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Items: 21


Upper Respiratory Dysbiosis with a Facultative-Dominated Ecotype in Advanced Lung Disease and Dynamic Change after Lung Transplant.

Simon-Soro A, Sohn MB, McGinniss JE, Imai I, Brown MC, Knecht VR, Bailey A, Clarke EL, Cantu E, Li H, Bittinger K, Diamond JM, Christie JD, Bushman FD, Collman RG.

Ann Am Thorac Soc. 2019 Aug 15. doi: 10.1513/AnnalsATS.201904-299OC. [Epub ahead of print]


Development and Evaluation of a Novel Point-of-Use Quality Assurance Tool for Digital Pathology.

Clarke EL, Brettle D, Sykes A, Wright A, Boden A, Treanor D.

Arch Pathol Lab Med. 2019 Apr 25. doi: 10.5858/arpa.2018-0210-OA. [Epub ahead of print]


Sunbeam: an extensible pipeline for analyzing metagenomic sequencing experiments.

Clarke EL, Taylor LJ, Zhao C, Connell A, Lee JJ, Fett B, Bushman FD, Bittinger K.

Microbiome. 2019 Mar 22;7(1):46. doi: 10.1186/s40168-019-0658-x.


Molecular analysis of bacterial contamination on stethoscopes in an intensive care unit.

Knecht VR, McGinniss JE, Shankar HM, Clarke EL, Kelly BJ, Imai I, Fitzgerald AS, Bittinger K, Bushman FD, Collman RG.

Infect Control Hosp Epidemiol. 2018 Dec 18:1-7. doi: 10.1017/ice.2018.319. [Epub ahead of print]


Lack of detection of a human placenta microbiome in samples from preterm and term deliveries.

Leiby JS, McCormick K, Sherrill-Mix S, Clarke EL, Kessler LR, Taylor LJ, Hofstaedter CE, Roche AM, Mattei LM, Bittinger K, Elovitz MA, Leite R, Parry S, Bushman FD.

Microbiome. 2018 Oct 30;6(1):196. doi: 10.1186/s40168-018-0575-4.


T cell dynamics and response of the microbiota after gene therapy to treat X-linked severe combined immunodeficiency.

Clarke EL, Connell AJ, Six E, Kadry NA, Abbas AA, Hwang Y, Everett JK, Hofstaedter CE, Marsh R, Armant M, Kelsen J, Notarangelo LD, Collman RG, Hacein-Bey-Abina S, Kohn DB, Cavazzana M, Fischer A, Williams DA, Pai SY, Bushman FD.

Genome Med. 2018 Sep 28;10(1):70. doi: 10.1186/s13073-018-0580-z.


Bidirectional transfer of Anelloviridae lineages between graft and host during lung transplantation.

Abbas AA, Young JC, Clarke EL, Diamond JM, Imai I, Haas AR, Cantu E, Lederer DJ, Meyer K, Milewski RK, Olthoff KM, Shaked A, Christie JD, Bushman FD, Collman RG.

Am J Transplant. 2019 Apr;19(4):1086-1097. doi: 10.1111/ajt.15116. Epub 2018 Oct 8.


Is Your Color My Color? Dividing the Labor of the Stroop Task Between Co-actors.

Yamaguchi M, Clarke EL, Egan DL.

Front Psychol. 2018 Aug 6;9:1407. doi: 10.3389/fpsyg.2018.01407. eCollection 2018.


Evaluation of a therapy for Idiopathic Chronic Enterocolitis in rhesus macaques (Macaca mulatta) and linked microbial community correlates.

Taylor JM, Clarke EL, Baker K, Lauder A, Kim D, Bailey A, Wu GD, Collman RG, Doyle-Meyers L, Russell-Lodrigue K, Blanchard J, Bushman FD, Bohm R.

PeerJ. 2018 Apr 11;6:e4612. doi: 10.7717/peerj.4612. eCollection 2018.


Community screening for visual impairment in older people.

Clarke EL, Evans JR, Smeeth L.

Cochrane Database Syst Rev. 2018 Feb 20;2:CD001054. doi: 10.1002/14651858.CD001054.pub3. Review.


Microbial Lineages in Sarcoidosis. A Metagenomic Analysis Tailored for Low-Microbial Content Samples.

Clarke EL, Lauder AP, Hofstaedter CE, Hwang Y, Fitzgerald AS, Imai I, Biernat W, Rękawiecki B, Majewska H, Dubaniewicz A, Litzky LA, Feldman MD, Bittinger K, Rossman MD, Patterson KC, Bushman FD, Collman RG.

Am J Respir Crit Care Med. 2018 Jan 15;197(2):225-234. doi: 10.1164/rccm.201705-0891OC.


swga: a primer design toolkit for selective whole genome amplification.

Clarke EL, Sundararaman SA, Seifert SN, Bushman FD, Hahn BH, Brisson D.

Bioinformatics. 2017 Jul 15;33(14):2071-2077. doi: 10.1093/bioinformatics/btx118.


Colour in digital pathology: a review.

Clarke EL, Treanor D.

Histopathology. 2017 Jan;70(2):153-163. doi: 10.1111/his.13079. Review.


A response to Campbell WS, Talmon GA, Foster KW, Lele SM, Kozel JA, West WW. Sixty-five thousand shades of gray: importance of color in surgical pathology diagnoses. HUM PATHOL 2015;6:1945-50.

Clarke EL, Mello-Thoms C, Magee D, Treanor D.

Hum Pathol. 2016 Oct;56:204-5. doi: 10.1016/j.humpath.2016.04.021. Epub 2016 Jun 17. No abstract available.


Convergence of HbA1c values towards target in 272 primary care patients following nine years of target-driven care.

Clarke EL, Richardson JR, Bhartia M, Kennedy DM, Milles JJ, Ramachandran S.

Qual Prim Care. 2013;21(5):287-92.


A task-based approach for Gene Ontology evaluation.

Clarke EL, Loguercio S, Good BM, Su AI.

J Biomed Semantics. 2013 Apr 15;4 Suppl 1:S4. doi: 10.1186/2041-1480-4-S1-S4. Epub 2013 Apr 15.


Plastic surgery in the undergraduate curriculum: a nationwide survey of students, senior lecturers and consultant plastic surgeons in the UK.

Wade RG, Clarke EL, Leinster S, Figus A.

J Plast Reconstr Aesthet Surg. 2013 Jun;66(6):878-80. doi: 10.1016/j.bjps.2012.11.015. Epub 2012 Dec 13. No abstract available.


Linking genes to diseases with a SNPedia-Gene Wiki mashup.

Good BM, Clarke EL, Loguercio S, Su AI.

J Biomed Semantics. 2012 Apr 24;3 Suppl 1:S6. doi: 10.1186/2041-1480-3-S1-S6.


Building a biomedical semantic network in Wikipedia with Semantic Wiki Links.

Good BM, Clarke EL, Loguercio S, Su AI.

Database (Oxford). 2012 Mar 20;2012:bar060. doi: 10.1093/database/bar060. Print 2012.


The Gene Wiki in 2011: community intelligence applied to human gene annotation.

Good BM, Clarke EL, de Alfaro L, Su AI.

Nucleic Acids Res. 2012 Jan;40(Database issue):D1255-61. doi: 10.1093/nar/gkr925. Epub 2011 Nov 10.


Variations in the water, fat, glycogen and iodine of the flesh of oysters (Ostrea virginica) during hibernation and storage at 4 degrees C.

Baker ME, Boyd EM, Clarke EL, Ronan AK.

J Physiol. 1942 Jun 2;101(1):36-43. No abstract available.

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