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Items: 1 to 50 of 134

1.

Characterizing Mutational Signatures in Human Cancer Cell Lines Reveals Episodic APOBEC Mutagenesis.

Petljak M, Alexandrov LB, Brammeld JS, Price S, Wedge DC, Grossmann S, Dawson KJ, Ju YS, Iorio F, Tubio JMC, Koh CC, Georgakopoulos-Soares I, Rodríguez-Martín B, Otlu B, O'Meara S, Butler AP, Menzies A, Bhosle SG, Raine K, Jones DR, Teague JW, Beal K, Latimer C, O'Neill L, Zamora J, Anderson E, Patel N, Maddison M, Ng BL, Graham J, Garnett MJ, McDermott U, Nik-Zainal S, Campbell PJ, Stratton MR.

Cell. 2019 Mar 7;176(6):1282-1294.e20. doi: 10.1016/j.cell.2019.02.012.

2.

Airway Compression by a Right Aortic Arch in the Absence of a Vascular Ring.

Agati S, Guerra Sousa C, Calvaruso FD, Ferro G, Zanai R, Campanella I, Secinaro A, Iorio FS, Anderson RH, Reali S.

World J Pediatr Congenit Heart Surg. 2019 Jan;10(1):103-104. doi: 10.1177/2150135118802787. No abstract available.

PMID:
30799717
3.

Structural rearrangements generate cell-specific, gene-independent CRISPR-Cas9 loss of fitness effects.

Gonçalves E, Behan FM, Louzada S, Arnol D, Stronach EA, Yang F, Yusa K, Stegle O, Iorio F, Garnett MJ.

Genome Biol. 2019 Feb 5;20(1):27. doi: 10.1186/s13059-019-1637-z.

4.

JACKS: joint analysis of CRISPR/Cas9 knockout screens.

Allen F, Behan F, Khodak A, Iorio F, Yusa K, Garnett M, Parts L.

Genome Res. 2019 Mar;29(3):464-471. doi: 10.1101/gr.238923.118. Epub 2019 Jan 23.

5.

CellMinerCDB for Integrative Cross-Database Genomics and Pharmacogenomics Analyses of Cancer Cell Lines.

Rajapakse VN, Luna A, Yamade M, Loman L, Varma S, Sunshine M, Iorio F, Sousa FG, Elloumi F, Aladjem MI, Thomas A, Sander C, Kohn KW, Benes CH, Garnett M, Reinhold WC, Pommier Y.

iScience. 2018 Dec 21;10:247-264. doi: 10.1016/j.isci.2018.11.029. Epub 2018 Dec 12.

6.

Drug repurposing: progress, challenges and recommendations.

Pushpakom S, Iorio F, Eyers PA, Escott KJ, Hopper S, Wells A, Doig A, Guilliams T, Latimer J, McNamee C, Norris A, Sanseau P, Cavalla D, Pirmohamed M.

Nat Rev Drug Discov. 2018 Oct 12. doi: 10.1038/nrd.2018.168. [Epub ahead of print] Review.

PMID:
30310233
7.

The germline genetic component of drug sensitivity in cancer cell lines.

Menden MP, Casale FP, Stephan J, Bignell GR, Iorio F, McDermott U, Garnett MJ, Saez-Rodriguez J, Stegle O.

Nat Commun. 2018 Aug 23;9(1):3385. doi: 10.1038/s41467-018-05811-3.

8.

Prenatal Echocardiographic Assessment of Right Aortic Arch.

Campanale CM, Pasquini L, Santangelo TP, Iorio FS, Bagolan P, Sanders SP, Toscano A.

Ultrasound Obstet Gynecol. 2018 Aug 20. doi: 10.1002/uog.20098. [Epub ahead of print]

PMID:
30125417
9.

Unsupervised correction of gene-independent cell responses to CRISPR-Cas9 targeting.

Iorio F, Behan FM, Gonçalves E, Bhosle SG, Chen E, Shepherd R, Beaver C, Ansari R, Pooley R, Wilkinson P, Harper S, Butler AP, Stronach EA, Saez-Rodriguez J, Yusa K, Garnett MJ.

BMC Genomics. 2018 Aug 13;19(1):604. doi: 10.1186/s12864-018-4989-y.

10.

Assessment of cardiac function in infants with transposition of the great arteries after surgery: comparison of two methods.

Yang F, Iacobelli R, Wang JM, Iorio FS.

World J Pediatr. 2018 Aug;14(4):373-377. doi: 10.1007/s12519-018-0178-y. Epub 2018 Jul 30.

PMID:
30062649
11.

Long-term survival and phenotypic spectrum in heterotaxy syndrome: A 25-year follow-up experience.

Baban A, Cantarutti N, Adorisio R, Lombardi R, Calcagni G, Piano Mortari E, Dallapiccola B, Marino B, Iorio FS, Carsetti R, Digilio MC, Giannico S, Drago F, Carotti A.

Int J Cardiol. 2018 Oct 1;268:100-105. doi: 10.1016/j.ijcard.2018.02.050.

PMID:
30041775
12.

Bradyarrhythmias in Repaired Atrioventricular Septal Defects: Single-Center Experience Based on 34 Years of Follow-Up of 522 Patients.

Di Mambro C, Calvieri C, Silvetti MS, Tamburri I, Giannico S, Baban A, Albanese S, Brancaccio G, Carotti A, Iorio FS, Drago F.

Pediatr Cardiol. 2018 Dec;39(8):1590-1597. doi: 10.1007/s00246-018-1934-4. Epub 2018 Jun 13.

PMID:
29948031
13.

Pathway-based dissection of the genomic heterogeneity of cancer hallmarks' acquisition with SLAPenrich.

Iorio F, Garcia-Alonso L, Brammeld JS, Martincorena I, Wille DR, McDermott U, Saez-Rodriguez J.

Sci Rep. 2018 Apr 30;8(1):6713. doi: 10.1038/s41598-018-25076-6.

14.

Loss of functional BAP1 augments sensitivity to TRAIL in cancer cells.

Kolluri KK, Alifrangis C, Kumar N, Ishii Y, Price S, Michaut M, Williams S, Barthorpe S, Lightfoot H, Busacca S, Sharkey A, Yuan Z, Sage EK, Vallath S, Le Quesne J, Tice DA, Alrifai D, von Karstedt S, Montinaro A, Guppy N, Waller DA, Nakas A, Good R, Holmes A, Walczak H, Fennell DA, Garnett M, Iorio F, Wessels L, McDermott U, Janes SM.

Elife. 2018 Jan 18;7. pii: e30224. doi: 10.7554/eLife.30224.

15.

Age and blood transfusion: relationship and prognostic implications in cardiac surgery.

De Santo LS, Romano G, Mango E, Iorio F, Savarese L, Numis F, Zebele C.

J Thorac Dis. 2017 Oct;9(10):3719-3727. doi: 10.21037/jtd.2017.08.126.

16.

Transcription Factor Activities Enhance Markers of Drug Sensitivity in Cancer.

Garcia-Alonso L, Iorio F, Matchan A, Fonseca N, Jaaks P, Peat G, Pignatelli M, Falcone F, Benes CH, Dunham I, Bignell G, McDade SS, Garnett MJ, Saez-Rodriguez J.

Cancer Res. 2018 Feb 1;78(3):769-780. doi: 10.1158/0008-5472.CAN-17-1679. Epub 2017 Dec 11.

17.

GDSCTools for mining pharmacogenomic interactions in cancer.

Cokelaer T, Chen E, Iorio F, Menden MP, Lightfoot H, Saez-Rodriguez J, Garnett MJ.

Bioinformatics. 2018 Apr 1;34(7):1226-1228. doi: 10.1093/bioinformatics/btx744.

18.

Comprehensive Pharmacogenomic Profiling of Malignant Pleural Mesothelioma Identifies a Subgroup Sensitive to FGFR Inhibition.

Quispel-Janssen JM, Badhai J, Schunselaar L, Price S, Brammeld J, Iorio F, Kolluri K, Garnett M, Berns A, Baas P, McDermott U, Neefjes J, Alifrangis C.

Clin Cancer Res. 2018 Jan 1;24(1):84-94. doi: 10.1158/1078-0432.CCR-17-1172. Epub 2017 Oct 23.

19.

Long-Term Outcomes After Extracardiac Fontan Takedown to an Intermediate Palliative Circulation.

Trezzi M, Cetrano E, Giannico S, Iorio FS, Albanese SB, Carotti A.

Ann Thorac Surg. 2018 Feb;105(2):599-605. doi: 10.1016/j.athoracsur.2017.05.068. Epub 2017 Sep 19.

PMID:
28935350
20.

Atrial septal defect morphology and stenting in hypoplastic left heart syndrome after hybrid palliation.

Oreto L, Mandraffino G, Manuri L, Saitta MB, Agati S, Zito C, Iorio FS, Carerj S, Guccione P.

Cardiol Young. 2018 Feb;28(2):252-260. doi: 10.1017/S1047951117001792. Epub 2017 Sep 11.

PMID:
28889828
21.

Early hybrid approach and enteral feeding algorithm could reduce the incidence of necrotising enterocolitis in neonates with ductus-dependent systemic circulation.

Manuri L, Morelli S, Agati S, Saitta MB, Oreto L, Mandraffino G, Iannace E, Iorio FS, Guccione P.

Cardiol Young. 2017 Jan;27(1):154-160. doi: 10.1017/S1047951116000275.

PMID:
28281412
22.

Genome-wide chemical mutagenesis screens allow unbiased saturation of the cancer genome and identification of drug resistance mutations.

Brammeld JS, Petljak M, Martincorena I, Williams SP, Alonso LG, Dalmases A, Bellosillo B, Robles-Espinoza CD, Price S, Barthorpe S, Tarpey P, Alifrangis C, Bignell G, Vidal J, Young J, Stebbings L, Beal K, Stratton MR, Saez-Rodriguez J, Garnett M, Montagut C, Iorio F, McDermott U.

Genome Res. 2017 Apr;27(4):613-625. doi: 10.1101/gr.213546.116. Epub 2017 Feb 8.

23.

Efficient randomization of biological networks while preserving functional characterization of individual nodes.

Iorio F, Bernardo-Faura M, Gobbi A, Cokelaer T, Jurman G, Saez-Rodriguez J.

BMC Bioinformatics. 2016 Dec 20;17(1):542. doi: 10.1186/s12859-016-1402-1.

24.

Stem cell-like transcriptional reprogramming mediates metastatic resistance to mTOR inhibition.

Mateo F, Arenas EJ, Aguilar H, Serra-Musach J, de Garibay GR, Boni J, Maicas M, Du S, Iorio F, Herranz-Ors C, Islam A, Prado X, Llorente A, Petit A, Vidal A, Català I, Soler T, Venturas G, Rojo-Sebastian A, Serra H, Cuadras D, Blanco I, Lozano J, Canals F, Sieuwerts AM, de Weerd V, Look MP, Puertas S, García N, Perkins AS, Bonifaci N, Skowron M, Gómez-Baldó L, Hernández V, Martínez-Aranda A, Martínez-Iniesta M, Serrat X, Cerón J, Brunet J, Barretina MP, Gil M, Falo C, Fernández A, Morilla I, Pernas S, Plà MJ, Andreu X, Seguí MA, Ballester R, Castellà E, Nellist M, Morales S, Valls J, Velasco A, Matias-Guiu X, Figueras A, Sánchez-Mut JV, Sánchez-Céspedes M, Cordero A, Gómez-Miragaya J, Palomero L, Gómez A, Gajewski TF, Cohen EEW, Jesiotr M, Bodnar L, Quintela-Fandino M, López-Bigas N, Valdés-Mas R, Puente XS, Viñals F, Casanovas O, Graupera M, Hernández-Losa J, Ramón Y Cajal S, García-Alonso L, Saez-Rodriguez J, Esteller M, Sierra A, Martín-Martín N, Matheu A, Carracedo A, González-Suárez E, Nanjundan M, Cortés J, Lázaro C, Odero MD, Martens JWM, Moreno-Bueno G, Barcellos-Hoff MH, Villanueva A, Gomis RR, Pujana MA.

Oncogene. 2017 May 11;36(19):2737-2749. doi: 10.1038/onc.2016.427. Epub 2016 Dec 19.

25.

Logic models to predict continuous outputs based on binary inputs with an application to personalized cancer therapy.

Knijnenburg TA, Klau GW, Iorio F, Garnett MJ, McDermott U, Shmulevich I, Wessels LF.

Sci Rep. 2016 Nov 23;6:36812. doi: 10.1038/srep36812.

26.

Hemopoietic-specific Sf3b1-K700E knock-in mice display the splicing defect seen in human MDS but develop anemia without ring sideroblasts.

Mupo A, Seiler M, Sathiaseelan V, Pance A, Yang Y, Agrawal AA, Iorio F, Bautista R, Pacharne S, Tzelepis K, Manes N, Wright P, Papaemmanuil E, Kent DG, Campbell PC, Buonamici S, Bolli N, Vassiliou GS.

Leukemia. 2017 Mar;31(3):720-727. doi: 10.1038/leu.2016.251. Epub 2016 Sep 8.

27.

A CRISPR Dropout Screen Identifies Genetic Vulnerabilities and Therapeutic Targets in Acute Myeloid Leukemia.

Tzelepis K, Koike-Yusa H, De Braekeleer E, Li Y, Metzakopian E, Dovey OM, Mupo A, Grinkevich V, Li M, Mazan M, Gozdecka M, Ohnishi S, Cooper J, Patel M, McKerrell T, Chen B, Domingues AF, Gallipoli P, Teichmann S, Ponstingl H, McDermott U, Saez-Rodriguez J, Huntly BJP, Iorio F, Pina C, Vassiliou GS, Yusa K.

Cell Rep. 2016 Oct 18;17(4):1193-1205. doi: 10.1016/j.celrep.2016.09.079.

28.

Thrombosis of Kommerell's diverticulum with subclavian steal phenomenon in a patient with non-small cell lung carcinoma under chemotherapy.

Faggioni L, Gabelloni M, Napoli V, Iorio F, Chella A, Caramella D.

Eur J Radiol Open. 2016 Jul 30;3:191-4. doi: 10.1016/j.ejro.2016.07.005. eCollection 2016.

29.

A Landscape of Pharmacogenomic Interactions in Cancer.

Iorio F, Knijnenburg TA, Vis DJ, Bignell GR, Menden MP, Schubert M, Aben N, Gonçalves E, Barthorpe S, Lightfoot H, Cokelaer T, Greninger P, van Dyk E, Chang H, de Silva H, Heyn H, Deng X, Egan RK, Liu Q, Mironenko T, Mitropoulos X, Richardson L, Wang J, Zhang T, Moran S, Sayols S, Soleimani M, Tamborero D, Lopez-Bigas N, Ross-Macdonald P, Esteller M, Gray NS, Haber DA, Stratton MR, Benes CH, Wessels LFA, Saez-Rodriguez J, McDermott U, Garnett MJ.

Cell. 2016 Jul 28;166(3):740-754. doi: 10.1016/j.cell.2016.06.017. Epub 2016 Jul 7.

30.

Locally vascularized pelvic accessory spleen.

Iorio F, Frantellizzi V, Drudi FM, Maghella F, Liberatore M.

J Ultrasound. 2015 Aug 6;19(2):141-4. doi: 10.1007/s40477-015-0178-x. eCollection 2016.

31.

Multilevel models improve precision and speed of IC50 estimates.

Vis DJ, Bombardelli L, Lightfoot H, Iorio F, Garnett MJ, Wessels LF.

Pharmacogenomics. 2016 May;17(7):691-700. doi: 10.2217/pgs.16.15. Epub 2016 May 16.

32.

Transcriptional response networks for elucidating mechanisms of action of multitargeted agents.

Kibble M, Khan SA, Saarinen N, Iorio F, Saez-Rodriguez J, Mäkelä S, Aittokallio T.

Drug Discov Today. 2016 Jul;21(7):1063-75. doi: 10.1016/j.drudis.2016.03.001. Epub 2016 Mar 12. Review.

PMID:
26979547
33.

Integrated transcriptomic and proteomic analysis identifies protein kinase CK2 as a key signaling node in an inflammatory cytokine network in ovarian cancer cells.

Kulbe H, Iorio F, Chakravarty P, Milagre CS, Moore R, Thompson RG, Everitt G, Canosa M, Montoya A, Drygin D, Braicu I, Sehouli J, Saez-Rodriguez J, Cutillas PR, Balkwill FR.

Oncotarget. 2016 Mar 29;7(13):15648-61. doi: 10.18632/oncotarget.7255.

34.

Unravelling druggable signalling networks that control F508del-CFTR proteostasis.

Hegde RN, Parashuraman S, Iorio F, Ciciriello F, Capuani F, Carissimo A, Carrella D, Belcastro V, Subramanian A, Bounti L, Persico M, Carlile G, Galietta L, Thomas DY, Di Bernardo D, Luini A.

Elife. 2015 Dec 23;4. pii: e10365. doi: 10.7554/eLife.10365.

35.

Blood transcriptomics of drug-naïve sporadic Parkinson's disease patients.

Calligaris R, Banica M, Roncaglia P, Robotti E, Finaurini S, Vlachouli C, Antonutti L, Iorio F, Carissimo A, Cattaruzza T, Ceiner A, Lazarevic D, Cucca A, Pangher N, Marengo E, di Bernardo D, Pizzolato G, Gustincich S.

BMC Genomics. 2015 Oct 28;16:876. doi: 10.1186/s12864-015-2058-3.

36.

A Semi-Supervised Approach for Refining Transcriptional Signatures of Drug Response and Repositioning Predictions.

Iorio F, Shrestha RL, Levin N, Boilot V, Garnett MJ, Saez-Rodriguez J, Draviam VM.

PLoS One. 2015 Oct 9;10(10):e0139446. doi: 10.1371/journal.pone.0139446. eCollection 2015.

37.

Prospective derivation of a living organoid biobank of colorectal cancer patients.

van de Wetering M, Francies HE, Francis JM, Bounova G, Iorio F, Pronk A, van Houdt W, van Gorp J, Taylor-Weiner A, Kester L, McLaren-Douglas A, Blokker J, Jaksani S, Bartfeld S, Volckman R, van Sluis P, Li VS, Seepo S, Sekhar Pedamallu C, Cibulskis K, Carter SL, McKenna A, Lawrence MS, Lichtenstein L, Stewart C, Koster J, Versteeg R, van Oudenaarden A, Saez-Rodriguez J, Vries RG, Getz G, Wessels L, Stratton MR, McDermott U, Meyerson M, Garnett MJ, Clevers H.

Cell. 2015 May 7;161(4):933-45. doi: 10.1016/j.cell.2015.03.053.

38.

Identification of drug-specific pathways based on gene expression data: application to drug induced lung injury.

Melas IN, Sakellaropoulos T, Iorio F, Alexopoulos LG, Loh WY, Lauffenburger DA, Saez-Rodriguez J, Bai JP.

Integr Biol (Camb). 2015 Aug;7(8):904-20. doi: 10.1039/c4ib00294f.

PMID:
25932872
39.

BRAF inhibitor resistance mediated by the AKT pathway in an oncogenic BRAF mouse melanoma model.

Perna D, Karreth FA, Rust AG, Perez-Mancera PA, Rashid M, Iorio F, Alifrangis C, Arends MJ, Bosenberg MW, Bollag G, Tuveson DA, Adams DJ.

Proc Natl Acad Sci U S A. 2015 Feb 10;112(6):E536-45. doi: 10.1073/pnas.1418163112. Epub 2015 Jan 26.

40.

Exploiting combinatorial patterns in cancer genomic data for personalized therapy and new target discovery.

Schubert M, Iorio F.

Pharmacogenomics. 2014 Dec;15(16):1943-6. doi: 10.2217/pgs.14.157. No abstract available.

41.

Fast randomization of large genomic datasets while preserving alteration counts.

Gobbi A, Iorio F, Dawson KJ, Wedge DC, Tamborero D, Alexandrov LB, Lopez-Bigas N, Garnett MJ, Jurman G, Saez-Rodriguez J.

Bioinformatics. 2014 Sep 1;30(17):i617-23. doi: 10.1093/bioinformatics/btu474.

42.

The antimicrobial effects of Citrus limonum and Citrus aurantium essential oils on multi-species biofilms.

Oliveira SA, Zambrana JR, Iorio FB, Pereira CA, Jorge AO.

Braz Oral Res. 2014;28:22-7.

PMID:
25000605
43.

Percutaneous closure of paravalvular leak in children after left ventricular outflow enlargement by the Konno procedure with aortic valve mechanical prosthesis.

Oreto L, Iorio FS, Pongiglione G, Guccione P.

J Thorac Cardiovasc Surg. 2014 May;147(5):e61-3. doi: 10.1016/j.jtcvs.2014.01.047. Epub 2014 Feb 8. No abstract available.

44.

Heterogeneity of genomic evolution and mutational profiles in multiple myeloma.

Bolli N, Avet-Loiseau H, Wedge DC, Van Loo P, Alexandrov LB, Martincorena I, Dawson KJ, Iorio F, Nik-Zainal S, Bignell GR, Hinton JW, Li Y, Tubio JM, McLaren S, O' Meara S, Butler AP, Teague JW, Mudie L, Anderson E, Rashid N, Tai YT, Shammas MA, Sperling AS, Fulciniti M, Richardson PG, Parmigiani G, Magrangeas F, Minvielle S, Moreau P, Attal M, Facon T, Futreal PA, Anderson KC, Campbell PJ, Munshi NC.

Nat Commun. 2014;5:2997. doi: 10.1038/ncomms3997.

45.

Network based elucidation of drug response: from modulators to targets.

Iorio F, Saez-Rodriguez J, di Bernardo D.

BMC Syst Biol. 2013 Dec 13;7:139. doi: 10.1186/1752-0509-7-139. Review.

46.

Machine learning prediction of cancer cell sensitivity to drugs based on genomic and chemical properties.

Menden MP, Iorio F, Garnett M, McDermott U, Benes CH, Ballester PJ, Saez-Rodriguez J.

PLoS One. 2013 Apr 30;8(4):e61318. doi: 10.1371/journal.pone.0061318. Print 2013.

47.

Phosphoproteomics data classify hematological cancer cell lines according to tumor type and sensitivity to kinase inhibitors.

Casado P, Alcolea MP, Iorio F, Rodríguez-Prados JC, Vanhaesebroeck B, Saez-Rodriguez J, Joel S, Cutillas PR.

Genome Biol. 2013 Apr 29;14(4):R37. doi: 10.1186/gb-2013-14-4-r37.

48.

Cantrell's Syndrome with left ventricular diverticulum: a case report.

Manieri S, Adurno G, Iorio F, Tomasco B, Vairo U.

Minerva Pediatr. 2013 Feb;65(1):93-6.

PMID:
23422578
49.

DvD: An R/Cytoscape pipeline for drug repurposing using public repositories of gene expression data.

Pacini C, Iorio F, Gonçalves E, Iskar M, Klabunde T, Bork P, Saez-Rodriguez J.

Bioinformatics. 2013 Jan 1;29(1):132-4. doi: 10.1093/bioinformatics/bts656. Epub 2012 Nov 4.

50.

[Hyperglycaemia and Acute Coronary Syndrome].

Grembiale A, Cloro C, Iorio F, Cufone S, Succurro E, Arturi F.

Clin Ter. 2012;163(5):403-9. Review. Italian.

PMID:
23099971

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