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Latest publications of CIBIO affiliates (last updated on March 1st, 2019)

Polsinelli I, Borruso L, Caliandro R, Triboli L, Esposito A, Benini S (2019) A genome-wide analysis of desferrioxamine mediated iron uptake in Erwinia spp. reveals genes exclusive of the Rosaceae infecting strains. Sci Rep, 9(1):2818, doi:10.1038/s41598-019-39787-x.
http://www.ncbi.nlm.nih.gov/pubmed/30808981

De Filippis F, Pasolli E, Tett A, Tarallo S, Naccarati A, De Angelis M, Neviani E, Cocolin L, Gobbetti M, Segata N, Ercolini D (2019) Distinct Genetic and Functional Traits of Human Intestinal Prevotella copri Strains Are Associated with Different Habitual Diets. Cell Host Microbe, doi:10.1016/j.chom.2019.01.004.
http://www.ncbi.nlm.nih.gov/pubmed/30799264

Uluşeker C, Torres-Bacete J, García JL, Hanczyc MM, Nogales J, Kahramanoğulları O (2019) Quantifying dynamic mechanisms of auto-regulation in Escherichia coli with synthetic promoter in response to varying external phosphate levels. Sci Rep, 9(1):2076, doi:10.1038/s41598-018-38223-w.
http://www.ncbi.nlm.nih.gov/pubmed/30765722

Guida M, Zanon A, Montibeller L, Lavdas AA, Ladurner J, Pischedda F, Rakovic A, Domingues FS, Piccoli G, Klein C, Pramstaller PP, Hicks AA, Pichler I (2019) Parkin Interacts with Apoptosis-Inducing Factor and Interferes with Its Translocation to the Nucleus in Neuronal Cells. Int J Mol Sci, 20(3), doi:10.3390/ijms20030748.
http://www.ncbi.nlm.nih.gov/pubmed/30754623

Avogaro L, Oss Pegorar C, Bettin N, Cusanelli E (2019) Generation of Cancer Cell Clones to Visualize Telomeric Repeat-containing RNA TERRA Expressed from a Single Telomere in Living Cells. J Vis Exp, (143), doi:10.3791/58790.
http://www.ncbi.nlm.nih.gov/pubmed/30735171

Bianconi I, D'Arcangelo S, Esposito A, Benedet M, Piffer E, Dinnella G, Gualdi P, Schinella M, Baldo E, Donati C, Jousson O (2018) Persistence and Microevolution of  Front Microbiol, 9:3242, doi:10.3389/fmicb.2018.03242.
http://www.ncbi.nlm.nih.gov/pubmed/30692969

Salama M, Benitez-Riquelme D, Elabd S, Munoz L, Zhang P, Glanemann M, Mione MC, Goldin R, Soussi T, Davidson G, Blattner C (2019) Fam83F induces p53 stabilisation and promotes its activity. Cell Death Differ., doi:10.1038/s41418-019-0281-1.
http://www.ncbi.nlm.nih.gov/pubmed/30692643

Cayuela ML, Claes KBM, Ferreira MG, Henriques CM, van Eeden F, Varga M, Vierstraete J, Mione MC (2018) The Zebrafish as an Emerging Model to Study DNA Damage in Aging, Cancer and Other Diseases. Front Cell Dev Biol, 6:178, doi:10.3389/fcell.2018.00178.
http://www.ncbi.nlm.nih.gov/pubmed/30687705

Grassi E, Santoro R, Umbach A, Grosso A, Oliviero S, Neri F, Conti L, Ala U, Provero P, DiCunto F, Merlo GR (2018) Choice of Alternative Polyadenylation Sites, Mediated by the RNA-Binding Protein Elavl3, Plays a Role in Differentiation of Inhibitory Neuronal Progenitors. Front Cell Neurosci, 12:518, doi:10.3389/fncel.2018.00518.
http://www.ncbi.nlm.nih.gov/pubmed/30687010

Pedron R, Esposito A, Bianconi I, Pasolli E, Tett A, Asnicar F, Cristofolini M, Segata N, Jousson O (2019) Genomic and metagenomic insights into the microbial community of a thermal spring. Microbiome, 7(1):8, doi:10.1186/s40168-019-0625-6.
http://www.ncbi.nlm.nih.gov/pubmed/30674352

Song Y, Rongvaux A, Taylor A, Jiang T, Tebaldi T, Balasubramanian K, Bagale A, Terzi YK, Gbyli R, Wang X, Fu X, Gao Y, Zhao J, Podoltsev N, Xu M, Neparidze N, Wong E, Torres R, Bruscia EM, Kluger Y, Manz MG, Flavell RA, Halene S (2019) A highly efficient and faithful MDS patient-derived xenotransplantation model for pre-clinical studies. Nat Commun, 10(1):366, doi:10.1038/s41467-018-08166-x.
http://www.ncbi.nlm.nih.gov/pubmed/30664659

Pasolli E, Asnicar F, Manara S, Zolfo M, Karcher N, Armanini F, Beghini F, Manghi P, Tett A, Ghensi P, Collado MC, Rice BL, DuLong C, Morgan XC, Golden CD, Quince C, Huttenhower C, Segata N (2019) Extensive Unexplored Human Microbiome Diversity Revealed by Over 150,000 Genomes from Metagenomes Spanning Age, Geography, and Lifestyle. Cell, 176(3):649-662.e20, doi:10.1016/j.cell.2019.01.001.
http://www.ncbi.nlm.nih.gov/pubmed/30661755

Profumo V, Forte B, Percio S, Rotundo F, Doldi V, Ferrari E, Fenderico N, Dugo M, Romagnoli D, Benelli M, Valdagni R, Dolfini D, Zaffaroni N, Gandellini P (2019) LEADeR role of miR-205 host gene as long noncoding RNA in prostate basal cell differentiation. Nat Commun, 10(1):307, doi:10.1038/s41467-018-08153-2.
http://www.ncbi.nlm.nih.gov/pubmed/30659180

Zielonka M, Probst J, Carl M, Hoffmann GF, Kölker S, Okun JG (2019) Bioenergetic dysfunction in a zebrafish model of acute hyperammonemic decompensation. Exp. Neurol., 314:91-99, doi:10.1016/j.expneurol.2019.01.008.
http://www.ncbi.nlm.nih.gov/pubmed/30653968

Cleverley RM, Rutter ZJ, Rismondo J, Corona F, Tsui HT, Alatawi FA, Daniel RA, Halbedel S, Massidda O, Winkler ME, Lewis RJ (2019) The cell cycle regulator GpsB functions as cytosolic adaptor for multiple cell wall enzymes. Nat Commun, 10(1):261, doi:10.1038/s41467-018-08056-2.
http://www.ncbi.nlm.nih.gov/pubmed/30651563

Zellweger F, De Frenne P, Lenoir J, Rocchini D, Coomes D (2019) Advances in Microclimate Ecology Arising from Remote Sensing. Trends Ecol. Evol. (Amst.), doi:10.1016/j.tree.2018.12.012.
http://www.ncbi.nlm.nih.gov/pubmed/30651180

Schiffer L, Azhar R, Shepherd L, Ramos M, Geistlinger L, Huttenhower C, Dowd JB, Segata N, Waldron L (2019) HMP16SData: Efficient Access to the Human Microbiome Project through Bioconductor. Am. J. Epidemiol., doi:10.1093/aje/kwz006.
http://www.ncbi.nlm.nih.gov/pubmed/30649166

Ciribilli Y, Borlak J (2018) Correction: Oncogenomics of c-Myc transgenic mice reveal novel regulators of extracellular signaling, angiogenesis and invasion with clinical significance for human lung adenocarcinoma. Oncotarget, 9(98):37269, doi:10.18632/oncotarget.26489.
http://www.ncbi.nlm.nih.gov/pubmed/30647859

Matsushita-Ishiodori Y, Hanczyc MM, Wang A, Szostak JW, Yomo T (2019) Using Imaging Flow Cytometry to Quantify and Optimize Giant Vesicle Production by Water-in-oil Emulsion Transfer Methods. Langmuir, 35(6):2375-2382, doi:10.1021/acs.langmuir.8b03635.
http://www.ncbi.nlm.nih.gov/pubmed/30645943

Smurova K, De Wulf P (2018) Centromere and Pericentromere Transcription: Roles and Regulation … in Sickness and in Health. Front Genet, 9:674, doi:10.3389/fgene.2018.00674.
http://www.ncbi.nlm.nih.gov/pubmed/30627137

Anelli V, Ordas A, Kneitz S, Sagredo LM, Gourain V, Schartl M, Meijer AH, Mione M (2018) Ras-Induced miR-146a and 193a Target Jmjd6 to Regulate Melanoma Progression. Front Genet, 9:675, doi:10.3389/fgene.2018.00675.
http://www.ncbi.nlm.nih.gov/pubmed/30619488

D'Agostino VG, Sighel D, Zucal C, Bonomo I, Micaelli M, Lolli G, Provenzani A, Quattrone A, Adami V (2019) Screening Approaches for Targeting Ribonucleoprotein Complexes: A New Dimension for Drug Discovery. SLAS Discov, 24(3):314-331, doi:10.1177/2472555218818065.
http://www.ncbi.nlm.nih.gov/pubmed/30616427

Sznarkowska A, Kostecka A, Kawiak A, Acedo P, Lion M, Inga A, Zawacka-Pankau J (2018) Reactivation of TAp73 tumor suppressor by protoporphyrin IX, a metabolite of aminolevulinic acid, induces apoptosis in  Cell Div, 13:10, doi:10.1186/s13008-018-0043-3.
http://www.ncbi.nlm.nih.gov/pubmed/30603043

Pasternak G, Yang Y, Santos BB, Brunello F, Hanczyc MM, Motta A (2019) Regenerated silk fibroin membranes as separators for transparent microbial fuel cells. Bioelectrochemistry, 126:146-155, doi:10.1016/j.bioelechem.2018.12.004.
http://www.ncbi.nlm.nih.gov/pubmed/30597451

Zizioli D, Mione M, Varinelli M, Malagola M, Bernardi S, Alghisi E, Borsani G, Finazzi D, Monti E, Presta M, Russo D (2019) Zebrafish disease models in hematology: Highlights on biological and translational impact. Biochim Biophys Acta Mol Basis Dis, 1865(3):620-633, doi:10.1016/j.bbadis.2018.12.015.
http://www.ncbi.nlm.nih.gov/pubmed/30593895

Chelini G, Zerbi V, Cimino L, Grigoli A, Markicevic M, Libera F, Robbiati S, Gadler M, Bronzoni S, Miorelli S, Galbusera A, Gozzi A, Casarosa S, Provenzano G, Bozzi Y (2019) Aberrant Somatosensory Processing and Connectivity in Mice Lacking  J. Neurosci., 39(8):1525-1538, doi:10.1523/JNEUROSCI.0612-18.2018.
http://www.ncbi.nlm.nih.gov/pubmed/30593497

Romagnoli D, Boccalini G, Bonechi M, Biagioni C, Fassan P, Bertorelli R, De Sanctis V, Di Leo A, Migliaccio I, Malorni L, Benelli M (2018) ddSeeker: a tool for processing Bio-Rad ddSEQ single cell RNA-seq data. BMC Genomics, 19(1):960, doi:10.1186/s12864-018-5249-x.
http://www.ncbi.nlm.nih.gov/pubmed/30583719

Poggi L, Casarosa S, Carl M (2018) An Eye on the Wnt Inhibitory Factor Wif1. Front Cell Dev Biol, 6:167, doi:10.3389/fcell.2018.00167.
http://www.ncbi.nlm.nih.gov/pubmed/30574494

de Sousa-Pereira P, Abrantes J, Bauernfried S, Pierini V, Esteves PJ, Keppler OT, Pizzato M, Hornung V, Fackler OT, Baldauf HM (2019) The antiviral activity of rodent and lagomorph SERINC3 and SERINC5 is counteracted by known viral antagonists. J. Gen. Virol., 100(2):278-288, doi:10.1099/jgv.0.001201.
http://www.ncbi.nlm.nih.gov/pubmed/30566072

Jurman G, Filosi M, Visintainer R, Riccadonna S, Furlanello C (2019) Stability in GRN Inference. Methods Mol. Biol., 1883:323-346, doi:10.1007/978-1-4939-8882-2_14.
http://www.ncbi.nlm.nih.gov/pubmed/30547407

Berto G, Ferreira-Cerca S, De Wulf P (2018) The Rio1 protein kinases/ATPases: conserved regulators of growth, division, and genomic stability. Curr. Genet., doi:10.1007/s00294-018-0912-y.
http://www.ncbi.nlm.nih.gov/pubmed/30515528

Toparlak OD, Mansy SS (2018) Progress in synthesizing protocells. Exp. Biol. Med. (Maywood), doi:10.1177/1535370218816657.
http://www.ncbi.nlm.nih.gov/pubmed/30509137

Berti A, Caporali R, Montecucco C, Paolazzi G, Monti S (2019) Aging in Primary Systemic Vasculitis: Implications for Diagnosis, Clinical Manifestations, and Management. Drugs Aging, 36(1):53-63, doi:10.1007/s40266-018-0617-4.
http://www.ncbi.nlm.nih.gov/pubmed/30484240

Muglia P, Filosi M, Da Ros L, Kam-Thong T, Nardocci F, Trabetti E, Ratti E, Rizzini P, Zuddas A, Bernardina BD, Domenici EItalian Autism Network,  (2018) The Italian autism network (ITAN): a resource for molecular genetics and biomarker investigations. BMC Psychiatry, 18(1):369, doi:10.1186/s12888-018-1937-y.
http://www.ncbi.nlm.nih.gov/pubmed/30463616

Borrenberghs D, Zurnic I, De Wit F, Acke A, Dirix L, Cereseto A, Debyser Z, Hendrix J (2018) Post-mitotic BET-induced reshaping of integrase quaternary structure supports wild-type MLV integration. Nucleic Acids Res., doi:10.1093/nar/gky1157.
http://www.ncbi.nlm.nih.gov/pubmed/30445610

Raneri M, Pinatel E, Peano C, Rampioni G, Leoni L, Bianconi I, Jousson O, Dalmasio C, Ferrante P, Briani F (2018) Pseudomonas aeruginosa mutants defective in glucose uptake have pleiotropic phenotype and altered virulence in non-mammal infection models. Sci Rep, 8(1):16912, doi:10.1038/s41598-018-35087-y.
http://www.ncbi.nlm.nih.gov/pubmed/30442901

Manara S, Pasolli E, Dolce D, Ravenni N, Campana S, Armanini F, Asnicar F, Mengoni A, Galli L, Montagnani C, Venturini E, Rota-Stabelli O, Grandi G, Taccetti G, Segata N (2018) Whole-genome epidemiology, characterisation, and phylogenetic reconstruction of Staphylococcus aureus strains in a paediatric hospital. Genome Med, 10(1):82, doi:10.1186/s13073-018-0593-7.
http://www.ncbi.nlm.nih.gov/pubmed/30424799

Maurer SE, Tølbøl Sørensen K, Iqbal Z, Nicholas J, Quirion K, Gioia M, Monnard PA, Hanczyc MM (2018) Vesicle Self-Assembly of Monoalkyl Amphiphiles under the Effects of High Ionic Strength, Extreme pH, and High Temperature Environments. Langmuir, 34(50):15560-15568, doi:10.1021/acs.langmuir.8b02830.
http://www.ncbi.nlm.nih.gov/pubmed/30407827

Ghensi P, Tonetto G, Soldini C, Bettio E, Mortellaro C, Soldini C (2018) Dental Implants With a Platform-Switched Morse Taper Connection and an Osteo Growth Induction Surface. J Craniofac Surg, doi:10.1097/SCS.0000000000004795.
http://www.ncbi.nlm.nih.gov/pubmed/30394965

Romanel A (2019) Allele-Specific Expression Analysis in Cancer Using Next-Generation Sequencing Data. Methods Mol. Biol., 1878:125-137, doi:10.1007/978-1-4939-8868-6_7.
http://www.ncbi.nlm.nih.gov/pubmed/30378073

Franzosa EA, McIver LJ, Rahnavard G, Thompson LR, Schirmer M, Weingart G, Lipson KS, Knight R, Caporaso JG, Segata N, Huttenhower C (2018) Species-level functional profiling of metagenomes and metatranscriptomes. Nat. Methods, 15(11):962-968, doi:10.1038/s41592-018-0176-y.
http://www.ncbi.nlm.nih.gov/pubmed/30377376

Cesaratto F, Sasset L, Myers MP, Re A, Petris G, Burrone OR (2019) BiP/GRP78 Mediates ERAD Targeting of Proteins Produced by Membrane-Bound Ribosomes Stalled at the STOP-Codon. J. Mol. Biol., 431(2):123-141, doi:10.1016/j.jmb.2018.10.009.
http://www.ncbi.nlm.nih.gov/pubmed/30367842

Pollini D, Loffredo R, Cardano M, Conti L, Lattante S, Notarangelo A, Sabatelli M, Provenzani A (2018) Generation and characterization of a human iPSC line from an ALS patient carrying the Q66K-MATR3 mutation. Stem Cell Res, 33:146-150, doi:10.1016/j.scr.2018.10.011.
http://www.ncbi.nlm.nih.gov/pubmed/30366341

O'Sullivan A, Salcedo J, Rubert J (2018) Correction to: Advanced analytical strategies for measuring free bioactive milk sugars: from composition and concentrations to human metabolic response. Anal Bioanal Chem, 410(30):7997, doi:10.1007/s00216-018-1389-8.
http://www.ncbi.nlm.nih.gov/pubmed/30353219

Nava Rodrigues D, Casiraghi N, Romanel A, Crespo M, Miranda S, Rescigno P, Figueiredo I, Riisnaes R, Carreira S, Sumanasuriya S, Gasperini P, Sharp A, Mateo J, Makay A, McNair C, Schiewer M, Knudsen K, Boysen G, Demichelis F, de Bono JS (2019) RB1 Heterogeneity in Advanced Metastatic Castration-Resistant Prostate Cancer. Clin. Cancer Res., 25(2):687-697, doi:10.1158/1078-0432.CCR-18-2068.
http://www.ncbi.nlm.nih.gov/pubmed/30257982

Beltran H, Oromendia C, Danila DC, Montgomery B, Hoimes C, Szmulewitz RZ, Vaishampayan U, Armstrong AJ, Stein M, Pinski J, Mosquera JM, Sailer V, Bareja R, Romanel A, Gumpeni N, Sboner A, Dardenne E, Puca L, Prandi D, Rubin MA, Scher HI, Rickman DS, Demichelis F, Nanus DM, Ballman KV, Tagawa ST (2019) A Phase II Trial of the Aurora Kinase A Inhibitor Alisertib for Patients with Castration-resistant and Neuroendocrine Prostate Cancer: Efficacy and Biomarkers. Clin. Cancer Res., 25(1):43-51, doi:10.1158/1078-0432.CCR-18-1912.
http://www.ncbi.nlm.nih.gov/pubmed/30232224

Liang Y, Tebaldi T, Rejeski K, Joshi P, Stefani G, Taylor A, Song Y, Vasic R, Maziarz J, Balasubramanian K, Ardasheva A, Ding A, Quattrone A, Halene S (2018) SRSF2 mutations drive oncogenesis by activating a global program of aberrant alternative splicing in hematopoietic cells. Leukemia, 32(12):2659-2671, doi:10.1038/s41375-018-0152-7.
http://www.ncbi.nlm.nih.gov/pubmed/29858584