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Sucrose Metabolism in Haloarchaea: Reassessment Using Genomics, Proteomics, and Metagenomics.

Williams TJ, Allen MA, Liao Y, Raftery MJ, Cavicchioli R.

Appl Environ Microbiol. 2019 Mar 6;85(6). pii: e02935-18. doi: 10.1128/AEM.02935-18. Print 2019 Mar 15.


Safety and tolerability of HIV-1 multiantigen pDNA vaccine given with IL-12 plasmid DNA via electroporation, boosted with a recombinant vesicular stomatitis virus HIV Gag vaccine in healthy volunteers in a randomized, controlled clinical trial.

Elizaga ML, Li SS, Kochar NK, Wilson GJ, Allen MA, Tieu HVN, Frank I, Sobieszczyk ME, Cohen KW, Sanchez B, Latham TE, Clarke DK, Egan MA, Eldridge JH, Hannaman D, Xu R, Ota-Setlik A, McElrath MJ, Hay CM; NIAID HIV Vaccine Trials Network (HVTN) 087 Study Team.

PLoS One. 2018 Sep 20;13(9):e0202753. doi: 10.1371/journal.pone.0202753. eCollection 2018.


Innovative approaches to track lymph node germinal center responses to evaluate development of broadly neutralizing antibodies in human HIV vaccine trials.

Patricia D'Souza M, Allen MA, Baumblatt JAG, Boggiano C, Crotty S, Grady C, Havenar-Daughton C, Heit A, Hu DJ, Kunwar N, McElrath MJ; Lymph Node Webinar Contributors.

Vaccine. 2018 Sep 11;36(38):5671-5677. doi: 10.1016/j.vaccine.2018.07.071. Epub 2018 Aug 7.


Genomic variation and biogeography of Antarctic haloarchaea.

Tschitschko B, Erdmann S, DeMaere MZ, Roux S, Panwar P, Allen MA, Williams TJ, Brazendale S, Hancock AM, Eloe-Fadrosh EA, Cavicchioli R.

Microbiome. 2018 Jun 20;6(1):113. doi: 10.1186/s40168-018-0495-3.


Detecting Differential Transcription Factor Activity from ATAC-Seq Data.

Tripodi IJ, Allen MA, Dowell RD.

Molecules. 2018 May 10;23(5). pii: E1136. doi: 10.3390/molecules23051136.


Opioid analgesics: Is it time for risk stratification prior to use? - ADDENDUM.

Allen MA.

CJEM. 2018 May 9:1. doi: 10.1017/cem.2018.399. [Epub ahead of print] No abstract available.


A versatile expression vector for the growth and amplification of unmodified phage display polypeptides.

Winton AJ, Baptiste JL, Allen MA.

Protein Expr Purif. 2018 Sep;149:31-36. doi: 10.1016/j.pep.2018.04.008. Epub 2018 Apr 17.


Enhancer RNA profiling predicts transcription factor activity.

Azofeifa JG, Allen MA, Hendrix JR, Read T, Rubin JD, Dowell RD.

Genome Res. 2018 Feb 15. doi: 10.1101/gr.225755.117. [Epub ahead of print]


Synthesis of N-Oxyureas by Substitution and Cope-Type Hydroamination Reactions Using O-Isocyanate Precursors.

Allen MA, Ivanovich RA, Polat DE, Beauchemin AM.

Org Lett. 2017 Dec 15;19(24):6574-6577. doi: 10.1021/acs.orglett.7b03288. Epub 2017 Nov 22.


Opioid analgesics: Is it time for risk stratification prior to use? - ERRATUM.

Allen MA.

CJEM. 2017 Nov 20:1. doi: 10.1017/cem.2017.424. [Epub ahead of print] No abstract available.


Human TFIIH Kinase CDK7 Regulates Transcription-Associated Chromatin Modifications.

Ebmeier CC, Erickson B, Allen BL, Allen MA, Kim H, Fong N, Jacobsen JR, Liang K, Shilatifard A, Dowell RD, Old WM, Bentley DL, Taatjes DJ.

Cell Rep. 2017 Aug 1;20(5):1173-1186. doi: 10.1016/j.celrep.2017.07.021.


Opioid Analgesics: Is it Time for Risk Stratification Prior to Use?

Allen MA.

CJEM. 2017 Sep;19(5):414. doi: 10.1017/cem.2017.359. Epub 2017 Jul 28. No abstract available.


RNA Pol II transcription model and interpretation of GRO-seq data.

Lladser ME, Azofeifa JG, Allen MA, Dowell RD.

J Math Biol. 2017 Jan;74(1-2):77-97. doi: 10.1007/s00285-016-1014-4. Epub 2016 May 3.


Ecophysiological Distinctions of Haloarchaea from a Hypersaline Antarctic Lake as Determined by Metaproteomics.

Tschitschko B, Williams TJ, Allen MA, Zhong L, Raftery MJ, Cavicchioli R.

Appl Environ Microbiol. 2016 May 16;82(11):3165-73. doi: 10.1128/AEM.00473-16. Print 2016 Jun 1.


An Annotation Agnostic Algorithm for Detecting Nascent RNA Transcripts in GRO-Seq.

Azofeifa JG, Allen MA, Lladser ME, Dowell RD.

IEEE/ACM Trans Comput Biol Bioinform. 2017 Sep-Oct;14(5):1070-1081. doi: 10.1109/TCBB.2016.2520919. Epub 2016 Jan 26.


Antarctic archaea-virus interactions: metaproteome-led analysis of invasion, evasion and adaptation.

Tschitschko B, Williams TJ, Allen MA, Páez-Espino D, Kyrpides N, Zhong L, Raftery MJ, Cavicchioli R.

ISME J. 2015 Sep;9(9):2094-107. doi: 10.1038/ismej.2015.110. Epub 2015 Jun 30.


Quality and equity of care in U.S. hospitals.

Trivedi AN, Nsa W, Hausmann LR, Lee JS, Ma A, Bratzler DW, Mor MK, Baus K, Larbi F, Fine MJ.

N Engl J Med. 2014 Dec 11;371(24):2298-308. doi: 10.1056/NEJMsa1405003.


HIV-specific humoral responses benefit from stronger prime in phase Ib clinical trial.

Bart PA, Huang Y, Karuna ST, Chappuis S, Gaillard J, Kochar N, Shen X, Allen MA, Ding S, Hural J, Liao HX, Haynes BF, Graham BS, Gilbert PB, McElrath MJ, Montefiori DC, Tomaras GD, Pantaleo G, Frahm N.

J Clin Invest. 2014 Nov;124(11):4843-56. doi: 10.1172/JCI75894. Epub 2014 Oct 1.


Medicare claims can be used to identify US hospitals with higher rates of surgical site infection following vascular surgery.

Calderwood MS, Kleinman K, Bratzler DW, Ma A, Kaganov RE, Bruce CB, Balaconis EC, Canning C, Platt R, Huang SS; CDC Prevention Epicenters Program; Oklahoma Foundation for Medical Quality.

Med Care. 2014 Oct;52(10):918-25. doi: 10.1097/MLR.0000000000000212.


Global analysis of p53-regulated transcription identifies its direct targets and unexpected regulatory mechanisms.

Allen MA, Andrysik Z, Dengler VL, Mellert HS, Guarnieri A, Freeman JA, Sullivan KD, Galbraith MD, Luo X, Kraus WL, Dowell RD, Espinosa JM.

Elife. 2014 May 27;3:e02200. doi: 10.7554/eLife.02200.


Antibody-conjugated paramagnetic nanobeads: kinetics of bead-cell binding.

Waseem S, Allen MA, Schreier S, Udomsangpetch R, Bhakdi SC.

Int J Mol Sci. 2014 May 19;15(5):8821-34. doi: 10.3390/ijms15058821.


A framework for the treatment of pain and addiction in the emergency department.

Allen MA, Jewers H, McDonald JS.

J Emerg Nurs. 2014 Nov;40(6):552-9. doi: 10.1016/j.jen.2013.12.020. Epub 2014 Mar 14. No abstract available.


Microbial ecology of an Antarctic hypersaline lake: genomic assessment of ecophysiology among dominant haloarchaea.

Williams TJ, Allen MA, DeMaere MZ, Kyrpides NC, Tringe SG, Woyke T, Cavicchioli R.

ISME J. 2014 Aug;8(8):1645-58. doi: 10.1038/ismej.2014.18. Epub 2014 Feb 20. Erratum in: ISME J. 2014 Aug;8(8):1752.


Activity of commonly used antimicrobial prophylaxis regimens against pathogens causing coronary artery bypass graft and arthroplasty surgical site infections in the United States, 2006-2009.

Berríos-Torres SI, Yi SH, Bratzler DW, Ma A, Mu Y, Zhu L, Jernigan JA.

Infect Control Hosp Epidemiol. 2014 Mar;35(3):231-9. doi: 10.1086/675289. Epub 2014 Jan 29.


A community-based approach to the treatment of pain and addiction.

Allen MA.

Can J Rural Med. 2014 Winter;19(1):27-30. No abstract available.


Harnessing claims to improve detection of surgical site infections following hysterectomy and colorectal surgery.

Letourneau AR, Calderwood MS, Huang SS, Bratzler DW, Ma A, Yokoe DS.

Infect Control Hosp Epidemiol. 2013 Dec;34(12):1321-3. doi: 10.1086/673975. Epub 2013 Oct 28.


Tmem79/Matt is the matted mouse gene and is a predisposing gene for atopic dermatitis in human subjects.

Saunders SP, Goh CS, Brown SJ, Palmer CN, Porter RM, Cole C, Campbell LE, Gierlinski M, Barton GJ, Schneider G, Balmain A, Prescott AR, Weidinger S, Baurecht H, Kabesch M, Gieger C, Lee YA, Tavendale R, Mukhopadhyay S, Turner SW, Madhok VB, Sullivan FM, Relton C, Burn J, Meggitt S, Smith CH, Allen MA, Barker JN, Reynolds NJ, Cordell HJ, Irvine AD, McLean WH, Sandilands A, Fallon PG.

J Allergy Clin Immunol. 2013 Nov;132(5):1121-9. doi: 10.1016/j.jaci.2013.08.046. Epub 2013 Sep 29.


High level of intergenera gene exchange shapes the evolution of haloarchaea in an isolated Antarctic lake.

DeMaere MZ, Williams TJ, Allen MA, Brown MV, Gibson JA, Rich J, Lauro FM, Dyall-Smith M, Davenport KW, Woyke T, Kyrpides NC, Tringe SG, Cavicchioli R.

Proc Natl Acad Sci U S A. 2013 Oct 15;110(42):16939-44. doi: 10.1073/pnas.1307090110. Epub 2013 Sep 30.


HIF1A employs CDK8-mediator to stimulate RNAPII elongation in response to hypoxia.

Galbraith MD, Allen MA, Bensard CL, Wang X, Schwinn MK, Qin B, Long HW, Daniels DL, Hahn WC, Dowell RD, Espinosa JM.

Cell. 2013 Jun 6;153(6):1327-39. doi: 10.1016/j.cell.2013.04.048.


Implications of Medicare procedure volumes on resident education.

Broughan TA, Crosby ME, Trickey AW, Ma A, Bratzler DW.

Am J Surg. 2013 Jun;205(6):737-44. doi: 10.1016/j.amjsurg.2012.11.006. Epub 2013 Mar 26.


Rare pathogenic variants in IL36RN underlie a spectrum of psoriasis-associated pustular phenotypes.

Setta-Kaffetzi N, Navarini AA, Patel VM, Pullabhatla V, Pink AE, Choon SE, Allen MA, Burden AD, Griffiths CE, Seyger MM, Kirby B, Trembath RC, Simpson MA, Smith CH, Capon F, Barker JN.

J Invest Dermatol. 2013 May;133(5):1366-9. doi: 10.1038/jid.2012.490. Epub 2013 Jan 10. No abstract available.


Use of Medicare claims to identify US hospitals with a high rate of surgical site infection after hip arthroplasty.

Calderwood MS, Kleinman K, Bratzler DW, Ma A, Bruce CB, Kaganov RE, Canning C, Platt R, Huang SS; Centers for Disease Control and Prevention Epicenters Program; Oklahoma Foundation for Medical Quality.

Infect Control Hosp Epidemiol. 2013 Jan;34(1):31-9. doi: 10.1086/668785. Epub 2012 Nov 20.


Temperature dependence of electron magnetic resonance spectra of iron oxide nanoparticles mineralized in Listeria innocua protein cages.

Usselman RJ, Russek SE, Klem MT, Allen MA, Douglas T, Young M, Idzerda YU, Singel DJ.

J Appl Phys. 2012 Oct 15;112(8):84701. Epub 2012 Oct 16.


Key microbial drivers in Antarctic aquatic environments.

Wilkins D, Yau S, Williams TJ, Allen MA, Brown MV, DeMaere MZ, Lauro FM, Cavicchioli R.

FEMS Microbiol Rev. 2013 May;37(3):303-35. doi: 10.1111/1574-6976.12007. Epub 2012 Nov 20. Review.


How should a commercial driver medical examiner approach determining fitness for duty in a commercial motor vehicle operator with a body mass index ≥33 kg/m2?

Gerbo R, Jin CF, Allen MA.

J Occup Environ Med. 2012 Oct;54(10):1315-7. doi: 10.1097/JOM.0b013e318222b0a0. No abstract available.


M13 bacteriophage display framework that allows sortase-mediated modification of surface-accessible phage proteins.

Hess GT, Cragnolini JJ, Popp MW, Allen MA, Dougan SK, Spooner E, Ploegh HL, Belcher AM, Guimaraes CP.

Bioconjug Chem. 2012 Jul 18;23(7):1478-87. doi: 10.1021/bc300130z. Epub 2012 Jul 3.


Biotemplated synthesis of perovskite nanomaterials for solar energy conversion.

Nuraje N, Dang X, Qi J, Allen MA, Lei Y, Belcher AM.

Adv Mater. 2012 Jun 5;24(21):2885-9. doi: 10.1002/adma.201200114. Epub 2012 Apr 20.


Graphene sheets stabilized on genetically engineered M13 viral templates as conducting frameworks for hybrid energy-storage materials.

Oh D, Dang X, Yi H, Allen MA, Xu K, Lee YJ, Belcher AM.

Small. 2012 Apr 10;8(7):1006-11. doi: 10.1002/smll.201102036. Epub 2012 Feb 16.


Use of Medicare diagnosis and procedure codes to improve detection of surgical site infections following hip arthroplasty, knee arthroplasty, and vascular surgery.

Calderwood MS, Ma A, Khan YM, Olsen MA, Bratzler DW, Yokoe DS, Hooper DC, Stevenson K, Fraser VJ, Platt R, Huang SS; CDC Prevention Epicenters Program.

Infect Control Hosp Epidemiol. 2012 Jan;33(1):40-9. doi: 10.1086/663207. Epub 2011 Nov 22.


Use of Medicare claims to rank hospitals by surgical site infection risk following coronary artery bypass graft surgery.

Huang SS, Placzek H, Livingston J, Ma A, Onufrak F, Lankiewicz J, Kleinman K, Bratzler D, Olsen MA, Lyles R, Khan Y, Wright P, Yokoe DS, Fraser VJ, Weinstein RA, Stevenson K, Hooper D, Vostok J, Datta R, Nsa W, Platt R.

Infect Control Hosp Epidemiol. 2011 Aug;32(8):775-83. doi: 10.1086/660874.


A global analysis of C. elegans trans-splicing.

Allen MA, Hillier LW, Waterston RH, Blumenthal T.

Genome Res. 2011 Feb;21(2):255-64. doi: 10.1101/gr.113811.110. Epub 2010 Dec 22.


Surgical care improvement project adherence and postoperative infections.

Bratzler DW, Ma A, Nsa W.

JAMA. 2010 Oct 20;304(15):1670; author reply 1671-2. doi: 10.1001/jama.2010.1461. No abstract available.


Polycistronic pre-mRNA processing in vitro: snRNP and pre-mRNA role reversal in trans-splicing.

Lasda EL, Allen MA, Blumenthal T.

Genes Dev. 2010 Aug 1;24(15):1645-58. doi: 10.1101/gad.1940010. Epub 2010 Jul 12.


The genome sequence of the psychrophilic archaeon, Methanococcoides burtonii: the role of genome evolution in cold adaptation.

Allen MA, Lauro FM, Williams TJ, Burg D, Siddiqui KS, De Francisci D, Chong KW, Pilak O, Chew HH, De Maere MZ, Ting L, Katrib M, Ng C, Sowers KR, Galperin MY, Anderson IJ, Ivanova N, Dalin E, Martinez M, Lapidus A, Hauser L, Land M, Thomas T, Cavicchioli R.

ISME J. 2009 Sep;3(9):1012-35. doi: 10.1038/ismej.2009.45. Epub 2009 Apr 30.


Bacterial, archaeal and eukaryotic diversity of smooth and pustular microbial mat communities in the hypersaline lagoon of Shark Bay.

Allen MA, Goh F, Burns BP, Neilan BA.

Geobiology. 2009 Jan;7(1):82-96. doi: 10.1111/j.1472-4669.2008.00187.x.


Determining the specific microbial populations and their spatial distribution within the stromatolite ecosystem of Shark Bay.

Goh F, Allen MA, Leuko S, Kawaguchi T, Decho AW, Burns BP, Neilan BA.

ISME J. 2009 Apr;3(4):383-96. doi: 10.1038/ismej.2008.114. Epub 2008 Dec 18.


Initial antibiotic selection and patient outcomes: observations from the National Pneumonia Project.

Bratzler DW, Ma A, Nsa W.

Clin Infect Dis. 2008 Dec 1;47 Suppl 3:S193-201. doi: 10.1086/591404.


Genes involved in pre-mRNA 3'-end formation and transcription termination revealed by a lin-15 operon Muv suppressor screen.

Cui M, Allen MA, Larsen A, Macmorris M, Han M, Blumenthal T.

Proc Natl Acad Sci U S A. 2008 Oct 28;105(43):16665-70. doi: 10.1073/pnas.0807104105. Epub 2008 Oct 22.


Management of open abdominal wounds with a dynamic fascial closure system.

Reimer MW, Yelle JD, Reitsma B, Doumit G, Allen MA, Bell MS.

Can J Surg. 2008 Jun;51(3):209-14.

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