Mutational Signatures in Breast Cancer: The Problem at the DNA Level by Nik-Zainal, Serena, Morganella, Sandro

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TimeDelay-ARACNE: Reverse engineering of gene networks from time-course data by an information theoretic approach by Zoppoli, Pietro, Morganella, Sandro, Ceccarelli, Michele

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A Compendium of Mutational Signatures of Environmental Agents by Kucab, Jill E., Zou, Xueqing, Morganella, Sandro, Joel, Madeleine, Nanda, A. Scott, Nagy, Eszter, Gomez, Celine, Degasperi, Andrea, Harris, Rebecca, Jackson, Stephen P., Arlt, Volker M., Phillips, David H., Nik-Zainal, Serena

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Noncanonical secondary structures arising from non-B DNA motifs are determinants of mutagenesis by Georgakopoulos-Soares, Ilias, Morganella, Sandro, Jain, Naman, Hemberg, Martin, Nik-Zainal, Serena

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Whole-Genome Sequencing Reveals Breast Cancers with Mismatch Repair Deficiency by Davies, Helen, Morganella, Sandro, Purdie, Colin A, Jang, Se Jin, Borgen, Elin, Russnes, Hege, Glodzik, Dominik, Zou, Xueqing, Viari, Alain, Richardson, Andrea L, Børresen-Dale, Anne-Lise, Thompson, Alastair, Eyfjord, Jorunn E, Kong, Gu, Stratton, Michael R, Nik-Zainal, Serena

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The Genomic and Immune Landscapes of Lethal Metastatic Breast Cancer by 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

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Partially methylated domains are hypervariable in breast cancer and fuel widespread CpG island hypermethylation by Brinkman, Arie B., Nik-Zainal, Serena, Simmer, Femke, Rodríguez-González, F. Germán, Smid, Marcel, Alexandrov, Ludmil B., Butler, Adam, Martin, Sancha, Davies, Helen, Glodzik, Dominik, Zou, Xueqing, Ramakrishna, Manasa, Staaf, Johan, Ringnér, Markus, Sieuwerts, Anieta, Ferrari, Anthony, Morganella, Sandro, Fleischer, Thomas, Kristensen, Vessela, Gut, Marta, van de Vijver, Marc J., Børresen-Dale, Anne-Lise, Richardson, Andrea L., Thomas, Gilles, Gut, Ivo G., Martens, John W. M., Foekens, John A., Stratton, Michael R., Stunnenberg, Hendrik G.

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Finding recurrent copy number alterations preserving within-sample homogeneity by Morganella, Sandro, Pagnotta, Stefano Maria, Ceccarelli, Michele

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ChromoTrace: Computational reconstruction of 3D chromosome configurations for super-resolution microscopy by Barton, Carl, Morganella, Sandro, Ødegård-Fougner, Øyvind, Alexander, Stephanie, Ries, Jonas, Fitzgerald, Tomas, Ellenberg, Jan, Birney, Ewan

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Genome-wide analysis of copy number alterations led to the characterisation of PDCD10 as oncogene in ovarian cancer by De Marco, Carmela, Zoppoli, Pietro, Rinaldo, Nicola, Morganella, Sandro, Morello, Matteo, Zuccalà, Valeria, Carriero, Maria Vincenza, Malanga, Donatella, Chirillo, Roberta, Bruni, Paola, Malzoni, Carmine, Di Vizio, Dolores, Venturella, Roberta, Zullo, Fulvio, Rizzuto, Antonia, Ceccarelli, Michele, Ciliberto, Gennaro, Viglietto, Giuseppe

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IRIS: a method for reverse engineering of regulatory relations in gene networks by Morganella, Sandro, Zoppoli, Pietro, Ceccarelli, Michele

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Landscape of somatic mutations in 560 breast cancer whole-genome sequences by Nik-Zainal, Serena, Davies, Helen, Staaf, Johan, Ramakrishna, Manasa, Glodzik, Dominik, Zou, Xueqing, Martincorena, Inigo, Alexandrov, Ludmil B., Martin, Sancha, Wedge, David C., Van Loo, Peter, Ju, Young Seok, Smid, Marcel, Brinkman, Arie B., Morganella, Sandro, Aure, Miriam R., Lingjærde, Ole Christian, Langerød, Anita, Ringnér, Markus, Ahn, Sung-Min, Boyault, Sandrine, Brock, Jane E., Broeks, Annegien, Butler, Adam, Desmedt, Christine, Dirix, Luc, Dronov, Serge, Fatima, Aquila, Foekens, John A., Gerstung, Moritz, Hooijer, Gerrit K. J., Jang, Se Jin, Jones, David R., Kim, Hyung-Yong, King, Tari A., Krishnamurthy, Savitri, Lee, Hee Jin, Lee, Jeong-Yeon, Li, Yilong, McLaren, Stuart, Menzies, Andrew, Mustonen, Ville, O’Meara, Sarah, Pauporté, Iris, Pivot, Xavier, Purdie, Colin A., Raine, Keiran, Ramakrishnan, Kamna, Rodríguez-González, F. Germán, Romieu, Gilles, Sieuwerts, Anieta M., Simpson, Peter T., Shepherd, Rebecca, Stebbings, Lucy, Stefansson, Olafur A., Teague, Jon, Tommasi, Stefania, Treilleux, Isabelle, Van den Eynden, Gert G., Vermeulen, Peter, Vincent-Salomon, Anne, Yates, Lucy, Caldas, Carlos, Veer, Laura van’t, Tutt, Andrew, Knappskog, Stian, Tan, Benita Kiat Tee, Jonkers, Jos, Borg, Åke, Ueno, Naoto T., Sotiriou, Christos, Viari, Alain, Futreal, P. Andrew, Campbell, Peter J., Span, Paul N., Van Laere, Steven, Lakhani, Sunil R., Eyfjord, Jorunn E., Thompson, Alastair M., Birney, Ewan, Stunnenberg, Hendrik G., van de Vijver, Marc J., Martens, John W. M., Børresen-Dale, Anne-Lise, Richardson, Andrea L., Kong, Gu, Thomas, Gilles, Stratton, Michael R.

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VegaMC: a R/bioconductor package for fast downstream analysis of large array comparative genomic hybridization datasets by MORGANELLA, Sandro, CECCARELLI, Michele

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The genome as a record of environmental exposure by Nik-Zainal, Serena, Kucab, Jill E, Morganella, Sandro, Glodzik, Dominik, Alexandrov, Ludmil B, Arlt, Volker M, Weninger, Annette, Hollstein, Monica, Stratton, Michael R, Phillips, David H

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Short inverted repeats contribute to localized mutability in human somatic cells by Zou, Xueqing, Morganella, Sandro, Glodzik, Dominik, Davies, Helen, Li, Yilin, Stratton, Michael R, Nik-Zainal, Serena

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Abstract LB-262: A somatic-mutational process in breast cancer genomes recurrently duplicates germline susceptibility loci and tissue-specific super-enhancers by Glodzik, Dominik, Morganella, Sandro, Davies, Helen, Nik-Zainal, Serena

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The topography of mutational processes in breast cancer genomes by Morganella, Sandro, Alexandrov, Ludmil B., Glodzik, Dominik, Zou, Xueqing, Davies, Helen, Staaf, Johan, Sieuwerts, Anieta M., Brinkman, Arie B., Martin, Sancha, Ramakrishna, Manasa, Butler, Adam, Kim, Hyung-Yong, Borg, Åke, Sotiriou, Christos, Futreal, P. Andrew, Campbell, Peter J., Span, Paul N., Van Laere, Steven, Lakhani, Sunil R., Eyfjord, Jorunn E., Thompson, Alastair M., Stunnenberg, Hendrik G., van de Vijver, Marc J., Martens, John W. M., Børresen-Dale, Anne-Lise, Richardson, Andrea L., Kong, Gu, Thomas, Gilles, Sale, Julian, Rada, Cristina, Stratton, Michael R., Birney, Ewan, Nik-Zainal, Serena

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Hydroxymethylation profile of cell-free DNA is a biomarker for early colorectal cancer by Walker, Nicolas J., Rashid, Mamunur, Yu, Shirong, Bignell, Helen, Lumby, Casper K., Livi, Carmen M., Howell, Kate, Morley, David J., Morganella, Sandro, Barrell, Daniel, Caim, Shabhonam, Gosal, Walraj, Füllgrabe, Jens, Charlesworth, Thomas J., Vasquez, Louella, Ahdesmäki, Miika, Eizenga, Jordan, Prabhat, Parul, Proutski, Vitali, Murat-Onana, Marie Laurie, Greenwood, Catherine J., Kirkwood, Lisa, Maisuria-Armer, Meeta, Li, Mengjie, Coats, Emma, Winfield, Victoria, MacBean, Lachlan, Stock, Toby, Tomé-Fernandez, Alice, Chan, Yat, Sheikh, Nasir, Golder, Paula, Steward, Michael, Ost, Tobias W. B., Stewart, Douglas, Vilella, Albert, Noursalehi, Mojtaba, Paten, Benedict, Lucarelli, Debora, Mason, Joanne, Ridge, Gareth, Mellad, Jason, Shirodkar, Suman, Balasubaramanian, Shankar, Holbrook, Joanna D.

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VEGA: variational segmentation for copy number detection by Morganella, Sandro, Cerulo, Luigi, Viglietto, Giuseppe, Ceccarelli, Michele

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VEGAWES: variational segmentation on whole exome sequencing for copy number detection by Anjum, Samreen, Morganella, Sandro, D'Angelo, Fulvio, Iavarone, Antonio, Ceccarelli, Michele

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