Synthetic Lethal Phenotype Identification through Cancer Evolution Analysis

Pubblicazioni

Mutation–selection balance and compensatory mechanisms in tumour evolution

Autori: Erez Persi, Yuri I. Wolf, David Horn, Eytan Ruppin, Francesca Demichelis, Robert A. Gatenby, Robert J. Gillies, Eugene V. Koonin
Pubblicato in: Nature Reviews Genetics, Numero 22/4, 2021, Pagina/e 251-262, ISSN 1471-0056
Editore: Nature Publishing Group
DOI: 10.1038/s41576-020-00299-4

Role of specialized composition of SWI/SNF complexes in prostate cancer lineage plasticity

Autori: Joanna Cyrta, Anke Augspach, Maria Rosaria De Filippo, Davide Prandi, Phillip Thienger, Matteo Benelli, Victoria Cooley, Rohan Bareja, David Wilkes, Sung-Suk Chae, Paola Cavaliere, Noah Dephoure, Anne-Christine Uldry, Sophie Braga Lagache, Luca Roma, Sandra Cohen, Muriel Jaquet, Laura P. Brandt, Mohammed Alshalalfa, Loredana Puca, Andrea Sboner, Felix Feng, Shangqian Wang, Himisha Beltran, Tamara
Pubblicato in: Nature Communications, Numero 11/1, 2020, ISSN 2041-1723
Editore: Nature Publishing Group
DOI: 10.1038/s41467-020-19328-1

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

Autori: Himisha Beltran, Alessandro Romanel, Vincenza Conteduca, Nicola Casiraghi, Michael Sigouros, Gian Marco Franceschini, Francesco Orlando, Tarcisio Fedrizzi, Sheng-Yu Ku, Emma Dann, Alicia Alonso, Juan Miguel Mosquera, Andrea Sboner, Jenny Xiang, Olivier Elemento, David M. Nanus, Scott T. Tagawa, Matteo Benelli, Francesca Demichelis
Pubblicato in: Journal of Clinical Investigation, Numero 130/4, 2020, Pagina/e 1653-1668, ISSN 0021-9738
Editore: American Society for Clinical Investigation
DOI: 10.1172/jci131041

Genomic correlates of clinical outcome in advanced prostate cancer

Autori: Wassim Abida, Joanna Cyrta, Glenn Heller, Davide Prandi, Joshua Armenia, Ilsa Coleman, Marcin Cieslik, Matteo Benelli, Dan Robinson, Eliezer M. Van Allen, Andrea Sboner, Tarcisio Fedrizzi, Juan Miguel Mosquera, Brian D. Robinson, Navonil De Sarkar, Lakshmi P. Kunju, Scott Tomlins, Yi Mi Wu, Daniel Nava Rodrigues, Massimo Loda, Anuradha Gopalan, Victor E. Reuter, Colin C. Pritchard, Joaquin Mateo,
Pubblicato in: Proceedings of the National Academy of Sciences, Numero 116/23, 2019, Pagina/e 11428-11436, ISSN 0027-8424
Editore: National Academy of Sciences
DOI: 10.1073/pnas.1902651116

N-Myc Induces an EZH2-Mediated Transcriptional Program Driving Neuroendocrine Prostate Cancer

Autori: 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, David S. Rickman
Pubblicato in: Cancer Cell, Numero 30/4, 2016, Pagina/e 563-577, ISSN 1535-6108
Editore: Cell Press
DOI: 10.1016/j.ccell.2016.09.005

Tumor purity quantification by clonal DNA methylation signatures

Autori: Matteo Benelli, Dario Romagnoli, Francesca Demichelis
Pubblicato in: Bioinformatics, 2018, ISSN 1367-4803
Editore: Oxford University Press
DOI: 10.1093/bioinformatics/bty011

Personalized In Vitro and In Vivo Cancer Models to Guide Precision Medicine

Autori: Chantal Pauli, Benjamin D. Hopkins, Davide Prandi, Reid Shaw, Tarcisio Fedrizzi, Andrea Sboner, Verena Sailer, Michael Augello, Loredana Puca, Rachele Rosati, Terra J. McNary, Yelena Churakova, Cynthia Cheung, Joanna Triscott, David Pisapia, Rema Rao, Juan Miguel Mosquera, Brian Robinson, Bishoy M. Faltas, Brooke E. Emerling, Vijayakrishna K. Gadi, Brady Bernard, Olivier Elemento, Himisha Beltran,
Pubblicato in: Cancer Discovery, Numero 7/5, 2017, Pagina/e 462-477, ISSN 2159-8274
Editore: American Association for Cancer Research Inc.
DOI: 10.1158/2159-8290.CD-16-1154

EthSEQ: ethnicity annotation from whole exome sequencing data

Autori: Alessandro Romanel, Tuo Zhang, Olivier Elemento, Francesca Demichelis
Pubblicato in: Bioinformatics, Numero 33/15, 2017, Pagina/e 2402-2404, ISSN 1367-4803
Editore: Oxford University Press
DOI: 10.1093/bioinformatics/btx165

Next-Generation Rapid Autopsies Enable Tumor Evolution Tracking and Generation of Preclinical Models

Autori: David J. Pisapia, Steven Salvatore, Chantal Pauli, Erika Hissong, Ken Eng, Davide Prandi, Verena-Wilbeth Sailer, Brian D. Robinson, Kyung Park, Joanna Cyrta, Scott T. Tagawa, Myriam Kossai, Jacqueline Fontugne, Robert Kim, Alexandros Sigaras, Rema Rao, Danielle Pancirer, Bishoy Faltas, Rohan Bareja, Ana M. Molina, David M. Nanus, Prajwal Rajappa, Mark M. Souweidane, Jeffrey Greenfield, Anne-Katrin
Pubblicato in: JCO Precision Oncology, Numero 1, 2017, Pagina/e 1-13, ISSN 2473-4284
Editore: American Society of Clinical Oncology
DOI: 10.1200/PO.16.00038

The long tail of oncogenic drivers in prostate cancer

Autori: Joshua Armenia, Stephanie A. M. Wankowicz, David Liu, Jianjiong Gao, Ritika Kundra, Ed Reznik, Walid K. Chatila, Debyani Chakravarty, G. Celine Han, Ilsa Coleman, Bruce Montgomery, Colin Pritchard, Colm Morrissey, Christopher E. Barbieri, Himisha Beltran, Andrea Sboner, Zafeiris Zafeiriou, Susana Miranda, Craig M. Bielski, Alexander V. Penson, Charlotte Tolonen, Franklin W. Huang, Dan Robinson, Yi
Pubblicato in: Nature Genetics, Numero 50/5, 2018, Pagina/e 645-651, ISSN 1061-4036
Editore: Nature Publishing Group
DOI: 10.1038/s41588-018-0078-z

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

Autori: Antonio Casini, Michele Olivieri, Gianluca Petris, Claudia Montagna, Giordano Reginato, Giulia Maule, Francesca Lorenzin, Davide Prandi, Alessandro Romanel, Francesca Demichelis, Alberto Inga, Anna Cereseto
Pubblicato in: Nature Biotechnology, Numero 36/3, 2018, Pagina/e 265-271, ISSN 1087-0156
Editore: Nature Publishing Group
DOI: 10.1038/nbt.4066

SOX2 promotes lineage plasticity and antiandrogen resistance in TP53 - and RB1 -deficient prostate cancer

Autori: Ping Mu, Zeda Zhang, Matteo Benelli, Wouter R. Karthaus, Elizabeth Hoover, Chi-Chao Chen, John Wongvipat, Sheng-Yu Ku, Dong Gao, Zhen Cao, Neel Shah, Elizabeth J. Adams, Wassim Abida, Philip A. Watson, Davide Prandi, Chun-Hao Huang, Elisa de Stanchina, Scott W. Lowe, Leigh Ellis, Himisha Beltran, Mark A. Rubin, David W. Goodrich, Francesca Demichelis, Charles L. Sawyers
Pubblicato in: Science, Numero 355/6320, 2017, Pagina/e 84-88, ISSN 0036-8075
Editore: American Association for the Advancement of Science
DOI: 10.1126/science.aah4307

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

Autori: Gianluca Petris, Antonio Casini, Claudia Montagna, Francesca Lorenzin, Davide Prandi, Alessandro Romanel, Jacopo Zasso, Luciano Conti, Francesca Demichelis, Anna Cereseto
Pubblicato in: Nature Communications, Numero 8, 2017, Pagina/e 15334, ISSN 2041-1723
Editore: Nature Publishing Group
DOI: 10.1038/ncomms15334

Divergent clonal evolution of castration-resistant neuroendocrine prostate cancer

Autori: Himisha Beltran, Davide Prandi, Juan Miguel Mosquera, Matteo Benelli, Loredana Puca, Joanna Cyrta, Clarisse Marotz, Eugenia Giannopoulou, Balabhadrapatruni V S K Chakravarthi, Sooryanarayana Varambally, Scott A Tomlins, David M Nanus, Scott T Tagawa, Eliezer M Van Allen, Olivier Elemento, Andrea Sboner, Levi A Garraway, Mark A Rubin, Francesca Demichelis
Pubblicato in: Nature Medicine, Numero 22/3, 2016, Pagina/e 298-305, ISSN 1078-8956
Editore: Nature Publishing Group
DOI: 10.1038/nm.4045

Clonal evolution of chemotherapy-resistant urothelial carcinoma

Autori: 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
Pubblicato in: Nature Genetics, Numero 48/12, 2016, Pagina/e 1490-1499, ISSN 1061-4036
Editore: Nature Publishing Group
DOI: 10.1038/ng.3692

TPES: tumor purity estimation from SNVs

Autori: Alessio Locallo, Davide Prandi, Tarcisio Fedrizzi, Francesca Demichelis
Pubblicato in: Bioinformatics, Numero 35/21, 2019, Pagina/e 4433-4435, ISSN 1367-4803
Editore: Oxford University Press
DOI: 10.1093/bioinformatics/btz406

Ploidy‐ and Purity‐Adjusted Allele‐Specific DNA Analysis Using CLONETv2

Autori: Davide Prandi, Francesca Demichelis
Pubblicato in: Current Protocols in Bioinformatics, Numero 67/1, 2019, ISSN 1934-3396
Editore: John Wiley & Sons Inc.
DOI: 10.1002/cpbi.81

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