Demichelis Lab - Computational Oncology

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ASEQ-Allele Specific Expression

CLONET-CLONality Estimate in Tumors

IgC2N-germline Copy Number Changes

SPIA-SNP panel identification assay

TO-DAG Timed Oncogenetic Directed Acyclic Graphs


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Prostate Cancer Innsbruck study

PRRs-Polymorphic Regulatory Regions


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Oligonucleotide probe

sequence analysis
Size Enrichment Test

zFish Project




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public:publications [2015/02/12 16:51]
f.demichelis@unitn.it 		public:publications [2016/10/18 14:27] (current)
f.demichelis@unitn.it
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-==== Selected Publications (2010-2015) ====+==== Selected Publications (2010-2016) ==== 
 + 
 +=== 2016 === 
 + 
 +Bishoy M. Faltas*, Davide Prandi*, Scott T. Tagawa, Ana M. Molina, David M. Nanus, Cora Sternberg, Jonathan Rosenberg, Juan Miguel Mosquera, Brian Robinson, Olivier Elemento, Andrea Sboner, Himisha Beltran*, Francesca Demichelis*, Mark A. Rubin*. **Clonal Evolution of Chemotherapy-resistant Urothelial Carcinoma.** Nat Genet. 2016 Oct 17. doi: 10.1038/ng.3692. 
 + 
 +Etienne Dardenne*, Himisha Beltran*, Matteo Benelli, Kaitlyn Gayvert, Adeline Berger, Loredana Puca, Joanna Cyrta, Andrea Sboner, Zohal Noorzad, Theresa MacDonald, Cynthia Cheung, Ka Shing Yuen, Dong Gao, Yu Chen, Martin Eilers, Juan-Miguel Mosquera, Brian D. Robinson, Olivier Elemento, Mark A. Rubin, Francesca Demichelis and David S. Rickman. **N-Myc induces an EZH2-mediated transcriptional program driving Neuroendocrine Prostate Cancer.** Cancer Cell. 2016 Oct 10;30(4):563-577. 
 + 
 + 
 +Beltran H*, Prandi D*, Mosquera JM, Benelli M, Puca L, Cyrta J, Marotz C, Giannopoulou E, Chakravarthi BV, Varambally S, Tomlins SA, Nanus DM, Tagawa ST, Van Allen EM, Elemento O, Sboner A, Garraway LA*, Rubin MA*, Demichelis F*. **Divergent clonal evolution of castration-resistant neuroendocrine prostate cancer.** Nat Med. 2016 Mar;22(3):298-305. 
 + 
 + 
 +Khurana E, Fu Y, Chakravarty D, Demichelis F, Rubin MA, Gerstein M. **Role of non-coding sequence variants in cancer.** Nat Rev Genet. 2016 Feb;17(2):93-108. doi: 10.1038/nrg.2015.17. Epub 2016 Jan 19. 
 + 
 + 
 +Rubin MA, Girelli G, Demichelis F. **Genomic Correlates to the newly proposed Grading Prognostic Groups for Prostate Cancer.** Eur Urol. 2016 Apr;69(4):557-60.
  
 === 2015 === === 2015 ===
  
-Romanel A, Lago S, Prandi D, Sboner A, Demichelis F. **ASEQ: fast allele-specific studies from next-generation sequencing data.** BMC Medical Genomics (in press)+The Cancer Genome Atlas Research Network (including Davide Prandi and Francesca Demichelis). **The Molecular Taxonomy of Primary Prostate Cancer**. Cell 4(163), 1011-1025, 2015. 
 + 
 +Romanel A*, Gasi Tandefelt D*, Conteduca C, 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*. **Plasma AR and abiraterone-resistant prostate cancer**. Science Translational Medicine 7, 312re10, 2015. 
 + 
 +Boysen G*, Barbieri CE*, Prandi D, Blattner M, Chae SS, Dahija A, Nataraj S, Huang D, Marotz C, Xu L, Huang J, Lecca P, Chhangawala S, Liu D, Zhou P, Sboner A, de Bono JS, Demichelis F*, Houvras Y*, Rubin MA*. **SPOP mutation leads to genomic instability in prostate cancer.** Elife. 2015 Sep 16;4. doi: 10.7554/eLife.09207.
  
-Garritano S*, Romanel A*, Ciribilli Y*, Bisio A, Gavoci A, Inga A#, Demichelis F#. **In-silico identification and functional validation of allele-dependent AR enhancers.** Oncotarget (in press)+Beltran H, Demichelis F. **Prostate cancer: Intrapatient heterogeneity in prostate cancer.** Nat Rev Urol. 2015 Aug;12(8):430-1. Nature Reviews Urology | News and Views
  
 +Robinson D, Van Allen EM, et al. **Integrative clinical genomics of advanced prostate cancer.** Cell. 2015 May 21;161(5):1215-28. doi: 10.1016/j.cell.2015.05.001. SU2C-PCF 
  
 +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 T, Herrscher E, Wilkes D, MacDonald T, Xue H, Vacic V, Emde AK, Oschwald D , Tan A, Chen Z, Collins C, Gleave M, Wang Y, Chakravarty D, Schiffman M, Kim R, Campagne F, Robinson B, Nanus D, Tagawa S, Xiang J, Smogorzewska A, Demichelis F, Rickman D, Sboner A, Elemento O, Rubin MA. **Whole-Exome Sequencing of Metastatic Cancer and Biomarkers of Treatment Response.** Jama Oncology, 2015.
  
 +Romanel A, Lago S, Prandi D, Sboner A, Demichelis F. **ASEQ: fast allele-specific studies from next-generation sequencing data.** BMC Medical Genomics  8(1):9, 2015.
  
 +Garritano S*, Romanel A*, Ciribilli Y*, Bisio A, Gavoci A, Inga A*, Demichelis F*. **In-silico identification and functional validation of allele-dependent AR enhancers.** Oncotarget 6(7):4816-4828, 2015.
  
  
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-===== 2013 =====+=== 2013 ===
  
 Park K, Chiu YL, Rubin MA, Demichelis F(*), Mosquera JM(*). **V-ets erythroblastosis virus E26 oncogene homolog (avian)/Trefoil factor 3/high-molecular-weight cytokeratin triple immunostain: a novel tissue-based biomarker in prostate cancer with potential clinical application.** Hum Pathol. 2013 Jul 12. doi:pii: S0046-8177(13)00199-8. 10.1016/j.humpath.2013.05.010. [Epub ahead of print] Park K, Chiu YL, Rubin MA, Demichelis F(*), Mosquera JM(*). **V-ets erythroblastosis virus E26 oncogene homolog (avian)/Trefoil factor 3/high-molecular-weight cytokeratin triple immunostain: a novel tissue-based biomarker in prostate cancer with potential clinical application.** Hum Pathol. 2013 Jul 12. doi:pii: S0046-8177(13)00199-8. 10.1016/j.humpath.2013.05.010. [Epub ahead of print]
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 Banerjee S, Oldridge D, Poptsova M, Hussain WM, Chakravarty D, Demichelis F. **A computational framework discovers new copy number variants with functional importance**. PLoS One. 2011 Mar 29;6(3):e17539. Banerjee S, Oldridge D, Poptsova M, Hussain WM, Chakravarty D, Demichelis F. **A computational framework discovers new copy number variants with functional importance**. PLoS One. 2011 Mar 29;6(3):e17539.
  
-===== 2010 =====+=== 2010 ===
  
 Setlur SR, Chen CX, Hossain RR, Ha JS, Van Doren VE, Stenzel B, Steiner E, Oldridge D, Katabayashi N, Banerjee S, Chen JY, Schäfer G, Horninger W, Lee C, Rubin MA, Klocker H, and Demichelis F. **Genetic Variation of Genes involved in Dihydrotestosterone Metabolism and the risk of prostate cancer**. Cancer Epidemiol Biomarkers Prev. 2010 Jan;19(1):229-39. Setlur SR, Chen CX, Hossain RR, Ha JS, Van Doren VE, Stenzel B, Steiner E, Oldridge D, Katabayashi N, Banerjee S, Chen JY, Schäfer G, Horninger W, Lee C, Rubin MA, Klocker H, and Demichelis F. **Genetic Variation of Genes involved in Dihydrotestosterone Metabolism and the risk of prostate cancer**. Cancer Epidemiol Biomarkers Prev. 2010 Jan;19(1):229-39.

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public/publications.txt · Last modified: 2016/10/18 14:27 by f.demichelis@unitn.it