Scientific publications
Research - Scientific Publications
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Publications by SIB Members for the year 2012. For older publications, please click on the date links below on the left.  


Peer-reviewed journal articles


  • Alcantara R, Axelsen KB, Morgat A, Belda E, Coudert E, Bridge A, Cao H, de Matos P, Ennis M, Turner S, Owen G, Bougueleret L, Xenarios I, Steinbeck C. Rhea--a manually curated resource of biochemical reactions. Nucleic Acids Res 2012;40(Database issue):D754-60. (url)

  • Ambatipudi S, Gerstung M, Pandey M, Samant T, Patil A, Kane S, Desai RS, Schaffer AA, Beerenwinkel N, Mahimkar MB. Genome-wide expression and copy number analysis identifies driver genes in gingivobuccal cancers. Genes Chromosomes Cancer 2012;51(2):161-73. (url)

  • Ambuhl ME, Brepsant C, Meister JJ, Verkhovsky AB, Sbalzarini IF. High-resolution cell outline segmentation and tracking from phase-contrast microscopy images. J Microsc 2012;245(2):161-70. (url)

  • Arenas M, Ray N, Currat M, Excoffier L. Consequences of range contractions and range shifts on molecular diversity. Mol Biol Evol 2012;29(1):207-18. (url)

  • Beysard M, Perrin N, Jaarola M, Heckel G, Vogel P. Asymmetric and differential gene introgression at a contact zone between two highly divergent lineages of field voles (Microtus agrestis). J Evol Biol 2012;25(2):400-8. (url)

  • Buescher JM, Liebermeister W, Jules M, Uhr M, Muntel J, Botella E, Hessling B, Kleijn RJ, Le Chat L, Lecointe F, Mader U, Nicolas P, Piersma S, Rugheimer F, Becher D, Bessieres P, Bidnenko E, Denham EL, Dervyn E, Devine KM, Doherty G, Drulhe S, Felicori L, Fogg MJ, Goelzer A, Hansen A, Harwood CR, Hecker M, Hubner S, Hultschig C, Jarmer H, Klipp E, Leduc A, Lewis P, Molina F, Noirot P, Peres S, Pigeonneau N, Pohl S, Rasmussen S, Rinn B, Schaffer M, Schnidder J, Schwikowski B, Van Dijl JM, Veiga P, Walsh S, Wilkinson AJ, Stelling J, Aymerich S, Sauer U. Global network reorganization during dynamic adaptations of Bacillus subtilis metabolism. Science 2012;335(6072):1099-103. (url)

  • Canella D, Bernasconi D, Gilardi F, Lemartelot G, Migliavacca E, Praz V, Cousin P, Delorenzi M, Hernandez N. A multiplicity of factors contributes to selective RNA polymerase III occupancy of a subset of RNA polymerase III genes in mouse liver. Genome Res 2012. (url)

  • Gene Ontology Consortium. The Gene Ontology: enhancements for 2011. Nucleic Acids Res 2012;40(Database issue):D559-64. (url)

  • Dimmer EC, Huntley RP, Alam-Faruque Y, Sawford T, O'Donovan C, Martin MJ, Bely B, Browne P, Mun Chan W, Eberhardt R, Gardner M, Laiho K, Legge D, Magrane M, Pichler K, Poggioli D, Sehra H, Auchincloss A, Axelsen K, Blatter MC, Boutet E, Braconi-Quintaje S, Breuza L, Bridge A, Coudert E, Estreicher A, Famiglietti L, Ferro-Rojas S, Feuermann M, Gos A, Gruaz-Gumowski N, Hinz U, Hulo C, James J, Jimenez S, Jungo F, Keller G, Lemercier P, Lieberherr D, Masson P, Moinat M, Pedruzzi I, Poux S, Rivoire C, Roechert B, Schneider M, Stutz A, Sundaram S, Tognolli M, Bougueleret L, Argoud-Puy G, Cusin I, Duek-Roggli P, Xenarios I, Apweiler R. The UniProt-GO Annotation database in 2011. Nucleic Acids Res 2012;40(Database issue):D565-70. (url)

  • Gheldof N, Leleu M, Noordermeer D, Rougemont J, Reymond A. Detecting long-range chromatin interactions using the chromosome conformation capture sequencing (4C-seq) method. Methods Mol Biol 2012;786:211-25. (url)

  • Hon GC, Hawkins RD, Caballero OL, Lo C, Lister R, Pelizzola M, Valsesia A, Ye Z, Kuan S, Edsall LE, Camargo AA, Stevenson BJ, Ecker JR, Bafna V, Strausberg RL, Simpson AJ, Ren B. Global DNA hypomethylation coupled to repressive chromatin domain formation and gene silencing in breast cancer. Genome Res 2012;22(2):246-58. (url)

  • Iber D. Inferring Biological Mechanisms by Data-Based Mathematical Modelling: Compartment-Specific Gene Activation during Sporulation in Bacillus subtilis as a Test Case. Adv Bioinformatics 2012;2011:124062. (url)

  • Jol S, Kümmel A, Terzer M, Stelling J, Heinemann M. System-Level Insights into Yeast Metabolism by Thermodynamic Analysis of Elementary Flux Modes. PLoS Computational Biology 2012;8(3). (url)

  • Jones AM, Aebersold R, Ahrens CH, Apweiler R, Baerenfaller K, Baker M, Bendixen E, Briggs S, Brownridge P, Brunner E, Daube M, Deutsch EW, Grossniklaus U, Heazlewood J, Hengartner MO, Hermjakob H, Jovanovic M, Lawless C, Lochnit G, Martens L, Ravnsborg C, Schrimpf SP, Shim YH, Subasic D, Tholey A, van Wijk K, von Mering C, Weiss M, Zheng X. The HUPO initiative on Model Organism Proteomes, iMOP. Proteomics 2012;12(3):340-5. (url)

  • Kami C, Hersch M, Trevisan M, Genoud T, Hiltbrunner A, Bergmann S, Fankhauser C. Nuclear Phytochrome A Signaling Promotes Phototropism in Arabidopsis. Plant Cell 2012. (url)

  • Lin Y, Rajan V, Moret BM. A Metric for Phylogenetic Trees Based on Matching. IEEE/ACM Trans Comput Biol Bioinform 2011. (url)

  • Lischer HE, Excoffier L. PGDSpider: an automated data conversion tool for connecting population genetics and genomics programs. Bioinformatics 2012;28(2):298-9. (url)

  • Louis A, Roest Crollius H, Robinson-Rechavi M. How much does the amphioxus genome represent the ancestor of chordates? Brief Funct Genomics 2012. (url)

  • Morgat A, Coissac E, Coudert E, Axelsen KB, Keller G, Bairoch A, Bridge A, Bougueleret L, Xenarios I, Viari A. UniPathway: a resource for the exploration and annotation of metabolic pathways. Nucleic Acids Res 2012;40(Database issue):D761-9. (url)

  • Nicolas P, Mader U, Dervyn E, Rochat T, Leduc A, Pigeonneau N, Bidnenko E, Marchadier E, Hoebeke M, Aymerich S, Becher D, Bisicchia P, Botella E, Delumeau O, Doherty G, Denham EL, Fogg MJ, Fromion V, Goelzer A, Hansen A, Hartig E, Harwood CR, Homuth G, Jarmer H, Jules M, Klipp E, Le Chat L, Lecointe F, Lewis P, Liebermeister W, March A, Mars RA, Nannapaneni P, Noone D, Pohl S, Rinn B, Rugheimer F, Sappa PK, Samson F, Schaffer M, Schwikowski B, Steil L, Stulke J, Wiegert T, Devine KM, Wilkinson AJ, van Dijl JM, Hecker M, Volker U, Bessieres P, Noirot P. Condition-dependent transcriptome reveals high-level regulatory architecture in Bacillus subtilis. Science 2012;335(6072):1103-6. (url)

  • Niknejad A, Comte A, Parmentier G, Roux J, Bastian FB, Robinson-Rechavi M. vHOG, a multi-species vertebrate ontology of homologous organs groups. Bioinformatics 2012. (url)

  • Orchard S, Albar JP, Deutsch EW, Eisenacher M, Binz PA, Martinez-Bartolome S, Vizcaino JA, Hermjakob H. From Proteomics Data Representation to Public Data Flow: A Report on the HUPO-PSI Workshop September 2011, Geneva, Switzerland. Proteomics 2012;12(3):351-5. (url)

  • Pedersen C, Axelsen K, Harper J, Palmgren M. Evolution of plant P-type ATPases. Frontiers in Plant Physiology 2012;3(31). (url)

  • Powell S, Szklarczyk D, Trachana K, Roth A, Kuhn M, Muller J, Arnold R, Rattei T, Letunic I, Doerks T, Jensen LJ, von Mering C, Bork P. eggNOG v3.0: orthologous groups covering 1133 organisms at 41 different taxonomic ranges. Nucleic Acids Res 2012;40(Database issue):D284-9. (url)

  • Reboux S, Schrader B, Sbalzarini I. A self-organizing Lagrangian particle method for adaptive-resolution advection–diffusion simulations. Journal of Computational Physics 2012;231(9):3623–3646. (url)

  • Rougemont J, Naef F. Computational analysis of protein-DNA interactions from ChIP-seq data. Methods Mol Biol 2012;786:263-73. (url)

  • Sakoparnig T, Kockmann T, Paro R, Beisel C, Beerenwinkel N. Binding profiles of chromatin-modifying proteins are predictive for transcriptional activity and promoter-proximal pausing. J Comput Biol 2012;19(2):126-38. (url)

  • Sansone SA, Rocca-Serra P, Field D, Maguire E, Taylor C, Hofmann O, Fang H, Neumann S, Tong W, Amaral-Zettler L, Begley K, Booth T, Bougueleret L, Burns G, Chapman B, Clark T, Coleman LA, Copeland J, Das S, de Daruvar A, de Matos P, Dix I, Edmunds S, Evelo CT, Forster MJ, Gaudet P, Gilbert J, Goble C, Griffin JL, Jacob D, Kleinjans J, Harland L, Haug K, Hermjakob H, Ho Sui SJ, Laederach A, Liang S, Marshall S, McGrath A, Merrill E, Reilly D, Roux M, Shamu CE, Shang CA, Steinbeck C, Trefethen A, Williams-Jones B, Wolstencroft K, Xenarios I, Hide W. Toward interoperable bioscience data. Nat Genet 2012;44(2):121-6. (url)

  • Schlegel M, Kindler E, Essbauer SS, Wolf R, Thiel J, Groschup MH, Heckel G, Oehme RM, Ulrich RG. Tula Virus Infections in the Eurasian Water Vole in Central Europe. Vector Borne Zoonotic Dis 2012. (url)

  • Schrimpf SP, von Mering C, Bendixen E, Heazlewood JL, Bumann D, Omenn G, Hengartner MO. The initiative on Model Organism Proteomes (iMOP) Session September 6, 2011, Geneva, Switzerland. Proteomics 2012;12(3):346-50. (url)

  • Silvan U, Boiteux C, Sutterlin R, Schroeder U, Mannherz HG, Jockusch BM, Berneche S, Aebi U, Schoenenberger CA. An antiparallel actin dimer is associated with the endocytic pathway in mammalian cells. J Struct Biol 2012;177(1):70-80. (url)

  • Slatkin M, Excoffier L. Serial Founder Effects During Range Expansion: A Spatial Analog of Genetic Drift. Genetics 2012. (url)

  • UniProt Consortium. Reorganizing the protein space at the Universal Protein Resource (UniProt). Nucleic Acids Res 2012;40(Database issue):D71-5. (url)

  • Zhu Z, Frey O, Ottoz DS, Rudolf F, Hierlemann A. Microfluidic single-cell cultivation chip with controllable immobilization and selective release of yeast cells. Lab Chip 2012;12(5):906-15. (url)

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Book chapters


  • Müller C, Ramaswamy R, Sbalzarini I. Global Parameter Identification of Stochastic Reaction Networks from Single Trajectories Advances in Systems Biology: Springer; 2012. p. 477-498. (url)

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Conference proceedings


  • Schabauer H, Valle M, Pacher C, Stockinger H, Stamatakis A, Robinson-Rechavi M, Yang Z, Salamin N. SlimCodeML: An Optimized Version of CodeML for the Branch-Site Model. IEEE, editor. HiCOMB (11th IEEE International Workshop on High Performance Computational Biology); 2012; Shanghai, China; 2012. (url)

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Other articles


  • Baillie Gerritsen V. get a grip. Protein Spotlight 2012(135). (url)

 

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