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Items: 1 to 50 of 183

1.

B-cell Receptor Recombinations in Lung Adenocarcinoma Exome Files Correlate With a Higher Overall Survival Rate.

Tu YN, Tong WL, Callahan BM, Chobrutskiy BI, Blanck G.

Anticancer Res. 2020 Apr;40(4):2043-2051. doi: 10.21873/anticanres.14161.

PMID:
32234895
2.

Subverting Hedgehog Protein Autoprocessing by Chemical Induction of Paracatalysis.

Smith CJ, Wagner AG, Stagnitta RT, Xu Z, Pezzullo JL, Giner JL, Xie J, Covey DF, Wang C, Callahan BP.

Biochemistry. 2020 Feb 18;59(6):736-741. doi: 10.1021/acs.biochem.0c00013. Epub 2020 Feb 4.

PMID:
32013401
3.

Operationalizing Impaired Performance in Neuropsychological Assessment: A Comparison of the Use of Published Versus Sample-Based Normative Data for the Prediction of Dementia.

Callahan BL; Alzheimer’s Disease Neuroimaging Initiative.

J Int Neuropsychol Soc. 2019 Dec 11:1-8. doi: 10.1017/S1355617719001309. [Epub ahead of print]

PMID:
31822300
4.

General Base Swap Preserves Activity and Expands Substrate Tolerance in Hedgehog Autoprocessing.

Zhao J, Ciulla DA, Xie J, Wagner AG, Castillo DA, Zwarycz AS, Lin Z, Beadle S, Giner JL, Li Z, Li H, Banavali N, Callahan BP, Wang C.

J Am Chem Soc. 2019 Nov 20;141(46):18380-18384. doi: 10.1021/jacs.9b08914. Epub 2019 Nov 7.

PMID:
31682419
5.

Protein-Nucleic Acid Conjugation with Sterol Linkers Using Hedgehog Autoprocessing.

Zhang X, Xu Z, Moumin DS, Ciulla DA, Owen TS, Mancusi RA, Giner JL, Wang C, Callahan BP.

Bioconjug Chem. 2019 Nov 20;30(11):2799-2804. doi: 10.1021/acs.bioconjchem.9b00550. Epub 2019 Oct 10.

PMID:
31600061
6.

Understanding and interpreting community sequencing measurements of the vaginal microbiome.

Berman HL, McLaren MR, Callahan BJ.

BJOG. 2020 Jan;127(2):139-146. doi: 10.1111/1471-0528.15978. Epub 2019 Nov 1. Review.

PMID:
31597208
7.

Ceftiofur formulation differentially affects the intestinal drug concentration, resistance of fecal Escherichia coli, and the microbiome of steers.

Foster DM, Jacob ME, Farmer KA, Callahan BJ, Theriot CM, Kathariou S, Cernicchiaro N, Prange T, Papich MG.

PLoS One. 2019 Oct 4;14(10):e0223378. doi: 10.1371/journal.pone.0223378. eCollection 2019.

8.

Consistent and correctable bias in metagenomic sequencing experiments.

McLaren MR, Willis AD, Callahan BJ.

Elife. 2019 Sep 10;8. pii: e46923. doi: 10.7554/eLife.46923.

9.

Author Correction: Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2.

Bolyen E, Rideout JR, Dillon MR, Bokulich NA, Abnet CC, Al-Ghalith GA, Alexander H, Alm EJ, Arumugam M, Asnicar F, Bai Y, Bisanz JE, Bittinger K, Brejnrod A, Brislawn CJ, Brown CT, Callahan BJ, Caraballo-Rodríguez AM, Chase J, Cope EK, Da Silva R, Diener C, Dorrestein PC, Douglas GM, Durall DM, Duvallet C, Edwardson CF, Ernst M, Estaki M, Fouquier J, Gauglitz JM, Gibbons SM, Gibson DL, Gonzalez A, Gorlick K, Guo J, Hillmann B, Holmes S, Holste H, Huttenhower C, Huttley GA, Janssen S, Jarmusch AK, Jiang L, Kaehler BD, Kang KB, Keefe CR, Keim P, Kelley ST, Knights D, Koester I, Kosciolek T, Kreps J, Langille MGI, Lee J, Ley R, Liu YX, Loftfield E, Lozupone C, Maher M, Marotz C, Martin BD, McDonald D, McIver LJ, Melnik AV, Metcalf JL, Morgan SC, Morton JT, Naimey AT, Navas-Molina JA, Nothias LF, Orchanian SB, Pearson T, Peoples SL, Petras D, Preuss ML, Pruesse E, Rasmussen LB, Rivers A, Robeson MS 2nd, Rosenthal P, Segata N, Shaffer M, Shiffer A, Sinha R, Song SJ, Spear JR, Swafford AD, Thompson LR, Torres PJ, Trinh P, Tripathi A, Turnbaugh PJ, Ul-Hasan S, van der Hooft JJJ, Vargas F, Vázquez-Baeza Y, Vogtmann E, von Hippel M, Walters W, Wan Y, Wang M, Warren J, Weber KC, Williamson CHD, Willis AD, Xu ZZ, Zaneveld JR, Zhang Y, Zhu Q, Knight R, Caporaso JG.

Nat Biotechnol. 2019 Sep;37(9):1091. doi: 10.1038/s41587-019-0252-6.

PMID:
31399723
10.

Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2.

Bolyen E, Rideout JR, Dillon MR, Bokulich NA, Abnet CC, Al-Ghalith GA, Alexander H, Alm EJ, Arumugam M, Asnicar F, Bai Y, Bisanz JE, Bittinger K, Brejnrod A, Brislawn CJ, Brown CT, Callahan BJ, Caraballo-Rodríguez AM, Chase J, Cope EK, Da Silva R, Diener C, Dorrestein PC, Douglas GM, Durall DM, Duvallet C, Edwardson CF, Ernst M, Estaki M, Fouquier J, Gauglitz JM, Gibbons SM, Gibson DL, Gonzalez A, Gorlick K, Guo J, Hillmann B, Holmes S, Holste H, Huttenhower C, Huttley GA, Janssen S, Jarmusch AK, Jiang L, Kaehler BD, Kang KB, Keefe CR, Keim P, Kelley ST, Knights D, Koester I, Kosciolek T, Kreps J, Langille MGI, Lee J, Ley R, Liu YX, Loftfield E, Lozupone C, Maher M, Marotz C, Martin BD, McDonald D, McIver LJ, Melnik AV, Metcalf JL, Morgan SC, Morton JT, Naimey AT, Navas-Molina JA, Nothias LF, Orchanian SB, Pearson T, Peoples SL, Petras D, Preuss ML, Pruesse E, Rasmussen LB, Rivers A, Robeson MS 2nd, Rosenthal P, Segata N, Shaffer M, Shiffer A, Sinha R, Song SJ, Spear JR, Swafford AD, Thompson LR, Torres PJ, Trinh P, Tripathi A, Turnbaugh PJ, Ul-Hasan S, van der Hooft JJJ, Vargas F, Vázquez-Baeza Y, Vogtmann E, von Hippel M, Walters W, Wan Y, Wang M, Warren J, Weber KC, Williamson CHD, Willis AD, Xu ZZ, Zaneveld JR, Zhang Y, Zhu Q, Knight R, Caporaso JG.

Nat Biotechnol. 2019 Aug;37(8):852-857. doi: 10.1038/s41587-019-0209-9. No abstract available. Erratum in: Nat Biotechnol. 2019 Sep;37(9):1091.

11.

Investigating the Association Between Verbal Forgetting and Pathological Markers of Alzheimer's and Lewy Body Diseases.

Schaeffer MJ, Callahan BL; Alzheimer’s Disease Neuroimaging Initiative.

J Alzheimers Dis. 2019;70(3):877-887. doi: 10.3233/JAD-180962.

PMID:
31282412
12.

High-throughput amplicon sequencing of the full-length 16S rRNA gene with single-nucleotide resolution.

Callahan BJ, Wong J, Heiner C, Oh S, Theriot CM, Gulati AS, McGill SK, Dougherty MK.

Nucleic Acids Res. 2019 Oct 10;47(18):e103. doi: 10.1093/nar/gkz569.

13.

Potential MMP2-mediated availability of HLA binding, mutant ECM peptides reflects better melanoma survival rates and greater T-cell infiltrates.

Zaman S, Chobrutskiy BI, Patel JS, Callahan BM, Mihyu MM, Diviney A, Blanck G.

Lab Invest. 2019 Sep;99(9):1287-1295. doi: 10.1038/s41374-019-0248-3. Epub 2019 Apr 24.

PMID:
31019293
14.

White matter hyperintensities in vascular contributions to cognitive impairment and dementia (VCID): Knowledge gaps and opportunities.

Alber J, Alladi S, Bae HJ, Barton DA, Beckett LA, Bell JM, Berman SE, Biessels GJ, Black SE, Bos I, Bowman GL, Brai E, Brickman AM, Callahan BL, Corriveau RA, Fossati S, Gottesman RF, Gustafson DR, Hachinski V, Hayden KM, Helman AM, Hughes TM, Isaacs JD, Jefferson AL, Johnson SC, Kapasi A, Kern S, Kwon JC, Kukolja J, Lee A, Lockhart SN, Murray A, Osborn KE, Power MC, Price BR, Rhodius-Meester HFM, Rondeau JA, Rosen AC, Rosene DL, Schneider JA, Scholtzova H, Shaaban CE, Silva NCBS, Snyder HM, Swardfager W, Troen AM, van Veluw SJ, Vemuri P, Wallin A, Wellington C, Wilcock DM, Xie SX, Hainsworth AH.

Alzheimers Dement (N Y). 2019 Apr 9;5:107-117. doi: 10.1016/j.trci.2019.02.001. eCollection 2019. Review.

15.

Matrix-Metalloprotease Resistant Mucin-16 (MUC16) Peptide Mutants Represent a Worse Lung Adenocarcinoma Outcome.

Patel JS, Callahan BM, Chobrutskiy BI, Blanck G.

Proteomics Clin Appl. 2019 Jul;13(4):e1800155. doi: 10.1002/prca.201800155. Epub 2019 Mar 12.

PMID:
30790454
16.

T-cell receptor V and J usage paired with specific HLA alleles associates with distinct cervical cancer survival rates.

Roca AM, Chobrutskiy BI, Callahan BM, Blanck G.

Hum Immunol. 2019 Apr;80(4):237-242. doi: 10.1016/j.humimm.2019.01.005. Epub 2019 Jan 23.

PMID:
30684568
17.

Sterol A-ring plasticity in hedgehog protein cholesterolysis supports a primitive substrate selectivity mechanism.

Ciulla DA, Wagner AG, Liu X, Cooper CL, Jorgensen MT, Wang C, Goyal P, Banavali NK, Pezzullo JL, Giner JL, Callahan BP.

Chem Commun (Camb). 2019 Feb 5;55(12):1829-1832. doi: 10.1039/c8cc09729a.

18.

Multiomics modeling of the immunome, transcriptome, microbiome, proteome and metabolome adaptations during human pregnancy.

Ghaemi MS, DiGiulio DB, Contrepois K, Callahan B, Ngo TTM, Lee-McMullen B, Lehallier B, Robaczewska A, Mcilwain D, Rosenberg-Hasson Y, Wong RJ, Quaintance C, Culos A, Stanley N, Tanada A, Tsai A, Gaudilliere D, Ganio E, Han X, Ando K, McNeil L, Tingle M, Wise P, Maric I, Sirota M, Wyss-Coray T, Winn VD, Druzin ML, Gibbs R, Darmstadt GL, Lewis DB, Partovi Nia V, Agard B, Tibshirani R, Nolan G, Snyder MP, Relman DA, Quake SR, Shaw GM, Stevenson DK, Angst MS, Gaudilliere B, Aghaeepour N.

Bioinformatics. 2019 Jan 1;35(1):95-103. doi: 10.1093/bioinformatics/bty537.

19.

Simple statistical identification and removal of contaminant sequences in marker-gene and metagenomics data.

Davis NM, Proctor DM, Holmes SP, Relman DA, Callahan BJ.

Microbiome. 2018 Dec 17;6(1):226. doi: 10.1186/s40168-018-0605-2.

20.

TRB-J1 usage, in combination with the HLA-A*01:01 allele, represents an apparent survival advantage for uterine corpus endometrial carcinoma: Comparisons with microscopic assessments of lymphocyte infiltrates.

Clark KR, Tong WL, Callahan BM, Yavorski JM, Tu YN, Blanck G.

Int J Immunogenet. 2019 Feb;46(1):31-37. doi: 10.1111/iji.12409. Epub 2018 Nov 26.

PMID:
30474304
21.

MMP7 sensitivity of mutant ECM proteins: An indicator of melanoma survival rates and T-cell infiltration.

Zaman S, Chobrutskiy BI, Patel JS, Callahan BM, Tong WL, Mihyu MM, Blanck G.

Clin Biochem. 2019 Jan;63:85-91. doi: 10.1016/j.clinbiochem.2018.11.004. Epub 2018 Nov 8.

PMID:
30414845
22.

Examining the validity of the ADHD concept in adults and older adults.

Callahan BL, Plamondon A.

CNS Spectr. 2019 Oct;24(5):518-525. doi: 10.1017/S1092852918001190.

PMID:
30295232
23.

Dosing Regimen of Enrofloxacin Impacts Intestinal Pharmacokinetics and the Fecal Microbiota in Steers.

Ferguson KM, Jacob ME, Theriot CM, Callahan BJ, Prange T, Papich MG, Foster DM.

Front Microbiol. 2018 Sep 19;9:2190. doi: 10.3389/fmicb.2018.02190. eCollection 2018.

24.

Immune receptor recombinations from breast cancer exome files, independently and in combination with specific HLA alleles, correlate with better survival rates.

Tong WL, Callahan BM, Tu YN, Zaman S, Chobrutskiy BI, Blanck G.

Breast Cancer Res Treat. 2019 Jan;173(1):167-177. doi: 10.1007/s10549-018-4961-1. Epub 2018 Sep 18.

PMID:
30229447
25.

Mutant cytoskeletal and ECM peptides sensitive to the ST14 protease are associated with a worse outcome for glioblastoma multiforme.

Zaman S, Chobrutskiy BI, Patel JS, Callahan BM, Tong WL, Blanck G.

Biochem Biophys Res Commun. 2018 Sep 18;503(4):2218-2225. doi: 10.1016/j.bbrc.2018.06.141. Epub 2018 Jul 17.

PMID:
29953855
26.

Pollen wall degradation in the Brassicaceae permits cell emergence after pollination.

Edlund AF, Olsen K, Mendoza C, Wang J, Buckley T, Nguyen M, Callahan B, Owen HA.

Am J Bot. 2017 Aug;104(8):1266-1273. doi: 10.3732/ajb.1700201.

27.

T cell receptor-β J usage, in combination with particular HLA class II alleles, correlates with better cancer survival rates.

Callahan BM, Tong WL, Blanck G.

Immunol Res. 2018 Apr;66(2):219-223. doi: 10.1007/s12026-018-8990-y.

PMID:
29594966
28.

T-cell receptor-β V and J usage, in combination with particular HLA class I and class II alleles, correlates with cancer survival patterns.

Callahan BM, Yavorski JM, Tu YN, Tong WL, Kinskey JC, Clark KR, Fawcett TJ, Blanck G.

Cancer Immunol Immunother. 2018 Jun;67(6):885-892. doi: 10.1007/s00262-018-2139-7. Epub 2018 Mar 5.

PMID:
29508024
29.

In Nature, There Is Only Diversity.

McLaren MR, Callahan BJ.

mBio. 2018 Jan 2;9(1). pii: e02149-17. doi: 10.1128/mBio.02149-17.

30.

Cytoskeleton and ECM tumor mutant peptides: Increased protease sensitivities and potential consequences for the HLA class I mutant epitope reservoir.

Callahan BM, Patel JS, Fawcett TJ, Blanck G.

Int J Cancer. 2018 Mar 1;142(5):988-998. doi: 10.1002/ijc.31111. Epub 2017 Nov 2.

31.

Chemical Bypass of General Base Catalysis in Hedgehog Protein Cholesterolysis Using a Hyper-Nucleophilic Substrate.

Ciulla DA, Jorgensen MT, Giner JL, Callahan BP.

J Am Chem Soc. 2018 Jan 24;140(3):916-918. doi: 10.1021/jacs.7b05161. Epub 2017 Sep 25.

32.

Incidental 131I Activity in the Deltoid Region on Posttherapy Radioiodine Scan.

Strober MD, Callahan BR.

Clin Nucl Med. 2017 Nov;42(11):899-900. doi: 10.1097/RLU.0000000000001828.

PMID:
28902736
33.

Replication and refinement of a vaginal microbial signature of preterm birth in two racially distinct cohorts of US women.

Callahan BJ, DiGiulio DB, Goltsman DSA, Sun CL, Costello EK, Jeganathan P, Biggio JR, Wong RJ, Druzin ML, Shaw GM, Stevenson DK, Holmes SP, Relman DA.

Proc Natl Acad Sci U S A. 2017 Sep 12;114(37):9966-9971. doi: 10.1073/pnas.1705899114. Epub 2017 Aug 28.

34.

Adult ADHD: Risk Factor for Dementia or Phenotypic Mimic?

Callahan BL, Bierstone D, Stuss DT, Black SE.

Front Aging Neurosci. 2017 Aug 3;9:260. doi: 10.3389/fnagi.2017.00260. eCollection 2017.

35.

Effect of conceptual and lexical errorless versus trial-and-error learning in amnestic mild cognitive impairment.

Callahan BL, Anderson ND.

Neuropsychol Rehabil. 2019 Jul;29(6):969-982. doi: 10.1080/09602011.2017.1361843. Epub 2017 Aug 11.

PMID:
28797212
36.

Exact sequence variants should replace operational taxonomic units in marker-gene data analysis.

Callahan BJ, McMurdie PJ, Holmes SP.

ISME J. 2017 Dec;11(12):2639-2643. doi: 10.1038/ismej.2017.119. Epub 2017 Jul 21.

37.

Antihypertensive Treatment is associated with MRI-Derived Markers of Neurodegeneration and Impaired Cognition: A Propensity-Weighted Cohort Study.

Edwards JD, Ramirez J, Callahan BL, Tobe SW, Oh P, Berezuk C, Lanctôt K, Swardfager W, Nestor S, Kiss A, Strother S, Black SE; Alzheimer’s Disease Neuroimaging Initiative.

J Alzheimers Dis. 2017;59(3):1113-1122. doi: 10.3233/JAD-170238.

PMID:
28731439
38.

Addressing Disparities in Diabetes Management Through Novel Approaches to Encourage Technology Adoption and Use.

Sheon AR, Bolen SD, Callahan B, Shick S, Perzynski AT.

JMIR Diabetes. 2017 Jul 13;2(2):e16. doi: 10.2196/diabetes.6751.

39.

The Ultimate Outlier: Transitional Care for Persons with Dementia and BPSD.

Cohen-Mansfield J, Ray CA, Hai T, Marcu C, Callahan BL, Freedman M.

Curr Alzheimer Res. 2017;14(9):969-977. doi: 10.2174/1567205014666170515141710.

PMID:
28521676
40.

Functional Reserve: Experience Participating in Instrumental Activities of Daily Living is Associated with Gender and Functional Independence in Mild Cognitive Impairment.

Berezuk C, Zakzanis KK, Ramirez J, Ruocco AC, Edwards JD, Callahan BL, Black SE; Alzheimer’s Disease Neuroimaging Initiative.

J Alzheimers Dis. 2017;58(2):425-434. doi: 10.3233/JAD-161227.

PMID:
28453478
41.

Development of cognitive screening test for the severely hearing impaired: Hearing-impaired MoCA.

Lin VY, Chung J, Callahan BL, Smith L, Gritters N, Chen JM, Black SE, Masellis M.

Laryngoscope. 2017 May;127 Suppl 1:S4-S11. doi: 10.1002/lary.26590.

PMID:
28409842
42.

Patient portals and broadband internet inequality.

Perzynski AT, Roach MJ, Shick S, Callahan B, Gunzler D, Cebul R, Kaelber DC, Huml A, Thornton JD, Einstadter D.

J Am Med Inform Assoc. 2017 Sep 1;24(5):927-932. doi: 10.1093/jamia/ocx020.

43.

Facial emotion recognition in patients with focal and diffuse axonal injury.

Yassin W, Callahan BL, Ubukata S, Sugihara G, Murai T, Ueda K.

Brain Inj. 2017;31(5):624-630. doi: 10.1080/02699052.2017.1285052. Epub 2017 Mar 28.

PMID:
28350176
44.

Illuminating cytochrome P450 binding: Ru(ii)-caged inhibitors of CYP17A1.

Li A, Yadav R, White JK, Herroon MK, Callahan BP, Podgorski I, Turro C, Scott EE, Kodanko JJ.

Chem Commun (Camb). 2017 Mar 28;53(26):3673-3676. doi: 10.1039/c7cc01459g.

45.

Radiological-Pathological Correlation in Alzheimer's Disease: Systematic Review of Antemortem Magnetic Resonance Imaging Findings.

Dallaire-Théroux C, Callahan BL, Potvin O, Saikali S, Duchesne S.

J Alzheimers Dis. 2017;57(2):575-601. doi: 10.3233/JAD-161028. Review.

PMID:
28282807
46.

Memory for emotional images differs according to the presence of depressive symptoms in individuals at risk for dementia.

Callahan BL, Laforce R, Dugas M, Hudon C.

Int Psychogeriatr. 2017 Apr;29(4):673-685. doi: 10.1017/S1041610216002179. Epub 2016 Dec 15.

PMID:
27974073
47.

Bioconductor Workflow for Microbiome Data Analysis: from raw reads to community analyses.

Callahan BJ, Sankaran K, Fukuyama JA, McMurdie PJ, Holmes SP.

Version 2. F1000Res. 2016 Jun 24 [revised 2016 Jan 1];5:1492. eCollection 2016.

48.

1,2-Dichloroethane Exposure Alters the Population Structure, Metabolism, and Kinetics of a Trichloroethene-Dechlorinating Dehalococcoides mccartyi Consortium.

Mayer-Blackwell K, Fincker M, Molenda O, Callahan B, Sewell H, Holmes S, Edwards EA, Spormann AM.

Environ Sci Technol. 2016 Nov 15;50(22):12187-12196. Epub 2016 Nov 3.

PMID:
27809491
49.

A Single Aspartate Coordinates Two Catalytic Steps in Hedgehog Autoprocessing.

Xie J, Owen T, Xia K, Callahan B, Wang C.

J Am Chem Soc. 2016 Aug 31;138(34):10806-9. doi: 10.1021/jacs.6b06928. Epub 2016 Aug 19.

50.

Hedgehog Proteins Consume Steroidal CYP17A1 Antagonists: Potential Therapeutic Significance in Advanced Prostate Cancer.

Bordeau BM, Ciulla DA, Callahan BP.

ChemMedChem. 2016 Sep 20;11(18):1983-6. doi: 10.1002/cmdc.201600238. Epub 2016 Jul 20.

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