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Recording development with single cell dynamic lineage tracing.

McKenna A, Gagnon JA.

Development. 2019 Jun 27;146(12). pii: dev169730. doi: 10.1242/dev.169730. Review.


Correction to "Comprehensive Analysis of Changes in Crude Oil Chemical Composition during Biosouring and Treatments".

Nowak JA, Shrestha PM, Weber RJ, McKenna AM, Chen H, Coates JD, Goldstein AH.

Environ Sci Technol. 2019 Jul 2;53(13):7921. doi: 10.1021/acs.est.9b03043. Epub 2019 Jun 15. No abstract available.


Massively parallel profiling and predictive modeling of the outcomes of CRISPR/Cas9-mediated double-strand break repair.

Chen W, McKenna A, Schreiber J, Haeussler M, Yin Y, Agarwal V, Noble WS, Shendure J.

Nucleic Acids Res. 2019 Sep 5;47(15):7989-8003. doi: 10.1093/nar/gkz487.


Molecular-Level Characterization of Oil-Soluble Ketone/Aldehyde Photo-Oxidation Products by Fourier Transform Ion Cyclotron Resonance Mass Spectrometry Reveals Similarity Between Microcosm and Field Samples.

Niles SF, Chacón-Patiño ML, Chen H, McKenna AM, Blakney GT, Rodgers RP, Marshall AG.

Environ Sci Technol. 2019 Jun 18;53(12):6887-6894. doi: 10.1021/acs.est.9b00908. Epub 2019 May 31.


Destabilization of the MiniChromosome Maintenance (MCM) complex modulates the cellular response to DNA double strand breaks.

Drissi R, Chauvin A, McKenna A, Lévesque D, Blais-Brochu S, Jean D, Boisvert FM.

Cell Cycle. 2018;17(23):2593-2609. doi: 10.1080/15384101.2018.1553336. Epub 2018 Dec 10.


Fremyella diplosiphon as a biodiesel agent: Identification of fatty acid methyl esters via microwave-assisted direct in situ transesterification.

Tabatabai B, Chen H, Lu J, Giwa-Otusajo J, McKenna AM, Shrivastava AK, Sitther V.

Bioenergy Res. 2018 Sep;11(3):528-537. doi: 10.1007/s12155-018-9919-y. Epub 2018 May 12.


Single Centre Experience - Clinical Presentation and Frequency of Paediatric Diabetic Ketoacidosis (DKA) At Diagnosis over a 5-Year Period.

McKenna A, Sandys N, Ryder K, Metwally N, Brennan A, O'Regan M, Hoey MCV, Roche EF.

Ir Med J. 2018 Mar 14;111(3):714.


Comprehensive Longitudinal Microbiome Analysis of the Chicken Cecum Reveals a Shift From Competitive to Environmental Drivers and a Window of Opportunity for Campylobacter.

Ijaz UZ, Sivaloganathan L, McKenna A, Richmond A, Kelly C, Linton M, Stratakos AC, Lavery U, Elmi A, Wren BW, Dorrell N, Corcionivoschi N, Gundogdu O.

Front Microbiol. 2018 Oct 15;9:2452. doi: 10.3389/fmicb.2018.02452. eCollection 2018.


Role of a pre-operative radiological scoring system in determining resectability for potentially resectable hilar cholangiocarcinoma.

Bird N, McKenna A, Dunne D, Francis B, Fenwick S, Poston G, Jones R, Malik H.

Eur J Surg Oncol. 2019 Feb;45(2):192-197. doi: 10.1016/j.ejso.2018.08.018. Epub 2018 Sep 11.


Synthesizing Signaling Pathways from Temporal Phosphoproteomic Data.

Köksal AS, Beck K, Cronin DR, McKenna A, Camp ND, Srivastava S, MacGilvray ME, Bodík R, Wolf-Yadlin A, Fraenkel E, Fisher J, Gitter A.

Cell Rep. 2018 Sep 25;24(13):3607-3618. doi: 10.1016/j.celrep.2018.08.085.


A Review of the Effect of Management Practices on Campylobacter Prevalence in Poultry Farms.

Sibanda N, McKenna A, Richmond A, Ricke SC, Callaway T, Stratakos AC, Gundogdu O, Corcionivoschi N.

Front Microbiol. 2018 Aug 24;9:2002. doi: 10.3389/fmicb.2018.02002. eCollection 2018. Review.


Extreme physiological plasticity in a hibernating basoendothermic mammal, Tenrec ecaudatus.

Treat MD, Scholer L, Barrett B, Khachatryan A, McKenna AJ, Reyes T, Rezazadeh A, Ronkon CF, Samora D, Santamaria JF, Silva Rubio C, Sutherland E, Richardson J, Lighton JRB, van Breukelen F.

J Exp Biol. 2018 Oct 18;221(Pt 20). pii: jeb185900. doi: 10.1242/jeb.185900.


Oxygen consumption of desert pupfish at ecologically relevant temperatures suggests a significant role for anaerobic metabolism.

Heuton M, Ayala L, Morante A, Dayton K, Jones AC, Hunt JR, McKenna A, van Breukelen F, Hillyard S.

J Comp Physiol B. 2018 Sep;188(5):821-830. doi: 10.1007/s00360-018-1174-1. Epub 2018 Jul 23.


The quality of randomized controlled trials of psychotherapy for eating disorders.

Grenon R, McKenna A, Maxwell H, Carlucci S, Brugnera A, Schwartze D, Hammond N, Ivanova I, Mcquaid N, Proulx G, Tasca GA.

Int J Methods Psychiatr Res. 2018 Sep;27(3):e1734. doi: 10.1002/mpr.1734. Epub 2018 Jul 20.


Meta-analysis of prognostic factors for overall survival in patients with resected hilar cholangiocarcinoma.

Bird NTE, McKenna A, Dodd J, Poston G, Jones R, Malik H.

Br J Surg. 2018 Oct;105(11):1408-1416. doi: 10.1002/bjs.10921. Epub 2018 Jul 12.


The Impact of Carbon Source as Electron Donor on Composition and Concentration of Dissolved Organic Nitrogen in Biosorption-Activated Media for Stormwater and Groundwater Co-Treatment.

Chang NB, Wen D, McKenna AM, Wanielista MP.

Environ Sci Technol. 2018 Aug 21;52(16):9380-9390. doi: 10.1021/acs.est.8b01788. Epub 2018 Aug 3.


1.1-billion-year-old porphyrins establish a marine ecosystem dominated by bacterial primary producers.

Gueneli N, McKenna AM, Ohkouchi N, Boreham CJ, Beghin J, Javaux EJ, Brocks JJ.

Proc Natl Acad Sci U S A. 2018 Jul 24;115(30):E6978-E6986. doi: 10.1073/pnas.1803866115. Epub 2018 Jul 9.


FlashFry: a fast and flexible tool for large-scale CRISPR target design.

McKenna A, Shendure J.

BMC Biol. 2018 Jul 5;16(1):74. doi: 10.1186/s12915-018-0545-0.


Simultaneous single-cell profiling of lineages and cell types in the vertebrate brain.

Raj B, Wagner DE, McKenna A, Pandey S, Klein AM, Shendure J, Gagnon JA, Schier AF.

Nat Biotechnol. 2018 Jun;36(5):442-450. doi: 10.1038/nbt.4103. Epub 2018 Mar 28.


Cheques and challenges: business performance in New Zealand general practice.

Greatbanks R, Doolan-Noble F, McKenna A.

J Prim Health Care. 2017 Sep;9(3):185-190. doi: 10.1071/HC17047.


Outcomes of Clinical Nurse Specialist Practice in the Implementation of Video Monitoring at an Academic Medical Center.

Purvis S, Kaun A, McKenna A, Weber Viste J, Fedorov E.

Clin Nurse Spec. 2018 Mar/Apr;32(2):90-96. doi: 10.1097/NUR.0000000000000356.


Comprehensive Analysis of Changes in Crude Oil Chemical Composition during Biosouring and Treatments.

Nowak JA, Shrestha PM, Weber RJ, McKenna AM, Chen H, Coates JD, Goldstein AH.

Environ Sci Technol. 2018 Feb 6;52(3):1290-1300. doi: 10.1021/acs.est.7b05346. Epub 2018 Jan 22. Erratum in: Environ Sci Technol. 2019 Jul 2;53(13):7921.


Organic coating on biochar explains its nutrient retention and stimulation of soil fertility.

Hagemann N, Joseph S, Schmidt HP, Kammann CI, Harter J, Borch T, Young RB, Varga K, Taherymoosavi S, Elliott KW, McKenna A, Albu M, Mayrhofer C, Obst M, Conte P, Dieguez-Alonso A, Orsetti S, Subdiaga E, Behrens S, Kappler A.

Nat Commun. 2017 Oct 20;8(1):1089. doi: 10.1038/s41467-017-01123-0.


CRISPR/Cas9-Mediated Scanning for Regulatory Elements Required for HPRT1 Expression via Thousands of Large, Programmed Genomic Deletions.

Gasperini M, Findlay GM, McKenna A, Milbank JH, Lee C, Zhang MD, Cusanovich DA, Shendure J.

Am J Hum Genet. 2017 Aug 3;101(2):192-205. doi: 10.1016/j.ajhg.2017.06.010. Epub 2017 Jul 14.


Systematic genomic and translational efficiency studies of uveal melanoma.

Johnson CP, Kim IK, Esmaeli B, Amin-Mansour A, Treacy DJ, Carter SL, Hodis E, Wagle N, Seepo S, Yu X, Lane AM, Gragoudas ES, Vazquez F, Nickerson E, Cibulskis K, McKenna A, Gabriel SB, Getz G, Van Allen EM, 't Hoen PAC, Garraway LA, Woodman SE.

PLoS One. 2017 Jun 8;12(6):e0178189. doi: 10.1371/journal.pone.0178189. eCollection 2017.


Spatiotemporal Evolution of Coherent Elastic Strain Waves in a Single MoS2 Flake.

McKenna AJ, Eliason JK, Flannigan DJ.

Nano Lett. 2017 Jun 14;17(6):3952-3958. doi: 10.1021/acs.nanolett.7b01565. Epub 2017 May 17.


The development of bodily self-consciousness: changing responses to the Full Body Illusion in childhood.

Cowie D, McKenna A, Bremner AJ, Aspell JE.

Dev Sci. 2018 May;21(3):e12557. doi: 10.1111/desc.12557. Epub 2017 Mar 22.


Is the incidence of type 1 diabetes in children and adolescents stabilising? The first 6 years of a National Register.

Roche EF, McKenna AM, Ryder KJ, Brennan AA, O'Regan M, Hoey HM.

Eur J Pediatr. 2016 Dec;175(12):1913-1919. Epub 2016 Sep 22.


4 Years after the Deepwater Horizon Spill: Molecular Transformation of Macondo Well Oil in Louisiana Salt Marsh Sediments Revealed by FT-ICR Mass Spectrometry.

Chen H, Hou A, Corilo YE, Lin Q, Lu J, Mendelssohn IA, Zhang R, Rodgers RP, McKenna AM.

Environ Sci Technol. 2016 Sep 6;50(17):9061-9. doi: 10.1021/acs.est.6b01156. Epub 2016 Aug 10.


Whole-organism lineage tracing by combinatorial and cumulative genome editing.

McKenna A, Findlay GM, Gagnon JA, Horwitz MS, Schier AF, Shendure J.

Science. 2016 Jul 29;353(6298):aaf7907. doi: 10.1126/science.aaf7907. Epub 2016 May 26.


A comparative assessment of clinical whole exome and transcriptome profiling across sequencing centers: implications for precision cancer medicine.

Van Allen EM, Robinson D, Morrissey C, Pritchard C, Imamovic A, Carter S, Rosenberg M, McKenna A, Wu YM, Cao X, Chinnaiyan A, Garraway L, Nelson PS.

Oncotarget. 2016 Aug 16;7(33):52888-52899. doi: 10.18632/oncotarget.9184.


Infection prevention in breast implant surgery - A review of the surgical evidence, guidelines and a checklist.

Barr SP, Topps AR, Barnes NL, Henderson J, Hignett S, Teasdale RL, McKenna A, Harvey JR, Kirwan CC; Northwest Breast Surgical Research Collaborative.

Eur J Surg Oncol. 2016 May;42(5):591-603. doi: 10.1016/j.ejso.2016.02.240. Epub 2016 Feb 27. Review.


Photochemical changes in water accommodated fractions of MC252 and surrogate oil created during solar exposure as determined by FT-ICR MS.

Vaughan PP, Wilson T, Kamerman R, Hagy ME, McKenna A, Chen H, Jeffrey WH.

Mar Pollut Bull. 2016 Mar 15;104(1-2):262-8. doi: 10.1016/j.marpolbul.2016.01.012. Epub 2016 Jan 14.


Direct and indirect effects of maltreatment typologies on suicidality in a representative Northern Irish sample: Psychopathology only partially mediates the relationship.

McKenna ÁE, Gillen AM.

J Psychiatr Res. 2016 Jan;72:82-90. doi: 10.1016/j.jpsychires.2015.11.001. Epub 2015 Nov 6.


A risk-adjusted financial model to estimate the cost of a video-assisted thoracoscopic surgery lobectomy programme.

Brunelli A, Tentzeris V, Sandri A, McKenna A, Liew SL, Milton R, Chaudhuri N, Kefaloyannis E, Papagiannopoulos K.

Eur J Cardiothorac Surg. 2016 May;49(5):1492-6. doi: 10.1093/ejcts/ezv339. Epub 2015 Sep 26.


Genomic Characterization of Brain Metastases Reveals Branched Evolution and Potential Therapeutic Targets.

Brastianos PK, Carter SL, Santagata S, Cahill DP, Taylor-Weiner A, Jones RT, Van Allen EM, Lawrence MS, Horowitz PM, Cibulskis K, Ligon KL, Tabernero J, Seoane J, Martinez-Saez E, Curry WT, Dunn IF, Paek SH, Park SH, McKenna A, Chevalier A, Rosenberg M, Barker FG 2nd, Gill CM, Van Hummelen P, Thorner AR, Johnson BE, Hoang MP, Choueiri TK, Signoretti S, Sougnez C, Rabin MS, Lin NU, Winer EP, Stemmer-Rachamimov A, Meyerson M, Garraway L, Gabriel S, Lander ES, Beroukhim R, Batchelor TT, Baselga J, Louis DN, Getz G, Hahn WC.

Cancer Discov. 2015 Nov;5(11):1164-1177. doi: 10.1158/2159-8290.CD-15-0369. Epub 2015 Sep 26.


Childhood adversity profiles and adult psychopathology in a representative Northern Ireland study.

McLafferty M, Armour C, McKenna A, O'Neill S, Murphy S, Bunting B.

J Anxiety Disord. 2015 Oct;35:42-8. doi: 10.1016/j.janxdis.2015.07.004. Epub 2015 Aug 12.


On the validity of empirical potentials for simulating radiation damage in graphite: a benchmark.

Latham CD, McKenna AJ, Trevethan TP, Heggie MI, Rayson MJ, Briddon PR.

J Phys Condens Matter. 2015 Aug 12;27(31):316301. doi: 10.1088/0953-8984/27/31/316301. Epub 2015 Jul 23.


Paired exome analysis of Barrett's esophagus and adenocarcinoma.

Stachler MD, Taylor-Weiner A, Peng S, McKenna A, Agoston AT, Odze RD, Davison JM, Nason KS, Loda M, Leshchiner I, Stewart C, Stojanov P, Seepo S, Lawrence MS, Ferrer-Torres D, Lin J, Chang AC, Gabriel SB, Lander ES, Beer DG, Getz G, Carter SL, Bass AJ.

Nat Genet. 2015 Sep;47(9):1047-55. doi: 10.1038/ng.3343. Epub 2015 Jul 20.


Genomic Correlate of Exceptional Erlotinib Response in Head and Neck Squamous Cell Carcinoma.

Van Allen EM, Lui VW, Egloff AM, Goetz EM, Li H, Johnson JT, Duvvuri U, Bauman JE, Stransky N, Zeng Y, Gilbert BR, Pendleton KP, Wang L, Chiosea S, Sougnez C, Wagle N, Zhang F, Du Y, Close D, Johnston PA, McKenna A, Carter SL, Golub TR, Getz G, Mills GB, Garraway LA, Grandis JR.

JAMA Oncol. 2015 May;1(2):238-44. doi: 10.1001/jamaoncol.2015.34.


Purchasing and Using Personal Emergency Response Systems (PERS): how decisions are made by community-dwelling seniors in Canada.

McKenna AC, Kloseck M, Crilly R, Polgar J.

BMC Geriatr. 2015 Jul 11;15:81. doi: 10.1186/s12877-015-0079-z.


Using visualization to derive insights from research funding portfolios.

Molnar A, McKenna AF, Liu Q, Vorvoreanu M, Madhavan K.

IEEE Comput Graph Appl. 2015 May-Jun;35(3):91-6, c3. doi: 10.1109/MCG.2015.68. No abstract available.


Prospective derivation of a living organoid biobank of colorectal cancer patients.

van de Wetering M, Francies HE, Francis JM, Bounova G, Iorio F, Pronk A, van Houdt W, van Gorp J, Taylor-Weiner A, Kester L, McLaren-Douglas A, Blokker J, Jaksani S, Bartfeld S, Volckman R, van Sluis P, Li VS, Seepo S, Sekhar Pedamallu C, Cibulskis K, Carter SL, McKenna A, Lawrence MS, Lichtenstein L, Stewart C, Koster J, Versteeg R, van Oudenaarden A, Saez-Rodriguez J, Vries RG, Getz G, Wessels L, Stratton MR, McDermott U, Meyerson M, Garnett MJ, Clevers H.

Cell. 2015 May 7;161(4):933-45. doi: 10.1016/j.cell.2015.03.053.


High field electron paramagnetic resonance characterization of electronic and structural environments for paramagnetic metal ions and organic free radicals in Deepwater Horizon oil spill tar balls.

Ramachandran V, van Tol J, McKenna AM, Rodgers RP, Marshall AG, Dalal NS.

Anal Chem. 2015 Feb 17;87(4):2306-13. doi: 10.1021/ac504080g. Epub 2015 Feb 3.


Complementary genomic approaches highlight the PI3K/mTOR pathway as a common vulnerability in osteosarcoma.

Perry JA, Kiezun A, Tonzi P, Van Allen EM, Carter SL, Baca SC, Cowley GS, Bhatt AS, Rheinbay E, Pedamallu CS, Helman E, Taylor-Weiner A, McKenna A, DeLuca DS, Lawrence MS, Ambrogio L, Sougnez C, Sivachenko A, Walensky LD, Wagle N, Mora J, de Torres C, Lavarino C, Dos Santos Aguiar S, Yunes JA, Brandalise SR, Mercado-Celis GE, Melendez-Zajgla J, Cárdenas-Cardós R, Velasco-Hidalgo L, Roberts CW, Garraway LA, Rodriguez-Galindo C, Gabriel SB, Lander ES, Golub TR, Orkin SH, Getz G, Janeway KA.

Proc Natl Acad Sci U S A. 2014 Dec 23;111(51):E5564-73. doi: 10.1073/pnas.1419260111. Epub 2014 Dec 15.


The incidence of childhood type 1 diabetes in Ireland and the National Childhood Diabetes Register.

Roche EF, McKenna A, Ryder K, Brennan A, O'Regan M, Hoey H.

Ir Med J. 2014 Oct;107(9):278-81.


Sunlight creates oxygenated species in water-soluble fractions of Deepwater Horizon oil.

Ray PZ, Chen H, Podgorski DC, McKenna AM, Tarr MA.

J Hazard Mater. 2014 Sep 15;280:636-43. doi: 10.1016/j.jhazmat.2014.08.059. Epub 2014 Sep 6.


The genomic landscape of pediatric Ewing sarcoma.

Crompton BD, Stewart C, Taylor-Weiner A, Alexe G, Kurek KC, Calicchio ML, Kiezun A, Carter SL, Shukla SA, Mehta SS, Thorner AR, de Torres C, Lavarino C, Suñol M, McKenna A, Sivachenko A, Cibulskis K, Lawrence MS, Stojanov P, Rosenberg M, Ambrogio L, Auclair D, Seepo S, Blumenstiel B, DeFelice M, Imaz-Rosshandler I, Schwarz-Cruz Y Celis A, Rivera MN, Rodriguez-Galindo C, Fleming MD, Golub TR, Getz G, Mora J, Stegmaier K.

Cancer Discov. 2014 Nov;4(11):1326-41. doi: 10.1158/2159-8290.CD-13-1037. Epub 2014 Sep 3.


Exome sequencing of pleuropulmonary blastoma reveals frequent biallelic loss of TP53 and two hits in DICER1 resulting in retention of 5p-derived miRNA hairpin loop sequences.

Pugh TJ, Yu W, Yang J, Field AL, Ambrogio L, Carter SL, Cibulskis K, Giannikopoulos P, Kiezun A, Kim J, McKenna A, Nickerson E, Getz G, Hoffher S, Messinger YH, Dehner LP, Roberts CW, Rodriguez-Galindo C, Williams GM, Rossi CT, Meyerson M, Hill DA.

Oncogene. 2014 Nov 6;33(45):5295-302. doi: 10.1038/onc.2014.150. Epub 2014 Jun 9.

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