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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.


MAPPs for the identification of immunogenic hotspots of biotherapeutics; an overview of the technology and its application to the biopharmaceutical arena.

Quarmby V, Phung QT, Lill JR.

Expert Rev Proteomics. 2018 Sep;15(9):733-748. doi: 10.1080/14789450.2018.1521279. Epub 2018 Sep 17.


Microwave-Assisted Protein Staining, Destaining, and In-Gel/In-Solution Digestion of Proteins.

Lill JR, Nesatyy VJ.

Methods Mol Biol. 2018;1853:75-86. doi: 10.1007/978-1-4939-8745-0_10.


Minimal Information About an Immuno-Peptidomics Experiment (MIAIPE).

Lill JR, van Veelen PA, Tenzer S, Admon A, Caron E, Elias JE, Heck AJR, Marcilla M, Marino F, Müller M, Peters B, Purcell A, Sette A, Sturm T, Ternette N, Vizcaíno JA, Bassani-Sternberg M.

Proteomics. 2018 Jun;18(12):e1800110. doi: 10.1002/pmic.201800110.


MHC class I presented antigens from malignancies: A perspective on analytical characterization & immunogenicity.

Schmidt M, Lill JR.

J Proteomics. 2019 Jan 16;191:48-57. doi: 10.1016/j.jprot.2018.04.021. Epub 2018 Apr 24.


Tumor suppressor BAP1 is essential for thymic development and proliferative responses of T lymphocytes.

Arenzana TL, Lianoglou S, Seki A, Eidenschenk C, Cheung T, Seshasayee D, Hagenbeek T, Sambandam A, Noubade R, Peng I, Lesch J, DeVoss J, Wu X, Lee WP, Caplazi P, Webster J, Liu J, Pham VC, Arnott D, Lill JR, Modrusan Z, Dey A, Rutz S.

Sci Immunol. 2018 Apr 20;3(22). pii: eaal1953. doi: 10.1126/sciimmunol.aal1953.


The kinase TPL2 activates ERK and p38 signaling to promote neutrophilic inflammation.

Senger K, Pham VC, Varfolomeev E, Hackney JA, Corzo CA, Collier J, Lau VWC, Huang Z, Hamidzhadeh K, Caplazi P, Peng I, Setiadi AF, Francis R, Paler-Martinez A, Kwon YC, Ramirez-Carrozzi V, Sun Y, Grigg PW, Roose-Girma M, Jeet S, Barck KH, Pham A, Ota N, Ha C, Stinson J, Guillory J, Tam L, Modrusan Z, Emson C, McKenzie BS, Townsend MJ, Carano RAD, Warming S, Vucic D, DeVoss J, Lee WP, Lill JR, Zarrin AA.

Sci Signal. 2017 Apr 18;10(475). pii: eaah4273. doi: 10.1126/scisignal.aah4273.


Characterization of Chain Pairing Variants of Bispecific IgG Expressed in a Single Host Cell by High-Resolution Native and Denaturing Mass Spectrometry.

Schachner L, Han G, Dillon M, Zhou J, McCarty L, Ellerman D, Yin Y, Spiess C, Lill JR, Carter PJ, Sandoval W.

Anal Chem. 2016 Dec 20;88(24):12122-12127. doi: 10.1021/acs.analchem.6b02866. Epub 2016 Dec 8.


A Common Variant of IL-6R is Associated with Elevated IL-6 Pathway Activity in Alzheimer's Disease Brains.

Haddick PC, Larson JL, Rathore N, Bhangale TR, Phung QT, Srinivasan K, Hansen DV, Lill JR; Alzheimer’s Disease Genetic Consortium (ADGC), Alzheimer’s Disease Neuroimaging Initiative (ADNI), Pericak-Vance MA, Haines J, Farrer LA, Kauwe JS, Schellenberg GD, Cruchaga C, Goate AM, Behrens TW, Watts RJ, Graham RR, Kaminker JS, van der Brug M.

J Alzheimers Dis. 2017;56(3):1037-1054. doi: 10.3233/JAD-160524.


Building proteomic tool boxes to monitor MHC class I and class II peptides.

Schumacher FR, Delamarre L, Jhunjhunwala S, Modrusan Z, Phung QT, Elias JE, Lill JR.

Proteomics. 2017 Jan;17(1-2). doi: 10.1002/pmic.201600061. Review.


RIPK1 inhibits ZBP1-driven necroptosis during development.

Newton K, Wickliffe KE, Maltzman A, Dugger DL, Strasser A, Pham VC, Lill JR, Roose-Girma M, Warming S, Solon M, Ngu H, Webster JD, Dixit VM.

Nature. 2016 Dec 1;540(7631):129-133. doi: 10.1038/nature20559. Epub 2016 Nov 7.


De Novo MS/MS Sequencing of Native Human Antibodies.

Guthals A, Gan Y, Murray L, Chen Y, Stinson J, Nakamura G, Lill JR, Sandoval W, Bandeira N.

J Proteome Res. 2017 Jan 6;16(1):45-54. doi: 10.1021/acs.jproteome.6b00608. Epub 2016 Nov 2.


Rapid, semi-automated protein terminal characterization using ISDetect.

Bakalarski CE, Gan Y, Wertz I, Lill JR, Sandoval W.

Nat Biotechnol. 2016 Aug 9;34(8):811-3. doi: 10.1038/nbt.3621. No abstract available.


Uncovering a Dual Regulatory Role for Caspases During Endoplasmic Reticulum Stress-induced Cell Death.

Anania VG, Yu K, Gnad F, Pferdehirt RR, Li H, Ma TP, Jeon D, Fortelny N, Forrest W, Ashkenazi A, Overall CM, Lill JR.

Mol Cell Proteomics. 2016 Jul;15(7):2293-307. doi: 10.1074/mcp.M115.055376. Epub 2016 Apr 28.


Caspase-11 cleaves gasdermin D for non-canonical inflammasome signalling.

Kayagaki N, Stowe IB, Lee BL, O'Rourke K, Anderson K, Warming S, Cuellar T, Haley B, Roose-Girma M, Phung QT, Liu PS, Lill JR, Li H, Wu J, Kummerfeld S, Zhang J, Lee WP, Snipas SJ, Salvesen GS, Morris LX, Fitzgerald L, Zhang Y, Bertram EM, Goodnow CC, Dixit VM.

Nature. 2015 Oct 29;526(7575):666-71. doi: 10.1038/nature15541. Epub 2015 Sep 16.


Transcription Factor ATF4 Induces NLRP1 Inflammasome Expression during Endoplasmic Reticulum Stress.

D'Osualdo A, Anania VG, Yu K, Lill JR, Kaufman RJ, Matsuzawa S, Reed JC.

PLoS One. 2015 Jun 18;10(6):e0130635. doi: 10.1371/journal.pone.0130635. eCollection 2015.


SUMO deconjugation is required for arsenic-triggered ubiquitylation of PML.

Fasci D, Anania VG, Lill JR, Salvesen GS.

Sci Signal. 2015 Jun 9;8(380):ra56. doi: 10.1126/scisignal.aaa3929.


Proteomic tools for the characterization of cell death mechanisms in drug discovery.

Anania VG, Lill JR.

Proteomics Clin Appl. 2015 Aug;9(7-8):671-83. doi: 10.1002/prca.201400151. Epub 2015 May 3. Review.


HSP105 recruits protein phosphatase 2A to dephosphorylate β-catenin.

Yu N, Kakunda M, Pham V, Lill JR, Du P, Wongchenko M, Yan Y, Firestein R, Huang X.

Mol Cell Biol. 2015 Apr;35(8):1390-400. doi: 10.1128/MCB.01307-14. Epub 2015 Feb 2.


Deubiquitinase DUBA is a post-translational brake on interleukin-17 production in T cells.

Rutz S, Kayagaki N, Phung QT, Eidenschenk C, Noubade R, Wang X, Lesch J, Lu R, Newton K, Huang OW, Cochran AG, Vasser M, Fauber BP, DeVoss J, Webster J, Diehl L, Modrusan Z, Kirkpatrick DS, Lill JR, Ouyang W, Dixit VM.

Nature. 2015 Feb 19;518(7539):417-21. doi: 10.1038/nature13979. Epub 2014 Dec 3.


Predicting immunogenic tumour mutations by combining mass spectrometry and exome sequencing.

Yadav M, Jhunjhunwala S, Phung QT, Lupardus P, Tanguay J, Bumbaca S, Franci C, Cheung TK, Fritsche J, Weinschenk T, Modrusan Z, Mellman I, Lill JR, Delamarre L.

Nature. 2014 Nov 27;515(7528):572-6. doi: 10.1038/nature14001.


Evolutionary divergence in the catalytic activity of the CAM-1, ROR1 and ROR2 kinase domains.

Bainbridge TW, DeAlmeida VI, Izrael-Tomasevic A, Chalouni C, Pan B, Goldsmith J, Schoen AP, Quiñones GA, Kelly R, Lill JR, Sandoval W, Costa M, Polakis P, Arnott D, Rubinfeld B, Ernst JA.

PLoS One. 2014 Jul 16;9(7):e102695. doi: 10.1371/journal.pone.0102695. eCollection 2014.


Stable-isotope-labeled histone peptide library for histone post-translational modification and variant quantification by mass spectrometry.

Lin S, Wein S, Gonzales-Cope M, Otte GL, Yuan ZF, Afjehi-Sadat L, Maile T, Berger SL, Rush J, Lill JR, Arnott D, Garcia BA.

Mol Cell Proteomics. 2014 Sep;13(9):2450-66. doi: 10.1074/mcp.O113.036459. Epub 2014 Jul 7.


Complementary methods for the identification of substrates of proteolysis.

Pham VC, Anania VG, Phung QT, Lill JR.

Methods Enzymol. 2014;544:359-80. doi: 10.1016/B978-0-12-417158-9.00014-5.


Toward understanding ubiquitin-modifying enzymes: from pharmacological targeting to proteomics.

Lill JR, Wertz IE.

Trends Pharmacol Sci. 2014 Apr;35(4):187-207. doi: 10.1016/ Epub 2014 Apr 6. Review.


Endosomes are specialized platforms for bacterial sensing and NOD2 signalling.

Nakamura N, Lill JR, Phung Q, Jiang Z, Bakalarski C, de Mazière A, Klumperman J, Schlatter M, Delamarre L, Mellman I.

Nature. 2014 May 8;509(7499):240-4. doi: 10.1038/nature13133. Epub 2014 Mar 30.


Combinatorial approach for large-scale identification of linked peptides from tandem mass spectrometry spectra.

Wang J, Anania VG, Knott J, Rush J, Lill JR, Bourne PE, Bandeira N.

Mol Cell Proteomics. 2014 Apr;13(4):1128-36. doi: 10.1074/mcp.M113.035758. Epub 2014 Feb 3.


A turn-key approach for large-scale identification of complex posttranslational modifications.

Wang J, Anania VG, Knott J, Rush J, Lill JR, Bourne PE, Bandeira N.

J Proteome Res. 2014 Mar 7;13(3):1190-9. doi: 10.1021/pr400368u. Epub 2014 Jan 29.


Peptide level immunoaffinity enrichment enhances ubiquitination site identification on individual proteins.

Anania VG, Pham VC, Huang X, Masselot A, Lill JR, Kirkpatrick DS.

Mol Cell Proteomics. 2014 Jan;13(1):145-56. doi: 10.1074/mcp.M113.031062. Epub 2013 Oct 18.


Phosphoproteomic analysis implicates the mTORC2-FoxO1 axis in VEGF signaling and feedback activation of receptor tyrosine kinases.

Zhuang G, Yu K, Jiang Z, Chung A, Yao J, Ha C, Toy K, Soriano R, Haley B, Blackwood E, Sampath D, Bais C, Lill JR, Ferrara N.

Sci Signal. 2013 Apr 16;6(271):ra25. doi: 10.1126/scisignal.2003572.


A Novel Peptide-Based SILAC Method to Identify the Posttranslational Modifications Provides Evidence for Unconventional Ubiquitination in the ER-Associated Degradation Pathway.

Anania VG, Bustos DJ, Lill JR, Kirkpatrick DS, Coscoy L.

Int J Proteomics. 2013;2013:857918. doi: 10.1155/2013/857918. Epub 2013 Feb 3.


Phosphorylation of Dishevelled by protein kinase RIPK4 regulates Wnt signaling.

Huang X, McGann JC, Liu BY, Hannoush RN, Lill JR, Pham V, Newton K, Kakunda M, Liu J, Yu C, Hymowitz SG, Hongo JA, Wynshaw-Boris A, Polakis P, Harland RM, Dixit VM.

Science. 2013 Mar 22;339(6126):1441-5. doi: 10.1126/science.1232253. Epub 2013 Jan 31.


The chromosome-centric human proteome project: a call to action.

Hühmer AF, Paulus A, Martin LB, Millis K, Agreste T, Saba J, Lill JR, Fischer SM, Dracup W, Lavery P.

J Proteome Res. 2013 Jan 4;12(1):28-32. doi: 10.1021/pr300933p. Epub 2012 Dec 21.


Loss of the tumor suppressor BAP1 causes myeloid transformation.

Dey A, Seshasayee D, Noubade R, French DM, Liu J, Chaurushiya MS, Kirkpatrick DS, Pham VC, Lill JR, Bakalarski CE, Wu J, Phu L, Katavolos P, LaFave LM, Abdel-Wahab O, Modrusan Z, Seshagiri S, Dong K, Lin Z, Balazs M, Suriben R, Newton K, Hymowitz S, Garcia-Manero G, Martin F, Levine RL, Dixit VM.

Science. 2012 Sep 21;337(6101):1541-6. Epub 2012 Aug 9.


Microwave-assisted protein staining, destaining, and in-gel/in-solution digestion of proteins.

Lill JR, Nesatyy VJ.

Methods Mol Biol. 2012;869:521-32. doi: 10.1007/978-1-61779-821-4_46.


Complementary proteomic tools for the dissection of apoptotic proteolysis events.

Pham VC, Pitti R, Anania VG, Bakalarski CE, Bustos D, Jhunjhunwala S, Phung QT, Yu K, Forrest WF, Kirkpatrick DS, Ashkenazi A, Lill JR.

J Proteome Res. 2012 May 4;11(5):2947-54. doi: 10.1021/pr300035k. Epub 2012 Mar 29.


Polyubiquitination of insulin-like growth factor I receptor (IGF-IR) activation loop promotes antibody-induced receptor internalization and down-regulation.

Mao Y, Shang Y, Pham VC, Ernst JA, Lill JR, Scales SJ, Zha J.

J Biol Chem. 2011 Dec 2;286(48):41852-61. doi: 10.1074/jbc.M111.288514. Epub 2011 Oct 12.


Ubiquitin ligase RNF146 regulates tankyrase and Axin to promote Wnt signaling.

Callow MG, Tran H, Phu L, Lau T, Lee J, Sandoval WN, Liu PS, Bheddah S, Tao J, Lill JR, Hongo JA, Davis D, Kirkpatrick DS, Polakis P, Costa M.

PLoS One. 2011;6(7):e22595. doi: 10.1371/journal.pone.0022595. Epub 2011 Jul 25.


Deubiquitinase USP37 is activated by CDK2 to antagonize APC(CDH1) and promote S phase entry.

Huang X, Summers MK, Pham V, Lill JR, Liu J, Lee G, Kirkpatrick DS, Jackson PK, Fang G, Dixit VM.

Mol Cell. 2011 May 20;42(4):511-23. doi: 10.1016/j.molcel.2011.03.027.


Sensitivity to antitubulin chemotherapeutics is regulated by MCL1 and FBW7.

Wertz IE, Kusam S, Lam C, Okamoto T, Sandoval W, Anderson DJ, Helgason E, Ernst JA, Eby M, Liu J, Belmont LD, Kaminker JS, O'Rourke KM, Pujara K, Kohli PB, Johnson AR, Chiu ML, Lill JR, Jackson PK, Fairbrother WJ, Seshagiri S, Ludlam MJ, Leong KG, Dueber EC, Maecker H, Huang DC, Dixit VM.

Nature. 2011 Mar 3;471(7336):110-4. doi: 10.1038/nature09779. Erratum in: Nature. 2011 Jul 7;475(7354):122.


Resurrection of a clinical antibody: template proteogenomic de novo proteomic sequencing and reverse engineering of an anti-lymphotoxin-α antibody.

Castellana NE, McCutcheon K, Pham VC, Harden K, Nguyen A, Young J, Adams C, Schroeder K, Arnott D, Bafna V, Grogan JL, Lill JR.

Proteomics. 2011 Feb;11(3):395-405. doi: 10.1002/pmic.201000487. Epub 2011 Jan 5.


Comparative analysis of techniques to purify plasma membrane proteins.

Weekes MP, Antrobus R, Lill JR, Duncan LM, Hör S, Lehner PJ.

J Biomol Tech. 2010 Sep;21(3):108-15.


Template proteogenomics: sequencing whole proteins using an imperfect database.

Castellana NE, Pham V, Arnott D, Lill JR, Bafna V.

Mol Cell Proteomics. 2010 Jun;9(6):1260-70. doi: 10.1074/mcp.M900504-MCP200. Epub 2010 Feb 17.


Deubiquitinase USP9X stabilizes MCL1 and promotes tumour cell survival.

Schwickart M, Huang X, Lill JR, Liu J, Ferrando R, French DM, Maecker H, O'Rourke K, Bazan F, Eastham-Anderson J, Yue P, Dornan D, Huang DC, Dixit VM.

Nature. 2010 Jan 7;463(7277):103-7. doi: 10.1038/nature08646. Epub 2009 Dec 20.


Cullin3-based polyubiquitination and p62-dependent aggregation of caspase-8 mediate extrinsic apoptosis signaling.

Jin Z, Li Y, Pitti R, Lawrence D, Pham VC, Lill JR, Ashkenazi A.

Cell. 2009 May 15;137(4):721-35. doi: 10.1016/j.cell.2009.03.015. Epub 2009 May 7.


Targeting interferon alpha subtypes in serum: a comparison of analytical approaches to the detection and quantitation of proteins in complex biological matrices.

Izrael-Tomasevic A, Phu L, Phung QT, Lill JR, Arnott D.

J Proteome Res. 2009 Jun;8(6):3132-40. doi: 10.1021/pr900076q.


The double-histone-acetyltransferase complex ATAC is essential for mammalian development.

Guelman S, Kozuka K, Mao Y, Pham V, Solloway MJ, Wang J, Wu J, Lill JR, Zha J.

Mol Cell Biol. 2009 Mar;29(5):1176-88. doi: 10.1128/MCB.01599-08. Epub 2008 Dec 22.


Automated de novo protein sequencing of monoclonal antibodies.

Bandeira N, Pham V, Pevzner P, Arnott D, Lill JR.

Nat Biotechnol. 2008 Dec;26(12):1336-8. doi: 10.1038/nbt1208-1336. No abstract available.


Recent developments in microwave-assisted protein chemistries - can this be integrated into the drug discovery and validation process?

Sandoval WN, Pham VC, Lill JR.

Drug Discov Today. 2008 Dec;13(23-24):1075-81. doi: 10.1016/j.drudis.2008.08.007. Epub 2008 Nov 7. Review.


Ubiquitin chain editing revealed by polyubiquitin linkage-specific antibodies.

Newton K, Matsumoto ML, Wertz IE, Kirkpatrick DS, Lill JR, Tan J, Dugger D, Gordon N, Sidhu SS, Fellouse FA, Komuves L, French DM, Ferrando RE, Lam C, Compaan D, Yu C, Bosanac I, Hymowitz SG, Kelley RF, Dixit VM.

Cell. 2008 Aug 22;134(4):668-78. doi: 10.1016/j.cell.2008.07.039.

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