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Automated Big Data Analytics for the Radiation Oncology Alternative Payment Model Proposal Using a Novel Health Care Software Technology.

Thaker NG, Holloway J, Hodapp C, Mellen M, Fryefield D, Meghani R, Tong K, Rose CM.

JCO Oncol Pract. 2020 Mar 10:JOP1900692. doi: 10.1200/JOP.19.00692. [Epub ahead of print]


Dynamic Regulation of Mitochondrial Import by the Ubiquitin System.

Phu L, Rose CM, Tea JS, Wall CE, Verschueren E, Cheung TK, Kirkpatrick DS, Bingol B.

Mol Cell. 2020 Mar 5;77(5):1107-1123.e10. doi: 10.1016/j.molcel.2020.02.012.


Quantitative Proteomics of the Cancer Cell Line Encyclopedia.

Nusinow DP, Szpyt J, Ghandi M, Rose CM, McDonald ER 3rd, Kalocsay M, Jané-Valbuena J, Gelfand E, Schweppe DK, Jedrychowski M, Golji J, Porter DA, Rejtar T, Wang YK, Kryukov GV, Stegmeier F, Erickson BK, Garraway LA, Sellers WR, Gygi SP.

Cell. 2020 Jan 23;180(2):387-402.e16. doi: 10.1016/j.cell.2019.12.023.


Chaperone mediated detection of small molecule target binding in cells.

Cho KF, Ma TP, Rose CM, Kirkpatrick DS, Yu K, Blake RA.

Nat Commun. 2020 Jan 23;11(1):465. doi: 10.1038/s41467-019-14033-0.


PIKES Analysis Reveals Response to Degraders and Key Regulatory Mechanisms of the CRL4 Network.

Reichermeier KM, Straube R, Reitsma JM, Sweredoski MJ, Rose CM, Moradian A, den Besten W, Hinkle T, Verschueren E, Petzold G, Thomä NH, Wertz IE, Deshaies RJ, Kirkpatrick DS.

Mol Cell. 2020 Mar 5;77(5):1092-1106.e9. doi: 10.1016/j.molcel.2019.12.013. Epub 2020 Jan 20.


Endothelial intercellular cell adhesion molecule 1 contributes to cell aggregate formation in CHO cells cultured in serum-free media.

Louie S, Heidersbach A, Blanco N, Haley B, Rose CM, Liu PS, Yim M, Tang D, Lam C, Sandoval WN, Shaw D, Snedecor B, Misaghi S.

Biotechnol Prog. 2019 Dec 17:e29251. doi: 10.1002/btpr.2951. [Epub ahead of print]


PPEF2 Opposes PINK1-Mediated Mitochondrial Quality Control by Dephosphorylating Ubiquitin.

Wall CE, Rose CM, Adrian M, Zeng YJ, Kirkpatrick DS, Bingol B.

Cell Rep. 2019 Dec 3;29(10):3280-3292.e7. doi: 10.1016/j.celrep.2019.10.130.


Transposable element expression in tumors is associated with immune infiltration and increased antigenicity.

Kong Y, Rose CM, Cass AA, Williams AG, Darwish M, Lianoglou S, Haverty PM, Tong AJ, Blanchette C, Albert ML, Mellman I, Bourgon R, Greally J, Jhunjhunwala S, Chen-Harris H.

Nat Commun. 2019 Nov 19;10(1):5228. doi: 10.1038/s41467-019-13035-2.


An uncommon case of arthrogryposis, renal dysfunction, and cholestasis (ARC) syndrome and review of the renal involvement: Answers.

Duong MD, Rose CM, Reidy KJ, Del Rio M.

Pediatr Nephrol. 2020 Feb;35(2):249-251. doi: 10.1007/s00467-019-04338-z. Epub 2019 Aug 28. No abstract available.


An uncommon case of arthrogryposis, renal dysfunction, and cholestasis (ARC) syndrome and review of the renal involvement: Questions.

Duong MD, Rose CM, Reidy KJ, Del Rio M.

Pediatr Nephrol. 2020 Feb;35(2):247-248. doi: 10.1007/s00467-019-04336-1. Epub 2019 Aug 28.


Consumption Patterns of Milk and 100% Juice in Relation to Diet Quality and Body Weight Among United States Children: Analyses of NHANES 2011-16 Data.

Maillot M, Vieux F, Rehm CD, Rose CM, Drewnowski A.

Front Nutr. 2019 Aug 8;6:117. doi: 10.3389/fnut.2019.00117. eCollection 2019.


Activity space metrics not associated with sociodemographic variables, diet or health outcomes in the Seattle Obesity Study II.

Drewnowski A, Aggarwal A, Rose CM, Gupta S, Delaney JA, Hurvitz PM.

Spat Spatiotemporal Epidemiol. 2019 Aug;30:100289. doi: 10.1016/j.sste.2019.100289. Epub 2019 Jul 12.


Enabling Global Clinical Collaborations on Identifiable Patient Data: The Minerva Initiative.

Nellåker C, Alkuraya FS, Baynam G, Bernier RA, Bernier FPJ, Boulanger V, Brudno M, Brunner HG, Clayton-Smith J, Cogné B, Dawkins HJS, deVries BBA, Douzgou S, Dudding-Byth T, Eichler EE, Ferlaino M, Fieggen K, Firth HV, FitzPatrick DR, Gration D, Groza T, Haendel M, Hallowell N, Hamosh A, Hehir-Kwa J, Hitz MP, Hughes M, Kini U, Kleefstra T, Kooy RF, Krawitz P, Küry S, Lees M, Lyon GJ, Lyonnet S, Marcadier JL, Meyn S, Moslerová V, Politei JM, Poulton CC, Raymond FL, Reijnders MRF, Robinson PN, Romano C, Rose CM, Sainsbury DCG, Schofield L, Sutton VR, Turnovec M, Van Dijck A, Van Esch H, Wilkie AOM; Minerva Consortium.

Front Genet. 2019 Jul 29;10:611. doi: 10.3389/fgene.2019.00611. eCollection 2019.


Interaction of cell culture process parameters for modulating mAb afucosylation.

Nguyen Dang A, Mun M, Rose CM, Ahyow P, Meier A, Sandoval W, Yuk IH.

Biotechnol Bioeng. 2019 Apr;116(4):831-845. doi: 10.1002/bit.26908. Epub 2019 Feb 4.


Discovery and Qualification of Candidate Urinary Biomarkers of Disease Activity in Lupus Nephritis.

Anania VG, Yu K, Pingitore F, Li Q, Rose CM, Liu P, Sandoval W, Herman AE, Lill JR, Mathews WR.

J Proteome Res. 2019 Mar 1;18(3):1264-1277. doi: 10.1021/acs.jproteome.8b00874. Epub 2019 Jan 3.


TomahaqCompanion: A Tool for the Creation and Analysis of Isobaric Label Based Multiplexed Targeted Assays.

Rose CM, Erickson BK, Schweppe DK, Viner R, Choi J, Rogers J, Bomgarden R, Gygi SP, Kirkpatrick DS.

J Proteome Res. 2019 Feb 1;18(2):594-605. doi: 10.1021/acs.jproteome.8b00767. Epub 2018 Dec 12.


Chronic platelet-derived growth factor receptor signaling exerts control over initiation of protein translation in glioma.

Zhou S, Appleman VA, Rose CM, Jun HJ, Yang J, Zhou Y, Bronson RT, Gygi SP, Charest A.

Life Sci Alliance. 2018 Jun 19;1(3):e201800029. doi: 10.26508/lsa.201800029. eCollection 2018 Jun.


A PDGFRα-driven mouse model of glioblastoma reveals a stathmin1-mediated mechanism of sensitivity to vinblastine.

Jun HJ, Appleman VA, Wu HJ, Rose CM, Pineda JJ, Yeo AT, Delcuze B, Lee C, Gyuris A, Zhu H, Woolfenden S, Bronisz A, Nakano I, Chiocca EA, Bronson RT, Ligon KL, Sarkaria JN, Gygi SP, Michor F, Mitchison TJ, Charest A.

Nat Commun. 2018 Aug 6;9(1):3116. doi: 10.1038/s41467-018-05036-4.


Beverage consumption patterns among 4-19 y old children in 2009-14 NHANES show that the milk and 100% juice pattern is associated with better diets.

Maillot M, Rehm CD, Vieux F, Rose CM, Drewnowski A.

Nutr J. 2018 May 24;17(1):54. doi: 10.1186/s12937-018-0363-9.


Investigation into the role of the germline epigenome in the transmission of glucocorticoid-programmed effects across generations.

Cartier J, Smith T, Thomson JP, Rose CM, Khulan B, Heger A, Meehan RR, Drake AJ.

Genome Biol. 2018 Apr 10;19(1):50. doi: 10.1186/s13059-018-1422-4.


Compositional Proteomics: Effects of Spatial Constraints on Protein Quantification Utilizing Isobaric Tags.

O'Brien JJ, O'Connell JD, Paulo JA, Thakurta S, Rose CM, Weekes MP, Huttlin EL, Gygi SP.

J Proteome Res. 2018 Jan 5;17(1):590-599. doi: 10.1021/acs.jproteome.7b00699. Epub 2017 Dec 15.


Prolonged Mek1/2 suppression impairs the developmental potential of embryonic stem cells.

Choi J, Huebner AJ, Clement K, Walsh RM, Savol A, Lin K, Gu H, Di Stefano B, Brumbaugh J, Kim SY, Sharif J, Rose CM, Mohammad A, Odajima J, Charron J, Shioda T, Gnirke A, Gygi S, Koseki H, Sadreyev RI, Xiao A, Meissner A, Hochedlinger K.

Nature. 2017 Aug 10;548(7666):219-223. doi: 10.1038/nature23274. Epub 2017 Jul 26.


Acromelia-oligodontia syndrome.

Talasila J, Pachigolla R, Yarlagadda KVSN, Vuppala R, Grzeschik KH, Kiran K V S S, Rose CM, Gottesman GS, Urban Z.

Clin Case Rep. 2017 May 5;5(6):968-974. doi: 10.1002/ccr3.956. eCollection 2017 Jun.


DUSP9 Modulates DNA Hypomethylation in Female Mouse Pluripotent Stem Cells.

Choi J, Clement K, Huebner AJ, Webster J, Rose CM, Brumbaugh J, Walsh RM, Lee S, Savol A, Etchegaray JP, Gu H, Boyle P, Elling U, Mostoslavsky R, Sadreyev R, Park PJ, Gygi SP, Meissner A, Hochedlinger K.

Cell Stem Cell. 2017 May 4;20(5):706-719.e7. doi: 10.1016/j.stem.2017.03.002. Epub 2017 Mar 30.


Dietary patterns in infancy are associated with child diet and weight outcomes at 6 years.

Rose CM, Birch LL, Savage JS.

Int J Obes (Lond). 2017 May;41(5):783-788. doi: 10.1038/ijo.2017.27. Epub 2017 Feb 28.


A Strategy to Combine Sample Multiplexing with Targeted Proteomics Assays for High-Throughput Protein Signature Characterization.

Erickson BK, Rose CM, Braun CR, Erickson AR, Knott J, McAlister GC, Wühr M, Paulo JA, Everley RA, Gygi SP.

Mol Cell. 2017 Jan 19;65(2):361-370. doi: 10.1016/j.molcel.2016.12.005. Epub 2017 Jan 5.


Highly Multiplexed Quantitative Mass Spectrometry Analysis of Ubiquitylomes.

Rose CM, Isasa M, Ordureau A, Prado MA, Beausoleil SA, Jedrychowski MP, Finley DJ, Harper JW, Gygi SP.

Cell Syst. 2016 Oct 26;3(4):395-403.e4. doi: 10.1016/j.cels.2016.08.009. Epub 2016 Sep 22.


The rise in bilateral mastectomies: Evidence, ethics, and physician's role.

Yang YT, Pike ER, Rose CM, Botnick LE.

Breast. 2016 Oct;29:160-2. doi: 10.1016/j.breast.2016.07.024. Epub 2016 Aug 9.


Open-label randomized trial of titrated disease management for patients with hypertension: Study design and baseline sample characteristics.

Jackson GL, Weinberger M, Kirshner MA, Stechuchak KM, Melnyk SD, Bosworth HB, Coffman CJ, Neelon B, Van Houtven C, Gentry PW, Morris IJ, Rose CM, Taylor JP, May CL, Han B, Wainwright C, Alkon A, Powell L, Edelman D.

Contemp Clin Trials. 2016 Sep;50:5-15. doi: 10.1016/j.cct.2016.07.009. Epub 2016 Jul 12.


NeuCode Proteomics Reveals Bap1 Regulation of Metabolism.

Baughman JM, Rose CM, Kolumam G, Webster JD, Wilkerson EM, Merrill AE, Rhoads TW, Noubade R, Katavolos P, Lesch J, Stapleton DS, Rabaglia ME, Schueler KL, Asuncion R, Domeyer M, Zavala-Solorio J, Reich M, DeVoss J, Keller MP, Attie AD, Hebert AS, Westphall MS, Coon JJ, Kirkpatrick DS, Dey A.

Cell Rep. 2016 Jul 12;16(2):583-595. doi: 10.1016/j.celrep.2016.05.096. Epub 2016 Jun 30.


PTP1B controls non-mitochondrial oxygen consumption by regulating RNF213 to promote tumour survival during hypoxia.

Banh RS, Iorio C, Marcotte R, Xu Y, Cojocari D, Rahman AA, Pawling J, Zhang W, Sinha A, Rose CM, Isasa M, Zhang S, Wu R, Virtanen C, Hitomi T, Habu T, Sidhu SS, Koizumi A, Wilkins SE, Kislinger T, Gygi SP, Schofield CJ, Dennis JW, Wouters BG, Neel BG.

Nat Cell Biol. 2016 Jul;18(7):803-813. doi: 10.1038/ncb3376. Epub 2016 Jun 20.


Temple-Baraitser Syndrome and Zimmermann-Laband Syndrome: one clinical entity?

Mégarbané A, Al-Ali R, Choucair N, Lek M, Wang E, Ladjimi M, Rose CM, Hobeika R, Macary Y, Temanni R, Jithesh PV, Chouchane A, Sastry KS, Thomas R, Tomei S, Liu W, Marincola FM, MacArthur D, Chouchane L.

BMC Med Genet. 2016 Jun 10;17(1):42. doi: 10.1186/s12881-016-0304-4.


Glucocorticoids accelerate maturation of the heme pathway in fetal liver through effects on transcription and DNA methylation.

Khulan B, Liu L, Rose CM, Boyle AK, Manning JR, Drake AJ.

Epigenetics. 2016;11(2):103-9. doi: 10.1080/15592294.2016.1144006. Epub 2016 Feb 18.


Neucode Labels for Multiplexed, Absolute Protein Quantification.

Potts GK, Voigt EA, Bailey DJ, Rose CM, Westphall MS, Hebert AS, Yin J, Coon JJ.

Anal Chem. 2016 Mar 15;88(6):3295-303. doi: 10.1021/acs.analchem.5b04773. Epub 2016 Feb 25.


Patterns of early dietary exposures have implications for maternal and child weight outcomes.

Rose CM, Savage JS, Birch LL.

Obesity (Silver Spring). 2016 Feb;24(2):430-8. doi: 10.1002/oby.21349. Epub 2015 Dec 31.


Multiplexed, Proteome-Wide Protein Expression Profiling: Yeast Deubiquitylating Enzyme Knockout Strains.

Isasa M, Rose CM, Elsasser S, Navarrete-Perea J, Paulo JA, Finley DJ, Gygi SP.

J Proteome Res. 2015 Dec 4;14(12):5306-17. doi: 10.1021/acs.jproteome.5b00802. Epub 2015 Nov 4.


The Negative Mode Proteome with Activated Ion Negative Electron Transfer Dissociation (AI-NETD).

Riley NM, Rush MJ, Rose CM, Richards AL, Kwiecien NW, Bailey DJ, Hebert AS, Westphall MS, Coon JJ.

Mol Cell Proteomics. 2015 Oct;14(10):2644-60. doi: 10.1074/mcp.M115.049726. Epub 2015 Jul 20.


Potential regulatory phosphorylation sites in a Medicago truncatula plasma membrane proton pump implicated during early symbiotic signaling in roots.

Nguyen TT, Volkening JD, Rose CM, Venkateshwaran M, Westphall MS, Coon JJ, Ané JM, Sussman MR.

FEBS Lett. 2015 Aug 4;589(17):2186-93. doi: 10.1016/j.febslet.2015.06.035. Epub 2015 Jul 17.


A calibration routine for efficient ETD in large-scale proteomics.

Rose CM, Rush MJ, Riley NM, Merrill AE, Kwiecien NW, Holden DD, Mullen C, Westphall MS, Coon JJ.

J Am Soc Mass Spectrom. 2015 Nov;26(11):1848-57. doi: 10.1007/s13361-015-1183-1. Epub 2015 Jun 26.


Breastfeeding outcome comparison by parity.

Hackman NM, Schaefer EW, Beiler JS, Rose CM, Paul IM.

Breastfeed Med. 2015 Apr;10(3):156-62. doi: 10.1089/bfm.2014.0119. Epub 2014 Dec 30.


Short-term testosterone manipulations do not affect cognition or motor function but differentially modulate emotions in young and older male rhesus monkeys.

Kelly B, Maguire-Herring V, Rose CM, Gore HE, Ferrigno S, Novak MA, Lacreuse A.

Horm Behav. 2014 Nov;66(5):731-42. doi: 10.1016/j.yhbeh.2014.08.016. Epub 2014 Oct 13.


Dynamic changes in DNA modification states during late gestation male germ line development in the rat.

Rose CM, van den Driesche S, Sharpe RM, Meehan RR, Drake AJ.

Epigenetics Chromatin. 2014 Aug 7;7:19. doi: 10.1186/1756-8935-7-19. eCollection 2014.


NeuCode labels for relative protein quantification.

Merrill AE, Hebert AS, MacGilvray ME, Rose CM, Bailey DJ, Bradley JC, Wood WW, El Masri M, Westphall MS, Gasch AP, Coon JJ.

Mol Cell Proteomics. 2014 Sep;13(9):2503-12. doi: 10.1074/mcp.M114.040287. Epub 2014 Jun 17.


Neutron-encoded mass signatures for quantitative top-down proteomics.

Rhoads TW, Rose CM, Bailey DJ, Riley NM, Molden RC, Nestler AJ, Merrill AE, Smith LM, Hebert AS, Westphall MS, Pagliarini DJ, Garcia BA, Coon JJ.

Anal Chem. 2014 Mar 4;86(5):2314-9. doi: 10.1021/ac403579s. Epub 2014 Feb 19.


F-box protein FBXL16 binds PP2A-B55α and regulates differentiation of embryonic stem cells along the FLK1+ lineage.

Honarpour N, Rose CM, Brumbaugh J, Anderson J, Graham RL, Sweredoski MJ, Hess S, Coon JJ, Deshaies RJ.

Mol Cell Proteomics. 2014 Mar;13(3):780-91. doi: 10.1074/mcp.M113.031765. Epub 2014 Jan 5.


Neutron-encoded signatures enable product ion annotation from tandem mass spectra.

Richards AL, Vincent CE, Guthals A, Rose CM, Westphall MS, Bandeira N, Coon JJ.

Mol Cell Proteomics. 2013 Dec;12(12):3812-23. doi: 10.1074/mcp.M113.028951. Epub 2013 Sep 16.


Practice-based evidence to evidence-based practice: building the National Radiation Oncology Registry.

Efstathiou JA, Nassif DS, McNutt TR, Bogardus CB, Bosch W, Carlin J, Chen RC, Chou H, Eggert D, Fraass BA, Goldwein J, Hoffman KE, Hotz K, Hunt M, Kessler M, Lawton CA, Mayo C, Michalski JM, Mutic S, Potters L, Rose CM, Sandler HM, Sharp G, Tomé W, Tran PT, Wall T, Zietman AL, Gabriel PE, Bekelman JE.

J Oncol Pract. 2013 May;9(3):e90-5. doi: 10.1200/JOP.2013.001003. Erratum in: J Oncol Pract. 2013 Jul;9(4):222.


The Cholesterol, Hypertension, And Glucose Education (CHANGE) study: results from a randomized controlled trial in African Americans with diabetes.

Crowley MJ, Powers BJ, Olsen MK, Grubber JM, Koropchak C, Rose CM, Gentry P, Bowlby L, Trujillo G, Maciejewski ML, Bosworth HB.

Am Heart J. 2013 Jul;166(1):179-86. doi: 10.1016/j.ahj.2013.04.004. Epub 2013 May 17.


Epigenetic reprogramming: preparing the epigenome for the next generation.

Rose CM, van den Driesche S, Meehan RR, Drake AJ.

Biochem Soc Trans. 2013 Jun;41(3):809-14. doi: 10.1042/BST20120356. Review.


Activated ion ETD performed in a modified collision cell on a hybrid QLT-Oribtrap mass spectrometer.

Ledvina AR, Rose CM, McAlister GC, Syka JE, Westphall MS, Griep-Raming J, Schwartz JC, Coon JJ.

J Am Soc Mass Spectrom. 2013 Nov;24(11):1623-33. doi: 10.1007/s13361-013-0621-1. Epub 2013 May 16.

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