• Zhurinsky J, Leonhard K, Watt S, Marguerat S, Bähler J, Nurse P. (2010). A Coordinated Global Control over Cellular Transcription.
    Curr Biol, 404, 183-201.

    PDF Pubmed Curr Biol

  • Nemoto N, Udagawa T, Ohira T, Jiang L, Hirota K, Wilkinson CR, Bähler J, Jones N, Ohta K, Wek RC, Asano K (2010). The Roles of Stress-Activated Sty1 and Gcn2 Kinases and of the Protooncoprotein Homologue Int6/eIF3e in Responses to Endogenous Oxidative Stress during Histidine Starvation.
    J. Mol.Biol., 26;404(2):183-201.

    PDF Pubmed JMB

  • Kiang L, Heichinger C, Watt S, Bähler J, Nurse P (2010). Specific replication origins promote DNA amplification in fission yeast.
    J. Cell Science, 123, 3047-3051.

    PDF Pubmed JCS

  • St-André O, Lemieux C, Perreault A, Lackner DH, Bähler J, Bachand F (2010). Negative regulation of meiotic gene expression by the nuclear poly(A)-binding protein in fission yeast.
    J. Biol. Chem., 285, 27859-27868.

    PDF Pubmed JBC

  • Wen WL, Stevenson AL, Wang CY, Chen HJ, Kearsey SE, Norbury CJ, Watt S, Bähler J, Wang SW (2010). Vgl1, a multi-KH domain protein, is a novel component of the fission yeast stress granules required for cell survival under thermal stress.
    Nucleic Acids Res., 38, 6555-6566.

    PDF Pubmed Nucleic Acids Res

  • Kaufmann I, White E, Azad A, Marguerat S, Bähler J, Proudfoot NJ (2010). Transcriptional activation of the general amino acid permease gene per1 by the histone deacetylase Clr6 Is regulated by Oca2 kinase.
    Mol. Cell. Biol., 30, 3396–3410.

    PDF Pubmed Mol Cell Biol

  • Onishi M, Koga T, Hirata A, Nakamura T, Asakawa H, Shimoda C, Bähler J, Wu JQ, Takegawa K, Tachikawa H, Pringle JR, Fukui Y (2010). Role of septins in the orientation of forespore membrane extension during sporulation in fission yeast.
    Mol. Cell Biol., 30, 2057-2074.

    PDF Pubmed Mol Cell Biol

  • Wilhelm B, Marguerat S, Goodhead I, Bähler J (2010). Defining transcribed regions in fission yeast using RNA-seq.
    Nature Protocols, 5:255-266.

    PDF Pubmed Nature Prot

  • Lemay J-F, D’Amours A, Lemieux C, Lackner DH, St-Sauveur VG, Bähler J, Bachand F (2010). The nuclear poly(A)-binding protein interacts with the exosome to promote synthesis of noncoding small nucleolar RNAs.
    Mol. Cell. 37:34-45.

    PDF Pubmed Mol Cell

  • Pancaldi V, Schubert F, Bähler J (2010). Meta-analysis of genome regulation and expression variability across hundreds of environmental and genetic perturbations in fission yeast.
    Mol. BioSystems, 6:543-552.

    PDF Pubmed Mol BioSystems Supplementary Data


  • Marguerat S, Bähler J (2009). RNA-seq: from technology to biology.
    Cell. Mol. Life. Sci. 67:569-579.

    PDF Pubmed Cell Mol Life Sci

  • Kim H-S, Vanoosthuyse V, Fillingham J, Roguev A, Watt S, Kislinger T, Treyer A, Carpenter LR, Bennett CS, Emili A, Greenblatt JF, Hardwick KG, Krogan NJ, Bähler J, Keogh M-C (2009). An acetylated form of histone H2A.Z regulates chromosome architecture in Schizosaccharomyces pombe.
    Nat. Struct. Mol. Biol. 16:1286-1293.

    PDF Pubmed Nat Struct Mol Biol

  • Croucher N, Fookes M, Perkins T, Turner D, Marguerat S, Keane T, Quail M, He M, Assefa S, Bähler J, Kingsley R, Parkhill J, Bentley S, Dougan G, Thomson N (2009). A simple method for directional transcriptome sequencing using Illumina technology.
    Nucleic Acids Res. 37:e148.

    PDF Pubmed Nucleic Acids Res

  • Aligianni S, Lackner DH, Klier S, Rustici G, Wilhelm BT, Marguerat S, Codlin S, Brazma A, de Bruin RAM, Bähler J (2009). The fission yeast homeodomain protein yox1p binds to MBF and confines MBF-dependent cell-cycle transcription to G1-S via negative feedback.
    PLoS Genetics, 5:e1000626.

    PDF Pubmed PLoS Genetics

  • Tinline-Purvis H, Cullen J, Savory AP, Davé A, Moss J, Bridge WL, Marguerat S, Bähler J, Ragoussis R, Mott R, Walker C, Humphrey TC (2009). Failed gene conversion leads to extensive end processing and chromosomal rearrangements.
    EMBO J. 28:3400–3412.

    PDF Pubmed EMBO J

  • Anderson HE, Wardle J, Vural Korkut S, Murton HE, López-Maury L, Bähler J, Whitehall SK (2009). The fission yeast HIRA histone chaperone is required for promoter silencing and the suppression of cryptic antisense transcripts.
    Mol. Cell. Biol. 29:5158.

    PDF Pubmed Mol Cell Biol

  • Kiang L, Heichinger C, Watt S, Bähler J, Nurse P (2009). Cyclin-dependent kinase inhibits reinitiation of a normal S-phase program during G2 in fission yeast.
    Mol. Cell. Biol. 29:4025-4032.

    PDF Pubmed MCB

  • Schonbrun M, Laor D, López-Maury L, Bähler J, Kupiec M, Weisman R (2009). TOR complex 2 controls gene silencing, telomere length maintenance and survival under DNA damaging conditions.
    Mol. Cell. Biol. 29:4584-4594.

    PDF Pubmed MCB

  • Bähler J (2009). Global approaches to study gene regulation.
    Methods 48:217.

    Pubmed Methods


  • Helmlinger D, Marguerat S, Villén J, Gygi SP, Bähler J, Winston F (2008). The SAGA coactivator complex controls sexual differentiation in fission yeast through the opposing regulatory roles of its subunits Gcn5 and Spt8.
    Genes & Dev. 22:3184-3195.

    PDF Pubmed Genes & Dev

  • Anders A, Watt S, Bähler J, Sawin KE (2008). Improved tools for efficient mapping of fission yeast genes: identification of microtubule nucleation modifier mod22-1 as an allele of chromatin-remodelling factor gene swr1.
    Yeast 25:913-925.

    PDF Pubmed Yeast

  • Monahan BJ, Villén J, Marguerat S, Bähler J, Gygi SP, Winston F (2008). A comprehensive analysis of fission yeast Swi/Snf and RSC reveals significant divergence from budding yeast and a role for Swi/Snf in transcriptional repression.
    Nat. Struct. Mol. Biol. 15:873-880.

    PDF Pubmed Nat Struct Mol Biol

  • Jeffares D, Penkett CJ, Bähler J (2008). Rapidly regulated genes are intron poor.
    Trends Genet. 24:375-378.

    PDF Pubmed Trends Genet

  • López-Maury L, Marguerat, S, Bähler J (2008). Gene expression tuning to changing environments: from rapid responses to evolutionary adaptation.
    Nat. Rev. Genet. 9:583-593.

    PDF Pubmed Nat Rev Genet

  • Marguerat S, Wilhelm BT, Bähler J (2008). Next-generation sequencing: applications beyond genomes.
    Biochem. Soc. Trans. 36:1091-1096.

  • PDF Pubmed Biochem Soc Trans

  • Lackner DH, Bähler J (2008). Translational control of gene expression: from transcripts to transcriptomes.
    Int. Rev. Cell. Mol. Biol. 271:199-251

  • PDF Pubmed Int Rev Cell Mol Biol

  • Wilhelm B, Marguerat S, Watt S, Schubert F, Wood V, Goodhead I, Penkett CJ, Rogers J, Bähler J (2008). Dynamic repertoire of a eukaryotic transcriptome surveyed at single nucleotide resolution.
    Nature 453:1239-43.

    PDF Pubmed Nature Supplementary Data TranscriptomeViewer

  • Udagawa T, Nemoto N, Wilkinson CRM, Narashimhan J, Jiang L, Watt S, Zook A, Jones N, Wek RC, Bähler J, Asano K (2008). Int6/eIF3e promotes general translation and Atf1 abundance to modulate Sty1 MAP kinase-dependent stress response in fission yeast.
    J. Biol. Chem. 283:22063-22075.

    PDF Pubmed JBC Supplementary Data

  • Ludin K, Mata J, Lehmann E, Bähler J, Kohli J (2008). Sites of strong Rec12/Spo11 binding in the fission yeast genome are associated with meiotic recombination and with centromeres.
    Chromosoma 117, 431-444.

    PDF Pubmed Chromosoma Supplementary Data

  • Reiter W, Watt S, Dawson D, Lawrence CL, Bähler J, Jones N, Wilkinson CRM (2008). Fission yeast MAP kinase Sty1 is recruited to stress-induced genes.
    J. Biol. Chem. 283:9945-9956.

    PDF Pubmed JBC

  • Mercier A, Watt S, Bähler J, Labbe S (2008). Key function for the CCAAT-binding factor Php4 to regulate gene expression in response to iron deficiency in fission yeast.
    Eukaryot. Cell 7:493-508.

    PDF Pubmed Eukaryot. Cell

  • Watt S, Mata J, Lopez-Maury L, Marguerat S, Burns G, Bähler J (2008). urg1: a uracil-regulatable promoter system for fission yeast with short induction and repression times.
    PLoS ONE 3:e1428

    PDF Pubmed PLoS ONE Supplementary Data

  • Dainty SJ, Kennedy CA, Watt S, Bähler J, Whitehall S (2008). The response of Schizosaccharomyces pombe to zinc deficiency.
    Eukaryot. Cell 7:454-464.

    PDF Pubmed Eukaryot. Cell Supplementary Data

  • Wang S-W, Stevenson AL, Kearsey SE, Watt S, Bähler J (2008). Global role for polyadenylation-assisted nuclear RNA degradation in post-transcriptional gene silencing.
    Mol. Cell. Biol. 28:656-665

    PDF Pubmed MCB Supplementary Data

  • Miklos I, Szilagyi Z, Watt S, Zilahi E, Batta G, Antunovics Z, Enczi K, Bähler J, Sipiczki M (2008). Genomic expression patterns in cell separation mutants of Schizosaccharomyces pombe defective in genes coding for the Mediator subunits Med8/Sep15 and Med31/Sep10.
    Mol. Genet. Genomics 279:225-238.

    PDF Pubmed MGG Supplementary Data

  • Chen D, Wilkinson CR, Watt S, Penkett, CJ, Toone WM, Jones N, Bähler J (2008). Multiple pathways differentially regulate global oxidative stress responses in fission yeast.
    Mol. Biol. Cell 19:308-317

    PDF Pubmed MBC Supplementary Data

  • Breitkreutz B-J, Stark C, Reguly T, Boucher L, Breitkreutz A, Livstone M, Oughtred R, Lackner DH, Bähler J, Wood V, Dolinski K, Tyers M (2008). The BioGRID interaction database: 2008 update.
    Nucleic Acids Res. 36:D637-D640



  • Kirmizis A, Santos-Rosa H, Penkett CJ, Singer MA, Vermeulen M, Mann M, Bähler J, Green RD, Kouzarides T (2007). Methylation of histone H3 arginine 2 regulates the genomic patterning of H3K4 methylation.
    Nature 449:928-932

    PDF Pubmed Nature

  • Marguerat S, Wilhelm BT, Bähler J (2007). Shaken not stirred: a global research cocktail served in Hinxton.
    Genome Biol. 8:320.

    PDF Pubmed Genome Biol.

  • Mata J, Wilbrey A, Bähler J (2007). Transcriptional regulatory network for sexual differentiation in fission yeast.
    Genome Biol. 8:R217.

    PDF Pubmed Genome Biol. Supplementary Data

  • Lackner DH, Beilharz TH, Marguerat S, Mata J, Watt S, Schubert F, Preiss T, and Bähler J (2007). A Network of Multiple Regulatory Layers Shapes Gene Expression in Fission Yeast.
    Mol. Cell 26:145-155.

    PDF Pubmed Mol. Cell Supplementary Data

  • Rustici G, van Bakel H, Lackner D, Holstege F, Wijmenga C, Bähler J, and Brazma A (2007). Global transcriptional responses of fission and budding yeast to changes in copper and iron levels: a comparative study.
    Genome Biol.8:R73.

    PDF Pubmed Genome Biol. Supp. Data 1/Data 2

  • Gordon M, Holt D, Panigrahi A, Wilhelm B, Erdjument-Bromage H, Tempst P, Bähler J, and Cairns B (2007). Genome-wide dynamics of SAPHIRE, an essential complex for gene activation and chromatin boundaries.
    Mol. Cell. Biol. 27:4058-4069.

    PDF Pubmed Mol. Cell. Biol.


  • Penkett CJ, Birtle ZE, and Bähler J (2006). Simplified primer design for PCR-based gene targeting and microarray primer database: two web tools for fission yeast.
    Yeast 23:921-928.

    PDF Pubmed Yeast Web Page

  • Mata J and Bähler J (2006). Global roles of Ste11p, cell type, and pheromone in the control of gene expression during early sexual differentiation in fission yeast.
    Proc. Natl. Acad. Sci. USA 103:15517-15522.

    PDF Pubmed PNAS Supplementary Data

  • Heichinger C, Penkett CJ, Bähler J, and Nurse P (2006). Genome-wide characterization of fission yeast DNA replication origins.
    EMBO J. 25:5171-5179.

    PDF Pubmed EMBO J. Supplementary Data

  • Sharma N, Marguerat S, Mehta S, Watt S, and Bähler J (2006). The fission yeast Rpb4 subunit of RNA polymerase II plays a specialized role in cell separation.
    Mol. Genet. Genomics 276:545-554.

    PDF Pubmed MGG Supplementary Data

  • Rodriguez-Gabriel MA, Watt S, Bähler J, and Russell P (2006). Upf1, an RNA helicase required for nonsense-mediated mRNA Decay, modulates the transcriptional response to oxidative stress in fission yeast.
    Mol. Cell. Biol. 26:6347-6356.

    PDF Pubmed MCB Supplementary Data

  • Penkett CJ, Morris JA, Wood V, and Bähler J (2006). YOGY: a web-based, integrated database to retrieve protein orthologs and associated Gene Ontology terms.
    Nucleic Acids Res. 34:W330-334.

    PDF Pubmed NAR Web Page

  • Marguerat S, Jensen TS, de Lichtenberg U, Wilhelm BT, Jensen LJ, and Bähler J (2006). The more the merrier: comparative analysis of microarray studies on cell cycle-regulated genes in fission yeast.
    Yeast 23:261-277.

    PDF Pubmed Yeast Supplementary Data

  • Martín V, Rodríguez-Gabriel MA, McDonald WH, Watt S, Yates III JR, Bähler J, and Russell P (2006). Cip1 and Cip2 are novel RNA-recognition-motif proteins that counteract Csx1 function during oxidative stress.
    Mol. Biol Cell. 17:1176-1183.

    PDF Pubmed MBC

  • Bachand F, Lackner DH, Bähler J, and Silver PA (2006). Autoregulation of ribosome biosynthesis by a translational response in fission yeast.
    Mol. Cell. Biol. 26:1731-1742.

    PDF Pubmed MCB

  • Wilhelm BT, Bähler J (2006). The genomics of stress response in Schizosaccharomyces pombe.
    In: The Mycota Volume XIII, Fungal Genomics, Transcriptomics, Proteomics and Metabolomics (A. Brown, ed.), pp. 97-111. Springer, Heidelberg.


  • Bähler J (2005). Cell-cycle control of gene expression in budding and fission yeast.
    Annu. Rev. Genet. 39:69-94.

    PDF Pubmed Annu. Rev. Genet.
  • Jenkins CC, Mata J, Crane RF, Thomas B, Akoulitchev A, Bähler J, and Norbury CJ (2005). Activation of AP-1-dependent transcription by a truncated translation initiation factor.
    Eukaryot. Cell. 4:1840-1850.

    PDF Pubmed Eukaryot. Cell Supplementary Data

  • Mata J, Marguerat S, and Bähler J (2005). Post-transcriptional control of gene expression: a genome-wide perspective.
    Trends Biochem. Sci. 30:506-514.

    PDF Pubmed TIBS
  • Bähler J and Svetina S (2005). A logical circuit for the regulation of fission yeast growth modes.
    J. Theor. Biol. 237:210-218.

    PDF Pubmed JTB

  • Lee KM, Miklos I, Du H, Watt S, Szilagyi Z, Saiz JE, Madabhushi R, Penkett CJ, Sipiczki M, Bähler J, and Fisher RP (2005). Impairment of the TFIIH-associated CDK-activating kinase selectively affects cell cycle-regulated gene expression in fission yeast.
    Mol. Biol. Cell 16:2734-2745.

    PDF Pubmed MBC Supplementary Data

  • Harrison C, Katayama S, Dhut S, Chen D, Jones N, Bähler J, and Toda T (2005). SCFPof1-ubiquitin and its target Zip1 transcription factor mediate cadmium response in fission yeast.
    EMBO J. 24:599-610.

    PDF Pubmed EMBO J. Supplementary Data

  • Mandell JG, Bähler J, Volpe TA, Martienssen RA, and Cech TR (2005). Global expression changes resulting from loss of telomeric DNA in fission yeast.
    Genome Biol. 6:R1.

    PDF Pubmed Genome Biology Supplementary Data

  • Hansen KR, Burns G, Mata J, Volpe TA, Martienssen RA, Bähler J, and Thon G (2005). Global effects on gene expression in fission yeast by silencing and RNA interference machineries.
    Mol. Cell. Biol. 25:590-601.

    PDF Pubmed MCB Supplementary Data

  • Bähler J (2005). A transcriptional pathway for cell separation in fission yeast.
    Cell Cycle 4:39-41.

    PDF Pubmed Cell Cycle
  • Mandell JG, Goodrich KJ, Bähler J, and Cech TR (2005). Expression of a recQ helicase homolog affects progression through crisis in fission yeast lacking telomerase.
    J. Biol. Chem. 280:5249-5257.

    PDF Pubmed JBC


  • Sanders SL, Portoso M, Mata J, Bähler J, Allshire RC, and Kouzarides T (2004). Methylation of histone H4 lysine 20 controls recruitment of Crb2 to sites of DNA damage.
    Cell 119:603-614.

    PDF Pubmed Cell Supplementary Data

  • Gatti L, Chen D, Beretta GL, Rustici G, Carenini N, Corna E, Colangelo D, Zunino F, Bähler J, and Perego P (2004). Global gene expression of fission yeast in response to cisplatin.
    Cell. Mol. Life Sci. 61:2253-2263.

    PDF Pubmed CMLS Supplementary Data

  • Rustici G, Mata J, Kivinen K, Lió P, Penkett CJ, Burns G, Hayles J, Brazma A, Nurse P, and Bähler J (2004). Periodic gene expression program of the fission yeast cell cycle.
    Nature Genet. 36:809-817.

    PDF Pubmed Nature Genet. Supplementary Data

  • Watson A, Mata J, Bähler J, Carr A, and Humphrey T (2004). Genomic expression responses to ionising radiation and the regulatory roles of the Rad3-checkpoint and Sty1 stress-response kinases in fission yeast.
    Mol. Biol. Cell 15:851-860.

    PDF Pubmed MBC Supplementary Data

  • Penkett CJ and Bähler J (2004). Navigating public microarray databases.
    Comp. Funct. Genom. 5:471-479.

    PDF Pubmed CFG

  • Penkett CJ and Bähler J (2004). Getting the most from public microarray data.
    European Pharmaceutical Review (Spring 2004) 1:8-17.

  • Bähler J and Wood V (2004). The genome and beyond.
    Molecular Biology of Schizosaccharomyces pombe. (R. Egel, ed.). pp. 13-25. Springer, Heidelberg.


  • Rodríguez-Gabriel MA, Burns G, McDonald WH, Martín V, Yates III JR, Bähler J, and Russell P (2003). RNA binding protein Csx1 mediates global control of gene expression in response to oxidative stress.
    EMBO J. 22:6256-6266.

    PDF Pubmed EMBO J. Supplementary Data

  • Mata J and Bähler J (2003). Correlations between gene expression and gene conservation in fission yeast.
    Genome Research 13:2686-2690.

    PDF Pubmed Genome Research

  • Lyne R, Burns G, Mata J, Penkett CJ, Rustici G, Chen D, Langford C, Vetrie D, and Bähler J (2003). Whole-genome microarrays of fission yeast: characteristics, accuracy, reproducibility, and processing of array data.
    BMC Genomics 4:27.

    PDF Pubmed BMC Genomics

  • Chen D, Toone WM, Mata J, Lyne R, Burns G, Kivinen K, Brazma A, Jones N, and Bähler J (2003). Global transcriptional responses of fission yeast to environmental stress.
    Mol. Biol. Cell 14:214-229.

    PDF Pubmed MBC Supplementary Data


  • Mata J, Lyne R, Burns G, and Bähler J (2002). The transcriptional program of meiosis and sporulation in fission yeast.
    Nature Genet. 32:143-147.

    PDF Pubmed Nature Genet. Supplementary Data

  • Smith DA, Toone WM, Chen D, Bähler J, Jones N, Morgan BA, and Quinn J (2002). The Srk1 protein kinase is a target for the Sty1 stress-activated MAPK in fission yeast.
    J. Biol. Chem. 277:33411-33421.

    PDF Pubmed JBC

  • Wood V and Bähler J (2002). How to get the best from fission yeast genome data.
    Comp. Funct. Genom. 3:282-288.

    PDF Pubmed CFG

Previous publications from Jürg