Publications by SIB Members for the year 2016

Peer-reviewed journal articles

  • Andreozzi S, Chakrabarti A, Soh KC, Burgard A, Yang TH, Van Dien S, Miskovic L, Hatzimanikatis V. Identification of metabolic engineering targets for the enhancement of 1,4-butanediol production in recombinant E. coli using large-scale kinetic models. Metab Eng 2016. (url)
  • Andreozzi S, Miskovic L, Hatzimanikatis V. iSCHRUNK - In Silico Approach to Characterization and Reduction of Uncertainty in the Kinetic Models of Genome-scale Metabolic Networks. Metab Eng 2016;33:158-68. (url)
  • Barillari C, Ottoz DS, Fuentes-Serna JM, Ramakrishnan C, Rinn B, Rudolf F. openBIS ELN-LIMS: an open-source database for academic laboratories. Bioinformatics 2016;32(4):638-40. (url)
  • Boutet E, Lieberherr D, Tognolli M, Schneider M, Bansal P, Bridge AJ, Poux S, Bougueleret L, Xenarios I. UniProtKB/Swiss-Prot, the Manually Annotated Section of the UniProt KnowledgeBase: How to Use the Entry View. Methods Mol Biol 2016;1374:23-54. (url)
  • Burri R, Antoniazza S, Gaigher A, Ducrest AL, Simon C, European Barn Owl N, Fumagalli L, Goudet J, Roulin A. The genetic basis of color-related local adaptation in a ring-like colonization around the Mediterranean. Evolution 2016;70(1):140-53. (url)
  • Christe C, Stolting KN, Bresadola L, Fussi B, Heinze B, Wegmann D, Lexer C. Selection against recombinant hybrids maintains reproductive isolation in hybridizing Populus species despite F fertility and recurrent gene flow. Mol Ecol 2016. (url)
  • Civenni G, Longoni N, Costales P, Dallavalle C, Garcia Inclan C, Albino D, Nunez LE, Moris F, Carbone GM, Catapano CV. EC-70124, a novel glycosylated indolocarbazole multi-kinase inhibitor, reverts tumorigenic and stem cell properties in prostate cancer by inhibiting STAT3 and NF-kappaB. Mol Cancer Ther 2016. (url)
  • Di Mitri D, Alimonti A. Non-Cell-Autonomous Regulation of Cellular Senescence in Cancer. Trends Cell Biol 2016;26(3):215-26. (url)
  • Dousse A, Junier T, Zdobnov EM. CEGA-a catalog of conserved elements from genomic alignments. Nucleic Acids Res 2016;44(D1):D96-D100. (url)
  • Ewing GB, Jensen JD. The consequences of not accounting for background selection in demographic inference. Mol Ecol 2016;25(1):135-41. (url)
  • Fabre G, Garroum I, Mazurek S, Daraspe J, Mucciolo A, Sankar M, Humbel BM, Nawrath C. The ABCG transporter PEC1/ABCG32 is required for the formation of the developing leaf cuticle in Arabidopsis. New Phytol 2016;209(1):192-201. (url)
  • Gaidatzis D, Burger L, Florescu M, Stadler MB. Erratum: Analysis of intronic and exonic reads in RNA-seq data characterizes transcriptional and post-transcriptional regulation. Nat Biotechnol 2016;34(2):210. (url)
  • Herve V, Junier T, Bindschedler S, Verrecchia E, Junier P. Diversity and ecology of oxalotrophic bacteria. World J Microbiol Biotechnol 2016;32(2):28. (url)
  • Huerta-Cepas J, Szklarczyk D, Forslund K, Cook H, Heller D, Walter MC, Rattei T, Mende DR, Sunagawa S, Kuhn M, Jensen LJ, von Mering C, Bork P. eggNOG 4.5: a hierarchical orthology framework with improved functional annotations for eukaryotic, prokaryotic and viral sequences. Nucleic Acids Res 2016;44(D1):D286-93. (url)
  • Ison J, Rapacki K, Menager H, Kalas M, Rydza E, Chmura P, Anthon C, Beard N, Berka K, Bolser D, Booth T, Bretaudeau A, Brezovsky J, Casadio R, Cesareni G, Coppens F, Cornell M, Cuccuru G, Davidsen K, Vedova GD, Dogan T, Doppelt-Azeroual O, Emery L, Gasteiger E, Gatter T, Goldberg T, Grosjean M, Gruning B, Helmer-Citterich M, Ienasescu H, Ioannidis V, Jespersen MC, Jimenez R, Juty N, Juvan P, Koch M, Laibe C, Li JW, Licata L, Mareuil F, Micetic I, Friborg RM, Moretti S, Morris C, Moller S, Nenadic A, Peterson H, Profiti G, Rice P, Romano P, Roncaglia P, Saidi R, Schafferhans A, Schwammle V, Smith C, Sperotto MM, Stockinger H, Varekova RS, Tosatto SC, de la Torre V, Uva P, Via A, Yachdav G, Zambelli F, Vriend G, Rost B, Parkinson H, Longreen P, Brunak S. Tools and data services registry: a community effort to document bioinformatics resources. Nucleic Acids Res 2016;44(D1):D38-47. (url)
  • Jensen JD, Foll M, Bernatchez L. The past, present and future of genomic scans for selection. Mol Ecol 2016;25(1):1-4. (url)
  • Kapopoulou A, Mathew L, Wong A, Trono D, Jensen JD. The evolution of gene expression and binding specificity of the largest transcription factor family in primates. Evolution 2016;70(1):167-80. (url)
  • Kapun M, Fabian DK, Goudet J, Flatt T. Genomic Evidence for Adaptive Inversion Clines in Drosophila melanogaster. Mol Biol Evol 2016. (url)
  • Kilpelainen TO & CO. Genome-wide meta-analysis uncovers novel loci influencing circulating leptin levels. Nat Commun 2016;7:10494. (url)
  • Kumar S, Bucher P. Predicting transcription factor site occupancy using DNA sequence intrinsic and cell-type specific chromatin features. BMC Bioinformatics 2016;17 Suppl 1:4. (url)
  • Lamparter D, Marbach D, Rueedi R, Kutalik Z, Bergmann S. Fast and Rigorous Computation of Gene and Pathway Scores from SNP-Based Summary Statistics. PLoS Comput Biol 2016;12(1):e1004714. (url)
  • Laurent S, Pfeifer SP, Settles ML, Hunter SS, Hardwick KM, Ormond L, Sousa VC, Jensen JD, Rosenblum EB. The population genomics of rapid adaptation: disentangling signatures of selection and demography in white sands lizards. Mol Ecol 2016;25(1):306-23. (url)
  • Li M, Luo XJ, Landen M, Bergen SE, Hultman CM, Li X, Zhang W, Yao YG, Zhang C, Liu J, Mattheisen M, Cichon S, Muhleisen TW, Degenhardt FA, Nothen MM, Schulze TG, Grigoroiu-Serbanescu M, Li H, Fuller CK, Chen C, Dong Q, Chen C, Jamain S, Leboyer M, Bellivier F, Etain B, Kahn JP, Henry C, Preisig M, Kutalik Z, Castelao E, Wright A, Mitchell PB, Fullerton JM, Schofield PR, Montgomery GW, Medland SE, Gordon SD, Martin NG, Moo DSC, Swedish Bipolar Study G, Rietschel M, Liu C, Kleinman JE, Hyde TM, Weinberger DR, Su B. Impact of a cis-associated gene expression SNP on chromosome 20q11.22 on bipolar disorder susceptibility, hippocampal structure and cognitive performance. Br J Psychiatry 2016;208(2):128-37. (url)
  • Liu F, Koval M, Ranganathan S, Fanayan S, Hancock WS, Lundberg EK, Beavis RC, Lane L, Duek P, McQuade L, Kelleher NL, Baker MS. Systems Proteomics View of the Endogenous Human Claudin Protein Family. J Proteome Res 2016;15(2):339-59. (url)
  • Mariethoz J, Khatib K, Alocci D, Campbell MP, Karlsson NG, Packer NH, Mullen EH, Lisacek F. SugarBindDB, a resource of glycan-mediated host-pathogen interactions. Nucleic Acids Res 2016;44(D1):D1243-50. (url)
  • Members SIBSIoB. The SIB Swiss Institute of Bioinformatics' resources: focus on curated databases. Nucleic Acids Res 2016;44(D1):D27-37. (url)
  • Moretti S, Martin O, Van Du Tran T, Bridge A, Morgat A, Pagni M. MetaNetX/MNXref - reconciliation of metabolites and biochemical reactions to bring together genome-scale metabolic networks. Nucleic Acids Res 2016;44(D1):D523-6. (url)
  • Nair NU, Hunter L, Shao M, Grnarova P, Lin Y, Bucher P, BM EM. A maximum-likelihood approach for building cell-type trees by lifting. BMC Genomics 2016;17 Suppl 1:14. (url)
  • Ormond L, Foll M, Ewing GB, Pfeifer SP, Jensen JD. Inferring the age of a fixed beneficial allele. Mol Ecol 2016;25(1):157-169. (url)
  • Otowa T, Hek K, Lee M, Byrne EM, Mirza SS, Nivard MG, Bigdeli T, Aggen SH, Adkins D, Wolen A, Fanous A, Keller MC, Castelao E, Kutalik Z, der Auwera SV, Homuth G, Nauck M, Teumer A, Milaneschi Y, Hottenga JJ, Direk N, Hofman A, Uitterlinden A, Mulder CL, Henders AK, Medland SE, Gordon S, Heath AC, Madden PA, Pergadia ML, van der Most PJ, Nolte IM, van Oort FV, Hartman CA, Oldehinkel AJ, Preisig M, Grabe HJ, Middeldorp CM, Penninx BW, Boomsma D, Martin NG, Montgomery G, Maher BS, van den Oord EJ, Wray NR, Tiemeier H, Hettema JM. Meta-analysis of genome-wide association studies of anxiety disorders. Mol Psychiatry 2016. (url)
  • Peraro MD, van der Goot FG. Pore-forming toxins: ancient, but never really out of fashion. Nat Rev Microbiol 2016;14(2):77-92. (url)
  • Renzette N, Kowalik TF, Jensen JD. On the relative roles of background selection and genetic hitchhiking in shaping human cytomegalovirus genetic diversity. Mol Ecol 2016;25(1):403-13. (url)
  • Ritpitakphong U, Falquet L, Vimoltust A, Berger A, Metraux JP, L'Haridon F. The microbiome of the leaf surface of Arabidopsis protects against a fungal pathogen. New Phytol 2016. (url)
  • Sayyab S, Viluma A, Bergvall K, Brunberg E, Jagannathan V, Leeb T, Andersson G, Bergstrom TF. Whole-Genome Sequencing of a Canine Family Trio Reveals a FAM83G Variant Associated with Hereditary Footpad Hyperkeratosis. G3 (Bethesda) 2016. (url)
  • Seifert D, Di Giallonardo F, Topfer A, Singer J, Schmutz S, Gunthard HF, Beerenwinkel N, Metzner KJ. A Comprehensive Analysis of Primer IDs to Study Heterogeneous HIV-1 Populations. J Mol Biol 2016;428(1):238-50. (url)
  • Shim H, Laurent S, Matuszewski S, Foll M, Jensen JD. Detecting and Quantifying Changing Selection Intensities from Time-Sampled Polymorphism Data. G3 (Bethesda) 2016. (url)
  • Soneson C, Matthes KL, Nowicka M, Law CW, Robinson MD. Isoform prefiltering improves performance of count-based methods for analysis of differential transcript usage. Genome Biol 2016;17(1):12. (url)
  • Szklarczyk D, Santos A, von Mering C, Jensen LJ, Bork P, Kuhn M. STITCH 5: augmenting protein-chemical interaction networks with tissue and affinity data. Nucleic Acids Res 2016;44(D1):D380-4. (url)
  • Teumer A & CO. Genome-wide Association Studies Identify Genetic Loci Associated With Albuminuria in Diabetes. Diabetes 2016;65(3):803-17. (url)
  • Urfer M, Bogdanovic J, Lo Monte F, Moehle K, Zerbe K, Omasits U, Ahrens CH, Pessi G, Eberl L, Robinson JA. A Peptidomimetic Antibiotic Targets Outer Membrane Proteins and Disrupts Selectively the Outer Membrane in Escherichia coli. J Biol Chem 2016;291(4):1921-32. (url)
  • Zoete V, Schuepbach T, Bovigny C, Chaskar P, Daina A, Rohrig UF, Michielin O. Attracting cavities for docking. Replacing the rough energy landscape of the protein by a smooth attracting landscape. J Comput Chem 2016;37(4):437-47. (url)

Other articles

  • Baillie Gerritsen V. Discerning change. Protein Spotlight 2016 (176). (url)
  • Baillie Gerritsen V. Shaping life. Protein Spotlight 2016 (175). (url)

Publications 2015