{"id":51,"date":"2020-01-24T16:16:10","date_gmt":"2020-01-24T16:16:10","guid":{"rendered":"http:\/\/localhost\/wordpress\/?page_id=51"},"modified":"2025-10-06T16:04:44","modified_gmt":"2025-10-06T14:04:44","slug":"publications","status":"publish","type":"page","link":"https:\/\/www.jacques-rougemont.ch\/?page_id=51&lang=en","title":{"rendered":"Publications-en"},"content":{"rendered":"\n<h1>Publications<\/h1>\n\n\n\n<h3>Research articles:<\/h3>\n\n\n\n<ol><li>Weinreb E, McBride JM, Siek M, et al., <em>Enzymes as viscoelastic catalytic machines<\/em>. <a href=\"https:\/\/www.nature.com\/articles\/s41567-025-02825-9\" target=\"_blank\" rel=\"noreferrer noopener\">Nat Phys <strong>21<\/strong>:787\u2014798 (2025)<\/a><\/li><li>Sala C, Benjak A, Goletti D, et al., <em>Multicenter analysis of sputum microbiota in tuberculosis patients.<\/em> <a rel=\"noreferrer noopener\" href=\"https:\/\/journals.plos.org\/plosone\/article?id=10.1371\/journal.pone.0240250\" target=\"_blank\">PLoS ONE <strong>15<\/strong>:e0240250 (2020)<\/a>.<\/li><li>Jeitziner R, Carri\u00e8re M, Rougemont J, et al., <em>Two-Tier Mapper, an unbiased topology-based clustering method for enhanced global gene expression analysis<\/em>. <a rel=\"noreferrer noopener\" aria-label=\" (opens in a new tab)\" href=\"https:\/\/academic.oup.com\/bioinformatics\/article\/35\/18\/3339\/5308599\" target=\"_blank\">Bioinformatics <strong>35<\/strong>:3339\u20143347 (2019)<\/a>.<\/li><li>Eckmann JP, Rougemont J &amp; Tlusty T, <em>Colloquium: Proteins: The physics of amorphous evolving matter<\/em>. <a rel=\"noreferrer noopener\" aria-label=\"Rev Modern Phys 91:031001 (2019) (opens in a new tab)\" href=\"https:\/\/journals.aps.org\/rmp\/abstract\/10.1103\/RevModPhys.91.031001\" target=\"_blank\">Rev Modern Phys <strong>91<\/strong>:031001 (2019)<\/a>.<\/li><li>Yeganeh M, Praz V, Carmeli C, et al., <em>Differential regulation of RNA polymerase III genes during liver regeneration<\/em>. <a rel=\"noreferrer noopener\" aria-label=\"Nucleic Acids Research 47:1786\u20141796 (2019) (opens in a new tab)\" href=\"https:\/\/academic.oup.com\/nar\/article\/47\/4\/1786\/5266946\" target=\"_blank\">Nucleic Acids Research <strong>47<\/strong>:1786\u20141796 (2019)<\/a>.<\/li><li>Scott CC, Vossio S, Rougemont J &amp; Gruenberg J, <em>TFAP2 transcription factors are regulators of lipid droplet biogenesis<\/em>, <a rel=\"noreferrer noopener\" aria-label=\"elife 7 (2018) (opens in a new tab)\" href=\"https:\/\/elifesciences.org\/articles\/36330\" target=\"_blank\">elife <strong>7<\/strong> (2018)<\/a>.<\/li><li>Rib L, Villeneuve D, Minocha S, et al., <em>Cycles of gene expression and genome response during mammalian tissue regeneration<\/em>, <a rel=\"noreferrer noopener\" aria-label=\"Epigenetics Chromatin 11:52 (2018) (opens in a new tab)\" href=\"https:\/\/epigeneticsandchromatin.biomedcentral.com\/articles\/10.1186\/s13072-018-0222-0\" target=\"_blank\">Epigenetics Chromatin <strong>11<\/strong>:52 (2018)<\/a>.<\/li><li>Dewhurst-Maridor G, Abegg D, David FPA, et al., <em>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<\/em>, <a rel=\"noreferrer noopener\" aria-label=\"Mol Biol Cell 28:2637\u20142649 (2017) (opens in a new tab)\" href=\"https:\/\/www.molbiolcell.org\/doi\/full\/10.1091\/mbc.E17-03-0169\" target=\"_blank\">Mol Biol Cell <strong>28<\/strong>:2637\u20142649 (2017)<\/a>.<\/li><li>Loviglio MN, Leleu M, M\u00e4nnik M, et al., <em>Chromosomal contacts connect loci associated with autism, BMI and head circumference phenotypes<\/em>, <a rel=\"noreferrer noopener\" aria-label=\"Mol Psychiatry 22:836\u2014849 (2017) (opens in a new tab)\" href=\"https:\/\/www.nature.com\/articles\/mp201684\" target=\"_blank\">Mol Psychiatry <strong>22<\/strong>:836\u2014849 (2017)<\/a>.<\/li><li>Mange F, Praz V, Migliavacca E, et al., <em>Diurnal regulation of RNA polymerase III transcription is under the control of both the feeding-fasting response and the circadian clock<\/em>, <a rel=\"noreferrer noopener\" aria-label=\"Genome Research 27:973\u2014984 (2017) (opens in a new tab)\" href=\"https:\/\/genome.cshlp.org\/content\/27\/6\/973.long\" target=\"_blank\">Genome Research <strong>27<\/strong>:973\u2014984 (2017)<\/a>.<\/li><li>David FPA, Rougemont J &amp; Deplancke B., <em>GETPrime 2.0: gene- and transcript-specific qPCR primers for 13 species including polymorphisms<\/em>, <a rel=\"noreferrer noopener\" aria-label=\"Nucleic Acids Research 45:D56\u2014D60 (2017) (opens in a new tab)\" href=\"https:\/\/academic.oup.com\/nar\/article\/45\/D1\/D56\/2770663\" target=\"_blank\">Nucleic Acids Research <strong>45<\/strong>:D56\u2014D60 (2017)<\/a>.<\/li><li>Loviglio MN, Beck CR, White JJ, et al., <em>Identification of a RAI1-associated disease network through integration of exome sequencing, transcriptomics, and 3D genomics<\/em>, <a rel=\"noreferrer noopener\" aria-label=\"Genome Med 8:105 (2016 (opens in a new tab)\" href=\"https:\/\/genomemedicine.biomedcentral.com\/articles\/10.1186\/s13073-016-0359-z\" target=\"_blank\">Genome Med <strong>8<\/strong>:105 (2016<\/a>).<\/li><li>Styles EB, Founk KJ, Zamparo LA, et al., <em>Exploring Quantitative Yeast Phenomics with Single-Cell Analysis of DNA Damage Foci<\/em>, <a rel=\"noreferrer noopener\" aria-label=\"Cell Syst 3:264\u2014277.e10 (2016) (opens in a new tab)\" href=\"https:\/\/www.cell.com\/cell-systems\/fulltext\/S2405-4712(16)30263-0\" target=\"_blank\">Cell Syst <strong>3<\/strong>:264\u2014277.e10 (2016)<\/a>.<\/li><li>SIB Swiss Institute of Bioinformatics Members. <em>The SIB Swiss Institute of Bioinformatics&#8217; resources: focus on curated databases<\/em>, <a rel=\"noreferrer noopener\" aria-label=\"Nucleic Acids Research 44:D27\u201437 (2016) (opens in a new tab)\" href=\"https:\/\/academic.oup.com\/nar\/article\/44\/D1\/D27\/2503101\" target=\"_blank\">Nucleic Acids Research <strong>44<\/strong>:D27\u201437 (2016)<\/a>.<\/li><li>Zaiss MM, Rapin A, Lebon L, et al., <em>The Intestinal Microbiota Contributes to the Ability of Helminths to Modulate Allergic Inflammation<\/em>, <a rel=\"noreferrer noopener\" aria-label=\"Immunity 43:998\u20141010 (2015) (opens in a new tab)\" href=\"https:\/\/www.cell.com\/immunity\/fulltext\/S1074-7613(15)00397-0\" target=\"_blank\">Immunity <strong>43<\/strong>:998\u20141010 (2015)<\/a>.<\/li><li>Kubik S, Bruzzone MJ, Jacquet P, et al., <em>Nucleosome Stability Distinguishes Two Different Promoter Types at All Protein-Coding Genes in Yeast<\/em>, <a rel=\"noreferrer noopener\" aria-label=\"Mol Cell 60:422\u2014434 (2015) (opens in a new tab)\" href=\"https:\/\/www.cell.com\/molecular-cell\/fulltext\/S1097-2765(15)00769-8\" target=\"_blank\">Mol Cell <strong>60<\/strong>:422\u2014434 (2015)<\/a>.<\/li><li>Lemaire L, Goulley J, Kim YH, et al., <em>Bicaudal C1 promotes pancreatic NEUROG3+ endocrine progenitor differentiation and ductal morphogenesis<\/em>, <a rel=\"noreferrer noopener\" aria-label=\"Development 142:858\u2014870, (2015) (opens in a new tab)\" href=\"https:\/\/dev.biologists.org\/content\/142\/5\/858.long\" target=\"_blank\">Development <strong>142<\/strong>:858\u2014870, (2015)<\/a>.<\/li><li>Droz-Georget Lathion S, Rochat A, Knott G, et al., <em>A single epidermal stem cell strategy for safe ex vivo gene therapy<\/em>, <a rel=\"noreferrer noopener\" aria-label=\"EMBO Mol Med 7:380\u2014393, (2015) (opens in a new tab)\" href=\"https:\/\/www.embopress.org\/doi\/full\/10.15252\/emmm.201404353\" target=\"_blank\">EMBO Mol Med <strong>7<\/strong>:380\u2014393, (2015)<\/a>.<\/li><li>Rajaram RD, Buric D, Caikovski M, et al., <em>Progesterone and Wnt4 control mammary stem cells via myoepithelial crosstalk<\/em>, <a rel=\"noreferrer noopener\" aria-label=\"EMBO Journal 34:641\u2014652, (2015) (opens in a new tab)\" href=\"https:\/\/www.embopress.org\/doi\/full\/10.15252\/embj.201490434\" target=\"_blank\">EMBO Journal <strong>34<\/strong>:641\u2014652, (2015)<\/a>.<\/li><li>Wachowicz P, Chasapi A, Krapp A, et al., <em>Analysis of S. pombe SIN protein SPB-association reveals two genetically separable states of the SIN<\/em>, <a rel=\"noreferrer noopener\" aria-label=\"J Cell Sci 128:741\u2014754, (2014 (opens in a new tab)\" href=\"https:\/\/jcs.biologists.org\/content\/128\/4\/741.long\" target=\"_blank\">J Cell Sci <strong>128<\/strong>:741\u2014754, (2014<\/a>).<\/li><li> Porro A, Feuerhahn S, Delafontaine J, et al., <em>Functional characterization of the TERRA transcriptome at damaged telomeres<\/em>, <a rel=\"noreferrer noopener\" aria-label=\"Nat Commun 5:5379, (2014) (opens in a new tab)\" href=\"https:\/\/www.nature.com\/articles\/ncomms6379\" target=\"_blank\">Nat Commun <strong>5<\/strong>:5379, (2014)<\/a>.<\/li><li> Knight B, Kubik S, Ghosh B, et al., <em>Two distinct promoter architectures centered on dynamic nucleosomes control ribosomal protein gene transcription<\/em>, <a rel=\"noreferrer noopener\" aria-label=\"Genes Dev 28:1695\u20141709 (2014) (opens in a new tab)\" href=\"http:\/\/genesdev.cshlp.org\/content\/28\/15\/1695.long\" target=\"_blank\">Genes Dev <strong>28<\/strong>:1695\u20141709 (2014)<\/a>.<\/li><li>Stockinger H, Altenhoff AM, Arnold K, et al., <em>Fifteen years SIB Swiss Institute of Bioinformatics: life science databases, tools and support<\/em>, <a rel=\"noreferrer noopener\" aria-label=\"Nucleic Acids Research 42:W436\u201441, (2014) (opens in a new tab)\" href=\"https:\/\/academic.oup.com\/nar\/article\/42\/W1\/W436\/2436660\" target=\"_blank\">Nucleic Acids Research <strong>42<\/strong>:W436\u201441, (2014)<\/a>.<\/li><li>Bonhoure N, Bounova G, Bernasconi D, et al., <em>Quantifying ChIP-seq data: a spiking method providing an internal reference for sample-to-sample normalization<\/em>, <a rel=\"noreferrer noopener\" aria-label=\"Genome Research 24:1157\u20141168, (2014) (opens in a new tab)\" href=\"https:\/\/genome.cshlp.org\/content\/24\/7\/1157.long\" target=\"_blank\">Genome Research <strong>24<\/strong>:1157\u20141168, (2014)<\/a>.<\/li><li>Solans L, Gonzalo-Asensio J, Sala C, et al., <em>The PhoP-Dependent ncRNA Mcr7 Modulates the TAT Secretion System in Mycobacterium tuberculosis<\/em>, <a rel=\"noreferrer noopener\" aria-label=\"PLoS pathogens 10:e1004183, (2014) (opens in a new tab)\" href=\"https:\/\/journals.plos.org\/plospathogens\/article?id=10.1371\/journal.ppat.1004183\" target=\"_blank\">PLoS pathogens <strong>10<\/strong>:e1004183, (2014)<\/a>.<\/li><li>Gilardi F, Migliavacca E, Naldi A, et al., <em>Genome-wide analysis of SREBP1 activity around the clock reveals its combined dependency on nutrient and circadian signals<\/em>, <a rel=\"noreferrer noopener\" aria-label=\"PLoS Genetics 10:e1004155, (2014) (opens in a new tab)\" href=\"https:\/\/journals.plos.org\/plosgenetics\/article?id=10.1371\/journal.pgen.1004155\" target=\"_blank\">PLoS Genetics <strong>10<\/strong>:e1004155, (2014)<\/a>.<\/li><li>Singh P, Benjak A, Carat S, et al., <em>Genome-wide re-sequencing of multidrug-resistant Mycobacterium leprae Airaku-3<\/em>, <a rel=\"noreferrer noopener\" aria-label=\"Clin Microbiol Infect 20:O619\u2014622, (2014) (opens in a new tab)\" href=\"https:\/\/www.clinicalmicrobiologyandinfection.com\/article\/S1198-743X(14)65395-7\/fulltext\" target=\"_blank\">Clin Microbiol Infect <strong>20<\/strong>:O619\u2014622, (2014)<\/a>.<\/li><li>David FPA, Delafontaine J, Carat S, et al., <em>HTSstation: A Web Application and Open-Access Libraries for High-Throughput Sequencing Data Analysis<\/em>, <a rel=\"noreferrer noopener\" aria-label=\"PLoS ONE 9:e85879, (2014) (opens in a new tab)\" href=\"https:\/\/journals.plos.org\/plosone\/article?id=10.1371\/journal.pone.0085879\" target=\"_blank\">PLoS ONE <strong>9<\/strong>:e85879, (2014)<\/a>.<\/li><li>Steijger T, Abril JF, Engstr\u00f6m PG, et al., <em>Assessment of transcript reconstruction methods for RNA-seq<\/em>, <a rel=\"noreferrer noopener\" aria-label=\"Nature methods 10:1177\u20141184, (2013) (opens in a new tab)\" href=\"https:\/\/www.nature.com\/articles\/nmeth.2714\" target=\"_blank\">Nature methods <strong>10<\/strong>:1177\u20141184, (2013)<\/a>.<\/li><li>Gheldof N, Witwicki RM, Migliavacca E, et al., <em>Structural variation-associated expression changes are paralleled by chromatin architecture modifications<\/em>, <a rel=\"noreferrer noopener\" aria-label=\"PLoS ONE 8:e79973 (2013) (opens in a new tab)\" href=\"https:\/\/journals.plos.org\/plosone\/article?id=10.1371\/journal.pone.0079973\" target=\"_blank\">PLoS ONE <strong>8<\/strong>:e79973 (2013)<\/a>.<\/li><li>Uplekar S, Rougemont J, Cole ST &amp; Sala C, <em>High-resolution transcriptome and genome-wide dynamics of RNA polymerase and NusA in Mycobacterium tuberculosis<\/em>, <a rel=\"noreferrer noopener\" aria-label=\"Nucleic Acids Research 41:961\u2014977 (2013) (opens in a new tab)\" href=\"https:\/\/academic.oup.com\/nar\/article\/41\/2\/961\/1071254\" target=\"_blank\">Nucleic Acids Research <strong>41<\/strong>:961\u2014977 (2013)<\/a>.<\/li><li>Le Martelot G, Canella D, Symul L, Migliavacca E et al., <em>Genome-Wide RNA Polymerase II Profiles and RNA Accumulation Reveal Kinetics of Transcription and Associated Epigenetic Changes During Diurnal Cycles<\/em>, <a rel=\"noreferrer noopener\" aria-label=\"PLoS Biology 10:e1001442 (2012) (opens in a new tab)\" href=\"https:\/\/journals.plos.org\/plosbiology\/article?id=10.1371\/journal.pbio.1001442\" target=\"_blank\">PLoS Biology <strong>10<\/strong>:e1001442 (2012)<\/a>.<\/li><li>Weissbrodt DG, Shani N, Sinclair L, Lefebvre G et al., <em>PyroTRF-ID: a novel bioinformatics methodology for the affiliation of terminal-restriction fragments using 16S rRNA gene pyrosequencing data<\/em>, <a rel=\"noreferrer noopener\" aria-label=\"BMC microbiology 12:306 (2012) (opens in a new tab)\" href=\"https:\/\/bmcmicrobiol.biomedcentral.com\/articles\/10.1186\/1471-2180-12-306\" target=\"_blank\">BMC microbiology <strong>12<\/strong>:306 (2012)<\/a>.<\/li><li>Hornitschek P, Kohnen MV, Lorrain S, et al., <em>Phytochrome interacting factors 4 and 5 control seedling growth in changing light conditions by directly controlling auxin signaling<\/em>, <a rel=\"noreferrer noopener\" aria-label=\"Plant J 71:699\u2014711 (2012) (opens in a new tab)\" href=\"https:\/\/onlinelibrary.wiley.com\/doi\/full\/10.1111\/j.1365-313X.2012.05033.x\" target=\"_blank\">Plant J <strong>71<\/strong>:699\u2014711 (2012)<\/a>.<\/li><li>Hartkoorn R, Sala C, Uplekar S, et al., <em>Genome-Wide Definition of the SigF Regulon in Mycobacterium tuberculosis<\/em>, <a rel=\"noreferrer noopener\" aria-label=\"J Bacteriol 194:2001\u20142009 (2012) (opens in a new tab)\" href=\"https:\/\/jb.asm.org\/content\/194\/8\/2001.long\" target=\"_blank\">J Bacteriol <strong>194<\/strong>:2001\u20142009 (2012)<\/a>.<\/li><li>Canella D, Bernasconi D, Gilardi F, et al., <em>A multiplicity of factors contributes to selective RNA polymerase III occupancy of a subset of RNA polymerase III genes in mouse liver<\/em>, <a rel=\"noreferrer noopener\" aria-label=\"Genome Res 22:666\u2014680 (2012) (opens in a new tab)\" href=\"https:\/\/genome.cshlp.org\/content\/22\/4\/666.long\" target=\"_blank\">Genome Res <strong>22<\/strong>:666\u2014680 (2012)<\/a>.<\/li><li>Blasco B, Chen JM, Hartkoorn R, et al., <em>Virulence Regulator EspR of Mycobacterium tuberculosis is a Nucleoid-Associated Protein<\/em>, <a rel=\"noreferrer noopener\" aria-label=\"PLoS pathogens 8:e1002621 (2012) (opens in a new tab)\" href=\"https:\/\/journals.plos.org\/plospathogens\/article?id=10.1371\/journal.ppat.1002621\" target=\"_blank\">PLoS pathogens <strong>8<\/strong>:e1002621 (2012)<\/a>.<\/li><li>Noordermeer D, Leleu M, Splinter E, et al., <em>The dynamic architecture of Hox gene clusters<\/em>, <a rel=\"noreferrer noopener\" aria-label=\"Science 334:222\u2014225 (2011) (opens in a new tab)\" href=\"https:\/\/science.sciencemag.org\/content\/334\/6053\/222.long\" target=\"_blank\">Science <strong>334<\/strong>:222\u2014225 (2011)<\/a>.<\/li><li>Gubelmann C, Gattiker A, Massouras A, et al., <em>GETPrime: a gene- or transcript-specific primer database for quantitative real-time PCR<\/em>, <a rel=\"noreferrer noopener\" aria-label=\"Database 2011:bar040 (2011) (opens in a new tab)\" href=\"https:\/\/academic.oup.com\/database\/article\/doi\/10.1093\/database\/bar040\/467059\" target=\"_blank\">Database <strong>2011<\/strong>:bar040 (2011)<\/a>.<\/li><li>Ayyanan A, Laribi O, Schuepbach-Mallepell S, et al., <em>Perinatal exposure to Bisphenol A increases adult mammary gland progesterone response and cell number<\/em>, <a rel=\"noreferrer noopener\" aria-label=\"Molecular Endocrinology 25:1915\u20141923 (2011) (opens in a new tab)\" href=\"https:\/\/academic.oup.com\/mend\/article\/25\/11\/1915\/2614776\" target=\"_blank\">Molecular Endocrinology <strong>25<\/strong>:1915\u20141923 (2011)<\/a>.<\/li><li>Meylan S, Groner AC, Ambrosini G, et al., <em>A gene-rich, transcriptionally active environment and the pre-deposition of repressive marks are predictive of susceptibility to KRAB\/KAP1-mediated silencing<\/em>, <a rel=\"noreferrer noopener\" aria-label=\"BMC Genomics 12:378 (2011) (opens in a new tab)\" href=\"https:\/\/bmcgenomics.biomedcentral.com\/articles\/10.1186\/1471-2164-12-378\" target=\"_blank\">BMC Genomics <strong>12<\/strong>:378 (2011)<\/a>.<\/li><li>Uplekar S, Heym B, Friocourt V, Rougemont J &amp; Cole ST, <em>Comparative genomics of esx genes from clinical isolates of Mycobacterium tuberculosis provides evidence for gene conversion and epitope variation<\/em>, <a rel=\"noreferrer noopener\" aria-label=\"Infection and Immunity 79:4042\u20144049 (2011) (opens in a new tab)\" href=\"https:\/\/iai.asm.org\/content\/79\/10\/4042.long\" target=\"_blank\">Infection and Immunity <strong>79<\/strong>:4042\u20144049 (2011)<\/a>.<\/li><li>Huber A, French SL, Tekotte H, et al., <em>Sch9 regulates ribosome biogenesis via Stb3, Dot6 and Tod6 and the histone deacetylase complex RPD3L<\/em>, <a rel=\"noreferrer noopener\" aria-label=\"EMBO Journal 20:3052-3064 (2011) (opens in a new tab)\" href=\"https:\/\/www.embopress.org\/doi\/10.1038\/emboj.2011.221\" target=\"_blank\">EMBO Journal <strong>20<\/strong>:3052-3064 (2011)<\/a>.<\/li><li>Lefebvre G, Beerenwinkel N, Rougemont J, Telenti A &amp; Ciuffi A, <em>Analysis of HIV-1 Expression Level and Sense of Transcription by High-Throughput Sequencing of the Infected Cell<\/em>, <a rel=\"noreferrer noopener\" aria-label=\"Journal of Virology 85:6205\u20146211 (2011) (opens in a new tab)\" href=\"https:\/\/jvi.asm.org\/content\/85\/13\/6205.long\" target=\"_blank\">Journal of Virology <strong>85<\/strong>:6205\u20146211 (2011)<\/a>.<\/li><li>Truman RW, Singh P, Sharma R, et al., <em>Probable zoonotic leprosy in the southern United States<\/em>, <a rel=\"noreferrer noopener\" aria-label=\"The New England Journal of Medicine 364:1626\u20141633, (2011) (opens in a new tab)\" href=\"https:\/\/www.nejm.org\/doi\/10.1056\/NEJMoa1010536\" target=\"_blank\">The New England Journal of Medicine <strong>364<\/strong>:1626\u20141633, (2011)<\/a>.<\/li><li>Rey G, Cesbron F, Rougemont J, et al., <em>Genome-wide and phase-specific DNA-binding rhythms of BMAL1 control circadian output functions in mouse liver<\/em>, <a rel=\"noreferrer noopener\" aria-label=\"PLoS Biology 9:e1000595 (2011) (opens in a new tab)\" href=\"https:\/\/journals.plos.org\/plosbiology\/article?id=10.1371\/journal.pbio.1000595\" target=\"_blank\">PLoS Biology <strong>9<\/strong>:e1000595 (2011)<\/a>.<\/li><li>Stoll G, et al., <em>Stabilizing patterning in the Drosophila segment polarity network by selecting models in silico<\/em>, <a rel=\"noreferrer noopener\" aria-label=\"Biosystems 102:3\u201410 (2010) (opens in a new tab)\" href=\"https:\/\/www.sciencedirect.com\/science\/article\/pii\/S030326471000122X\" target=\"_blank\">Biosystems <strong>102<\/strong>:3\u201410 (2010)<\/a>.<\/li><li>Leleu M, Lefebvre G &amp; Rougemont J, <em>Processing and analyzing ChIP-seq data: from short reads to regulatory interactions<\/em>, <a rel=\"noreferrer noopener\" aria-label=\"Briefings in Functional Genomics 9:466\u2014476 (2010) (opens in a new tab)\" href=\"https:\/\/academic.oup.com\/bfg\/article\/9\/5-6\/466\/181894\" target=\"_blank\">Briefings in Functional Genomics <strong>9<\/strong>:466\u2014476 (2010)<\/a>.<\/li><li>Massouras A, Hens K, Gubelmann C, et al. <em>Primer-initiated sequence synthesis to detect and assemble structural variants<\/em>, <a rel=\"noreferrer noopener\" aria-label=\"Nature Methods 7:485\u2014486 (2010) (opens in a new tab)\" href=\"https:\/\/www.nature.com\/articles\/nmeth.f.308\" target=\"_blank\">Nature Methods <strong>7<\/strong>:485\u2014486 (2010)<\/a>.<\/li><li>Preti M, Ribeyre C, Pascali C, et al., <em>The telomere-binding protein Tbf1 demarcates snoRNA gene promoters in Saccharomyces cerevisiae<\/em>, <a rel=\"noreferrer noopener\" aria-label=\"Molecular Cell 38:614\u2014620 (2010) (opens in a new tab)\" href=\"https:\/\/www.cell.com\/molecular-cell\/fulltext\/S1097-2765(10)00329-1\" target=\"_blank\">Molecular Cell <strong>38<\/strong>:614\u2014620 (2010)<\/a>.<\/li><li>Rowe HM, Jakobsson J, Mesnard D, et al. <em>KAP1 controls endogenous retroviruses in embryonic stem cells<\/em>, <a rel=\"noreferrer noopener\" aria-label=\"Nature 463:237\u2014240 (2010) (opens in a new tab)\" href=\"https:\/\/www.nature.com\/articles\/nature08674\" target=\"_blank\">Nature <strong>463<\/strong>:237\u2014240 (2010)<\/a>.<\/li><li>Monot M, Honor\u00e9 N, Garnier Th, et al., <em>Comparative genomic and phylogeographic analysis of Mycobacterium leprae<\/em>, <a rel=\"noreferrer noopener\" aria-label=\"Nat Genet 41:1282\u20141289 (2009) (opens in a new tab)\" href=\"https:\/\/www.nature.com\/articles\/ng.477\" target=\"_blank\">Nat Genet <strong>41<\/strong>:1282\u20141289 (2009)<\/a>.<\/li><li>Nikolaev SI, Iseli Ch, Sharp AJ, et al., <em>Detection of genomic variation by selection of a 9 mb DNA region and high throughput sequencing<\/em>, <a rel=\"noreferrer noopener\" aria-label=\"PLoS ONE 4:e6659 (2009) (opens in a new tab)\" href=\"https:\/\/journals.plos.org\/plosone\/article?id=10.1371\/journal.pone.0006659\" target=\"_blank\">PLoS ONE <strong>4<\/strong>:e6659 (2009)<\/a>.<\/li><li>Gattiker A, Dessimoz Ch, Schneider A, et al., <em>The Microbe browser for comparative genomics<\/em>, <a rel=\"noreferrer noopener\" aria-label=\"Nucleic Acids Res 37:W296\u2014299 (2009) (opens in a new tab)\" href=\"https:\/\/academic.oup.com\/nar\/article\/37\/suppl_2\/W296\/1125264\" target=\"_blank\">Nucleic Acids Res <strong>37<\/strong>:W296\u2014299 (2009)<\/a>.<\/li><li>Gattiker A, Hermida L, Liechti R, et al., <em>MIMAS 3.0 is a Multiomics Information Management and Annotation System<\/em>, <a rel=\"noreferrer noopener\" aria-label=\"BMC Bioinformatics 10:151 (2009) (opens in a new tab)\" href=\"https:\/\/bmcbioinformatics.biomedcentral.com\/articles\/10.1186\/1471-2105-10-151\" target=\"_blank\">BMC Bioinformatics <strong>10<\/strong>:151 (2009)<\/a>.<\/li><li>Rougemont J, Amzallag A, Iseli Ch, et al., <em>Probabilistic base calling of Solexa sequencing data<\/em>, <a rel=\"noreferrer noopener\" aria-label=\"BMC Bioinformatics, 9:431 (2008) (opens in a new tab)\" href=\"https:\/\/bmcbioinformatics.biomedcentral.com\/articles\/10.1186\/1471-2105-9-431\" target=\"_blank\">BMC Bioinformatics, <strong>9<\/strong>:431 (2008)<\/a>.<\/li><li>Stamatakis A, Hoover P &amp; Rougemont J, <em>A rapid bootstrap algorithm for the RAxML Web servers<\/em>, <a rel=\"noreferrer noopener\" aria-label=\"Syst Biol,  57, 758\u2014771 (2008) (opens in a new tab)\" href=\"https:\/\/academic.oup.com\/sysbio\/article\/57\/5\/758\/1618491\" target=\"_blank\">Syst Biol,  <strong>57<\/strong>, 758\u2014771 (2008)<\/a>.<\/li><li>Stoll G, Rougemont J &amp; Naef F, <em>Representing perturbed dynamics in biological network models<\/em>, <a rel=\"noreferrer noopener\" aria-label=\"Phys Rev E, 76, 011917 (2007) (opens in a new tab)\" href=\"https:\/\/journals.aps.org\/pre\/abstract\/10.1103\/PhysRevE.76.011917\" target=\"_blank\">Phys Rev E, <strong>76<\/strong>, 011917 (2007)<\/a>.<\/li><li>Rougemont J &amp; Naef F, <em>Dynamical signatures of cellular fluctuations and oscillator stability in peripheral circadian clocks<\/em>, <a rel=\"noreferrer noopener\" aria-label=\"Mol Syst Biol, 3:93 (2007) (opens in a new tab)\" href=\"https:\/\/www.embopress.org\/doi\/full\/10.1038\/msb4100130\" target=\"_blank\">Mol Syst Biol, <strong>3<\/strong>:93 (2007)<\/a>.<\/li><li>Nikolaev SI, Montoya-Burgos JI, Margulies EH, NISC Comparative Sequencing Program, Rougemont J, Nyffeler B &amp; Antonarakis SE, <em>Early History of Mammals is Elucidated with the ENCODE Multiple Species Sequencing Data<\/em>, <a rel=\"noreferrer noopener\" aria-label=\"PLoS Genet, 3:e2 (2007) (opens in a new tab)\" href=\"https:\/\/journals.plos.org\/plosgenetics\/article?id=10.1371\/journal.pgen.0030002\" target=\"_blank\">PLoS Genet, <strong>3<\/strong>:e2 (2007)<\/a>.<\/li><li>Guillaume F, &amp; Rougemont J, <em>Nemo: an evolutionary and population genetics programming framework<\/em>, <a rel=\"noreferrer noopener\" aria-label=\"Bioinformatics, 22:2556\u20142557 (2006) (opens in a new tab)\" href=\"https:\/\/academic.oup.com\/bioinformatics\/article\/22\/20\/2556\/218293\" target=\"_blank\">Bioinformatics, <strong>22<\/strong>:2556\u20142557 (2006)<\/a>.<\/li><li>Stoll G, Rougemont J &amp; Naef F, <em>Few crucial links assure checkpoint efficiency in the yeast cell-cycle network<\/em>, <a rel=\"noreferrer noopener\" aria-label=\"Bioinformatics, 22:2539\u20142546 (2006) (opens in a new tab)\" href=\"https:\/\/academic.oup.com\/bioinformatics\/article\/22\/20\/2539\/218727\" target=\"_blank\">Bioinformatics, <strong>22<\/strong>:2539\u20142546 (2006)<\/a>.<\/li><li>Honor\u00e9 P, Granjeaud S, Tagett R, et al., <em>MicroArray Facility: a laboratory information management system with extended support for Nylon based technologies<\/em>, <a rel=\"noreferrer noopener\" aria-label=\"BMC Genomics, 7:240 (2006) (opens in a new tab)\" href=\"https:\/\/bmcgenomics.biomedcentral.com\/articles\/10.1186\/1471-2164-7-240\" target=\"_blank\">BMC Genomics, <strong>7<\/strong>:240 (2006)<\/a>.<\/li><li>Rougemont J &amp; Naef F, <em>Collective Synchronization in Populations of Globally Coupled Phase Oscillators with Drifting Frequencies<\/em>, <a rel=\"noreferrer noopener\" aria-label=\"Phys Rev E 73:011104 (2006) (opens in a new tab)\" href=\"https:\/\/journals.aps.org\/pre\/abstract\/10.1103\/PhysRevE.73.011104\" target=\"_blank\">Phys Rev E <strong>73<\/strong>:011104 (2006)<\/a>.<\/li><li>Deutsch S, Lyle R, Dermitzakis ET, et al., <em>Gene Expression Variation and Expression Quantitative Trait Mapping of Human Chromosome 21 Genes<\/em>, <a rel=\"noreferrer noopener\" aria-label=\"Hum Mol Genet 14:3741\u20143749 (2005) (opens in a new tab)\" href=\"https:\/\/academic.oup.com\/hmg\/article\/14\/23\/3741\/559486\" target=\"_blank\">Hum Mol Genet <strong>14<\/strong>:3741\u20143749 (2005)<\/a>.<\/li><li>Bertucci F, Finetti P, Rougemont J, et al., <em>Gene Expression Profiling Identifies Molecular Subtypes of Inflammatory Breast Cancer<\/em>, <a rel=\"noreferrer noopener\" aria-label=\"Cancer Res 65:2170\u20142178 (2005) (opens in a new tab)\" href=\"https:\/\/cancerres.aacrjournals.org\/content\/65\/6\/2170.long\" target=\"_blank\">Cancer Res <strong>65<\/strong>:2170\u20142178 (2005)<\/a>.<\/li><li>Jacquemier J, Ginestier Ch, Rougemont J, et al., <em>Protein Expression Profiling Identifies Subclasses of Breast Cancers and Predicts Prognosis<\/em>, <a rel=\"noreferrer noopener\" aria-label=\"Cancer Res 65:767\u2014779 (2005) (opens in a new tab)\" href=\"https:\/\/cancerres.aacrjournals.org\/content\/65\/3\/767.long\" target=\"_blank\">Cancer Res <strong>65<\/strong>:767\u2014779 (2005)<\/a>.<\/li><li>Bertucci F, Finetti P, Rougemont J, et al., <em>Gene Expression Profiling for Molecular Characterization of Inflammatory Breast Cancer and Prediction of Response to Chemotherapy<\/em>, <a rel=\"noreferrer noopener\" aria-label=\"Cancer Res 64:8558\u20148565 (2004) (opens in a new tab)\" href=\"https:\/\/cancerres.aacrjournals.org\/content\/64\/23\/8558\" target=\"_blank\">Cancer Res <strong>64<\/strong>:8558\u20148565 (2004)<\/a>.<\/li><li>Lord GJ &amp; Rougemont J, <em>A Numerical Scheme for Stochastic PDEs with Gevrey Regularity<\/em>, <a rel=\"noreferrer noopener\" aria-label=\"IMA J Numer Anal 24:587\u2014604 (2004) (opens in a new tab)\" href=\"https:\/\/academic.oup.com\/imajna\/article\/24\/4\/587\/687374\" target=\"_blank\">IMA J Numer Anal <strong>24<\/strong>:587\u2014604 (2004)<\/a>.<\/li><li>Lopez F, Rougemont J, Loriod B, et al., <em>Feature Extraction and Signal Processing for Nylon DNA Microarrays<\/em>, <a rel=\"noreferrer noopener\" aria-label=\"BMC Genomics 5:38 (2004) (opens in a new tab)\" href=\"https:\/\/bmcgenomics.biomedcentral.com\/articles\/10.1186\/1471-2164-5-38\" target=\"_blank\">BMC Genomics <strong>5<\/strong>:38 (2004)<\/a>.<\/li><li>Lord GJ &amp; Rougemont J, <em>Numerical Computation of $\\epsilon$-Entropy for Parabolic Equations with Analytic Solutions<\/em>, <a rel=\"noreferrer noopener\" aria-label=\"Physica D 194:65\u201474 (2004) (opens in a new tab)\" href=\"https:\/\/www.sciencedirect.com\/science\/article\/abs\/pii\/S016727890400065X\" target=\"_blank\">Physica D <strong>194<\/strong>:65\u201474 (2004)<\/a>.<\/li><li>Rougemont J &amp; Hingamp P, <em>DNA Microarray Data and Contextual Analysis of Correlation Graphs<\/em>,  <a rel=\"noreferrer noopener\" aria-label=\"BMC Bioinformatics 4:15 (2003) (opens in a new tab)\" href=\"https:\/\/bmcbioinformatics.biomedcentral.com\/articles\/10.1186\/1471-2105-4-15\" target=\"_blank\">BMC Bioinformatics <strong>4<\/strong>:15 (2003)<\/a>.<\/li><li>Lord GJ &amp; Rougemont J, <em>Topological and $\\epsilon$-entropy for Large Volume Limits of Discretised Parabolic Equations<\/em>, <a rel=\"noreferrer noopener\" aria-label=\"SIAM J Numer Anal 40:1311\u20141329 (2002) (opens in a new tab)\" href=\"https:\/\/epubs.siam.org\/doi\/10.1137\/S0036142901392328\" target=\"_blank\">SIAM J Numer Anal <strong>40<\/strong>:1311\u20141329 (2002)<\/a>.<\/li><li>Rougemont J, <em>Space-Time Invariant Measures, Entropy, and Dimension for Stochastic Ginzburg-Landau Equations<\/em>, <a rel=\"noreferrer noopener\" aria-label=\"Commun Math Phys 225:423\u2014448 (2002) (opens in a new tab)\" href=\"https:\/\/link.springer.com\/article\/10.1007\/s002200100586\" target=\"_blank\">Commun Math Phys <strong>225<\/strong>:423\u2014448 (2002)<\/a>.<\/li><li>Rougemont J, <em>Evaporation of Droplets in the Two-Dimensional Ginzburg-Landau Equation<\/em>, <a rel=\"noreferrer noopener\" aria-label=\"Physica D 140:267\u2014282 (2000) (opens in a new tab)\" href=\"https:\/\/www.sciencedirect.com\/science\/article\/abs\/pii\/S0167278900000099\" target=\"_blank\">Physica D <strong>140<\/strong>:267\u2014282 (2000)<\/a>.<\/li><li>Rougemont J, <em>Dynamics of Kinks in the Ginzburg-Landau Equation: Approach to a Metastable Shape and Collapse of Embedded Pairs of Kinks<\/em>, <a rel=\"noreferrer noopener\" aria-label=\"Nonlinearity 12:539\u2014554 (1999) (opens in a new tab)\" href=\"https:\/\/iopscience.iop.org\/article\/10.1088\/0951-7715\/12\/3\/007\" target=\"_blank\">Nonlinearity <strong>12<\/strong>:539\u2014554 (1999)<\/a>.<\/li><li>Eckmann JP &amp; Rougemont J, <em>Coarsening by Ginzburg-Landau Dynamics<\/em>, <a rel=\"noreferrer noopener\" aria-label=\"Commun Math Phys 199:441\u2014470 (1998) (opens in a new tab)\" href=\"https:\/\/link.springer.com\/article\/10.1007\/s002200050508\" target=\"_blank\">Commun Math Phys <strong>199<\/strong>:441\u2014470 (1998)<\/a>. <\/li><\/ol>\n\n\n\n<h3>Conference proceedings, book chapters, and other publications:<\/h3>\n\n\n\n<ol><li>Ayday E, Raisaro JL, Rougemont J &amp; Hubaux JP, <em>Protecting and evaluating genomic privacy in medical tests and personalized medicine<\/em>, <a rel=\"noreferrer noopener\" aria-label=\"The 12th ACM workshop (2013) (opens in a new tab)\" href=\"https:\/\/dl.acm.org\/doi\/10.1145\/2517840.2517843\" target=\"_blank\">The 12th ACM workshop (2013)<\/a>.<\/li><li>Rougemont J &amp; Naef F, <em>Computational Analysis of Protein-DNA Interactions from ChIP-seq Data<\/em>, <a rel=\"noreferrer noopener\" aria-label=\"Methods in Molecular Biology 786:263\u2014273 (2012) (opens in a new tab)\" href=\"https:\/\/link.springer.com\/protocol\/10.1007\/978-1-61779-292-2_16\" target=\"_blank\">Methods in Molecular Biology <strong>786<\/strong>:263\u2014273 (2012)<\/a>, Springer.<\/li><li>Gheldof N, Leleu M, Noordermeer D, Rougemont J, Reymond A, <em>Detecting Long-Range Chromatin Interactions Using the Chromosome Conformation Capture Sequencing (4C-seq) Method<\/em>, <a rel=\"noreferrer noopener\" aria-label=\"Methods in Molecular Biology 786:211\u2014225 (2012) (opens in a new tab)\" href=\"https:\/\/link.springer.com\/protocol\/10.1007\/978-1-61779-292-2_13\" target=\"_blank\">Methods in Molecular Biology <strong>786<\/strong>:211\u2014225 (2012)<\/a>, Springer.<\/li><li>Rougemont J &amp; Naef F, <em>Stochastic phase oscillator models for circadian clocks<\/em>, <a rel=\"noreferrer noopener\" aria-label=\"Cellular Oscillatory Mechanisms, M Maroto, N Monk (eds.) (2008) (opens in a new tab)\" href=\"https:\/\/link.springer.com\/chapter\/10.1007\/978-0-387-09794-7_10\" target=\"_blank\">Cellular Oscillatory Mechanisms, M Maroto, N Monk (eds.) (2008)<\/a>, Springer.<\/li><li>Rougemont J &amp; Naef F, <em>Stochastic phase oscillators and bioluminescence recordings<\/em>, <a rel=\"noreferrer noopener\" aria-label=\"Cold Spring Harbor Symposia on Quantitative Biology LXXII (2007) (opens in a new tab)\" href=\"http:\/\/symposium.cshlp.org\/content\/72\/405.long\" target=\"_blank\">Cold Spring Harbor Symposia on Quantitative Biology <strong>LXXII<\/strong> (2007)<\/a>, Cold Spring Harbor Laboratory Press.<\/li><li>Bittner F, Denteneer D, Kronemeijer S, et al., <em>On Lossless Compression of 1-bit Audio Signals<\/em>, <a href=\"http:\/\/www.maths-in-industry.org\/miis\/92\/\" target=\"_blank\" rel=\"noreferrer noopener\" aria-label=\"Proceedings of the forty-second European study group with industry, G.M. Hek (ed.) (2002) (opens in a new tab)\">Proceedings of the forty-second European study group with industry, G.M. Hek (ed.) (2002)<\/a>.<\/li><li>Rougemont J, <em>Book Review: Global Attractors in Abstract Parabolic Problems by J. W. Cholewa &amp; T. Dlotko<\/em>, <a href=\"https:\/\/londmathsoc.onlinelibrary.wiley.com\/doi\/abs\/10.1112\/S0024609301218840\" target=\"_blank\" rel=\"noreferrer noopener\" aria-label=\"Bull London Math Soc, 33:758\u2014759 (2001) (opens in a new tab)\">Bull London Math Soc, <strong>33<\/strong>:758\u2014759 (2001)<\/a>.<\/li><li>Rougemont J, <em>Equation de Ginzburg-Landau et ph\u00e9nom\u00e8ne d&#8217;homog\u00e9n\u00e9isation en dimensions 1 et 2<\/em>, PhD Thesis, University of Geneva, 1999.<\/li><li>Eckmann JP, Rougemont J &amp; Schenkel A, <em>How to Park a Truck with n Trailers<\/em>, Lecture Notes, University of Geneva, 1996.<\/li><li>Rougemont J, <em>Dualit\u00e9 spectrale pour une cha\u00eene de billards quantiques<\/em>, Master thesis, University of Geneva, 1995.<\/li><\/ol>\n","protected":false},"excerpt":{"rendered":"<p>Publications Research articles: Weinreb E, McBride JM, Siek M, et al., Enzymes as viscoelastic catalytic machines. Nat Phys 21:787\u2014798 (2025) Sala C, Benjak A, Goletti D, et al., Multicenter analysis of sputum microbiota in tuberculosis patients. PLoS ONE 15:e0240250 (2020). Jeitziner R, Carri\u00e8re M, Rougemont J, et al., Two-Tier Mapper, an unbiased topology-based clustering method [&hellip;]<\/p>\n","protected":false},"author":1,"featured_media":0,"parent":45,"menu_order":0,"comment_status":"closed","ping_status":"closed","template":"","meta":[],"_links":{"self":[{"href":"https:\/\/www.jacques-rougemont.ch\/index.php?rest_route=\/wp\/v2\/pages\/51"}],"collection":[{"href":"https:\/\/www.jacques-rougemont.ch\/index.php?rest_route=\/wp\/v2\/pages"}],"about":[{"href":"https:\/\/www.jacques-rougemont.ch\/index.php?rest_route=\/wp\/v2\/types\/page"}],"author":[{"embeddable":true,"href":"https:\/\/www.jacques-rougemont.ch\/index.php?rest_route=\/wp\/v2\/users\/1"}],"replies":[{"embeddable":true,"href":"https:\/\/www.jacques-rougemont.ch\/index.php?rest_route=%2Fwp%2Fv2%2Fcomments&post=51"}],"version-history":[{"count":12,"href":"https:\/\/www.jacques-rougemont.ch\/index.php?rest_route=\/wp\/v2\/pages\/51\/revisions"}],"predecessor-version":[{"id":752,"href":"https:\/\/www.jacques-rougemont.ch\/index.php?rest_route=\/wp\/v2\/pages\/51\/revisions\/752"}],"up":[{"embeddable":true,"href":"https:\/\/www.jacques-rougemont.ch\/index.php?rest_route=\/wp\/v2\/pages\/45"}],"wp:attachment":[{"href":"https:\/\/www.jacques-rougemont.ch\/index.php?rest_route=%2Fwp%2Fv2%2Fmedia&parent=51"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}