Synthetic Lethal Phenotype Identification through Cancer Evolution Analysis

Publications

Mutation–selection balance and compensatory mechanisms in tumour evolution

Auteurs: Erez Persi, Yuri I. Wolf, David Horn, Eytan Ruppin, Francesca Demichelis, Robert A. Gatenby, Robert J. Gillies, Eugene V. Koonin
Publié dans: Nature Reviews Genetics, Numéro 22/4, 2021, Page(s) 251-262, ISSN 1471-0056
Éditeur: Nature Publishing Group
DOI: 10.1038/s41576-020-00299-4

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

Auteurs: 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
Publié dans: Nature Communications, Numéro 11/1, 2020, ISSN 2041-1723
Éditeur: Nature Publishing Group
DOI: 10.1038/s41467-020-19328-1

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

Auteurs: 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
Publié dans: Journal of Clinical Investigation, Numéro 130/4, 2020, Page(s) 1653-1668, ISSN 0021-9738
Éditeur: American Society for Clinical Investigation
DOI: 10.1172/jci131041

Genomic correlates of clinical outcome in advanced prostate cancer

Auteurs: 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,
Publié dans: Proceedings of the National Academy of Sciences, Numéro 116/23, 2019, Page(s) 11428-11436, ISSN 0027-8424
Éditeur: National Academy of Sciences
DOI: 10.1073/pnas.1902651116

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

Auteurs: 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
Publié dans: Cancer Cell, Numéro 30/4, 2016, Page(s) 563-577, ISSN 1535-6108
Éditeur: Cell Press
DOI: 10.1016/j.ccell.2016.09.005

Tumor purity quantification by clonal DNA methylation signatures

Auteurs: Matteo Benelli, Dario Romagnoli, Francesca Demichelis
Publié dans: Bioinformatics, 2018, ISSN 1367-4803
Éditeur: Oxford University Press
DOI: 10.1093/bioinformatics/bty011

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

Auteurs: 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,
Publié dans: Cancer Discovery, Numéro 7/5, 2017, Page(s) 462-477, ISSN 2159-8274
Éditeur: American Association for Cancer Research Inc.
DOI: 10.1158/2159-8290.CD-16-1154

EthSEQ: ethnicity annotation from whole exome sequencing data

Auteurs: Alessandro Romanel, Tuo Zhang, Olivier Elemento, Francesca Demichelis
Publié dans: Bioinformatics, Numéro 33/15, 2017, Page(s) 2402-2404, ISSN 1367-4803
Éditeur: Oxford University Press
DOI: 10.1093/bioinformatics/btx165

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

Auteurs: 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
Publié dans: JCO Precision Oncology, Numéro 1, 2017, Page(s) 1-13, ISSN 2473-4284
Éditeur: American Society of Clinical Oncology
DOI: 10.1200/PO.16.00038

The long tail of oncogenic drivers in prostate cancer

Auteurs: 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
Publié dans: Nature Genetics, Numéro 50/5, 2018, Page(s) 645-651, ISSN 1061-4036
Éditeur: Nature Publishing Group
DOI: 10.1038/s41588-018-0078-z

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

Auteurs: Antonio Casini, Michele Olivieri, Gianluca Petris, Claudia Montagna, Giordano Reginato, Giulia Maule, Francesca Lorenzin, Davide Prandi, Alessandro Romanel, Francesca Demichelis, Alberto Inga, Anna Cereseto
Publié dans: Nature Biotechnology, Numéro 36/3, 2018, Page(s) 265-271, ISSN 1087-0156
Éditeur: Nature Publishing Group
DOI: 10.1038/nbt.4066

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

Auteurs: 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
Publié dans: Science, Numéro 355/6320, 2017, Page(s) 84-88, ISSN 0036-8075
Éditeur: American Association for the Advancement of Science
DOI: 10.1126/science.aah4307

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

Auteurs: Gianluca Petris, Antonio Casini, Claudia Montagna, Francesca Lorenzin, Davide Prandi, Alessandro Romanel, Jacopo Zasso, Luciano Conti, Francesca Demichelis, Anna Cereseto
Publié dans: Nature Communications, Numéro 8, 2017, Page(s) 15334, ISSN 2041-1723
Éditeur: Nature Publishing Group
DOI: 10.1038/ncomms15334

Divergent clonal evolution of castration-resistant neuroendocrine prostate cancer

Auteurs: 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
Publié dans: Nature Medicine, Numéro 22/3, 2016, Page(s) 298-305, ISSN 1078-8956
Éditeur: Nature Publishing Group
DOI: 10.1038/nm.4045

Clonal evolution of chemotherapy-resistant urothelial carcinoma

Auteurs: 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
Publié dans: Nature Genetics, Numéro 48/12, 2016, Page(s) 1490-1499, ISSN 1061-4036
Éditeur: Nature Publishing Group
DOI: 10.1038/ng.3692

TPES: tumor purity estimation from SNVs

Auteurs: Alessio Locallo, Davide Prandi, Tarcisio Fedrizzi, Francesca Demichelis
Publié dans: Bioinformatics, Numéro 35/21, 2019, Page(s) 4433-4435, ISSN 1367-4803
Éditeur: Oxford University Press
DOI: 10.1093/bioinformatics/btz406

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

Auteurs: Davide Prandi, Francesca Demichelis
Publié dans: Current Protocols in Bioinformatics, Numéro 67/1, 2019, ISSN 1934-3396
Éditeur: John Wiley & Sons Inc.
DOI: 10.1002/cpbi.81

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