Simone Zaccaria

Scopus Author ID ORCID

Publication Activity (10 Years)

Years Active: 2020-2024
Publications (10 Years): 29

Top Venues

Nature communications

Genome biology

Nature

bioRxiv : the preprint server for biology

Princeton University

This page only lists publications with an associated author ORCID identifier.

Affiliation History

Princeton University Apr 20 2017

United States

Postdoctoral Research Associate :: Computer Science Department

Publications

Michelle Dietzen, Haoran Zhai, Olivia Lucas, Oriol Pich, Christopher Barrington, Wei-Ting Lu, Sophia Ward, Yanping Guo, Robert Edward Hynds, Simone Zaccaria, Charles Swanton, Nicholas McGranahan, Nnennaya Kanu
Replication timing alterations are associated with mutation acquisition during breast and lung cancer evolution. Nature communications 15 (1) (2024)
Matthew A Myers, Brian J Arnold, Vineet Bansal, Metin Balaban, Katelyn M Mullen, Simone Zaccaria, Benjamin J Raphael
HATCHet2: clone- and haplotype-specific copy number inference from bulk tumor sequencing data. Genome biology 25 (1) (2024)
Matthew A Myers, Brian J Arnold, Vineet Bansal, Metin Balaban, Katelyn M Mullen, Simone Zaccaria, Benjamin J Raphael
HATCHet2: clone- and haplotype-specific copy number inference from bulk tumor sequencing data. Genome biology 25 (1) (2024)
Sebastijan Hobor, Maise Al Bakir, Crispin T Hiley, Marcin Skrzypski, Alexander M Frankell, Bjorn Bakker, Thomas B K Watkins, Aleksandra Markovets, Jonathan R Dry, Andrew P Brown, Jasper van der Aart, Hilda van den Bos, Diana Carolina Johanna Spierings, Dahmane Oukrif, Marco Novelli, Turja Chakrabarti, Adam H Rabinowitz, Laila Ait Hassou, Saskia Litière, D Lucas Kerr, Lisa Tan, Gavin P Kelly, David Allan Moore, Matthew J Renshaw, Subramanian Venkatesan, William Hill, Ariana Huebner, Carlos Martínez-Ruiz, James R M Black, Wei Wu, Mihaela Angelova, Nicholas McGranahan, Julian Downward, Juliann Chmielecki, Carl Barrett, Kevin Litchfield, Su Kit Chew, Collin M Blakely, Elza C de Bruin, Floris Foijer, Karen H Vousden, Trever G Bivona, null null, Robert Edward Hynds, Nnennaya Kanu, Simone Zaccaria, Eva Grönroos, Charles Swanton
Mixed responses to targeted therapy driven by chromosomal instability through p53 dysfunction and genome doubling. Nature communications 15 (1) (2024)
Sebastijan Hobor, Maise Al Bakir, Crispin T Hiley, Marcin Skrzypski, Alexander M Frankell, Bjorn Bakker, Thomas B K Watkins, Aleksandra Markovets, Jonathan R Dry, Andrew P Brown, Jasper van der Aart, Hilda van den Bos, Diana Carolina Johanna Spierings, Dahmane Oukrif, Marco Novelli, Turja Chakrabarti, Adam H Rabinowitz, Laila Ait Hassou, Saskia Litière, D Lucas Kerr, Lisa Tan, Gavin P Kelly, David Allan Moore, Matthew J Renshaw, Subramanian Venkatesan, William Hill, Ariana Huebner, Carlos Martínez-Ruiz, James R M Black, Wei Wu, Mihaela Angelova, Nicholas McGranahan, Julian Downward, Juliann Chmielecki, Carl Barrett, Kevin Litchfield, Su Kit Chew, Collin M Blakely, Elza C de Bruin, Floris Foijer, Karen H Vousden, Trever G Bivona, null null, Robert Edward Hynds, Nnennaya Kanu, Simone Zaccaria, Eva Grönroos, Charles Swanton
Mixed responses to targeted therapy driven by chromosomal instability through p53 dysfunction and genome doubling. Nature communications 15 (1) (2024)
Alexander M Frankell, Michelle Dietzen, Maise Al Bakir, Emilia L Lim, Takahiro Karasaki, Sophia Ward, Selvaraju Veeriah, Emma C Colliver, Ariana Huebner, Abigail Bunkum, Mark S Hill, Kristiana Grigoriadis, David Allan Moore, James R M Black, Wing Kin Liu, Kerstin Thol, Oriol Pich, Thomas B K Watkins, Cristina Naceur-Lombardelli, Daniel E Cook, Roberto Salgado, Gareth A Wilson, Chris Bailey, Mihaela Angelova, Robert Bentham, Carlos Martínez-Ruiz, Christopher Abbosh, Andrew G Nicholson, John P C Le Quesne, Dhruva Biswas, Rachel Rosenthal, Clare Puttick, Sonya Hessey, Claudia S Y Lee, Paulina Prymas, Antonia Toncheva, Jon Smith, Wei Xing, Jérôme Nicod, Gillian Price, Keith M Kerr, Babu Naidu, Gary M Middleton, Kevin G Blyth, Dean A Fennell, Martin D Forster, Siow Ming Lee, Mary Falzon, Madeleine Hewish, Michael J Shackcloth, Eric Lim, Sarah Benafif, Peter Russell, Ekaterini Boleti, Matthew G Krebs, Jason F Lester, Dionysis Papadatos-Pastos, Tanya Ahmad, Ricky M Thakrar, David Lawrence, Neal Navani, Sam M Janes, Caroline Dive, Fiona H Blackhall, Yvonne Summers, Judith Cave, Teresa Marafioti, Javier Herrero, Sergio A Quezada, Karl S Peggs, Roland F Schwarz, Peter Van Loo, Daniël M Miedema, Nicolai Juul Birkbak, Crispin T Hiley, Allan Hackshaw, Simone Zaccaria, null null, Mariam Jamal-Hanjani, Nicholas McGranahan, Charles Swanton
Author Correction: The evolution of lung cancer and impact of subclonal selection in TRACERx. Nature (2024)
Michelle Dietzen, Haoran Zhai, Olivia Lucas, Oriol Pich, Christopher Barrington, Wei-Ting Lu, Sophia Ward, Yanping Guo, Robert Edward Hynds, Simone Zaccaria, Charles Swanton, Nicholas McGranahan, Nnennaya Kanu
Replication timing alterations are associated with mutation acquisition during breast and lung cancer evolution. Nature communications 15 (1) (2024)
Michelle Dietzen, Haoran Zhai, Olivia Lucas, Oriol Pich, Christopher Barrington, Wei-Ting Lu, Sophia Ward, Yanping Guo, Robert Edward Hynds, Simone Zaccaria, Charles Swanton, Nicholas McGranahan, Nnennaya Kanu
Replication timing alterations are associated with mutation acquisition during breast and lung cancer evolution. Nature communications 15 (1) (2024)
Matthew A Myers, Brian J Arnold, Vineet Bansal, Metin Balaban, Katelyn M Mullen, Simone Zaccaria, Benjamin J Raphael
HATCHet2: clone- and haplotype-specific copy number inference from bulk tumor sequencing data. Genome biology 25 (1) (2024)
Sebastijan Hobor, Maise Al Bakir, Crispin T Hiley, Marcin Skrzypski, Alexander M Frankell, Bjorn Bakker, Thomas B K Watkins, Aleksandra Markovets, Jonathan R Dry, Andrew P Brown, Jasper van der Aart, Hilda van den Bos, Diana Carolina Johanna Spierings, Dahmane Oukrif, Marco Novelli, Turja Chakrabarti, Adam H Rabinowitz, Laila Ait Hassou, Saskia Litière, D Lucas Kerr, Lisa Tan, Gavin P Kelly, David Allan Moore, Matthew J Renshaw, Subramanian Venkatesan, William Hill, Ariana Huebner, Carlos Martínez-Ruiz, James R M Black, Wei Wu, Mihaela Angelova, Nicholas McGranahan, Julian Downward, Juliann Chmielecki, Carl Barrett, Kevin Litchfield, Su Kit Chew, Collin M Blakely, Elza C de Bruin, Floris Foijer, Karen H Vousden, Trever G Bivona, null null, Robert Edward Hynds, Nnennaya Kanu, Simone Zaccaria, Eva Grönroos, Charles Swanton
Mixed responses to targeted therapy driven by chromosomal instability through p53 dysfunction and genome doubling. Nature communications 15 (1) (2024)
Matthew A Myers, Brian J Arnold, Vineet Bansal, Metin Balaban, Katelyn M Mullen, Simone Zaccaria, Benjamin J Raphael
HATCHet2: clone- and haplotype-specific copy number inference from bulk tumor sequencing data. Genome biology 25 (1) (2024)
Sebastijan Hobor, Maise Al Bakir, Crispin T Hiley, Marcin Skrzypski, Alexander M Frankell, Bjorn Bakker, Thomas B K Watkins, Aleksandra Markovets, Jonathan R Dry, Andrew P Brown, Jasper van der Aart, Hilda van den Bos, Diana Carolina Johanna Spierings, Dahmane Oukrif, Marco Novelli, Turja Chakrabarti, Adam H Rabinowitz, Laila Ait Hassou, Saskia Litière, D Lucas Kerr, Lisa Tan, Gavin P Kelly, David Allan Moore, Matthew J Renshaw, Subramanian Venkatesan, William Hill, Ariana Huebner, Carlos Martínez-Ruiz, James R M Black, Wei Wu, Mihaela Angelova, Nicholas McGranahan, Julian Downward, Juliann Chmielecki, Carl Barrett, Kevin Litchfield, Su Kit Chew, Collin M Blakely, Elza C de Bruin, Floris Foijer, Karen H Vousden, Trever G Bivona, null null, Robert Edward Hynds, Nnennaya Kanu, Simone Zaccaria, Eva Grönroos, Charles Swanton
Mixed responses to targeted therapy driven by chromosomal instability through p53 dysfunction and genome doubling. Nature communications 15 (1) (2024)
Matthew A Myers, Brian J Arnold, Vineet Bansal, Metin Balaban, Katelyn M Mullen, Simone Zaccaria, Benjamin J Raphael
HATCHet2: clone- and haplotype-specific copy number inference from bulk tumor sequencing data. Genome biology 25 (1) (2024)
Matthew A Myers, Brian J Arnold, Vineet Bansal, Metin Balaban, Katelyn M Mullen, Simone Zaccaria, Benjamin J Raphael
HATCHet2: clone- and haplotype-specific copy number inference from bulk tumor sequencing data. Genome biology 25 (1) (2024)
Sebastijan Hobor, Maise Al Bakir, Crispin T Hiley, Marcin Skrzypski, Alexander M Frankell, Bjorn Bakker, Thomas B K Watkins, Aleksandra Markovets, Jonathan R Dry, Andrew P Brown, Jasper van der Aart, Hilda van den Bos, Diana Carolina Johanna Spierings, Dahmane Oukrif, Marco Novelli, Turja Chakrabarti, Adam H Rabinowitz, Laila Ait Hassou, Saskia Litière, D Lucas Kerr, Lisa Tan, Gavin P Kelly, David Allan Moore, Matthew J Renshaw, Subramanian Venkatesan, William Hill, Ariana Huebner, Carlos Martínez-Ruiz, James R M Black, Wei Wu, Mihaela Angelova, Nicholas McGranahan, Julian Downward, Juliann Chmielecki, Carl Barrett, Kevin Litchfield, Su Kit Chew, Collin M Blakely, Elza C de Bruin, Floris Foijer, Karen H Vousden, Trever G Bivona, null null, Robert Edward Hynds, Nnennaya Kanu, Simone Zaccaria, Eva Grönroos, Charles Swanton
Mixed responses to targeted therapy driven by chromosomal instability through p53 dysfunction and genome doubling. Nature communications 15 (1) (2024)
Ieva Usaite, Dhruva Biswas, Krijn Dijkstra, Thomas Bk Watkins, Oriol Pich, Clare Puttick, Mihaela Angelova, Krupa Thakkar, Crispin Hiley, Nicolai Juul Birkbak, Marleen Kok, Simone Zaccaria, Yin Wu, Kevin Litchfield, Charles Swanton, Nnennaya Kanu
Quantifying the impact of immunotherapy on RNA dynamics in cancer. Journal for immunotherapy of cancer 11 (11) (2023)
Michael D Kinnaman, Simone Zaccaria, Alvin P Makohon-Moore, Brian J Arnold, Max Fine Levine, Gunes Gundem, Juan Esteban Arango Ossa, Dominik Głodzik, M Irene Rodríguez-Sánchez, Nancy Bouvier, Shanita Li, Emily Stockfisch, Marisa Dunigan, Cassidy Cobbs, Umesh Bhanot, Daoqi You, Katelyn Mullen, Jerry P Melchor, Michael V Ortiz, Tara J O'Donohue, Emily K Slotkin, Leonard H Wexler, Filemon Dela Cruz, Meera R Hameed, Julia L Glade Bender, William D Tap, Paul A Meyers, Elli Papaemmanuil, Andrew L Kung, Christine A Iacobuzio-Donahue
Subclonal somatic copy number alterations emerge and dominate in recurrent osteosarcoma. bioRxiv : the preprint server for biology (2023)
Takahiro Karasaki, David Allan Moore, Selvaraju Veeriah, Cristina Naceur-Lombardelli, Antonia Toncheva, Neil Magno, Sophia Ward, Maise Al Bakir, Thomas B K Watkins, Kristiana Grigoriadis, Ariana Huebner, Mark S Hill, Alexander M Frankell, Christopher Abbosh, Clare Puttick, Haoran Zhai, Francisco Gimeno-Valiente, Sadegh Saghafinia, Nnennaya Kanu, Michelle Dietzen, Oriol Pich, Emilia L Lim, Carlos Martínez-Ruiz, James R M Black, Dhruva Biswas, Brittany B Campbell, Claudia S Y Lee, Emma C Colliver, Katey S S Enfield, Sonya Hessey, Crispin T Hiley, Simone Zaccaria, Kevin Litchfield, Nicolai Juul Birkbak, Elizabeth Larose Cadieux, Jonas Demeulemeester, Peter Van Loo, Prasad S Adusumilli, Kay See Tan, Waseem Cheema, Francisco Sanchez-Vega, David R Jones, Natasha Rekhtman, William D Travis, Allan Hackshaw, Teresa Marafioti, Roberto Salgado, John P C Le Quesne, Andrew G Nicholson, null null, Nicholas McGranahan, Charles Swanton, Mariam Jamal-Hanjani
Evolutionary characterization of lung adenocarcinoma morphology in TRACERx. Nature medicine (2023)
Michael D Kinnaman, Simone Zaccaria, Alvin P Makohon-Moore, Brian J Arnold, Max Fine Levine, Gunes Gundem, Juan Esteban Arango Ossa, Dominik Głodzik, M Irene Rodríguez-Sánchez, Nancy Bouvier, Shanita Li, Emily Stockfisch, Marisa Dunigan, Cassidy Cobbs, Umeshkumar K Bhanot, Daoqi You, Katelyn Mullen, Jerry P Melchor, Michael V Ortiz, Tara J O'Donohue, Emily K Slotkin, Leonard H Wexler, Filemon Dela Cruz, Meera R Hameed, Julia L Glade Bender, William D Tap, Paul A Meyers, Elli Papaemmanuil, Andrew L Kung, Christine A Iacobuzio-Donahue
Subclonal Somatic Copy-Number Alterations Emerge and Dominate in Recurrent Osteosarcoma. Cancer research (2023)
Kristiana Grigoriadis, Ariana Huebner, Abigail Bunkum, Emma C Colliver, Alexander M Frankell, Mark S Hill, Kerstin Thol, Nicolai Juul Birkbak, Charles Swanton, Simone Zaccaria, Nicholas McGranahan
CONIPHER: a computational framework for scalable phylogenetic reconstruction with error correction. Nature protocols (2023)
Alexander M Frankell, Michelle Dietzen, Maise Al Bakir, Emilia L Lim, Takahiro Karasaki, Sophia Ward, Selvaraju Veeriah, Emma C Colliver, Ariana Huebner, Abigail Bunkum, Mark S Hill, Kristiana Grigoriadis, David Allan Moore, James R M Black, Wing Kin Liu, Kerstin Thol, Oriol Pich, Thomas B K Watkins, Cristina Naceur-Lombardelli, Daniel E Cook, Roberto Salgado, Gareth A Wilson, Chris Bailey, Mihaela Angelova, Robert Bentham, Carlos Martínez-Ruiz, Christopher Abbosh, Andrew G Nicholson, John P C Le Quesne, Dhruva Biswas, Rachel Rosenthal, Clare Puttick, Sonya Hessey, Claudia S Y Lee, Paulina Prymas, Antonia Toncheva, Jon Smith, Wei Xing, Jérôme Nicod, Gillian Price, Keith M Kerr, Babu Naidu, Gary M Middleton, Kevin G Blyth, Dean A Fennell, Martin D Forster, Siow Ming Lee, Mary Falzon, Madeleine Hewish, Michael J Shackcloth, Eric Lim, Sarah Benafif, Peter Russell, Ekaterini Boleti, Matthew G Krebs, Jason F Lester, Dionysis Papadatos-Pastos, Tanya Ahmad, Ricky M Thakrar, David Lawrence, Neal Navani, Sam M Janes, Caroline Dive, Fiona H Blackhall, Yvonne Summers, Judith Cave, Teresa Marafioti, Javier Herrero, Sergio A Quezada, Karl S Peggs, Roland F Schwarz, Peter Van Loo, Daniël M Miedema, Nicolai Juul Birkbak, Crispin T Hiley, Allan Hackshaw, Simone Zaccaria, null null, Mariam Jamal-Hanjani, Nicholas McGranahan, Charles Swanton
The evolution of lung cancer and impact of subclonal selection in TRACERx. Nature (2023)
Michael D Kinnaman, Simone Zaccaria, Alvin P Makohon-Moore, Brian J Arnold, Max Fine Levine, Gunes Gundem, Juan Esteban Arango Ossa, Dominik Głodzik, M Irene Rodríguez-Sánchez, Nancy Bouvier, Shanita Li, Emily Stockfisch, Marisa Dunigan, Cassidy Cobbs, Umesh Bhanot, Daoqi You, Katelyn Mullen, Jerry P Melchor, Michael V Ortiz, Tara J O'Donohue, Emily K Slotkin, Leonard H Wexler, Filemon Dela Cruz, Meera R Hameed, Julia L Glade Bender, William D Tap, Paul A Meyers, Elli Papaemmanuil, Andrew L Kung, Christine A Iacobuzio-Donahue
Subclonal somatic copy number alterations emerge and dominate in recurrent osteosarcoma. bioRxiv : the preprint server for biology (2023)
Sanjana Rajan, Simone Zaccaria, Matthew V Cannon, Maren Cam, Amy C Gross, Benjamin J Raphael, Ryan D Roberts
Structurally Complex Osteosarcoma Genomes Exhibit Limited Heterogeneity within Individual Tumors and across Evolutionary Time. Cancer research communications 3 (4) (2023)
Maise Al Bakir, Ariana Huebner, Carlos Martínez-Ruiz, Kristiana Grigoriadis, Thomas B K Watkins, Oriol Pich, David Allan Moore, Selvaraju Veeriah, Sophia Ward, Joanne Laycock, Diana Johnson, Andrew Rowan, Maryam Razaq, Mita Akther, Cristina Naceur-Lombardelli, Paulina Prymas, Antonia Toncheva, Sonya Hessey, Michelle Dietzen, Emma C Colliver, Alexander M Frankell, Abigail Bunkum, Emilia L Lim, Takahiro Karasaki, Christopher Abbosh, Crispin T Hiley, Mark S Hill, Daniel E Cook, Gareth A Wilson, Roberto Salgado, Emma Nye, Richard Kevin Stone, Dean A Fennell, Gillian Price, Keith M Kerr, Babu Naidu, Gary M Middleton, Yvonne Summers, Colin R Lindsay, Fiona H Blackhall, Judith Cave, Kevin G Blyth, Arjun Nair, Asia Ahmed, Magali N Taylor, Alexander James Procter, Mary Falzon, David Lawrence, Neal Navani, Ricky M Thakrar, Samuel M Janes, Dionysis Papadatos-Pastos, Martin D Forster, Siow Ming Lee, Tanya Ahmad, Sergio A Quezada, Karl S Peggs, Peter Van Loo, Caroline Dive, Allan Hackshaw, Nicolai Juul Birkbak, Simone Zaccaria, null null, Mariam Jamal-Hanjani, Nicholas McGranahan, Charles Swanton
The evolution of non-small cell lung cancer metastases in TRACERx. Nature (2023)
Michael D Kinnaman, Simone Zaccaria, Alvin P Makohon-Moore, Brian J Arnold, Max Fine Levine, Gunes Gundem, Juan Esteban Arango Ossa, Dominik Głodzik, M Irene Rodríguez-Sánchez, Nancy Bouvier, Shanita Li, Emily Stockfisch, Marisa Dunigan, Cassidy Cobbs, Umesh Bhanot, Daoqi You, Katelyn Mullen, Jerry P Melchor, Michael V Ortiz, Tara J O'Donohue, Emily K Slotkin, Leonard H Wexler, Filemon Dela Cruz, Meera R Hameed, Julia L Glade Bender, William D Tap, Paul A Meyers, Elli Papaemmanuil, Andrew L Kung, Christine A Iacobuzio-Donahue
Subclonal somatic copy number alterations emerge and dominate in recurrent osteosarcoma. bioRxiv : the preprint server for biology (2023)
Hua Sun, Song Cao, R Jay Mashl, Chia-Kuei Mo, Simone Zaccaria, Michael C Wendl, Sherri R Davies, Matthew H Bailey, Tina M Primeau, Jeremy Hoog, Jacqueline L Mudd, Dennis A Dean, Rajesh Patidar, Li Chen, Matthew A Wyczalkowski, Reyka G Jayasinghe, Fernanda Martins Rodrigues, Nadezhda V Terekhanova, Yize Li, Kian-Huat Lim, Andrea Wang-Gillam, Brian Andrew Van Tine, Cynthia X Ma, Rebecca Aft, Katherine C Fuh, Julie K Schwarz, Jose P Zevallos, Sidharth V Puram, John F Dipersio, null null, Brandi Davis-Dusenbery, Matthew J Ellis, Michael T Lewis, Michael A Davies, Meenhard Herylyn, Bingliang Fang, Jack A Roth, Alana L Welm, Bryan E Welm, Funda Meric-Bernstam, Feng Chen, Ryan C Fields, Shunqiang Li, Ramaswamy Govindan, James H Doroshow, Jeffrey A Moscow, Yvonne A Evrard, Jeffrey H Chuang, Benjamin J Raphael, Li Ding
Author Correction: Comprehensive characterization of 536 patient-derived xenograft models prioritizes candidates for targeted treatment. Nature communications 13 (1) (2022)
Hua Sun, Song Cao, R Jay Mashl, Chia-Kuei Mo, Simone Zaccaria, Michael C Wendl, Sherri R Davies, Matthew H Bailey, Tina M Primeau, Jeremy Hoog, Jacqueline L Mudd, Dennis A Dean, Rajesh Patidar, Li Chen, Matthew A Wyczalkowski, Reyka G Jayasinghe, Fernanda Martins Rodrigues, Nadezhda V Terekhanova, Yize Li, Kian-Huat Lim, Andrea Wang-Gillam, Brian Andrew Van Tine, Cynthia X Ma, Rebecca Aft, Katherine C Fuh, Julie K Schwarz, Jose P Zevallos, Sidharth V Puram, John F Dipersio, null null, Brandi Davis-Dusenbery, Matthew J Ellis, Michael T Lewis, Michael A Davies, Meenhard Herylyn, Bingliang Fang, Jack A Roth, Alana L Welm, Bryan E Welm, Funda Meric-Bernstam, Feng Chen, Ryan C Fields, Shunqiang Li, Ramaswamy Govindan, James H Doroshow, Jeffrey A Moscow, Yvonne A Evrard, Jeffrey H Chuang, Benjamin J Raphael, Li Ding
Comprehensive characterization of 536 patient-derived xenograft models prioritizes candidatesfor targeted treatment. Nature communications 12 (1) (2021)
Simone Zaccaria, Benjamin J Raphael
Characterizing allele- and haplotype-specific copy numbers in single cells with CHISEL. Nature biotechnology 39 (2) (2020)
Simone Zaccaria, Benjamin J Raphael
Accurate quantification of copy-number aberrations and whole-genome duplications in multi-sample tumor sequencing data. Nature communications 11 (1) (2020)

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Publication Activity (10 Years)

Top Topics

Top Venues

Simone Zaccaria