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The XFP (17-BM) beamline for X-ray footprinting at NSLS-II.

Asuru A, Farquhar ER, Sullivan M, Abel D, Toomey J, Chance MR, Bohon J.

J Synchrotron Radiat. 2019 Jul 1;26(Pt 4):1388-1399. doi: 10.1107/S1600577519003576. Epub 2019 Jun 4.


Interplay of transcriptional signaling by progesterone, cyclic AMP, and inflammation in myometrial cells: implications for the control of human parturition.

Stanfield Z, Amini P, Wang J, Yi L, Tan H, Chance MR, Koyutürk M, Mesiano S.

Mol Hum Reprod. 2019 Jul 1;25(7):408-422. doi: 10.1093/molehr/gaz028.


Corrigendum: Myometrial Transcriptional Signatures of Human Parturition.

Stanfield Z, Lai PF, Lei K, Johnson MR, Blanks AM, Romero R, Chance MR, Mesiano S, Koyutürk M.

Front Genet. 2019 May 28;10:515. doi: 10.3389/fgene.2019.00515. eCollection 2019.


Assembly of a GPCR-G Protein Complex.

Du Y, Duc NM, Rasmussen SGF, Hilger D, Kubiak X, Wang L, Bohon J, Kim HR, Wegrecki M, Asuru A, Jeong KM, Lee J, Chance MR, Lodowski DT, Kobilka BK, Chung KY.

Cell. 2019 May 16;177(5):1232-1242.e11. doi: 10.1016/j.cell.2019.04.022. Epub 2019 May 9.


Myometrial Transcriptional Signatures of Human Parturition.

Stanfield Z, Lai PF, Lei K, Johnson MR, Blanks AM, Romero R, Chance MR, Mesiano S, Koyutürk M.

Front Genet. 2019 Apr 1;10:185. doi: 10.3389/fgene.2019.00185. eCollection 2019. Erratum in: Front Genet. 2019 May 28;10:515.


CoPhosK: A method for comprehensive kinase substrate annotation using co-phosphorylation analysis.

Ayati M, Wiredja D, Schlatzer D, Maxwell S, Li M, Koyutürk M, Chance MR.

PLoS Comput Biol. 2019 Feb 27;15(2):e1006678. doi: 10.1371/journal.pcbi.1006678. eCollection 2019 Feb.


A Metastable Contact and Structural Disorder in the Estrogen Receptor Transactivation Domain.

Peng Y, Cao S, Kiselar J, Xiao X, Du Z, Hsieh A, Ko S, Chen Y, Agrawal P, Zheng W, Shi W, Jiang W, Yang L, Chance MR, Surewicz WK, Buck M, Yang S.

Structure. 2019 Feb 5;27(2):229-240.e4. doi: 10.1016/j.str.2018.10.026. Epub 2018 Dec 20.


Multidomain architecture of estrogen receptor reveals interfacial cross-talk between its DNA-binding and ligand-binding domains.

Huang W, Peng Y, Kiselar J, Zhao X, Albaqami A, Mendez D, Chen Y, Chakravarthy S, Gupta S, Ralston C, Kao HY, Chance MR, Yang S.

Nat Commun. 2018 Aug 30;9(1):3520. doi: 10.1038/s41467-018-06034-2.


High-Resolution Hydroxyl Radical Protein Footprinting: Biophysics Tool for Drug Discovery.

Kiselar J, Chance MR.

Annu Rev Biophys. 2018 Mar 14. doi: 10.1146/annurev-biophys-070317-033123. [Epub ahead of print]


Integrated microRNA and mRNA network analysis of the human myometrial transcriptome in the transition from quiescence to labor.

Ackerman WE 4th, Buhimschi IA, Brubaker D, Maxwell S, Rood KM, Chance MR, Jing H, Mesiano S, Buhimschi CS.

Biol Reprod. 2018 Jun 1;98(6):834-845. doi: 10.1093/biolre/ioy040.


A Practical Guide to iSPOT Modeling: An Integrative Structural Biology Platform.

Hsieh A, Lu L, Chance MR, Yang S.

Adv Exp Med Biol. 2017;1009:229-238. doi: 10.1007/978-981-10-6038-0_14.


Proteomics and Network Analyses Reveal Inhibition of Akt-mTOR Signaling in CD4+ T Cells by Mycobacterium tuberculosis Mannose-Capped Lipoarabinomannan.

Karim AF, Sande OJ, Tomechko SE, Ding X, Li M, Maxwell S, Ewing RM, Harding CV, Rojas RE, Chance MR, Boom WH.

Proteomics. 2017 Nov;17(22). doi: 10.1002/pmic.201700233.


Phosphoproteomics Profiling of Nonsmall Cell Lung Cancer Cells Treated with a Novel Phosphatase Activator.

Wiredja DD, Ayati M, Mazhar S, Sangodkar J, Maxwell S, Schlatzer D, Narla G, Koyutürk M, Chance MR.

Proteomics. 2017 Nov;17(22). doi: 10.1002/pmic.201700214. Epub 2017 Oct 25. Erratum in: Proteomics. 2018 Dec;18(24):e1870214.


Regulation of endothelial hemoglobin alpha expression by Kruppel-like factors.

Sangwung P, Zhou G, Lu Y, Liao X, Wang B, Mutchler SM, Miller M, Chance MR, Straub AC, Jain MK.

Vasc Med. 2017 Oct;22(5):363-369. doi: 10.1177/1358863X17722211. Epub 2017 Aug 19.


The KSEA App: a web-based tool for kinase activity inference from quantitative phosphoproteomics.

Wiredja DD, Koyutürk M, Chance MR.

Bioinformatics. 2017 Jun 26. doi: 10.1093/bioinformatics/btx415. [Epub ahead of print]


Proteomic profiling of the hypothalamus in two mouse models of narcolepsy.

Azzam S, Schlatzer D, Nethery D, Saleh D, Li X, Akladious A, Chance MR, Strohl KP.

Proteomics. 2017 Jul;17(13-14). doi: 10.1002/pmic.201600478. Epub 2017 Jun 26.


Activation of tumor suppressor protein PP2A inhibits KRAS-driven tumor growth.

Sangodkar J, Perl A, Tohme R, Kiselar J, Kastrinsky DB, Zaware N, Izadmehr S, Mazhar S, Wiredja DD, O'Connor CM, Hoon D, Dhawan NS, Schlatzer D, Yao S, Leonard D, Borczuk AC, Gokulrangan G, Wang L, Svenson E, Farrington CC, Yuan E, Avelar RA, Stachnik A, Smith B, Gidwani V, Giannini HM, McQuaid D, McClinch K, Wang Z, Levine AC, Sears RC, Chen EY, Duan Q, Datt M, Haider S, Ma'ayan A, DiFeo A, Sharma N, Galsky MD, Brautigan DL, Ioannou YA, Xu W, Chance MR, Ohlmeyer M, Narla G.

J Clin Invest. 2017 Jun 1;127(6):2081-2090. doi: 10.1172/JCI89548. Epub 2017 May 15.


A Targeted Mass Spectrometry Assay for Detection of HIV Gag Protein Following Induction of Latent Viral Reservoirs.

Schlatzer D, Haqqani AA, Li X, Dobrowolski C, Chance MR, Tilton JC.

Anal Chem. 2017 May 16;89(10):5325-5332. doi: 10.1021/acs.analchem.6b05070. Epub 2017 May 3.


Linearity of network proximity measures: implications for set-based queries and significance testing.

Maxwell S, Chance MR, Koyutürk M.

Bioinformatics. 2017 May 1;33(9):1354-1361. doi: 10.1093/bioinformatics/btw733.


Proteome and Protein Network Analyses of Memory T Cells Find Altered Translation and Cell Stress Signaling in Treated Human Immunodeficiency Virus Patients Exhibiting Poor CD4 Recovery.

Azzam S, Schlatzer D, Maxwell S, Li X, Bazdar D, Chen Y, Asaad R, Barnholtz-Sloan J, Chance MR, Sieg SF.

Open Forum Infect Dis. 2016 Mar 15;3(2):ofw037. doi: 10.1093/ofid/ofw037. eCollection 2016 Mar.


Protein Footprinting Comes of Age: Mass Spectrometry for Biophysical Structure Assessment.

Wang L, Chance MR.

Mol Cell Proteomics. 2017 May;16(5):706-716. doi: 10.1074/mcp.O116.064386. Epub 2017 Mar 8. Review.


Structural basis of ligand interaction with atypical chemokine receptor 3.

Gustavsson M, Wang L, van Gils N, Stephens BS, Zhang P, Schall TJ, Yang S, Abagyan R, Chance MR, Kufareva I, Handel TM.

Nat Commun. 2017 Jan 18;8:14135. doi: 10.1038/ncomms14135.


Finding lost genes in GWAS via integrative-omics analysis reveals novel sub-networks associated with preterm birth.

Brubaker D, Liu Y, Wang J, Tan H, Zhang G, Jacobsson B, Muglia L, Mesiano S, Chance MR.

Hum Mol Genet. 2016 Dec 1;25(23):5254-5264. doi: 10.1093/hmg/ddw325.


During Hepatitis C Virus (HCV) Infection and HCV-HIV Coinfection, an Elevated Plasma Level of Autotaxin Is Associated With Lysophosphatidic Acid and Markers of Immune Activation That Normalize During Interferon-Free HCV Therapy.

Kostadinova L, Shive CL, Judge C, Zebrowski E, Compan A, Rife K, Hirsch A, Falck-Ytter Y, Schlatzer DM, Li X, Chance MR, Rodriguez B, Popkin DL, Anthony DD.

J Infect Dis. 2016 Nov 1;214(9):1438-1448. Epub 2016 Aug 17.


Probing the structure of ribosome assembly intermediates in vivo using DMS and hydroxyl radical footprinting.

Hulscher RM, Bohon J, Rappé MC, Gupta S, D'Mello R, Sullivan M, Ralston CY, Chance MR, Woodson SA.

Methods. 2016 Jul 1;103:49-56. doi: 10.1016/j.ymeth.2016.03.012. Epub 2016 Mar 22.


Apigenin blocks IKKα activation and suppresses prostate cancer progression.

Shukla S, Kanwal R, Shankar E, Datt M, Chance MR, Fu P, MacLennan GT, Gupta S.

Oncotarget. 2015 Oct 13;6(31):31216-32. doi: 10.18632/oncotarget.5157.


Proteomic and bioinformatics profile of paired human alveolar macrophages and peripheral blood monocytes.

Tomechko SE, Lundberg KC, Jarvela J, Bebek G, Chesnokov NG, Schlatzer D, Ewing RM, Boom WH, Chance MR, Silver RF.

Proteomics. 2015 Nov;15(22):3797-805. doi: 10.1002/pmic.201400496.


MOBAS: identification of disease-associated protein subnetworks using modularity-based scoring.

Ayati M, Erten S, Chance MR, Koyutürk M.

EURASIP J Bioinform Syst Biol. 2015 Jun 30;2015:7. doi: 10.1186/s13637-015-0025-6. eCollection 2015 Dec.


Characterizing monoclonal antibody structure by carboxyl group footprinting.

Kaur P, Tomechko SE, Kiselar J, Shi W, Deperalta G, Wecksler AT, Gokulrangan G, Ling V, Chance MR.

MAbs. 2015;7(3):540-52. doi: 10.1080/19420862.2015.1023683.


Phosphorylation of HEXIM1 at Tyr271 and Tyr274 Promotes Release of P-TEFb from the 7SK snRNP Complex and Enhances Proviral HIV Gene Expression.

Mbonye UR, Wang B, Gokulrangan G, Chance MR, Karn J.

Proteomics. 2015 Jun;15(12):2078-86. doi: 10.1002/pmic.201500038. Epub 2015 May 15. Erratum in: Proteomics. 2016 Aug;16(15-16):2302.


Detection of structural waters and their role in structural dynamics of rhodopsin activation.

Wang L, Chance MR.

Methods Mol Biol. 2015;1271:97-111. doi: 10.1007/978-1-4939-2330-4_7.


Quantitative protein topography analysis and high-resolution structure prediction using hydroxyl radical labeling and tandem-ion mass spectrometry (MS).

Kaur P, Kiselar J, Yang S, Chance MR.

Mol Cell Proteomics. 2015 Apr;14(4):1159-68. doi: 10.1074/mcp.O114.044362. Epub 2015 Feb 16.


Acetyl-L-carnitine increases mitochondrial protein acetylation in the aged rat heart.

Kerner J, Yohannes E, Lee K, Virmani A, Koverech A, Cavazza C, Chance MR, Hoppel C.

Mech Ageing Dev. 2015 Jan;145:39-50. doi: 10.1016/j.mad.2015.01.003. Epub 2015 Feb 7.


Tissue specific dysregulated protein subnetworks in type 2 diabetic bladder urothelium and detrusor muscle.

Tomechko SE, Liu G, Tao M, Schlatzer D, Powell CT, Gupta S, Chance MR, Daneshgari F.

Mol Cell Proteomics. 2015 Mar;14(3):635-45. doi: 10.1074/mcp.M114.041863. Epub 2015 Jan 8.


Quantitative mapping of protein structure by hydroxyl radical footprinting-mediated structural mass spectrometry: a protection factor analysis.

Huang W, Ravikumar KM, Chance MR, Yang S.

Biophys J. 2015 Jan 6;108(1):107-15. doi: 10.1016/j.bpj.2014.11.013. Erratum in: Biophys J. 2015 Feb 3;108(3):780.


Characterizing monoclonal antibody structure by carbodiimide/GEE footprinting.

Kaur P, Tomechko S, Kiselar J, Shi W, Deperalta G, Wecksler AT, Gokulrangan G, Ling V, Chance MR.

MAbs. 2014;6(6):1486-99. doi: 10.4161/19420862.2014.975096. Retraction in: MAbs. 2015;7(3):651.


A synchrotron-based hydroxyl radical footprinting analysis of amyloid fibrils and prefibrillar intermediates with residue-specific resolution.

Klinger AL, Kiselar J, Ilchenko S, Komatsu H, Chance MR, Axelsen PH.

Biochemistry. 2014 Dec 16;53(49):7724-34. doi: 10.1021/bi5010409. Epub 2014 Dec 3.


Proteomics of skin proteins in psoriasis: from discovery and verification in a mouse model to confirmation in humans.

Lundberg KC, Fritz Y, Johnston A, Foster AM, Baliwag J, Gudjonsson JE, Schlatzer D, Gokulrangan G, McCormick TS, Chance MR, Ward NL.

Mol Cell Proteomics. 2015 Jan;14(1):109-19. doi: 10.1074/mcp.M114.042242. Epub 2014 Oct 28.


Integrating phosphoproteomics in systems biology.

Liu Y, Chance MR.

Comput Struct Biotechnol J. 2014 Aug 1;10(17):90-7. doi: 10.1016/j.csbj.2014.07.003. eCollection 2014 Jul. Review.


Electron microscopic and proteomic comparison of terminal branches of the trigeminal nerve in patients with and without migraine headaches.

Guyuron B, Yohannes E, Miller R, Chim H, Reed D, Chance MR.

Plast Reconstr Surg. 2014 Nov;134(5):796e-805e. doi: 10.1097/PRS.0000000000000696.


Crystal structure of Clostridium acetobutylicum Aspartate kinase (CaAK): An important allosteric enzyme for amino acids production.

Manjasetty BA, Chance MR, Burley SK, Panjikar S, Almo SC.

Biotechnol Rep (Amst). 2014 Sep 1;3:73-85.


Discovery of common sequences absent in the human reference genome using pooled samples from next generation sequencing.

Liu Y, Koyutürk M, Maxwell S, Xiang M, Veigl M, Cooper RS, Tayo BO, Li L, LaFramboise T, Wang Z, Zhu X, Chance MR.

BMC Genomics. 2014 Aug 16;15:685. doi: 10.1186/1471-2164-15-685.


Visualizing the kinetic power stroke that drives proton-coupled zinc(II) transport.

Gupta S, Chai J, Cheng J, D'Mello R, Chance MR, Fu D.

Nature. 2014 Aug 7;512(7512):101-4. doi: 10.1038/nature13382. Epub 2014 Jun 22.


Development of a microsecond X-ray protein footprinting facility at the Advanced Light Source.

Gupta S, Celestre R, Petzold CJ, Chance MR, Ralston C.

J Synchrotron Radiat. 2014 Jul;21(Pt 4):690-9. doi: 10.1107/S1600577514007000. Epub 2014 May 16.


Multiple glycosaminoglycan-binding epitopes of monocyte chemoattractant protein-3/CCL7 enable it to function as a non-oligomerizing chemokine.

Salanga CL, Dyer DP, Kiselar JG, Gupta S, Chance MR, Handel TM.

J Biol Chem. 2014 May 23;289(21):14896-912. doi: 10.1074/jbc.M114.547737. Epub 2014 Apr 11.


Reliable determination of site-specific in vivo protein N-glycosylation based on collision-induced MS/MS and chromatographic retention time.

Wang B, Tsybovsky Y, Palczewski K, Chance MR.

J Am Soc Mass Spectrom. 2014 May;25(5):729-41. doi: 10.1007/s13361-013-0823-6. Epub 2014 Feb 19.


Synchrotron X-ray footprinting on tour.

Bohon J, D'Mello R, Ralston C, Gupta S, Chance MR.

J Synchrotron Radiat. 2014 Jan;21(Pt 1):24-31. doi: 10.1107/S1600577513024715. Epub 2013 Nov 2.


Pathway analyses and understanding disease associations.

Liu Y, Chance MR.

Curr Genet Med Rep. 2013 Dec 1;1(4). doi: 10.1007/s40142-013-0025-3.


SAHA enhances Proteostasis of epilepsy-associated α1(A322D)β2γ2 GABA(A) receptors.

Di XJ, Han DY, Wang YJ, Chance MR, Mu TW.

Chem Biol. 2013 Dec 19;20(12):1456-68. doi: 10.1016/j.chembiol.2013.09.020. Epub 2013 Nov 7.

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