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Distinct Features of Stress Granule Proteins Predict Localization in Membraneless Organelles.

Kuechler ER, Budzyńska PM, Bernardini JP, Gsponer J, Mayor T.

J Mol Biol. 2020 Feb 24. pii: S0022-2836(20)30193-5. doi: 10.1016/j.jmb.2020.02.020. [Epub ahead of print]


Computational Disorder Analysis in Ethylene Response Factors Uncovers Binding Motifs Critical to Their Diverse Functions.

Sun X, Malhis N, Zhao B, Xue B, Gsponer J, Rikkerink EHA.

Int J Mol Sci. 2019 Dec 20;21(1). pii: E74. doi: 10.3390/ijms21010074.


Phase separation and clustering of an ABC transporter in Mycobacterium tuberculosis.

Heinkel F, Abraham L, Ko M, Chao J, Bach H, Hui LT, Li H, Zhu M, Ling YM, Rogalski JC, Scurll J, Bui JM, Mayor T, Gold MR, Chou KC, Av-Gay Y, McIntosh LP, Gsponer J.

Proc Natl Acad Sci U S A. 2019 Aug 13;116(33):16326-16331. doi: 10.1073/pnas.1820683116. Epub 2019 Jul 31.


Predicting Protein-Protein Interfaces that Bind Intrinsically Disordered Protein Regions.

Wong ETC, Gsponer J.

J Mol Biol. 2019 Aug 9;431(17):3157-3178. doi: 10.1016/j.jmb.2019.06.010. Epub 2019 Jun 15.


Improved measures for evolutionary conservation that exploit taxonomy distances.

Malhis N, Jones SJM, Gsponer J.

Nat Commun. 2019 Apr 5;10(1):1556. doi: 10.1038/s41467-019-09583-2.


Inverse Correlation between Amyloid Stiffness and Size.

Nassar R, Wong E, Gsponer J, Lamour G.

J Am Chem Soc. 2019 Jan 9;141(1):58-61. doi: 10.1021/jacs.8b10142. Epub 2018 Dec 20.


Mechanical Anisotropy in GNNQQNY Amyloid Crystals.

Nassar R, Wong E, Bui JM, Yip CK, Li H, Gsponer J, Lamour G.

J Phys Chem Lett. 2018 Sep 6;9(17):4901-4909. doi: 10.1021/acs.jpclett.8b02027. Epub 2018 Aug 15.


Biophysical Characterization of the Tandem FHA Domain Regulatory Module from the Mycobacterium tuberculosis ABC Transporter Rv1747.

Heinkel F, Shen L, Richard-Greenblatt M, Okon M, Bui JM, Gee CL, Gay LM, Alber T, Av-Gay Y, Gsponer J, McIntosh LP.

Structure. 2018 Jul 3;26(7):972-986.e6. doi: 10.1016/j.str.2018.04.018. Epub 2018 May 31.


The [PSI +] yeast prion does not wildly affect proteome composition whereas selective pressure exerted on [PSI +] cells can promote aneuploidy.

Chan PHW, Lee L, Kim E, Hui T, Stoynov N, Nassar R, Moksa M, Cameron DM, Hirst M, Gsponer J, Mayor T.

Sci Rep. 2017 Aug 16;7(1):8442. doi: 10.1038/s41598-017-07999-8.


Topological Dissection of the Membrane Transport Protein Mhp1 Derived from Cysteine Accessibility and Mass Spectrometry.

Calabrese AN, Jackson SM, Jones LN, Beckstein O, Heinkel F, Gsponer J, Sharples D, Sans M, Kokkinidou M, Pearson AR, Radford SE, Ashcroft AE, Henderson PJF.

Anal Chem. 2017 Sep 5;89(17):8844-8852. doi: 10.1021/acs.analchem.7b01310. Epub 2017 Aug 9.


Mapping the Broad Structural and Mechanical Properties of Amyloid Fibrils.

Lamour G, Nassar R, Chan PHW, Bozkurt G, Li J, Bui JM, Yip CK, Mayor T, Li H, Wu H, Gsponer JA.

Biophys J. 2017 Feb 28;112(4):584-594. doi: 10.1016/j.bpj.2016.12.036.


Distinct genetic evolution patterns of relapsing diffuse large B-cell lymphoma revealed by genome-wide copy number aberration and targeted sequencing analysis.

Juskevicius D, Lorber T, Gsponer J, Perrina V, Ruiz C, Stenner-Liewen F, Dirnhofer S, Tzankov A.

Leukemia. 2016 Dec;30(12):2385-2395. doi: 10.1038/leu.2016.135. Epub 2016 May 20.


MoRFchibi SYSTEM: software tools for the identification of MoRFs in protein sequences.

Malhis N, Jacobson M, Gsponer J.

Nucleic Acids Res. 2016 Jul 8;44(W1):W488-93. doi: 10.1093/nar/gkw409. Epub 2016 May 12.


Systems-wide Identification of cis-Regulatory Elements in Proteins.

Yeon JH, Heinkel F, Sung M, Na D, Gsponer J.

Cell Syst. 2016 Feb 24;2(2):89-100. doi: 10.1016/j.cels.2016.02.004. Epub 2016 Feb 24.


Free energies of solvation in the context of protein folding: Implications for implicit and explicit solvent models.

Cumberworth A, Bui JM, Gsponer J.

J Comput Chem. 2016 Mar 15;37(7):629-40. doi: 10.1002/jcc.24235. Epub 2015 Nov 12.


Determination of Protein Folding Intermediate Structures Consistent with Data from Oxidative Footprinting Mass Spectrometry.

Heinkel F, Gsponer J.

J Mol Biol. 2016 Jan 29;428(2 Pt A):365-371. doi: 10.1016/j.jmb.2015.10.022. Epub 2015 Oct 30.


Computational Identification of MoRFs in Protein Sequences Using Hierarchical Application of Bayes Rule.

Malhis N, Wong ET, Nassar R, Gsponer J.

PLoS One. 2015 Oct 30;10(10):e0141603. doi: 10.1371/journal.pone.0141603. eCollection 2015.


Computational identification of MoRFs in protein sequences.

Malhis N, Gsponer J.

Bioinformatics. 2015 Jun 1;31(11):1738-44. doi: 10.1093/bioinformatics/btv060. Epub 2015 Jan 30.


Early development of human lymphomas in a prostate cancer xenograft program using triple knock-out immunocompromised mice.

Wetterauer C, Vlajnic T, Schüler J, Gsponer JR, Thalmann GN, Cecchini M, Schneider J, Zellweger T, Pueschel H, Bachmann A, Ruiz C, Dirnhofer S, Bubendorf L, Rentsch CA.

Prostate. 2015 May;75(6):585-92. doi: 10.1002/pros.22939. Epub 2015 Jan 13.


Categorizer: a tool to categorize genes into user-defined biological groups based on semantic similarity.

Na D, Son H, Gsponer J.

BMC Genomics. 2014 Dec 11;15:1091. doi: 10.1186/1471-2164-15-1091.


A feature analysis of lower solubility proteins in three eukaryotic systems.

Albu RF, Chan GT, Zhu M, Wong ET, Taghizadeh F, Hu X, Mehran AE, Johnson JD, Gsponer J, Mayor T.

J Proteomics. 2015 Apr 6;118:21-38. doi: 10.1016/j.jprot.2014.10.011. Epub 2014 Oct 25.


Rsp5/Nedd4 is the main ubiquitin ligase that targets cytosolic misfolded proteins following heat stress.

Fang NN, Chan GT, Zhu M, Comyn SA, Persaud A, Deshaies RJ, Rotin D, Gsponer J, Mayor T.

Nat Cell Biol. 2014 Dec;16(12):1227-37. doi: 10.1038/ncb3054. Epub 2014 Oct 26.


Incidental prostate cancer prevalence at radical cystoprostatectomy--importance of the histopathological work-up.

Wetterauer C, Weibel M, Gsponer JR, Vlajnic T, Zellweger T, Bütikofer S, Müller G, Püschel H, Bachmann A, Gasser TC, Bubendorf L, Rentsch CA.

Virchows Arch. 2014 Dec;465(6):629-36. doi: 10.1007/s00428-014-1656-9. Epub 2014 Oct 1.


Intrinsically disordered segments affect protein half-life in the cell and during evolution.

van der Lee R, Lang B, Kruse K, Gsponer J, Sánchez de Groot N, Huynen MA, Matouschek A, Fuxreiter M, Babu MM.

Cell Rep. 2014 Sep 25;8(6):1832-1844. doi: 10.1016/j.celrep.2014.07.055. Epub 2014 Sep 15.


Maximum tumor diameter adjusted to the risk profile predicts biochemical recurrence after radical prostatectomy.

Müller G, Rieken M, Bonkat G, Gsponer JR, Vlajnic T, Wetterauer C, Gasser TC, Wyler SF, Bachmann A, Bubendorf L.

Virchows Arch. 2014 Oct;465(4):429-37. doi: 10.1007/s00428-014-1643-1. Epub 2014 Aug 17.


Easyworm: an open-source software tool to determine the mechanical properties of worm-like chains.

Lamour G, Kirkegaard JB, Li H, Knowles TP, Gsponer J.

Source Code Biol Med. 2014 Jul 10;9:16. doi: 10.1186/1751-0473-9-16. eCollection 2014.


Mechanically tightening a protein slipknot into a trefoil knot.

He C, Lamour G, Xiao A, Gsponer J, Li H.

J Am Chem Soc. 2014 Aug 27;136(34):11946-55. doi: 10.1021/ja503997h. Epub 2014 Aug 13.


Phosphorylation of an intrinsically disordered segment in Ets1 shifts conformational sampling toward binding-competent substates.

Bui JM, Gsponer J.

Structure. 2014 Aug 5;22(8):1196-1203. doi: 10.1016/j.str.2014.06.002. Epub 2014 Jul 10.


Upregulation of the miR-17-92 cluster and its two paraloga in osteosarcoma - reasons and consequences.

Arabi L, Gsponer JR, Smida J, Nathrath M, Perrina V, Jundt G, Ruiz C, Quagliata L, Baumhoer D.

Genes Cancer. 2014 Apr;5(1-2):56-63.


Classification of intrinsically disordered regions and proteins.

van der Lee R, Buljan M, Lang B, Weatheritt RJ, Daughdrill GW, Dunker AK, Fuxreiter M, Gough J, Gsponer J, Jones DT, Kim PM, Kriwacki RW, Oldfield CJ, Pappu RV, Tompa P, Uversky VN, Wright PE, Babu MM.

Chem Rev. 2014 Jul 9;114(13):6589-631. doi: 10.1021/cr400525m. Epub 2014 Apr 29. Review. No abstract available.


Bacillus Calmette-Guérin strain differences have an impact on clinical outcome in bladder cancer immunotherapy.

Rentsch CA, Birkhäuser FD, Biot C, Gsponer JR, Bisiaux A, Wetterauer C, Lagranderie M, Marchal G, Orgeur M, Bouchier C, Bachmann A, Ingersoll MA, Brosch R, Albert ML, Thalmann GN.

Eur Urol. 2014 Oct;66(4):677-88. doi: 10.1016/j.eururo.2014.02.061. Epub 2014 Mar 12.


High intrinsic mechanical flexibility of mouse prion nanofibrils revealed by measurements of axial and radial Young's moduli.

Lamour G, Yip CK, Li H, Gsponer J.

ACS Nano. 2014 Apr 22;8(4):3851-61. doi: 10.1021/nn5007013. Epub 2014 Mar 6.


ERG rearrangement and protein expression in the progression to castration-resistant prostate cancer.

Gsponer JR, Braun M, Scheble VJ, Zellweger T, Bachmann A, Perner S, Vlajnic T, Srivastava M, Tan SH, Dobi A, Sesterhenn IA, Srivastava S, Bubendorf L, Ruiz C.

Prostate Cancer Prostatic Dis. 2014 Jun;17(2):126-31. doi: 10.1038/pcan.2013.62. Epub 2014 Jan 28.


Impaired autophagy in the lipid-storage disorder Niemann-Pick type C1 disease.

Sarkar S, Carroll B, Buganim Y, Maetzel D, Ng AH, Cassady JP, Cohen MA, Chakraborty S, Wang H, Spooner E, Ploegh H, Gsponer J, Korolchuk VI, Jaenisch R.

Cell Rep. 2013 Dec 12;5(5):1302-15. doi: 10.1016/j.celrep.2013.10.042. Epub 2013 Nov 27.


NeuroGeM, a knowledgebase of genetic modifiers in neurodegenerative diseases.

Na D, Rouf M, O'Kane CJ, Rubinsztein DC, Gsponer J.

BMC Med Genomics. 2013 Nov 14;6:52. doi: 10.1186/1755-8794-6-52.


VEGFA gene locus analysis across 80 human tumour types reveals gene amplification in several neoplastic entities.

Andreozzi M, Quagliata L, Gsponer JR, Ruiz C, Vuaroqueaux V, Eppenberger-Castori S, Tornillo L, Terracciano LM.

Angiogenesis. 2014 Jul;17(3):519-27. doi: 10.1007/s10456-013-9396-z. Epub 2013 Oct 11.


Protein synthesis rate is the predominant regulator of protein expression during differentiation.

Kristensen AR, Gsponer J, Foster LJ.

Mol Syst Biol. 2013;9:689. doi: 10.1038/msb.2013.47.


On the importance of polar interactions for complexes containing intrinsically disordered proteins.

Wong ET, Na D, Gsponer J.

PLoS Comput Biol. 2013;9(8):e1003192. doi: 10.1371/journal.pcbi.1003192. Epub 2013 Aug 22.


Promiscuity as a functional trait: intrinsically disordered regions as central players of interactomes.

Cumberworth A, Lamour G, Babu MM, Gsponer J.

Biochem J. 2013 Sep 15;454(3):361-9. doi: 10.1042/BJ20130545. Review.


Characterization and clinical relevance of ALDHbright populations in prostate cancer.

Le Magnen C, Bubendorf L, Rentsch CA, Mengus C, Gsponer J, Zellweger T, Rieken M, Thalmann GN, Cecchini MG, Germann M, Bachmann A, Wyler S, Heberer M, Spagnoli GC.

Clin Cancer Res. 2013 Oct 1;19(19):5361-71. doi: 10.1158/1078-0432.CCR-12-2857. Epub 2013 Aug 22.


System-wide analysis reveals intrinsically disordered proteins are prone to ubiquitylation after misfolding stress.

Ng AH, Fang NN, Comyn SA, Gsponer J, Mayor T.

Mol Cell Proteomics. 2013 Sep;12(9):2456-67. doi: 10.1074/mcp.M112.023416. Epub 2013 May 28.


Estrogen receptor β expression and androgen receptor phosphorylation correlate with a poor clinical outcome in hormone-naive prostate cancer and are elevated in castration-resistant disease.

Zellweger T, Stürm S, Rey S, Zlobec I, Gsponer JR, Rentsch CA, Terracciano LM, Bachmann A, Bubendorf L, Ruiz C.

Endocr Relat Cancer. 2013 May 21;20(3):403-13. doi: 10.1530/ERC-12-0402. Print 2013 Jun.


What's in a name? Why these proteins are intrinsically disordered: Why these proteins are intrinsically disordered.

Dunker AK, Babu MM, Barbar E, Blackledge M, Bondos SE, Dosztányi Z, Dyson HJ, Forman-Kay J, Fuxreiter M, Gsponer J, Han KH, Jones DT, Longhi S, Metallo SJ, Nishikawa K, Nussinov R, Obradovic Z, Pappu RV, Rost B, Selenko P, Subramaniam V, Sussman JL, Tompa P, Uversky VN.

Intrinsically Disord Proteins. 2013 Apr 1;1(1):e24157. doi: 10.4161/idp.24157. eCollection 2013 Jan-Dec. Review.


BCG-mediated bladder cancer immunotherapy: identifying determinants of treatment response using a calibrated mathematical model.

Rentsch CA, Biot C, Gsponer JR, Bachmann A, Albert ML, Breban R.

PLoS One. 2013;8(2):e56327. doi: 10.1371/journal.pone.0056327. Epub 2013 Feb 25.


Structure and intrinsic disorder in protein autoinhibition.

Trudeau T, Nassar R, Cumberworth A, Wong ET, Woollard G, Gsponer J.

Structure. 2013 Mar 5;21(3):332-41. doi: 10.1016/j.str.2012.12.013. Epub 2013 Jan 31.


The molecular mechanism underlying mechanical anisotropy of the protein GB1.

Li YD, Lamour G, Gsponer J, Zheng P, Li H.

Biophys J. 2012 Dec 5;103(11):2361-8. doi: 10.1016/j.bpj.2012.10.035.


Deep clonal profiling of formalin fixed paraffin embedded clinical samples.

Holley T, Lenkiewicz E, Evers L, Tembe W, Ruiz C, Gsponer JR, Rentsch CA, Bubendorf L, Stapleton M, Amorese D, Legendre C, Cunliffe HE, McCullough AE, Pockaj B, Craig D, Carpten J, Von Hoff D, Iacobuzio-Donahue C, Barrett MT.

PLoS One. 2012;7(11):e50586. doi: 10.1371/journal.pone.0050586. Epub 2012 Nov 30.


Cellular strategies for regulating functional and nonfunctional protein aggregation.

Gsponer J, Babu MM.

Cell Rep. 2012 Nov 29;2(5):1425-37. doi: 10.1016/j.celrep.2012.09.036. Epub 2012 Nov 15.


A defect in ATP-citrate lyase links acetyl-CoA production, virulence factor elaboration and virulence in Cryptococcus neoformans.

Griffiths EJ, Hu G, Fries B, Caza M, Wang J, Gsponer J, Gates-Hollingsworth MA, Kozel TR, De Repentigny L, Kronstad JW.

Mol Microbiol. 2012 Dec;86(6):1404-23. doi: 10.1111/mmi.12065. Epub 2012 Nov 1.


Evolutionary selection for protein aggregation.

Sanchez de Groot N, Torrent M, Villar-Piqué A, Lang B, Ventura S, Gsponer J, Babu MM.

Biochem Soc Trans. 2012 Oct;40(5):1032-7. Review.


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