Scientific publications 2017

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Publications by SIB Members published in 2017

Listed in Europe PMC, latest update: 2018-01-03.

Peer-reviewed articles and conference proceedings

Aalders KC, Kuijer A, Straver ME, Slaets L, Litiere S, Viale G, Van't Veer LJ, Glas AM, Delorenzi M, van Dalen T, Tryfonidis K, Piccart MJ, Cardoso F, Rutgers EJ, TRANSBIG Consortium and the MINDACT Investigators. Characterisation of multifocal breast cancer using the 70-gene signature in clinical low-risk patients enrolled in the EORTC 10041/BIG 03-04 MINDACT trial. Eur J Cancer 2017;79:98-105
Abel L, Fellay J, Haas DW, Schurr E, Srikrishna G, Urbanowski M, Chaturvedi N, Srinivasan S, Johnson DH, Bishai WR. Genetics of human susceptibility to active and latent tuberculosis: present knowledge and future perspectives. Lancet Infect Dis 2017
Abriata LA, Albanesi D, Dal Peraro M, de Mendoza D. Signal Sensing and Transduction by Histidine Kinases as Unveiled through Studies on a Temperature Sensor. Acc Chem Res 2017;50(6):1359-1366
Abriata LA, Rodrigues JPGLM, Salathé M, Patiny L. Augmenting Research, Education, and Outreach with Client-Side Web Programming. Trends Biotechnol 2017
Abriata LA, Tamò GE, Monastyrskyy B, Kryshtafovych A, Dal Peraro M. Assessment of hard target modeling in CASP12 reveals an emerging role of alignment-based contact prediction methods. Proteins 2017
Aeschbacher S, Selby JP, Willis JH, Coop G. Population-genomic inference of the strength and timing of selection against gene flow. Proc Natl Acad Sci U S A 2017;114(27):7061-7066
Aeschimann F, Kumari P, Bartake H, Gaidatzis D, Xu L, Ciosk R, Großhans H. LIN41 Post-transcriptionally Silences mRNAs by Two Distinct and Position-Dependent Mechanisms. Mol Cell 2017;65(3):476-489.e4
Aguilar-Rodríguez J, Payne JL, Wagner A. A thousand empirical adaptive landscapes and their navigability. Nat Ecol Evol 2017;1(2):45
Ahlstrand E, Buetti-Dinh A, Friedman R. An interactive computer lab of the galvanic cell for students in biochemistry. Biochem Mol Biol Educ 2017
Akhmedov M, Kedaigle A, Chong RE, Montemanni R, Bertoni F, Fraenkel E, Kwee I. PCSF: An R-package for network-based interpretation of high-throughput data. PLoS Comput Biol 2017;13(7):e1005694
Alberti-Servera L, von Muenchow L, Tsapogas P, Capoferri G, Eschbach K, Beisel C, Ceredig R, Ivanek R, Rolink A. Single-cell RNA sequencing reveals developmental heterogeneity among early lymphoid progenitors. EMBO J 2017;36(24):3619-3633
Alexanian M, Maric D, Jenkinson SP, Mina M, Friedman CE, Ting CC, Micheletti R, Plaisance I, Nemir M, Maison D, Kernen J, Pezzuto I, Villeneuve D, Burdet F, Ibberson M, Leib SL, Palpant NJ, Hernandez N, Ounzain S, Pedrazzini T. A transcribed enhancer dictates mesendoderm specification in pluripotency. Nat Commun 2017;8(1):1806
Alghanem B, Nikitin F, Stricker T, Duchoslav E, Luban J, Strambio-De-Castillia C, Muller M, Lisacek F, Varesio E, Hopfgartner G. Optimization by infusion of multiple reaction monitoring transitions for sensitive quantification of peptides by liquid chromatography/mass spectrometry. Rapid Commun Mass Spectrom 2017;31(9):753-761
An J, Ponthier CM, Sack R, Seebacher J, Stadler MB, Donovan KA, Fischer ES. pSILAC mass spectrometry reveals ZFP91 as IMiD-dependent substrate of the CRL4CRBN ubiquitin ligase. Nat Commun 2017;8:15398
Anderson WP, Global Life Science Data Resources Working Group. Data management: A global coalition to sustain core data. Nature 2017;543(7644):179
Anikster Y, Haack TB, Vilboux T, Pode-Shakked B, Thöny B, Shen N, Guarani V, Meissner T, Mayatepek E, Trefz FK, Marek-Yagel D, Martinez A, Huttlin EL, Paulo JA, Berutti R, Benoist JF, Imbard A, Dorboz I, Heimer G, Landau Y, Ziv-Strasser L, Malicdan MCV, Gemperle-Britschgi C, Cremer K, Engels H, Meili D, Keller I, Bruggmann R, Strom TM, Meitinger T, Mullikin JC, Schwartz G, Ben-Zeev B, Gahl WA, Harper JW, Blau N, Hoffmann GF, Prokisch H, Opladen T, Schiff M. Biallelic Mutations in DNAJC12 Cause Hyperphenylalaninemia, Dystonia, and Intellectual Disability. Am J Hum Genet 2017;100(2):257-266
Ansar M, Riazuddin S, Sarwar MT, Makrythanasis P, Paracha SA, Iqbal Z, Khan J, Assir MZ, Hussain M, Razzaq A, Polla DL, Taj AS, Holmgren A, Batool N, Misceo D, Iwaszkiewicz J, de Brouwer APM, Guipponi M, Hanquinet S, Zoete V, Santoni FA, Frengen E, Ahmed J, Riazuddin S, van Bokhoven H, Antonarakis SE. Biallelic variants in LINGO1 are associated with autosomal recessive intellectual disability, microcephaly, speech and motor delay. Genet Med 2017
Antiochos P, Marques-Vidal P, Virzi J, Pagano S, Satta N, Hartley O, Montecucco F, Mach F, Kutalik Z, Waeber G, Vollenweider P, Vuilleumier N. Impact of CD14 Polymorphisms on Anti-Apolipoprotein A-1 IgG-Related Coronary Artery Disease Prediction in the General Population. Arterioscler Thromb Vasc Biol 2017;37(12):2342-2349
Antiochos P, Marques-Vidal P, Virzi J, Pagano S, Satta N, Hartley O, Montecucco F, Mach F, Kutalik Z, Waeber G, Vollenweider P, Vuilleumier N. Anti-Apolipoprotein A-1 IgG Predict All-Cause Mortality and Are Associated with Fc Receptor-Like 3 Polymorphisms. Front Immunol 2017;8:437
Arvaniti E, Claassen M. Sensitive detection of rare disease-associated cell subsets via representation learning. Nat Commun 2017;8:14825
Asgari S, Schlapbach LJ, Anchisi S, Hammer C, Bartha I, Junier T, Mottet-Osman G, Posfay-Barbe KM, Longchamp D, Stocker M, Cordey S, Kaiser L, Riedel T, Kenna T, Long D, Schibler A, Telenti A, Tapparel C, McLaren PJ, Garcin D, Fellay J. Severe viral respiratory infections in children with IFIH1 loss-of-function mutations. Proc Natl Acad Sci U S A 2017;114(31):8342-8347
Avalle L, Incarnato D, Savino A, Gai M, Marino F, Pensa S, Barbieri I, Stadler MB, Provero P, Oliviero S, Poli V. MicroRNAs-143 and -145 induce epithelial to mesenchymal transition and modulate the expression of junction proteins. Cell Death Differ 2017;24(10):1750-1760
Awasthi Mishra N, Drögemüller C, Jagannathan V, Keller I, Wüthrich D, Bruggmann R, Beck J, Schütz E, Brenig B, Demmel S, Moser S, Signer-Hasler H, Pieńkowska-Schelling A, Schelling C, Sande M, Rongen R, Rieder S, Kelsh RN, Mercader N, Leeb T. A structural variant in the 5'-flanking region of the TWIST2 gene affects melanocyte development in belted cattle. PLoS One 2017;12(6):e0180170
Barido-Sottani J, Bošková V, Plessis LD, Kühnert D, Magnus C, Mitov V, Müller NF, PecErska J, Rasmussen DA, Zhang C, Drummond AJ, Heath TA, Pybus OG, Vaughan TG, Stadler T. Taming the BEAST-A Community Teaching Material Resource for BEAST 2. Syst Biol 2018;67(1):170-174
Bartha I, McLaren PJ, Brumme C, Harrigan R, Telenti A, Fellay J. Estimating the Respective Contributions of Human and Viral Genetic Variation to HIV Control. PLoS Comput Biol 2017;13(2):e1005339
Basaldella M, Furrer L, Tasso C, Rinaldi F. Entity recognition in the biomedical domain using a hybrid approach. J Biomed Semantics 2017;8(1):51
Bassani-Sternberg M, Chong C, Guillaume P, Solleder M, Pak H, Gannon PO, Kandalaft LE, Coukos G, Gfeller D. Deciphering HLA-I motifs across HLA peptidomes improves neo-antigen predictions and identifies allostery regulating HLA specificity. PLoS Comput Biol 2017;13(8):e1005725
Becker E, Schmidt TSB, Bengs S, Poveda L, Opitz L, Atrott K, Stanzel C, Biedermann L, Rehman A, Jonas D, von Mering C, Rogler G, Frey-Wagner I. Effects of oral antibiotics and isotretinoin on the murine gut microbiota. Int J Antimicrob Agents 2017;50(3):342-351
Benedetti F, Racko D, Dorier J, Burnier Y, Stasiak A. Transcription-induced supercoiling explains formation of self-interacting chromatin domains in S. pombe. Nucleic Acids Res 2017;45(17):9850-9859
Bernasconi E, Gaudio E, Lejeune P, Tarantelli C, Cascione L, Kwee I, Spriano F, Rinaldi A, Mensah AA, Chung E, Stathis A, Siegel S, Schmees N, Ocker M, Zucca E, Haendler B, Bertoni F. Preclinical evaluation of the BET bromodomain inhibitor BAY 1238097 for the treatment of lymphoma. Br J Haematol 2017;178(6):936-948
Bertelli C, Mueller L, Thomas V, Pillonel T, Jacquier N, Greub G. Cedratvirus lausannensis - digging into Pithoviridae diversity. Environ Microbiol 2017;19(10):4022-4034
Bhosale PG, Cristea S, Ambatipudi S, Desai RS, Kumar R, Patil A, Kane S, Borges AM, Schäffer AA, Beerenwinkel N, Mahimkar MB. Chromosomal Alterations and Gene Expression Changes Associated with the Progression of Leukoplakia to Advanced Gingivobuccal Cancer. Transl Oncol 2017;10(3):396-409
Bhosale PG, Pandey M, Cristea S, Shah M, Patil A, Beerenwinkel N, Schäffer AA, Mahimkar MB. Recurring Amplification at 11q22.1-q22.2 Locus Plays an Important Role in Lymph Node Metastasis and Radioresistance in OSCC. Sci Rep 2017;7(1):16051
Binder V, Bergum B, Jaisson S, Gillery P, Scavenius C, Spriet E, Nyhaug AK, Roberts HM, Chapple ILC, Hellvard A, Delaleu N, Mydel P. Impact of fibrinogen carbamylation on fibrin clot formation and stability. Thromb Haemost 2017;117(5):899-910
Blanquart F, Wymant C, Cornelissen M, Gall A, Bakker M, Bezemer D, Hall M, Hillebregt M, Ong SH, Albert J, Bannert N, Fellay J, Fransen K, Gourlay AJ, Grabowski MK, Gunsenheimer-Bartmeyer B, Günthard HF, Kivelä P, Kouyos R, Laeyendecker O, Liitsola K, Meyer L, Porter K, Ristola M, van Sighem A, Vanham G, Berkhout B, Kellam P, Reiss P, Fraser C, BEEHIVE collaboration. Viral genetic variation accounts for a third of variability in HIV-1 set-point viral load in Europe. PLoS Biol 2017;15(6):e2001855
Boareto M, Iber D, Taylor V. Differential interactions between Notch and ID factors control neurogenesis by modulating Hes factor autoregulation. Development 2017;144(19):3465-3474
Borghesi A, Stronati M, Fellay J. Neonatal Group B Streptococcal Disease in Otherwise Healthy Infants: Failure of Specific Neonatal Immune Responses. Front Immunol 2017;8:215
Bosshard L, Dupanloup I, Tenaillon O, Bruggmann R, Ackermann M, Peischl S, Excoffier L. Accumulation of Deleterious Mutations During Bacterial Range Expansions. Genetics 2017;207(2):669-684
Bovay A, Zoete V, Dolton G, Bulek AM, Cole DK, Rizkallah PJ, Fuller A, Beck K, Michielin O, Speiser DE, Sewell AK, Fuertes Marraco SA. T cell receptor alpha variable 12-2 bias in the immunodominant response to Yellow fever virus. Eur J Immunol 2017
Bramsen JB, Rasmussen MH, Ongen H, Mattesen TB, Ørntoft MW, Árnadóttir SS, Sandoval J, Laguna T, Vang S, Øster B, Lamy P, Madsen MR, Laurberg S, Esteller M, Dermitzakis ET, Ørntoft TF, Andersen CL. Molecular-Subtype-Specific Biomarkers Improve Prediction of Prognosis in Colorectal Cancer. Cell Rep 2017;19(6):1268-1280
Bratulic S, Toll-Riera M, Wagner A. Mistranslation can enhance fitness through purging of deleterious mutations. Nat Commun 2017;8:15410
Britschgi A, Duss S, Kim S, Couto JP, Brinkhaus H, Koren S, De Silva D, Mertz KD, Kaup D, Varga Z, Voshol H, Vissieres A, Leroy C, Roloff T, Stadler MB, Scheel CH, Miraglia LJ, Orth AP, Bonamy GM, Reddy VA, Bentires-Alj M. The Hippo kinases LATS1 and 2 control human breast cell fate via crosstalk with ERα. Nature 2017;541(7638):541-545
Brown AA, Viñuela A, Delaneau O, Spector TD, Small KS, Dermitzakis ET. Predicting causal variants affecting expression by using whole-genome sequencing and RNA-seq from multiple human tissues. Nat Genet 2017;49(12):1747-1751
Brown AA. veqtl-mapper: variance association mapping for molecular phenotypes. Bioinformatics 2017;33(17):2772-2773
Bryois J, Buil A, Ferreira PG, Panousis NI, Brown AA, Viñuela A, Planchon A, Bielser D, Small K, Spector T, Dermitzakis ET. Time-dependent genetic effects on gene expression implicate aging processes. Genome Res 2017;27(4):545-552
Burley SK, Kurisu G, Markley JL, Nakamura H, Velankar S, Berman HM, Sali A, Schwede T, Trewhella J. PDB-Dev: a Prototype System for Depositing Integrative/Hybrid Structural Models. Structure 2017;25(9):1317-1318
Campbell MP, Peterson RA, Gasteiger E, Mariethoz J, Lisacek F, Packer NH. Navigating the Glycome Space and Connecting the Glycoproteome. Methods Mol Biol 2017;1558:139-158
Carapito C, Duek P, Macron C, Seffals M, Rondel K, Delalande F, Lindskog C, Fréour T, Vandenbrouck Y, Lane L, Pineau C. Validating Missing Proteins in Human Sperm Cells by Targeted Mass-Spectrometry- and Antibody-based Methods. J Proteome Res 2017;16(12):4340-4351
Carmona SJ, Teichmann SA, Ferreira L, Macaulay IC, Stubbington MJ, Cvejic A, Gfeller D. Single-cell transcriptome analysis of fish immune cells provides insight into the evolution of vertebrate immune cell types. Genome Res 2017;27(3):451-461
Carrat GR, Hu M, Nguyen-Tu MS, Chabosseau P, Gaulton KJ, van de Bunt M, Siddiq A, Falchi M, Thurner M, Canouil M, Pattou F, Leclerc I, Pullen TJ, Cane MC, Prabhala P, Greenwald W, Schulte A, Marchetti P, Ibberson M, MacDonald PE, Manning Fox JE, Gloyn AL, Froguel P, Solimena M, McCarthy MI, Rutter GA. Decreased STARD10 Expression Is Associated with Defective Insulin Secretion in Humans and Mice. Am J Hum Genet 2017;100(2):238-256
Carratalà A, Shim H, Zhong Q, Bachmann V, Jensen JD, Kohn T. Experimental adaptation of human echovirus 11 to ultraviolet radiation leads to resistance to disinfection and ribavirin. Virus Evol 2017;3(2):vex035
Cascione L, Rinaldi A, Chiappella A, Kwee I, Ciccone G, Altenbuchinger M, Kohler C, Vitolo U, Inghirami G, Bertoni F. Diffuse large B cell lymphoma cell of origin by digital expression profiling in the REAL07 Phase 1-2 study. Br J Haematol 2017
Castelli M, Clementi N, Pfaff J, Sautto GA, Diotti RA, Burioni R, Doranz BJ, Dal Peraro M, Clementi M, Mancini N. A Biologically-validated HCV E1E2 Heterodimer Structural Model. Sci Rep 2017;7(1):214
Castelo-Szekely V, Arpat AB, Janich P, Gatfield D. Translational contributions to tissue specificity in rhythmic and constitutive gene expression. Genome Biol 2017;18(1):116
Cavoto E, Neuenschwander S, Goudet J, Perrin N. Sex-antagonistic genes, XY recombination, and feminized Y chromosomes. J Evol Biol 2017
Chang H, Hoshina N, Zhang C, Ma Y, Cao H, Wang Y, Wu DD, Bergen SE, Landén M, Hultman CM, Preisig M, Kutalik Z, Castelao E, Grigoroiu-Serbanescu M, Forstner AJ, Strohmaier J, Hecker J, Schulze TG, Müller-Myhsok B, Reif A, Mitchell PB, Martin NG, Schofield PR, Cichon S, Nöthen MM, Swedish Bipolar Study Group, MooDS Bipolar Consortium, Walter H, Erk S, Heinz A, Amin N, van Duijn CM, Meyer-Lindenberg A, Tost H, Xiao X, Yamamoto T, Rietschel M, Li M. The protocadherin 17 gene affects cognition, personality, amygdala structure and function, synapse development and risk of major mood disorders. Mol Psychiatry 2017
Chen H, Cade BE, Gleason KJ, Bjonnes AC, Stilp AM, Sofer T, Conomos MP, Ancoli-Israel S, Arens R, Azarbarzin A, Bell GI, Below JE, Chun S, Evans DS, Ewert R, Frazier-Wood AC, Gharib SA, Haba-Rubio J, Hagen EW, Heinzer R, Hillman DR, Johnson WC, Kutalik Z, Lane JM, Larkin EK, Lee SK, Liang J, Loredo JS, Mukherjee S, Palmer LJ, Papanicolaou GJ, Penzel T, Peppard PE, Post WS, Ramos AR, Rice K, Rotter JI, Sands SA, Shah NA, Shin C, Stone KL, Stubbe B, Sul JH, Tafti M, Taylor KD, Teumer A, Thornton TA, Tranah GJ, Wang C, Wang H, Warby SC, Wellman DA, Zee PC, Hanis CL, Laurie CC, Gottlieb DJ, Patel SR, Zhu X, Sunyaev SR, Saxena R, Lin X, Redline S. Multi-ethnic Meta-analysis Identifies RAI1 as a Possible Obstructive Sleep Apnea Related Quantitative Trait Locus in Men. Am J Respir Cell Mol Biol 2017
Chen W, Gardeux V, Meireles-Filho A, Deplancke B. Profiling of Single-Cell Transcriptomes. Curr Protoc Mouse Biol 2017;7(3):145-175
Chevalier MF, Trabanelli S, Racle J, Salomé B, Cesson V, Gharbi D, Bohner P, Domingos-Pereira S, Dartiguenave F, Fritschi AS, Speiser DE, Rentsch CA, Gfeller D, Jichlinski P, Nardelli-Haefliger D, Jandus C, Derré L. ILC2-modulated T cell-to-MDSC balance is associated with bladder cancer recurrence. J Clin Invest 2017;127(8):2916-2929
Chevrier S, Levine JH, Zanotelli VRT, Silina K, Schulz D, Bacac M, Ries CH, Ailles L, Jewett MAS, Moch H, van den Broek M, Beisel C, Stadler MB, Gedye C, Reis B, Pe'er D, Bodenmiller B. An Immune Atlas of Clear Cell Renal Cell Carcinoma. Cell 2017;169(4):736-749.e18
Christel S, Herold M, Bellenberg S, El Hajjami M, Buetti-Dinh A, Pivkin IV, Sand W, Wilmes P, Poetsch A, Dopson M. Multi-omics reveal the lifestyle of the acidophilic, mineral-oxidizing model species Leptospirillum ferriphilum(T). Appl Environ Microbiol 2017
Colombo DF, Burger L, Baubec T, Schübeler D. Binding of high mobility group A proteins to the mammalian genome occurs as a function of AT-content. PLoS Genet 2017;13(12):e1007102
Corre T, Arjona FJ, Hayward C, Youhanna S, de Baaij JHF, Belge H, Nägele N, Debaix H, Blanchard MG, Traglia M, Harris SE, Ulivi S, Rueedi R, Lamparter D, Macé A, Sala C, Lenarduzzi S, Ponte B, Pruijm M, Ackermann D, Ehret G, Baptista D, Polasek O, Rudan I, Hurd TW, Hastie ND, Vitart V, Waeber G, Kutalik Z, Bergmann S, Vargas-Poussou R, Konrad M, Gasparini P, Deary IJ, Starr JM, Toniolo D, Vollenweider P, Hoenderop JGJ, Bindels RJM, Bochud M, Devuyst O. Genome-Wide Meta-Analysis Unravels Interactions between Magnesium Homeostasis and Metabolic Phenotypes. J Am Soc Nephrol 2018;29(1):335-348
Cosset É, Ilmjärv S, Dutoit V, Elliott K, von Schalscha T, Camargo MF, Reiss A, Moroishi T, Seguin L, Gomez G, Moo JS, Preynat-Seauve O, Krause KH, Chneiweiss H, Sarkaria JN, Guan KL, Dietrich PY, Weis SM, Mischel PS, Cheresh DA. Glut3 Addiction Is a Druggable Vulnerability for a Molecularly Defined Subpopulation of Glioblastoma. Cancer Cell 2017;32(6):856-868.e5
Crippa S, Ancey PB, Vazquez J, Angelino P, Rougemont AL, Guettier C, Zoete V, Delorenzi M, Michielin O, Meylan E. Mutant CTNNB1 and histological heterogeneity define metabolic subtypes of hepatoblastoma. EMBO Mol Med 2017;9(11):1589-1604
Crona K, Gavryushkin A, Gavryushkin A, Greene D, Beerenwinkel N, Beerenwinkel N. Inferring genetic interactions from comparative fitness data. Elife 2017;6
Cruciani-Guglielmacci C, Bellini L, Denom J, Oshima M, Fernandez N, Normandie-Levi P, Berney XP, Kassis N, Rouch C, Dairou J, Gorman T, Smith DM, Marley A, Liechti R, Kuznetsov D, Wigger L, Burdet F, Lefèvre AL, Wehrle I, Uphues I, Hildebrandt T, Rust W, Bernard C, Ktorza A, Rutter GA, Scharfmann R, Xenarios I, Le Stunff H, Thorens B, Magnan C, Ibberson M. Molecular phenotyping of multiple mouse strains under metabolic challenge uncovers a role for Elovl2 in glucose-induced insulin secretion. Mol Metab 2017;6(4):340-351
Daina A, Michielin O, Zoete V. SwissADME: a free web tool to evaluate pharmacokinetics, drug-likeness and medicinal chemistry friendliness of small molecules. Sci Rep 2017;7:42717
Darwiche R, Mène-Saffrané L, Gfeller D, Asojo OA, Schneiter R. The pathogen-related yeast protein Pry1, a member of the CAP protein superfamily, is a fatty acid-binding protein. J Biol Chem 2017;292(20):8304-8314
Daub JT, Moretti S, Davydov II, Excoffier L, Robinson-Rechavi M. Detection of Pathways Affected by Positive Selection in Primate Lineages Ancestral to Humans. Mol Biol Evol 2017;34(6):1391-1402
Davydov II, Robinson-Rechavi M, Salamin N. State aggregation for fast likelihood computations in molecular evolution. Bioinformatics 2017;33(3):354-362
de la Harpe M, Paris M, Karger DN, Rolland J, Kessler M, Salamin N, Lexer C. Molecular ecology studies of species radiations: current research gaps, opportunities and challenges. Mol Ecol 2017;26(10):2608-2622
Delachat AM, Guidotti N, Bachmann AL, Meireles-Filho ACA, Pick H, Lechner CC, Deluz C, Deplancke B, Suter DM, Fierz B. Engineered Multivalent Sensors to Detect Coexisting Histone Modifications in Living Stem Cells. Cell Chem Biol 2017
Dhillon DS, Milinkovitch MC, Zwicker M. Bifurcation Analysis of Reaction Diffusion Systems on Arbitrary Surfaces. Bull Math Biol 2017;79(4):788-827
Ding R, Boutet E, Lieberherr D, Schneider M, Tognolli M, Wu CH, Vijay-Shanker K, Arighi CN. eGenPub, a text mining system for extending computationally mapped bibliography for UniProt Knowledgebase by capturing centrality. Database (Oxford) 2017;2017
Ding W, Baumdicker F, Neher RA. panX: pan-genome analysis and exploration. Nucleic Acids Res 2017
Djordjevic M, Djordjevic M, Zdobnov E. Scoring Targets of Transcription in Bacteria Rather than Focusing on Individual Binding Sites. Front Microbiol 2017;8:2314
Dobay MP, Lemonnier F, Missiaglia E, Bastard C, Vallois D, Jais JP, Scourzic L, Dupuy A, Fataccioli V, Pujals A, Parrens M, Le Bras F, Rousset T, Picquenot JM, Martin N, Haioun C, Delarue R, Bernard OA, Delorenzi M, de Leval L, Gaulard P. Integrative clinicopathological and molecular analyses of angioimmunoblastic T-cell lymphoma and other nodal lymphomas of follicular helper T-cell origin. Haematologica 2017;102(4):e148-e151
Dréos R, Ambrosini G, Groux R, Périer RC, Bucher P. MGA repository: a curated data resource for ChIP-seq and other genome annotated data. Nucleic Acids Res 2017
Egli T, Vukojevic V, Sengstag T, Jacquot M, Cabezón R, Coynel D, Freytag V, Heck A, Vogler C, de Quervain DJ, Papassotiropoulos A, Milnik A. Exhaustive search for epistatic effects on the human methylome. Sci Rep 2017;7(1):13669
Essaidi-Laziosi M, Brito F, Benaoudia S, Royston L, Cagno V, Fernandes-Rocha M, Piuz I, Zdobnov E, Huang S, Constant S, Boldi MO, Kaiser L, Tapparel C. Propagation of respiratory viruses in human airway epithelia reveals persistent virus-specific signatures. J Allergy Clin Immunol 2017
Faget J, Contat C, Zangger N, Peters S, Meylan E. RANKL signaling sustains primary tumor growth in genetically engineered mouse models of lung adenocarcinoma. J Thorac Oncol 2017
Faget J, Groeneveld S, Boivin G, Sankar M, Zangger N, Garcia M, Guex N, Zlobec I, Steiner L, Piersigilli A, Xenarios I, Meylan E. Neutrophils and Snail Orchestrate the Establishment of a Pro-tumor Microenvironment in Lung Cancer. Cell Rep 2017;21(11):3190-3204
Feigelman R, Kahlert CR, Baty F, Rassouli F, Kleiner RL, Kohler P, Brutsche MH, von Mering C. Sputum DNA sequencing in cystic fibrosis: non-invasive access to the lung microbiome and to pathogen details. Microbiome 2017;5(1):20
Fonseca Costa SS, Wegmann D, Ripperger JA. Normalisation against Circadian and Age-Related Disturbances Enables Robust Detection of Gene Expression Changes in Liver of Aged Mice. PLoS One 2017;12(1):e0169615
Forslund K, Pereira C, Capella-Gutierrez S, Sousa da Silva A, Altenhoff A, Huerta-Cepas J, Muffato M, Patricio M, Vandepoele K, Ebersberger I, Blake J, Fernández Breis JT, Quest for Orthologs Consortium, Boeckmann B, Gabaldón T, Sonnhammer E, Dessimoz C, Lewis S. Gearing up to handle the mosaic nature of life in the quest for orthologs. Bioinformatics 2017
Frismantas V, Dobay MP, Rinaldi A, Tchinda J, Dunn SH, Kunz J, Richter-Pechanska P, Marovca B, Pail O, Jenni S, Diaz-Flores E, Chang BH, Brown TJ, Collins RH, Uhrig S, Balasubramanian GP, Bandapalli OR, Higi S, Eugster S, Voegeli P, Delorenzi M, Cario G, Loh ML, Schrappe M, Stanulla M, Kulozik AE, Muckenthaler MU, Saha V, Irving JA, Meisel R, Radimerski T, Von Stackelberg A, Eckert C, Tyner JW, Horvath P, Bornhauser BC, Bourquin JP. Ex vivo drug response profiling detects recurrent sensitivity patterns in drug-resistant acute lymphoblastic leukemia. Blood 2017;129(11):e26-e37
Gardeux V, David FPA, Shajkofci A, Schwalie PC, Deplancke B. ASAP: a web-based platform for the analysis and interactive visualization of single-cell RNA-seq data. Bioinformatics 2017;33(19):3123-3125
Garieri M, Delaneau O, Santoni F, Fish RJ, Mull D, Carninci P, Dermitzakis ET, Antonarakis SE, Fort A. The effect of genetic variation on promoter usage and enhancer activity. Nat Commun 2017;8(1):1358
Gegenschatz-Schmid K, Verkauskas G, Demougin P, Bilius V, Dasevicius D, Stadler MB, Hadziselimovic F. DMRTC2, PAX7, BRACHYURY/T and TERT Are Implicated in Male Germ Cell Development Following Curative Hormone Treatment for Cryptorchidism-Induced Infertility. Genes (Basel) 2017;8(10)
Gille D, Zangger N, Soneson C, Bütikofer U, Delorenzi M, Schwander F, Kopf-Bolanz KA, Chollet M, Walther B, Laederach K, Vergères G. Caloric dose-responsive genes in blood cells differentiate the metabolic status of obese men. J Nutr Biochem 2017;43:156-165
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