Scientific publications
Research - Scientific Publications
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Publications by SIB Members for the year 2014. For older publications, please click on the date links below on the left.  


Peer-reviewed journal articles


  • Ali HS, Drewes S, Sadowska ET, Mikowska M, Groschup MH, Heckel G, Koteja P, Ulrich RG. First molecular evidence for Puumala hantavirus in Poland. Viruses 2014;6(1):340-53. (url)

  • Bachler M, Menshykau D, De Geyter C, Iber D. Species-specific differences in follicular antral sizes result from diffusion-based limitations on the thickness of the granulosa cell layer. Mol Hum Reprod 2014;20(3):208-21. (url)

  • Bank C, Hietpas RT, Wong A, Bolon DN, Jensen JD. A Bayesian MCMC Approach To Assess the Complete Distribution of Fitness Effects of New Mutations: Uncovering the Potential for Adaptive Walks in Challenging Environments. Genetics 2014. (url)

  • Beerenwinkel N, Beretta S, Bonizzoni P, Dondi R, Pirola Y. Covering Pairs in Directed Acyclic Graphs. Computer Science 2014(Data Structures and Algorithms). (url)

  • Bernard T, Bridge A, Morgat A, Moretti S, Xenarios I, Pagni M. Reconciliation of metabolites and biochemical reactions for metabolic networks. Brief Bioinform 2014;15(1):123-35. (url)

  • Beysard M, Heckel G. Structure and dynamics of hybrid zones at different stages of speciation in the common vole (Microtus arvalis). Mol Ecol 2014;23(3):673-87. (url)

  • Blaser O, Neuenschwander S, Perrin N. Sex-chromosome turnovers: the hot-potato model. Am Nat 2014;183(1):140-6. (url)

  • Cai H, Kumar N, Ai N, Gupta S, Rath P, Baudis M. Progenetix: 12 years of oncogenomic data curation. Nucleic Acids Res 2014;42(Database issue):D1055-62. (url)

  • Cai H, Kumar N, Bagheri HC, von Mering C, Robinson MD, Baudis M. Chromothripsis-like patterns are recurring but heterogeneously distributed features in a survey of 22,347 cancer genome screens. BMC Genomics 2014;15:82. (url)

  • Christin PA, Spriggs E, Osborne CP, Stromberg CA, Salamin N, Edwards EJ. Molecular dating, evolutionary rates, and the age of the grasses. Syst Biol 2014;63(2):153-65. (url)

  • Constantinescu S, Hecht K, Sobotzki N, Erzinger MM, Bovet C, Shay JW, Wollscheid B, Sturla SJ, Marra G, Beerenwinkel N. Transcriptomic Responses of Cancerous and Noncancerous Human Colon Cells to Sulforaphane and Selenium. Chem Res Toxicol 2014. (url)

  • David FP, Delafontaine J, Carat S, Ross FJ, Lefebvre G, Jarosz Y, Sinclair L, Noordermeer D, Rougemont J, Leleu M. HTSstation: A Web Application and Open-Access Libraries for High-Throughput Sequencing Data Analysis. PLoS One 2014;9(1):e85879. (url)

  • Dumcke S, Brauer J, Anchang B, Spang R, Beerenwinkel N, Tresch A. Exact likelihood computation in Boolean networks with probabilistic time delays, and its application in signal network reconstruction. Bioinformatics 2014;30(3):414-9. (url)

  • Ewing GB, Jensen JD. Distinguishing neutral from deleterious mutations in growing populations. Front Genet 2014;5:7. (url)

  • Foll M, Poh YP, Renzette N, Ferrer-Admetlla A, Bank C, Shim H, Malaspinas AS, Ewing G, Liu P, Wegmann D, Caffrey DR, Zeldovich KB, Bolon DN, Wang JP, Kowalik TF, Schiffer CA, Finberg RW, Jensen JD. Influenza virus drug resistance: a time-sampled population genetics perspective. PLoS Genet 2014;10(2):e1004185. (url)

  • Gallo Cassarino T, Bordoli L, Schwede T. Assessment of ligand binding site predictions in CASP10. Proteins 2014;82 Suppl 2:154-63. (url)

  • Ganter M, Kaltenbach HM, Stelling J. Predicting network functions with nested patterns. Nat Commun 2014;5:3006. (url)

  • Jacquemont S, Coe BP, Hersch M, Duyzend MH, Krumm N, Bergmann S, Beckmann JS, Rosenfeld JA, Eichler EE. A Higher Mutational Burden in Females Supports a "Female Protective Model" in Neurodevelopmental Disorders. Am J Hum Genet 2014. (url)

  • Jorjani H, Zavolan M. TSSer: an automated method to identify transcription start sites in prokaryotic genomes from differential RNA sequencing data. Bioinformatics 2014. (url)

  • Katayama T, Wilkinson MD, Aoki-Kinoshita KF, Kawashima S, Yamamoto Y, Yamaguchi A, Okamoto S, Kawano S, Kim JD, Wang Y, Wu H, Kano Y, Ono H, Bono H, Kocbek S, Aerts J, Akune Y, Antezana E, Arakawa K, Aranda B, Baran J, Bolleman J, Bonnal RJ, Buttigieg PL, Campbell MP, Chen YA, Chiba H, Cock PJ, Cohen KB, Constantin A, Duck G, Dumontier M, Fujisawa T, Fujiwara T, Goto N, Hoehndorf R, Igarashi Y, Itaya H, Ito M, Iwasaki W, Kala M, Katoda T, Kim T, Kokubu A, Komiyama Y, Kotera M, Laibe C, Lapp H, Lutteke T, Marshall MS, Mori T, Mori H, Morita M, Murakami K, Nakao M, Narimatsu H, Nishide H, Nishimura Y, Nystrom-Persson J, Ogishima S, Okamura Y, Okuda S, Oshita K, Packer NH, Prins P, Ranzinger R, Rocca-Serra P, Sansone S, Sawaki H, Shin SH, Splendiani A, Strozzi F, Tadaka S, Toukach P, Uchiyama I, Umezaki M, Vos R, Whetzel PL, Yamada I, Yamasaki C, Yamashita R, York WS, Zmasek CM, Kawamoto S, Takagi T. BioHackathon series in 2011 and 2012: penetration of ontology and linked data in life science domains. J Biomed Semantics 2014;5(1):5. (url)

  • Kishore S, Piscuoglio S, Kovac MB, Gylling A, Wenzel F, Trapani F, Altermatt HJ, Mele V, Marra G, Peltomaki P, Terracciano L, Zavolan M, Heinimann K. 3'-UTR poly(T/U) tract deletions and altered expression of EWSR1 are a hallmark of mismatch repair-deficient cancers. Cancer Res 2014;74(1):224-34. (url)

  • Kryshtafovych A, Barbato A, Fidelis K, Monastyrskyy B, Schwede T, Tramontano A. Assessment of the assessment: Evaluation of the model quality estimates in CASP10. Proteins 2014;82 Suppl 2:112-26. (url)

  • Kryshtafovych A, Moult J, Bales P, Bazan JF, Biasini M, Burgin A, Chen C, Cochran FV, Craig TK, Das R, Fass D, Garcia-Doval C, Herzberg O, Lorimer D, Luecke H, Ma X, Nelson DC, van Raaij MJ, Rohwer F, Segall A, Seguritan V, Zeth K, Schwede T. Challenging the state of the art in protein structure prediction: Highlights of experimental target structures for the 10th Critical Assessment of Techniques for Protein Structure Prediction Experiment CASP10. Proteins 2014;82 Suppl 2:26-42. (url)

  • Kryuchkova N, Robinson-Rechavi M. Determinants of protein evolutionary rates in light of ENCODE functional genomics. BMC Bioinformatics 2014;15((Suppl 3):A9). (url)

  • Ledda M, Kutalik Z, Souza Destito MC, Souza MM, Cirillo CA, Zamboni A, Martin N, Morya E, Sameshima K, Beckmann JS, le Coutre J, Bergmann S, Genick UK. GWAS of human bitter taste perception identifies new loci and reveals additional complexity of bitter taste genetics. Hum Mol Genet 2014;23(1):259-67. (url)

  • Lischer HE, Excoffier L, Heckel G. Ignoring Heterozygous Sites Biases Phylogenomic Estimates of Divergence Times: Implications for the Evolutionary History of Microtus Voles. Mol Biol Evol 2014. (url)

  • Litsios G, Wuest RO, Kostikova A, Forest F, Lexer C, Linder HP, Pearman PB, Zimmermann NE, Salamin N. Effects of a fire response trait on diversification in replicated radiations. Evolution 2014;68(2):453-65. (url)

  • Luisier R, Unterberger EB, Goodman JI, Schwarz M, Moggs J, Terranova R, van Nimwegen E. Computational modeling identifies key gene regulatory interactions underlying phenobarbital-mediated tumor promotion. Nucleic Acids Res 2014. (url)

  • Marz M, Beerenwinkel N, Drosten C, Fricke M, Frishman D, Hofacker IL, Hoffmann D, Middendorf M, Rattei T, Stadler PF, Topfer A. Challenges in RNA Virus Bioinformatics. Bioinformatics 2014. (url)

  • Matias Rodrigues JF, von Mering C. HPC-CLUST: distributed hierarchical clustering for large sets of nucleotide sequences. Bioinformatics 2014;30(2):287-8. (url)

  • Mauvoisin D, Wang J, Jouffe C, Martin E, Atger F, Waridel P, Quadroni M, Gachon F, Naef F. Circadian clock-dependent and -independent rhythmic proteomes implement distinct diurnal functions in mouse liver. Proc Natl Acad Sci U S A 2014;111(1):167-72. (url)

  • Mittal N, Zavolan M. Seq and CLIP through the miRNA world. Genome Biol 2014;15(1):202. (url)

  • Moretti S, Laurenczy B, Gharib WH, Castella B, Kuzniar A, Schabauer H, Studer RA, Valle M, Salamin N, Stockinger H, Robinson-Rechavi M. Selectome update: quality control and computational improvements to a database of positive selection. Nucleic Acids Res 2014;42(Database issue):D917-21. (url)

  • Moult J, Fidelis K, Kryshtafovych A, Schwede T, Tramontano A. Critical assessment of methods of protein structure prediction (CASP) - round x. Proteins 2014;82 Suppl 2:1-6. (url)

  • Necsulea A, Soumillon M, Warnefors M, Liechti A, Daish T, Zeller U, Baker JC, Grutzner F, Kaessmann H. The evolution of lncRNA repertoires and expression patterns in tetrapods. Nature 2014;505(7485):635-40. (url)

  • Olden M, Corre T, Hayward C, Toniolo D, Ulivi S, Gasparini P, Pistis G, Hwang SJ, Bergmann S, Campbell H, Cocca M, Gandin I, Girotto G, Glaudemans B, Hastie ND, Loffing J, Polasek O, Rampoldi L, Rudan I, Sala C, Traglia M, Vollenweider P, Vuckovic D, Youhanna S, Weber J, Wright AF, Kutalik Z, Bochud M, Fox CS, Devuyst O. Common Variants in UMOD Associate with Urinary Uromodulin Levels: A Meta-Analysis. J Am Soc Nephrol 2014. (url)

  • Pasche E, Gobeill J, Kreim O, Oezdemir-Zaech F, Vachon T, Lovis C, Ruch P. Development and tuning of an original search engine for patent libraries in medicinal chemistry. BMC Bioinformatics 2014;15 Suppl 1:S15. (url)

  • Pedersen BP, Ifrim G, Liboriussen P, Axelsen KB, Palmgren MG, Nissen P, Wiuf C, Pedersen CN. Large scale identification and categorization of protein sequences using structured logistic regression. PLoS One 2014;9(1):e85139. (url)

  • Prabhakaran S, Rey M, Zagordi O, Beerenwinkel N, Roth V. HIV Haplotype Inference Using a Propagating Dirichlet Process Mixture Model. IEEE/ACM Trans Comput Biol Bioinform 2014. (url)

  • Renaud M, Praz V, Vieu E, Florens L, Washburn MP, l'Hote P, Hernandez N. Gene duplication and neofunctionalization: POLR3G and POLR3GL. Genome Res 2014;24(1):37-51. (url)

  • Renzette N, Caffrey DR, Zeldovich KB, Liu P, Gallagher GR, Aiello D, Porter AJ, Kurt-Jones EA, Bolon DN, Poh YP, Jensen JD, Schiffer CA, Kowalik TF, Finberg RW, Wang JP. Evolution of the influenza A virus genome during development of oseltamivir resistance in vitro. J Virol 2014;88(1):272-81. (url)

  • Rueedi R, Ledda M, Nicholls AW, Salek RM, Marques-Vidal P, Morya E, Sameshima K, Montoliu I, Da Silva L, Collino S, Martin FP, Rezzi S, Steinbeck C, Waterworth DM, Waeber G, Vollenweider P, Beckmann JS, Le Coutre J, Mooser V, Bergmann S, Genick UK, Kutalik Z. Genome-wide association study of metabolic traits reveals novel gene-metabolite-disease links. PLoS Genet 2014;10(2):e1004132. (url)

  • Sankar M, Nieminen K, Ragni L, Xenarios I, Hardtke CS. Automated quantitative histology reveals vascular morphodynamics during Arabidopsis hypocotyl secondary growth. Elife 2014;3:e01567. (url)

  • Silvestro D, Zizka G, Schulte K. Disentangling the effects of key innovations on the diversification of Bromelioideae (bromeliaceae). Evolution 2014;68(1):163-75. (url)

  • Tafti M, Hor H, Dauvilliers Y, Lammers GJ, Overeem S, Mayer G, Javidi S, Iranzo A, Santamaria J, Peraita-Adrados R, Vicario JL, Arnulf I, Plazzi G, Bayard S, Poli F, Pizza F, Geisler P, Wierzbicka A, Bassetti CL, Mathis J, Lecendreux M, Donjacour CE, van der Heide A, Heinzer R, Haba-Rubio J, Feketeova E, Hogl B, Frauscher B, Beneto A, Khatami R, Canellas F, Pfister C, Scholz S, Billiard M, Baumann CR, Ercilla G, Verduijn W, Claas FH, Dubois V, Nowak J, Eberhard HP, Pradervand S, Hor CN, Testi M, Tiercy JM, Kutalik Z. DQB1 locus alone explains most of the risk and protection in narcolepsy with cataplexy in Europe. Sleep 2014;37(1):19-25. (url)

  • Valle M, Schabauer H, Pacher C, Stockinger H, Stamatakis A, Robinson-Rechavi M, Salamin N. Optimization strategies for fast detection of positive selection on phylogenetic trees. Bioinformatics 2014. (url)

  • Warinner C, Rodrigues JF, Vyas R, Trachsel C, Shved N, Grossmann J, Radini A, Hancock Y, Tito RY, Fiddyment S, Speller C, Hendy J, Charlton S, Luder HU, Salazar-Garcia DC, Eppler E, Seiler R, Hansen LH, Castruita JA, Barkow-Oesterreicher S, Teoh KY, Kelstrup CD, Olsen JV, Nanni P, Kawai T, Willerslev E, von Mering C, Lewis CM, Jr., Collins MJ, Gilbert MT, Ruhli F, Cappellini E. Pathogens and host immunity in the ancient human oral cavity. Nat Genet 2014. (url)

  • Waszak SM, Kilpinen H, Gschwind AR, Orioli A, Raghav SK, Witwicki RM, Migliavacca E, Yurovsky A, Lappalainen T, Hernandez N, Reymond A, Dermitzakis ET, Deplancke B. Identification and removal of low-complexity sites in allele-specific analysis of ChIP-seq data. Bioinformatics 2014;30(2):165-71. (url)

  • Wegmann D, Currat M. Recipient of the 2013 Molecular Ecology Prize: Laurent Excoffier. Mol Ecol 2014;23(1):16-9. (url)

  • Woltering JM, Noordermeer D, Leleu M, Duboule D. Conservation and divergence of regulatory strategies at Hox Loci and the origin of tetrapod digits. PLoS Biol 2014;12(1):e1001773. (url)

  • Zawistowski M, Reppell M, Wegmann D, St Jean PL, Ehm MG, Nelson MR, Novembre J, Zollner S. Analysis of rare variant population structure in Europeans explains differential stratification of gene-based tests. Eur J Hum Genet 2014. (url)

Conference proceedings


  • Shao M, Lin Y, Moret BME. An exact algorithm to compute the DCJ distance for genomes with duplicate genes. Science LNiC, editor. RECOMB'14; 2014; Pittsburgh, Pennsylvania, USA: Springer; 2014. p. 280-292. (url)

Other articles


  • Baillie Gerritsen V. a pain soothed. Protein Spotlight 2014 (157). (url)

  • Baillie Gerritsen V. a gut's tale. Protein Spotlight 2014 (158). (url)
 

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