Synthetic Lethal Phenotype Identification through Cancer Evolution Analysis

Publicaciones

Mutation–selection balance and compensatory mechanisms in tumour evolution

Autores: Erez Persi, Yuri I. Wolf, David Horn, Eytan Ruppin, Francesca Demichelis, Robert A. Gatenby, Robert J. Gillies, Eugene V. Koonin
Publicado en: Nature Reviews Genetics, Edición 22/4, 2021, Página(s) 251-262, ISSN 1471-0056
Editor: Nature Publishing Group
DOI: 10.1038/s41576-020-00299-4

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

Autores: 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
Publicado en: Nature Communications, Edición 11/1, 2020, ISSN 2041-1723
Editor: Nature Publishing Group
DOI: 10.1038/s41467-020-19328-1

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

Autores: 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
Publicado en: Journal of Clinical Investigation, Edición 130/4, 2020, Página(s) 1653-1668, ISSN 0021-9738
Editor: American Society for Clinical Investigation
DOI: 10.1172/jci131041

Genomic correlates of clinical outcome in advanced prostate cancer

Autores: 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,
Publicado en: Proceedings of the National Academy of Sciences, Edición 116/23, 2019, Página(s) 11428-11436, ISSN 0027-8424
Editor: National Academy of Sciences
DOI: 10.1073/pnas.1902651116

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

Autores: 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
Publicado en: Cancer Cell, Edición 30/4, 2016, Página(s) 563-577, ISSN 1535-6108
Editor: Cell Press
DOI: 10.1016/j.ccell.2016.09.005

Tumor purity quantification by clonal DNA methylation signatures

Autores: Matteo Benelli, Dario Romagnoli, Francesca Demichelis
Publicado en: Bioinformatics, 2018, ISSN 1367-4803
Editor: Oxford University Press
DOI: 10.1093/bioinformatics/bty011

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

Autores: 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,
Publicado en: Cancer Discovery, Edición 7/5, 2017, Página(s) 462-477, ISSN 2159-8274
Editor: American Association for Cancer Research Inc.
DOI: 10.1158/2159-8290.CD-16-1154

EthSEQ: ethnicity annotation from whole exome sequencing data

Autores: Alessandro Romanel, Tuo Zhang, Olivier Elemento, Francesca Demichelis
Publicado en: Bioinformatics, Edición 33/15, 2017, Página(s) 2402-2404, ISSN 1367-4803
Editor: Oxford University Press
DOI: 10.1093/bioinformatics/btx165

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

Autores: 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
Publicado en: JCO Precision Oncology, Edición 1, 2017, Página(s) 1-13, ISSN 2473-4284
Editor: American Society of Clinical Oncology
DOI: 10.1200/PO.16.00038

The long tail of oncogenic drivers in prostate cancer

Autores: 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
Publicado en: Nature Genetics, Edición 50/5, 2018, Página(s) 645-651, ISSN 1061-4036
Editor: Nature Publishing Group
DOI: 10.1038/s41588-018-0078-z

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

Autores: Antonio Casini, Michele Olivieri, Gianluca Petris, Claudia Montagna, Giordano Reginato, Giulia Maule, Francesca Lorenzin, Davide Prandi, Alessandro Romanel, Francesca Demichelis, Alberto Inga, Anna Cereseto
Publicado en: Nature Biotechnology, Edición 36/3, 2018, Página(s) 265-271, ISSN 1087-0156
Editor: Nature Publishing Group
DOI: 10.1038/nbt.4066

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

Autores: 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
Publicado en: Science, Edición 355/6320, 2017, Página(s) 84-88, ISSN 0036-8075
Editor: American Association for the Advancement of Science
DOI: 10.1126/science.aah4307

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

Autores: Gianluca Petris, Antonio Casini, Claudia Montagna, Francesca Lorenzin, Davide Prandi, Alessandro Romanel, Jacopo Zasso, Luciano Conti, Francesca Demichelis, Anna Cereseto
Publicado en: Nature Communications, Edición 8, 2017, Página(s) 15334, ISSN 2041-1723
Editor: Nature Publishing Group
DOI: 10.1038/ncomms15334

Divergent clonal evolution of castration-resistant neuroendocrine prostate cancer

Autores: 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
Publicado en: Nature Medicine, Edición 22/3, 2016, Página(s) 298-305, ISSN 1078-8956
Editor: Nature Publishing Group
DOI: 10.1038/nm.4045

Clonal evolution of chemotherapy-resistant urothelial carcinoma

Autores: 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
Publicado en: Nature Genetics, Edición 48/12, 2016, Página(s) 1490-1499, ISSN 1061-4036
Editor: Nature Publishing Group
DOI: 10.1038/ng.3692

TPES: tumor purity estimation from SNVs

Autores: Alessio Locallo, Davide Prandi, Tarcisio Fedrizzi, Francesca Demichelis
Publicado en: Bioinformatics, Edición 35/21, 2019, Página(s) 4433-4435, ISSN 1367-4803
Editor: Oxford University Press
DOI: 10.1093/bioinformatics/btz406

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

Autores: Davide Prandi, Francesca Demichelis
Publicado en: Current Protocols in Bioinformatics, Edición 67/1, 2019, ISSN 1934-3396
Editor: John Wiley & Sons Inc.
DOI: 10.1002/cpbi.81

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