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The principles of tomorrow's university.

Katz DS, Allen G, Barba LA, Berg DR, Bik H, Boettiger C, Borgman CL, Brown CT, Buck S, Burd R, de Waard A, Eve MP, Granger BE, Greenberg J, Howe A, Howe B, Khanna M, Killeen TL, Mayernik M, McKiernan E, Mentzel C, Merchant N, Niemeyer KE, Noren L, Nusser SM, Reed DA, Seidel E, Smith M, Spies JR, Turk M, Van Horn JD, Walsh J.

F1000Res. 2018 Dec 11;7:1926. doi: 10.12688/f1000research.17425.1. eCollection 2018.


Re-assembly, quality evaluation, and annotation of 678 microbial eukaryotic reference transcriptomes.

Johnson LK, Alexander H, Brown CT.

Gigascience. 2018 Dec 13. doi: 10.1093/gigascience/giy158. [Epub ahead of print]


Keeping it light: (re)analyzing community-wide datasets without major infrastructure.

Alexander H, Johnson LK, Brown CT.

Gigascience. 2019 Feb 1;8(2). doi: 10.1093/gigascience/giy159.


Whole genome variant association across 100 dogs identifies a frame shift mutation in DISHEVELLED 2 which contributes to Robinow-like syndrome in Bulldogs and related screw tail dog breeds.

Mansour TA, Lucot K, Konopelski SE, Dickinson PJ, Sturges BK, Vernau KL, Choi S, Stern JA, Thomasy SM, Döring S, Verstraete FJM, Johnson EG, York D, Rebhun RB, Ho HH, Brown CT, Bannasch DL.

PLoS Genet. 2018 Dec 6;14(12):e1007850. doi: 10.1371/journal.pgen.1007850. eCollection 2018 Dec.


Biosynthetic capacity, metabolic variety and unusual biology in the CPR and DPANN radiations.

Castelle CJ, Brown CT, Anantharaman K, Probst AJ, Huang RH, Banfield JF.

Nat Rev Microbiol. 2018 Oct;16(10):629-645. doi: 10.1038/s41579-018-0076-2.


A Missense Mutation in the Vacuolar Protein Sorting 11 (VPS11) Gene Is Associated with Neuroaxonal Dystrophy in Rottweiler Dogs.

Lucot KL, Dickinson PJ, Finno CJ, Mansour TA, Letko A, Minor KM, Mickelson JR, Drögemüller C, Brown CT, Bannasch DL.

G3 (Bethesda). 2018 Jul 31;8(8):2773-2780. doi: 10.1534/g3.118.200376.


A novel light source with tuneable uniformity of light distribution for artificial daylight photodynamic therapy.

O'Mahoney P, Haigh N, Wood K, Brown CTA, Ibbotson S, Eadie E.

Photodiagnosis Photodyn Ther. 2018 Sep;23:144-150. doi: 10.1016/j.pdpdt.2018.06.013. Epub 2018 Jun 18.


Exploration of the effect of violent crime on recreational and transportation walking by path and structural equation models.

Deka D, Brown CT, Sinclair J.

Health Place. 2018 Jul;52:34-45. doi: 10.1016/j.healthplace.2018.05.004. Epub 2018 May 26.


Quantifying Direct DNA Damage in the Basal Layer of Skin Exposed to UV Radiation from Sunbeds.

Barnard IRM, Tierney P, Campbell CL, McMillan L, Moseley H, Eadie E, Brown CTA, Wood K.

Photochem Photobiol. 2018 Sep;94(5):1017-1025. doi: 10.1111/php.12935. Epub 2018 Jun 26.


Alterations in Lipid, Amino Acid, and Energy Metabolism Distinguish Crohn's Disease from Ulcerative Colitis and Control Subjects by Serum Metabolomic Profiling.

Scoville EA, Allaman MM, Brown CT, Motley AK, Horst SN, Williams CS, Koyama T, Zhao Z, Adams DW, Beaulieu DB, Schwartz DA, Wilson KT, Coburn LA.

Metabolomics. 2018 Jan;14(1):17. doi: 10.1007/s11306-017-1311-y. Epub 2017 Dec 29.


Hospitalized Premature Infants Are Colonized by Related Bacterial Strains with Distinct Proteomic Profiles.

Brown CT, Xiong W, Olm MR, Thomas BC, Baker R, Firek B, Morowitz MJ, Hettich RL, Banfield JF.

MBio. 2018 Apr 10;9(2). pii: e00441-18. doi: 10.1128/mBio.00441-18.


Diode-pumped femtosecond Tm3+-doped LuScO3 laser near 2.1  μm.

Stevenson NK, Brown CTA, Hopkins JM, Dawson MD, Kränkel C, Lagatsky AA.

Opt Lett. 2018 Mar 15;43(6):1287-1290. doi: 10.1364/OL.43.001287.


Exogenous mineralization of hard tissues using photo-absorptive minerals and femto-second lasers; the case of dental enamel.

Anastasiou AD, Strafford S, Thomson CL, Gardy J, Edwards TJ, Malinowski M, Hussain SA, Metzger NK, Hassanpour A, Brown CTA, Brown AP, Duggal MS, Jha A.

Acta Biomater. 2018 Apr 15;71:86-95. doi: 10.1016/j.actbio.2018.02.012. Epub 2018 Feb 17.


Non-traumatic testicular rupture following episode of epididymo-orchitis.

Brown CT, Wan JC, DaJusta DG.

Urol Case Rep. 2018 Jan 8;17:48-49. doi: 10.1016/j.eucr.2018.01.005. eCollection 2018 Mar. No abstract available.


Draft genome of tule elk Cervus canadensis nannodes.

Mizzi JE, Lounsberry ZT, Brown CT, Sacks BN.

Version 2. F1000Res. 2017 Sep 15 [revised 2017 Jan 1];6:1691. doi: 10.12688/f1000research.12636.2. eCollection 2017.


Central nervous system transcriptome of Biomphalaria alexandrina, an intermediate host for schistosomiasis.

Mansour TA, Habib MR, Rodríguez LCV, Vázquez AH, Alers JM, Ghezzi A, Croll RP, Brown CT, Miller MW.

BMC Res Notes. 2017 Dec 11;10(1):729. doi: 10.1186/s13104-017-3018-6.


ANISEED 2017: extending the integrated ascidian database to the exploration and evolutionary comparison of genome-scale datasets.

Brozovic M, Dantec C, Dardaillon J, Dauga D, Faure E, Gineste M, Louis A, Naville M, Nitta KR, Piette J, Reeves W, Scornavacca C, Simion P, Vincentelli R, Bellec M, Aicha SB, Fagotto M, Guéroult-Bellone M, Haeussler M, Jacox E, Lowe EK, Mendez M, Roberge A, Stolfi A, Yokomori R, Brown CT, Cambillau C, Christiaen L, Delsuc F, Douzery E, Dumollard R, Kusakabe T, Nakai K, Nishida H, Satou Y, Swalla B, Veeman M, Volff JN, Lemaire P.

Nucleic Acids Res. 2018 Jan 4;46(D1):D718-D725. doi: 10.1093/nar/gkx1108.


FGF4 retrogene on CFA12 is responsible for chondrodystrophy and intervertebral disc disease in dogs.

Brown EA, Dickinson PJ, Mansour T, Sturges BK, Aguilar M, Young AE, Korff C, Lind J, Ettinger CL, Varon S, Pollard R, Brown CT, Raudsepp T, Bannasch DL.

Proc Natl Acad Sci U S A. 2017 Oct 24;114(43):11476-11481. doi: 10.1073/pnas.1709082114. Epub 2017 Oct 11.


Percutaneous Vesicoscopic Approach for Retrograde Ureteroscopy Following Cohen Cross-trigonal Ureteral Reimplantation.

Brown CT, Jayanthi VR.

Urology. 2018 Jan;111:186-188. doi: 10.1016/j.urology.2017.09.028. Epub 2017 Oct 10.


1.9 µm waveguide laser fabricated by ultrafast laser inscription in Tm:Lu2O3 ceramic.

Morris J, Stevenson NK, Bookey HT, Kar AK, Brown CTA, Hopkins JM, Dawson MD, Lagatsky AA.

Opt Express. 2017 Jun 26;25(13):14910-14917. doi: 10.1364/OE.25.014910.


dRep: a tool for fast and accurate genomic comparisons that enables improved genome recovery from metagenomes through de-replication.

Olm MR, Brown CT, Brooks B, Banfield JF.

ISME J. 2017 Dec;11(12):2864-2868. doi: 10.1038/ismej.2017.126. Epub 2017 Jul 25.


Evolutionary loss of melanogenesis in the tunicate Molgula occulta.

Racioppi C, Valoroso MC, Coppola U, Lowe EK, Brown CT, Swalla BJ, Christiaen L, Stolfi A, Ristoratore F.

Evodevo. 2017 Jul 18;8:11. doi: 10.1186/s13227-017-0074-x. eCollection 2017.


Genome-resolved metaproteomic characterization of preterm infant gut microbiota development reveals species-specific metabolic shifts and variabilities during early life.

Xiong W, Brown CT, Morowitz MJ, Banfield JF, Hettich RL.

Microbiome. 2017 Jul 10;5(1):72. doi: 10.1186/s40168-017-0290-6.


Identification of long non-coding RNA in the horse transcriptome.

Scott EY, Mansour T, Bellone RR, Brown CT, Mienaltowski MJ, Penedo MC, Ross PJ, Valberg SJ, Murray JD, Finno CJ.

BMC Genomics. 2017 Jul 4;18(1):511. doi: 10.1186/s12864-017-3884-2.


Characterization of ciliate diversity in bromeliad tank waters from the Brazilian Atlantic Forest.

Simão TLL, Borges AG, Gano KA, Davis-Richardson AG, Brown CT, Fagen JR, Triplett EW, Dias R, Mondin CA, da Silva RM, Eizirik E, Utz LRP.

Eur J Protistol. 2017 Oct;61(Pt B):359-365. doi: 10.1016/j.ejop.2017.05.005. Epub 2017 May 17.


β-pyrophosphate: A potential biomaterial for dental applications.

Anastasiou AD, Strafford S, Posada-Estefan O, Thomson CL, Hussain SA, Edwards TJ, Malinowski M, Hondow N, Metzger NK, Brown CTA, Routledge MN, Brown AP, Duggal MS, Jha A.

Mater Sci Eng C Mater Biol Appl. 2017 Jun 1;75:885-894. doi: 10.1016/j.msec.2017.02.116. Epub 2017 Feb 24.


A quantitative study of in vivo protoporphyrin IX fluorescence build up during occlusive treatment phases.

Campbell CL, Brown CTA, Wood K, Salvio AG, Inada NM, Bagnato VS, Moseley H.

Photodiagnosis Photodyn Ther. 2017 Jun;18:204-207. doi: 10.1016/j.pdpdt.2017.02.004. Epub 2017 Feb 28.


Centromere location in Arabidopsis is unaltered by extreme divergence in CENH3 protein sequence.

Maheshwari S, Ishii T, Brown CT, Houben A, Comai L.

Genome Res. 2017 Mar;27(3):471-478. doi: 10.1101/gr.214619.116. Epub 2017 Feb 21.


Genome-Resolved Meta-Omics Ties Microbial Dynamics to Process Performance in Biotechnology for Thiocyanate Degradation.

Kantor RS, Huddy RJ, Iyer R, Thomas BC, Brown CT, Anantharaman K, Tringe S, Hettich RL, Harrison ST, Banfield JF.

Environ Sci Technol. 2017 Mar 7;51(5):2944-2953. doi: 10.1021/acs.est.6b04477. Epub 2017 Feb 13.


Tissue resolved, gene structure refined equine transcriptome.

Mansour TA, Scott EY, Finno CJ, Bellone RR, Mienaltowski MJ, Penedo MC, Ross PJ, Valberg SJ, Murray JD, Brown CT.

BMC Genomics. 2017 Jan 20;18(1):103. doi: 10.1186/s12864-016-3451-2.


Identical bacterial populations colonize premature infant gut, skin, and oral microbiomes and exhibit different in situ growth rates.

Olm MR, Brown CT, Brooks B, Firek B, Baker R, Burstein D, Soenjoyo K, Thomas BC, Morowitz M, Banfield JF.

Genome Res. 2017 Apr;27(4):601-612. doi: 10.1101/gr.213256.116. Epub 2017 Jan 10.


Unusual respiratory capacity and nitrogen metabolism in a Parcubacterium (OD1) of the Candidate Phyla Radiation.

Castelle CJ, Brown CT, Thomas BC, Williams KH, Banfield JF.

Sci Rep. 2017 Jan 9;7:40101. doi: 10.1038/srep40101.


A New Chicken Genome Assembly Provides Insight into Avian Genome Structure.

Warren WC, Hillier LW, Tomlinson C, Minx P, Kremitzki M, Graves T, Markovic C, Bouk N, Pruitt KD, Thibaud-Nissen F, Schneider V, Mansour TA, Brown CT, Zimin A, Hawken R, Abrahamsen M, Pyrkosz AB, Morisson M, Fillon V, Vignal A, Chow W, Howe K, Fulton JE, Miller MM, Lovell P, Mello CV, Wirthlin M, Mason AS, Kuo R, Burt DW, Dodgson JB, Cheng HH.

G3 (Bethesda). 2017 Jan 5;7(1):109-117. doi: 10.1534/g3.116.035923.


Channeling Community Contributions to Scientific Software: A Sprint Experience.

Crusoe MR, Brown CT.

J Open Res Softw. 2016;4(1). pii: e27. Epub 2016 Jul 19.


Measurement of bacterial replication rates in microbial communities.

Brown CT, Olm MR, Thomas BC, Banfield JF.

Nat Biotechnol. 2016 Dec;34(12):1256-1263. doi: 10.1038/nbt.3704. Epub 2016 Nov 7.


RubisCO of a nucleoside pathway known from Archaea is found in diverse uncultivated phyla in bacteria.

Wrighton KC, Castelle CJ, Varaljay VA, Satagopan S, Brown CT, Wilkins MJ, Thomas BC, Sharon I, Williams KH, Tabita FR, Banfield JF.

ISME J. 2016 Nov;10(11):2702-2714. doi: 10.1038/ismej.2016.53. Epub 2016 May 3.


Thousands of microbial genomes shed light on interconnected biogeochemical processes in an aquifer system.

Anantharaman K, Brown CT, Hug LA, Sharon I, Castelle CJ, Probst AJ, Thomas BC, Singh A, Wilkins MJ, Karaoz U, Brodie EL, Williams KH, Hubbard SS, Banfield JF.

Nat Commun. 2016 Oct 24;7:13219. doi: 10.1038/ncomms13219.


Modelling topical photodynamic therapy treatment including the continuous production of Protoporphyrin IX.

Campbell CL, Brown CT, Wood K, Moseley H.

Phys Med Biol. 2016 Nov 7;61(21):7507-7521. Epub 2016 Oct 7.


A new view of the tree of life.

Hug LA, Baker BJ, Anantharaman K, Brown CT, Probst AJ, Castelle CJ, Butterfield CN, Hernsdorf AW, Amano Y, Ise K, Suzuki Y, Dudek N, Relman DA, Finstad KM, Amundson R, Thomas BC, Banfield JF.

Nat Microbiol. 2016 Apr 11;1:16048. doi: 10.1038/nmicrobiol.2016.48.


Transcriptome of the Caribbean stony coral Porites astreoides from three developmental stages.

Mansour TA, Rosenthal JJ, Brown CT, Roberson LM.

Gigascience. 2016 Aug 2;5(1):33. doi: 10.1186/s13742-016-0138-1.


How open science helps researchers succeed.

McKiernan EC, Bourne PE, Brown CT, Buck S, Kenall A, Lin J, McDougall D, Nosek BA, Ram K, Soderberg CK, Spies JR, Thaney K, Updegrove A, Woo KH, Yarkoni T.

Elife. 2016 Jul 7;5. pii: e16800. doi: 10.7554/eLife.16800.


Monte Carlo modelling of photodynamic therapy treatments comparing clustered three dimensional tumour structures with homogeneous tissue structures.

Campbell CL, Wood K, Brown CT, Moseley H.

Phys Med Biol. 2016 Jul 7;61(13):4840-54. doi: 10.1088/0031-9155/61/13/4840. Epub 2016 Jun 8.


Evidence for persistent and shared bacterial strains against a background of largely unique gut colonization in hospitalized premature infants.

Raveh-Sadka T, Firek B, Sharon I, Baker R, Brown CT, Thomas BC, Morowitz MJ, Banfield JF.

ISME J. 2016 Dec;10(12):2817-2830. doi: 10.1038/ismej.2016.83. Epub 2016 Jun 3.


Warmer temperature modifies effects of polybrominated diphenyl ethers on hormone profiles in leopard frog tadpoles (Lithobates pipiens).

Freitas MB, Brown CT, Karasov WH.

Environ Toxicol Chem. 2017 Jan;36(1):120-127. doi: 10.1002/etc.3506. Epub 2016 Jul 26.


Serum Fatty Acids Are Correlated with Inflammatory Cytokines in Ulcerative Colitis.

Wiese DM, Horst SN, Brown CT, Allaman MM, Hodges ME, Slaughter JC, Druce JP, Beaulieu DB, Schwartz DA, Wilson KT, Coburn LA.

PLoS One. 2016 May 26;11(5):e0156387. doi: 10.1371/journal.pone.0156387. eCollection 2016.


Genomic resolution of a cold subsurface aquifer community provides metabolic insights for novel microbes adapted to high CO2 concentrations.

Probst AJ, Castelle CJ, Singh A, Brown CT, Anantharaman K, Sharon I, Hug LA, Burstein D, Emerson JB, Thomas BC, Banfield JF.

Environ Microbiol. 2017 Feb;19(2):459-474. doi: 10.1111/1462-2920.13362. Epub 2016 Jul 7.


L-Arginine Availability and Metabolism Is Altered in Ulcerative Colitis.

Coburn LA, Horst SN, Allaman MM, Brown CT, Williams CS, Hodges ME, Druce JP, Beaulieu DB, Schwartz DA, Wilson KT.

Inflamm Bowel Dis. 2016 Aug;22(8):1847-58. doi: 10.1097/MIB.0000000000000790.


Analysis of five complete genome sequences for members of the class Peribacteria in the recently recognized Peregrinibacteria bacterial phylum.

Anantharaman K, Brown CT, Burstein D, Castelle CJ, Probst AJ, Thomas BC, Williams KH, Banfield JF.

PeerJ. 2016 Jan 28;4:e1607. doi: 10.7717/peerj.1607. eCollection 2016.


Major bacterial lineages are essentially devoid of CRISPR-Cas viral defence systems.

Burstein D, Sun CL, Brown CT, Sharon I, Anantharaman K, Probst AJ, Thomas BC, Banfield JF.

Nat Commun. 2016 Feb 3;7:10613. doi: 10.1038/ncomms10613.

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