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Comparative Genomics and Transcriptomics to Analyze Fruiting Body Development in Filamentous Ascomycetes.

Lütkenhaus R, Traeger S, Breuer J, Carreté L, Kuo A, Lipzen A, Pangilinan J, Dilworth D, Sandor L, Pöggeler S, Gabaldón T, Barry K, Grigoriev IV, Nowrousian M.

Genetics. 2019 Oct 11. pii: genetics.302749.2019. doi: 10.1534/genetics.119.302749. [Epub ahead of print]


Ingested nitrate and nitrite and bladder cancer in Northern New England.

Barry KH, Jones RR, Cantor KP, Freeman LEB, Wheeler DC, Baris D, Johnson AT, Hosain GMM, Schwenn M, Zhang H, Sinha R, Koutros S, Karagas MR, Silverman DT, Ward MH.

Epidemiology. 2019 Sep 30. doi: 10.1097/EDE.0000000000001112. [Epub ahead of print]


Variation and inheritance of small RNAs in maize inbreds and F1 hybrids.

Crisp PA, Hammond R, Zhou P, Vaillancourt B, Lipzen AM, Daum C, Barry KW, de Leon N, Buell CR, Kaeppler SM, Meyers BC, Hirsch C, Springer NM.

Plant Physiol. 2019 Oct 1. pii: pp.00817.2019. doi: 10.1104/pp.19.00817. [Epub ahead of print]


Genome expansion by allopolyploidization in the fungal strain Coniochaeta 2T2.1 and its exceptional lignocellulolytic machinery.

Mondo SJ, Jiménez DJ, Hector RE, Lipzen A, Yan M, LaButti K, Barry K, van Elsas JD, Grigoriev IV, Nichols NN.

Biotechnol Biofuels. 2019 Sep 23;12:229. doi: 10.1186/s13068-019-1569-6. eCollection 2019.


Limited evidence for spatial resource partitioning across temperate grassland biodiversity experiments.

Barry KE, van Ruijven J, Mommer L, Bai Y, Beierkuhnlein C, Buchmann N, de Kroon H, Ebeling A, Eisenhauer N, Guimaraes-Steinicke C, Hildebrandt A, Isbell F, Milcu A, Neßhöver C, Reich PB, Roscher C, Sauheitl L, Scherer-Lorenzen M, Schmid B, Tilman D, von Felten S, Weigelt A.

Ecology. 2019 Sep 27. doi: 10.1002/ecy.2905. [Epub ahead of print]


Prophylactic negative wound therapy in laparotomy wounds (PROPEL trial): randomized controlled trial.

Donlon NE, Boland PA, Kelly ME, Schmidt K, Cooke F, Neary PM, Barry KM, Reynolds JV.

Int J Colorectal Dis. 2019 Sep 16. doi: 10.1007/s00384-019-03398-9. [Epub ahead of print]


Overexpression of a Prefoldin β subunit gene reduces biomass recalcitrance in the bioenergy crop Populus.

Zhang J, Xie M, Li M, Ding J, Pu Y, Bryan AC, Rottmann W, Winkeler KA, Collins CM, Singan V, Lindquist EA, Jawdy SS, Gunter LE, Engle NL, Yang X, Barry K, Tschaplinski TJ, Schmutz J, Tuskan GA, Muchero W, Chen JG.

Plant Biotechnol J. 2019 Sep 9. doi: 10.1111/pbi.13254. [Epub ahead of print]


A retrospective review of dupilumab and psoriasis biologic combination therapy.

Barry K, Zancanaro P, Casseres R, Dumont N, Rosmarin D.

J Dermatolog Treat. 2019 Sep 2:1-2. doi: 10.1080/09546634.2019.1659481. [Epub ahead of print] No abstract available.


Construction and comparison of three reference-quality genome assemblies for soybean.

Valliyodan B, Cannon SB, Bayer PE, Shu S, Brown AV, Ren L, Jenkins J, Chung CY, Chan TF, Daum CG, Plott C, Hastie A, Baruch K, Barry KW, Huang W, Patil G, Varshney RK, Hu H, Batley J, Yuan Y, Song Q, Stupar RM, Goodstein DM, Stacey G, Lam HM, Jackson SA, Schmutz J, Grimwood J, Edwards D, Nguyen HT.

Plant J. 2019 Aug 21. doi: 10.1111/tpj.14500. [Epub ahead of print]


Pharmacokinetics of 99mTc-HMPAO in Isolated Perfused Rat Lungs.

Clough AV, Barry K, Rizzo BM, Jacobs ER, Audi SH.

J Appl Physiol (1985). 2019 Aug 15. doi: 10.1152/japplphysiol.00717.2018. [Epub ahead of print]


Correction to: Ancient polymorphisms contribute to genome-wide variation by long-term balancing selection and divergent sorting in Boechera stricta.

Wang B, Mojica JP, Perera N, Lee CR, Lovell JT, Sharma A, Adam C, Lipzen A, Barry K, Rokhsar DS, Schmutz J, Mitchell-Olds T.

Genome Biol. 2019 Aug 9;20(1):161. doi: 10.1186/s13059-019-1781-5.


Managing All the Genotypic Knowledge: Approach to a Septic Patient Colonized by Different Enterobacteriales with Unique Carbapenemases.

Park SC, Wailan AM, Barry KE, Vegesana K, Carroll J, Mathers AJ, Miller WR, Munita JM.

Antimicrob Agents Chemother. 2019 Jul 25;63(8). pii: e00029-19. doi: 10.1128/AAC.00029-19. Print 2019 Aug.


The Role of fosA in Challenges with Fosfomycin Susceptibility Testing of Multispecies Klebsiella pneumoniae Carbapenemase-Producing Clinical Isolates.

Elliott ZS, Barry KE, Cox HL, Stoesser N, Carroll J, Vegesana K, Kotay S, Sheppard AE, Wailan A, Crook DW, Parikh H, Mathers AJ.

J Clin Microbiol. 2019 Sep 24;57(10). pii: e00634-19. doi: 10.1128/JCM.00634-19. Print 2019 Oct.


Multiple Maize Reference Genomes Impact the Identification of Variants by Genome-Wide Association Study in a Diverse Inbred Panel.

Gage JL, Vaillancourt B, Hamilton JP, Manrique-Carpintero NC, Gustafson TJ, Barry K, Lipzen A, Tracy WF, Mikel MA, Kaeppler SM, Buell CR, de Leon N.

Plant Genome. 2019 Jun;12(2). doi: 10.3835/plantgenome2018.09.0069.


Mediation of plant-mycorrhizal interaction by a lectin receptor-like kinase.

Labbé J, Muchero W, Czarnecki O, Wang J, Wang X, Bryan AC, Zheng K, Yang Y, Xie M, Zhang J, Wang D, Meidl P, Wang H, Morrell-Falvey JL, Cope KR, Maia LGS, Ané JM, Mewalal R, Jawdy SS, Gunter LE, Schackwitz W, Martin J, Le Tacon F, Li T, Zhang Z, Ranjan P, Lindquist E, Yang X, Jacobson DA, Tschaplinski TJ, Barry K, Schmutz J, Chen JG, Tuskan GA.

Nat Plants. 2019 Jul;5(7):676-680. doi: 10.1038/s41477-019-0469-x. Epub 2019 Jul 8.


Standard Fixed-Schedule Methadone Taper Versus Symptom-Triggered Methadone Approach for Treatment of Neonatal Opioid Withdrawal Syndrome.

Wachman EM, Minear S, Hirashima M, Hansbury A, Hutton E, Shrestha H, Combs G, Barry K, Slater C, Stickney D, Walley AY.

Hosp Pediatr. 2019 Aug;9(8):576-584. doi: 10.1542/hpeds.2018-0165. Epub 2019 Jul 3.


Not even wrong: Comment by Wagg et al.

Wagg C, Barry KE, O'Brien MJ, McKenzie-Gopsill A, Roscher C, Eisenhauer N, Schmid B.

Ecology. 2019 Oct;100(10):e02805. doi: 10.1002/ecy.2805. Epub 2019 Jul 31. No abstract available.


Ancient polymorphisms contribute to genome-wide variation by long-term balancing selection and divergent sorting in Boechera stricta.

Wang B, Mojica JP, Perera N, Lee CR, Lovell JT, Sharma A, Adam C, Lipzen A, Barry K, Rokhsar DS, Schmutz J, Mitchell-Olds T.

Genome Biol. 2019 Jun 21;20(1):126. doi: 10.1186/s13059-019-1729-9. Erratum in: Genome Biol. 2019 Aug 9;20(1):161.


The adequacy of lymph node clearance in colon cancer surgery performed in a non-specialist centre; implications for practice.

Higgins P, Nemeth T, Bennani F, Khan W, Khan I, Waldron R, Barry K.

Ir J Med Sci. 2019 Jun 19. doi: 10.1007/s11845-019-02044-1. [Epub ahead of print]


Obscure gastrointestinal bleeding resulting from small bowel neoplasia; A case series.

Teh JW, Fowler AL, Donlon NE, Khan W, Khan IZ, Waldron M, Barry K.

Int J Surg Case Rep. 2019;60:87-90. doi: 10.1016/j.ijscr.2019.05.006. Epub 2019 May 10.


QTL × environment interactions underlie adaptive divergence in switchgrass across a large latitudinal gradient.

Lowry DB, Lovell JT, Zhang L, Bonnette J, Fay PA, Mitchell RB, Lloyd-Reilley J, Boe AR, Wu Y, Rouquette FM Jr, Wynia RL, Weng X, Behrman KD, Healey A, Barry K, Lipzen A, Bauer D, Sharma A, Jenkins J, Schmutz J, Fritschi FB, Juenger TE.

Proc Natl Acad Sci U S A. 2019 Jun 25;116(26):12933-12941. doi: 10.1073/pnas.1821543116. Epub 2019 Jun 10.


Community-Based Recreation Therapy and Mental Health Recovery: A Mixed-Media Participatory Action Research Study.

Ariss JJ, Gerlach A, Baker JB, Barry K, Cooper L, de Vries TL, Halligan K, Lacroix M.

Prog Community Health Partnersh. 2019;13(2):161-170. doi: 10.1353/cpr.2019.0016.


Community-Based Recreation Therapy and Mental Health Recovery: A Mixed-Media Participatory Action Research Study.

Ariss JJ, Gerlach A, Baker JB, Barry K, Cooper L, de Vries TL, Halligan K, Lacroix M.

Prog Community Health Partnersh. 2019;13(2):125-126. doi: 10.1353/cpr.2019.0025. No abstract available.


A new reference genome for Sorghum bicolor reveals high levels of sequence similarity between sweet and grain genotypes: implications for the genetics of sugar metabolism.

Cooper EA, Brenton ZW, Flinn BS, Jenkins J, Shu S, Flowers D, Luo F, Wang Y, Xia P, Barry K, Daum C, Lipzen A, Yoshinaga Y, Schmutz J, Saski C, Vermerris W, Kresovich S.

BMC Genomics. 2019 May 27;20(1):420. doi: 10.1186/s12864-019-5734-x.


Four Years of CHEER: Cost and QALY Savings of a Free Nurse-run Walk-in Clinic Serving an Uninsured, Predominantly Spanish-speaking Immigrant Population in Providence.

Barry K, McCarthy M, Buckley J, Jacques S, Johnson H, Almeida-Monroe V, De Groot AS.

J Health Care Poor Underserved. 2019;30(2):806-819. doi: 10.1353/hpu.2019.0057.


Changes in auditory thalamus neural firing patterns after acoustic trauma in rats.

Barry KM, Robertson D, Mulders WHAM.

Hear Res. 2019 Aug;379:89-97. doi: 10.1016/j.heares.2019.05.001. Epub 2019 May 4.


Oxidative opening of the aromatic ring: Tracing the natural history of a large superfamily of dioxygenase domains and their relatives.

Burroughs AM, Glasner ME, Barry KP, Taylor EA, Aravind L.

J Biol Chem. 2019 Jun 28;294(26):10211-10235. doi: 10.1074/jbc.RA119.007595. Epub 2019 May 15.


Draft Genome Sequences of Three Monokaryotic Isolates of the White-Rot Basidiomycete Fungus Dichomitus squalens.

Casado López S, Peng M, Daly P, Andreopoulos B, Pangilinan J, Lipzen A, Riley R, Ahrendt S, Ng V, Barry K, Daum C, Grigoriev IV, Hildén KS, Mäkelä MR, de Vries RP.

Microbiol Resour Announc. 2019 May 2;8(18). pii: e00264-19. doi: 10.1128/MRA.00264-19.


Unleashing Type-2 Dendritic Cells to Drive Protective Antitumor CD4+ T Cell Immunity.

Binnewies M, Mujal AM, Pollack JL, Combes AJ, Hardison EA, Barry KC, Tsui J, Ruhland MK, Kersten K, Abushawish MA, Spasic M, Giurintano JP, Chan V, Daud AI, Ha P, Ye CJ, Roberts EW, Krummel MF.

Cell. 2019 Apr 18;177(3):556-571.e16. doi: 10.1016/j.cell.2019.02.005. Epub 2019 Apr 4.


Transcriptional and Chemical Changes in Soybean Leaves in Response to Long-Term Aphid Colonization.

Hohenstein JD, Studham ME, Klein A, Kovinich N, Barry K, Lee YJ, MacIntosh GC.

Front Plant Sci. 2019 Mar 13;10:310. doi: 10.3389/fpls.2019.00310. eCollection 2019.


Don't overlook the little guy: An evaluation of the frequency of small plasmids co-conjugating with larger carbapenemase gene containing plasmids.

Barry KE, Wailan AM, Sheppard AE, Crook D, Vegesana K, Stoesser N, Parikh HI, Sebra R, Mathers AJ.

Plasmid. 2019 May;103:1-8. doi: 10.1016/j.plasmid.2019.03.005. Epub 2019 Mar 27.


Klebsiella quasipneumoniae Provides a Window into Carbapenemase Gene Transfer, Plasmid Rearrangements, and Patient Interactions with the Hospital Environment.

Mathers AJ, Crook D, Vaughan A, Barry KE, Vegesana K, Stoesser N, Parikh HI, Sebra R, Kotay S, Walker AS, Sheppard AE.

Antimicrob Agents Chemother. 2019 May 24;63(6). pii: e02513-18. doi: 10.1128/AAC.02513-18. Print 2019 Jun.


Transcriptomic atlas of mushroom development reveals conserved genes behind complex multicellularity in fungi.

Krizsán K, Almási É, Merényi Z, Sahu N, Virágh M, Kószó T, Mondo S, Kiss B, Bálint B, Kües U, Barry K, Cseklye J, Hegedüs B, Henrissat B, Johnson J, Lipzen A, Ohm RA, Nagy I, Pangilinan J, Yan J, Xiong Y, Grigoriev IV, Hibbett DS, Nagy LG.

Proc Natl Acad Sci U S A. 2019 Apr 9;116(15):7409-7418. doi: 10.1073/pnas.1817822116. Epub 2019 Mar 22.


Megaphylogeny resolves global patterns of mushroom evolution.

Varga T, Krizsán K, Földi C, Dima B, Sánchez-García M, Sánchez-Ramírez S, Szöllősi GJ, Szarkándi JG, Papp V, Albert L, Andreopoulos W, Angelini C, Antonín V, Barry KW, Bougher NL, Buchanan P, Buyck B, Bense V, Catcheside P, Chovatia M, Cooper J, Dämon W, Desjardin D, Finy P, Geml J, Haridas S, Hughes K, Justo A, Karasiński D, Kautmanova I, Kiss B, Kocsubé S, Kotiranta H, LaButti KM, Lechner BE, Liimatainen K, Lipzen A, Lukács Z, Mihaltcheva S, Morgado LN, Niskanen T, Noordeloos ME, Ohm RA, Ortiz-Santana B, Ovrebo C, Rácz N, Riley R, Savchenko A, Shiryaev A, Soop K, Spirin V, Szebenyi C, Tomšovský M, Tulloss RE, Uehling J, Grigoriev IV, Vágvölgyi C, Papp T, Martin FM, Miettinen O, Hibbett DS, Nagy LG.

Nat Ecol Evol. 2019 Apr;3(4):668-678. doi: 10.1038/s41559-019-0834-1. Epub 2019 Mar 18.


Utilisation of critical care services for surgical patients in a model three hospital.

Fowler AL, Cullivan O, Sibartie S, O'Shea A, Waldron R, Khan I, Khan W, Barry KM.

Ir J Med Sci. 2019 Feb 9. doi: 10.1007/s11845-019-01981-1. [Epub ahead of print]


Genome-wide association analysis of stalk biomass and anatomical traits in maize.

Mazaheri M, Heckwolf M, Vaillancourt B, Gage JL, Burdo B, Heckwolf S, Barry K, Lipzen A, Ribeiro CB, Kono TJY, Kaeppler HF, Spalding EP, Hirsch CN, Robin Buell C, de Leon N, Kaeppler SM.

BMC Plant Biol. 2019 Jan 31;19(1):45. doi: 10.1186/s12870-019-1653-x.


Genomic and Genetic Insights Into a Cosmopolitan Fungus, Paecilomyces variotii (Eurotiales).

Urquhart AS, Mondo SJ, Mäkelä MR, Hane JK, Wiebenga A, He G, Mihaltcheva S, Pangilinan J, Lipzen A, Barry K, de Vries RP, Grigoriev IV, Idnurm A.

Front Microbiol. 2018 Dec 13;9:3058. doi: 10.3389/fmicb.2018.03058. eCollection 2018.


Reclaiming Health Policy: Models for Graduate-Level Education and Military-Civilian Teamwork.

Barry KM, Robb DJ.

Annu Rev Nurs Res. 2018 Dec;36(1):151-204. doi: 10.1891/0739-6686.36.1.151. Review. No abstract available.


The genomic landscape of molecular responses to natural drought stress in Panicum hallii.

Lovell JT, Jenkins J, Lowry DB, Mamidi S, Sreedasyam A, Weng X, Barry K, Bonnette J, Campitelli B, Daum C, Gordon SP, Gould BA, Khasanova A, Lipzen A, MacQueen A, Palacio-Mejía JD, Plott C, Shakirov EV, Shu S, Yoshinaga Y, Zane M, Kudrna D, Talag JD, Rokhsar D, Grimwood J, Schmutz J, Juenger TE.

Nat Commun. 2018 Dec 6;9(1):5213. doi: 10.1038/s41467-018-07669-x.


Draft Genome Assemblies of Five Robust Yarrowia lipolytica Strains Exhibiting High Lipid Production, Pentose Sugar Utilization, and Sugar Alcohol Secretion from Undetoxified Lignocellulosic Biomass Hydrolysates.

Walker C, Ryu S, Na H, Zane M, LaButti K, Lipzen A, Haridas S, Barry K, Grigoriev IV, Quarterman J, Slininger P, Dien B, Trinh CT.

Microbiol Resour Announc. 2018 Sep 27;7(12). pii: e01040-18. doi: 10.1128/MRA.01040-18. eCollection 2018 Sep.


The Future of Complementarity: Disentangling Causes from Consequences.

Barry KE, Mommer L, van Ruijven J, Wirth C, Wright AJ, Bai Y, Connolly J, De Deyn GB, de Kroon H, Isbell F, Milcu A, Roscher C, Scherer-Lorenzen M, Schmid B, Weigelt A.

Trends Ecol Evol. 2019 Feb;34(2):167-180. doi: 10.1016/j.tree.2018.10.013. Epub 2018 Dec 4. Review.


Does soil track-in contribute to house dust concentrations of perfluoroalkyl acids (PFAAs) in areas affected by soil or water contamination?

Scher DP, Kelly JE, Huset CA, Barry KM, Yingling VL.

J Expo Sci Environ Epidemiol. 2019 Mar;29(2):218-226. doi: 10.1038/s41370-018-0101-6. Epub 2018 Dec 5.


Regulation of Yeast-to-Hyphae Transition in Yarrowia lipolytica.

Pomraning KR, Bredeweg EL, Kerkhoven EJ, Barry K, Haridas S, Hundley H, LaButti K, Lipzen A, Yan M, Magnuson JK, Simmons BA, Grigoriev IV, Nielsen J, Baker SE.

mSphere. 2018 Dec 5;3(6). pii: e00541-18. doi: 10.1128/mSphere.00541-18.


Alcohol use severity and age moderate the effects of brief interventions in an emergency department randomized controlled trial.

Fernandez AC, Waller R, Walton MA, Bonar EE, Ignacio RV, Chermack ST, Cunningham RM, Booth BM, Ilgen MA, Barry KL, Blow FC.

Drug Alcohol Depend. 2019 Jan 1;194:386-394. doi: 10.1016/j.drugalcdep.2018.10.021. Epub 2018 Nov 14.


Phylogenomics of Endogonaceae and evolution of mycorrhizas within Mucoromycota.

Chang Y, Desirò A, Na H, Sandor L, Lipzen A, Clum A, Barry K, Grigoriev IV, Martin FM, Stajich JE, Smith ME, Bonito G, Spatafora JW.

New Phytol. 2019 Apr;222(1):511-525. doi: 10.1111/nph.15613. Epub 2019 Jan 12.


Pezizomycetes genomes reveal the molecular basis of ectomycorrhizal truffle lifestyle.

Murat C, Payen T, Noel B, Kuo A, Morin E, Chen J, Kohler A, Krizsán K, Balestrini R, Da Silva C, Montanini B, Hainaut M, Levati E, Barry KW, Belfiori B, Cichocki N, Clum A, Dockter RB, Fauchery L, Guy J, Iotti M, Le Tacon F, Lindquist EA, Lipzen A, Malagnac F, Mello A, Molinier V, Miyauchi S, Poulain J, Riccioni C, Rubini A, Sitrit Y, Splivallo R, Traeger S, Wang M, Žifčáková L, Wipf D, Zambonelli A, Paolocci F, Nowrousian M, Ottonello S, Baldrian P, Spatafora JW, Henrissat B, Nagy LG, Aury JM, Wincker P, Grigoriev IV, Bonfante P, Martin FM.

Nat Ecol Evol. 2018 Dec;2(12):1956-1965. doi: 10.1038/s41559-018-0710-4. Epub 2018 Nov 12.


Community clinic-based lifestyle change for prevention of metabolic syndrome: Rationale, design and methods of the 'Vida Sana/healthy life' program.

Risica PM, McCarthy M, Barry K, Oliverio SP, De Groot AS.

Contemp Clin Trials Commun. 2018 Oct 25;12:123-128. doi: 10.1016/j.conctc.2018.10.002. eCollection 2018 Dec.


A randomized controlled trial of the effects of mindfulness practice on doctoral candidate psychological status.

Barry KM, Woods M, Martin A, Stirling C, Warnecke E.

J Am Coll Health. 2019 May-Jun;67(4):299-307. doi: 10.1080/07448481.2018.1515760. Epub 2018 Nov 2.


Population genomics and climate adaptation of a C4 perennial grass, Panicum hallii (Poaceae).

Gould BA, Palacio-Mejia JD, Jenkins J, Mamidi S, Barry K, Schmutz J, Juenger TE, Lowry DB.

BMC Genomics. 2018 Nov 1;19(1):792. doi: 10.1186/s12864-018-5179-7.


Bridging the [Health Equity] Gap at a Free Clinic for Uninsured Residents of Rhode Island.

Hindocha P, Nair NJ, Pigoga JL, Barry K, McCarthy M, Almeida-Monroe V, De Groot AS.

R I Med J (2013). 2018 Nov 1;101(9):27-31.


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