
Microevolutionary genomics of bacteria.
Jordan, I.K., Rogozin, I.B., Wolf, Y.I. and Koonin, E.V., 2002
Theor Popul Biol 61: 435-447
[Link] [Google Scholar]
Essential genes are more evolutionarily conserved than non-essential genes in bacteria.
Jordan, I.K., Rogozin, I.B., Wolf, Y.I. and Koonin, E.V., 2002
Genome Res 12: 962-968
[Link] [Google Scholar]
Purifying and directional selection in overlapping prokaryotic genes.
Rogozin, I.B., Spiridonov, A.N., Sorokin, A.V., Wolf, Y.I., Jordan, I.K., Tatusov, R.L. and Koonin, E.V., 2002
Trends Genet 18: 228-232
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2001

Constant relative rate of protein evolution and detection of functional diversification among bacterial, archaeal and eukaryotic proteins.
Jordan, I.K., Kondrashov, F.A., Rogozin, I.B., Tatusov, R.L., Wolf, Y.I. and Koonin, E.V., 2001
Genome Biology 2: 0053 1-0053 9
[Link] [Google Scholar]
Independent evolution of heavy metal-associated domains in copper chaperones and copper-transporting atpases.
Jordan, I.K., Natale, D.A., Koonin, E.V. and Galperin, M.Y., 2001
J Mol Evol 53:622-633 \
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Sequence and structural aspects of functional diversification in class I alpha-mannosidase evolution.
Jordan, I.K., Bishop, G.R. and Gonzalez, D.S., 2001
Bioinformatics 17: 965-976
[Link] [Google Scholar]
Lineage-specific gene expansions in bacterial and archaeal genomes.
Jordan, I.K., Makarova, K.S., Spouge, J.L., Wolf, Y.I. and Koonin, E.V., 2001
Genome Res 11: 555-565
[Link] [Google Scholar]
Gene conversions in genes encoding outer-membrane proteins in H.
Jordan, I.K., Makarova, K.S., Wolf, Y.I. and Koonin, E.V., 2001
pylori and C pneumoniae Trends Genet 17: 7-10
[Link] [Google Scholar]

2000

Copper chaperones in bacteria: association with copper-transporting ATPases.
Jordan, I.K., Natale, D.A. and Galperin, M.Y., 2000
Trends Biochem Sci 25: 480-481
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The alpha-mannosidases: phylogeny and adaptive diversification.
Gonzalez, D.S. and Jordan, I.K., 2000
Mol Biol Evol 17: 292-300
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Molecular evolution of the Paramyxoviridae and Rhabdoviridae multiple protein encoding P gene.
Jordan, I.K., Sutter, B.A. and McClure, M.A., 2000
Mol Biol Evol 17: 75-86
[Link] [Google Scholar]

1999

Comparative genomics and evolutionary dynamics of Saccharomyces cerevisiae Ty elements.
Jordan, I.K. and McDonald, J.F., 1999
Genetica 107: 3-13
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Genomic demography: A life history analysis of transposable element evolution.
Promislow, D.E.L., Jordan, I.K. and McDonald, J.F., 1999
Proc Roy Soc Lon B Biol 266: 1555-1560
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Evidence for the recent horizontal transfer of a long terminal repeat retrotransposon.
Jordan, I.K. and McDonald, J.F., 1999
Proc Natl Acad Sci USA 96: 12621-12625
[Link] [Google Scholar]
The role of interelement selection in Saccharomyces cerevisiae Ty element evolution.
Jordan, I.K. and McDonald, J.F., 1999
J Mol Evol 49: 352-357
[Link] [Google Scholar]
Tempo and mode of Ty element evolution in Saccharomyces cerevisiae.
Jordan, I.K. and McDonald, J.F., 1999
Genetics 151: 1341-1351
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Phylogenetic perspective reveals abundant Ty1/Ty2 hybrid elements in the Saccharomyces cerevisiae genome.
Jordan, I.K. and McDonald, J.F., 1999
Mol Biol Evol 16: 419-422
[Link] [Google Scholar]

1998

Inter-element selection in the regulatory region of the copia retrotransposon.
Jordan, I.K. and McDonald, J.F., 1998
J Mol Evol 47: 670-676
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Evolution of the copia retrotransposon in the Drosophila melanogaster species subgroup.
Jordan , I.K. and McDonald, J.F., 1998
Mol Biol Evol 15: 1160-1171
[Link] [Google Scholar]
Evidence for the role of recombination in the regulatory evolution of Saccharomyces cerevisiae Ty elements.
Jordan, I.K. and McDonald, J.F., 1998
J Mol Evol 47: 14-20
[Link] [Google Scholar]

1997

LTR retrotransposons and the evolution of eukaryotic enhancers.
McDonald, J.F., Matyunina, L.V., Wilson, S., Jordan, I.K., Bowen, N.J. and Miller, W.J., 1997
Genetica 100: 3-13
[Link] [Google Scholar]

1996

Naturally occurring variation in copia expression is due to both element (cis) and host (trans) regulatory variation.
Matyunina, LV., Jordan, I.K. and McDonald, J.F., 1996
Proc Natl Acad Sci USA 93: 7097-7102
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