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A Western-Type Dietary Pattern Induces an Atherogenic Gene Expression Profile in the Coronary Arteries of the Ossabaw Pig.

Walker ME, Matthan NR, Lamon-Fava S, Solano-Aguilar G, Jang S, Lakshman S, Molokin A, Urban JF Jr, Faits T, Johnson WE, Lichtenstein AH.

Curr Dev Nutr. 2019 Mar 30;3(5):nzz023. doi: 10.1093/cdn/nzz023. eCollection 2019 May.


scruff: an R/Bioconductor package for preprocessing single-cell RNA-sequencing data.

Wang Z, Hu J, Johnson WE, Campbell JD.

BMC Bioinformatics. 2019 May 2;20(1):222. doi: 10.1186/s12859-019-2797-2.


Whole Genome Sequencing and Re-sequencing of the Sable Antelope (Hippotragus niger): A Resource for Monitoring Diversity in ex Situ and in Situ Populations.

Koepfli KP, Tamazian G, Wildt D, Dobrynin P, Kim C, Frandsen PB, Godinho R, Yurchenko AA, Komissarov A, Krasheninnikova K, Kliver S, Kolchanova S, Gonçalves M, Carneiro M, Pinto PV, Ferrand N, Maldonado JE, Ferrie GM, Chemnick L, Ryder OA, Johnson WE, Comizzoli P, O'Brien SJ, Pukazhenthi BS.

G3 (Bethesda). 2019 Jun 5;9(6):1785-1793. doi: 10.1534/g3.119.400084.


A Western-type dietary pattern and atorvastatin induce epicardial adipose tissue interferon signaling in the Ossabaw pig.

Walker ME, Matthan NR, Solano-Aguilar G, Jang S, Lakshman S, Molokin A, Faits T, Urban JF Jr, Johnson WE, Lamon-Fava S, Lichtenstein AH.

J Nutr Biochem. 2019 May;67:212-218. doi: 10.1016/j.jnutbio.2019.02.003. Epub 2019 Feb 20.


Improving Illumina assemblies with Hi-C and long reads: An example with the North African dromedary.

Elbers JP, Rogers MF, Perelman PL, Proskuryakova AA, Serdyukova NA, Johnson WE, Horin P, Corander J, Murphy D, Burger PA.

Mol Ecol Resour. 2019 Jul;19(4):1015-1026. doi: 10.1111/1755-0998.13020. Epub 2019 May 17.


Origins and evolutionary consequences of ancient endogenous retroviruses.

Johnson WE.

Nat Rev Microbiol. 2019 Jun;17(6):355-370. doi: 10.1038/s41579-019-0189-2. Review.


CD271-selected mesenchymal stem cells from adipose tissue enhance cartilage repair and are less angiogenic than plastic adherent mesenchymal stem cells.

Kohli N, Al-Delfi IRT, Snow M, Sakamoto T, Miyazaki T, Nakajima H, Uchida K, Johnson WEB.

Sci Rep. 2019 Feb 28;9(1):3194. doi: 10.1038/s41598-019-39715-z.


Evolution of gene regulation in ruminants differs between evolutionary breakpoint regions and homologous synteny blocks.

Farré M, Kim J, Proskuryakova AA, Zhang Y, Kulemzina AI, Li Q, Zhou Y, Xiong Y, Johnson JL, Perelman PL, Johnson WE, Warren WC, Kukekova AV, Zhang G, O'Brien SJ, Ryder OA, Graphodatsky AS, Ma J, Lewin HA, Larkin DM.

Genome Res. 2019 Apr;29(4):576-589. doi: 10.1101/gr.239863.118. Epub 2019 Feb 13.


Game Changers: A Critical Race Theory Analysis of the Economic, Social, and Political Factors Impacting Black Fatherhood and Family Formation.

Lemmons BP, Johnson WE.

Soc Work Public Health. 2019;34(1):86-101. doi: 10.1080/19371918.2018.1562406. Epub 2019 Jan 22.


C57BL/6 substrain differences in inflammatory and neuropathic nociception and genetic mapping of a major quantitative trait locus underlying acute thermal nociception.

Bryant CD, Bagdas D, Goldberg LR, Khalefa T, Reed ER, Kirkpatrick SL, Kelliher JC, Chen MM, Johnson WE, Mulligan MK, Imad Damaj M.

Mol Pain. 2019 Jan-Dec;15:1744806918825046. doi: 10.1177/1744806918825046.


Genetic Variation in Coat Colour Genes MC1R and ASIP Provides Insights Into Domestication and Management of South American Camelids.

Marín JC, Rivera R, Varas V, Cortés J, Agapito A, Chero A, Chávez A, Johnson WE, Orozco-terWengel P.

Front Genet. 2018 Nov 13;9:487. doi: 10.3389/fgene.2018.00487. eCollection 2018.


Human adipose tissue-derived mesenchymal stem/stromal cells adhere to and inhibit the growth of Staphylococcus aureus and Pseudomonas aeruginosa.

Wood CR, Al Dhahri D, Al Delfi I, Pickles NA, Sammons RL, Worthington T, Wright KT, Johnson WEB.

J Med Microbiol. 2018 Dec;67(12):1789-1795. doi: 10.1099/jmm.0.000861. Epub 2018 Oct 23.


Nomenclature for endogenous retrovirus (ERV) loci.

Gifford RJ, Blomberg J, Coffin JM, Fan H, Heidmann T, Mayer J, Stoye J, Tristem M, Johnson WE.

Retrovirology. 2018 Aug 28;15(1):59. doi: 10.1186/s12977-018-0442-1. Review.


Exploring Host-Microbe Interactions in Lung Cancer.

Zhao Y, Johnson WE.

Am J Respir Crit Care Med. 2018 Nov 1;198(9):1116-1118. doi: 10.1164/rccm.201807-1225ED. No abstract available.


Alternative empirical Bayes models for adjusting for batch effects in genomic studies.

Zhang Y, Jenkins DF, Manimaran S, Johnson WE.

BMC Bioinformatics. 2018 Jul 13;19(1):262. doi: 10.1186/s12859-018-2263-6.


Comparison of Mesenchymal Stromal Cells Isolated from Murine Adipose Tissue and Bone Marrow in the Treatment of Spinal Cord Injury.

Takahashi A, Nakajima H, Uchida K, Takeura N, Honjoh K, Watanabe S, Kitade M, Kokubo Y, Johnson WEB, Matsumine A.

Cell Transplant. 2018 Jul;27(7):1126-1139. doi: 10.1177/0963689718780309. Epub 2018 Jun 27.


Detection of multiple perturbations in multi-omics biological networks.

Griffin PJ, Zhang Y, Johnson WE, Kolaczyk ED.

Biometrics. 2018 Dec;74(4):1351-1361. doi: 10.1111/biom.12893. Epub 2018 May 17.


Earth BioGenome Project: Sequencing life for the future of life.

Lewin HA, Robinson GE, Kress WJ, Baker WJ, Coddington J, Crandall KA, Durbin R, Edwards SV, Forest F, Gilbert MTP, Goldstein MM, Grigoriev IV, Hackett KJ, Haussler D, Jarvis ED, Johnson WE, Patrinos A, Richards S, Castilla-Rubio JC, van Sluys MA, Soltis PS, Xu X, Yang H, Zhang G.

Proc Natl Acad Sci U S A. 2018 Apr 24;115(17):4325-4333. doi: 10.1073/pnas.1720115115.


Exposing mesenchymal stem cells to chondroitin sulphated proteoglycans reduces their angiogenic and neuro-adhesive paracrine activity.

Wood CR, Al Delfi IRT, Innes JF, Myint P, Johnson WEB.

Biochimie. 2018 Dec;155:26-36. doi: 10.1016/j.biochi.2018.04.011. Epub 2018 Apr 19.


Substitution-Inert Polynuclear Platinum Complexes as Metalloshielding Agents for Heparan Sulfate.

Gorle AK, Katner SJ, Johnson WE, Lee DE, Daniel AG, Ginsburg EP, von Itzstein M, Berners-Price SJ, Farrell NP.

Chemistry. 2018 May 2;24(25):6606-6616. doi: 10.1002/chem.201706030. Epub 2018 Apr 14.


Clinical Cell Therapy Guidelines for Neurorestoration (IANR/CANR 2017).

Huang H, Young W, Chen L, Feng S, Zoubi ZMA, Sharma HS, Saberi H, Moviglia GA, He X, Muresanu DF, Sharma A, Otom A, Andrews RJ, Al-Zoubi A, Bryukhovetskiy AS, Chernykh ER, Domańska-Janik K, Jafar E, Johnson WE, Li Y, Li D, Luan Z, Mao G, Shetty AK, Siniscalco D, Skaper S, Sun T, Wang Y, Wiklund L, Xue Q, You SW, Zheng Z, Dimitrijevic MR, Masri WSE, Sanberg PR, Xu Q, Luan G, Chopp M, Cho KS, Zhou XF, Wu P, Liu K, Mobasheri H, Ohtori S, Tanaka H, Han F, Feng Y, Zhang S, Lu Y, Zhang Z, Rao Y, Tang Z, Xi H, Wu L, Shen S, Xue M, Xiang G, Guo X, Yang X, Hao Y, Hu Y, Li J, Ao Q, Wang B, Zhang Z, Lu M, Li T.

Cell Transplant. 2018 Feb;27(2):310-324. doi: 10.1177/0963689717746999.


Existing blood transcriptional classifiers accurately discriminate active tuberculosis from latent infection in individuals from south India.

Leong S, Zhao Y, Joseph NM, Hochberg NS, Sarkar S, Pleskunas J, Hom D, Lakshminarayanan S, Horsburgh CR Jr, Roy G, Ellner JJ, Johnson WE, Salgame P.

Tuberculosis (Edinb). 2018 Mar;109:41-51. doi: 10.1016/ Epub 2018 Jan 31.


Comparison of Metal-Ammine Compounds Binding to DNA and Heparin. Glycans as Ligands in Bioinorganic Chemistry.

Katner SJ, Johnson WE, Peterson EJ, Page P, Farrell NP.

Inorg Chem. 2018 Mar 19;57(6):3116-3125. doi: 10.1021/acs.inorgchem.7b03043. Epub 2018 Feb 23.


Publisher Correction: Combating subclonal evolution of resistant cancer phenotypes.

Brady SW, McQuerry JA, Qiao Y, Piccolo SR, Shrestha G, Jenkins DF, Layer RM, Pedersen BS, Miller RH, Esch A, Selitsky SR, Parker JS, Anderson LA, Dalley BK, Factor RE, Reddy CB, Boltax JP, Li DY, Moos PJ, Gray JW, Heiser LM, Buys SS, Cohen AL, Johnson WE, Quinlan AR, Marth G, Werner TL, Bild AH.

Nat Commun. 2018 Feb 5;9(1):572. doi: 10.1038/s41467-017-02383-6.


Adaptive genomic evolution of opsins reveals that early mammals flourished in nocturnal environments.

Borges R, Johnson WE, O'Brien SJ, Gomes C, Heesy CP, Antunes A.

BMC Genomics. 2018 Feb 5;19(1):121. doi: 10.1186/s12864-017-4417-8.


High-Resolution Sequencing of Viral Populations during Early Simian Immunodeficiency Virus Infection Reveals Evolutionary Strategies for Rapid Escape from Emerging Env-Specific Antibody Responses.

Ita S, Hill AK, Lam EC, Dufort FJ, Yang X, Newman R, Leviyang S, Fofana IB, Johnson WE.

J Virol. 2018 Mar 14;92(7). pii: e01574-17. doi: 10.1128/JVI.01574-17. Print 2018 Apr 1.


Landscape genomics: natural selection drives the evolution of mitogenome in penguins.

Ramos B, González-Acuña D, Loyola DE, Johnson WE, Parker PG, Massaro M, Dantas GPM, Miranda MD, Vianna JA.

BMC Genomics. 2018 Jan 16;19(1):53. doi: 10.1186/s12864-017-4424-9.


The Complete Phylogeny of Pangolins: Scaling Up Resources for the Molecular Tracing of the Most Trafficked Mammals on Earth.

Gaubert P, Antunes A, Meng H, Miao L, Peigné S, Justy F, Njiokou F, Dufour S, Danquah E, Alahakoon J, Verheyen E, Stanley WT, O'Brien SJ, Johnson WE, Luo SJ.

J Hered. 2018 May 11;109(4):347-359. doi: 10.1093/jhered/esx097.


Combating subclonal evolution of resistant cancer phenotypes.

Brady SW, McQuerry JA, Qiao Y, Piccolo SR, Shrestha G, Jenkins DF, Layer RM, Pedersen BS, Miller RH, Esch A, Selitsky SR, Parker JS, Anderson LA, Dalley BK, Factor RE, Reddy CB, Boltax JP, Li DY, Moos PJ, Gray JW, Heiser LM, Buys SS, Cohen AL, Johnson WE, Quinlan AR, Marth G, Werner TL, Bild AH.

Nat Commun. 2017 Nov 1;8(1):1231. doi: 10.1038/s41467-017-01174-3. Erratum in: Nat Commun. 2018 Feb 5;9(1):572.


Retroviruses of the RDR superinfection interference group: ancient origins and broad host distribution of a promiscuous Env gene.

Sinha A, Johnson WE.

Curr Opin Virol. 2017 Aug;25:105-112. doi: 10.1016/j.coviro.2017.07.020. Epub 2017 Aug 19. Review.


Conservation Genetics of the Cheetah: Lessons Learned and New Opportunities.

O'Brien SJ, Johnson WE, Driscoll CA, Dobrynin P, Marker L.

J Hered. 2017 Sep 1;108(6):671-677. doi: 10.1093/jhered/esx047. Review.


Y-chromosome and mtDNA variation confirms independent domestications and directional hybridization in South American camelids.

Marín JC, Romero K, Rivera R, Johnson WE, González BA.

Anim Genet. 2017 Oct;48(5):591-595. doi: 10.1111/age.12570. Epub 2017 Jul 11.


Casein kinase 1-epsilon deletion increases mu opioid receptor-dependent behaviors and binge eating1.

Goldberg LR, Kirkpatrick SL, Yazdani N, Luttik KP, Lacki OA, Babbs RK, Jenkins DF, Johnson WE, Bryant CD.

Genes Brain Behav. 2017 Sep;16(7):725-738. doi: 10.1111/gbb.12397. Epub 2017 Jul 6. Erratum in: Genes Brain Behav. 2017 Nov;16(8):823.


Biomarkers of oxidatively induced DNA damage in dreissenid mussels: A genotoxicity assessment tool for the Laurentian Great Lakes.

Jaruga P, Coskun E, Kimbrough K, Jacob A, Johnson WE, Dizdaroglu M.

Environ Toxicol. 2017 Sep;32(9):2144-2153. doi: 10.1002/tox.22427. Epub 2017 Jun 1.


Activity of distinct growth factor receptor network components in breast tumors uncovers two biologically relevant subtypes.

Rahman M, MacNeil SM, Jenkins DF, Shrestha G, Wyatt SR, McQuerry JA, Piccolo SR, Heiser LM, Gray JW, Johnson WE, Bild AH.

Genome Med. 2017 Apr 26;9(1):40. doi: 10.1186/s13073-017-0429-x.


A penalized regression approach to haplotype reconstruction of viral populations arising in early HIV/SIV infection.

Leviyang S, Griva I, Ita S, Johnson WE.

Bioinformatics. 2017 Aug 15;33(16):2455-2463. doi: 10.1093/bioinformatics/btx187.


Analysis of SIVmac Envelope-Specific Antibodies Selected Through Phage Display.

Ita S, Agostinho MR, Sullivan K, Yub Han S, Akleh R, Johnson WE, Fofana IBF.

AIDS Res Hum Retroviruses. 2017 Aug;33(8):869-879. doi: 10.1089/AID.2016.0247. Epub 2017 Feb 16.


An Intact Retroviral Gene Conserved in Spiny-Rayed Fishes for over 100 My.

Henzy JE, Gifford RJ, Kenaley CP, Johnson WE.

Mol Biol Evol. 2017 Mar 1;34(3):634-639. doi: 10.1093/molbev/msw262.


The developing landscape of diagnostic and prognostic biomarkers for spinal cord injury in cerebrospinal fluid and blood.

Hulme CH, Brown SJ, Fuller HR, Riddell J, Osman A, Chowdhury J, Kumar N, Johnson WE, Wright KT.

Spinal Cord. 2017 Feb;55(2):114-125. doi: 10.1038/sc.2016.174. Epub 2016 Dec 20. Review.


Cytoplasmic FMR1-Interacting Protein 2 Is a Major Genetic Factor Underlying Binge Eating.

Kirkpatrick SL, Goldberg LR, Yazdani N, Babbs RK, Wu J, Reed ER, Jenkins DF, Bolgioni AF, Landaverde KI, Luttik KP, Mitchell KS, Kumar V, Johnson WE, Mulligan MK, Cottone P, Bryant CD.

Biol Psychiatry. 2017 May 1;81(9):757-769. doi: 10.1016/j.biopsych.2016.10.021. Epub 2016 Oct 25.


Canine mesenchymal stem cells are neurotrophic and angiogenic: An in vitro assessment of their paracrine activity.

Al Delfi IR, Sheard JJ, Wood CR, Vernallis A, Innes JF, Myint P, Johnson WE.

Vet J. 2016 Nov;217:10-17. doi: 10.1016/j.tvjl.2016.09.003. Epub 2016 Sep 19.


TRIM5α Resistance Escape Mutations in the Capsid Are Transferable between Simian Immunodeficiency Virus Strains.

Wu F, Kirmaier A, White E, Ourmanov I, Whitted S, Matsuda K, Riddick N, Hall LR, Morgan JS, Plishka RJ, Buckler-White A, Johnson WE, Hirsch VM.

J Virol. 2016 Nov 28;90(24):11087-11095. Print 2016 Dec 15.


PGD: a pangolin genome hub for the research community.

Tan TK, Tan KY, Hari R, Mohamed Yusoff A, Wong GJ, Siow CC, Mutha NV, Rayko M, Komissarov A, Dobrynin P, Krasheninnikova K, Tamazian G, Paterson IC, Warren WC, Johnson WE, O'Brien SJ, Choo SW.

Database (Oxford). 2016 Sep 11;2016. pii: baw063. doi: 10.1093/database/baw063. Print 2016.


Positive Selection Linked with Generation of Novel Mammalian Dentition Patterns.

Machado JP, Philip S, Maldonado E, O'Brien SJ, Johnson WE, Antunes A.

Genome Biol Evol. 2016 Sep 11;8(9):2748-59. doi: 10.1093/gbe/evw200.


Molecular assessment of the phylogeny and biogeography of a recently diversified endemic group of South American canids (Mammalia: Carnivora: Canidae).

Tchaicka L, Freitas TR, Bager A, Vidal SL, Lucherini M, Iriarte A, Novaro A, Geffen E, Garcez FS, Johnson WE, Wayne RK, Eizirik E.

Genet Mol Biol. 2016 Jul-Sep;39(3):442-51. doi: 10.1590/1678-4685-GMB-2015-0189. Epub 2016 Jul 25.


BatchQC: interactive software for evaluating sample and batch effects in genomic data.

Manimaran S, Selby HM, Okrah K, Ruberman C, Leek JT, Quackenbush J, Haibe-Kains B, Bravo HC, Johnson WE.

Bioinformatics. 2016 Dec 15;32(24):3836-3838. Epub 2016 Aug 18.


Pangolin genomes and the evolution of mammalian scales and immunity.

Choo SW, Rayko M, Tan TK, Hari R, Komissarov A, Wee WY, Yurchenko AA, Kliver S, Tamazian G, Antunes A, Wilson RK, Warren WC, Koepfli KP, Minx P, Krasheninnikova K, Kotze A, Dalton DL, Vermaak E, Paterson IC, Dobrynin P, Sitam FT, Rovie-Ryan JJ, Johnson WE, Yusoff AM, Luo SJ, Karuppannan KV, Fang G, Zheng D, Gerstein MB, Lipovich L, O'Brien SJ, Wong GJ.

Genome Res. 2016 Oct;26(10):1312-1322. Epub 2016 Aug 10.


Phylogeny and History of the Lost SIV from Crab-Eating Macaques: SIVmfa.

McCarthy KR, Johnson WE, Kirmaier A.

PLoS One. 2016 Jul 14;11(7):e0159281. doi: 10.1371/journal.pone.0159281. eCollection 2016.


Phylogenetic sleuthing reveals pair of paralogous genes.

Henzy JE, Johnson WE.

Elife. 2016 May 31;5. pii: e17224. doi: 10.7554/eLife.17224.


Striatal transcriptome analysis of a congenic mouse line (chromosome 11: 50-60Mb) exhibiting reduced methamphetamine sensitivity.

Yazdani N, Shen Y, Johnson WE, Bryant CD.

Genom Data. 2016 Apr 11;8:77-80. doi: 10.1016/j.gdata.2016.03.009. eCollection 2016 Jun.

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