Accurate quantification of copy-number aberrations and whole-genome duplications in multi-sample tumor sequencing data

por Zaccaria, Simone, Raphael, Benjamin J.
Publicado 2020

Characterizing allele- and haplotype-specific copy numbers in single cells with CHISEL

por Zaccaria, Simone, Raphael, Benjamin J.
Publicado 2021

Parsimonious Clone Tree Integration in cancer

por Sashittal, Palash, Zaccaria, Simone, El-Kebir, Mohammed
Publicado 2022

Identifying tumor clones in sparse single-cell mutation data

por Myers, Matthew A, Zaccaria, Simone, Raphael, Benjamin J
Publicado 2020

On the inversion-indel distance

por Willing, Eyla, Zaccaria, Simone, Braga, Marília DV, Stoye, Jens
Publicado 2013

HapCHAT: adaptive haplotype assembly for efficiently leveraging high coverage in long reads

por Beretta, Stefano, Patterson, Murray D., Zaccaria, Simone, Della Vedova, Gianluca, Bonizzoni, Paola
Publicado 2018

CNAViz: An interactive webtool for user-guided segmentation of tumor DNA sequencing data

por Lalani, Zubair, Chu, Gillian, Hsu, Silas, Kagawa, Shaw, Xiang, Michael, Zaccaria, Simone, El-Kebir, Mohammed
Publicado 2022

HATCHet2: clone- and haplotype-specific copy number inference from bulk tumor sequencing data

por Myers, Matthew A., Arnold, Brian J., Bansal, Vineet, Mullen, Katelyn M., Zaccaria, Simone, Raphael, Benjamin J.
Publicado 2023

Complexity and algorithms for copy-number evolution problems

por El-Kebir, Mohammed, Raphael, Benjamin J., Shamir, Ron, Sharan, Roded, Zaccaria, Simone, Zehavi, Meirav, Zeira, Ron
Publicado 2017

Structurally Complex Osteosarcoma Genomes Exhibit Limited Heterogeneity within Individual Tumors and across Evolutionary Time

por Rajan, Sanjana, Zaccaria, Simone, Cannon, Matthew V., Cam, Maren, Gross, Amy C., Raphael, Benjamin J., Roberts, Ryan D.
Publicado 2023

Quantifying the impact of immunotherapy on RNA dynamics in cancer

por Usaite, Ieva, Biswas, Dhruva, Dijkstra, Krijn, Watkins, Thomas BK, Pich, Oriol, Puttick, Clare, Angelova, Mihaela, Thakkar, Krupa, Hiley, Crispin, Birkbak, Nicolai, Kok, Marleen, Zaccaria, Simone, Wu, Yin, Litchfield, Kevin, Swanton, Charles, Kanu, Nnennaya
Publicado 2023

Subclonal somatic copy number alterations emerge and dominate in recurrent osteosarcoma

por Kinnaman, Michael D., Zaccaria, Simone, Makohon-Moore, Alvin, Arnold, Brian, Levine, Max, Gundem, Gunes, Ossa, Juan E. Arango, Glodzik, Dominik, Rodríguez-Sánchez, M. Irene, Bouvier, Nancy, Li, Shanita, Stockfisch, Emily, Dunigan, Marisa, Cobbs, Cassidy, Bhanot, Umesh, You, Daoqi, Mullen, Katelyn, Melchor, Jerry, Ortiz, Michael V., O’Donohue, Tara, Slotkin, Emily, Wexler, Leonard H., Dela Cruz, Filemon S., Hameed, Meera, Glade Bender, Julia L., Tap, William D., Meyers, Paul A., Papaemmanuil, Elli, Kung, Andrew L., Iacobuzio-Donahue, Christine A
Publicado 2023

Subclonal Somatic Copy-Number Alterations Emerge and Dominate in Recurrent Osteosarcoma

por Kinnaman, Michael D., Zaccaria, Simone, Makohon-Moore, Alvin, Arnold, Brian, Levine, Max F., Gundem, Gunes, Arango Ossa, Juan E., Glodzik, Dominik, Rodríguez-Sánchez, M. Irene, Bouvier, Nancy, Li, Shanita, Stockfisch, Emily, Dunigan, Marisa, Cobbs, Cassidy, Bhanot, Umesh K., You, Daoqi, Mullen, Katelyn, Melchor, Jerry P., Ortiz, Michael V., O'Donohue, Tara J., Slotkin, Emily K., Wexler, Leonard H., Dela Cruz, Filemon S., Hameed, Meera R., Glade Bender, Julia L., Tap, William D., Meyers, Paul A., Papaemmanuil, Elli, Kung, Andrew L., Iacobuzio-Donahue, Christine A.
Publicado 2023

Comprehensive characterization of 536 patient-derived xenograft models prioritizes candidates for targeted treatment

por Sun, Hua, Cao, Song, Mashl, R. Jay, Mo, Chia-Kuei, Zaccaria, Simone, Wendl, Michael C., Davies, Sherri R., Bailey, Matthew H., Primeau, Tina M., Hoog, Jeremy, Mudd, Jacqueline L., Dean, Dennis A., Patidar, Rajesh, Chen, Li, Wyczalkowski, Matthew A., Jayasinghe, Reyka G., Rodrigues, Fernanda Martins, Terekhanova, Nadezhda V., Li, Yize, Lim, Kian-Huat, Wang-Gillam, Andrea, Van Tine, Brian A., Ma, Cynthia X., Aft, Rebecca, Fuh, Katherine C., Schwarz, Julie K., Zevallos, Jose P., Puram, Sidharth V., Dipersio, John F., Davis-Dusenbery, Brandi, Ellis, Matthew J., Lewis, Michael T., Davies, Michael A., Herlyn, Meenhard, Fang, Bingliang, Roth, Jack A., Welm, Alana L., Welm, Bryan E., Meric-Bernstam, Funda, Chen, Feng, Fields, Ryan C., Li, Shunqiang, Govindan, Ramaswamy, Doroshow, James H., Moscow, Jeffrey A., Evrard, Yvonne A., Chuang, Jeffrey H., Raphael, Benjamin J., Ding, Li
Publicado 2021

Author Correction: Comprehensive characterization of 536 patient-derived xenograft models prioritizes candidates for targeted treatment

por Sun, Hua, Cao, Song, Mashl, R. Jay, Mo, Chia-Kuei, Zaccaria, Simone, Wendl, Michael C., Davies, Sherri R., Bailey, Matthew H., Primeau, Tina M., Hoog, Jeremy, Mudd, Jacqueline L., Dean, Dennis A., Patidar, Rajesh, Chen, Li, Wyczalkowski, Matthew A., Jayasinghe, Reyka G., Rodrigues, Fernanda Martins, Terekhanova, Nadezhda V., Li, Yize, Lim, Kian-Huat, Wang-Gillam, Andrea, Van Tine, Brian A., Ma, Cynthia X., Aft, Rebecca, Fuh, Katherine C., Schwarz, Julie K., Zevallos, Jose P., Puram, Sidharth V., Dipersio, John F., Davis-Dusenbery, Brandi, Ellis, Matthew J., Lewis, Michael T., Davies, Michael A., Herlyn, Meenhard, Fang, Bingliang, Roth, Jack A., Welm, Alana L., Welm, Bryan E., Meric-Bernstam, Funda, Chen, Feng, Fields, Ryan C., Li, Shunqiang, Govindan, Ramaswamy, Doroshow, James H., Moscow, Jeffrey A., Evrard, Yvonne A., Chuang, Jeffrey H., Raphael, Benjamin J., Ding, Li
Publicado 2022

The evolution of non-small cell lung cancer metastases in TRACERx

por Al Bakir, Maise, Huebner, Ariana, Martínez-Ruiz, Carlos, Grigoriadis, Kristiana, Watkins, Thomas B. K., Pich, Oriol, Moore, David A., Veeriah, Selvaraju, Ward, Sophia, Laycock, Joanne, Johnson, Diana, Rowan, Andrew, Razaq, Maryam, Akther, Mita, Naceur-Lombardelli, Cristina, Prymas, Paulina, Toncheva, Antonia, Hessey, Sonya, Dietzen, Michelle, Colliver, Emma, Frankell, Alexander M., Bunkum, Abigail, Lim, Emilia L., Karasaki, Takahiro, Abbosh, Christopher, Hiley, Crispin T., Hill, Mark S., Cook, Daniel E., Wilson, Gareth A., Salgado, Roberto, Nye, Emma, Stone, Richard Kevin, Fennell, Dean A., Price, Gillian, Kerr, Keith M., Naidu, Babu, Middleton, Gary, Summers, Yvonne, Lindsay, Colin R., Blackhall, Fiona H., Cave, Judith, Blyth, Kevin G., Nair, Arjun, Ahmed, Asia, Taylor, Magali N., Procter, Alexander James, Falzon, Mary, Lawrence, David, Navani, Neal, Thakrar, Ricky M., Janes, Sam M., Papadatos-Pastos, Dionysis, Forster, Martin D., Lee, Siow Ming, Ahmad, Tanya, Quezada, Sergio A., Peggs, Karl S., Van Loo, Peter, Dive, Caroline, Hackshaw, Allan, Birkbak, Nicolai J., Zaccaria, Simone, Jamal-Hanjani, Mariam, McGranahan, Nicholas, Swanton, Charles
Publicado 2023

Evolutionary characterisation of lung adenocarcinoma morphology in TRACERx

por Karasaki, Takahiro, Moore, David A., Veeriah, Selvaraju, Naceur-Lombardelli, Cristina, Toncheva, Antonia, Magno, Neil, Ward, Sophia, Al Bakir, Maise, Watkins, Thomas B.K., Grigoriadis, Kristiana, Huebner, Ariana, Hill, Mark S., Frankell, Alexander M., Abbosh, Christopher, Gimeno-Valiente, Francisco, Saghafinia, Sadegh, Kanu, Nnennaya, Dietzen, Michelle, Pich, Oriol, Lim, Emilia, Martinez-Ruiz, Carlos, Black, James R.M., Puttick, Clare, Biswas, Dhruva, Campbell, Brittany B., Lee, Claudia, Colliver, Emma, Enfield, Katey S.S., Hessey, Sonya, Hiley, Crispin T., Zaccaria, Simone, Litchfield, Kevin, Birkbak, Nicolai J., Cadieux, Elizabeth Larose, Demeulemeester, Jonas, Van Loo, Peter, Adusumilli, Prasad S., Tan, Kay See, Cheema, Waseem, Sanchez-Vega, Francisco, Jones, David R., Rekhtman, Natasha, Travis, William D., Hackshaw, Allan, Marafioti, Teresa, Salgado, Roberto, Le Quesne, John, Nicholson, Andrew G., McGranahan, Nicholas, Swanton, Charles, Jamal-Hanjani, Mariam, Jamal-Hanjani, Mariam, McGranahan, Nicholas, Swanton, Charles, McGranahan, Nicholas, Birkbak, Nicolai J., Litchfield, Kevin, Zaccaria, Simone, Swanton, Charles, Karasaki, Takahiro, Moore, David A., Al Bakir, Maise, Campbell, Brittany B., Abbosh, Christopher, Hessey, Sonya, Hiley, Crispin T., Jamal-Hanjani, Mariam, Swanton, Charles, Hackshaw, Allan, Moore, David A., Nicholson, Andrew G., Le Quesne, John, Salgado, Roberto, Al Bakir, Maise, Karasaki, Takahiro, Veeriah, Selvaraju, Naceur-Lombardelli, Cristina, Toncheva, Antonia, Magno, Neil, Ward, Sophia, Karasaki, Takahiro, Moore, David A., Dietzen, Michelle, Karasaki, Takahiro, Grigoriadis, Kristiana, Frankell, Alexander M., Watkins, Thomas B.K., Lim, Emilia, Hill, Mark S., Campbell, Brittany B., Karasaki, Takahiro, Martinez-Ruiz, Carlos, Black, James R.M., Puttick, Clare, Biswas, Dhruva, Gimeno-Valiente, Francisco, Saghafinia, Sadegh, Kanu, Nnennaya, Karasaki, Takahiro, Huebner, Ariana, Al Bakir, Maise, Abbosh, Christopher, Frankell, Alexander M., Karasaki, Takahiro, Birkbak, Nicolai J., Swanton, Charles, Karasaki, Takahiro, Puttick, Clare, Pich, Oriol, Puttick, Clare, Lee, Claudia, Grigoriadis, Kristiana, Colliver, Emma, Enfield, Katey S.S., Hiley, Crispin T., McGranahan, Nicholas, Swanton, Charles, Karasaki, Takahiro, Hill, Mark S., Litchfield, Kevin, Hackshaw, Allan, Adusumilli, Prasad S., Tan, Kay See, Cheema, Waseem, Sanchez-Vega, Francisco, Jones, David R., Rekhtman, Natasha, Travis, William D., Moore, David A., Karasaki, Takahiro, Watkins, Thomas B.K., Frankell, Alexander M., Grigoriadis, Kristiana, Colliver, Emma, Enfield, Katey S.S., Cadieux, Elizabeth Larose, Demeulemeester, Jonas, Van Loo, Peter, Sanchez-Vega, Francisco, Jones, David R., Rekhtman, Natasha, Travis, William D., Marafioti, Teresa, Salgado, Roberto, Le Quesne, John, Nicholson, Andrew G., McGranahan, Nicholas, Jamal-Hanjani, Mariam, Swanton, Charles
Publicado 2023

The evolution of lung cancer and impact of subclonal selection in TRACERx

por Frankell, Alexander M., Dietzen, Michelle, Al Bakir, Maise, Lim, Emilia L., Karasaki, Takahiro, Ward, Sophia, Veeriah, Selvaraju, Colliver, Emma, Huebner, Ariana, Bunkum, Abigail, Hill, Mark S., Grigoriadis, Kristiana, Moore, David A., Black, James R. M., Liu, Wing Kin, Thol, Kerstin, Pich, Oriol, Watkins, Thomas B. K., Naceur-Lombardelli, Cristina, Cook, Daniel E., Salgado, Roberto, Wilson, Gareth A., Bailey, Chris, Angelova, Mihaela, Bentham, Robert, Martínez-Ruiz, Carlos, Abbosh, Christopher, Nicholson, Andrew G., Le Quesne, John, Biswas, Dhruva, Rosenthal, Rachel, Puttick, Clare, Hessey, Sonya, Lee, Claudia, Prymas, Paulina, Toncheva, Antonia, Smith, Jon, Xing, Wei, Nicod, Jerome, Price, Gillian, Kerr, Keith M., Naidu, Babu, Middleton, Gary, Blyth, Kevin G., Fennell, Dean A., Forster, Martin D., Lee, Siow Ming, Falzon, Mary, Hewish, Madeleine, Shackcloth, Michael J., Lim, Eric, Benafif, Sarah, Russell, Peter, Boleti, Ekaterini, Krebs, Matthew G., Lester, Jason F., Papadatos-Pastos, Dionysis, Ahmad, Tanya, Thakrar, Ricky M., Lawrence, David, Navani, Neal, Janes, Sam M., Dive, Caroline, Blackhall, Fiona H., Summers, Yvonne, Cave, Judith, Marafioti, Teresa, Herrero, Javier, Quezada, Sergio A., Peggs, Karl S., Schwarz, Roland F., Van Loo, Peter, Miedema, Daniël M., Birkbak, Nicolai J., Hiley, Crispin T., Hackshaw, Allan, Zaccaria, Simone, Jamal-Hanjani, Mariam, McGranahan, Nicholas, Swanton, Charles
Publicado 2023