Matthew Settles

Title(s)Bioinformatics Programmer 4, Biochemistry and Biophysics
SchoolSchool of Medicine
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    Altmetrics Details PMC Citations indicate the number of times the publication was cited by articles in PubMed Central, and the Altmetric score represents citations in news articles and social media. (Note that publications are often cited in additional ways that are not shown here.) Fields are based on how the National Library of Medicine (NLM) classifies the publication's journal and might not represent the specific topic of the publication. Translation tags are based on the publication type and the MeSH terms NLM assigns to the publication. Some publications (especially newer ones and publications not in PubMed) might not yet be assigned Field or Translation tags.) Click a Field or Translation tag to filter the publications.
    1. High-volume hybridoma sequencing on the NeuroMabSeq platform enables efficient generation of recombinant monoclonal antibodies and scFvs for neuroscience research. Sci Rep. 2023 09 27; 13(1):16200. Mitchell KG, Gong B, Hunter SS, Burkart-Waco D, Gavira-O'Neill CE, Templeton KM, Goethel ME, Bzymek M, MacNiven LM, Murray KD, Settles ML, Froenicke L, Trimmer JS. PMID: 37758930; PMCID: PMC10533561.
      View in: PubMed   Mentions:    Fields:    Translation:AnimalsCells
    2. NeuroMabSeq: high volume acquisition, processing, and curation of hybridoma sequences and their use in generating recombinant monoclonal antibodies and scFvs for neuroscience research. bioRxiv. 2023 Jun 30. Mitchell KG, Gong B, Hunter SS, Burkart-Waco D, Gavira-O'Neill CE, Templeton KM, Goethel ME, Bzymek M, MacNiven LM, Murray KD, Settles ML, Froenicke L, Trimmer JS. PMID: 37425915; PMCID: PMC10327083.
      View in: PubMed   Mentions:
    3. Human soft tissue sarcomas harbor an intratumoral viral microbiome which is linked with natural killer cell infiltrate and prognosis. J Immunother Cancer. 2023 01; 11(1). Perry LM, Cruz SM, Kleber KT, Judge SJ, Darrow MA, Jones LB, Basmaci UN, Joshi N, Settles ML, Durbin-Johnson BP, Gingrich AA, Monjazeb AM, Carr-Ascher J, Thorpe SW, Murphy WJ, Eisen JA, Canter RJ. PMID: 36599469; PMCID: PMC9815021.
      View in: PubMed   Mentions: 5     Fields:    Translation:HumansCells
    4. Workshop-based learning and networking: a scalable model for research capacity strengthening in low- and middle-income countries. Glob Health Action. 2022 12 31; 15(1):2062175. Perier C, Nasinghe E, Charles I, Ssetaba LJ, Ahyong V, Bangs D, Beatty PR, Czudnochowski N, Diallo A, Dugan E, Fabius JM, Fong Baker H, Gardner J, Isaacs S, Joanah B, Kalantar K, Kateete D, Knight M, Krasilnikov M, Krogan NJ, Langelier C, Lee E, Li LM, Licht D, Lien K, Lyons Z, Mboowa G, Mwebaza I, Mwesigwa S, Nalwadda G, Nichols R, Penaranda ME, Petnic S, Phelps M, Popper SJ, Rape M, Reingold A, Robbins R, Rosenberg OS, Savage DF, Schildhauer S, Settles ML, Sserwadda I, Stanley S, Tato CM, Tsitsiklis A, Van Dis E, Vanaerschot M, Vinden J, Cox JS, Joloba ML, Schaletzky J. PMID: 35730550; PMCID: PMC9225690.
      View in: PubMed   Mentions:    Fields:    Translation:HumansPHPublic Health
    5. Biofilms preserve the transmissibility of a multi-drug resistance plasmid. NPJ Biofilms Microbiomes. 2022 12 09; 8(1):95. Metzger GA, Ridenhour BJ, France M, Gliniewicz K, Millstein J, Settles ML, Forney LJ, Stalder T, Top EM. PMID: 36481746; PMCID: PMC9732292.
      View in: PubMed   Mentions: 6     Fields:    
    6. A two-stage digestion of whole murine knee joints for single-cell RNA sequencing. Osteoarthr Cartil Open. 2022 Dec; 4(4):100321. Leale DM, Li L, Settles ML, Mitchell K, Froenicke L, Yik JHN, Haudenschild DR. PMID: 36474787; PMCID: PMC9718180.
      View in: PubMed   Mentions:
    7. Comparative Transcriptional Analyses in the Nucleus Accumbens Identifies RGS2 as a Key Mediator of Depression-Related Behavior. Biol Psychiatry. 2022 12 15; 92(12):942-951. Williams AV, Peña CJ, Ramos-Maciel S, Laman-Maharg A, Ordoñez-Sanchez E, Britton M, Durbin-Johnson B, Settles M, Hao R, Yokoyama S, Xu C, Luo PX, Dwyer T, Bhela S, Black AM, Labonté B, Serafini RA, Ruiz A, Neve RL, Zachariou V, Nestler EJ, Trainor BC. PMID: 36075764; PMCID: PMC9794384.
      View in: PubMed   Mentions: 4     Fields:    Translation:Animals
    8. Effects of pairing on color change and central gene expression in lined seahorses. Genes Brain Behav. 2022 06; 21(5):e12812. Mederos SL, Duarte RC, Mastoras M, Dennis MY, Settles ML, Lau AR, Scott A, Woodward K, Johnson C, Seelke AMH, Bales KL. PMID: 35652318; PMCID: PMC9744553.
      View in: PubMed   Mentions: 4     Fields:    Translation:HumansAnimals
    9. Sex disparate gut microbiome and metabolome perturbations precede disease progression in a mouse model of Rett syndrome. Commun Biol. 2021 12 16; 4(1):1408. Neier K, Grant TE, Palmer RL, Chappell D, Hakam SM, Yasui KM, Rolston M, Settles ML, Hunter SS, Madany A, Ashwood P, Durbin-Johnson B, LaSalle JM, Yasui DH. PMID: 34916612; PMCID: PMC8677842.
      View in: PubMed   Mentions: 5  Translation:Animals
    10. Dual transcriptomic analysis reveals metabolic changes associated with differential persistence of human pathogenic bacteria in leaves of Arabidopsis and lettuce. G3 (Bethesda). 2021 Dec 08; 11(12). Jacob C, Velásquez AC, Josh NA, Settles M, He SY, Melotto M. PMID: 34550367; PMCID: PMC8664426.
      View in: PubMed   Mentions: 4     Fields:    Translation:HumansAnimalsCells
    11. Establishment of quantitative RNAi-based forward genetics in Entamoeba histolytica and identification of genes required for growth. PLoS Pathog. 2021 11; 17(11):e1010088. Bettadapur A, Hunter SS, Suleiman RL, Ruyechan MC, Huang W, Barbieri CG, Miller HW, Tam TSY, Settles ML, Ralston KS. PMID: 34843592; PMCID: PMC8716031.
      View in: PubMed   Mentions: 2     Fields:    Translation:Animals
    12. Protective heterologous T cell immunity in COVID-19 induced by the trivalent MMR and Tdap vaccine antigens. Med. 2021 09 10; 2(9):1050-1071.e7. Mysore V, Cullere X, Settles ML, Ji X, Kattan MW, Desjardins M, Durbin-Johnson B, Gilboa T, Baden LR, Walt DR, Lichtman AH, Jehi L, Mayadas TN. PMID: 34414383; PMCID: PMC8363466.
      View in: PubMed   Mentions: 23     Fields:    Translation:HumansCells
    13. Diversification, Introgression, and Rampant Cytonuclear Discordance in Rocky Mountains Chipmunks (Sciuridae: Tamias). Syst Biol. 2021 08 11; 70(5):908-921. Sarver BAJ, Herrera ND, Sneddon D, Hunter SS, Settles ML, Kronenberg Z, Demboski JR, Good JM, Sullivan J. PMID: 33410870; PMCID: PMC8786503.
      View in: PubMed   Mentions: 9     Fields:    Translation:HumansAnimals
    14. Inhibition of MET Signaling with Ficlatuzumab in Combination with Chemotherapy in Refractory AML: Clinical Outcomes and High-Dimensional Analysis. Blood Cancer Discov. 2021 09; 2(5):434-449. Wang VE, Blaser BW, Patel RK, Behbehani GK, Rao AA, Durbin-Johnson B, Jiang T, Logan AC, Settles M, Mannis GN, Olin R, Damon LE, Martin TG, Sayre PH, Gaensler KM, McMahon E, Flanders M, Weinberg V, Ye CJ, Carbone DP, Munster PN, Fragiadakis GK, McCormick F, Andreadis C. PMID: 34514432; PMCID: PMC8425277.
      View in: PubMed   Mentions: 3     Fields:    Translation:Humans
    15. Wilson Disease: Intersecting DNA Methylation and Histone Acetylation Regulation of Gene Expression in a Mouse Model of Hepatic Copper Accumulation. Cell Mol Gastroenterol Hepatol. 2021; 12(4):1457-1477. Sarode GV, Neier K, Shibata NM, Shen Y, Goncharov DA, Goncharova EA, Mazi TA, Joshi N, Settles ML, LaSalle JM, Medici V. PMID: 34098115; PMCID: PMC8487080.
      View in: PubMed   Mentions: 4     Fields:    Translation:HumansAnimalsCells
    16. The auxin-producing Bacillus thuringiensis RZ2MS9 promotes the growth and modifies the root architecture of tomato (Solanum lycopersicum cv. Micro-Tom). Arch Microbiol. 2021 Sep; 203(7):3869-3882. Batista BD, Dourado MN, Figueredo EF, Hortencio RO, Marques JPR, Piotto FA, Bonatelli ML, Settles ML, Azevedo JL, Quecine MC. PMID: 34013419.
      View in: PubMed   Mentions: 20     Fields:    Translation:AnimalsCells
    17. Protective heterologous T cell immunity in COVID-19 induced by MMR and Tdap vaccine antigens. bioRxiv. 2021 May 04. Mysore V, Cullere X, Settles ML, Ji X, Kattan MW, Desjardins M, Durbin-Johnson B, Gilboa T, Baden LR, Walt DR, Lichtman A, Jehi L, Mayadas TN. PMID: 33972940; PMCID: PMC8109200.
      View in: PubMed   Mentions:
    18. Disruption of global hypothalamic microRNA (miR) profiles and associated behavioral changes in California mice (Peromyscus californicus) developmentally exposed to endocrine disrupting chemicals. Horm Behav. 2021 02; 128:104890. Kaur S, Kinkade JA, Green MT, Martin RE, Willemse TE, Bivens NJ, Schenk AK, Helferich WG, Trainor BC, Fass J, Settles M, Mao J, Rosenfeld CS. PMID: 33221288; PMCID: PMC7897400.
      View in: PubMed   Mentions: 12     Fields:    Translation:Animals
    19. Chromatin accessibility in canine stromal cells and its implications for canine somatic cell reprogramming. Stem Cells Transl Med. 2020 Nov 16. Questa M, Moshref M, Jimenez RJ, Lopez-Cervantes V, Crawford CK, Settles ML, Ross PJ, Kol A. PMID: 33210453; PMCID: PMC7900587.
      View in: PubMed   Mentions: 3     Fields:    
    20. Association of the Lactase Persistence Haplotype Block With Disease Risk in Populations of European Descent. Front Genet. 2020; 11:558762. Joslin SEK, Durbin-Johnson BP, Britton M, Settles ML, Korf I, Lemay DG. PMID: 33193640; PMCID: PMC7658388.
      View in: PubMed   Mentions: 2  
    21. Transcriptomic response to elevated water temperatures in adult migrating Yukon River Chinook salmon (Oncorhynchus tshawytscha). Conserv Physiol. 2020; 8(1):coaa084. Bowen L, von Biela VR, McCormick SD, Regish AM, Waters SC, Durbin-Johnson B, Britton M, Settles ML, Donnelly DS, Laske SM, Carey MP, Brown RJ, Zimmerman CE. PMID: 34512988; PMCID: PMC7486460.
      View in: PubMed   Mentions: 5  
    22. MYBPC3 Haplotype Linked to Hypertrophic Cardiomyopathy in Rhesus Macaques (Macaca mulatta). Comp Med. 2020 10 01; 70(5):358-367. Oldt RF, Bussey KJ, Settles ML, Fass JN, Roberts JA, Reader JR, Komandoor S, Abrich VA, Kanthaswamy S. PMID: 32753092; PMCID: PMC7574221.
      View in: PubMed   Mentions:    Fields:    Translation:HumansAnimals
    23. Complete Genome Sequence of Bacillus sp. Strain RZ2MS9, a Multitrait Plant Growth Promoter. Microbiol Resour Announc. 2020 Jul 30; 9(31). Bonatelli ML, Li J, Dumaresq A, Quecine MC, Settles ML. PMID: 32732234; PMCID: PMC7393963.
      View in: PubMed   Mentions: 1  
    24. Bioinformatics Core Survey Highlights the Challenges Facing Data Analysis Facilities. J Biomol Tech. 2020 07; 31(2):66-73. Dragon JA, Gates C, Sui SH, Hutchinson JN, Karuturi RKM, Kucukural A, Polson S, Riva A, Settles ML, Thimmapuram J, Levine SS. PMID: 32382253; PMCID: PMC7192196.
      View in: PubMed   Mentions: 2     Fields:    Translation:Humans
    25. Proximal femoral head transcriptome reveals novel candidate genes related to epiphysiolysis in broiler chickens. BMC Genomics. 2019 Dec 30; 20(1):1031. de Oliveira Peixoto J, Savoldi IR, Ibelli AMG, Cantão ME, Jaenisch FRF, Giachetto PF, Settles ML, Zanella R, Marchesi JAP, Pandolfi JR, Coutinho LL, Ledur MC. PMID: 31888477; PMCID: PMC6937697.
      View in: PubMed   Mentions: 8     Fields:    Translation:AnimalsCells
    26. Rectal Microbiome Composition Correlates with Humoral Immunity to HIV-1 in Vaccinated Rhesus Macaques. mSphere. 2019 12 11; 4(6). Elizaldi SR, Verma A, Walter KA, Rolston M, Dinasarapu AR, Durbin-Johnson BP, Settles M, Kozlowski PA, Raeman R, Iyer SS. PMID: 31826975; PMCID: PMC6908426.
      View in: PubMed   Mentions: 12     Fields:    Translation:AnimalsCells
    27. Single-Cell RNA-seq Reveals Profound Alterations in Mechanosensitive Dorsal Root Ganglion Neurons with Vitamin E Deficiency. iScience. 2019 Nov 22; 21:720-735. Finno CJ, Peterson J, Kang M, Park S, Bordbari MH, Durbin-Johnson B, Settles M, Perez-Flores MC, Lee JH, Yamoah EN. PMID: 31733517; PMCID: PMC6864320.
      View in: PubMed   Mentions: 7  
    28. Additional Evidence for DDB2 T338M as a Genetic Risk Factor for Ocular Squamous Cell Carcinoma in Horses. Int J Genomics. 2019; 2019:3610965. Singer-Berk MH, Knickelbein KE, Lounsberry ZT, Crausaz M, Vig S, Joshi N, Britton M, Settles ML, Reilly CM, Bentley E, Nunnery C, Dwyer A, Lassaline ME, Bellone RR. PMID: 31637255; PMCID: PMC6766160.
      View in: PubMed   Mentions: 3  
    29. Ultrahigh-Throughput Multiplexing and Sequencing of >500-Base-Pair Amplicon Regions on the Illumina HiSeq 2500 Platform. mSystems. 2019 Jan-Feb; 4(1). Holm JB, Humphrys MS, Robinson CK, Settles ML, Ott S, Fu L, Yang H, Gajer P, He X, McComb E, Gravitt PE, Ghanem KG, Brotman RM, Ravel J. PMID: 30801027; PMCID: PMC6381223.
      View in: PubMed   Mentions: 66     Fields:    
    30. Transcriptome Analysis of Salmonella Heidelberg after Exposure to Cetylpyridinium Chloride, Acidified Calcium Hypochlorite, and Peroxyacetic Acid. J Food Prot. 2019 01; 82(1):109-119. Cadena M, Froenicke L, Britton M, Settles ML, Durbin-Johnson B, Kumimoto E, Gallardo RA, Ferreiro A, Chylkova T, Zhou H, Pitesky M. PMID: 30702951.
      View in: PubMed   Mentions: 5     Fields:    Translation:AnimalsCellsPHPublic Health
    31. Fatherhood alters gene expression within the MPOA. Environ Epigenet. 2018 Oct; 4(4):dvy026. Seelke AMH, Bond JM, Simmons TC, Joshi N, Settles ML, Stolzenberg D, Rhemtulla M, Bales KL. PMID: 30568805; PMCID: PMC6305489.
      View in: PubMed   Mentions: 6  
    32. Obesity treatment by epigallocatechin-3-gallate-regulated bile acid signaling and its enriched Akkermansia muciniphila. FASEB J. 2018 Jun 08; fj201800370R. Sheng L, Jena PK, Liu HX, Hu Y, Nagar N, Bronner DN, Settles ML, Bäumler AJ, Wan YY. PMID: 29882708; PMCID: PMC6219838.
      View in: PubMed   Mentions: 44     Fields:    
    33. High-Quality Complete Genome Sequences of Three Bovine Shiga Toxin-Producing Escherichia coli O177:H- (fliCH25) Isolates Harboring Virulent stx2 and Multiple Plasmids. Genome Announc. 2018 Feb 15; 6(7). Sheng H, Duan M, Hunter SS, Minnich SA, Settles ML, New DD, Chase JR, Fagnan MW, Hovde CJ. PMID: 29449403; PMCID: PMC5814490.
      View in: PubMed   Mentions: 3  
    34. 16S rRNA analysis of diversity of manure microbial community in dairy farm environment. PLoS One. 2018; 13(1):e0190126. Pandey P, Chiu C, Miao M, Wang Y, Settles M, Del Rio NS, Castillo A, Souza A, Pereira R, Jeannotte R. PMID: 29304047; PMCID: PMC5755784.
      View in: PubMed   Mentions: 14     Fields:    Translation:Animals
    35. Human Milk Microbial Community Structure Is Relatively Stable and Related to Variations in Macronutrient and Micronutrient Intakes in Healthy Lactating Women. J Nutr. 2017 09; 147(9):1739-1748. Williams JE, Carrothers JM, Lackey KA, Beatty NF, York MA, Brooker SL, Shafii B, Price WJ, Settles ML, McGuire MA, McGuire MK. PMID: 28724659; PMCID: PMC5572491.
      View in: PubMed   Mentions: 69     Fields:    Translation:HumansCells
    36. Unlocking the story in the swab: A new genotyping assay for the amphibian chytrid fungus Batrachochytrium dendrobatidis. Mol Ecol Resour. 2017 Nov; 17(6):1283-1292. Byrne AQ, Rothstein AP, Poorten TJ, Erens J, Settles ML, Rosenblum EB. PMID: 28371384.
      View in: PubMed   Mentions: 13     Fields:    Translation:Animals
    37. Genomic Methods and Microbiological Technologies for Profiling Novel and Extreme Environments for the Extreme Microbiome Project (XMP). J Biomol Tech. 2017 04; 28(1):31-39. Tighe S, Afshinnekoo E, Rock TM, McGrath K, Alexander N, McIntyre A, Ahsanuddin S, Bezdan D, Green SJ, Joye S, Stewart Johnson S, Baldwin DA, Bivens N, Ajami N, Carmical JR, Herriott IC, Colwell R, Donia M, Foox J, Greenfield N, Hunter T, Hoffman J, Hyman J, Jorgensen E, Krawczyk D, Lee J, Levy S, Garcia-Reyero N, Settles M, Thomas K, Gómez F, Schriml L, Kyrpides N, Zaikova E, Penterman J, Mason CE. PMID: 28337070; PMCID: PMC5345951.
      View in: PubMed   Mentions: 24     Fields:    Translation:PHPublic Health
    38. Erratum to: Small RNAs from a Big Genome: The piRNA Pathway and Transposable Elements in the Salamander Species Desmognathus fuscus. J Mol Evol. 2017 01; 84(1):67. Madison-Villar MJ, Sun C, Lau NC, Settles ML, Mueller RL. PMID: 27909757.
      View in: PubMed   Mentions: 1     Fields:    
    39. Small RNAs from a Big Genome: The piRNA Pathway and Transposable Elements in the Salamander Species Desmognathus fuscus. J Mol Evol. 2016 Oct; 83(3-4):126-136. Madison-Villar MJ, Sun C, Lau NC, Settles ML, Mueller RL. PMID: 27743003.
      View in: PubMed   Mentions: 7     Fields:    Translation:AnimalsCells
    40. Love the one you're with: replicate viral adaptations converge on the same phenotypic change. PeerJ. 2016; 4:e2227. Miller CR, Nagel AC, Scott L, Settles M, Joyce P, Wichman HA. PMID: 27547540; PMCID: PMC4958007.
      View in: PubMed   Mentions: 5     Fields:    
    41. A Phylogenomic Approach Based on PCR Target Enrichment and High Throughput Sequencing: Resolving the Diversity within the South American Species of Bartsia L. (Orobanchaceae). PLoS One. 2016; 11(2):e0148203. Uribe-Convers S, Settles ML, Tank DC. PMID: 26828929; PMCID: PMC4734709.
      View in: PubMed   Mentions: 26     Fields:    Translation:AnimalsCells
    42. Full Mitochondrial Genome Sequence of the Sugar Beet Wireworm Limonius californicus (Coleoptera: Elateridae), a Common Agricultural Pest. Genome Announc. 2016 Jan 21; 4(1). Gerritsen AT, New DD, Robison BD, Rashed A, Hohenlohe P, Forney L, Rashidi M, Wilson CM, Settles ML. PMID: 26798113; PMCID: PMC4722280.
      View in: PubMed   Mentions: 5  
    43. Mitochondrial Genome Sequence of the Galápagos Endemic Land Snail Naesiotus nux. Genome Announc. 2016 Jan 21; 4(1). Hunter SS, Settles ML, New DD, Parent CE, Gerritsen AT. PMID: 26798085; PMCID: PMC4722252.
      View in: PubMed   Mentions: 4  
    44. Evolutionary Paths That Expand Plasmid Host-Range: Implications for Spread of Antibiotic Resistance. Mol Biol Evol. 2016 Apr; 33(4):885-97. Loftie-Eaton W, Yano H, Burleigh S, Simmons RS, Hughes JM, Rogers LM, Hunter SS, Settles ML, Forney LJ, Ponciano JM, Top EM. PMID: 26668183; PMCID: PMC4840908.
      View in: PubMed   Mentions: 56     Fields:    Translation:HumansCells
    45. The population genomics of rapid adaptation: disentangling signatures of selection and demography in white sands lizards. Mol Ecol. 2016 01; 25(1):306-23. Laurent S, Pfeifer SP, Settles ML, Hunter SS, Hardwick KM, Ormond L, Sousa VC, Jensen JD, Rosenblum EB. PMID: 26363411.
      View in: PubMed   Mentions: 19     Fields:    Translation:Animals
    46. Fecal Microbial Community Structure Is Stable over Time and Related to Variation in Macronutrient and Micronutrient Intakes in Lactating Women. J Nutr. 2015 Oct; 145(10):2379-88. Carrothers JM, York MA, Brooker SL, Lackey KA, Williams JE, Shafii B, Price WJ, Settles ML, McGuire MA, McGuire MK. PMID: 26311809; PMCID: PMC4580954.
      View in: PubMed   Mentions: 34     Fields:    Translation:Humans
    47. Draft Genome Sequence of Pseudomonas sp. nov. H2. Genome Announc. 2015 Apr 02; 3(2). Loftie-Eaton W, Suzuki H, Bashford K, Heuer H, Stragier P, De Vos P, Settles ML, Top EM. PMID: 25838493; PMCID: PMC4384497.
      View in: PubMed   Mentions: 1  
    48. Vaginal microbiota of adolescent girls prior to the onset of menarche resemble those of reproductive-age women. mBio. 2015 Mar 24; 6(2). Hickey RJ, Zhou X, Settles ML, Erb J, Malone K, Hansmann MA, Shew ML, Van Der Pol B, Fortenberry JD, Forney LJ. PMID: 25805726; PMCID: PMC4453513.
      View in: PubMed   Mentions: 68     Fields:    Translation:HumansCells
    49. Fine-scale analysis of 16S rRNA sequences reveals a high level of taxonomic diversity among vaginal Atopobium spp. Pathog Dis. 2015 Jun; 73(4). Mendes-Soares H, Krishnan V, Settles ML, Ravel J, Brown CJ, Forney LJ. PMID: 25778779; PMCID: PMC4542641.
      View in: PubMed   Mentions: 7     Fields:    Translation:HumansCells
    50. Elevated dairy fat intake in lactating women alters milk lipid and fatty acids without detectible changes in expression of genes related to lipid uptake or synthesis. Nutr Res. 2015 Mar; 35(3):221-8. Yahvah KM, Brooker SL, Williams JE, Settles M, McGuire MA, McGuire MK. PMID: 25661476.
      View in: PubMed   Mentions: 12     Fields:    Translation:HumansCells
    51. Comparative analysis of microbial community of novel lactic acid fermentation inoculated with different undefined mixed cultures. Bioresour Technol. 2015 Mar; 179:268-274. Liang S, Gliniewicz K, Mendes-Soares H, Settles ML, Forney LJ, Coats ER, McDonald AG. PMID: 25545096.
      View in: PubMed   Mentions: 8     Fields:    Translation:CellsPHPublic Health
    52. Influence of organic loading rate and solid retention time on polyhydroxybutyrate production from hybrid poplar hydrolysates using mixed microbial cultures. Bioresour Technol. 2015 Jan; 175:23-33. Dai J, Gliniewicz K, Settles ML, Coats ER, McDonald AG. PMID: 25459800.
      View in: PubMed   Mentions: 6     Fields:    Translation:AnimalsCells
    53. Prenatal exposure to BPA alters the epigenome of the rat mammary gland and increases the propensity to neoplastic development. PLoS One. 2014; 9(7):e99800. Dhimolea E, Wadia PR, Murray TJ, Settles ML, Treitman JD, Sonnenschein C, Shioda T, Soto AM. PMID: 24988533; PMCID: PMC4079328.
      View in: PubMed   Mentions: 45     Fields:    Translation:AnimalsCells
    54. Vaginal microbiome changes with levonorgestrel intrauterine system placement. Contraception. 2014 Aug; 90(2):130-5. Jacobson JC, Turok DK, Dermish AI, Nygaard IE, Settles ML. PMID: 24835828.
      View in: PubMed   Mentions: 16     Fields:    Translation:HumansCellsCTClinical Trials
    55. Phase variation in Myxococcus xanthus yields cells specialized for iron sequestration. PLoS One. 2014; 9(4):e95189. Dziewanowska K, Settles M, Hunter S, Linquist I, Schilkey F, Hartzell PL. PMID: 24733297; PMCID: PMC3986340.
      View in: PubMed   Mentions: 7     Fields:    Translation:Cells
    56. Maternal bisphenol a exposure impacts the fetal heart transcriptome. PLoS One. 2014; 9(2):e89096. Chapalamadugu KC, Vandevoort CA, Settles ML, Robison BD, Murdoch GK. PMID: 24586524; PMCID: PMC3934879.
      View in: PubMed   Mentions: 24     Fields:    Translation:AnimalsCellsPHPublic Health
    57. Draft Genome Sequence of Pseudomonas moraviensis R28-S. Genome Announc. 2014 Feb 20; 2(1). Hunter SS, Yano H, Loftie-Eaton W, Hughes J, De Gelder L, Stragier P, De Vos P, Settles ML, Top EM. PMID: 24558233; PMCID: PMC3931354.
      View in: PubMed   Mentions: 7  
    58. Microbiota of the seminal fluid from healthy and infertile men. Fertil Steril. 2013 Nov; 100(5):1261-9. Hou D, Zhou X, Zhong X, Settles ML, Herring J, Wang L, Abdo Z, Forney LJ, Xu C. PMID: 23993888; PMCID: PMC3888793.
      View in: PubMed   Mentions: 91     Fields:    Translation:HumansCells
    59. SlopMap: a software application tool for quick and flexible identification of similar sequences using exact k-mer matching. J Data Mining Genomics Proteomics. 2013 Aug 01; 4(3). Zhbannikov IY, Hunter SS, Settles ML, Foster JA. PMID: 24404406; PMCID: PMC3882202.
      View in: PubMed   Mentions: 2  
    60. Sex-specific transcriptional responses of the zebrafish (Danio rerio) brain selenoproteome to acute sodium selenite supplementation. Physiol Genomics. 2013 Aug 01; 45(15):653-66. Benner MJ, Settles ML, Murdoch GK, Hardy RW, Robison BD. PMID: 23737534; PMCID: PMC3742966.
      View in: PubMed   Mentions: 5     Fields:    Translation:Animals
    61. MasABK proteins interact with proteins of the type IV pilin system to affect social motility of Myxococcus xanthus. PLoS One. 2013; 8(1):e54557. Fremgen S, Williams A, Furusawa G, Dziewanowska K, Settles M, Hartzell P. PMID: 23342171; PMCID: PMC3546991.
      View in: PubMed   Mentions: 1     Fields:    Translation:Cells
    62. A forward genetic screen reveals that calcium-dependent protein kinase 3 regulates egress in Toxoplasma. PLoS Pathog. 2012; 8(11):e1003049. Garrison E, Treeck M, Ehret E, Butz H, Garbuz T, Oswald BP, Settles M, Boothroyd J, Arrizabalaga G. PMID: 23209419; PMCID: PMC3510250.
      View in: PubMed   Mentions: 74     Fields:    Translation:Animals
    63. Substrate-specific gene expression in Batrachochytrium dendrobatidis, the chytrid pathogen of amphibians. PLoS One. 2012; 7(11):e49924. Rosenblum EB, Poorten TJ, Joneson S, Settles M. PMID: 23185485; PMCID: PMC3502224.
      View in: PubMed   Mentions: 22     Fields:    Translation:Animals
    64. Epigenetic transgenerational inheritance of vinclozolin induced mouse adult onset disease and associated sperm epigenome biomarkers. Reprod Toxicol. 2012 Dec; 34(4):694-707. Guerrero-Bosagna C, Covert TR, Haque MM, Settles M, Nilsson EE, Anway MD, Skinner MK. PMID: 23041264; PMCID: PMC3513496.
      View in: PubMed   Mentions: 118     Fields:    Translation:AnimalsCells
    65. An improved algorithm for the detection of genomic variation using short oligonucleotide expression microarrays. Mol Ecol Resour. 2012 Nov; 12(6):1079-89. Settles ML, Coram T, Soule T, Robison BD. PMID: 22966828; PMCID: PMC3470765.
      View in: PubMed   Mentions:    Fields:    Translation:Animals
    66. Brain transcriptome variation among behaviorally distinct strains of zebrafish (Danio rerio). BMC Genomics. 2012 Jul 20; 13:323. Drew RE, Settles ML, Churchill EJ, Williams SM, Balli S, Robison BD. PMID: 22817472; PMCID: PMC3434030.
      View in: PubMed   Mentions: 24     Fields:    Translation:HumansAnimalsCells
    67. The role of clonal interference in the evolutionary dynamics of plasmid-host adaptation. mBio. 2012; 3(4):e00077-12. Hughes JM, Lohman BK, Deckert GE, Nichols EP, Settles M, Abdo Z, Top EM. PMID: 22761390; PMCID: PMC3398533.
      View in: PubMed   Mentions: 18     Fields:    Translation:Cells
    68. mcaGUI: microbial community analysis R-Graphical User Interface (GUI). Bioinformatics. 2012 Aug 15; 28(16):2198-9. Copeland WK, Krishnan V, Beck D, Settles M, Foster JA, Cho KC, Day M, Hickey R, Schütte UM, Zhou X, Williams CJ, Forney LJ, Abdo Z. PMID: 22692220; PMCID: PMC3413388.
      View in: PubMed   Mentions: 4     Fields:    
    69. Meta-analysis of two genome-wide association studies of bovine paratuberculosis. PLoS One. 2012; 7(3):e32578. Minozzi G, Williams JL, Stella A, Strozzi F, Luini M, Settles ML, Taylor JF, Whitlock RH, Zanella R, Neibergs HL. PMID: 22396781; PMCID: PMC3292576.
      View in: PubMed   Mentions: 29     Fields:    Translation:Animals
    70. Only skin deep: shared genetic response to the deadly chytrid fungus in susceptible frog species. Mol Ecol. 2012 Jul; 21(13):3110-20. Rosenblum EB, Poorten TJ, Settles M, Murdoch GK. PMID: 22332717.
      View in: PubMed   Mentions: 40     Fields:    Translation:AnimalsCells
    71. Experimental sink removal induces stress responses, including shifts in amino acid and phenylpropanoid metabolism, in soybean leaves. Planta. 2012 May; 235(5):939-54. Turner GW, Cuthbertson DJ, Voo SS, Settles ML, Grimes HD, Lange BM. PMID: 22109846; PMCID: PMC3551543.
      View in: PubMed   Mentions: 1     Fields:    Translation:AnimalsCells
    72. Genome-wide scan identifies loci associated with classical BSE occurrence. PLoS One. 2011; 6(11):e26819. Murdoch BM, Murdoch GK, Settles M, McKay S, Williams JL, Moore SS. PMID: 22073200; PMCID: PMC3208576.
      View in: PubMed   Mentions: 6     Fields:    Translation:HumansAnimals
    73. Global analysis of phase variation in Myxococcus xanthus. Mol Microbiol. 2011 Aug; 81(3):784-804. Furusawa G, Dziewanowska K, Stone H, Settles M, Hartzell P. PMID: 21722202; PMCID: PMC3192537.
      View in: PubMed   Mentions: 11     Fields:    Translation:Cells
    74. OTUbase: an R infrastructure package for operational taxonomic unit data. Bioinformatics. 2011 Jun 15; 27(12):1700-1. Beck D, Settles M, Foster JA. PMID: 21498398; PMCID: PMC3106189.
      View in: PubMed   Mentions: 7     Fields:    
    75. Epigenetic transgenerational actions of vinclozolin on promoter regions of the sperm epigenome. PLoS One. 2010 Sep 30; 5(9). Guerrero-Bosagna C, Settles M, Lucker B, Skinner MK. PMID: 20927350; PMCID: PMC2948035.
      View in: PubMed   Mentions: 199     Fields:    Translation:AnimalsCells
    76. PRNP haplotype associated with classical BSE incidence in European Holstein cattle. PLoS One. 2010 Sep 16; 5(9). Murdoch BM, Clawson ML, Yue S, Basu U, McKay S, Settles M, Capoferri R, Laegreid WW, Williams JL, Moore SS. PMID: 20862290; PMCID: PMC2940907.
      View in: PubMed   Mentions: 8     Fields:    Translation:AnimalsCells
    77. GSEA-SNP identifies genes associated with Johne's disease in cattle. Mamm Genome. 2010 Aug; 21(7-8):419-25. Neibergs HL, Settles ML, Whitlock RH, Taylor JF. PMID: 20706723.
      View in: PubMed   Mentions: 16     Fields:    Translation:AnimalsCells
    78. Alterations in the developing testis transcriptome following embryonic vinclozolin exposure. Reprod Toxicol. 2010 Nov; 30(3):353-64. Clement TM, Savenkova MI, Settles M, Anway MD, Skinner MK. PMID: 20566332; PMCID: PMC2944409.
      View in: PubMed   Mentions: 13     Fields:    Translation:Animals
    79. A 2cM genome-wide scan of European Holstein cattle affected by classical BSE. BMC Genet. 2010 Mar 29; 11:20. Murdoch BM, Clawson ML, Laegreid WW, Stothard P, Settles M, McKay S, Prasad A, Wang Z, Moore SS, Williams JL. PMID: 20350325; PMCID: PMC2853485.
      View in: PubMed   Mentions: 9     Fields:    Translation:AnimalsCells
    80. Meta-analysis of transcripts associated with race-specific resistance to stripe rust in wheat demonstrates common induction of blue copper-binding protein, heat-stress transcription factor, pathogen-induced WIR1A protein, and ent-kaurene synthase transcripts. Funct Integr Genomics. 2010 Aug; 10(3):383-92. Coram TE, Huang X, Zhan G, Settles ML, Chen X. PMID: 19937262.
      View in: PubMed   Mentions: 24     Fields:    Translation:Animals
    81. Genome-wide transcriptional response of Silurana (Xenopus) tropicalis to infection with the deadly chytrid fungus. PLoS One. 2009 Aug 04; 4(8):e6494. Rosenblum EB, Poorten TJ, Settles M, Murdoch GK, Robert J, Maddox N, Eisen MB. PMID: 19701481; PMCID: PMC2727658.
      View in: PubMed   Mentions: 43     Fields:    Translation:AnimalsCells
    82. Large-scale analysis of antisense transcription in wheat using the Affymetrix GeneChip Wheat Genome Array. BMC Genomics. 2009 May 29; 10:253. Coram TE, Settles ML, Chen X. PMID: 19480707; PMCID: PMC2694213.
      View in: PubMed   Mentions: 21     Fields:    Translation:AnimalsCells
    83. Effect of starvation on transcriptomes of brain and liver in adult female zebrafish (Danio rerio). Physiol Genomics. 2008 Nov 12; 35(3):283-95. Drew RE, Rodnick KJ, Settles M, Wacyk J, Churchill E, Powell MS, Hardy RW, Murdoch GK, Hill RA, Robison BD. PMID: 18728227; PMCID: PMC2585019.
      View in: PubMed   Mentions: 43     Fields:    Translation:AnimalsCells
    84. Transcriptome analysis of high-temperature adult-plant resistance conditioned by Yr39 during the wheat-Puccinia striiformis f. sp. tritici interaction. Mol Plant Pathol. 2008 Jul; 9(4):479-93. Coram TE, Settles ML, Chen X. PMID: 18705862; PMCID: PMC6640281.
      View in: PubMed   Mentions: 40     Fields:    Translation:Animals
    85. Surveying expression level polymorphism and single-feature polymorphism in near-isogenic wheat lines differing for the Yr5 stripe rust resistance locus. Theor Appl Genet. 2008 Aug; 117(3):401-11. Coram TE, Settles ML, Wang M, Chen X. PMID: 18470504.
      View in: PubMed   Mentions: 12     Fields:    Translation:AnimalsCells
    86. Sexual dimorphism in hepatic gene expression and the response to dietary carbohydrate manipulation in the zebrafish (Danio rerio). Comp Biochem Physiol Part D Genomics Proteomics. 2008 Jun; 3(2):141-54. Robison BD, Drew RE, Murdoch GK, Powell M, Rodnick KJ, Settles M, Stone D, Churchill E, Hill RA, Papasani MR, Lewis SS, Hardy RW. PMID: 20483215; PMCID: PMC3047473.
      View in: PubMed   Mentions: 30     Fields:    
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