Onyia NE, Osagie E, Akhigbe P, Idemudia NL, Obuekwe O, Omoigberale A, Richards VP, Coker MO (2024) Impact of perinatal HIV exposure and infection on salivary properties among Nigerian children. BMC Oral Health (In press). [DOI]
Mann AE, Chakraborty B, O’Connell LM, Nascimento MM, Burne RA, Coker MO, Richards VP (2024) Heterogeneous lineage-specific arginine deiminase expression within dental microbiome species. Microbiology Spectrum. [DOI]
O’Connell LM, Mann AE, Osagie E, Akhigbe P, Blouin T, Soule A, Obuekwe O, Omoigberale A, Burne RA, Coker MO, Richards VP (2023) Supragingival mycobiome of HIV-exposed-but-uninfected children reflects a stronger correlation with caries-free associated taxa compared to HIV-infected or uninfected children. Microbiology Spectrum. [DOI]
Mann AE, O'Connell LM, Osagie E, Akhigbe P, Obuekwe O, Omoigberale A, Kelly C, Coker MO, and Richards VP (2023) The impact of HIV on the oral microbiome of children living in Sub-Saharan Africa using a rpoC gene-fragment metataxonomic approach. Microbiology Spectrum. [DOI]
Onyia NE, Akhigbe P, Osagie E, Obuekwe O, Omoigberale A, Richards VP, Coker MO (2023) Prevalence and associated factors of developmental defects of enamel among Nigerian children with HIV exposure. Journal of Clinical Pediatric Dentistry. [DOI]
Akhigbe P, Chukwumah NM, Adebiyi R, Folayan MO, Divaris K, Obuekwe O, Omoigberale A, Jedy-Agba E, Kim M, Charurat M, Richards VP, Coker MO (2022) Age-specific associations with dental caries in HIV-infected, exposed but uninfected and HIV-unexposed uninfected children in Nigeria. BMC Oral Health, 22(1):429 [DOI]
O’Connell LM, Blouin T, Soule A, Burne RA, Nascimento MM, Richards VP (2022) Optimization and evaluation of the 30S-S11 rDNA gene for taxonomic profiling of oral streptococci. Applied and Environmental Microbiology. [PDF] Hassler HB, Probert B, Moore C, Lawson E, Jackson RW, Russell BT, Richards VP (2022) Phylogenies of the 16S rRNA gene and its hypervariable regions lack concordance with core genome phylogenies. Microbiome. [DOI]
Rathbone T, Ates I, Fernando L, Addlestone E, Lee CM, Richards VP, Cottle RN (2022) Electroporation-mediated delivery of cas9 ribonucleoproteins results in high levels of gene editing in primary hepatocytes. The CRISPR Journal. [DOI]
Coker MO, Akhigbe P, Osagie E, Idemudia NL, Igedegbe O, Chukwumah N, Adebiyi R, Mann AE, O’Connell LM, Obuekwe O, Omoigberale A, Charurat M, Richards VP (2021) Dental caries and its association with the oral microbiomes and HIV in young children – Nigeria (DOMHaIN): a cohort study. BMC Oral Health 21, 620. [DOI]
Richards VP, Nigsch A, Pavinski Bitar P, Sun Q, Stuber T, Ceres K, Robbe Austerman S, Schukken Y, Grohn YT, and Stanhope MJ (2021) Evolutionary genomic and bacteria GWAS analysis of Mycobacterium avium subsp. paratuberculosis and dairy cattle Johne’s disease phenotypes. Applied and Environmental Microbiology. [PDF] Ma X, Agudelo P, Richards VP, Baeza AJ (2020) The complete mitochondrial genome of the Columbia lance nematode, Hoplolaimus columbus, a major agricultural pathogen in North America. Parasites & Vectors, 13:321. [DOI] Cushman LJ, Richards VP, McMillan PD (2020) Micranthes petiolaris variety shealyi: A New Variety of Micranthes (Section Stellares, Saxifragaceae) from South Carolina. Phytotaxa, 452:2 O'Connell LM, Santos R, Springer G, Burne RA, Nascimento MM, Richards VP (2020) Site-specific profiling of the dental mycobiome reveals strong taxonomic shifts during progression of early childhood caries. Applied and Environmental Microbiology, 18;86(7). [PDF] Richards VP, Velsko IM, Alam TM, Zadoks RN, Manning SD, Pavinski Bitar PD, Hassler HB, Crestani C, Springer G, Probert B, Town CD, Stanhope MJ (2019) Population gene introgression and high genome plasticity for the zoonotic pathogen Streptococcus agalactiae. Molecular Biology and Evolution. [DOI] Nascimento MM, Alvarez AJ, Huang X, Browngardt C, Jenkins R, Sinhoreti MC, Ribeiro APD, Dilbone DA, Richards VP, Garrett TJ, Burne RA (2019) Metabolic profile of supragingival plaque exposed to arginine and fluoride. Journal of Dental Research. [DOI] Kaspar J, Godwin M, Velsko IM, Richards VP, Burne RA (2019) Spontaneously arising Streptococcus mutans variants with reduced susceptibility to chlorhexidine display genetic defects and diminished fitness. Antimicrobial Agents and Chemotherapy. [DOI] Velsko IM, Perez MS, Richards VP (2019) Resolving phylogenetic relationships for Streptococcus mitis and Streptococcus oralis, through core and pan genome analyses. Genome Biology and Evolution. [DOI] Nascimento MM, Alvarez AJ, Huang X, Hanway S, Perry S, Luce A, Richards VP, Burne RA (2019). Arginine metabolism in supragingival oral biofilms as a predictor of caries risk. JDR Clinical & Translational Research. [DOI] Marra NJ, Stanhope MJ, Jue N, Wang M, Sun Q, Pavinski Bitar P, Richards VP, Komissarov A, Rayko M, Kliver S, Stanhope BJ, Winkler C, O’Brien SJ, Antunes A, Jorgensen S, Shivji MS (2019) White shark genome: ancient elasmobranch adaptations addressing genome stability. PNAS 201819778. [DOI] Velsko IM, Chakraborty B, Nascimento M, Burne RA, Richards VP (2018) Species designations belie phenotypic and genotypic heterogeneity in oral Streptococci. mSystems, 3 (6) e00158-18; doi: 10.1128/mSystems.00158-18 [PDF] Abranches J, Zeng L, Kajfasz JK, Palmer SR, Chakraborty B, Wen ZT, Richards VP, Burne, RA, Brady LJ, Lemos JA. Biology of oral Streptococci (2018). Microbiol Spectrum 6(5). [DOI] Richards VP, DeBiasse M, Shivji MS (2018) Deep mitochondrial lineage divergence among populations of the southern stingray (Hypanus americana) throughout the Southeastern United States and Caribbean. Marine Biodiversity. [DOI] Bernard AM, Richards VP, Stanhope MJ, Shivji MS (2018) Transcriptome derived simple sequence repeats confirm the genetic isolation of Northeast Pacific white sharks. Journal of Heredity, 109, 771 – 779. [DOI] Chen Y, Hammer EE, Richards VP. (2018) Phylogenetic signature of lateral exchange of genes for antibiotic production and resistance among bacteria highlights a pattern of global transmission of pathogens between humans and livestock. Molecular Phylogenetics and Evolution, 125, 255-264. [PDF] He J, Kim D, Zhou X, Ahn S, Burne R, Richards VP, Koo H. (2017). RNA-seq reveals transcriptomic changes of Streptococcus mutans co-culturing with Candida albicans within mixed-species biofilms. Frontiers in Microbiology. [DOI]
Richards VP, Alvarez AJ, Luce A, Perry S, Bedenbaugh M, Mitchell M, Hong H, Shaddox LM, Burne RA, Nascimento MM. (2017). Microbiomes of site-specific dental plaque of children with different caries status. Infection and Immunity. [PDF] Marra NJ, Richards VP, Early A, Bogdanowicz SM, Pavinski Bitar P, Stanhope MJ, Shivji MS. (2017) Comparative transcriptomics of elasmobranchs and teleosts highlight important processes in adaptive immunity and regional endothermy. BMC Genomics, 18-87. [DOI] Jacob A, O'Brien Andersen L, Pavinski Bitar P, Richards VP, Shah S, Stanhope MJ, Stensvold R, Clark G (2016). Blastocystis mitochondrial genomes appear to show multiple independent gains and losses of start and stop codons. Genome Biology and Evolution, 8, 3340-3350. [DOI] Palmer A, Painter J, Hassler HB, Richards VP, Bruce T, Morrison S, Brown E, Kozak NA, Lucas C, McNealy TL. (2016) Legionella clemsonensis sp. nov., - a green fluorescing Legionella strain from a patient with pneumonia. Microbiology and Immunology, 60, 694-701. [DOI] DeBiasse MB, Richards VP, Shivji MS, Hellberg ME. (2016) Shared phylogeographic breaks in a Caribbean coral reef sponge and its invertebrate commensals. Journal of Biogeography. [DOI] Richards VP, Bernard AM, Feldheim KA, Shivji MS. (2016) Patterns of population structure and dispersal in the long-lived "redwood" of the coral reef, the giant barrel sponge (Xestospongia muta). Coral Reefs, 1-11. [PDF] Huang X, Palmer SR, Ahn SJ, Richards VP, Williams ML, Nascimento MM, Burne R (2016) A Highly Arginolytic Streptococcus Species That Potently Antagonizes Streptococcus mutans. Applied and environmental microbiology. 82, 2187-2201. [DOI] Richards VP, Lefébure T, Pavinski Bitar PD, Simpson KW, Schukken YH, Stanhope MJ. (2015) Genome based phylogeny and comparative genomic analysis of intra-mammary pathogenic Escherichia coli. PloS One, 10(3):e0119799. [DOI] Richards VP, DeBiasse MB, Shivji MS (2014) Genetic evidence supports larval retention in the Western Caribbean for an invertebrate with high dispersal capability (Ophiothrix suensonii: Echinodermata, Ophiuroidea). Coral Reefs, DOI: 10.1007/s00338-014-1237-z [PDF] Choi SC, Parker J, Richards VP, Ross K, Jilly B, Chen J. (2014) Draft genome sequence of an atypical strain of Streptococcus pneumoniae isolated from a respiratory infection. Genome announcements 2, 4. [DOI] Richards VP, Palmer SR, Highlander S, Pavinski Bitar PD, Qin X, Weinstock GM, Highlander SK, Town CD, Burne RA, Stanhope MJ (2014) Phylogenomics and the dynamic genome evolution of the genus Streptococcus. Genome Biology and Evolution, 6, 741 - 753. [PDF] Richards VP, Choi SC, Pavinski Bitar PD, Gurjar AA, Stanhope MJ (2013) Transcriptomic and genomic evidence for Streptococcus agalactiae adaptation to the bovine environment. BMC Genomics, 14, 920. [PDF] Richards VP, Suzuki H, Stanhope MJ, Shivji MS (2013) Characterization of the heart transcriptome of the white shark (Carcharodon carcharias). BMC Genomics, 14, 697. [PDF] Richards VP, Greig TW, Fair PA, McCulloch SD, Politz C, Natoli A, Driscoll CA, Hoelzel RA, David V, Bossart GD, Lopez JV (2013) Patterns of population structure for inshore bottlenose dolphins along the eastern United States. Journal of Heredity, 104, 765 – 778. [PDF] Palmer SR, Miller JH, Abranches J, Zeng L, Lefébure T, Richards VP, Lemos JA, Stanhope MJ, Burne RA (2013) Phenotypic heterogeneity of genomically-diverse isolates of Streptococcus mutans. PloS One, 10(1371): e0061358. [DOI] Richards VP, Lefébure T, Pavinski Bitar PD, Stanhope MJ (2012) Comparative characterization of the virulence gene clusters (lipooligosaccharide [LOS] and capsular polysaccharide [CPS]) for Campylobacter coli, Campylobacter jejuni subsp. jejuni and related Campylobacter species. Infection Genetics and Evolution, 14, 200 – 213. [PDF] Richards VP, Zadoks RN, Pavinski Bitar PD, Lefébure T, Lang P, Werner B, Tikofsky L, Moroni P, Stanhope MJ (2012) Genome characterization and population genetic structure of the zoonotic pathogen, Streptococcus canis. BMC Microbiology, 12, 293. [PDF] Cornejo OE, Lefébure T, Pavinski Bitar PD, Lang P, Richards VP, Eilertson K, Do T, Beighton D, Zeng L, Ahn SJ, Burne RA, Siepel A, Carlos D. Bustamante CD, Stanhope MJ (2012) Evolutionary and population genomics of the cavity causing bacteria Streptococcus mutans. Molecular Biology and Evolution, 30, 881 – 893. [DOI] Bernard AM, Feldheim KA, Richards VP, Nemeth RS, Shivji MS (2012) Development and characterization of fifteen novel microsatellite loci for the Nassau grouper (Epinephelus striatus) and their utility for cross-amplification on a suite of closely related species. Conservation Genetic Resources, 4, 983 – 986. [DOI] Lefébure T, Richards VP, Lang P, Pavinski-Bitar P, Stanhope MJ (2012) Gene repertoire evolution of Streptococcus pyogenes inferred from phylogenomic analysis with Streptococcus canis and Streptococcus dysgalactiae. PLoS One, 7(5): e37607. [DOI] Richards VP, Stanhope MJ, Shivji MS (2012) Island endemism, morphological stasis, and possible cryptic speciation in two coral reef, commensal Leucothoid amphipod species throughout Florida and the Caribbean. Biodiversity and Conservation, 21, 343 – 361. [PDF] Richards VP, Lang P, Bitar PD, Lefébure T, Schukken YH, Zadoks RN, Stanhope MJ (2011) Comparative genomics and the role of lateral gene transfer in the evolution of bovine adapted Streptococcus agalactiae. Infection Genetics and Evolution, 11, 1263 – 1275. [PDF] Feldheim KA, Chapman DD, Simpfendorfer CA, Richards VP, Shivji MS, Wiley TR, Poulakis GR, Carlson JK, Eng R, Sargarese S (2009) Genetic tools to support the conservation of the endangered smalltooth sawfish, Pristis pectinata. Conservation Genetics Resources, 2, 105 – 113. DeBiasse MB, Richards VP, Shivji MS (2009) Genetic assessment of connectivity in the common reef sponge, Callyspongia vaginalis (Demospongiae: Haplosclerida) reveals high population structure along the Florida reef tract. Coral Reefs, 29, 47 – 55. Smith WD, Bizzarro JJ, Richards VP, Nielsen J, Márquez-Farías F, Shivji MS (2009) Morphometric convergence and molecular divergence: the taxonomic status and evolutionary history of Gymnura crebripunctata and Gymnura marmorata in the eastern Pacific Ocean. Journal of Fish Biology, 75, 761 – 783. Richards VP, Henning M, Witzell W, Shivji MS (2009) Species delineation and evolutionary history of the globally distributed spotted eagle ray (Aetobatus narinari). Journal of Heredity, 100, 273 – 283. [PDF] Banks KW, Riegl BM, Richards VP, Walker BK, Helmle KP, Jordan LKB, Phipps J, Shivji MS, Spieler RE, Dodge RE (2008) The reef tract of continental Southeast Florida (Miami-Dade, Broward and Palm Beach Counties, USA). In: Coral reefs of the USA (eds. Riegl BM, Dodge RE), pp 175 220. Springer.com. Richards VP, Thomas JD, Stanhope MJ, Shivji MS (2007) Genetic connectivity in the Florida reef system: comparative phylogeography of commensal invertebrates with contrasting reproductive strategies. Molecular Ecology, 16, 139 – 157. [PDF]
Department of Biological Sciences, College of Science, Clemson University, Clemson, SC 29634