Intersect-then-combine approach: improving the performance of somatic variant calling in whole exome sequencing data using multiple aligners and callers

por Callari, Maurizio, Sammut, Stephen-John, De Mattos-Arruda, Leticia, Bruna, Alejandra, Rueda, Oscar M., Chin, Suet-Feung, Caldas, Carlos
Publicado 2017

Computational approach to discriminate human and mouse sequences in patient-derived tumour xenografts

por Callari, Maurizio, Batra, Ankita Sati, Batra, Rajbir Nath, Sammut, Stephen-John, Greenwood, Wendy, Clifford, Harry, Hercus, Colin, Chin, Suet-Feung, Bruna, Alejandra, Rueda, Oscar M., Caldas, Carlos
Publicado 2018

The Pfam protein families database

por Finn, Robert D., Tate, John, Mistry, Jaina, Coggill, Penny C., Sammut, Stephen John, Hotz, Hans-Rudolf, Ceric, Goran, Forslund, Kristoffer, Eddy, Sean R., Sonnhammer, Erik L. L., Bateman, Alex
Publicado 2008

Prognostic Value of MammaPrint(®) in Invasive Lobular Breast Cancer

por Beumer, Inès J., Persoon, Marion, Witteveen, Anke, Dreezen, Christa, Chin, Suet-Feung, Sammut, Stephen-John, Snel, Mireille, Caldas, Carlos, Linn, Sabine, van ’t Veer, Laura J., Bernards, Rene, Glas, Annuska M.
Publicado 2016

Next Generation-Targeted Amplicon Sequencing (NG-TAS): an optimised protocol and computational pipeline for cost-effective profiling of circulating tumour DNA

por Gao, Meiling, Callari, Maurizio, Beddowes, Emma, Sammut, Stephen-John, Grzelak, Marta, Biggs, Heather, Jones, Linda, Boumertit, Abdelhamid, Linn, Sabine C., Cortes, Javier, Oliveira, Mafalda, Baird, Richard, Chin, Suet-Feung, Caldas, Carlos
Publicado 2019

Shallow whole genome sequencing for robust copy number profiling of formalin-fixed paraffin-embedded breast cancers

por Chin, Suet-Feung, Santonja, Angela, Grzelak, Marta, Ahn, Soomin, Sammut, Stephen-John, Clifford, Harry, Rueda, Oscar M., Pugh, Michelle, Goldgraben, Mae A., Bardwell, Helen A., Cho, Eun Yoon, Provenzano, Elena, Rojo, Federico, Alba, Emilio, Caldas, Carlos
Publicado 2018

The molecular landscape of Asian breast cancers reveals clinically relevant population-specific differences

por Pan, Jia-Wern, Zabidi, Muhammad Mamduh Ahmad, Ng, Pei-Sze, Meng, Mei-Yee, Hasan, Siti Norhidayu, Sandey, Bethan, Sammut, Stephen-John, Yip, Cheng-Har, Rajadurai, Pathmanathan, Rueda, Oscar M., Caldas, Carlos, Chin, Suet-Feung, Teo, Soo-Hwang
Publicado 2020

The temporal mutational and immune tumour microenvironment remodelling of HER2-negative primary breast cancers

por De Mattos-Arruda, Leticia, Cortes, Javier, Blanco-Heredia, Juan, Tiezzi, Daniel G., Villacampa, Guillermo, Gonçalves-Ribeiro, Samuel, Paré, Laia, Souza, Carla Anjos, Ortega, Vanesa, Sammut, Stephen-John, Cusco, Pol, Fasani, Roberta, Chin, Suet-Feung, Perez-Garcia, Jose, Dienstmann, Rodrigo, Nuciforo, Paolo, Villagrasa, Patricia, Rubio, Isabel T., Prat, Aleix, Caldas, Carlos
Publicado 2021

AACR Project GENIE: 100,000 Cases and Beyond

por Pugh, Trevor J., Bell, Jonathan L., Bruce, Jeff P., Doherty, Gary J., Galvin, Matthew, Green, Michelle F., Hunter-Zinck, Haley, Kumari, Priti, Lenoue-Newton, Michele L., Li, Marilyn M., Lindsay, James, Mazor, Tali, Ovalle, Andrea, Sammut, Stephen-John, Schultz, Nikolaus, Yu, Thomas V., Sweeney, Shawn M., Bernard, Brady
Publicado 2022

Multi-omic machine learning predictor of breast cancer therapy response

por Sammut, Stephen-John, Crispin-Ortuzar, Mireia, Chin, Suet-Feung, Provenzano, Elena, Bardwell, Helen A., Ma, Wenxin, Cope, Wei, Dariush, Ali, Dawson, Sarah-Jane, Abraham, Jean E., Dunn, Janet, Hiller, Louise, Thomas, Jeremy, Cameron, David A., Bartlett, John M. S., Hayward, Larry, Pharoah, Paul D., Markowetz, Florian, Rueda, Oscar M., Earl, Helena M., Caldas, Carlos
Publicado 2021

DNA methylation landscapes of 1538 breast cancers reveal a replication-linked clock, epigenomic instability and cis-regulation

por Batra, Rajbir Nath, Lifshitz, Aviezer, Vidakovic, Ana Tufegdzic, Chin, Suet-Feung, Sati-Batra, Ankita, Sammut, Stephen-John, Provenzano, Elena, Ali, H. Raza, Dariush, Ali, Bruna, Alejandra, Murphy, Leigh, Purushotham, Arnie, Ellis, Ian, Green, Andrew, Garrett-Bakelman, Francine E., Mason, Chris, Melnick, Ari, Aparicio, Samuel A. J. R., Rueda, Oscar M., Tanay, Amos, Caldas, Carlos
Publicado 2021

Comparison of tumor‐informed and tumor‐naïve sequencing assays for ctDNA detection in breast cancer

por Santonja, Angela, Cooper, Wendy N, Eldridge, Matthew D, Edwards, Paul A W, Morris, James A, Edwards, Abigail R, Zhao, Hui, Heider, Katrin, Couturier, Dominique‐Laurent, Vijayaraghavan, Aadhitthya, Mennea, Paulius, Ditter, Emma‐Jane, Smith, Christopher G, Boursnell, Chris, Manzano García, Raquel, Rueda, Oscar M, Beddowes, Emma, Biggs, Heather, Sammut, Stephen‐John, Rosenfeld, Nitzan, Caldas, Carlos, Abraham, Jean E, Gale, Davina
Publicado 2023

Dynamics of breast cancer relapse reveal late recurring ER-positive genomic subgroups

por Rueda, Oscar M., Sammut, Stephen-John, Seoane, Jose A, Chin, Suet-Feung, Caswell-Jin, Jennifer L, Callari, Maurizio, Batra, Rajbir, Pereira, Bernard, Bruna, Alejandra, Ali, H Raza, Provenzano, Elena, Liu, Bin, Parisien, Michelle, Gillett, Cheryl, McKinney, Steven, Green, Andrew R., Murphy, Leigh, Purushotham, Arnie, Ellis, Ian O., Pharoah, Paul D., Rueda, Cristina, Aparicio, Samuel AJR, Caldas, Carlos, Curtis, Christina
Publicado 2019

Prediction of cancer treatment response from histopathology images through imputed transcriptomics

por Hoang, Danh-Tai, Dinstag, Gal, Hermida, Leandro C., Ben-Zvi, Doreen S., Elis, Efrat, Caley, Katherine, Sammut, Stephen-John, Sinha, Sanju, Sinha, Neelam, Dampier, Christopher H., Stossel, Chani, Patil, Tejas, Rajan, Arun, Lassoued, Wiem, Strauss, Julius, Bailey, Shania, Allen, Clint, Redman, Jason, Beker, Tuvik, Jiang, Peng, Golan, Talia, Wilkinson, Scott, Sowalsky, Adam G., Pine, Sharon R., Caldas, Carlos, Gulley, James L., Aldape, Kenneth, Aharonov, Ranit, Stone, Eric A., Ruppin, Eytan
Publicado 2023

A Biobank of Breast Cancer Explants with Preserved Intra-tumor Heterogeneity to Screen Anticancer Compounds

por Bruna, Alejandra, Rueda, Oscar M., Greenwood, Wendy, Batra, Ankita Sati, Callari, Maurizio, Batra, Rajbir Nath, Pogrebniak, Katherine, Sandoval, Jose, Cassidy, John W., Tufegdzic-Vidakovic, Ana, Sammut, Stephen-John, Jones, Linda, Provenzano, Elena, Baird, Richard, Eirew, Peter, Hadfield, James, Eldridge, Matthew, McLaren-Douglas, Anne, Barthorpe, Andrew, Lightfoot, Howard, O’Connor, Mark J., Gray, Joe, Cortes, Javier, Baselga, Jose, Marangoni, Elisabetta, Welm, Alana L., Aparicio, Samuel, Serra, Violeta, Garnett, Mathew J., Caldas, Carlos
Publicado 2016

The Genomic and Immune Landscapes of Lethal Metastatic Breast Cancer

por De Mattos-Arruda, Leticia, Sammut, Stephen-John, Ross, Edith M., Bashford-Rogers, Rachael, Greenstein, Erez, Markus, Havell, Morganella, Sandro, Teng, Yvonne, Maruvka, Yosef, Pereira, Bernard, Rueda, Oscar M., Chin, Suet-Feung, Contente-Cuomo, Tania, Mayor, Regina, Arias, Alexandra, Ali, H. Raza, Cope, Wei, Tiezzi, Daniel, Dariush, Aliakbar, Dias Amarante, Tauanne, Reshef, Dan, Ciriaco, Nikaoly, Martinez-Saez, Elena, Peg, Vicente, Ramon y Cajal, Santiago, Cortes, Javier, Vassiliou, George, Getz, Gad, Nik-Zainal, Serena, Murtaza, Muhammed, Friedman, Nir, Markowetz, Florian, Seoane, Joan, Caldas, Carlos
Publicado 2019

The somatic mutation profiles of 2,433 breast cancers refines their genomic and transcriptomic landscapes

por Pereira, Bernard, Chin, Suet-Feung, Rueda, Oscar M., Vollan, Hans-Kristian Moen, Provenzano, Elena, Bardwell, Helen A., Pugh, Michelle, Jones, Linda, Russell, Roslin, Sammut, Stephen-John, Tsui, Dana W. Y., Liu, Bin, Dawson, Sarah-Jane, Abraham, Jean, Northen, Helen, Peden, John F., Mukherjee, Abhik, Turashvili, Gulisa, Green, Andrew R., McKinney, Steve, Oloumi, Arusha, Shah, Sohrab, Rosenfeld, Nitzan, Murphy, Leigh, Bentley, David R., Ellis, Ian O., Purushotham, Arnie, Pinder, Sarah E., Børresen-Dale, Anne-Lise, Earl, Helena M., Pharoah, Paul D., Ross, Mark T., Aparicio, Samuel, Caldas, Carlos
Publicado 2016

Erratum: The somatic mutation profiles of 2,433 breast cancers refine their genomic and transcriptomic landscapes

por Pereira, Bernard, Chin, Suet-Feung, Rueda, Oscar M., Vollan, Hans-Kristian Moen, Provenzano, Elena, Bardwell, Helen A., Pugh, Michelle, Jones, Linda, Russell, Roslin, Sammut, Stephen-John, Tsui, Dana W. Y., Liu, Bin, Dawson, Sarah-Jane, Abraham, Jean, Northen, Helen, Peden, John F., Mukherjee, Abhik, Turashvili, Gulisa, Green, Andrew R., McKinney, Steve, Oloumi, Arusha, Shah, Sohrab, Rosenfeld, Nitzan, Murphy, Leigh, Bentley, David R., Ellis, Ian O., Purushotham, Arnie, Pinder, Sarah E., Børresen-Dale, Anne-Lise, Earl, Helena M., Pharoah, Paul D., Ross, Mark T., Aparicio, Samuel, Caldas, Carlos
Publicado 2016

Integration of genomic, transcriptomic and proteomic data identifies two biologically distinct subtypes of invasive lobular breast cancer

por Michaut, Magali, Chin, Suet-Feung, Majewski, Ian, Severson, Tesa M., Bismeijer, Tycho, de Koning, Leanne, Peeters, Justine K., Schouten, Philip C., Rueda, Oscar M., Bosma, Astrid J., Tarrant, Finbarr, Fan, Yue, He, Beilei, Xue, Zheng, Mittempergher, Lorenza, Kluin, Roelof J.C., Heijmans, Jeroen, Snel, Mireille, Pereira, Bernard, Schlicker, Andreas, Provenzano, Elena, Ali, Hamid Raza, Gaber, Alexander, O’Hurley, Gillian, Lehn, Sophie, Muris, Jettie J.F., Wesseling, Jelle, Kay, Elaine, Sammut, Stephen John, Bardwell, Helen A., Barbet, Aurélie S., Bard, Floriane, Lecerf, Caroline, O’Connor, Darran P., Vis, Daniël J., Benes, Cyril H., McDermott, Ultan, Garnett, Mathew J., Simon, Iris M., Jirström, Karin, Dubois, Thierry, Linn, Sabine C., Gallagher, William M., Wessels, Lodewyk F.A., Caldas, Carlos, Bernards, Rene
Publicado 2016

Residual cancer burden after neoadjuvant chemotherapy and long-term survival outcomes in breast cancer: a multicentre pooled analysis of 5161 patients

por Yau, Christina, Osdoit, Marie, van der Noordaa, Marieke, Shad, Sonal, Wei, Jane, de Croze, Diane, Hamy, Anne-Sophie, Laé, Marick, Reyal, Fabien, Sonke, Gabe S, Steenbruggen, Tessa G, van Seijen, Maartje, Wesseling, Jelle, Martín, Miguel, del Monte-Millán, Maria, López-Tarruella, Sara, Boughey, Judy C, Goetz, Matthew P, Hoskin, Tanya, Gould, Rebekah, Valero, Vicente, Edge, Stephen B, Abraham, Jean E, Bartlett, John M S, Caldas, Carlos, Dunn, Janet, Earl, Helena, Hayward, Larry, Hiller, Louise, Provenzano, Elena, Sammut, Stephen-John, Thomas, Jeremy S, Cameron, David, Graham, Ashley, Hall, Peter, Mackintosh, Lorna, Fan, Fang, Godwin, Andrew K, Schwensen, Kelsey, Sharma, Priyanka, DeMichele, Angela M, Cole, Kimberly, Pusztai, Lajos, Kim, Mi-Ok, van ‘t Veer, Laura J, Esserman, Laura J, Symmans, W Fraser
Publicado 2022