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2011

Publications 2011

Alfano G, Conte I, Caramico T, Avellino R, Arno B, Pizzo MT, Tanimoto N, Beck SC, Huber G, Dolle P, Seeliger MW, Banfi S (2011). Vax2 regulates retinoic acid distribution and cone opsin expression in the vertebrate eye. Development 138 (2):261-271.

Allocca M, Manfredi A, Iodice C, Di Vicino U, Auricchio A (2011). AAV-mediated gene replacement, either alone or in combination with physical and pharmacological agents, results in partial and transient protection from photoreceptor degeneration associated with betaPDE deficiency. Invest Ophthalmol Vis Sci 52(8):5713-5719.

Angelini C, Grisold W, Nigro V (2011). Diagnosis by protein analysis of dysferlinopathy in two patients mistaken as polymyositis. Acta Myol 30 (3):185-187.

Ashtari M, Cyckowski LL, Monroe JF, Marshall KA, Chung DC, Auricchio A, Simonelli F, Leroy BP, Maguire AM, Shindler KS, Bennett J (2011). The human visual cortex responds to gene therapy-mediated recovery of retinal function. J Clin Invest 121 (6):2160-2168.

Auricchio A (2011). Fighting blindness with adeno-associated virus serotype 8. Hum Gene Ther 22(10):1169-1170.

Bai M, Gad H, Turacchio G, Cocucci E, Yang JS, Li J, Beznoussenko GV, Nie Z, Luo R, Fu L, Collawn JF, Kirchhausen T, Luini A, Hsu VW (2011). ARFGAP1 promotes AP-2-dependent endocytosis. Nat Cell Biol13 (5):559-567.

Belcastro V, Gregoretti F, Siciliano V, Santoro M, D'Angelo G, Oliva G, di Bernardo D (2011). Reverse-Engineering and Analysis of Genome-Wide Gene Regulatory Networks from Gene Expression Profiles Using High-Performance Computing. IEEE/ACM Trans Comput Biol Bioinform.

Belcastro V, Siciliano V, Gregoretti F, Mithbaokar P, Dharmalingam G, Berlingieri S, Iorio F, Oliva G, Polishchuck R, Brunetti-Pierri N, di Bernardo D (2011). Transcriptional gene network inference from a massive dataset elucidates transcriptome organization and gene function. Nucleic Acids Res 39 (20):8677-8688.

Bertola F, Filocamo M, Casati G, Mort M, Rosano C, Tylki-Szymanska A, Tuysuz B, Gabrielli O, Grossi S, Scarpa M, Parenti G, Antuzzi D, Dalmau J, Di Rocco M, Vici CD, Okur I, Rosell J, Rovelli A, Furlan F, Rigoldi M, Biondi A, Cooper DN, Parini R (2011). IDUA mutational profiling of a cohort of 102 European patients with mucopolysaccharidosis type I: identification and characterization of 35 novel alpha-L-iduronidase (IDUA) alleles. Hum Mutat 32 (6):E2189-2210.

Bimonte S, De Angelis A, Quagliata L, Giusti F, Tammaro R, Dallai R, Ascenzi MG, Diez-Roux G, Franco B (2011). Ofd1 is required in limb bud patterning and endochondral bone development. Dev Biol 349 (2):179-191.

Bojarski P, Kulak L, Walczewska-Szewc K, Synak A, Marzullo VM, Luini A, D'Auria S (2011). Long-Distance FRET Analysis: A Monte Carlo Simulation Study. J Phys Chem B 115 (33):10120-10125.

Bousquet J, Anto JM, Sterk PJ, Adcock IM, Chung KF, Roca J, Agusti A, Brightling C, Cambon-Thomsen A, Cesario A, Abdelhak S, Antonarakis SE, Avignon A, Ballabio A, Baraldi E, Baranov A, Bieber T, Bockaert J, Brahmachari S, Brambilla C, Bringer J, Dauzat M, Ernberg I, Fabbri L, Froguel P, Galas D, Gojobori T, Hunter P, Jorgensen C, Kauffmann F, Kourilsky P, Kowalski ML, Lancet D, Pen CL, Mallet J, Mayosi B, Mercier J, Metspalu A, Nadeau JH, Ninot G, Noble D, Ozturk M, Palkonen S, Prefaut C, Rabe K, Renard E, Roberts RG, Samolinski B, Schunemann HJ, Simon HU, Soares MB, Superti-Furga G, Tegner J, Verjovski-Almeida S, Wellstead P, Wolkenhauer O, Wouters E, Balling R, Brookes AJ, Charron D, Pison C, Chen Z, Hood L, Auffray C (2011). Systems medicine and integrated care to combat chronic noncommunicable diseases. Genome Med 3 (7):43.

Brunetti-Pierri N, Lanpher B, Erez A, Ananieva EA, Islam M, Marini JC, Sun Q, Yu C, Hegde M, Li J, Wynn RM, Chuang DT, Hutson S, Lee B (2011). Phenylbutyrate therapy for maple syrup urine disease. Hum Mol Genet 20 (4):631-640.

Brunetti-Pierri N, Ng P (2011). Helper-dependent adenoviral vectors for liver-directed gene therapy. Hum Mol Genet 20 (R1):R7-13.

Brunetti-Pierri N, Paciorkowski AR, Ciccone R, Della Mina E, Bonaglia MC, Borgatti R, Schaaf CP, Sutton VR, Xia Z, Jelluma N, Ruivenkamp C, Bertrand M, de Ravel TJ, Jayakar P, Belli S, Rocchetti K, Pantaleoni C, D'Arrigo S, Hughes J, Cheung SW, Zuffardi O, Stankiewicz P (2011). Duplications of FOXG1 in 14q12 are associated with developmental epilepsy, mental retardation, and severe speech impairment. Eur J Hum Genet 19 (1):102-107.

Brunetti-Pierri N, Piccolo P, Morava E, Wevers RA, McGuirk M, Johnson YR, Urban Z, Dishop MK, Potocki L (2011). Cutis laxa and fatal pulmonary hypertension: a newly recognized syndrome? Clin Dysmorphol 20(2):77-81.

Cacciottolo M, Belcastro V, Laval S, Bushby K, di Bernardo D, Nigro V (2011). Reverse engineering gene network identifies new dysferlin-interacting proteins. J Biol Chem 286 (7):5404-5413.

Cacciottolo M, Numitone G, Aurino S, Caserta IR, Fanin M, Politano L, Minetti C, Ricci E, Piluso G, Angelini C, Nigro V (2011). Muscular dystrophy with marked Dysferlin deficiency is consistently caused by primary dysferlin gene mutations. Eur J Hum Genet 19 (9):974-980.

Cervigni RI, Barretta ML, Persico A, Corda D, Colanzi A (2011). The role of Aurora-A kinase in the Golgi-dependent control of mitotic entry. Bioarchitecture 1 (2):61-65.

Colella P, Iodice C, Di Vicino U, Annunziata I, Surace EM, Auricchio A (2011). Non-erythropoietic erythropoietin derivatives protect from light-induced and genetic photoreceptor degeneration. Hum Mol Genet 20 (11):2251-2262.

Cotugno G, Annunziata P, Tessitore A, O'Malley T, Capalbo A, Faella A, Bartolomeo R, O'Donnell P, Wang P, Russo F, Sleeper MM, Knox VW, Fernandez S, Levanduski L, Hopwood J, De Leonibus E, Haskins M, Auricchio A (2011). Long-term amelioration of feline Mucopolysaccharidosis VI after AAV-mediated liver gene transfer. Mol Ther 19 (3):461-469.

Cotugno G, Aurilio M, Annunziata P, Capalbo A, Faella A, Rinaldi V, Strisciuglio C, Di Tommaso M, Aloj L, Auricchio A (2011). Noninvasive repetitive imaging of somatostatin receptor 2 gene transfer with positron emission tomography. Hum Gene Ther 22 (2):189-196.

Cozzolino M, Augello B, Carella M, Palumbo O, Tavazzi B, Amorini AM, Lazzarino G, Merla G, Brunetti-Pierri N (2011). Chromosomal 17p13.3 microdeletion unmasking recessive Canavan disease mutation. Mol Genet Metab 104 (4):706-707.

Cuccato G, Polynikis A, Siciliano V, Graziano M, di Bernardo M, di Bernardo D (2011). Modeling RNA interference in mammalian cells. BMC Syst Biol 5 19.

D'Angelo A, Franco B (2011). The primary cilium in different tissues-lessons from patients and animal models. Pediatr Nephrol 26 (5):655-662.

d'Aquino R, Tirino V, Desiderio V, Studer M, De Angelis GC, Laino L, De Rosa A, Di Nucci D, Martino S, Paino F, Sampaolesi M, Papaccio G (2011). Human neural crest-derived postnatal cells exhibit remarkable embryonic attributes either in vitro or in vivo. Eur Cell Mater 21 304-316.

De Matteis MA, Luini A (2011). Mendelian disorders of membrane trafficking. N Engl J Med 365 (10):927-938.

Diez-Roux G, Banfi S, Sultan M, Geffers L, Anand S, Rozado D, Magen A, Canidio E, Pagani M, Peluso I, Lin-Marq N, Koch M, Bilio M, Cantiello I, Verde R, De Masi C, Bianchi SA, Cicchini J, Perroud E, Mehmeti S, Dagand E, Schrinner S, Nurnberger A, Schmidt K, Metz K, Zwingmann C, Brieske N, Springer C, Hernandez AM, Herzog S, Grabbe F, Sieverding C, Fischer B, Schrader K, Brockmeyer M, Dettmer S, Helbig C, Alunni V, Battaini MA, Mura C, Henrichsen CN, Garcia-Lopez R, Echevarria D, Puelles E, Garcia-Calero E, Kruse S, Uhr M, Kauck C, Feng G, Milyaev N, Ong CK, Kumar L, Lam M, Semple CA, Gyenesei A, Mundlos S, Radelof U, Lehrach H, Sarmientos P, Reymond A, Davidson DR, Dolle P, Antonarakis SE, Yaspo ML, Martinez S, Baldock RA, Eichele G, Ballabio A (2011). A high-resolution anatomical atlas of the transcriptome in the mouse embryo. PLoS Biol 9 (1):e1000582.

Dimmock D, Brunetti-Pierri N, Palmer DJ, Beaudet AL, Ng P (2011). Correction of hyperbilirubinemia in gunn rats using clinically relevant low doses of helper-dependent adenoviral vectors. Hum Gene Ther 22(4):483-488.

Dindot S, Piccolo P, Grove N, Palmer D, Brunetti-Pierri N (2011). Intrathecal injection of helper-dependent adenoviral vectors results in long-term transgene expression in neuroependymal cells and neurons. Hum Gene Ther 22 (6):745-751.

Eichele G, Diez-Roux G (2011). High-throughput analysis of gene expression on tissue sections by in situ hybridization. Methods 53 (4):417-423.

Fecarotta S, Amitrano M, Romano A, Della Casa R, Bruschini D, Astarita L, Parenti G, Andria G (2011). The videofluoroscopic swallowing study shows a sustained improvement of dysphagia in children with Niemann-Pick disease type C after therapy with miglustat. Am J Med Genet 155A (3):540-547.

Gargiulo A, Testa F, Rossi S, Di Iorio V, Fecarotta S, de Berardinis T, Iovine A, Magli A, Signorini S, Fazzi E, Galantuomo MS, Fossarello M, Montefusco S, Ciccodicola A, Neri A, Macaluso C, Simonelli F, Surace EM (2011). Molecular and clinical characterization of albinism in a large cohort of Italian patients. Invest Ophthalmol Vis Sci 52 (3):1281-1289.

Gennarino VA, Sardiello M, Mutarelli M, Dharmalingam G, Maselli V, Lago G, Banfi S (2011). HOCTAR database: a unique resource for microRNA target prediction. Gene 480 (1-2):51-58.

Glick BS, Luini A (2011). Models for Golgi traffic: a critical assessment. Cold Spring Harbor Perspectives in Biology 3 (11):a005215.

Kahn RA, Luini A, Segev N (2011). The Cellular Logistics Blog (CellLogBlog): A place for reviews and reasoned debate. Cellular logistics 1 (1):3.

Karali M, Manfredi A, Puppo A, Marrocco E, Gargiulo A, Allocca M, Corte MD, Rossi S, Giunti M, Bacci ML, Simonelli F, Surace EM, Banfi S, Auricchio A (2011). MicroRNA-restricted transgene expression in the retina. PLoS One 6 (7):e22166.

Lancioni A, Rotundo IL, Kobayashi YM, D'Orsi L, Aurino S, Nigro G, Piluso G, Acampora D, Cacciottolo M, Campbell KP, Nigro V (2011). Combined deficiency of alpha and epsilon sarcoglycan disrupts the cardiac dystrophin complex. Hum Mol Genet 20 (23):4644-4654.

Lodato S, Tomassy GS, De Leonibus E, Uzcategui YG, Andolfi G, Armentano M, Touzot A, Gaztelu JM, Arlotta P, Menendez de la Prida L, Studer M (2011). Loss of COUP-TFI alters the balance between caudal ganglionic eminence- and medial ganglionic eminence-derived cortical interneurons and results in resistance to epilepsy. J Neurosci 31 (12):4650-4662.

Luciani A, Villella VR, Esposito S, Brunetti-Pierri N, Medina DL, Settembre C, Gavina M, Raia V, Ballabio A, Maiuri L (2011). Cystic fibrosis: a disorder with defective autophagy. Autophagy 7 (1):104-106.

Luini A (2011). A brief history of the cisternal progression-maturation model. Cellular logistics 1 (1):6-11.

Medina DL, Fraldi A, Bouche V, Annunziata F, Mansueto G, Spampanato C, Puri C, Pignata A, Martina JA, Sardiello M, Palmieri M, Polishchuk R, Puertollano R, Ballabio A (2011). Transcriptional activation of lysosomal exocytosis promotes cellular clearance. Developmental cell 21 (3):421-430.

Mussolino C, della Corte M, Rossi S, Viola F, Di Vicino U, Marrocco E, Neglia S, Doria M, Testa F, Giovannoni R, Crasta M, Giunti M, Villani E, Lavitrano M, Bacci ML, Ratiglia R, Simonelli F, Auricchio A, Surace EM (2011). AAV-mediated photoreceptor transduction of the pig cone-enriched retina. Gene Ther18 (7):637-645.

Mussolino C, Sanges D, Marrocco E, Bonetti C, Di Vicino U, Marigo V, Auricchio A, Meroni G, Surace EM (2011). Zinc-finger-based transcriptional repression of rhodopsin in a model of dominant retinitis pigmentosa. EMBO Mol Med 3 (3):118-128.

Napolitano LM, Jaffray EG, Hay RT, Meroni G (2011). Functional interactions between ubiquitin E2 enzymes and TRIM proteins. Biochem J 434 (2):309-319.

Nigro V, Aurino S, Piluso G (2011). Limb girdle muscular dystrophies: update on genetic diagnosis and therapeutic approaches. Curr Opin Neurol 24 (5):429-436.

Palmieri G, Bergamo P, Luini A, Ruvo M, Gogliettino M, Langella E, Saviano M, Hegde RN, Sandomenico A, Rossi M (2011). Acylpeptide hydrolase inhibition as targeted strategy to induce proteasomal down-regulation. PLoS One 6 (10):e25888

Palmieri M, Impey S, Kang H, di Ronza A, Pelz C, Sardiello M, Ballabio A (2011). Characterization of the CLEAR network reveals an integrated control of cellular clearance pathways. Hum Mol Genet 20 (19):3852-3866.

Piluso G, Dionisi M, Del Vecchio Blanco F, Torella A, Aurino S, Savarese M, Giugliano T, Bertini E, Terracciano A, Vainzof M, Criscuolo C, Politano L, Casali C, Santorelli FM, Nigro V (2011). Motor chip: a comparative genomic hybridization microarray for copy-number mutations in 245 neuromuscular disorders.Clin Chem 57 (11):1584-1596.

Polynikis A, Cuccato G, Criscuolo S, Hogan SJ, Di Bernardo M, Di Bernardo D (2011). Design and construction of a versatile synthetic network for bistable gene expression in mammalian systems. J Comput Biol 18 (2):195-203.

Roncarati R, Latronico MV, Musumeci B, Aurino S, Torella A, Bang ML, Jotti GS, Puca AA, Volpe M, Nigro V, Autore C, Condorelli G (2011). Unexpectedly low mutation rates in beta-myosin heavy chain and cardiac myosin binding protein genes in Italian patients with hypertrophic cardiomyopathy. J Cell Physiol 226(11):2894-2900.

Rotundo IL, Faraso S, De Leonibus E, Nigro G, Vitiello C, Lancioni A, Di Napoli D, Castaldo S, Russo V, Russo F, Piluso G, Auricchio A, Nigro V (2011). Worsening of cardiomyopathy using deflazacort in an animal model rescued by gene therapy. PLoS One 6 (9):e24729.

Settembre C, Ballabio A (2011). TFEB regulates autophagy: an integrated coordination of cellular degradation and recycling processes. Autophagy 7 (11):1379-1381.

Settembre C, Di Malta C, Polito VA, Garcia Arencibia M, Vetrini F, Erdin S, Erdin SU, Huynh T, Medina D, Colella P, Sardiello M, Rubinsztein DC, Ballabio A (2011). TFEB links autophagy to lysosomal biogenesis.Science 332 (6036):1429-1433.

Siciliano V, Menolascina F, Marucci L, Fracassi C, Garzilli I, Moretti MN, di Bernardo D (2011). Construction and modelling of an inducible positive feedback loop stably integrated in a mammalian cell-line. PLoS Comput Biol 7 (6):e1002074.

Spampanato C, De Leonibus E, Dama P, Gargiulo A, Fraldi A, Sorrentino NC, Russo F, Nusco E, Auricchio A, Surace EM, Ballabio A (2011). Efficacy of a combined intracerebral and systemic gene delivery approach for the treatment of a severe lysosomal storage disorder. Mol Ther 19 (5):860-869.

Tammaro A, Di Martino A, Bracco A, Cozzolino S, Savoia G, Andria B, Cannavo A, Spagnuolo M, Piluso G, Aurino S, Nigro V (2011). Novel missense mutations and unexpected multiple changes of RYR1 gene in 75 malignant hyperthermia families. Clin Genet 79 (5):438-447.

Testa F, Surace EM, Rossi S, Marrocco E, Gargiulo A, Di Iorio V, Ziviello C, Nesti A, Fecarotta S, Bacci ML, Giunti M, Della Corte M, Banfi S, Auricchio A, Simonelli F (2011). Evaluation of Italian patients with leber congenital amaurosis due to AIPL1 mutations highlights the potential applicability of gene therapy.Invest Ophthalmol Vis Sci 52 (8):5618-5624.

Thauvin-Robinet C, Lesca G, Aral B, Gigot N, Lambert S, Gueneau L, Macca M, Franco B, Huet F, Zabot MT, Attie-Bitach T, Attia-Sobol J, Faivre L (2011). Cerebral dysgenesis does not exclude OFD I syndrome.Am J Med Genet A 155 (2):455-457.

Vicinanza M, Di Campli A, Polishchuk E, Santoro M, Di Tullio G, Godi A, Levtchenko E, De Leo MG, Polishchuk R, Sandoval L, Marzolo MP, De Matteis MA (2011). OCRL controls trafficking through early endosomes via PtdIns4,5P-dependent regulation of endosomal actin. EMBO J 30 (24):4970-4985.

Vozzi D, Aaspollu A, Athanasakis E, Berto A, Fabretto A, Licastro D, Kulm M, Testa F, Trevisi P, Vahter M, Ziviello C, Martini A, Simonelli F, Banfi S, Gasparini P (2011). Molecular epidemiology of Usher syndrome in Italy. Mol Vis 17 1662-1668.

Yang JS, Valente C, Polishchuk RS, Turacchio G, Layre E, Moody DB, Leslie CC, Gelb MH, Brown WJ, Corda D, Luini A, Hsu VW (2011). COPI acts in both vesicular and tubular transport. Nat Cell Biol 13(8):996-1003.