Publications by SIB Members for the year 2013. For older publications, please click on the date links below on the left.  

Peer-reviewed journal articles

• Arnold P, Scholer A, Pachkov M, Balwierz PJ, Jorgensen H, Stadler MB, van Nimwegen E, Schubeler D. Modeling of epigenome dynamics identifies transcription factors that mediate Polycomb targeting. Genome Res 2013;23(1):60-73. (url)


• Bert SA, Robinson MD, Strbenac D, Statham AL, Song JZ, Hulf T, Sutherland RL, Coolen MW, Stirzaker C, Clark SJ. Regional activation of the cancer genome by long-range epigenetic remodeling. Cancer Cell 2013;23(1):9-22. (url)


• Christinat Y, Moret BM. A Transcript Perspective on Evolution. IEEE/ACM Trans Comput Biol Bioinform 2012. (url)


• Cisse OH, Pagni M, Hauser PM. De novo assembly of the Pneumocystis jirovecii genome from a single bronchoalveolar lavage fluid specimen from a patient. MBio 2012;4(1):e00428-12. (url)


• Dimitrieva S, Bucher P. UCNEbase--a database of ultraconserved non-coding elements and genomic regulatory blocks. Nucleic Acids Res 2013;41(Database issue):D101-9. (url)


• Franco D, Milde F, Klingauf M, Orsenigo F, Dejana E, Poulikakos D, Cecchini M, Koumoutsakos P, Ferrari A, Kurtcuoglu V. Accelerated endothelial wound healing on microstructured substrates under flow. Biomaterials 2013;34(5):1488-97. (url)


• Ganter M, Bernard T, Moretti S, Stelling J, Pagni M. MetaNetX.org: a website and repository for accessing, analyzing, and manipulating metabolic networks. Bioinformatics 2013. (url)


• Gaudet P, Argoud-Puy G, Cusin I, Duek P, Evalet O, Gateau A, Gleizes A, Pereira M, Zahn-Zabal M, Zwahlen C, Bairoch A, Lane L. neXtProt: Organizing Protein Knowledge in the Context of Human Proteome Projects. J Proteome Res 2013;12(1):293-8. (url)


• Kindler E, Trojnar E, Heckel G, Otto PH, Johne R. Analysis of rotavirus species diversity and evolution including the newly determined full-length genome sequences of rotavirus F and G. Infect Genet Evol 2012;14C:58-67. (url)


• Koumoutsakos P, Pivkin I, Milde F. The Fluid Mechanics of Cancer and Its Therapy. Annual Review Fluid Mechanics 2013;45:325-55. (url)


• Lew JM, Mao C, Shukla M, Warren A, Will R, Kuznetsov D, Xenarios I, Robertson BD, Gordon SV, Schnappinger D, Cole ST, Sobral B. Database resources for the tuberculosis community. Tuberculosis (Edinb) 2013. (url)


• Mayer C, Dimopoulos S, Rudolf F, Stelling J. Using CellX to Quantify Intracellular Events. Curr Protoc Mol Biol 2013;Chapter 14:Unit14 22. (url)


• Mohammadi P, Desfarges S, Bartha I, Joos B, Zangger N, Munoz M, Gunthard HF, Beerenwinkel N, Telenti A, Ciuffi A. 24 Hours in the Life of HIV-1 in a T Cell Line. PLoS Pathog 2013;9(1):e1003161. (url)


• Pachkov M, Balwierz PJ, Arnold P, Ozonov E, van Nimwegen E. SwissRegulon, a database of genome-wide annotations of regulatory sites: recent updates. Nucleic Acids Res 2013;41(Database issue):D214-20. (url)


• Pedruzzi I, Rivoire C, Auchincloss AH, Coudert E, Keller G, de Castro E, Baratin D, Cuche BA, Bougueleret L, Poux S, Redaschi N, Xenarios I, Bridge A. HAMAP in 2013, new developments in the protein family classification and annotation system. Nucleic Acids Res 2013;41(Database issue):D584-9. (url)


• Rajan V. A method of alignment masking for refining the phylogenetic signal of multiple sequence alignments. Mol Biol Evol 2013;30(3):689-712. (url)


• Salaverria I, Martin-Guerrero I, Burkhardt B, Kreuz M, Zenz T, Oschlies I, Arnold N, Baudis M, Bens S, Garcia-Orad A, Lisfeld J, Schwaenen C, Szczepanowski M, Wessendorf S, Pfreundschuh M, Trumper L, Klapper W, Siebert R. High resolution copy number analysis of IRF4 translocation-positive diffuse large B-cell and follicular lymphomas. Genes Chromosomes Cancer 2013;52(2):150-5. (url)


• Sigrist CJ, de Castro E, Cerutti L, Cuche BA, Hulo N, Bridge A, Bougueleret L, Xenarios I. New and continuing developments at PROSITE. Nucleic Acids Res 2013;41(Database issue):D344-7. (url)


• Singh ND, Jensen JD, Clark AG, Aquadro CF. Inferences of Demography and Selection in an African Population of Drosophila melanogaster. Genetics 2013;193(1):215-28. (url)


• Slayden RA, Jackson M, Zucker J, Ramirez MV, Dawson CC, Crew R, Sampson NS, Thomas ST, Jamshidi N, Sisk P, Caspi R, Crick DC, McNeil MR, Pavelka MS, Niederweis M, Siroy A, Dona V, McFadden J, Boshoff H, Lew JM. Updating and curating metabolic pathways of TB. Tuberculosis (Edinb) 2013. (url)


• Sunnaker M, Busetto AG, Numminen E, Corander J, Foll M, Dessimoz C. Approximate bayesian computation. PLoS Comput Biol 2013;9(1):e1002803. (url)


• Sutter A, Beysard M, Heckel G. Sex-specific clines support incipient speciation in a common European mammal. Heredity (Edinb) 2013. (url)


• Topfer A, Zagordi O, Prabhakaran S, Roth V, Halperin E, Beerenwinkel N. Probabilistic inference of viral quasispecies subject to recombination. J Comput Biol 2013;20(2):113-23. (url)


• 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 Res 2013;41(2):961-77. (url)


• Wang J, Wurm Y, Nipitwattanaphon M, Riba-Grognuz O, Huang YC, Shoemaker D, Keller L. A Y-like social chromosome causes alternative colony organization in fire ants. Nature 2013;493(7434):664-8. (url)

Other articles

• Baillie Gerritsen V. a wretched tale. Protein Spotlight 2013 (146). (url)