PUBLICATIONS
2021
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., and Jordan, I.K. 2021. Genomic characterization and computational phenotyping of nitrogen-fixing bacteria isolated from Colombian sugarcane fields. Sci Rep. 11: 9187.
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. Colistin heteroresistance is largely undetected among carbapenem-resistant Enterobacterales in the United States. mBio. 12: e02881-20.
Nagar, S.D., Conley, A.B., and Jordan, I.K., 2019. Deconvolving human evolutionary history: using network-based approaches to better understand our past. In: Systems Medicine; Integrative Qualitative and Computational Approaches
2020
Chande, A.T., Lee, S., Harris, M., Nguyen, Q., Beckett, S.J., Hilley, T., Andris, C. and Weitz, J.S. 2020. Real-time, interactive website for US-county-level COVID-19 event risk assessment. Nature Hum Behav. https://doi.org/10.1038/s41562-020-01000-9
Nagar, S.D., Conley, A.B. and Jordan, I.K. 2020. Population structure and pharmacogenomic risk stratification in the United States. BMC Biol. 18(1):140. doi: 10.1186/s12915-020-00875-4.
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. The phenotypic and functional consequences of genetic divergence between admixed Latin American populations: Antioquia and Chocó, Colombia. Genome Biol Evol. evaa154.
Espitia-Navarro, H.F., Chande, A.T., Nagar, S.D., Smith, H., Jordan, I.K. and Rishishwar, L., 2020. STing: accurate and ultrafast genomic profiling with exact sequence matches. Nucleic Acids Res. 48(14):7681-7689.
Chande, A.T., Rishishwar, L., Conley, A.B., Valderrama-Aguirre, A., Medina-Rivas, M.A. and Jordan, I.K., 2020. Ancestry effects on type 2 diabetes genetic risk inference in Hispanic/Latino populations. BMC Medical Genetics. 21(Suppl 2):132.
Norris, E.T., Rishishwar, L., and Jordan, I.K., 2019. Rapid, adaptive human evolution facilitated by admixture in the Americas. In: Human Migration: Biocultural Perspectives. Oxford University Press, USA. In Press.
Weitz, J.S., Harris, M., Chande, A.T., Gussler, J.W., Rishishwar, L. and Jordan, I.K., 2020 Online COVID-19 Dashboard Calculates How Risky Reopenings and Gatherings Can Be. Scientific American.
Clayton, E.A., Rishishwar, L., Huang, T-C., Gulati, S., Ban, D., McDonald, J.F., and Jordan, I.K., 2020. An atlas of transposable element derived alternative splicing in cancer. Philos Trans R Soc Lond B Biol Sci. 375: 20190342.
Norris, E.T., Rishishwar, L., Chande, A.T., Conley, A.B., Ye, K., Valderrama-Aguirre, A., Jordan, I.K., 2020. Admixture-enabled selection for adaptive evolution in the Americas. Genome Biol. 21:29.
McLaughlin HP, Bugrysheva JV, Conley AB, Gulvik CA, Cherney B, Kolton CB, et al., 2020. Rapid nanopore whole-genome sequencing for anthrax emergency preparedness. Emerg Infect Dis. 26(2).
Espitia-Navarro, H.F., Rishishwar, L., Mayer, L.W., and Jordan, I.K., 2019. Rapid bacterial typing in the post-genomic era. n: Budowle, B., Schutzer, S., and Morse, S. (Eds.), Microbial Forensics (3rd ed., pp. 267-282). Elsevier.
2019
Gargis AS, Cherney B, Conley AB, McLaughlin HP, and Sue D., 2019. Rapid Detection of Genetic Engineering, Structural Variation, and Antimicrobial Resistance Markers in Bacterial Biothreat Pathogens by Nanopore Sequencing. Sci Rep. 9(1):13501.
Gargis AS, Lascols C, McLaughlin HP, Conley AB, Hoffmaster AR, and Sue D., 2019. Genome Sequences of Penicillin-Resistant Bacillus anthracis Strains. Microbiol Resour Announc. 8(2).
Jordan, I.K., Rishishwar, L. and Conley, A.B. 2019. Native American admixture recapitulates population-specific migration and settlement of the continental United States. PLoS Genetics. 15:e1008225.
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. Analysis of Vibrio cholerae genomes identifies new Type VI Secretion System gene clusters. Genome Biol. 20:163.
Norris, E.T., Rishishwar, L., Wang, L., Conley, A.B., Chande, A.T., Dabrowski, A.M., Valderrama-Aguirre, A.E., and Jordan, I.K., 2019. Assortative mating on ancestry-variant traits in admixed Latin American populations. Front Genet. 10:241. doi:10.3389/fgene.2019.00241.
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., and Weiss, D.S., 2019. A Nationwide Screen of carbapenem-resistant Klebsiella pneumoniae reveals an isolate with enhanced virulence and clinically undetected colistin-heteroresistance. Antimicrob Agents Chemother. doi: 10.1128/AAC.00107-19. [Epub ahead of print]
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. Population pharmacogenomics for precision public health in Colombia. Front Genet. 10:241.
Bernardy, E.E., Petit, R., Moller, A., Blumenthal, J., McAdam, A., Priebe, G., Chande, A.T., Rishishwar, L., Jordan, I.K., Read, T., and Goldberg, J., 2019. Whole Genome Sequences of Staphylococcus aureus Isolates from Cystic Fibrosis Lung Infections. Microbiol Resour Announc. 8: e01564-18.
2018
Norris, E.T., Wang, L., Conley, A.B., Rishishwar, L., Mariño-Ramírez, L., Valderrama-Aguirre, A., and Jordan, I.K., 2018. Genetic ancestry, admixture and health determinants in Latin America. BMC Genomics. 19: 861.
Rishishwar, L., Wang, L., Wang, J., Yi, S.V., Lachance, J., and Jordan, I.K., 2018. Evidence for positive selection on recent human transposable element insertions. Gene. 675: 69-79.
Chande, A.T., Wang, L., Rishishwar, L., Conley, A.B., Norris, E.T., Valderrama-Aguirre, A., and Jordan, I.K., 2018. GlobAl Distribution of GEnetic Traits (GADGET) web server: polygenic trait scores worldwide. Nucleic Acids Research. 46: W121-W126.
Medina-Cordoba, L.K., Chande, A.T., Rishishwar, L., Mayer, L.W., Mariño-Ramírez, L., Valderrama-Aguirre, L., Valderrama-Aguirre, A., Kostka, J.E, and Jordan, I.K., 2018. Genome sequences of 15 Klebsiella spp. isolates from sugarcane fields in Colombia’s Cauca Valley. Genome Announcements. 6: e00104-18.
Gaby, J.C., Rishishwar, L., Valderrama-Aguirre, L., Green, S.J., Valderrama-Aguirre, A., Jordan, I.K., and Kostka , J.E., 2018. Diazotroph community characterization via a high-throughput nifH amplicon sequencing and analysis pipeline. Applied and Environmental Microbiology. 84: e01512-17.
2017
McLaughlin HP, Cherney B, Hakovirta JR, Priestley RA, Conley AB, Carter A, et al., 2017. Phylogenetic inference of Coxiella burnetii by 16S rRNA gene sequencing. PLoS One. 12(12):e0189910.
Chande, A.T., Rowell, J., Rishishwar, L., Conley, A.B., Norris, E.T., Valderrama-Aguirre, A., Medina-Rivas, M., and Jordan, I.K., 2017. Influence of genetic ancestry and socioeconomic status on type 2 diabetes in the diverse Colombian populations of Chocó and Antioquia. Scientific Reports. 7: 17127.
Rishishwar, L., Mariño-Ramírez, L., and Jordan, I.K., 2017. Benchmarking computational tools for polymorphic transposable element detection. Brief Bioinform. 18: 908–918.
Conley, A.B., Rishishwar, L., Norris, E.T., Valderrama-Aguirre, A., Mariño-Ramírez, L., Medina-Rivas, M., and Jordan, I.K., 2017. A comparative analysis of genetic ancestry and admixture in the Colombian populations of Chocó and Medellín. G3: Genes, Genomes, Genetics. 7: 3435-3447.
Wang, L., Norris, E.T., and Jordan, I.K., 2017. Human retrotransposon insertion polymorphisms are associated with health and disease via gene regulatory phenotypes. Frontiers in Microbiology. 8: 1418.
Sepúlveda-Torres, L.d.C., Rishishwar L., Rogers, M.L., Ríos-Olivares, E., Boukli, N., Jordan, I.K., and Cubano, L.A., 2017. A decade of viral mutations and associated drug resistance in a population of HIV-1+ Puerto Ricans: 2002–2011. PLoS ONE. E 12(5): e0177452.
Wang, L., Rishishwar, L., Mariño-Ramírez, L., and Jordan I.K., 2017. Human population-specific gene expression and transcriptional network modification with polymorphic transposable elements. Nuc. Acids Res. 45: 2318–2328.
Rishishwar, L. and Jordan, I.K., 2017. Implications of human evolution and admixture for mitochondrial replacement therapy. BMC Genomics. 18: 140.
Rishishwar, L., Wang, L., Clayton, E.A., Mariño-Ramírez, L., McDonald, J.F., and Jordan I.K., 2017. Population and clinical genetics of human transposable elements in the (post) genomic era. Mob Genet Elements. 7: 1-20.
Gupta, A., Jordan, I.K., and Rishishwar, L., 2017. stringMLST: a fast k-mer based tool for multi locus sequence typing. Bioinformatics. 33: 119-121.
Topaz, N., Mojib, N., Chande, A.T., Kubanek, J., and Jordan, I.K., 2017. RampDB: a web application and database for the exploration and prediction of receptor activity modifying protein interactions. Database. 2017: bax067.
2016
Bugrysheva JV, Cherney B, Sue D, Conley AB, Rowe LA, Knipe KM, et al., 2016. Complete Genome Sequences for Three Chromosomes of the Burkholderia stabilis Type Strain (ATCC BAA-67). Genome Announc. 4(6).
Clayton, E.A., Wang, L., Rishishwar, L., Wang, J., McDonald, J.F., and Jordan I.K., 2016. Patterns of transposable element expression and insertion in cancer. Front. Mol. Biosci. 3: 76.
Watve, S., Chande, A.T., Rishishwar, L., Bernardy, E.E., Mariño-Ramírez, L., Jordan, I.K., and Hammer, B.K., 2016. Whole genome sequence of 26 environmental Vibrio cholerae isolates. Genome Announcements. 4: e01396-16
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. Comparative genomic analysis of Haemophilus haemolyticus and non-typeable Haemophilus influenzae and a new testing scheme for their discrimination. J. Clin. Micro. 54: 3010-3017.
Orata, F.D., Xu, Y., Gladney, L.M., Rishishwar, L., Case, R.J., Boucher, Y., Jordan, I.K., and Tarr, C.L., 2016. Characterization of clinical and environmental isolates of Vibrio cidicii sp. nov., a close relative of Vibrio navarrensis. Int J Syst Evol Microbiol. 66: 4148-4155.
Rishishwar, L., Kraft, C.S., and Jordan, I.K., 2016. Population genomics of reduced vancomycin susceptibility in Staphylococcus aureus. mSphere. 1: e00094-16.
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. Lateral gene transfer in a heavy metal-contaminated groundwater microbial community. mBio. 7: e02234-15.
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. 6: 45-54.