Structual Biology

Method Development

Data Analysis

Publications

 

 

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Guex N, Crespo I, Bron S, Ifticene-Treboux A, Faes-Van't Hull E, Kharoubi S, Liechti R, Werffeli P, Ibberson M, Majo F, Nicolas M, Laurent J, Garg A, Zaman K, Lehr HA, Stevenson BJ, Rüegg C, Coukos G, Delaloye JF, Xenarios I, Doucey MA (2015). Angiogenic activity of breast cancer patients' monocytes reverted by combined use of systems modeling and experimental approaches . PLoS Comput Biol. 13:11(3):e1004050

 

 

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Scott CC, Vossio S, Vacca F, Snijder B, Larios J, Schaad O, Guex N, Kuznetsov D, Martin O, Chambon M, Turcatti G, Pelkmans L, Gruenberg J (2015). Wnt directs the endosomal flux of LDL-derived cholesterol and lipid droplet homeostasis. . EMBO Rep. 16:(6):741-52

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von Alpen D., Tran H.V., Guex N, Venturini G., Munier F.L., Schorderet D.F., Haider B.N. and Escher P. (2015). Differential dimerization of variants linked to enhanced S-Cone Sensitivity Syndrome (ESCS) located in the NR2E3 ligand-binding domain . Human mutation 36(6):599-610

 

 

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Pellissier L, Niculita-Hirzel H, Dubuis A, Pagni M, Guex N, Ndiribe C, Salamin N, Xenarios I, Goudet J, Sanders I.R, Guisan A (2014). Soil fungal communities of grasslands are environmentally structured at a regional scale in the Alps . Mol. Ecol. 23:4274-4290

 

 

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Gilardi F., Migliavacca E., Naldi A., Baruchet M., Canella D., Le Martelot G. Guex N [co-last] ,Desvergne B. (2014). Genome-wide analysis of SREBP1 activity around the clock reveals its combined dependency on nutrient and circadian signals . PLOS Genetics: Mar 6;10(3):e1004155

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Johansson, M.U., Zoete V., Guex N. (2013). Recurrent structural motifs in non-homologous protein structures. Int. J. Mol. Sci. 14(4):7795-7814

 

 

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Pagni M, Niculita-Hirzel H, Pelissier L,
Dubuis A, Xenarios I, Guisan A, Sanders I, Goudet J,
Guex N (2013). Density-based hierarchical clustering of pyro-sequences on a large scale – the case of fungal ITS1. Bioinformatics. 15;29(10):1268-74.

 

 

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Rotman N, Guex N ,Gouranton E, Wahli W. (2013). PPAR interprets a chromatin signature of pluripotency to promote embryonic differentiation at gastrulation . PLosOne. Dec 18;8(12):e83300. doi: 10.1371

 

 

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Pellissier L, Pinto-Figueroa E, Niculita-Hirzel H, Moora M, Villard L, Goudet J, Guex N, Pagni M, Xenarios I, Sanders I, Guisan A (2013). Plant species distributions along environmental gradients: do belowground interactions with fungi matter? . Front Plant Sci. doi: 10.3389/fpls.2013.00500

 

 

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Ibberson M, Bron S, Guex N, Faes-vanÕt Hull E, Ifticene-Treboux A, Henry L, Lehr H-A, Delaloye J-F, Coukos G, Xenarios I, Doucey M-A
 (2013). TIE-2 and VEGFR kinase activities drive TIE-2-expressing monocytes immunosuppressive function in human breast tumors. Clinical Cancer Research. June 5 - doi: 10.1158/1078-0432

 

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Guex N, Iseli C, Syngelaki A, Deluen A, Pescia G, Nicolaides KH, Xenarios I, Conrad B (2013). A robust 2nd generation genome-wide test for fetal aneuploidy based on shotgun sequencing cell-free DNA in maternal blood. Prenatal Diagnosis. Accepted

 

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Aghaeepour N, Finak G; FlowCAP Consortium, Dougall D, Khodabakhshi AH, Mah P, Obermoser G, Spidlen J, Taylor I, Wuensch SA, Bramson J, Eaves C, Weng AP, Iii ES, Ho K, Kollmann T, Rogers W, De Rosa S, Dalal B, Azad A, Pothen A, Brandes A, Bretschneider H, Bruggner R, Finck R, Jia R, Zimmerman N, Linderman M, Dill D, Nolan G, Chan C, Khettabi FE, O'Neill K, Chikina M, Ge Y, Sealfon S, Sug‡r I, Gupta A, Shooshtari P, Zare H, De Jager PL, Jiang M, Keilwagen J, Maisog JM, Luta G, Barbo AA, M‡jek P, Vilček J, Manninen T, Huttunen H, Ruusuvuori P, Nykter M, McLachlan GJ, Wang K, Naim I, Sharma G, Nikolic R, Pyne S, Qian Y, Qiu P, Quinn J, Roth A; DREAM Consortium, Meyer P, Stolovitzky G, Saez-Rodriguez J, Norel R, Bhattacharjee M, Biehl M, Bucher P, Bunte K, Di Camillo B, Sambo F, Sanavia T, Trifoglio E, Toffolo G, Dimitrieva S, Dreos R, Ambrosini G, Grau J, Grosse I, Posch S, Guex N, Keilwagen J, Kursa M, Rudnicki W, Liu B, Maienschein-Cline M, Manninen T, Huttunen H, Ruusuvuori P, Nykter M, Schneider P, Seifert M, Strickert M, Vilar JM, Hoos H, Mosmann TR, Brinkman R, Gottardo R, Scheuermann RH (2013). Critical assessment of automated flow cytometry data analysis techniques. Nat Methods. 10(3):228-38

 

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Le Martelot G, Canella D, Symul L, Migliavacca E, Gilardi F, Liechti R, Martin O, Harshman K, Delorenzi M, Desvergne B, Herr W, Deplancke B, Schibler U, Rougemont J, Guex N [coordinated all Bioinformatics analyses], Hernandez N, Naef F; CycliX Consortium. (2012). Genome-wide RNA polymerase II profiles and RNA accumulation reveal kinetics of transcription and associated epigenetic changes during diurnal cycles. PLoS Biol. 10(11).

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Johansson, M.U., Zoete V., Michielin O. & Guex N. (2012). Defining and searching for structural motifs using DeepView/Swiss-PdbViewer. BMC Bioinformatics, 13:173.

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Hor H., Bartesaghi L., Kutalik Z., Vic‡rio J.L., de Andrˇs C., Pfister C., Lammers G.J. Guex N., Chrast R., Tafti M., Peraita-Adrados R. (2011) A Missense Mutation in Myelin Oligodendrocyte Glycoprotein as a Cause of Familial Narcolepsy with Cataplexy. Am. J Hum Genet., 89(3):474-9.

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Deuquet J., Lausch E., Guex N., Abrami L., Salvi S., Lakka R., Ramirez M.C.M, Martignetti J., Rokicki, Bonafe L., Superti-Furga A. &  van der Goot G. (2011). Hyaline Fibromatosis Syndrome inducing mutations in the ectodomain of anthrax toxin receptor 2 can be rescued by proteasome inhibitors. EMBO Mol Med, 3(4):208-221

 

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Guex N., Migliavacca, E. & Xenarios, I. (2010). Multiple Imputations Applied to the DREAM3 Phosphoproteomics Challenge: A Winning Strategy. PloSOne, 5(1): e8012. doi:10.1371 / journal.pone.0008012

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Guex N., Peitsch, MC, & Schwede T. (2009). Automated comparative protein structure modeling with SWISS-MODEL and Swiss-PdbViewer: a historical perspective. Electrophoresis, Jun;30 Suppl 1:S162-73

 

 

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Ortiz M, Guex N., Patin E, Martin O, Xenarios I, Ciuffi A, Quintana-Murci L & Telenti A. (2009). Evolutionary Trajectories of Primate Genes Involved in HIV Pathogenesis. Molecular Biology and Evolution 26(12):2865-2875

 

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Simmons, C. A., Bledsoe, R. K., Guex, N. & Pearce, K. H. (2008). Expression, purification, and characterization of multiple, multifunctional human glucocorticoid receptor proteins. Protein Expr Purif. 62(1) 29-35

 

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Vasa, S. M., Guex, N. [ two first authors contributed equally ], Wilkinson, K. A., Weeks, K. M. & Giddings, M. C. (2008). ShapeFinder: A software system for high-throughput quantitative analysis of nucleic acid reactivity information resolved by capillary electrophoresis. RNA 14, 1979-1990.

 

 

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Wilkinson, K. A., Gorelick, R. J., Vasa, S. M., Guex, N., Rein, A., Mathews, D. H., Giddings, M. C. & Weeks, K. M. (2008). High-throughput SHAPE analysis reveals structures in HIV-1 genomic RNA strongly conserved across distinct biological states. PLoS Biol 6(4), e96

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O'Hara, F. P., Guex, N., Word, J. M., Miller, L. A., Becker, J. A., Walsh, S. L., Scangarella, N. E., West, J. M., Shawar, R. M., Amrine-Madsen, H. (2008). A geographic variant of the Staphylococcus aureus Panton-Valentine leukocidin toxin and the origin of community-associated methicillin-resistant S. aureus USA300. J Infect Dis 197, 187-94

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Pajerowska-Mukhtar, K. M., Mukhtar, M. S., Guex, N., Halim, V. A., Rosahl, S., Somssich, I. E. Gebhardt, C. (2008). Natural variation of potato allene oxide synthase 2 causes differential levels of jasmonates and pathogen resistance in Arabidopsis. Planta 228, 293-306

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Scheib H, McLay I, Guex N, Clare J, Blaney F, Dale T, Tate S, Robertson G (2006) Modeling the pore structure of voltage-gated sodium channels in closed, open, and fast-inactivated conformation reveals details of site 1 toxin and local anesthetic binding. J Mol Model 12(6)-813-22

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Schwede T, Kopp J , Guex N and Peitsch MC (2003) SWISS-MODEL: an automated protein homology-modeling server. Nucleic Acids Research 31:3381-3385.  (highly cited)

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Peitsch MC, Schwede T, Diemand A and Guex N (2003) Protein homology modelling. in: The Encyclopaedia of the Human Genome, DN. Cooper and A. Lockyer. eds.,  Nature publishing Group

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Guex N, Schwede T and Peitsch MC (2002) Imaging in Biochemistry. In: The Encyclopaedia of Imaging Science and Technology. Wiley & Sons, New York.
DOI: 10.1002/0471443395.img052

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Peitsch MC, Schwede T, Diemand A and Guex N (2002) Protein Structure Prediction by Comparison: Homology-based modelling. In: Current Topics in Computational Biology, p 449-466, T. Jiang et al. eds., MIT Press, Cambridge

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Guex N, Schwede T and Peitsch MC (2001) Protein tertiary structure modelling. Current Protocols in Protein Science. Unit 2.8:2.8.1-2.8.17.

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Peitsch MC, Schwede T and Guex N (2000) Automated protein modelling - the proteome in 3D. Pharmacogenomics. 1:257-266.

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Schwede T, Diemand A, Guex N and Peitsch MC (2000) Protein structure computing in the genomic era. Research in Microbiology 151:107-112. PMID: 10865955; UI: 20322324

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Guex N, Diemand A and Peitsch MC (1999) Protein modelling for all. TiBS 24:364-367. PMID: 10470037; UI: 99400974.

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Guex N and Peitsch MC (1999) Molecular modelling of proteinsImmunology News 6:132-134

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Mehenni H, Gerhig C, Nezu J-I, Oku A, Shimanand M, Rossier C, Guex N, Blouin J-L, Scott HS, Antonarakis SE (1998) Loss of LKB1 kinase activity in Peutz-Jeghers syndrome and evidence for allelic and locus heterogeneity. Am. J. Hum. Genet. 63, 1641-1650.

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Duret L, Guex N, Peitsch MC, Bairoch A (1998). New Insulin-Like Proteins with Atypical Disulfide Bond Pattern Characterized in Caenorhabditis elegans by Comparative Sequence Analysis and Homology Modeling. Genome Research 8, 348-353

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Peitsch MC, Guex N (1997) Large Scale Comparative Protein Modelling. in: Proteome Research: New Fontiers in Fuctional Genomics. Springer Verlag, ISBN 3-540-62753-7. pp 143-146 and pp. 177-186

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Guex N, Peitsch MC (1997) SWISS-MODEL and the Swiss-PdbViewer: An environment for comparative protein modelling. Electrophoresis 18, 2714-2723  (highly cited)

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Guex N and Peitsch MC (1997) Protein modelling via the Internet. Bio-World  5/97:9-13

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Guex N, Peitsch MC (1996) SWISS-PDBVIEWER: A fast and easy to use pdb viewer for Macintosh and PC. Protein data Bank Quaterly Newsletter 77,7

 

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Guex N, Henry H, Flach J, Richter H, Widmer F (1995) Glyoxysomal malate dehydrogenase and malate synthase from soybean cotyledons (Glycine max. L.) : enzyme association, antibody production and cDNA cloning. Planta  197(2) 369-375

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Guex N, Widmer F, Gaillard P, Carrupt P-A Testa B (1993) 3D Modelling of soybean glyoxysomal malate dehydrogenase (gMDH). Trends in QSAR and Molecular Modeling 9. Wermuth, C.G., Ed. Escom, Leiden, pp. 485-486.