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Items: 30

1.

Circulating tumor DNA profile recognizes transformation to castration-resistant neuroendocrine prostate cancer.

Beltran H, Romanel A, Conteduca V, Casiraghi N, Sigouros M, Franceschini GM, Orlando F, Fedrizzi T, Ku SY, Dann E, Alonso A, Mosquera JM, Sboner A, Xiang J, Elemento O, Nanus DM, Tagawa ST, Benelli M, Demichelis F.

J Clin Invest. 2020 Apr 1;130(4):1653-1668. doi: 10.1172/JCI131041.

2.

ABEMUS: platform specific and data informed detection of somatic SNVs in cfDNA.

Casiraghi N, Orlando F, Ciani Y, Xiang J, Sboner A, Elemento O, Attard G, Beltran H, Demichelis F, Romanel A.

Bioinformatics. 2020 Jan 10. pii: btaa016. doi: 10.1093/bioinformatics/btaa016. [Epub ahead of print]

PMID:
31922552
3.

PaCBAM: fast and scalable processing of whole exome and targeted sequencing data.

Valentini S, Fedrizzi T, Demichelis F, Romanel A.

BMC Genomics. 2019 Dec 26;20(1):1018. doi: 10.1186/s12864-019-6386-6.

4.

Truncated BRPF1 Cooperates with Smoothened to Promote Adult Shh Medulloblastoma.

Aiello G, Ballabio C, Ruggeri R, Fagnocchi L, Anderle M, Morassut I, Caron D, Garilli F, Gianno F, Giangaspero F, Piazza S, Romanel A, Zippo A, Tiberi L.

Cell Rep. 2019 Dec 17;29(12):4036-4052.e10. doi: 10.1016/j.celrep.2019.11.046.

5.

Integrative Molecular Analysis of Patients With Advanced and Metastatic Cancer.

Sailer V, Eng KW, Zhang T, Bareja R, Pisapia DJ, Sigaras A, Bhinder B, Romanel A, Wilkes D, Sticca E, Cyrta J, Rao R, Sahota S, Pauli C, Beg S, Motanagh S, Kossai M, Fontunge J, Puca L, Rennert H, Zhaoying Xiang J, Greco N, Kim R, MacDonald TY, McNary T, Blattner-Johnson M, Schiffman MH, Faltas BM, Greenfield JP, Rickman D, Andreopoulou E, Holcomb K, Vahdat LT, Scherr DS, van Besien K, Barbieri CE, Robinson BD, Fine HA, Ocean AJ, Molina A, Shah MA, Nanus DM, Pan Q, Demichelis F, Tagawa ST, Song W, Mosquera JM, Sboner A, Rubin MA, Elemento O, Beltran H.

JCO Precis Oncol. 2019;3. doi: 10.1200/PO.19.00047. Epub 2019 Sep 20.

6.

Core Biopsies from Prostate Cancer Patients in Active Surveillance Protocols Harbor PTEN and MYC Alterations.

Gandellini P, Casiraghi N, Rancati T, Benelli M, Doldi V, Romanel A, Colecchia M, Marenghi C, Valdagni R, Demichelis F, Zaffaroni N.

Eur Urol Oncol. 2019 May;2(3):277-285. doi: 10.1016/j.euo.2018.08.010. Epub 2018 Sep 10.

7.

Third generation EGFR inhibitor osimertinib combined with pemetrexed or cisplatin exerts long-lasting anti-tumor effect in EGFR-mutated pre-clinical models of NSCLC.

La Monica S, Minari R, Cretella D, Flammini L, Fumarola C, Bonelli M, Cavazzoni A, Digiacomo G, Galetti M, Madeddu D, Falco A, Lagrasta CA, Squadrilli A, Barocelli E, Romanel A, Quaini F, Petronini PG, Tiseo M, Alfieri R.

J Exp Clin Cancer Res. 2019 May 28;38(1):222. doi: 10.1186/s13046-019-1240-x.

8.

Allele-Specific Expression Analysis in Cancer Using Next-Generation Sequencing Data.

Romanel A.

Methods Mol Biol. 2019;1878:125-137. doi: 10.1007/978-1-4939-8868-6_7.

PMID:
30378073
9.

RB1 Heterogeneity in Advanced Metastatic Castration-Resistant Prostate Cancer.

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.

Clin Cancer Res. 2019 Jan 15;25(2):687-697. doi: 10.1158/1078-0432.CCR-18-2068. Epub 2018 Sep 26.

10.

A Phase II Trial of the Aurora Kinase A Inhibitor Alisertib for Patients with Castration-resistant and Neuroendocrine Prostate Cancer: Efficacy and Biomarkers.

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.

Clin Cancer Res. 2019 Jan 1;25(1):43-51. doi: 10.1158/1078-0432.CCR-18-1912. Epub 2018 Sep 19.

11.

A highly specific SpCas9 variant is identified by in vivo screening in yeast.

Casini A, Olivieri M, Petris G, Montagna C, Reginato G, Maule G, Lorenzin F, Prandi D, Romanel A, Demichelis F, Inga A, Cereseto A.

Nat Biotechnol. 2018 Mar;36(3):265-271. doi: 10.1038/nbt.4066. Epub 2018 Jan 29.

12.

Inherited determinants of early recurrent somatic mutations in prostate cancer.

Romanel A, Garritano S, Stringa B, Blattner M, Dalfovo D, Chakravarty D, Soong D, Cotter KA, Petris G, Dhingra P, Gasperini P, Cereseto A, Elemento O, Sboner A, Khurana E, Inga A, Rubin MA, Demichelis F.

Nat Commun. 2017 Jun 29;8(1):48. doi: 10.1038/s41467-017-00046-0.

13.

Hit and go CAS9 delivered through a lentiviral based self-limiting circuit.

Petris G, Casini A, Montagna C, Lorenzin F, Prandi D, Romanel A, Zasso J, Conti L, Demichelis F, Cereseto A.

Nat Commun. 2017 May 22;8:15334. doi: 10.1038/ncomms15334.

14.

Exome Sequencing of African-American Prostate Cancer Reveals Loss-of-Function ERF Mutations.

Huang FW, Mosquera JM, Garofalo A, Oh C, Baco M, Amin-Mansour A, Rabasha B, Bahl S, Mullane SA, Robinson BD, Aldubayan S, Khani F, Karir B, Kim E, Chimene-Weiss J, Hofree M, Romanel A, Osborne JR, Kim JW, Azabdaftari G, Woloszynska-Read A, Sfanos K, De Marzo AM, Demichelis F, Gabriel S, Van Allen EM, Mesirov J, Tamayo P, Rubin MA, Powell IJ, Garraway LA.

Cancer Discov. 2017 Sep;7(9):973-983. doi: 10.1158/2159-8290.CD-16-0960. Epub 2017 May 17.

15.

Androgen receptor gene status in plasma DNA associates with worse outcome on enzalutamide or abiraterone for castration-resistant prostate cancer: a multi-institution correlative biomarker study.

Conteduca V, Wetterskog D, Sharabiani MTA, Grande E, Fernandez-Perez MP, Jayaram A, Salvi S, Castellano D, Romanel A, Lolli C, Casadio V, Gurioli G, Amadori D, Font A, Vazquez-Estevez S, González Del Alba A, Mellado B, Fernandez-Calvo O, Méndez-Vidal MJ, Climent MA, Duran I, Gallardo E, Rodriguez A, Santander C, Sáez MI, Puente J, Gasi Tandefelt D, Wingate A, Dearnaley D; PREMIERE Collaborators; Spanish Oncology Genitourinary Group, Demichelis F, De Giorgi U, Gonzalez-Billalabeitia E, Attard G.

Ann Oncol. 2017 Jul 1;28(7):1508-1516. doi: 10.1093/annonc/mdx155.

16.

Erratum to: Unraveling the clonal hierarchy of somatic genomic aberrations.

Prandi D, Baca SC, Romanel A, Barbieri CE, Mosquera JM, Fontugne J, Beltran H, Sboner A, Garraway LA, Rubin MA, Demichelis F.

Genome Biol. 2017 May 2;18(1):80. doi: 10.1186/s13059-017-1183-5. No abstract available.

17.

EthSEQ: ethnicity annotation from whole exome sequencing data.

Romanel A, Zhang T, Elemento O, Demichelis F.

Bioinformatics. 2017 Aug 1;33(15):2402-2404. doi: 10.1093/bioinformatics/btx165.

18.

Development and validation of a whole-exome sequencing test for simultaneous detection of point mutations, indels and copy-number alterations for precision cancer care.

Rennert H, Eng K, Zhang T, Tan A, Xiang J, Romanel A, Kim R, Tam W, Liu YC, Bhinder B, Cyrta J, Beltran H, Robinson B, Mosquera JM, Fernandes H, Demichelis F, Sboner A, Kluk M, Rubin MA, Elemento O.

NPJ Genom Med. 2016;1. pii: 16019. doi: 10.1038/npjgenmed.2016.19. Epub 2016 Jul 20.

19.

Plasma AR and abiraterone-resistant prostate cancer.

Romanel A, Gasi Tandefelt D, Conteduca V, Jayaram A, Casiraghi N, Wetterskog D, Salvi S, Amadori D, Zafeiriou Z, Rescigno P, Bianchini D, Gurioli G, Casadio V, Carreira S, Goodall J, Wingate A, Ferraldeschi R, Tunariu N, Flohr P, De Giorgi U, de Bono JS, Demichelis F, Attard G.

Sci Transl Med. 2015 Nov 4;7(312):312re10. doi: 10.1126/scitranslmed.aac9511.

20.

Whole-Exome Sequencing of Metastatic Cancer and Biomarkers of Treatment Response.

Beltran H, Eng K, Mosquera JM, Sigaras A, Romanel A, Rennert H, Kossai M, Pauli C, Faltas B, Fontugne J, Park K, Banfelder J, Prandi D, Madhukar N, Zhang T, Padilla J, Greco N, McNary TJ, Herrscher E, Wilkes D, MacDonald TY, Xue H, Vacic V, Emde AK, Oschwald D, Tan AY, Chen Z, Collins C, Gleave ME, Wang Y, Chakravarty D, Schiffman M, Kim R, Campagne F, Robinson BD, Nanus DM, Tagawa ST, Xiang JZ, Smogorzewska A, Demichelis F, Rickman DS, Sboner A, Elemento O, Rubin MA.

JAMA Oncol. 2015 Jul;1(4):466-74. doi: 10.1001/jamaoncol.2015.1313.

21.

On the impact of discreteness and abstractions on modelling noise in gene regulatory networks.

Bodei C, Bortolussi L, Chiarugi D, Guerriero ML, Policriti A, Romanel A.

Comput Biol Chem. 2015 Jun;56:98-108. doi: 10.1016/j.compbiolchem.2015.04.004. Epub 2015 Apr 8.

PMID:
25909953
22.

ASEQ: fast allele-specific studies from next-generation sequencing data.

Romanel A, Lago S, Prandi D, Sboner A, Demichelis F.

BMC Med Genomics. 2015 Mar 1;8:9. doi: 10.1186/s12920-015-0084-2.

23.

In-silico identification and functional validation of allele-dependent AR enhancers.

Garritano S, Romanel A, Ciribilli Y, Bisio A, Gavoci A, Inga A, Demichelis F.

Oncotarget. 2015 Mar 10;6(7):4816-28.

24.

Tumor clone dynamics in lethal prostate cancer.

Carreira S, Romanel A, Goodall J, Grist E, Ferraldeschi R, Miranda S, Prandi D, Lorente D, Frenel JS, Pezaro C, Omlin A, Rodrigues DN, Flohr P, Tunariu N, S de Bono J, Demichelis F, Attard G.

Sci Transl Med. 2014 Sep 17;6(254):254ra125. doi: 10.1126/scitranslmed.3009448.

25.

Unraveling the clonal hierarchy of somatic genomic aberrations.

Prandi D, Baca SC, Romanel A, Barbieri CE, Mosquera JM, Fontugne J, Beltran H, Sboner A, Garraway LA, Rubin MA, Demichelis F.

Genome Biol. 2014 Aug 26;15(8):439. doi: 10.1186/s13059-014-0439-6. Erratum in: Genome Biol. 2017 May 2;18(1):80.

26.

Punctuated evolution of prostate cancer genomes.

Baca SC, Prandi D, Lawrence MS, Mosquera JM, Romanel A, Drier Y, Park K, Kitabayashi N, MacDonald TY, Ghandi M, Van Allen E, Kryukov GV, Sboner A, Theurillat JP, Soong TD, Nickerson E, Auclair D, Tewari A, Beltran H, Onofrio RC, Boysen G, Guiducci C, Barbieri CE, Cibulskis K, Sivachenko A, Carter SL, Saksena G, Voet D, Ramos AH, Winckler W, Cipicchio M, Ardlie K, Kantoff PW, Berger MF, Gabriel SB, Golub TR, Meyerson M, Lander ES, Elemento O, Getz G, Demichelis F, Rubin MA, Garraway LA.

Cell. 2013 Apr 25;153(3):666-77. doi: 10.1016/j.cell.2013.03.021.

27.

Distinct ERG rearrangement prevalence in prostate cancer: higher frequency in young age and in low PSA prostate cancer.

Schaefer G, Mosquera JM, Ramoner R, Park K, Romanel A, Steiner E, Horninger W, Bektic J, Ladurner-Rennau M, Rubin MA, Demichelis F, Klocker H.

Prostate Cancer Prostatic Dis. 2013 Jun;16(2):132-8. doi: 10.1038/pcan.2013.4. Epub 2013 Feb 5.

28.

Transcriptional regulation is a major controller of cell cycle transition dynamics.

Romanel A, Jensen LJ, Cardelli L, Csikász-Nagy A.

PLoS One. 2012;7(1):e29716. doi: 10.1371/journal.pone.0029716. Epub 2012 Jan 6.

29.

Estimating the divisibility of complex biological networks by sparseness indices.

Mazza T, Romanel A, Jordán F.

Brief Bioinform. 2010 May;11(3):364-74. doi: 10.1093/bib/bbp060. Epub 2010 Jan 11.

PMID:
20064873
30.

The Beta Workbench: a computational tool to study the dynamics of biological systems.

Dematté L, Priami C, Romanel A.

Brief Bioinform. 2008 Sep;9(5):437-49. doi: 10.1093/bib/bbn023. Epub 2008 May 7.

PMID:
18463130

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