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

Rossi M, Bucci G, Rizzotto D, Bordo D, Marzi MJ, Puppo M, Flinois A, Spadaro D, Citi S, Emionite L, Cilli M, Nicassio F, Inga A, Briata P, Gherzi R (2019) LncRNA EPR controls epithelial proliferation by coordinating Cdkn1a transcription and mRNA decay response to TGF-β. Nat Commun, 10(1):1969, doi:10.1038/s41467-019-09754-1.
http://www.ncbi.nlm.nih.gov/pubmed/31036808

Delgado-Gonzalez A, Robles-Remacho A, Marin-Romero A, Detassis S, Lopez-Longarela B, Lopez-Delgado FJ, de Miguel-Perez D, Guardia-Monteagudo JJ, Fara MA, Tabraue-Chavez M, Pernagallo S, Sanchez-Martin RM, Diaz-Mochon JJ (2019) PCR-free and chemistry-based technology for miR-21 rapid detection directly from tumour cells. Talanta, 200:51-56, doi:10.1016/j.talanta.2019.03.039.
http://www.ncbi.nlm.nih.gov/pubmed/31036216

Precazzini F, Pancher M, Gatto P, Tushe A, Adami V, Anelli V, Mione MC (2019) Automated in vivo screen in zebrafish identifies Clotrimazole as targeting a metabolic vulnerability in a melanoma model. Dev. Biol., doi:10.1016/j.ydbio.2019.04.005.
http://www.ncbi.nlm.nih.gov/pubmed/30998907

Della Volpe S, Nasti R, Queirolo M, Unver MY, Jumde VK, Dömling A, Vasile F, Potenza D, Ambrosio FA, Costa G, Alcaro S, Zucal C, Provenzani A, Di Giacomo M, Rossi D, Hirsch AKH, Collina S (2019) Novel Compounds Targeting the RNA-Binding Protein HuR. Structure-Based Design, Synthesis, and Interaction Studies. ACS Med Chem Lett, 10(4):615-620, doi:10.1021/acsmedchemlett.8b00600.
http://www.ncbi.nlm.nih.gov/pubmed/30996806

Breuer M, Guglielmi L, Zielonka M, Hemberger V, Kölker S, Okun JG, Hoffmann GF, Carl M, Sauer SW, Opladen T (2019) QDPR homologues in Danio rerio regulate melanin synthesis, early gliogenesis, and glutamine homeostasis. PLoS ONE, 14(4):e0215162, doi:10.1371/journal.pone.0215162.
http://www.ncbi.nlm.nih.gov/pubmed/30995231

Detassis S, Grasso M, Tabraue-Chávez M, Marín-Romero A, López-Longarela B, Ilyine H, Ress C, Ceriani S, Erspan M, Maglione A, Díaz-Mochón JJ, Pernagallo S, Denti MA (2019) New Platform for the Direct Profiling of microRNAs in Biofluids. Anal. Chem., doi:10.1021/acs.analchem.9b00213.
http://www.ncbi.nlm.nih.gov/pubmed/30994325

Zhang X, Piano I, Messina A, D'Antongiovanni V, Crò F, Provenzano G, Bozzi Y, Gargini C, Casarosa S (2019) Retinal defects in mice lacking the autism-associated gene Engrailed-2. Neuroscience, 408:177-190, doi:10.1016/j.neuroscience.2019.03.061.
http://www.ncbi.nlm.nih.gov/pubmed/30980901

Castro-Díez P, Vaz AS, Silva JS, van Loo M, Alonso Á, Aponte C, Bayón Á, Bellingham PJ, Chiuffo MC, DiManno N, Julian K, Kandert S, Porta N, Marchante H, Maule HG, Mayfield MM, Metcalfe D, Monteverdi MC, Núñez MA, Ostertag R, Parker IM, Peltzer DA, Potgieter LJ, Raymundo M, Rayome D, Reisman-Berman O, Richardson DM, Roos RE, Saldaña A, Shackleton RT, Torres A, Trudgen M, Urban J, Vicente JR, Vilà M, Ylioja T, Zenni RD, Godoy O (2019) Global effects of non-native tree species on multiple ecosystem services. Biol Rev Camb Philos Soc, doi:10.1111/brv.12511.
http://www.ncbi.nlm.nih.gov/pubmed/30974048

Infantino V, Tutucci E, Yeh Martin N, Zihlmann A, Garcia-Molinero V, Silvano G, Palancade B, Stutz F (2019) The mRNA export adaptor Yra1 contributes to DNA double-strand break repair through its C-box domain. PLoS ONE, 14(4):e0206336, doi:10.1371/journal.pone.0206336.
http://www.ncbi.nlm.nih.gov/pubmed/30951522

Biasini E (2019) A designer chaperone against prion diseases. Nat Biomed Eng, 3(3):167-168, doi:10.1038/s41551-019-0367-6.
http://www.ncbi.nlm.nih.gov/pubmed/30948815

Knezović Florijan M, Ozretić P, Bujak M, Pezzè L, Ciribilli Y, Kaštelan Ž, Slade N, Hudolin T (2019) The role of p53 isoforms' expression and p53 mutation status in renal cell cancer prognosis. Urol. Oncol., doi:10.1016/j.urolonc.2019.03.007.
http://www.ncbi.nlm.nih.gov/pubmed/30948335

Thomas AM, Manghi P, Asnicar F, Pasolli E, Armanini F, Zolfo M, Beghini F, Manara S, Karcher N, Pozzi C, Gandini S, Serrano D, Tarallo S, Francavilla A, Gallo G, Trompetto M, Ferrero G, Mizutani S, Shiroma H, Shiba S, Shibata T, Yachida S, Yamada T, Wirbel J, Schrotz-King P, Ulrich CM, Brenner H, Arumugam M, Bork P, Zeller G, Cordero F, Dias-Neto E, Setubal JC, Tett A, Pardini B, Rescigno M, Waldron L, Naccarati A, Segata N (2019) Metagenomic analysis of colorectal cancer datasets identifies cross-cohort microbial diagnostic signatures and a link with choline degradation. Nat. Med., 25(4):667-678, doi:10.1038/s41591-019-0405-7.
http://www.ncbi.nlm.nih.gov/pubmed/30936548

Wirbel J, Pyl PT, Kartal E, Zych K, Kashani A, Milanese A, Fleck JS, Voigt AY, Palleja A, Ponnudurai R, Sunagawa S, Coelho LP, Schrotz-King P, Vogtmann E, Habermann N, Niméus E, Thomas AM, Manghi P, Gandini S, Serrano D, Mizutani S, Shiroma H, Shiba S, Shibata T, Yachida S, Yamada T, Waldron L, Naccarati A, Segata N, Sinha R, Ulrich CM, Brenner H, Arumugam M, Bork P, Zeller G (2019) Meta-analysis of fecal metagenomes reveals global microbial signatures that are specific for colorectal cancer. Nat. Med., 25(4):679-689, doi:10.1038/s41591-019-0406-6.
http://www.ncbi.nlm.nih.gov/pubmed/30936547

Cardano M, Zasso J, Ruggiero L, Di Giacomo G, Marcatili M, Cremona O, Conti L (2019) Epsins Regulate Mouse Embryonic Stem Cell Exit from Pluripotency and Neural Commitment by Controlling Notch Activation. Stem Cells Int, 2019:4084351, doi:10.1155/2019/4084351.
http://www.ncbi.nlm.nih.gov/pubmed/30930949

Bizzego A, Bussola N, Chierici M, Maggio V, Francescatto M, Cima L, Cristoforetti M, Jurman G, Furlanello C (2019) Evaluating reproducibility of AI algorithms in digital pathology with DAPPER. PLoS Comput. Biol., 15(3):e1006269, doi:10.1371/journal.pcbi.1006269.
http://www.ncbi.nlm.nih.gov/pubmed/30917113

Huckins LM, Dobbyn A, Ruderfer DM, Hoffman G, Wang W, Pardiñas AF, Rajagopal VM, Als TD, T Nguyen H, Girdhar K, Boocock J, Roussos P, Fromer M, Kramer R, Domenici E, Gamazon ER, Purcell S, CommonMind Consortium, Schizophrenia Working Group of the PsyUniversity of Copenhagenchiatric Genomics Consortium, iPSYCH-GEMS Schizophrenia Working Group, Demontis D, Børglum AD, Walters JTR, O'Donovan MC, Sullivan P, Owen MJ, Devlin B, Sieberts SK, Cox NJ, Im HK, Sklar P, Stahl EA (2019) Gene expression imputation across multiple brain regions provides insights into schizophrenia risk. Nat. Genet., 51(4):659-674, doi:10.1038/s41588-019-0364-4.
http://www.ncbi.nlm.nih.gov/pubmed/30911161

Dolce D, Neri S, Grisotto L, Campana S, Ravenni N, Miselli F, Camera E, Zavataro L, Braggion C, Fiscarelli EV, Lucidi V, Cariani L, Girelli D, Faelli N, Colombo C, Lucanto C, Lombardo M, Magazzù G, Tosco A, Raia V, Manara S, Pasolli E, Armanini F, Segata N, Biggeri A, Taccetti G (2019) Methicillin-resistant Staphylococcus aureus eradication in cystic fibrosis patients: A randomized multicenter study. PLoS ONE, 14(3):e0213497, doi:10.1371/journal.pone.0213497.
http://www.ncbi.nlm.nih.gov/pubmed/30901344

Le Gall G, Guttula K, Kellingray L, Tett AJ, Hoopen RT, Kemsley EK, Savva GM, Ibrahim A, Narbad A (2019) Correction: Metabolite quantification of faecal extracts from colorectal cancer patients and healthy controls. Oncotarget, 10(17):1660, doi:10.18632/oncotarget.26766.
http://www.ncbi.nlm.nih.gov/pubmed/30899435

Murthy V, Tebaldi T, Yoshida T, Erdin S, Calzonetti T, Vijayvargia R, Tripathi T, Kerschbamer E, Seong IS, Quattrone A, Talkowski ME, Gusella JF, Georgopoulos K, MacDonald ME, Biagioli M (2019) Hypomorphic mutation of the mouse Huntington's disease gene orthologue. PLoS Genet., 15(3):e1007765, doi:10.1371/journal.pgen.1007765.
http://www.ncbi.nlm.nih.gov/pubmed/30897080

Bettin N, Oss Pegorar C, Cusanelli E (2019) The Emerging Roles of TERRA in Telomere Maintenance and Genome Stability. Cells, 8(3), doi:10.3390/cells8030246.
http://www.ncbi.nlm.nih.gov/pubmed/30875900

Dickmeis T, Feng Y, Mione MC, Ninov N, Santoro M, Spaink HP, Gut P (2019) Nano-Sampling and Reporter Tools to Study Metabolic Regulation in Zebrafish. Front Cell Dev Biol, 7:15, doi:10.3389/fcell.2019.00015.
http://www.ncbi.nlm.nih.gov/pubmed/30873407

Battistutta R, Lolli G (2019) Inhibitory Properties of ATP-Competitive Coumestrol and Boldine Are Correlated to Different Modulations of CK2 Flexibility. J. Nat. Prod., 82(4):1014-1018, doi:10.1021/acs.jnatprod.8b00889.
http://www.ncbi.nlm.nih.gov/pubmed/30840451

Grasso M, Piscopo P, Talarico G, Ricci L, Crestini A, Tosto G, Gasparini M, Bruno G, Denti MA, Confaloni A (2019) Plasma microRNA profiling distinguishes patients with frontotemporal dementia from healthy subjects. Neurobiol. Aging, doi:10.1016/j.neurobiolaging.2019.01.024.
http://www.ncbi.nlm.nih.gov/pubmed/30826067

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, 25(3):444-453.e3, 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

Wodak SJ, Paci E, Dokholyan NV, Berezovsky IN, Horovitz A, Li J, Hilser VJ, Bahar I, Karanicolas J, Stock G, Hamm P, Stote RH, Eberhardt J, Chebaro Y, Dejaegere A, Cecchini M, Changeux JP, Bolhuis PG, Vreede J, Faccioli P, Orioli S, Ravasio R, Yan L, Brito C, Wyart M, Gkeka P, Rivalta I, Palermo G, McCammon JA, Panecka-Hofman J, Wade RC, Di Pizio A, Niv MY, Nussinov R, Tsai CJ, Jang H, Padhorny D, Kozakov D, McLeish T (2019) Allostery in Its Many Disguises: From Theory to Applications. Structure, 27(4):566-578, doi:10.1016/j.str.2019.01.003.
http://www.ncbi.nlm.nih.gov/pubmed/30744993

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.), 34(4):327-341, 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

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

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

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

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

Berto G, Ferreira-Cerca S, De Wulf P (2019) The Rio1 protein kinases/ATPases: conserved regulators of growth, division, and genomic stability. Curr. Genet., 65(2):457-466, doi:10.1007/s00294-018-0912-y.
http://www.ncbi.nlm.nih.gov/pubmed/30515528

Toparlak OD, Mansy SS (2019) Progress in synthesizing protocells. Exp. Biol. Med. (Maywood), 244(4):304-313, doi:10.1177/1535370218816657.
http://www.ncbi.nlm.nih.gov/pubmed/30509137

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

Mezzavilla M, Notarangelo M, Concas MP, Catamo E, Gasparini P, Grillotti MG, Robino A (2019) Investigation of the link between PROP taste perception and vegetables consumption using FAOSTAT data. Int J Food Sci Nutr, 70(4):484-490, doi:10.1080/09637486.2018.1519527.
http://www.ncbi.nlm.nih.gov/pubmed/30304964

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

Rubin MA, Demichelis F (2019) The Genomics of Prostate Cancer: A Historic Perspective. Cold Spring Harb Perspect Med, 9(3), doi:10.1101/cshperspect.a034942.
http://www.ncbi.nlm.nih.gov/pubmed/29712681