August publications

Take a tour of SIB members' latest peer-reviewed articles and conference proceedings




  1. Bick JT, Flöter VL, Robinson MD, Bauersachs S, Ulbrich SE. Small RNA-seq analysis of single porcine blastocysts revealed that maternal estradiol-17beta exposure does not affect miRNA isoform (isomiR) expression. BMC Genomics 2018;19(1):590
  2. Chevalier M, Vermij SH, Wyler K, Gillet L, Keller I, Abriel H. Transcriptomic analyses of murine ventricular cardiomyocytes. Sci Data 2018;5:180170
  3. Cuendet MA, Margul DT, Schneider E, Vogt-Maranto L, Tuckerman ME. Endpoint-restricted adiabatic free energy dynamics approach for the exploration of biomolecular conformational equilibria. J Chem Phys 2018;149(7):072316
  4. Diessler S, Jan M, Emmenegger Y, Guex N, Middleton B, Skene DJ, Ibberson M, Burdet F, Götz L, Pagni M, Sankar M, Liechti R, Hor CN, Xenarios I, Franken P. A systems genetics resource and analysis of sleep regulation in the mouse. PLoS Biol 2018;16(8):e2005750
  5. Dyke SOM, Linden M, Lappalainen I, De Argila JR, Carey K, Lloyd D, Spalding JD, Cabili MN, Kerry G, Foreman J, Cutts T, Shabani M, Rodriguez LL, Haeussler M, Walsh B, Jiang X, Wang S, Perrett D, Boughtwood T, Matern A, Brookes AJ, Cupak M, Fiume M, Pandya R, Tulchinsky I, Scollen S, Törnroos J, Das S, Evans AC, Malin BA, Beck S, Brenner SE, Nyrönen T, Blomberg N, Firth HV, Hurles M, Philippakis AA, Rätsch G, Brudno M, Boycott KM, Rehm HL, Baudis M, Sherry ST, Kato K, Knoppers BM, Baker D, Flicek P. Registered access: authorizing data access. Eur J Hum Genet 2018
  6. Garcia V, Zoller S, Anisimova M. Accounting for Programmed Ribosomal Frameshifting in the Computation of Codon Usage Bias Indices. G3 (Bethesda) 2018
  7. Hadziselimovic F, Cathomas G, Verkauskas G, Dasevicius D, Stadler MB. PRDM Histone Methyltransferase mRNA Levels Increase in Response to Curative Hormone Treatment for Cryptorchidism-Dependent Male Infertility. Genes (Basel) 2018;9(8)
  8. He X, Folkman L, Borgwardt K. Kernelized rank learning for personalized drug recommendation. Bioinformatics 2018;34(16):2808-2816
  9. Kahles A, Lehmann KV, Toussaint NC, Hüser M, Stark SG, Sachsenberg T, Stegle O, Kohlbacher O, Sander C, Cancer Genome Atlas Research Network, Rätsch G. Comprehensive Analysis of Alternative Splicing Across Tumors from 8,705 Patients. Cancer Cell 2018;34(2):211-224.e6
  10. Lee K, Famiglietti ML, McMahon A, Wei CH, MacArthur JAL, Poux S, Breuza L, Bridge A, Cunningham F, Xenarios I, Lu Z. Scaling up data curation using deep learning: An application to literature triage in genomic variation resources. PLoS Comput Biol 2018;14(8):e1006390
  11. Macron C, Lane L, Núñez Galindo A, Dayon L. Identification of Missing Proteins in Normal Human Cerebrospinal Fluid. J Proteome Res 2018
  12. Macron C, Lane L, Núñez Galindo A, Dayon L. Deep Dive on the Proteome of Human Cerebrospinal Fluid: A Valuable Data Resource for Biomarker Discovery and Missing Protein Identification. J Proteome Res 2018
  13. Mariethoz J, Alocci D, Gastaldello A, Horlacher O, Gasteiger E, Rojas-Macias M, Karlsson NG, Packer N, Lisacek F. Glycomics@ExPASy: Bridging the gap. Mol Cell Proteomics 2018
  14. Nisa L, Barras D, Medová M, Aebersold DM, Medo M, Poliaková M, Koch J, Bojaxhiu B, Elicin O, Dettmer MS, Angelino P, Giger R, Borner U, Caversaccio MD, Carey TE, Ho L, McKee TA, Delorenzi M, Zimmer Y. Comprehensive Genomic Profiling of Patient-matched Head and Neck Cancer cells: a Preclinical Pipeline for Metastatic and Recurrent Disease. Mol Cancer Res 2018
  15. Omenn GS, Lane L, Overall CM, Corrales FJ, Schwenk JM, Paik YK, Van Eyk JE, Liu S, Snyder M, Baker MS, Deutsch EW. Progress on Identifying and Characterizing the Human Proteome: 2018 Metrics from the HUPO Human Proteome Project. J Proteome Res 2018
  16. Perez-Shibayama C, Gil-Cruz C, Cheng HW, Onder L, Printz A, Mörbe U, Novkovic M, Li C, Lopez-Macias C, Buechler MB, Turley SJ, Mack M, Soneson C, Robinson MD, Scandella E, Gommerman J, Ludewig B. Fibroblastic reticular cells initiate immune responses in visceral adipose tissues and secure peritoneal immunity. Sci Immunol 2018;3(26)
  17. Rzepiela AJ, Ghosh S, Breda J, Vina-Vilaseca A, Syed AP, Gruber AJ, Eschbach K, Beisel C, van Nimwegen E, Zavolan M. Single-cell mRNA profiling reveals the hierarchical response of miRNA targets to miRNA induction. Mol Syst Biol 2018;14(8):e8266
  18. Sulaimanov N, Kumar S, Burdet F, Ibberson M, Pagni M, Koeppl H. Inferring gene expression networks with hubs using a degree weighted Lasso approach. Bioinformatics 2018