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Sex, obesity, diabetes, and exposure to particulate matter among patients with severe asthma: Scientific insights from a comparative analysis of open clinical data sources during a five-day hackathon.

Fecho K, Ahalt SC, Arunachalam S, Champion J, Chute CG, Davis S, Gersing K, Glusman G, Hadlock J, Lee J, Pfaff E, Robinson M, Sid E, Ta C, Xu H, Zhu R, Zhu Q, Peden DB; Biomedical Data Translator Consortium.

J Biomed Inform. 2019 Oct 30;100:103325. doi: 10.1016/j.jbi.2019.103325. [Epub ahead of print]


Ensembles of natural language processing systems for portable phenotyping solutions.

Liu C, Ta CN, Rogers JR, Li Z, Lee J, Butler AM, Shang N, Kury FSP, Wang L, Shen F, Liu H, Ena L, Friedman C, Weng C.

J Biomed Inform. 2019 Oct 23;100:103318. doi: 10.1016/j.jbi.2019.103318. [Epub ahead of print]


Making work visible for electronic phenotype implementation: Lessons learned from the eMERGE network.

Shang N, Liu C, Rasmussen LV, Ta CN, Caroll RJ, Benoit B, Lingren T, Dikilitas O, Mentch FD, Carrell DS, Wei WQ, Luo Y, Gainer VS, Kullo IJ, Pacheco JA, Hakonarson H, Walunas TL, Denny JC, Wiley K, Murphy SN, Hripcsak G, Weng C.

J Biomed Inform. 2019 Nov;99:103293. doi: 10.1016/j.jbi.2019.103293. Epub 2019 Sep 19.


Detecting Systemic Data Quality Issues in Electronic Health Records.

Ta CN, Weng C.

Stud Health Technol Inform. 2019 Aug 21;264:383-387. doi: 10.3233/SHTI190248.


DQueST: dynamic questionnaire for search of clinical trials.

Liu C, Yuan C, Butler AM, Carvajal RD, Li ZR, Ta CN, Weng C.

J Am Med Inform Assoc. 2019 Nov 1;26(11):1333-1343. doi: 10.1093/jamia/ocz121.


Doc2Hpo: a web application for efficient and accurate HPO concept curation.

Liu C, Peres Kury FS, Li Z, Ta C, Wang K, Weng C.

Nucleic Acids Res. 2019 Jul 2;47(W1):W566-W570. doi: 10.1093/nar/gkz386.


Clinical Data: Sources and Types, Regulatory Constraints, Applications.

Ahalt SC, Chute CG, Fecho K, Glusman G, Hadlock J, Taylor CO, Pfaff ER, Robinson PN, Solbrig H, Ta C, Tatonetti N, Weng C; Biomedical Data Translator Consortium.

Clin Transl Sci. 2019 Jul;12(4):329-333. doi: 10.1111/cts.12638. Epub 2019 May 9. No abstract available.


Criteria2Query: a natural language interface to clinical databases for cohort definition.

Yuan C, Ryan PB, Ta C, Guo Y, Li Z, Hardin J, Makadia R, Jin P, Shang N, Kang T, Weng C.

J Am Med Inform Assoc. 2019 Apr 1;26(4):294-305. doi: 10.1093/jamia/ocy178.


Avian Intestinal Mucus Modulates Campylobacter jejuni Gene Expression in a Host-Specific Manner.

Looft T, Cai G, Choudhury B, Lai LX, Lippolis JD, Reinhardt TA, Sylte MJ, Casey TA.

Front Microbiol. 2019 Jan 7;9:3215. doi: 10.3389/fmicb.2018.03215. eCollection 2018.


Columbia Open Health Data, clinical concept prevalence and co-occurrence from electronic health records.

Ta CN, Dumontier M, Hripcsak G, Tatonetti NP, Weng C.

Sci Data. 2018 Nov 27;5:180273. doi: 10.1038/sdata.2018.273.


Using Fluorescence Spectroscopy To Identify Milk from Grass-Fed Dairy Cows and To Monitor Its Photodegradation.

Bhattacharjee U, Jarashow D, Casey TA, Petrich JW, Rasmussen MA.

J Agric Food Chem. 2018 Mar 7;66(9):2168-2173. doi: 10.1021/acs.jafc.7b05287. Epub 2018 Feb 5.


Multidrug-Resistant Salmonella enterica Serovar Typhimurium Isolates Are Resistant to Antibiotics That Influence Their Swimming and Swarming Motility.

Brunelle BW, Bearson BL, Bearson SMD, Casey TA.

mSphere. 2017 Nov 1;2(6). pii: e00306-17. doi: 10.1128/mSphere.00306-17. eCollection 2017 Nov-Dec.


Focal Liver Lesions: Computer-aided Diagnosis by Using Contrast-enhanced US Cine Recordings.

Ta CN, Kono Y, Eghtedari M, Oh YT, Robbin ML, Barr RG, Kummel AC, Mattrey RF.

Radiology. 2018 Mar;286(3):1062-1071. doi: 10.1148/radiol.2017170365. Epub 2017 Oct 25.


Genomic and Transcriptomic Analysis of Escherichia coli Strains Associated with Persistent and Transient Bovine Mastitis and the Role of Colanic Acid.

Lippolis JD, Holman DB, Brunelle BW, Thacker TC, Bearson BL, Reinhardt TA, Sacco RE, Casey TA.

Infect Immun. 2017 Dec 19;86(1). pii: e00566-17. doi: 10.1128/IAI.00566-17. Print 2018 Jan.


Genome Sequences of Escherichia coli Strains That Cause Persistent and Transient Mastitis.

Thacker TC, Lippolis JD, Brunelle BW, Casey TA, Reinhardt TA, Sacco RE, Holman DB.

Genome Announc. 2017 Aug 24;5(34). pii: e00775-17. doi: 10.1128/genomeA.00775-17.


Extended Lifetime In Vivo Pulse Stimulated Ultrasound Imaging.

Wang J, Barback CV, Ta CN, Weeks J, Gude N, Mattrey RF, Blair SL, Trogler WC, Lee H, Kummel AC.

IEEE Trans Med Imaging. 2018 Jan;37(1):222-229. doi: 10.1109/TMI.2017.2740784. Epub 2017 Aug 17.


Fermentation products as feed additives mitigate some ill-effects of heat stress in pigs.

Kumar S, Bass BE, Bandrick M, Loving CL, Brockmeier SL, Looft T, Trachsel J, Madson DM, Thomas M, Casey TA, Frank JW, Stanton TB, Allen HK.

J Anim Sci. 2017 Jan;95(1):279-290. doi: 10.2527/jas.2016.0662.


Ultrasound Responsive Macrophase-Segregated Microcomposite Films for in Vivo Biosensing.

Yang J, Wang J, Ta CN, Ward E, Barback CV, Sung TW, Mendez N, Blair SL, Kummel AC, Trogler WC.

ACS Appl Mater Interfaces. 2017 Jan 18;9(2):1719-1727. doi: 10.1021/acsami.6b10728. Epub 2017 Jan 5.


Differential Gene Expression of Three Mastitis-Causing Escherichia coli Strains Grown under Planktonic, Swimming, and Swarming Culture Conditions.

Lippolis JD, Brunelle BW, Reinhardt TA, Sacco RE, Thacker TC, Looft TP, Casey TA.

mSystems. 2016 Aug 9;1(4). pii: e00064-16. eCollection 2016 Jul-Aug.


Pipeline for amplifying and analyzing amplicons of the V1-V3 region of the 16S rRNA gene.

Allen HK, Bayles DO, Looft T, Trachsel J, Bass BE, Alt DP, Bearson SM, Nicholson T, Casey TA.

BMC Res Notes. 2016 Aug 2;9:380. doi: 10.1186/s13104-016-2172-6.


Fluorescence Spectroscopy of the Retina for the Screening of Bovine Spongiform Encephalopathy.

Bhattacharjee U, Graham C, Czub S, Dudas S, Rasmussen MA, Casey TA, Petrich JW.

J Agric Food Chem. 2016 Jan 13;64(1):320-5. doi: 10.1021/acs.jafc.5b04218. Epub 2015 Dec 30.


Carbadox has both temporary and lasting effects on the swine gut microbiota.

Looft T, Allen HK, Casey TA, Alt DP, Stanton TB.

Front Microbiol. 2014 Jun 10;5:276. doi: 10.3389/fmicb.2014.00276. eCollection 2014.


Finding alternatives to antibiotics.

Allen HK, Trachsel J, Looft T, Casey TA.

Ann N Y Acad Sci. 2014 Sep;1323:91-100. doi: 10.1111/nyas.12468. Epub 2014 Jun 20. Review.


2-tier in-plane motion correction and out-of-plane motion filtering for contrast-enhanced ultrasound.

Ta CN, Eghtedari M, Mattrey RF, Kono Y, Kummel AC.

Invest Radiol. 2014 Nov;49(11):707-19. doi: 10.1097/RLI.0000000000000074.


Determining the relative contribution and hierarchy of hha and qseBC in the regulation of flagellar motility of Escherichia coli O157:H7.

Sharma VK, Casey TA.

PLoS One. 2014 Jan 21;9(1):e85866. doi: 10.1371/journal.pone.0085866. eCollection 2014.


Escherichia coli O157:H7 lacking the qseBC-encoded quorum-sensing system outcompetes the parental strain in colonization of cattle intestines.

Sharma VK, Casey TA.

Appl Environ Microbiol. 2014 Mar;80(6):1882-92. doi: 10.1128/AEM.03198-13. Epub 2014 Jan 10.


Integrated processing of contrast pulse sequencing ultrasound imaging for enhanced active contrast of hollow gas filled silica nanoshells and microshells.

Ta CN, Liberman A, Paul Martinez H, Barback CV, Mattrey RF, Blair SL, Trogler WC, Kummel AC, Wu Z.

J Vac Sci Technol B Nanotechnol Microelectron. 2012 Mar;30(2):2C104. Epub 2012 Mar 23.


Automating tumor classification with pixel-by-pixel contrast-enhanced ultrasound perfusion kinetics.

Ta CN, Kono Y, Barback CV, Mattrey RF, Kummel AC.

J Vac Sci Technol B Nanotechnol Microelectron. 2012 Mar;30(2):2C103. Epub 2012 Mar 22.


Treatment, promotion, commotion: antibiotic alternatives in food-producing animals.

Allen HK, Levine UY, Looft T, Bandrick M, Casey TA.

Trends Microbiol. 2013 Mar;21(3):114-9. doi: 10.1016/j.tim.2012.11.001. Review.


Fluorescence spectroscopy of the retina from scrapie-infected mice.

Bose S, Schönenbrücher H, Richt JA, Casey TA, Rasmussen MA, Kehrli ME Jr, Petrich JW.

Photochem Photobiol. 2013 Jul-Aug;89(4):864-8. doi: 10.1111/php.12056. Epub 2013 Mar 4.


Hollow silica and silica-boron nano/microparticles for contrast-enhanced ultrasound to detect small tumors.

Liberman A, Martinez HP, Ta CN, Barback CV, Mattrey RF, Kono Y, Blair SL, Trogler WC, Kummel AC, Wu Z.

Biomaterials. 2012 Jul;33(20):5124-9. doi: 10.1016/j.biomaterials.2012.03.066. Epub 2012 Apr 11.


Evaluation of heat-labile enterotoxins type IIa and type IIb in the pathogenicity of enterotoxigenic Escherichia coli for neonatal pigs.

Casey TA, Connell TD, Holmes RK, Whipp SC.

Vet Microbiol. 2012 Sep 14;159(1-2):83-9. doi: 10.1016/j.vetmic.2012.03.018. Epub 2012 Mar 16.


Evaluation of hha and hha sepB mutant strains of Escherichia coli O157:H7 as bacterins for reducing E. coli O157:H7 shedding in cattle.

Sharma VK, Dean-Nystrom EA, Casey TA.

Vaccine. 2011 Jul 12;29(31):5078-86. doi: 10.1016/j.vaccine.2011.04.073. Epub 2011 May 6.


Quantitative automated image analysis system with automated debris filtering for the detection of breast carcinoma cells.

Martin DT, Sandoval S, Ta CN, Ruidiaz ME, Cortes-Mateos MJ, Messmer D, Kummel AC, Blair SL, Wang-Rodriguez J.

Acta Cytol. 2011;55(3):271-80. doi: 10.1159/000324029. Epub 2011 Apr 27.


Fluorescence spectroscopy of the retina for diagnosis of transmissible spongiform encephalopathies.

Adhikary R, Mukherjee P, Krishnamoorthy G, Kunkle RA, Casey TA, Rasmussen MA, Petrich JW.

Anal Chem. 2010 May 15;82(10):4097-101. doi: 10.1021/ac100179u.


A comparison of the fluorescence spectra of murine and bovine central nervous system and other tissues.

Adhikary R, Schönenbrücher H, Rasmussen MA, Casey TA, Hamir AN, Kehrli ME, Richt JA, Petrich JW.

Photochem Photobiol. 2009 Nov-Dec;85(6):1322-6. doi: 10.1111/j.1751-1097.2009.00593.x.


Effect of chlorate, molybdate, and shikimic acid on Salmonella enterica serovar Typhimurium in aerobic and anaerobic cultures.

Oliver CE, Beier RC, Hume ME, Horrocks SM, Casey TA, Caton JS, Nisbet DJ, Smith DJ, Krueger NA, Anderson RC.

Anaerobe. 2010 Apr;16(2):106-13. doi: 10.1016/j.anaerobe.2009.05.006. Epub 2009 Jun 11.


Escherichia coli O157 : H7 glutamate- and arginine-dependent acid-resistance systems protect against oxidative stress during extreme acid challenge.

Bearson BL, Lee IS, Casey TA.

Microbiology. 2009 Mar;155(Pt 3):805-12. doi: 10.1099/mic.0.022905-0.


Monitoring the accumulation of lipofuscin in aging murine eyes by fluorescence spectroscopy.

Mukherjee P, Bose S, Hurd AA, Adhikary R, Schönenbrücher H, Hamir AN, Richt JA, Casey TA, Rasmussen MA, Petrich JW.

Photochem Photobiol. 2009 Jan-Feb;85(1):234-8. doi: 10.1111/j.1751-1097.2008.00425.x. Epub 2008 Aug 27.


Fluorescence-based method, exploiting lipofuscin, for real-time detection of central nervous system tissues on bovine carcasses.

Schönenbrücher H, Adhikary R, Mukherjee P, Casey TA, Rasmussen MA, Maistrovich FD, Hamir AN, Kehrli ME Jr, Richt JA, Petrich JW.

J Agric Food Chem. 2008 Aug 13;56(15):6220-6. doi: 10.1021/jf0734368. Epub 2008 Jul 12.


Bovine immune response to shiga-toxigenic Escherichia coli O157:H7.

Hoffman MA, Menge C, Casey TA, Laegreid W, Bosworth BT, Dean-Nystrom EA.

Clin Vaccine Immunol. 2006 Dec;13(12):1322-7. Epub 2006 Oct 18.


Generation of fluorescent adducts of malondialdehyde and amino acids: toward an understanding of lipofuscin.

Chowdhury PK, Halder M, Choudhury PK, Kraus GA, Desai MJ, Armstrong DW, Casey TA, Rasmussen MA, Petrich JW.

Photochem Photobiol. 2004 Jan;79(1):21-5.


Fluorescence of dietary porphyrins as a basis for real-time detection of fecal contamination on meat.

Ashby KD, Wen J, Chowdhury P, Casey TA, Rasmussen MA, Petrich JW.

J Agric Food Chem. 2003 May 21;51(11):3502-7.


Environmental and food safety aspects of Escherichia coli O157:H7 infections in cattle.

Rasmussen MA, Casey TA.

Crit Rev Microbiol. 2001;27(2):57-73. Review.


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