Articles de recherche:

1. Sala C, Benjak A, Goletti D, et al., Multicenter analysis of sputum microbiota in tuberculosis patients. PLoS ONE 15:e0240250 (2020).
2. Jeitziner R, Carrière M, Rougemont J, et al., Two-Tier Mapper, an unbiased topology-based clustering method for enhanced global gene expression analysis. Bioinformatics 35:3339—3347 (2019).
3. Eckmann JP, Rougemont J & Tlusty T, Colloquium: Proteins: The physics of amorphous evolving matter. Rev Modern Phys 91:031001 (2019).
4. Yeganeh M, Praz V, Carmeli C, et al., Differential regulation of RNA polymerase III genes during liver regeneration. Nucleic Acids Research 47:1786—1796 (2019).
5. Scott CC, Vossio S, Rougemont J & Gruenberg J, TFAP2 transcription factors are regulators of lipid droplet biogenesis, elife 7 (2018).
6. Rib L, Villeneuve D, Minocha S, et al., Cycles of gene expression and genome response during mammalian tissue regeneration, Epigenetics Chromatin 11:52 (2018).
7. Dewhurst-Maridor G, Abegg D, David FPA, et al., The SAGA complex, together with transcription factors and the endocytic protein Rvs167p, coordinates the reprofiling of gene expression in response to changes in sterol composition in Saccharomyces cerevisiae, Mol Biol Cell 28:2637—2649 (2017).
8. Loviglio MN, Leleu M, Männik M, et al., Chromosomal contacts connect loci associated with autism, BMI and head circumference phenotypes, Mol Psychiatry 22:836—849 (2017).
9. Mange F, Praz V, Migliavacca E, et al., Diurnal regulation of RNA polymerase III transcription is under the control of both the feeding-fasting response and the circadian clock, Genome Research 27:973—984 (2017).
10. David FPA, Rougemont J & Deplancke B., GETPrime 2.0: gene- and transcript-specific qPCR primers for 13 species including polymorphisms, Nucleic Acids Research 45:D56—D60 (2017).
11. Loviglio MN, Beck CR, White JJ, et al., Identification of a RAI1-associated disease network through integration of exome sequencing, transcriptomics, and 3D genomics, Genome Med 8:105 (2016).
12. Styles EB, Founk KJ, Zamparo LA, et al., Exploring Quantitative Yeast Phenomics with Single-Cell Analysis of DNA Damage Foci, Cell Syst 3:264—277.e10 (2016).
13. SIB Swiss Institute of Bioinformatics Members. The SIB Swiss Institute of Bioinformatics’ resources: focus on curated databases, Nucleic Acids Research 44:D27—37 (2016).
14. Zaiss MM, Rapin A, Lebon L, et al., The Intestinal Microbiota Contributes to the Ability of Helminths to Modulate Allergic Inflammation, Immunity 43:998—1010 (2015).
15. Kubik S, Bruzzone MJ, Jacquet P, et al., Nucleosome Stability Distinguishes Two Different Promoter Types at All Protein-Coding Genes in Yeast, Mol Cell 60:422—434 (2015).
16. Lemaire L, Goulley J, Kim YH, et al., Bicaudal C1 promotes pancreatic NEUROG3+ endocrine progenitor differentiation and ductal morphogenesis, Development 142:858—870, (2015).
17. Droz-Georget Lathion S, Rochat A, Knott G, et al., A single epidermal stem cell strategy for safe ex vivo gene therapy, EMBO Mol Med 7:380—393, (2015).
18. Rajaram RD, Buric D, Caikovski M, et al., Progesterone and Wnt4 control mammary stem cells via myoepithelial crosstalk, EMBO Journal 34:641—652, (2015).
19. Wachowicz P, Chasapi A, Krapp A, et al., Analysis of S. pombe SIN protein SPB-association reveals two genetically separable states of the SIN, J Cell Sci 128:741—754, (2014).
20. Porro A, Feuerhahn S, Delafontaine J, et al., Functional characterization of the TERRA transcriptome at damaged telomeres, Nat Commun 5:5379, (2014).
21. Knight B, Kubik S, Ghosh B, et al., Two distinct promoter architectures centered on dynamic nucleosomes control ribosomal protein gene transcription, Genes Dev 28:1695—1709 (2014).
22. Stockinger H, Altenhoff AM, Arnold K, et al., Fifteen years SIB Swiss Institute of Bioinformatics: life science databases, tools and support, Nucleic Acids Research 42:W436—41, (2014).
23. Bonhoure N, Bounova G, Bernasconi D, et al., Quantifying ChIP-seq data: a spiking method providing an internal reference for sample-to-sample normalization, Genome Research 24:1157—1168, (2014).
24. Solans L, Gonzalo-Asensio J, Sala C, et al., The PhoP-Dependent ncRNA Mcr7 Modulates the TAT Secretion System in Mycobacterium tuberculosis, PLoS pathogens 10:e1004183, (2014).
25. Gilardi F, Migliavacca E, Naldi A, et al., Genome-wide analysis of SREBP1 activity around the clock reveals its combined dependency on nutrient and circadian signals, PLoS Genetics 10:e1004155, (2014).
26. Singh P, Benjak A, Carat S, et al., Genome-wide re-sequencing of multidrug-resistant Mycobacterium leprae Airaku-3, Clin Microbiol Infect 20:O619—622, (2014).
27. David FPA, Delafontaine J, Carat S, et al., HTSstation: A Web Application and Open-Access Libraries for High-Throughput Sequencing Data Analysis, PLoS ONE 9:e85879, (2014).
28. Steijger T, Abril JF, Engström PG, et al., Assessment of transcript reconstruction methods for RNA-seq, Nature methods 10:1177—1184, (2013).
29. Gheldof N, Witwicki RM, Migliavacca E, et al., Structural variation-associated expression changes are paralleled by chromatin architecture modifications, PLoS ONE 8:e79973 (2013).
30. Uplekar S, Rougemont J, Cole ST & Sala C, High-resolution transcriptome and genome-wide dynamics of RNA polymerase and NusA in Mycobacterium tuberculosis, Nucleic Acids Research 41:961—977 (2013).
31. Le Martelot G, Canella D, Symul L, Migliavacca E et al., Genome-Wide RNA Polymerase II Profiles and RNA Accumulation Reveal Kinetics of Transcription and Associated Epigenetic Changes During Diurnal Cycles, PLoS Biology 10:e1001442 (2012).
32. Weissbrodt DG, Shani N, Sinclair L, Lefebvre G et al., PyroTRF-ID: a novel bioinformatics methodology for the affiliation of terminal-restriction fragments using 16S rRNA gene pyrosequencing data, BMC microbiology 12:306 (2012).
33. Hornitschek P, Kohnen MV, Lorrain S, et al., Phytochrome interacting factors 4 and 5 control seedling growth in changing light conditions by directly controlling auxin signaling, Plant J 71:699—711 (2012).
34. Hartkoorn R, Sala C, Uplekar S, et al., Genome-Wide Definition of the SigF Regulon in Mycobacterium tuberculosis, J Bacteriol 194:2001—2009 (2012).
35. Canella D, Bernasconi D, Gilardi F, et al., A multiplicity of factors contributes to selective RNA polymerase III occupancy of a subset of RNA polymerase III genes in mouse liver, Genome Res 22:666—680 (2012).
36. Blasco B, Chen JM, Hartkoorn R, et al., Virulence Regulator EspR of Mycobacterium tuberculosis is a Nucleoid-Associated Protein, PLoS pathogens 8:e1002621 (2012).
37. Noordermeer D, Leleu M, Splinter E, et al., The dynamic architecture of Hox gene clusters, Science 334:222—225 (2011).
38. Gubelmann C, Gattiker A, Massouras A, et al., GETPrime: a gene- or transcript-specific primer database for quantitative real-time PCR, Database 2011:bar040 (2011).
39. Ayyanan A, Laribi O, Schuepbach-Mallepell S, et al., Perinatal exposure to Bisphenol A increases adult mammary gland progesterone response and cell number, Molecular Endocrinology 25:1915—1923 (2011).
40. Meylan S, Groner AC, Ambrosini G, et al., A gene-rich, transcriptionally active environment and the pre-deposition of repressive marks are predictive of susceptibility to KRAB/KAP1-mediated silencing, BMC Genomics 12:378 (2011).
41. Uplekar S, Heym B, Friocourt V, Rougemont J & Cole ST, Comparative genomics of esx genes from clinical isolates of Mycobacterium tuberculosis provides evidence for gene conversion and epitope variation, Infection and Immunity 79:4042—4049 (2011).
42. Huber A, French SL, Tekotte H, et al., Sch9 regulates ribosome biogenesis via Stb3, Dot6 and Tod6 and the histone deacetylase complex RPD3L, EMBO Journal 20:3052-3064 (2011).
43. Lefebvre G, Beerenwinkel N, Rougemont J, Telenti A & Ciuffi A, Analysis of HIV-1 Expression Level and Sense of Transcription by High-Throughput Sequencing of the Infected Cell, Journal of Virology 85:6205—6211 (2011).
44. Truman RW, Singh P, Sharma R, et al., Probable zoonotic leprosy in the southern United States, The New England Journal of Medicine 364:1626—1633, (2011).
45. Rey G, Cesbron F, Rougemont J, et al., Genome-wide and phase-specific DNA-binding rhythms of BMAL1 control circadian output functions in mouse liver, PLoS Biology 9:e1000595 (2011).
46. Stoll G, et al., Stabilizing patterning in the Drosophila segment polarity network by selecting models in silico, Biosystems 102:3—10 (2010).
47. Leleu M, Lefebvre G & Rougemont J, Processing and analyzing ChIP-seq data: from short reads to regulatory interactions, Briefings in Functional Genomics 9:466—476 (2010).
48. Massouras A, Hens K, Gubelmann C, et al. Primer-initiated sequence synthesis to detect and assemble structural variants, Nature Methods 7:485—486 (2010).
49. Preti M, Ribeyre C, Pascali C, et al., The telomere-binding protein Tbf1 demarcates snoRNA gene promoters in Saccharomyces cerevisiae, Molecular Cell 38:614—620 (2010).
50. Rowe HM, Jakobsson J, Mesnard D, et al. KAP1 controls endogenous retroviruses in embryonic stem cells, Nature 463:237—240 (2010).
51. Monot M, Honoré N, Garnier Th, et al., Comparative genomic and phylogeographic analysis of Mycobacterium leprae, Nat Genet 41:1282—1289 (2009).
52. Nikolaev SI, Iseli Ch, Sharp AJ, et al., Detection of genomic variation by selection of a 9 mb DNA region and high throughput sequencing, PLoS ONE 4:e6659 (2009).
53. Gattiker A, Dessimoz Ch, Schneider A, et al., The Microbe browser for comparative genomics, Nucleic Acids Res 37:W296—299 (2009).
54. Gattiker A, Hermida L, Liechti R, et al., MIMAS 3.0 is a Multiomics Information Management and Annotation System, BMC Bioinformatics 10:151 (2009).
55. Rougemont J, Amzallag A, Iseli Ch, et al., Probabilistic base calling of Solexa sequencing data, BMC Bioinformatics, 9:431 (2008).
56. Stamatakis A, Hoover P & Rougemont J, A rapid bootstrap algorithm for the RAxML Web servers, Syst Biol, 57, 758—771 (2008).
57. Stoll G, Rougemont J & Naef F, Representing perturbed dynamics in biological network models, Phys Rev E, 76, 011917 (2007).
58. Rougemont J & Naef F, Dynamical signatures of cellular fluctuations and oscillator stability in peripheral circadian clocks, Mol Syst Biol, 3:93 (2007).
59. Nikolaev SI, Montoya-Burgos JI, Margulies EH, NISC Comparative Sequencing Program, Rougemont J, Nyffeler B & Antonarakis SE, Early History of Mammals is Elucidated with the ENCODE Multiple Species Sequencing Data, PLoS Genet, 3:e2 (2007).
60. Guillaume F, & Rougemont J, Nemo: an evolutionary and population genetics programming framework, Bioinformatics, 22:2556—2557 (2006).
61. Stoll G, Rougemont J & Naef F, Few crucial links assure checkpoint efficiency in the yeast cell-cycle network, Bioinformatics, 22:2539—2546 (2006).
62. Honoré P, Granjeaud S, Tagett R, et al., MicroArray Facility: a laboratory information management system with extended support for Nylon based technologies, BMC Genomics, 7:240 (2006).
63. Rougemont J & Naef F, Collective Synchronization in Populations of Globally Coupled Phase Oscillators with Drifting Frequencies, Phys Rev E 73:011104 (2006).
64. Deutsch S, Lyle R, Dermitzakis ET, et al., Gene Expression Variation and Expression Quantitative Trait Mapping of Human Chromosome 21 Genes, Hum Mol Genet 14:3741—3749 (2005).
65. Bertucci F, Finetti P, Rougemont J, et al., Gene Expression Profiling Identifies Molecular Subtypes of Inflammatory Breast Cancer, Cancer Res 65:2170—2178 (2005).
66. Jacquemier J, Ginestier Ch, Rougemont J, et al., Protein Expression Profiling Identifies Subclasses of Breast Cancers and Predicts Prognosis, Cancer Res 65:767—779 (2005).
67. Bertucci F, Finetti P, Rougemont J, et al., Gene Expression Profiling for Molecular Characterization of Inflammatory Breast Cancer and Prediction of Response to Chemotherapy, Cancer Res 64:8558—8565 (2004).
68. Lord GJ & Rougemont J, A Numerical Scheme for Stochastic PDEs with Gevrey Regularity, IMA J Numer Anal 24:587—604 (2004).
69. Lopez F, Rougemont J, Loriod B, et al., Feature Extraction and Signal Processing for Nylon DNA Microarrays, BMC Genomics 5:38 (2004).
70. Lord GJ & Rougemont J, Numerical Computation of $\epsilon$-Entropy for Parabolic Equations with Analytic Solutions, Physica D 194:65—74 (2004).
71. Rougemont J & Hingamp P, DNA Microarray Data and Contextual Analysis of Correlation Graphs, BMC Bioinformatics 4:15 (2003).
72. Lord GJ & Rougemont J, Topological and $\epsilon$-entropy for Large Volume Limits of Discretised Parabolic Equations, SIAM J Numer Anal 40:1311—1329 (2002).
73. Rougemont J, Space-Time Invariant Measures, Entropy, and Dimension for Stochastic Ginzburg-Landau Equations, Commun Math Phys 225:423—448 (2002).
74. Rougemont J, Evaporation of Droplets in the Two-Dimensional Ginzburg-Landau Equation, Physica D 140:267—282 (2000).
75. Rougemont J, Dynamics of Kinks in the Ginzburg-Landau Equation: Approach to a Metastable Shape and Collapse of Embedded Pairs of Kinks, Nonlinearity 12:539—554 (1999).
76. Eckmann JP & Rougemont J, Coarsening by Ginzburg-Landau Dynamics, Commun Math Phys 199:441—470 (1998).