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Items: 32

1.

Spatially clustered loci with multiple enhancers are frequent targets of HIV-1 integration.

Lucic B, Chen HC, Kuzman M, Zorita E, Wegner J, Minneker V, Wang W, Fronza R, Laufs S, Schmidt M, Stadhouders R, Roukos V, Vlahovicek K, Filion GJ, Lusic M.

Nat Commun. 2019 Sep 6;10(1):4059. doi: 10.1038/s41467-019-12046-3.

2.

AAVvector-mediated in vivo reprogramming into pluripotency.

Senís E, Mosteiro L, Wilkening S, Wiedtke E, Nowrouzi A, Afzal S, Fronza R, Landerer H, Abad M, Niopek D, Schmidt M, Serrano M, Grimm D.

Nat Commun. 2018 Jul 9;9(1):2651. doi: 10.1038/s41467-018-05059-x.

3.

Mapping Active Gene-Regulatory Regions in Human Repopulating Long-Term HSCs.

Wünsche P, Eckert ESP, Holland-Letz T, Paruzynski A, Hotz-Wagenblatt A, Fronza R, Rath T, Gil-Farina I, Schmidt M, von Kalle C, Klein C, Ball CR, Herbst F, Glimm H.

Cell Stem Cell. 2018 Jul 5;23(1):132-146.e9. doi: 10.1016/j.stem.2018.06.003.

4.

Systematic comparative study of computational methods for T-cell receptor sequencing data analysis.

Afzal S, Gil-Farina I, Gabriel R, Ahmad S, von Kalle C, Schmidt M, Fronza R.

Brief Bioinform. 2019 Jan 18;20(1):222-234. doi: 10.1093/bib/bbx111.

PMID:
29028876
5.

Lentiviral Vector Promoter is Decisive for Aberrant Transcript Formation.

Scholz SJ, Fronza R, Bartholomä CC, Cesana D, Montini E, von Kalle C, Gil-Farina I, Schmidt M.

Hum Gene Ther. 2017 Oct;28(10):875-885. doi: 10.1089/hum.2017.162. Epub 2017 Aug 18.

PMID:
28825370
6.

Genetic subclone architecture of tumor clone-initiating cells in colorectal cancer.

Giessler KM, Kleinheinz K, Huebschmann D, Balasubramanian GP, Dubash TD, Dieter SM, Siegl C, Herbst F, Weber S, Hoffmann CM, Fronza R, Buchhalter I, Paramasivam N, Eils R, Schmidt M, von Kalle C, Schneider M, Ulrich A, Scholl C, Fröhling S, Weichert W, Brors B, Schlesner M, Ball CR, Glimm H.

J Exp Med. 2017 Jul 3;214(7):2073-2088. doi: 10.1084/jem.20162017. Epub 2017 Jun 1.

7.

The Clonal Fate of Live Cells.

Wang W, Fronza R, Schmidt M.

Mol Ther Methods Clin Dev. 2017 Apr 14;5:93-95. doi: 10.1016/j.omtm.2017.03.007. eCollection 2017 Jun 16. Review. No abstract available.

8.

GENE-IS: Time-Efficient and Accurate Analysis of Viral Integration Events in Large-Scale Gene Therapy Data.

Afzal S, Wilkening S, von Kalle C, Schmidt M, Fronza R.

Mol Ther Nucleic Acids. 2017 Mar 17;6:133-139. doi: 10.1016/j.omtn.2016.12.001. Epub 2016 Dec 10.

9.

Common integration sites of published datasets identified using a graph-based framework.

Vasciaveo A, Velevska I, Politano G, Savino A, Schmidt M, Fronza R.

Comput Struct Biotechnol J. 2015 Nov 29;14:87-90. doi: 10.1016/j.csbj.2015.11.004. eCollection 2016.

10.

A Graph Based Framework to Model Virus Integration Sites.

Fronza R, Vasciaveo A, Benso A, Schmidt M.

Comput Struct Biotechnol J. 2015 Nov 30;14:69-77. doi: 10.1016/j.csbj.2015.10.006. eCollection 2016.

11.

Recombinant AAV Integration Is Not Associated With Hepatic Genotoxicity in Nonhuman Primates and Patients.

Gil-Farina I, Fronza R, Kaeppel C, Lopez-Franco E, Ferreira V, D'Avola D, Benito A, Prieto J, Petry H, Gonzalez-Aseguinolaza G, Schmidt M.

Mol Ther. 2016 Jun;24(6):1100-1105. doi: 10.1038/mt.2016.52. Epub 2016 Mar 7.

12.

Tracking genetically engineered lymphocytes long-term reveals the dynamics of T cell immunological memory.

Oliveira G, Ruggiero E, Stanghellini MT, Cieri N, D'Agostino M, Fronza R, Lulay C, Dionisio F, Mastaglio S, Greco R, Peccatori J, Aiuti A, Ambrosi A, Biasco L, Bondanza A, Lambiase A, Traversari C, Vago L, von Kalle C, Schmidt M, Bordignon C, Ciceri F, Bonini C.

Sci Transl Med. 2015 Dec 9;7(317):317ra198. doi: 10.1126/scitranslmed.aac8265. Erratum in: Sci Transl Med. 2015 Dec 23;7(319):319er9. D'Agostino, Mattio [corrected to D'Agostino, Mattia].

PMID:
26659572
13.

High-resolution analysis of the human T-cell receptor repertoire.

Ruggiero E, Nicolay JP, Fronza R, Arens A, Paruzynski A, Nowrouzi A, Ürenden G, Lulay C, Schneider S, Goerdt S, Glimm H, Krammer PH, Schmidt M, von Kalle C.

Nat Commun. 2015 Sep 1;6:8081. doi: 10.1038/ncomms9081.

14.

Generation of lentivirus-induced dendritic cells under GMP-compliant conditions for adaptive immune reconstitution against cytomegalovirus after stem cell transplantation.

Sundarasetty BS, Kloess S, Oberschmidt O, Naundorf S, Kuehlcke K, Daenthanasanmak A, Gerasch L, Figueiredo C, Blasczyk R, Ruggiero E, Fronza R, Schmidt M, von Kalle C, Rothe M, Ganser A, Koehl U, Stripecke R.

J Transl Med. 2015 Jul 22;13:240. doi: 10.1186/s12967-015-0599-5.

15.

Presence of a trs-Like Motif Promotes Rep-Mediated Wild-Type Adeno-Associated Virus Type 2 Integration.

Petri K, Gabriel R, Agundez L, Fronza R, Afzal S, Kaeppel C, Linden RM, Henckaerts E, Schmidt M.

J Virol. 2015 Jul;89(14):7428-32. doi: 10.1128/JVI.00426-15. Epub 2015 May 13.

16.

Preclinical evaluation of efficacy and safety of an improved lentiviral vector for the treatment of β-thalassemia and sickle cell disease.

Negre O, Bartholomae C, Beuzard Y, Cavazzana M, Christiansen L, Courne C, Deichmann A, Denaro M, de Dreuzy E, Finer M, Fronza R, Gillet-Legrand B, Joubert C, Kutner R, Leboulch P, Maouche L, Paulard A, Pierciey FJ, Rothe M, Ryu B, Schmidt M, von Kalle C, Payen E, Veres G.

Curr Gene Ther. 2015;15(1):64-81.

17.

Reply to: NGS library preparation may generate artifactual integration sites of AAV vectors.

Kaeppel C, Beattie SG, Fronza R, van Logtenstein R, Salmon F, Schmidt S, Wolf S, Nowrouzi A, Glimm H, von Kalle C, Petry H, Gaudet D, Schmidt M.

Nat Med. 2014 Jun;20(6):578-9. doi: 10.1038/nm.3584. No abstract available.

PMID:
24901561
18.

Comparative next-generation sequencing of adeno-associated virus inverted terminal repeats.

Petri K, Fronza R, Gabriel R, Käppel C, Nowrouzi A, Linden RM, Henckaerts E, Schmidt M.

Biotechniques. 2014 May 1;56(5):269-73. doi: 10.2144/000114170. eCollection 2014 May.

19.

Gene therapy for Wiskott-Aldrich syndrome--long-term efficacy and genotoxicity.

Braun CJ, Boztug K, Paruzynski A, Witzel M, Schwarzer A, Rothe M, Modlich U, Beier R, Göhring G, Steinemann D, Fronza R, Ball CR, Haemmerle R, Naundorf S, Kühlcke K, Rose M, Fraser C, Mathias L, Ferrari R, Abboud MR, Al-Herz W, Kondratenko I, Maródi L, Glimm H, Schlegelberger B, Schambach A, Albert MH, Schmidt M, von Kalle C, Klein C.

Sci Transl Med. 2014 Mar 12;6(227):227ra33. doi: 10.1126/scitranslmed.3007280.

20.

From bench to bedside: preclinical evaluation of a self-inactivating gammaretroviral vector for the gene therapy of X-linked chronic granulomatous disease.

Stein S, Scholz S, Schwäble J, Sadat MA, Modlich U, Schultze-Strasser S, Diaz M, Chen-Wichmann L, Müller-Kuller U, Brendel C, Fronza R, Kaufmann KB, Naundorf S, Pech NK, Travers JB, Matute JD, Presson RG Jr, Sandusky GE, Kunkel H, Rudolf E, Dillmann A, von Kalle C, Kühlcke K, Baum C, Schambach A, Dinauer MC, Schmidt M, Grez M.

Hum Gene Ther Clin Dev. 2013 Jun;24(2):86-98. doi: 10.1089/humc.2013.019.

21.

A largely random AAV integration profile after LPLD gene therapy.

Kaeppel C, Beattie SG, Fronza R, van Logtenstein R, Salmon F, Schmidt S, Wolf S, Nowrouzi A, Glimm H, von Kalle C, Petry H, Gaudet D, Schmidt M.

Nat Med. 2013 Jul;19(7):889-91. doi: 10.1038/nm.3230. Epub 2013 Jun 16.

PMID:
23770691
22.

Integrase-deficient lentiviral vectors mediate efficient gene transfer to human vascular smooth muscle cells with minimal genotoxic risk.

Chick HE, Nowrouzi A, Fronza R, McDonald RA, Kane NM, Alba R, Delles C, Sessa WC, Schmidt M, Thrasher AJ, Baker AH.

Hum Gene Ther. 2012 Dec;23(12):1247-57. doi: 10.1089/hum.2012.042. Epub 2012 Oct 26.

23.

Identification and association analysis of several hundred single nucleotide polymorphisms within candidate genes for back fat thickness in Italian Large White pigs using a selective genotyping approach.

Fontanesi L, Galimberti G, Calò DG, Fronza R, Martelli PL, Scotti E, Colombo M, Schiavo G, Casadio R, Buttazzoni L, Russo V.

J Anim Sci. 2012 Aug;90(8):2450-64. doi: 10.2527/jas.2011-4797. Epub 2012 Feb 24.

PMID:
22367074
24.

Brain cancer prognosis: independent validation of a clinical bioinformatics approach.

Fronza R, Tramonti M, Atchley WR, Nardini C.

J Clin Bioinforma. 2012 Feb 1;2:2. doi: 10.1186/2043-9113-2-2.

25.

Joint analysis of transcriptional and post- transcriptional brain tumor data: searching for emergent properties of cellular systems.

Fronza R, Tramonti M, Atchley WR, Nardini C.

BMC Bioinformatics. 2011 Mar 30;12:86. doi: 10.1186/1471-2105-12-86.

26.

The bologna annotation resource: a non hierarchical method for the functional and structural annotation of protein sequences relying on a comparative large-scale genome analysis.

Bartoli L, Montanucci L, Fronza R, Martelli PL, Fariselli P, Carota L, Donvito G, Maggi GP, Casadio R.

J Proteome Res. 2009 Sep;8(9):4362-71. doi: 10.1021/pr900204r.

PMID:
19552451
27.

G1 cell-cycle arrest and apoptosis by histone deacetylase inhibition in MLL-AF9 acute myeloid leukemia cells is p21 dependent and MLL-AF9 independent.

Tonelli R, Sartini R, Fronza R, Freccero F, Franzoni M, Dongiovanni D, Ballarini M, Ferrari S, D'Apolito M, Di Cola G, Capranico G, Khobta A, Campanini R, Paolucci P, Minucci S, Pession A.

Leukemia. 2006 Jul;20(7):1307-10. Epub 2006 Apr 13. No abstract available.

PMID:
16617320
28.

Global alterations in mRNA polysomal recruitment in a cell model of colorectal cancer progression to metastasis.

Provenzani A, Fronza R, Loreni F, Pascale A, Amadio M, Quattrone A.

Carcinogenesis. 2006 Jul;27(7):1323-33. Epub 2006 Mar 10.

PMID:
16531451
29.

Anti-gene peptide nucleic acid specifically inhibits MYCN expression in human neuroblastoma cells leading to cell growth inhibition and apoptosis.

Tonelli R, Purgato S, Camerin C, Fronza R, Bologna F, Alboresi S, Franzoni M, Corradini R, Sforza S, Faccini A, Shohet JM, Marchelli R, Pession A.

Mol Cancer Ther. 2005 May;4(5):779-86.

30.

p21Waf1/Cip1 is a common target induced by short-chain fatty acid HDAC inhibitors (valproic acid, tributyrin and sodium butyrate) in neuroblastoma cells.

Rocchi P, Tonelli R, Camerin C, Purgato S, Fronza R, Bianucci F, Guerra F, Pession A, Ferreri AM.

Oncol Rep. 2005 Jun;13(6):1139-44.

PMID:
15870934
31.

Targeted inhibition of NMYC by peptide nucleic acid in N-myc amplified human neuroblastoma cells: cell-cycle inhibition with induction of neuronal cell differentiation and apoptosis.

Pession A, Tonelli R, Fronza R, Sciamanna E, Corradini R, Sforza S, Tedeschi T, Marchelli R, Montanaro L, Camerin C, Franzoni M, Paolucci G.

Int J Oncol. 2004 Feb;24(2):265-72.

PMID:
14719101
32.

Real-time RT-PCR of tyrosine hydroxylase to detect bone marrow involvement in advanced neuroblastoma.

Pession A, Libri V, Sartini R, Conforti R, Magrini E, Bernardi L, Fronza R, Olivotto E, Prete A, Tonelli R, Paolucci G.

Oncol Rep. 2003 Mar-Apr;10(2):357-62.

PMID:
12579272

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