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


  • Adrion JR, Kousathanas A, Pascual M, Burrack HJ, Haddad NM, Bergland AO, Machado H, Sackton TB, Schlenke TA, Watada M, Wegmann D, Singh ND. Drosophila suzukii: The Genetic Footprint of a Recent, Worldwide Invasion. Mol Biol Evol 2014. (url)

  • Aguilar-Bultet L, Calderon-Copete SP, Frey J, Falquet L. Draft Genome Sequence of the Virulent Avibacterium paragallinarum Serotype A Strain JF4211 and Identification of Two Toxins. Genome Announc 2013;1(4). (url)

  • Alcala N, Goudet J, Vuilleumier S. On the transition of genetic differentiation from isolation to panmixia: what we can learn from GST and D. Theor Popul Biol 2014;93:75-84. (url)

  • Alfaiz AA, Micale L, Mandriani B, Augello B, Pellico MT, Chrast J, Xenarios I, Zelante L, Merla G, Reymond A. TBC1D7 mutations are associated with intellectual disability, macrocrania, patellar dislocation, and celiac disease. Hum Mutat 2014;35(4):447-51. (url)

  • 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)

  • Almouzni G, Altucci L, Amati B, Ashley N, Baulcombe D, Beaujean N, Bock C, Bongcam-Rudloff E, Bousquet J, Braun S, Paillerets BB, Bussemakers M, Clarke L, Conesa A, Estivill X, Fazeli A, Grgurevic N, Gut I, Heijmans BT, Hermouet S, Houwing-Duistermaat J, Iacobucci I, Ilas J, Kandimalla R, Krauss-Etschmann S, Lasko P, Lehmann S, Lindroth A, Majdic G, Marcotte E, Martinelli G, Martinet N, Meyer E, Miceli C, Mills K, Moreno-Villanueva M, Morvan G, Nickel D, Niesler B, Nowacki M, Nowak J, Ossowski S, Pelizzola M, Pochet R, Potocnik U, Radwanska M, Raes J, Rattray M, Robinson MD, Roelen B, Sauer S, Schinzer D, Slagboom E, Spector T, Stunnenberg HG, Tiligada E, Torres-Padilla ME, Tsonaka R, Soom AV, Vidakovic M, Widschwendter M. Relationship between genome and epigenome - challenges and requirements for future research. BMC Genomics 2014;15:487. (url)

  • Andersson R, Gebhard C, Miguel-Escalada I, Hoof I, Bornholdt J, Boyd M, Chen Y, Zhao X, Schmidl C, Suzuki T, Ntini E, Arner E, Valen E, Li K, Schwarzfischer L, Glatz D, Raithel J, Lilje B, Rapin N, Bagger FO, Jorgensen M, Andersen PR, Bertin N, Rackham O, Burroughs AM, Baillie JK, Ishizu Y, Shimizu Y, Furuhata E, Maeda S, Negishi Y, Mungall CJ, Meehan TF, Lassmann T, Itoh M, Kawaji H, Kondo N, Kawai J, Lennartsson A, Daub CO, Heutink P, Hume DA, Jensen TH, Suzuki H, Hayashizaki Y, Muller F, Forrest AR, Carninci P, Rehli M, Sandelin A. An atlas of active enhancers across human cell types and tissues. Nature 2014;507(7493):455-61. (url)

  • Angelard C, Tanner CJ, Fontanillas P, Niculita-Hirzel H, Masclaux F, Sanders IR. Rapid genotypic change and plasticity in arbuscular mycorrhizal fungi is caused by a host shift and enhanced by segregation. ISME J 2014;8(2):284-94. (url)

  • Antoniazza S, Kanitz R, Neuenschwander S, Burri R, Gaigher A, Roulin A, Goudet J. Natural selection in a postglacial range expansion: the case of the colour cline in the European barn owl. Mol Ecol 2014;23(22):5508-23. (url)

  • Anzai H, Chopard B, Ohta M. Combinational Optimization of Strut Placement for Intracranial Stent Using a Realistic Aneurysm. Journal of Flow Control, Measurement & Visualization 2014;2:67-77. (url)

  • Arner E, Forrest AR, Ehrlund A, Mejhert N, Itoh M, Kawaji H, Lassmann T, Laurencikiene J, Ryden M, Arner P. Ceruloplasmin is a novel adipokine which is overexpressed in adipose tissue of obese subjects and in obesity-associated cancer cells. PLoS One 2014;9(3):e80274. (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)

  • Bachmann NL, Fraser TA, Bertelli C, Jelocnik M, Gillett A, Funnell O, Flanagan C, Myers GS, Timms P, Polkinghorne A. Comparative genomics of koala, cattle and sheep strains of Chlamydia pecorum. BMC Genomics 2014;15:667. (url)

  • Balwierz PJ, Pachkov M, Arnold P, Gruber AJ, Zavolan M, van Nimwegen E. ISMARA: automated modeling of genomic signals as a democracy of regulatory motifs. Genome Res 2014;24(5):869-84. (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)

  • Bank C, Hietpas RT, Jensen JD, Bolon DN. A systematic survey of an intragenic epistatic landscape. Mol Biol Evol 2014. (http://www.ncbi.nlm.nih.gov/pubmed/25371431"target="_blank">url)

  • Baresic M, Salatino S, Kupr B, van Nimwegen E, Handschin C. Transcriptional Network Analysis in Muscle Reveals AP-1 as a Partner of PGC-1alpha in the Regulation of the Hypoxic Gene Program. Mol Cell Biol 2014;34(16):2996-3012. (url)

  • Barras D, Chevalier N, Zoete V, Dempsey R, Lapouge K, Olayioye MA, Michielin O, Widmann C. A WXW motif is required for the anticancer activity of the TAT-RasGAP317-326 peptide. J Biol Chem 2014;289(34):23701-11. (url)

  • Barreto-Hernandez E, Falquet L, Reguero MT, Mantilla JR, Valenzuela EM, Gonzalez E, Cepeda A, Escalante A. Draft Genome Sequences of Multidrug-Resistant Acinetobacter sp. Strains from Colombian Hospitals. Genome Announc 2013;1(6). (url)

  • Bartha I, McLaren PJ, Ciuffi A, Fellay J, Telenti A. GuavaH: a compendium of host genomic data in HIV biology and disease. Retrovirology 2014;11:6. (url)

  • Barve A, Hosseini SR, Martin OC, Wagner A. Historical contingency and the gradual evolution of metabolic properties in central carbon and genome-scale metabolisms. BMC Syst Biol 2014;8:48. (url)

  • Bashirova AA, Martin-Gayo E, Jones DC, Qi Y, Apps R, Gao X, Burke PS, Taylor CJ, Rogich J, Wolinsky S, Bream JH, Duggal P, Hussain S, Martinson J, Weintrob A, Kirk GD, Fellay J, Buchbinder SP, Goedert JJ, Deeks SG, Pereyra F, Trowsdale J, Lichterfeld M, Telenti A, Walker BD, Allen RL, Carrington M, Yu XG. LILRB2 interaction with HLA class I correlates with control of HIV-1 infection. PLoS Genet 2014;10(3):e1004196. (url)

  • Beerenwinkel N, Schwarz RF, Gerstung M, Markowetz F. Cancer evolution: mathematical models and computational inference. Syst Biol 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)

  • Benedetti F, Dorier J, Burnier Y, Stasiak A. Models that include supercoiling of topological domains reproduce several known features of interphase chromosomes. Nucleic Acids Res 2014;42(5):2848-55. (url)

  • Benyamin B, Esko T, Ried JS, Radhakrishnan A, Vermeulen SH, Traglia M, Gogele M, Anderson D, Broer L, Podmore C, Luan J, Kutalik Z, Sanna S, van der Meer P, Tanaka T, Wang F, Westra HJ, Franke L, Mihailov E, Milani L, Haldin J, Winkelmann J, Meitinger T, Thiery J, Peters A, Waldenberger M, Rendon A, Jolley J, Sambrook J, Kiemeney LA, Sweep FC, Sala CF, Schwienbacher C, Pichler I, Hui J, Demirkan A, Isaacs A, Amin N, Steri M, Waeber G, Verweij N, Powell JE, Nyholt DR, Heath AC, Madden PA, Visscher PM, Wright MJ, Montgomery GW, Martin NG, Hernandez D, Bandinelli S, van der Harst P, Uda M, Vollenweider P, Scott RA, Langenberg C, Wareham NJ, InterAct C, van Duijn C, Beilby J, Pramstaller PP, Hicks AA, Ouwehand WH, Oexle K, Gieger C, Metspalu A, Camaschella C, Toniolo D, Swinkels DW, Whitfield JB. Novel loci affecting iron homeostasis and their effects in individuals at risk for hemochromatosis. Nat Commun 2014;5:4926. (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)

  • Bertels F, Silander OK, Pachkov M, Rainey PB, van Nimwegen E. Automated reconstruction of whole-genome phylogenies from short-sequence reads. Mol Biol Evol 2014;31(5):1077-88. (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)

  • Biasini M, Bienert S, Waterhouse A, Arnold K, Studer G, Schmidt T, Kiefer F, Cassarino TG, Bertoni M, Bordoli L, Schwede T. SWISS-MODEL: modelling protein tertiary and quaternary structure using evolutionary information. Nucleic Acids Res 2014;42(Web Server issue):W252-8. (url)

  • Bieler J, Cannavo R, Gustafson K, Gobet C, Gatfield D, Naef F. Robust synchronization of coupled circadian and cell cycle oscillators in single mammalian cells. Mol Syst Biol 2014;10(7):739. (url)

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

  • Bonafe L, Liang J, Gorna MW, Zhang Q, Ha-Vinh R, Campos-Xavier AB, Unger S, Beckmann JS, Le Bechec A, Stevenson B, Giedion A, Liu X, Superti-Furga G, Wang W, Spahr A, Superti-Furga A. MMP13 mutations are the cause of recessive metaphyseal dysplasia, Spahr type. Am J Med Genet A 2014;164A(5):1175-9. (url)

  • Bonhoure N, Bounova G, Bernasconi D, Praz V, Lammers F, Canella D, Willis IM, Herr W, Hernandez N, Delorenzi M. Quantifying ChIP-seq data: a spiking method providing an internal reference for sample-to-sample normalization. Genome Res 2014;24(7):1157-68. (url)

  • Borgdorff J, Ben Belgacem M, Bona-Casas C, Fazendeiro L, Groen D, Hoenen O, Mizeranschi A, Suter JL, Coster D, Coveney PV, Dubitzky W, Hoekstra AG, Strand P, Chopard B. Performance of distributed multiscale simulations. Philos Trans A Math Phys Eng Sci 2014;372(2021). (url)

  • Bryois J, Buil A, Evans DM, Kemp JP, Montgomery SB, Conrad DF, Ho KM, Ring S, Hurles M, Deloukas P, Davey Smith G, Dermitzakis ET. Cis and trans effects of human genomic variants on gene expression. PLoS Genet 2014;10(7):e1004461. (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)

  • Cannarozzi G, Plaza-Wuthrich S, Esfeld K, Larti S, Wilson YS, Girma D, de Castro E, Chanyalew S, Blosch R, Farinelli L, Lyons E, Schneider M, Falquet L, Kuhlemeier C, Assefa K, Tadele Z. Genome and transcriptome sequencing identifies breeding targets in the orphan crop tef (Eragrostis tef). BMC Genomics 2014;15(1):581. (url)

  • Cerase A, Smeets D, Tang YA, Gdula M, Kraus F, Spivakov M, Moindrot B, Leleu M, Tattermusch A, Demmerle J, Nesterova TB, Green C, Otte AP, Schermelleh L, Brockdorff N. Spatial separation of Xist RNA and polycomb proteins revealed by superresolution microscopy. Proc Natl Acad Sci U S A 2014;111(6):2235-40. (url)

  • Charpilloz C, Veuthey AL, Chopard B, Falcone JL. Motifs tree: a new method for predicting post-translational modifications. Bioinformatics 2014;30(14):1974-82. (url)

  • Chopard B, Borgdorff J, Hoekstra A. A framework for multi-scale modelling. Phil. Trans. R. Soc. A, 2014;372: 20130376. (url)

  • Choudhary V, Darwiche R, Gfeller D, Zoete V, Michielin O, Schneiter R. The caveolin-binding motif of the pathogen-related yeast protein Pry1, a member of the CAP protein superfamily, is required for in vivo export of cholesteryl acetate. J Lipid Res 2014;55(5):883-94. (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)

  • Cisse OH, Pagni M, Hauser PM. Comparative genomics suggests that the human pathogenic fungus Pneumocystis jirovecii acquired obligate biotrophy through gene loss. Genome Biol Evol 2014;6(8):1938-48. (url)

  • Claes F, Kuznetsov D, Liechti R, Von Dobschuetz S, Truong BD, Gleizes A, Conversa D, Colonna A, Demaio E, Ramazzotto S, Larfaoui F, Pinto J, Le Mercier P, Xenarios I, Dauphin G. The EMPRES-i genetic module: a novel tool linking epidemiological outbreak information and genetic characteristics of influenza viruses. Database (Oxford) 2014;2014:bau008. (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)

  • Cornelis G, Vernochet C, Malicorne S, Souquere S, Tzika AC, Goodman SM, Catzeflis F, Robinson TJ, Milinkovitch MC, Pierron G, Heidmann O, Dupressoir A, Heidmann T. Retroviral envelope syncytin capture in an ancestrally diverged mammalian clade for placentation in the primitive Afrotherian tenrecs. Proc Natl Acad Sci U S A 2014;111(41):E4332-41. (url)

  • Cortez D, Marin R, Toledo-Flores D, Froidevaux L, Liechti A, Waters PD, Grutzner F, Kaessmann H. Origins and functional evolution of Y chromosomes across mammals. Nature 2014;508(7497):488-93. (url)

  • Crouse J, Bedenikovic G, Wiesel M, Ibberson M, Xenarios I, Von Laer D, Kalinke U, Vivier E, Jonjic S, Oxenius A. Type I Interferons Protect T Cells against NK Cell Attack Mediated by the Activating Receptor NCR1. Immunity 2014;40(6):961-73. (url)

  • Cucchi T, Barnett R, Martinkova N, Renaud S, Renvoise E, Evin A, Sheridan A, Mainland I, Wickham-Jones C, Tougard C, Quere JP, Pascal M, Heckel G, O'Higgins P, Searle JB, Dobney KM. The Changing Pace of Insular Life: 5000 Years of Microevolution in the Orkney Vole (Microtus Arvalis Orcadensis). Evolution 2014. (url)

  • da Silveira Dos Santos AX, Riezman I, Aguilera-Romero MA, David F, Piccolis M, Loewith R, Schaad O, Riezman H. Systematic lipidomic analysis of yeast protein kinase and phosphatase mutants reveals novel insights into regulation of lipid homeostasis. Mol Biol Cell 2014;25(20):3234-46. (url)

  • Daubner GM, Brummer A, Tocchini C, Gerhardy S, Ciosk R, Zavolan M, Allain FH. Structural and functional implications of the QUA2 domain on RNA recognition by GLD-1. Nucleic Acids Res 2014;42(12):8092-105. (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)

  • Dhar R, Bergmiller T, Wagner A. Increased gene dosage plays a predominant role in the initial stages of evolution of duplicate TEM-1 beta lactamase genes. Evolution 2014;68(6):1775-91. (url)

  • Diepenbruck M, Waldmeier L, Ivanek R, Berninger P, Arnold P, van Nimwegen E, Christofori G. Tead2 expression levels control the subcellular distribution of Yap and Taz, zyxin expression and epithelial-mesenchymal transition. J Cell Sci 2014;127(Pt 7):1523-36. (url)

  • Dill MT, Makowska Z, Trincucci G, Gruber AJ, Vogt JE, Filipowicz M, Calabrese D, Krol I, Lau DT, Terracciano L, van Nimwegen E, Roth V, Heim MH. Pegylated IFN-alpha regulates hepatic gene expression through transient Jak/STAT activation. J Clin Invest 2014;124(4):1568-81. (url)

  • Dimopoulos S, Mayer CE, Rudolf F, Stelling J. Accurate cell segmentation in microscopy images using membrane patterns. Bioinformatics 2014. (url)

  • Drogemuller M, Jagannathan V, Becker D, Drogemuller C, Schelling C, Plassais J, Kaerle C, Dufaure de Citres C, Thomas A, Muller EJ, Welle MM, Roosje P, Leeb T. A mutation in the FAM83G gene in dogs with hereditary footpad hyperkeratosis (HFH). PLoS Genet 2014;10(5):e1004370. (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)

  • Dummer R, Goldinger SM, Turtschi CP, Eggmann NB, Michielin O, Mitchell L, Veronese L, Hilfiker PR, Felderer L, Rinderknecht JD. Vemurafenib in patients with BRAF(V600) mutation-positive melanoma with symptomatic brain metastases: final results of an open-label pilot study. Eur J Cancer 2014;50(3):611-21. (url)

  • Dussex N, Wegmann D, Robertson BC. Postglacial expansion and not human influence best explains the population structure in the endangered kea (Nestor notabilis). Mol Ecol 2014;23(9):2193-209. (url)

  • Engler R, Teplyakov V, Adams JM. An assessment of forest cover trends in South and North Korea, from 1980 to 2010. Environ Manage 2014;53(1):194-201. (url)

  • Erhard F, Haas J, Lieber D, Malterer G, Jaskiewicz L, Zavolan M, Dolken L, Zimmer R. Widespread context dependency of microRNA-mediated regulation. Genome Res 2014;24(6):906-19. (url)

  • Ettema TJ, Lindas AC, Hjort K, Poplawski AB, Kaessmann H, Grogan DW, Kelman Z, Andersson AF, Pelve EA, Lundgren M, Svard SG. Rolf Bernander (1956-2014): pioneer of the archaeal cell cycle. Mol Microbiol 2014;92(5):903-9. (url)

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

  • Falquet L, Calderon-Copete SP, Frey J. Draft Genome Sequence of the Virulent Clostridium chauvoei Reference Strain JF4335. Genome Announc 2013;1(4). (url)

  • Falquet L, Rossier G, Yael Maoz T. Report on the ALLBIO minisymposium and workshop: "Next Generation Sequencing (NGS) methods for identification of mutations and large structural variants”. EMBnet journal 2014;20. (http://journal.embnet.org/index.php/embnetjournal/article/view/766)

    Feldberg K, Schneider H, Stadler T, Schafer-Verwimp A, Schmidt AR, Heinrichs J. Epiphytic leafy liverworts diversified in angiosperm-dominated forests. Sci Rep 2014;4:5974. (url)


  • Famiglietti ML, Estreicher A, Gos A, Bolleman J, Gehant S, Breuza L, Bridge A, Poux S, Redaschi N, Bougueleret L, Xenarios I. Genetic Variations and Diseases in UniProtKB/Swiss-Prot: The Ins and Outs of Expert Manual Curation. Hum Mutat 2014;35(8):927-35. (url)

  • Feldberg K, Schneider H, Stadler T, Schafer-Verwimp A, Schmidt AR, Heinrichs J. Epiphytic leafy liverworts diversified in angiosperm-dominated forests. Sci Rep 2014;4:5974. (url)

  • Felizzi F, Iber D. Integrin clustering as a result of local membrane deformations and local signaling feedbacks. Physica A 2014;408:198-211. (url)

  • Fengos G, Schmidt A, Martin K, Fluri E, Aebersold R, Iber D, Pertz O. Spatial proteomic and phospho-proteomic organization in three prototypical cell migration modes. Proteome Sci 2014;12:23. (url)

  • Ferrer-Admetlla A, Liang M, Korneliussen T, Nielsen R. On detecting incomplete soft or hard selective sweeps using haplotype structure. Mol Biol Evol 2014;31(5):1275-91. (url)

  • Fodor A, Segura V, Denis M, Neuenschwander S, Fournier-Level A, Chatelet P, Homa FA, Lacombe T, This P, Le Cunff L. Genome-Wide Prediction Methods in Highly Diverse and Heterozygous Species: Proof-of-Concept through Simulation in Grapevine. PLoS One 2014;9(11):e110436. (url)

  • Foll M, Gaggiotti OE, Daub JT, Vatsiou A, Excoffier L. Widespread signals of convergent adaptation to high altitude in Asia and america. Am J Hum Genet 2014;95(4):394-407. (url)

  • Foll M, Shim H, Jensen JD. WFABC: a Wright-Fisher ABC-based approach for inferring effective population sizes and selection coefficients from time-sampled data. Mol Ecol Resour 2014. (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)

  • Forrest AR, Kawaji H, Rehli M, Baillie JK, de Hoon MJ, Lassmann T, Itoh M, Summers KM, Suzuki H, Daub CO, Kawai J, Heutink P, Hide W, Freeman TC, Lenhard B, Bajic VB, Taylor MS, Makeev VJ, Sandelin A, Hume DA, Carninci P, Hayashizaki Y. A promoter-level mammalian expression atlas. Nature 2014;507(7493):462-70. (url)

  • Franceschini A, Meier R, Casanova A, Kreibich S, Daga N, Andritschke D, Dilling S, Ramo P, Emmenlauer M, Kaufmann A, Conde-Alvarez R, Low SH, Pelkmans L, Helenius A, Hardt WD, Dehio C, von Mering C. Specific inhibition of diverse pathogens in human cells by synthetic microRNA-like oligonucleotides inferred from RNAi screens. Proc Natl Acad Sci U S A 2014;111(12):4548-53. (url)

  • Fried P, Iber D. Dynamic scaling of morphogen gradients on growing domains. Nat Commun 2014;5:5077. (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)

  • Genolet R, Leignadier J, Osteras M, Farinelli L, Stevenson BJ, Luescher IF. Duality of the murine CD8 compartment. Proc Natl Acad Sci U S A 2014;111(11):E1007-15. (url)

  • Gfeller D, Grosdidier A, Wirth M, Daina A, Michielin O, Zoete V. SwissTargetPrediction: a web server for target prediction of bioactive small molecules. Nucleic Acids Res 2014;42(Web Server issue):W32-8. (url)

  • Ghiurcuta CG, Moret BM. Evaluating synteny for improved comparative studies. Bioinformatics 2014;30(12):i9-i18. (url)

  • Giallonardo FD, Topfer A, Rey M, Prabhakaran S, Duport Y, Leemann C, Schmutz S, Campbell NK, Joos B, Lecca MR, Patrignani A, Daumer M, Beisel C, Rusert P, Trkola A, Gunthard HF, Roth V, Beerenwinkel N, Metzner KJ. Full-length haplotype reconstruction to infer the structure of heterogeneous virus populations. Nucleic Acids Res 2014. (url)

  • Giannuzzi G, Migliavacca E, Reymond A. Novel H3K4me3 marks are enriched at human- and chimpanzee-specific cytogenetic structures. Genome Res 2014;24(9):1455-68. (url)

  • Gilardi F, Migliavacca E, Naldi A, Baruchet M, Canella D, Le Martelot G, Guex N, Desvergne B. Genome-wide analysis of SREBP1 activity around the clock reveals its combined dependency on nutrient and circadian signals. PLoS Genet 2014;10(3):e1004155. (url)

  • Girma D, Assefa K, Chanyalew S, Cannarozzi G, Kuhlemeier C, Tadele Z. The origins and progress of genomics research on Tef (Eragrostis tef). Plant Biotechnol J 2014;12(5):534-40. (url)

  • Gopalakrishnan S, Montazeri H, Menz S, Beerenwinkel N, Huisinga W. Estimating HIV-1 Fitness Characteristics from Cross-Sectional Genotype Data. PLoS Comput Biol 2014;10(11):e1003886. (url)

  • Gotz L, Abrahams JL, Mariethoz J, Rudd PM, Karlsson NG, Packer NH, Campbell MP, Lisacek F. GlycoDigest: a tool for the targeted use of exoglycosidase digestions in glycan structure determination. Bioinformatics 2014;30(21):3131-3. (url)

  • Gray MM, Wegmann D, Haasl RJ, White MA, Gabriel SI, Searle JB, Cuthbert RJ, Ryan PG, Payseur BA. Demographic history of a recent invasion of house mice on the isolated Island of Gough. Mol Ecol 2014;23(8):1923-39. (url)

  • Gu Y, Liu GH, Plongthongkum N, Benner C, Yi F, Qu J, Suzuki K, Yang J, Zhang W, Li M, Montserrat N, Crespo I, Del Sol A, Esteban CR, Zhang K, Izpisua Belmonte JC. Global DNA methylation and transcriptional analyses of human ESC-derived cardiomyocytes. Protein Cell 2014;5(1):59-68. (url)

  • Hadadi N, Cher Soh K, Seijo M, Zisaki A, Guan X, Wenk MR, Hatzimanikatis V. A computational framework for integration of lipidomics data into metabolic pathways. Metab Eng 2014;23:1-8. (url)

  • Haendel MA, Balhoff JP, Bastian FB, Blackburn DC, Blake JA, Bradford Y, Comte A, Dahdul WM, Dececchi TA, Druzinsky RE, Hayamizu TF, Ibrahim N, Lewis SE, Mabee PM, Niknejad A, Robinson-Rechavi M, Sereno PC, Mungall CJ. Unification of multi-species vertebrate anatomy ontologies for comparative biology in Uberon. J Biomed Semantics 2014;5:21. (url)

  • Hauser PM, Bernard T, Greub G, Jaton K, Pagni M, Hafen GM. Microbiota present in cystic fibrosis lungs as revealed by whole genome sequencing. PLoS One 2014;9(3):e90934. (url)

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  • 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)

  • Warnefors M, Liechti A, Halbert J, Valloton D, Kaessmann H. Conserved microRNA editing in mammalian evolution, development and disease. Genome Biol 2014;15(6):R83. (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)

  • Wiedemar N, Tetens J, Jagannathan V, Menoud A, Neuenschwander S, Bruggmann R, Thaller G, Drogemuller C. Independent polled mutations leading to complex gene expression differences in cattle. PLoS One 2014;9(3):e93435. (url)

  • Winkler TW, Day FR, Croteau-Chonka DC, Wood AR, Locke AE, Magi R, Ferreira T, Fall T, Graff M, Justice AE, Luan J, Gustafsson S, Randall JC, Vedantam S, Workalemahu T, Kilpelainen TO, Scherag A, Esko T, Kutalik Z, Heid IM, Loos RJ. Quality control and conduct of genome-wide association meta-analyses. Nat Protoc 2014;9(5):1192-212. (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)

  • Wu H, Fujiwara T, Yamamoto Y, Bolleman J, Yamaguchi A. BioBenchmark Toyama 2012: an evaluation of the performance of triple stores on biological data. Journal of Biomedical Semantics 2014;5:32. (url)

  • Wunderlin T, Junier T, Roussel-Delif L, Jeanneret N, Junier P. Stage 0 sporulation gene A as a molecular marker to study diversity of endospore-forming Firmicutes. Environ Microbiol Rep 2013;5(6):911-24. (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)

  • Zhou X, Lindsay H, Robinson MD. Robustly detecting differential expression in RNA sequencing data using observation weights. Nucleic Acids Res 2014;42(11):e91. (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)

  • Baillie Gerritsen V. On the garden pea. Protein Spotlight 2014 (159) (url)

  • Baillie Gerritsen V. An unusual chemistry. Protein Spotlight 2014 (160) (url)

  • Baillie Gerritsen V. The senses confused. Protein Spotlight 2014 (161) (url)

  • Baillie Gerritsen V. It did it its way. Protein Spotlight 2014 (162) (url)

 

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