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Macroalgae as spatial and temporal bioindicators of coastal metal pollution following remediation and diversion of acid mine drainage.

Chalkley R, Child F, Al-Thaqafi K, Dean AP, White KN, Pittman JK.

Ecotoxicol Environ Saf. 2019 Oct 30;182:109458. doi: 10.1016/j.ecoenv.2019.109458. Epub 2019 Jul 26.


A two-step probing method to compare lysine accessibility across macromolecular complex conformations.

MacRae AJ, Coltri P, Hrabeta-Robinson E, Chalkley RJ, Burlingame AL, Jurica MS.

RNA Biol. 2019 Oct;16(10):1346-1354. doi: 10.1080/15476286.2019.1632777. Epub 2019 Jun 29.


Smeloff-Cutter Mechanical Prosthesis in the Aortic Position for 49 Years.

Chalkley RA, Kim CW, Choi JW, Roberts WC, Schussler JM.

Am J Cardiol. 2019 Aug 1;124(3):457-459. doi: 10.1016/j.amjcard.2019.05.004. Epub 2019 May 8.


Proteomics Standards Initiative Extended FASTA Format.

Binz PA, Shofstahl J, Vizcaíno JA, Barsnes H, Chalkley RJ, Menschaert G, Alpi E, Clauser K, Eng JK, Lane L, Seymour SL, Sánchez LFH, Mayer G, Eisenacher M, Perez-Riverol Y, Kapp EA, Mendoza L, Baker PR, Collins A, Van Den Bossche T, Deutsch EW.

J Proteome Res. 2019 Jun 7;18(6):2686-2692. doi: 10.1021/acs.jproteome.9b00064. Epub 2019 May 23.


The GRE over the entire range of scores lacks predictive ability for PhD outcomes in the biomedical sciences.

Sealy L, Saunders C, Blume J, Chalkley R.

PLoS One. 2019 Mar 21;14(3):e0201634. doi: 10.1371/journal.pone.0201634. eCollection 2019.


Faculty perceptions and knowledge of career development of trainees in biomedical science: What do we (think we) know?

Watts SW, Chatterjee D, Rojewski JW, Shoshkes Reiss C, Baas T, Gould KL, Brown AM, Chalkley R, Brandt P, Wefes I, Hyman L, Ford JK.

PLoS One. 2019 Jan 30;14(1):e0210189. doi: 10.1371/journal.pone.0210189. eCollection 2019.


Initial Guidelines for Manuscripts Employing Data-independent Acquisition Mass Spectrometry for Proteomic Analysis.

Chalkley RJ, MacCoss MJ, Jaffe JD, Röst HL.

Mol Cell Proteomics. 2019 Jan;18(1):1-2. doi: 10.1074/mcp.E118.001286. No abstract available.


Molecular High-Grade B-Cell Lymphoma: Defining a Poor-Risk Group That Requires Different Approaches to Therapy.

Sha C, Barrans S, Cucco F, Bentley MA, Care MA, Cummin T, Kennedy H, Thompson JS, Uddin R, Worrillow L, Chalkley R, van Hoppe M, Ahmed S, Maishman T, Caddy J, Schuh A, Mamot C, Burton C, Tooze R, Davies A, Du MQ, Johnson PWM, Westhead DR.

J Clin Oncol. 2019 Jan 20;37(3):202-212. doi: 10.1200/JCO.18.01314. Epub 2018 Dec 3. Erratum in: J Clin Oncol. 2019 Apr 20;37(12):1035.


Evolution of a Functional Taxonomy of Career Pathways for Biomedical Trainees.

Mathur A, Brandt P, Chalkley R, Daniel L, Labosky P, Stayart C, Meyers F.

J Clin Transl Sci. 2018 Apr;2(2):63-65. doi: 10.1017/cts.2018.22. Epub 2018 Aug 8.


Expanding the Use of Spectral Libraries in Proteomics.

Deutsch EW, Perez-Riverol Y, Chalkley RJ, Wilhelm M, Tate S, Sachsenberg T, Walzer M, Käll L, Delanghe B, Böcker S, Schymanski EL, Wilmes P, Dorfer V, Kuster B, Volders PJ, Jehmlich N, Vissers JPC, Wolan DW, Wang AY, Mendoza L, Shofstahl J, Dowsey AW, Griss J, Salek RM, Neumann S, Binz PA, Lam H, Vizcaíno JA, Bandeira N, Röst H.

J Proteome Res. 2018 Dec 7;17(12):4051-4060. doi: 10.1021/acs.jproteome.8b00485. Epub 2018 Oct 11. Review.


Prp8 positioning of U5 snRNA is linked to 5' splice site recognition.

MacRae AJ, Mayerle M, Hrabeta-Robinson E, Chalkley RJ, Guthrie C, Burlingame AL, Jurica MS.

RNA. 2018 Jun;24(6):769-777. doi: 10.1261/rna.065458.117. Epub 2018 Feb 27.


Revealing nascent proteomics in signaling pathways and cell differentiation.

Forester CM, Zhao Q, Phillips NJ, Urisman A, Chalkley RJ, Oses-Prieto JA, Zhang L, Ruggero D, Burlingame AL.

Proc Natl Acad Sci U S A. 2018 Mar 6;115(10):2353-2358. doi: 10.1073/pnas.1707514115. Epub 2018 Feb 21.


Survey of checkpoints along the pathway to diverse biomedical research faculty.

Meyers LC, Brown AM, Moneta-Koehler L, Chalkley R.

PLoS One. 2018 Jan 16;13(1):e0190606. doi: 10.1371/journal.pone.0190606. eCollection 2018.


A comparative analysis of clinical outcomes and disposable costs of different catheter ablation methods for the treatment of atrioventricular nodal reentrant tachycardia.

Berman AE, Rivner H, Chalkley R, Heboyan V.

Clinicoecon Outcomes Res. 2017 Nov 6;9:677-683. doi: 10.2147/CEOR.S139861. eCollection 2017.


Peripheral Elevation of a Klotho Fragment Enhances Brain Function and Resilience in Young, Aging, and α-Synuclein Transgenic Mice.

Leon J, Moreno AJ, Garay BI, Chalkley RJ, Burlingame AL, Wang D, Dubal DB.

Cell Rep. 2017 Aug 8;20(6):1360-1371. doi: 10.1016/j.celrep.2017.07.024.


The genomic road to invasion-examining the similarities and differences in the genomes of associated oral pre-cancer and cancer samples.

Wood HM, Daly C, Chalkley R, Senguven B, Ross L, Egan P, Chengot P, Graham J, Sethi N, Ong TK, MacLennan K, Rabbitts P, Conway C.

Genome Med. 2017 Jun 7;9(1):53. doi: 10.1186/s13073-017-0442-0.


The mzIdentML Data Standard Version 1.2, Supporting Advances in Proteome Informatics.

Vizcaíno JA, Mayer G, Perkins S, Barsnes H, Vaudel M, Perez-Riverol Y, Ternent T, Uszkoreit J, Eisenacher M, Fischer L, Rappsilber J, Netz E, Walzer M, Kohlbacher O, Leitner A, Chalkley RJ, Ghali F, Martínez-Bartolomé S, Deutsch EW, Jones AR.

Mol Cell Proteomics. 2017 Jul;16(7):1275-1285. doi: 10.1074/mcp.M117.068429. Epub 2017 May 17.


PPKs mediate direct signal transfer from phytochrome photoreceptors to transcription factor PIF3.

Ni W, Xu SL, González-Grandío E, Chalkley RJ, Huhmer AFR, Burlingame AL, Wang ZY, Quail PH.

Nat Commun. 2017 May 11;8:15236. doi: 10.1038/ncomms15236.


Hyper-O-GlcNAcylation activates nuclear factor κ-light-chain-enhancer of activated B cells (NF-κB) signaling through interplay with phosphorylation and acetylation.

Ma Z, Chalkley RJ, Vosseller K.

J Biol Chem. 2017 Jun 2;292(22):9150-9163. doi: 10.1074/jbc.M116.766568. Epub 2017 Apr 17.


New Guidelines for Publication of Manuscripts Describing Development and Application of Targeted Mass Spectrometry Measurements of Peptides and Proteins.

Abbatiello S, Ackermann BL, Borchers C, Bradshaw RA, Carr SA, Chalkley R, Choi M, Deutsch E, Domon B, Hoofnagle AN, Keshishian H, Kuhn E, Liebler DC, MacCoss M, MacLean B, Mani DR, Neubert H, Smith D, Vitek O, Zimmerman L.

Mol Cell Proteomics. 2017 Mar;16(3):327-328. doi: 10.1074/mcp.E117.067801. Epub 2017 Feb 9. No abstract available.


Proteomic analysis reveals O-GlcNAc modification on proteins with key regulatory functions in Arabidopsis.

Xu SL, Chalkley RJ, Maynard JC, Wang W, Ni W, Jiang X, Shin K, Cheng L, Savage D, Hühmer AF, Burlingame AL, Wang ZY.

Proc Natl Acad Sci U S A. 2017 Feb 21;114(8):E1536-E1543. doi: 10.1073/pnas.1610452114. Epub 2017 Feb 2.


The Limitations of the GRE in Predicting Success in Biomedical Graduate School.

Moneta-Koehler L, Brown AM, Petrie KA, Evans BJ, Chalkley R.

PLoS One. 2017 Jan 11;12(1):e0166742. doi: 10.1371/journal.pone.0166742. eCollection 2017.


Modification Site Localization in Peptides.

Chalkley RJ.

Adv Exp Med Biol. 2016;919:243-247. Review.


A quantitative immunoassay for lung cancer biomarker CIZ1b in patient plasma.

Coverley D, Higgins G, West D, Jackson OT, Dowle A, Haslam A, Ainscough E, Chalkley R, White J.

Clin Biochem. 2017 Apr;50(6):336-343. doi: 10.1016/j.clinbiochem.2016.11.015. Epub 2016 Nov 17.


Use of a glycosylation site database to improve glycopeptide identification from complex mixtures.

Chalkley RJ, Baker PR.

Anal Bioanal Chem. 2017 Jan;409(2):571-577. doi: 10.1007/s00216-016-9981-2. Epub 2016 Oct 8.


Glyco-centric lectin magnetic bead array (LeMBA) - proteomics dataset of human serum samples from healthy, Barrett׳s esophagus and esophageal adenocarcinoma individuals.

Shah AK, Lê Cao KA, Choi E, Chen D, Gautier B, Nancarrow D, Whiteman DC, Baker PR, Clauser KR, Chalkley RJ, Saunders NA, Barbour AP, Joshi V, Hill MM.

Data Brief. 2016 Apr 1;7:1058-62. doi: 10.1016/j.dib.2016.03.081. eCollection 2016 Jun.


N-Glycopeptide Profiling in Arabidopsis Inflorescence.

Xu SL, Medzihradszky KF, Wang ZY, Burlingame AL, Chalkley RJ.

Mol Cell Proteomics. 2016 Jun;15(6):2048-54. doi: 10.1074/mcp.M115.056101. Epub 2016 Apr 11.


Use of a mutant OGA for detecting O-GlcNAc modified proteins.

Chalkley RJ.

Biochem J. 2015 Dec 1;472(2):e25-6. doi: 10.1042/BJ20150970.


Elucidating drivers of oral epithelial dysplasia formation and malignant transformation to cancer using RNAseq.

Conway C, Graham JL, Chengot P, Daly C, Chalkley R, Ross L, Droop A, Rabbitts P, Stead LF.

Oncotarget. 2015 Nov 24;6(37):40186-201. doi: 10.18632/oncotarget.5529.


The origin and implementation of the Broadening Experiences in Scientific Training programs: an NIH common fund initiative.

Meyers FJ, Mathur A, Fuhrmann CN, O'Brien TC, Wefes I, Labosky PA, Duncan DS, August A, Feig A, Gould KL, Friedlander MJ, Schaffer CB, Van Wart A, Chalkley R.

FASEB J. 2016 Feb;30(2):507-14. doi: 10.1096/fj.15-276139. Epub 2015 Oct 2.


The clonal relationships between pre-cancer and cancer revealed by ultra-deep sequencing.

Wood HM, Conway C, Daly C, Chalkley R, Berri S, Senguven B, Stead L, Ross L, Egan P, Chengot P, Graham J, Sethi N, Ong TK, High A, MacLennan K, Rabbitts P.

J Pathol. 2015 Nov;237(3):296-306. doi: 10.1002/path.4576. Epub 2015 Jul 24.


Proteotranscriptomic Profiling of 231-BR Breast Cancer Cells: Identification of Potential Biomarkers and Therapeutic Targets for Brain Metastasis.

Dun MD, Chalkley RJ, Faulkner S, Keene S, Avery-Kiejda KA, Scott RJ, Falkenby LG, Cairns MJ, Larsen MR, Bradshaw RA, Hondermarck H.

Mol Cell Proteomics. 2015 Sep;14(9):2316-30. doi: 10.1074/mcp.M114.046110. Epub 2015 Jun 3.


On Credibility, Clarity, and Compliance.

Burlingame A, Carr SA, Bradshaw RA, Chalkley RJ.

Mol Cell Proteomics. 2015 Jul;14(7):1731-3. doi: 10.1074/mcp.E115.052506. Epub 2015 Jun 3. No abstract available.


A novel genomic signature reclassifies an oral cancer subtype.

Samman M, Wood HM, Conway C, Stead L, Daly C, Chalkley R, Berri S, Senguven B, Ross L, Egan P, Chengot P, Ong TK, Pentenero M, Gandolfo S, Cassenti A, Cassoni P, Al Ajlan A, Samkari A, Barrett W, MacLennan K, High A, Rabbitts P.

Int J Cancer. 2015 Nov 15;137(10):2364-73. doi: 10.1002/ijc.29615. Epub 2015 Jun 9.


Tissue-Specific Glycosylation at the Glycopeptide Level.

Medzihradszky KF, Kaasik K, Chalkley RJ.

Mol Cell Proteomics. 2015 Aug;14(8):2103-10. doi: 10.1074/mcp.M115.050393. Epub 2015 May 20.


Validity of the Medical College Admission Test for predicting MD-PhD student outcomes.

Bills JL, VanHouten J, Grundy MM, Chalkley R, Dermody TS.

Adv Health Sci Educ Theory Pract. 2016 Mar;21(1):33-49. doi: 10.1007/s10459-015-9609-x. Epub 2015 May 8.


Transforming training to reflect the workforce.

Mathur A, Meyers FJ, Chalkley R, O'Brien TC, Fuhrmann CN.

Sci Transl Med. 2015 Apr 29;7(285):285ed4. doi: 10.1126/scitranslmed.aaa8200. No abstract available.


Lessons in de novo peptide sequencing by tandem mass spectrometry.

Medzihradszky KF, Chalkley RJ.

Mass Spectrom Rev. 2015 Jan-Feb;34(1):43-63. Review.


Characterizing sialic acid variants at the glycopeptide level.

Medzihradszky KF, Kaasik K, Chalkley RJ.

Anal Chem. 2015 Mar 3;87(5):3064-71. doi: 10.1021/ac504725r. Epub 2015 Feb 17.


NGF and ProNGF: Regulation of neuronal and neoplastic responses through receptor signaling.

Bradshaw RA, Pundavela J, Biarc J, Chalkley RJ, Burlingame AL, Hondermarck H.

Adv Biol Regul. 2015 May;58:16-27. doi: 10.1016/j.jbior.2014.11.003. Epub 2014 Nov 20. Review.


Molecular architecture of photoreceptor phosphodiesterase elucidated by chemical cross-linking and integrative modeling.

Zeng-Elmore X, Gao XZ, Pellarin R, Schneidman-Duhovny D, Zhang XJ, Kozacka KA, Tang Y, Sali A, Chalkley RJ, Cote RH, Chu F.

J Mol Biol. 2014 Nov 11;426(22):3713-3728. doi: 10.1016/j.jmb.2014.07.033. Epub 2014 Aug 19.


A standardized framing for reporting protein identifications in mzIdentML 1.2.

Seymour SL, Farrah T, Binz PA, Chalkley RJ, Cottrell JS, Searle BC, Tabb DL, Vizcaíno JA, Prieto G, Uszkoreit J, Eisenacher M, Martínez-Bartolomé S, Ghali F, Jones AR.

Proteomics. 2014 Nov;14(21-22):2389-99. doi: 10.1002/pmic.201400080. Epub 2014 Sep 23.


ProteomeXchange provides globally coordinated proteomics data submission and dissemination.

Vizcaíno JA, Deutsch EW, Wang R, Csordas A, Reisinger F, Ríos D, Dianes JA, Sun Z, Farrah T, Bandeira N, Binz PA, Xenarios I, Eisenacher M, Mayer G, Gatto L, Campos A, Chalkley RJ, Kraus HJ, Albar JP, Martinez-Bartolomé S, Apweiler R, Omenn GS, Martens L, Jones AR, Hermjakob H.

Nat Biotechnol. 2014 Mar;32(3):223-6. doi: 10.1038/nbt.2839. No abstract available.


Adding value to rare tissue samples donated to biobanks: characterisation of breast tissue and primary cell cultures obtained from a female-to-male transgender patient.

Millican-Slater R, Good R, Nash C, Heads JA, Pollock S, Chalkley R, Gomm J, Jones JL, Sundara-Rajan S, Horgan K, Hanby AM, Speirs V.

Cell Tissue Bank. 2015 Mar;16(1):27-34. doi: 10.1007/s10561-014-9444-y. Epub 2014 Apr 9.


Double impact of cigarette smoke and mechanical ventilation on the alveolar epithelial type II cell.

Hirsch J, Chalkley RJ, Bentley T, Burlingame AL, Frank JA.

Crit Care. 2014 Mar 25;18(2):R50. doi: 10.1186/cc13795.


MS-viewer: a web-based spectral viewer for proteomics results.

Baker PR, Chalkley RJ.

Mol Cell Proteomics. 2014 May;13(5):1392-6. doi: 10.1074/mcp.O113.037200. Epub 2014 Mar 3.


Matching cross-linked peptide spectra: only as good as the worse identification.

Trnka MJ, Baker PR, Robinson PJ, Burlingame AL, Chalkley RJ.

Mol Cell Proteomics. 2014 Feb;13(2):420-34. doi: 10.1074/mcp.M113.034009. Epub 2013 Dec 12.


O-linked β-N-acetylglucosamine (O-GlcNAc) site thr-87 regulates synapsin I localization to synapses and size of the reserve pool of synaptic vesicles.

Skorobogatko Y, Landicho A, Chalkley RJ, Kossenkov AV, Gallo G, Vosseller K.

J Biol Chem. 2014 Feb 7;289(6):3602-12. doi: 10.1074/jbc.M113.512814. Epub 2013 Nov 26.


Proteome informatics research group (iPRG)_2012: a study on detecting modified peptides in a complex mixture.

Chalkley RJ, Bandeira N, Chambers MC, Clauser KR, Cottrell JS, Deutsch EW, Kapp EA, Lam HH, McDonald WH, Neubert TA, Sun RX.

Mol Cell Proteomics. 2014 Jan;13(1):360-71. doi: 10.1074/mcp.M113.032813. Epub 2013 Oct 31.


Multisite light-induced phosphorylation of the transcription factor PIF3 is necessary for both its rapid degradation and concomitant negative feedback modulation of photoreceptor phyB levels in Arabidopsis.

Ni W, Xu SL, Chalkley RJ, Pham TN, Guan S, Maltby DA, Burlingame AL, Wang ZY, Quail PH.

Plant Cell. 2013 Jul;25(7):2679-98. doi: 10.1105/tpc.113.112342. Epub 2013 Jul 31.

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