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A Multisite Randomized Controlled Two-Phase Trial of the Early Start Denver Model Compared to Treatment as Usual.

Rogers SJ, Estes A, Lord C, Munson J, Rocha M, Winter J, Greenson J, Colombi C, Dawson G, Vismara LA, Sugar CA, Hellemann G, Whelan F, Talbott M.

J Am Acad Child Adolesc Psychiatry. 2019 Sep;58(9):853-865. doi: 10.1016/j.jaac.2019.01.004. Epub 2019 Jan 24.


Implementing Patient-Reported Outcomes to Improve the Quality of Care for Weight of Patients with Schizophrenia.

Young AS, Cohen AN, Hamilton AB, Hellemann G, Reist C, Whelan F.

J Behav Health Serv Res. 2019 Jan;46(1):129-139. doi: 10.1007/s11414-018-9641-8.


Culture and Molecular Profiling of the Respiratory Tract Microbiota.

Whelan FJ, Rossi L, Stearns JC, Surette MG.

Methods Mol Biol. 2018;1849:49-61. doi: 10.1007/978-1-4939-8728-3_4.


Enhancing Low-Intensity Coaching in Parent Implemented Early Start Denver Model Intervention for Early Autism: A Randomized Comparison Treatment Trial.

Rogers SJ, Estes A, Vismara L, Munson J, Zierhut C, Greenson J, Dawson G, Rocha M, Sugar C, Senturk D, Whelan F, Talbott M.

J Autism Dev Disord. 2019 Feb;49(2):632-646. doi: 10.1007/s10803-018-3740-5.


A comprehensive evaluation of the sl1p pipeline for 16S rRNA gene sequencing analysis.

Whelan FJ, Surette MG.

Microbiome. 2017 Aug 14;5(1):100. doi: 10.1186/s40168-017-0314-2.


Streptococcus pneumoniae Colonization Is Required To Alter the Nasal Microbiota in Cigarette Smoke-Exposed Mice.

Shen P, Whelan FJ, Schenck LP, McGrath JJC, Vanderstocken G, Bowdish DME, Surette MG, Stämpfli MR.

Infect Immun. 2017 Sep 20;85(10). pii: e00434-17. doi: 10.1128/IAI.00434-17. Print 2017 Oct.


The Evolving Cystic Fibrosis Microbiome: A Comparative Cohort Study Spanning 16 Years.

Acosta N, Whelan FJ, Somayaji R, Poonja A, Surette MG, Rabin HR, Parkins MD.

Ann Am Thorac Soc. 2017 Aug;14(8):1288-1297. doi: 10.1513/AnnalsATS.201609-668OC.


Investigating the Structural Compaction of Biomolecules Upon Transition to the Gas-Phase Using ESI-TWIMS-MS.

Devine PWA, Fisher HC, Calabrese AN, Whelan F, Higazi DR, Potts JR, Lowe DC, Radford SE, Ashcroft AE.

J Am Soc Mass Spectrom. 2017 Sep;28(9):1855-1862. doi: 10.1007/s13361-017-1689-9. Epub 2017 May 8.


The effects of inhaled aztreonam on the cystic fibrosis lung microbiome.

Heirali AA, Workentine ML, Acosta N, Poonja A, Storey DG, Somayaji R, Rabin HR, Whelan FJ, Surette MG, Parkins MD.

Microbiome. 2017 May 5;5(1):51. doi: 10.1186/s40168-017-0265-7.


Prevalence and Outcomes of Achromobacter Species Infections in Adults with Cystic Fibrosis: a North American Cohort Study.

Edwards BD, Greysson-Wong J, Somayaji R, Waddell B, Whelan FJ, Storey DG, Rabin HR, Surette MG, Parkins MD.

J Clin Microbiol. 2017 Jul;55(7):2074-2085. doi: 10.1128/JCM.02556-16. Epub 2017 Apr 26.


Improving Weight in People with Serious Mental Illness: The Effectiveness of Computerized Services with Peer Coaches.

Young AS, Cohen AN, Goldberg R, Hellemann G, Kreyenbuhl J, Niv N, Nowlin-Finch N, Oberman R, Whelan F.

J Gen Intern Med. 2017 Apr;32(Suppl 1):48-55. doi: 10.1007/s11606-016-3963-0.


Longitudinal sampling of the lung microbiota in individuals with cystic fibrosis.

Whelan FJ, Heirali AA, Rossi L, Rabin HR, Parkins MD, Surette MG.

PLoS One. 2017 Mar 2;12(3):e0172811. doi: 10.1371/journal.pone.0172811. eCollection 2017.


Clinical Factors Associated with Successful Discharge from Assertive Community Treatment.

Bromley E, Mikesell L, Whelan F, Hellemann G, Hunt M, Cuddeback G, Bradford DW, Young AS.

Community Ment Health J. 2017 Nov;53(8):916-921. doi: 10.1007/s10597-017-0083-1. Epub 2017 Jan 23.


Reemergence of Lower-Airway Microbiota in Lung Transplant Patients with Cystic Fibrosis.

Syed SA, Whelan FJ, Waddell B, Rabin HR, Parkins MD, Surette MG.

Ann Am Thorac Soc. 2016 Dec;13(12):2132-2142.


Disorder drives cooperative folding in a multidomain protein.

Gruszka DT, Mendonça CA, Paci E, Whelan F, Hawkhead J, Potts JR, Clarke J.

Proc Natl Acad Sci U S A. 2016 Oct 18;113(42):11841-11846. Epub 2016 Oct 3.


Cognitive Effects of Stimulant, Guanfacine, and Combined Treatment in Child and Adolescent Attention-Deficit/Hyperactivity Disorder.

Bilder RM, Loo SK, McGough JJ, Whelan F, Hellemann G, Sugar C, Del'Homme M, Sturm A, Cowen J, Hanada G, McCracken JT.

J Am Acad Child Adolesc Psychiatry. 2016 Aug;55(8):667-73. doi: 10.1016/j.jaac.2016.05.016. Epub 2016 Jun 7.


Combined Stimulant and Guanfacine Administration in Attention-Deficit/Hyperactivity Disorder: A Controlled, Comparative Study.

McCracken JT, McGough JJ, Loo SK, Levitt J, Del'Homme M, Cowen J, Sturm A, Whelan F, Hellemann G, Sugar C, Bilder RM.

J Am Acad Child Adolesc Psychiatry. 2016 Aug;55(8):657-666.e1. doi: 10.1016/j.jaac.2016.05.015. Epub 2016 Jun 3.


Capturing the diversity of the human gut microbiota through culture-enriched molecular profiling.

Lau JT, Whelan FJ, Herath I, Lee CH, Collins SM, Bercik P, Surette MG.

Genome Med. 2016 Jul 1;8(1):72. doi: 10.1186/s13073-016-0327-7.


Early life nasal microbiota in infants with cystic fibrosis.

Whelan FJ, Surette MG.

Lancet Respir Med. 2016 Aug;4(8):595-596. doi: 10.1016/S2213-2600(16)30153-9. Epub 2016 Jun 21. No abstract available.


Partitioning and correlating subgroup characteristics from Aligned Pattern Clusters.

Lee ES, Whelan FJ, Bowdish DM, Wong AK.

Bioinformatics. 2016 Aug 15;32(16):2427-34. doi: 10.1093/bioinformatics/btw211. Epub 2016 Apr 22.


Streptococcus pneumoniae Colonization Disrupts the Microbial Community within the Upper Respiratory Tract of Aging Mice.

Thevaranjan N, Whelan FJ, Puchta A, Ashu E, Rossi L, Surette MG, Bowdish DM.

Infect Immun. 2016 Mar 24;84(4):906-16. doi: 10.1128/IAI.01275-15. Print 2016 Apr.


Health intervention pilots: thinking big before thinking small.

Hannay EJ, Whelan F.

Healthc (Amst). 2015 Dec;3(4):235-7. doi: 10.1016/j.hjdsi.2015.06.007. Epub 2015 Jul 29.


Clinical Insights into Pulmonary Exacerbations in Cystic Fibrosis from the Microbiome. What Are We Missing?

Whelan FJ, Surette MG.

Ann Am Thorac Soc. 2015 Nov;12 Suppl 2:S207-11. doi: 10.1513/AnnalsATS.201506-353AW.


Two repetitive, biofilm-forming proteins from Staphylococci: from disorder to extension.

Whelan F, Potts JR.

Biochem Soc Trans. 2015 Oct;43(5):861-6. doi: 10.1042/BST20150088. Review.


Pregnancy-related changes in the maternal gut microbiota are dependent upon the mother's periconceptional diet.

Gohir W, Whelan FJ, Surette MG, Moore C, Schertzer JD, Sloboda DM.

Gut Microbes. 2015;6(5):310-20. doi: 10.1080/19490976.2015.1086056.


Structural basis for DNA strand separation by a hexameric replicative helicase.

Chaban Y, Stead JA, Ryzhenkova K, Whelan F, Lamber EP, Antson A, Sanders CM, Orlova EV.

Nucleic Acids Res. 2015 Sep 30;43(17):8551-63. doi: 10.1093/nar/gkv778. Epub 2015 Aug 3.


The Evolution of the Scavenger Receptor Cysteine-Rich Domain of the Class A Scavenger Receptors.

Yap NV, Whelan FJ, Bowdish DM, Golding GB.

Front Immunol. 2015 Jul 6;6:342. doi: 10.3389/fimmu.2015.00342. eCollection 2015.


From bacterial to human dihydrouridine synthase: automated structure determination.

Whelan F, Jenkins HT, Griffiths SC, Byrne RT, Dodson EJ, Antson AA.

Acta Crystallogr D Biol Crystallogr. 2015 Jul;71(Pt 7):1564-71. doi: 10.1107/S1399004715009220. Epub 2015 Jun 30.


Cooperative folding of intrinsically disordered domains drives assembly of a strong elongated protein.

Gruszka DT, Whelan F, Farrance OE, Fung HK, Paci E, Jeffries CM, Svergun DI, Baldock C, Baumann CG, Brockwell DJ, Potts JR, Clarke J.

Nat Commun. 2015 Jun 1;6:7271. doi: 10.1038/ncomms8271.


Major reorientation of tRNA substrates defines specificity of dihydrouridine synthases.

Byrne RT, Jenkins HT, Peters DT, Whelan F, Stowell J, Aziz N, Kasatsky P, Rodnina MV, Koonin EV, Konevega AL, Antson AA.

Proc Natl Acad Sci U S A. 2015 May 12;112(19):6033-7. doi: 10.1073/pnas.1500161112. Epub 2015 Apr 22.


Culture and molecular-based profiles show shifts in bacterial communities of the upper respiratory tract that occur with age.

Stearns JC, Davidson CJ, McKeon S, Whelan FJ, Fontes ME, Schryvers AB, Bowdish DM, Kellner JD, Surette MG.

ISME J. 2015 May;9(5):1268. doi: 10.1038/ismej.2015.49. No abstract available.


Experience of primary care among homeless individuals with mental health conditions.

Chrystal JG, Glover DL, Young AS, Whelan F, Austin EL, Johnson NK, Pollio DE, Holt CL, Stringfellow E, Gordon AJ, Kim TA, Daigle SG, Steward JL, Kertesz SG.

PLoS One. 2015 Feb 6;10(2):e0117395. doi: 10.1371/journal.pone.0117395. eCollection 2015.


Culture and molecular-based profiles show shifts in bacterial communities of the upper respiratory tract that occur with age.

Stearns JC, Davidson CJ, McKeon S, Whelan FJ, Fontes ME, Schryvers AB, Bowdish DM, Kellner JD, Surette MG.

ISME J. 2015 May;9(5):1246-59. doi: 10.1038/ismej.2014.250. Epub 2015 Jan 9. Erratum in: ISME J. 2015 May;9(5):1268.


The loss of topography in the microbial communities of the upper respiratory tract in the elderly.

Whelan FJ, Verschoor CP, Stearns JC, Rossi L, Luinstra K, Loeb M, Smieja M, Johnstone J, Surette MG, Bowdish DM.

Ann Am Thorac Soc. 2014 May;11(4):513-21. doi: 10.1513/AnnalsATS.201310-351OC.


Contact endoscopy as a novel technique in the detection and diagnosis of oral cavity and oropharyngeal mucosal lesions in the head and neck.

Dowthwaite S, Szeto C, Wehrli B, Daley T, Whelan F, Franklin J, Nichols A, Yoo J, Fung K.

J Laryngol Otol. 2014 Feb;128(2):147-52. doi: 10.1017/S0022215113003332. Epub 2014 Jan 24.


A guide to bioinformatics for immunologists.

Whelan FJ, Yap NV, Surette MG, Golding GB, Bowdish DM.

Front Immunol. 2013 Dec 4;4:416. doi: 10.3389/fimmu.2013.00416. Review.


Implementation of evidence-based employment services in specialty mental health.

Hamilton AB, Cohen AN, Glover DL, Whelan F, Chemerinski E, McNagny KP, Mullins D, Reist C, Schubert M, Young AS.

Health Serv Res. 2013 Dec;48(6 Pt 2):2224-44. doi: 10.1111/1475-6773.12115. Epub 2013 Oct 21.


Positive effects of methylphenidate on hyperactivity are moderated by monoaminergic gene variants in children with autism spectrum disorders.

McCracken JT, Badashova KK, Posey DJ, Aman MG, Scahill L, Tierney E, Arnold LE, Vitiello B, Whelan F, Chuang SZ, Davies M, Shah B, McDougle CJ, Nurmi EL.

Pharmacogenomics J. 2014 Jun;14(3):295-302. doi: 10.1038/tpj.2013.23. Epub 2013 Jul 16.


Moderation of antipsychotic-induced weight gain by energy balance gene variants in the RUPP autism network risperidone studies.

Nurmi EL, Spilman SL, Whelan F, Scahill LL, Aman MG, McDougle CJ, Arnold LE, Handen B, Johnson C, Sukhodolsky DG, Posey DJ, Lecavalier L, Stigler KA, Ritz L, Tierney E, Vitiello B, McCracken JT; Research Units on Pediatric Psychopharmacology Autism Network.

Transl Psychiatry. 2013 Jun 25;3:e274. doi: 10.1038/tp.2013.26.


S-Adenosyl-S-carboxymethyl-L-homocysteine: a novel cofactor found in the putative tRNA-modifying enzyme CmoA.

Byrne RT, Whelan F, Aller P, Bird LE, Dowle A, Lobley CM, Reddivari Y, Nettleship JE, Owens RJ, Antson AA, Waterman DG.

Acta Crystallogr D Biol Crystallogr. 2013 Jun;69(Pt 6):1090-8. doi: 10.1107/S0907444913004939. Epub 2013 May 15.


Using patient-facing kiosks to support quality improvement at mental health clinics.

Cohen AN, Chinman MJ, Hamilton AB, Whelan F, Young AS.

Med Care. 2013 Mar;51(3 Suppl 1):S13-20. doi: 10.1097/MLR.0b013e31827da859.


The evolution of the class A scavenger receptors.

Whelan FJ, Meehan CJ, Golding GB, McConkey BJ, Bowdish DM.

BMC Evol Biol. 2012 Nov 27;12:227. doi: 10.1186/1471-2148-12-227.


Ki-67 expression predicts radiotherapy failure in early glottic cancer.

Nichols AC, Whelan F, Basmaji J, Dhaliwal S, Dowthwaite S, Chapeskie C, Read N, Palma DA, Fung K, Venkatesan V, Hammond JA, Franklin JH, Siddiqui I, Wehrli B, Kwan K, Koropatnick J, Mymryk JS, Barrett JW, Yoo J.

J Otolaryngol Head Neck Surg. 2012 Apr;41(2):124-30.


Crystallization and preliminary X-ray crystallographic analysis of the catalytic domain of human dihydrouridine synthase.

Griffiths S, Byrne RT, Antson AA, Whelan F.

Acta Crystallogr Sect F Struct Biol Cryst Commun. 2012 Mar 1;68(Pt 3):333-6. doi: 10.1107/S1744309112003831. Epub 2012 Feb 22.


A flexible brace maintains the assembly of a hexameric replicative helicase during DNA unwinding.

Whelan F, Stead JA, Shkumatov AV, Svergun DI, Sanders CM, Antson AA.

Nucleic Acids Res. 2012 Mar;40(5):2271-83. doi: 10.1093/nar/gkr906. Epub 2011 Nov 8.


Comparison of endoscopic laser resection versus radiation therapy for the treatment of early glottic carcinoma.

Osborn HA, Hu A, Venkatesan V, Nichols A, Franklin JH, Yoo JH, Ceron M, Whelan F, Fung K.

J Otolaryngol Head Neck Surg. 2011 Jun;40(3):200-4.


Contact endoscopy as a novel technique in the detection and diagnosis of mucosal lesions in the head and neck: a brief review.

Szeto C, Wehrli B, Whelan F, Franklin J, Nichols A, Yoo J, Fung K.

J Oncol. 2011;2011:196302. doi: 10.1155/2011/196302. Epub 2010 Dec 16.


Amino acid substitutions in the aryl hydrocarbon receptor ligand binding domain reveal YH439 as an atypical AhR activator.

Whelan F, Hao N, Furness SG, Whitelaw ML, Chapman-Smith A.

Mol Pharmacol. 2010 Jun;77(6):1037-46. doi: 10.1124/mol.109.062927. Epub 2010 Mar 15.


Possible influence of variant of the P-glycoprotein gene (MDR1/ABCB1) on clinical response to guanfacine in children with pervasive developmental disorders and hyperactivity.

McCracken JT, Aman MG, McDougle CJ, Tierney E, Shiraga S, Whelan F, Arnold LE, Posey D, Ritz L, Vitiello B, Scahill L.

J Child Adolesc Psychopharmacol. 2010 Feb;20(1):1-5. doi: 10.1089/cap.2009.0059.


The pleiotropy of dioxin toxicity--xenobiotic misappropriation of the aryl hydrocarbon receptor's alternative physiological roles.

Furness SG, Whelan F.

Pharmacol Ther. 2009 Dec;124(3):336-53. doi: 10.1016/j.pharmthera.2009.09.004. Epub 2009 Sep 23.


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