Items where Author is "Brewer, Daniel"

Article

Wilson, Emma, Jennings, Barbara Anne, Khondoker, Mizanur, Philpott, Carl M., Prinsley, Peter and Brewer, Daniel S. (2025) Epidemiology of Cholesteatoma in the UK Biobank. Clinical Otolaryngology, 50 (2). pp. 316-329. ISSN 1749-4478

Swart, Maarten, Redpath, Andia N., Ogbechi, Joy, Cardenas, Ryan, Topping, Louise, Compeer, Ewoud B., Goddard, Michael, Chanalaris, Anastasios, Williams, Richard, Brewer, Daniel S., Smart, Nicola, Monaco, Claudia and Troeberg, Linda (2024) The extracellular heparan sulfatase SULF2 limits myeloid IFNβ signaling and Th17 responses in inflammatory arthritis. Cellular and Molecular Life Sciences, 81. ISSN 1420-682X

Smith, Stephanie F., Brewer, Daniel S., Hurst, Rachel and Cooper, Colin S. (2024) Applications of urinary extracellular vesicles in the diagnosis and active surveillance of prostate cancer. Cancers, 16 (9). ISSN 2072-6694

Pope, Bernard, Park, Gahee, Lau, Edmund, Belic, Jelena, Lach, Radoslaw, George, Anne, McCoy, Patrick, Nguyen, Anne, Grima, Corrina, Campbell, Bethany, Jung, Chol-hee, Ditter, Emma-Jane, Zhao, Hui, Wedge, David C., Brewer, Daniel S., Lynch, Andy G., Dev, Harveer, Gnanapragasam, Vincent J., Rosenfeld, Nitzan, Hovens, Chris M., Corcoran, Niall M. and Massie, Charlie E. and The Pan Prostate Cancer Group (PPCG) (2024) Ultra-sensitive detection of circulating tumour DNA enriches for patients with greater risk of recurrence in clinically localised prostate cancer. European Urology, 85 (4). pp. 407-410. ISSN 0302-2838

Hurst, Rachel, Brewer, Daniel S., Gihawi, Abraham, Wain, John and Cooper, Colin S. (2024) Cancer invasion and anaerobic bacteria: New insights into mechanisms. Journal of Medical Microbiology, 73 (3). ISSN 0022-2615

Woodcock, Dan J., Sahli, Atef, Teslo, Ruxandra, Bhandari, Vinayak, Gruber, Andreas J., Ziubroniewicz, Aleksandra, Gundem, Gunes, Xu, Yaobo, Butler, Adam, Anokian, Ezequiel, Pope, Bernard J., Jung, Chol-Hee, Tarabichi, Maxime, Dentro, Stefan C., Farmery, J. Henry R., Van Loo, Peter, Warren, Anne Y., Gnanapragasam, Vincent, Hamdy, Freddie C., Bova, G. Steven, Foster, Christopher S., Neal, David E., Lu, Yong-Jie, Kote-Jarai, Zsofia, Fraser, Michael, Bristow, Robert G., Boutros, Paul C., Costello, Anthony J., Corcoran, Niall M., Hovens, Christopher M., Massie, Charlie E., Lynch, Andy G., Brewer, Daniel S., Eeles, Rosalind A., Cooper, Colin S. and Wedge, David C. (2024) Genomic evolution shapes prostate cancer disease type. Cell Genomics, 4 (3). ISSN 2666-979X

Gihawi, Abraham, Ge, Yuchen, Lu, Jennifer, Puiu, Daniela, Xu, Amanda, Cooper, Colin S., Brewer, Daniel S., Pertea, Mihaela and Salzberg, Steven L. (2023) Major data analysis errors invalidate cancer microbiome findings. mBIO, 14 (5). ISSN 2150-7511

Gihawi, Abraham, Cooper, Colin S. and Brewer, Daniel S. (2023) Caution regarding the specificities of pan-cancer microbial structure. Microbial Genomics, 9 (8). ISSN 2057-5858

Cardenas, Ryan, Prinsley, Peter, Philpott, Carl, Bhutta, Mahmood F., Wilson, Emma, Brewer, Daniel S. and Jennings, Barbara A. (2023) Whole exome sequencing study identifies candidate loss of function variants and locus heterogeneity in familial cholesteatoma. PLoS One, 18 (3). ISSN 1932-6203

Yazbek Hanna, Marcelino, Winterbone, Mark, O'Connell, Shea P., Olivan, Mireia, Hurst, Rachel, Mills, Rob, Cooper, Colin S., Brewer, Daniel S. and Clark, Jeremy (2023) Gene-transcript expression in urine supernatant and urine cell-sediment are different but equally useful for detecting prostate cancer. Cancers, 15 (3). ISSN 2072-6694

Wardale, Lewis, Cardenas, Ryan, Gnanapragasam, Vincent J., Cooper, Colin S., Clark, Jeremy and Brewer, Daniel S. (2023) Combining molecular subtypes with multivariable clinical models has the potential to improve prediction of treatment outcomes in prostate cancer at diagnosis. Current Oncology, 30 (1). pp. 157-170. ISSN 1198-0052

Buhigas, Claudia, Warren, Anne Y., Leung, Wing-Kit, Whitaker, Hayley C., Luxton, Hayley J., Hawkins, Steve, Kay, Jonathan, Butler, Adam, Xu, Yaobo, Woodcock, Dan J., Merson, Susan, Frame, Fiona M., Sahli, Atef, Abascal, Federico, Martincorena, Inigo, Bova, G. Steven, Foster, Christopher S., Campbell, Peter, Maitland, Norman J., Neal, David E., Massie, Charlie E., Lynch, Andy G., Eeles, Rosalind A., Cooper, Colin S., Wedge, David C. and Brewer, Daniel S. and CRUK-ICGC Prostate Cancer Group (2022) The architecture of clonal expansions in morphologically normal tissue from cancerous and non-cancerous prostates. Molecular Cancer, 21. ISSN 1476-4598

Burns, Daniel, Anokian, Ezequiel, Saunders, Edward J., Bristow, Robert G., Fraser, Michael, Reimand, Jüri, Schlomm, Thorsten, Sauter, Guido, Brors, Benedikt, Korbel, Jan, Weischenfeldt, Joachim, Waszak, Sebastian M., Corcoran, Niall M., Jung, Chol-Hee, Pope, Bernard J., Hovens, Chris M., Cancel-Tassin, Géraldine, Cussenot, Olivier, Loda, Massimo, Sander, Chris, Hayes, Vanessa M., Dalsgaard Sorensen, Karina, Lu, Yong-Jie, Hamdy, Freddie C., Foster, Christopher S., Gnanapragasam, Vincent, Butler, Adam, Lynch, Andy G., Massie, Charlie E., Woodcock, Dan J., Cooper, Colin S., Wedge, David C., Brewer, Daniel S., Kote-Jarai, Zsofia and Eeles, Rosalind A. and CR-UK/Prostate Cancer UK, ICGC, The PPCG (2022) Rare germline variants are associated with rapid biochemical recurrence after radical prostate cancer treatment: a PPCG study. European Urology, 82 (2). pp. 201-211. ISSN 0302-2838

Hurst, Rachel, Meader, Emma, Gihawi, Abraham, Rallapalli, Ghanasyam, Clark, Jeremy, Kay, Gemma L., Webb, Martyn, Manley, Kate, Curley, Helen, Walker, Helen, Kumar, Ravi, Schmidt, Katarzyna, Crossman, Lisa, Eeles, Rosalind A., Wedge, David C., Lynch, Andy G., Massie, Charlie E., Yazbek-Hanna, Marcelino, Rochester, Mark, Mills, Robert D., Mithen, Richard F., Traka, Maria H., Ball, Richard Y., O'Grady, Justin, Brewer, Daniel S., Wain, John and Cooper, Colin S. (2022) Microbiomes of urine and the prostate are linked to human prostate cancer risk groups. European Urology Oncology, 5 (4). pp. 412-419. ISSN 2588-9311

Cardenas, Ryan, Prinsley, Peter, Philpott, Carl, Bhutta, Mahmood F, Wilson, Emma, Brewer, Daniel S. and Jennings, Barbara A. (2022) Whole exome sequencing study identifies candidate loss of function variants and locus heterogeneity in familial cholesteatoma.

Jakobsdottir, G. Maria, Brewer, Daniel S., Cooper, Colin, Green, Catherine and Wedge, David C. (2022) APOBEC3 mutational signatures are associated with extensive and diverse genomic instability across multiple tumour types. BMC Biology, 20. ISSN 1741-7007

Connell, Shea, Frantzi, Maria, Latosinska, Agnieszka, Webb, Martyn, Mullen, William, Pejchinovski, Martin, Salji, Mark, Mischak, Harald, Cooper, Colin, Clark, Jeremy and Brewer, Daniel (2022) A model to detect significant prostate cancer integrating urinary peptide and extracellular vesicle RNA data. Cancers, 14 (8). ISSN 2072-6694

Ball, Richard, Cardenas, Ryan, Winterbone, Mark, Yazbek Hanna, Marcelino, Parker, Christopher C., Hurst, Rachel, Brewer, Daniel, D'Sa, Lauren, Mills, Robert, Cooper, Colin and Clark, Jeremy (2021) The urine biomarker PUR-4 is positively associated with the amount of Gleason 4 in human prostate cancers. Life, 11 (11). ISSN 2075-1729

Connell, Shea P., Mills, Robert, Pandha, Hardev, Morgan, Richard, Cooper, Colin, Clark, Jeremy and Brewer, Daniel (2021) Integration of urinary EN2 protein & cell-free RNA data in the development of a multivariable risk model for the detection of prostate cancer prior to biopsy. Cancers, 13 (9). ISSN 2072-6694

Woodcock, Dan, Riabchenko, Ekaterina, Taavitsainen, Sinja, Kankainen, Matti, Gundem, Gunes, Brewer, Daniel, Ellonen, Pekka, Lepistö, Maija, Golubeva, Yelena, Warner, Andrew, Tolonen, Teemu, Jasu, Juho, Isaacs, William B., Emmert-Buck, Michael R., Nykter, Matti, Visakorpi, Tapio, Bova, G. Steven and Wedge, David C. (2020) Prostate cancer evolution from multilineage primary to single lineage metastases with implications for liquid biopsy. Nature Communications, 11. ISSN 2041-1723

Luca, Bogdan, Moulton, Vincent, Ellis, Christopher, Connell, Shea P., Brewer, Daniel and Cooper, Colin (2020) Convergence of prognostic gene signatures suggests underlying mechanisms of human prostate cancer progression. Genes, 11 (7). ISSN 2073-4425

Connell, Shea P, O'Reilly, Eve, Tuzova, Alexandra, Webb, Martyn, Hurst, Rachel, Mills, Robert, Zhao, Fang, Bapat, Bharati, Cooper, Colin, Perry, Antoinette, Clark, Jeremy and Brewer, Daniel (2020) Development of a multivariable risk model integrating urinary cell DNA methylation and cell-free RNA data for the detection of significant prostate cancer. The Prostate, 80 (7). pp. 547-558. ISSN 0270-4137

Luca, Bogdan, Moulton, Vincent, Ellis, Christopher, Edwards, Dylan R., Campbell, Colin, Cooper, Rosalin A., Clark, Jeremy, Brewer, Daniel S. and Cooper, Colin S. (2020) A novel stratification framework for predicting outcome in patients with prostate cancer. British Journal of Cancer, 122 (10). 1467–1476. ISSN 0007-0920

Zapatka, Marc, Borozan, Ivan, Brewer, Daniel, Iskar, Murat, Grundhoff, Adam, Alawi, Malik, Desai, Nikita, Sültmann, Holger, Moch, Holger, Cooper, Colin, Eils, Roland, Ferretti, Vincent and Lichter, Peter (2020) The landscape of viral associations in human cancers. Nature Genetics, 52 (3). 320–330. ISSN 1061-4036

Gihawi, Abraham, Rallapalli, Ghanasyam, Hurst, Rachel, Cooper, Colin, Leggett, Richard M. and Brewer, Daniel (2019) SEPATH: Benchmarking the search for pathogens in human tissue whole genome sequence data leads to template pipelines. Genome Biology, 20. ISSN 1474-760X

Magiorkinis, Gkikas, Matthews, Philippa C., Wallace, Susan E., Jeffery, Katie, Dunbar, Kevin, Tedder, Richard, Mbisa, Jean L., Hannigan, Bernadette, Vayena, Effy, Simmonds, Peter, Brewer, Daniel S., Gihawi, Abraham, Rallapalli, Ghanasyam, Lahnstein, Lea, Fowler, Tom, Patch, Christine, Maleady-Crowe, Fiona, Lucassen, Anneke and Cooper, Colin (2019) Potential for diagnosis of infectious disease from the 100,000 Genomes Project Metagenomic Dataset: Recommendations for reporting results. Wellcome Open Research, 4.

Connell, Shea P., Yazbek Hanna, Marcelino, McCarthy, Frank, Hurst, Rachel, Webb, Martyn, Curley, Helen, Walker, Helen, Mills, Robert, Ball, Richard, Sanda, Martin, Pellegrini, Kathryn, Patil, Dattatraya, Perry, Antoinette, Schalken, Jack, Pandha, Hardev, Whitaker, Hayley C, Dennis, Nening, Stuttle, Christine, Mills, Ian, Guldvik, Ingrid, Parker, Christopher C., Brewer, Daniel, Cooper, Colin and Clark, Jeremy (2019) A four-group urine risk classifier for predicting outcome in prostate cancer patients. BJU International, 124 (4). pp. 609-620. ISSN 1464-4096

Alshaker, Heba, Wang, Qi, Brewer, Daniel and Pshezhetskiy, Dmitry (2019) Transcriptome-wide effects of sphingosine kinases knockdown in metastatic prostate and breast cancer cells: Implications for therapeutic targeting. Frontiers in Pharmacology, 10. ISSN 1663-9812

O'Reilly, Eve, Tuzova, Alexandra, Walsh, Anna, Russell, Niamh, O’Brien, Odharnaith, Kelly, Sarah, Dhomhnallain, Odharna, DeBarra, Liam, Dale, Connie, Brugman, Rick, Clarke, Gavin, Schmidt, Olivia, O'Meachair, Shane, Patil, Dattatraya, Pellegrini, Kathryn, Fleshner, Neil, Garcia, Julia, Zhao, Fang, Finn, Stephen, Mills, Robert, Y. Hanna, Marcelino, Hurst, Rachel, McEvoy, Elizabeth, Gallagher, William, Manecksha, Rustom, Cooper, Colin, Brewer, Daniel, Bapat, Bharati, Sanda, Martin, Clark, Jeremy and Perry, Antoinette (2019) epiCaPture: a urine DNA methylation test for early detection of aggressive prostate cancer. JCO Precision Oncology, 3 (3). pp. 1-18. ISSN 2473-4284

Webb, Martyn, Manley, Kate, Olivan, Mireia, Guldvik, Ingrid, Palczynska, Malgorzata, Hurst, Rachel, Connell, Shea P, Mills, Ian, Brewer, Daniel, Mills, Robert, Cooper, Colin and Clark, Jeremy (2019) Methodology for the at-home collection of urine samples for prostate cancer detection. Biotechniques, 68 (2). pp. 65-71. ISSN 0736-6205

Luca, Bogdan-Alexandru, Brewer, Daniel S., Edwards, Dylan R., Edward, Sandra, Whitaker, Hayley C., Merson, Sue, Denis, Nening, Cooper, Rosalin A., Hazell, Steven, Warren, Anne Y., Eeles, Rosalind, Lynch, Andy G., Ross-Adams, Helen, Lamb, Alastair D., Neal, David E., Sethia, Krishna, Mills, Robert D, Ball, Richard Y., Curley, Helen, Clark, Jeremy, Moulton, Vincent and Cooper, Colin S. and The CancerMap Group (2018) DESNT: a poor prognosis category of human prostate cancer. European Urology Focus, 4 (6). pp. 842-850. ISSN 2405-4569

Zhao, Fang, Olkhov-Mitsel, Ekaterina, Kamdar, Shivani, Jeyapala, Renu, Garcia, Julia, Hurst, Rachel, Yazbek Hanna, Marcelino, Mills, Robert, Tuzova, Alexandra, O'Reilly, Eve, Kelly, Sarah, Cooper, Colin, Brewer, Daniel, Perry, Antoinette, Clark, Jeremy, Fleshner, Neil and Bapat, Bharati (2018) A urine based DNA methylation Assay, ProCUrE, to identify clinically significant prostate cancer. Clinical Epigenetics, 10. ISSN 1868-7075

Wedge, David C., Gundem, Gunes, Mitchell, Thomas, Woodcock, Dan J., Martincorena, Inigo, Ghori, Mohammed, Zamora, Jorge, Butler, Adam, Whitaker, Hayley, Kote-Jarai, Zsofia, Alexandrov, Ludmil B., Van Loo, Peter, Massie, Charlie E., Dentro, Stefan, Warren, Anne Y., Verrill, Clare, Berney, Dan M., Dennis, Nening, Merson, Sue, Hawkins, Steve, Howat, William, Lu, Yong-Jie, Lambert, Adam, Kay, Jonathan, Kremeyer, Barbara, Karaszi, Katalin, Luxton, Hayley, Camacho, Niedzica, Marsden, Luke, Edwards, Sandra, Matthews, Lucy, Bo, Valeria, Leongamornlert, Daniel, McLaren, Stuart, Ng, Anthony, Yu, Yongwei, Zhang, Hongwei, Dadaev, Tokhir, Thomas, Sarah, Easton, Douglas F., Ahmed, Mahbubl, Bancroft, Elizabeth, Fisher, Cyril, Livni, Naomi, Nicol, David, Tavaré, Simon, Gill, Pelvender, Greenman, Christopher, Khoo, Vincent, Van As, Nicholas, Kumar, Pardeep, Ogden, Christopher, Cahill, Declan, Thompson, Alan, Mayer, Erik, Rowe, Edward, Dudderidge, Tim, Gnanapragasam, Vincent, Shah, Nimish C., Raine, Keiran, Jones, David, Menzies, Andrew, Stebbings, Lucy, Teague, Jon, Hazell, Steven, Corbishley, Cathy, de Bono, Johann, Attard, Gerhardt, Isaacs, William, Visakorpi, Tapio, Fraser, Michael, Boutros, Paul C., Bristow, Robert G., Workman, Paul, Sander, Chris, Hamdy, Freddie C., Futreal, Andrew, McDermott, Ultan, Al-Lazikani, Bissan, Lynch, Andrew G., Bova, G. Steven, Foster, Christopher S., Brewer, Daniel S., Neal, David E., Cooper, Colin S. and Eeles, Rosalind A. (2018) Sequencing of prostate cancers identifies new cancer genes, routes of progression and drug targets. Nature Genetics, 50. 682–692. ISSN 1061-4036

Camacho, Niedzica, Van Loo, Peter, Edwards, Sandra, Kay, Jonathan, Matthews, Lucy, Haase, Kerstin, Clark, Jeremy, Dennis, Nening, Thomas, Sarah, Kremeyer, Barbara, Zamora, Jorge, Butler, Adam P., Gundem, Gunes, Merson, Sue, Luxton, Hayley, Hawkins, Steve, Ghori, Mohammed, Marsden, Luke, Lambert, Adam, Karaszi, Katalin, Pelvender, Gill, Massie, Charlie, Kote-Jarai, ZSofia, Raine, Keiran, Jones, David, Howat, William, Hazell, Steven, Livni, Naomi, Fisher, Cyril, Ogden, Christopher, Kumar, Pardeep, Thompson, Alan, Nicol, David, Mayer, Erik, Dudderidge, Tim, Yu, Yongwei, Zhang, Hongwei, Shah, Nimish, Gnanapragasam, Vincent, Isaacs, William, Visakorpi, Tapio, Hamdy, Freddie, Berney, Dan, Verrill, Clare, Warren, Anne, Wedge, David, Lynch, Andrew, Foster, Christopher, Lu, Yong Jie, Bova, G. Steven, Whitaker, Hayley, McDermott, Ultan, Neal, David, Eeles, Rosalind, Cooper, Colin and Brewer, Daniel (2017) Appraising the relevance of DNA copy number loss and gain in prostate cancer using whole genome DNA sequence data. PLoS Genetics, 13 (9). ISSN 1553-7390

Behjati, Sam, Gundem, Gunes, Wedge, David C., Roberts, Nicola D., Tarpey, Patrick S., Cooke, Susanna L., Van Loo, Peter, Alexandrov, Ludmil B., Ramakrishna, Manasa, Davies, Helen, Nik-Zainal, Serena, Hardy, Claire, Latimer, Calli, Raine, Keiran M., Stebbings, Lucy, Menzies, Andy, Jones, David, Shepherd, Rebecca, Butler, Adam P., Teague, Jon W., Jorgensen, Mette, Khatri, Bhavisha, Pillay, Nischalan, Shlien, Adam, Futreal, P. Andrew, Badie, Christophe, Cooper, Colin S., Eeles, Rosalind A., Easton, Douglas, Foster, Christopher, Neal, David E., Brewer, Daniel S., Hamdy, Freddie, Lu, Yong-Jie, Lynch, Andrew G., Massi, Charlie E., Ng, Anthony, Whitaker, Hayley C., Yu, Yongwei, Zhang, Hongwei, Bancroft, Elizabeth, Berney, Dan, Camacho, Niedzica, Corbishley, Cathy, Dadaev, Tokhir, Dennis, Nening, Dudderidge, Tim, Edwards, Sandra, Fisher, Cyril, Ghori, Jilur, Gnanapragasam, Vincent J., Greenman, Christopher, Hawkins, Steve, Hazell, Steven, Howat, Will, Karaszi, Katalin, Kay, Jonathan, Kote-Jarai, Zsofia, Kremeyer, Barbara, Kumar, Pardeep, Lambert, Adam, Leongamornlert, Daniel, Livni, Naomi, Luxton, Hayley, Matthews, Lucy, Mayer, Erik, Merson, Susan, Nicol, David, Ogden, Christopher, O'Meara, Sarah, Pelvender, Gill, Shah, Nimish C., Tavare, Simon, Thomas, Sarah, Thompson, Alan, Verrill, Claire, Warren, Anne, Zamora, Jorge, McDermott, Ultan, Bova, G. Steven, Richardson, Andrea L., Flanagan, Adrienne M., Stratton, Michael R. and Campbell, Peter J. (2016) Mutational signatures of ionizing radiation in second malignancies. Nature Communications, 7. ISSN 2041-1723

Cooper, Colin S., Clark, Jeremy, Brewer, Daniel S. and Edwards, Dylan R. (2016) Prostate single nucleotide polymorphism provides a crucial clue to cancer aggression in active surveillance patients. European Urology, 69 (2). pp. 229-230. ISSN 0302-2838

Gundem, Gunes, Van Loo, Peter, Kremeyer, Barbara, Alexandrov, Ludmil B., Tubio, Jose M. C., Papaemmanuil, Elli, Brewer, Daniel, Kallio, Heini, Högnäs, Högnäs, Annala, Matti, Kivinummi, Kati, Goody, Victoria, Latimer, Calli, O'Meara, Sarah, Dawson, Kevin, Isaacs, William, Emmert-Buck, Michael R., Nykter, Matti, Foster, Christopher S., Kote-Jarai, Zsofia, Easton, Douglas F., Whitaker, Hayley C., Neal, David E., Cooper, Colin S., Eeles, Rosalind A., Visakorpi, Tapio, Campbell, Peter, McDermott, Ultan, Wedge, David C. and Bova, G. Steven and ICGC Prostate UK Group* (2015) The evolutionary history of lethal metastatic prostate cancer. Nature, 520 (7547). 353–357. ISSN 1476-4687

Massie, Charlie E., Spiteri, Inmaculada, Ross-Adams, Helen, Luxton, Hayley J., Kay, Jonathan, Whitaker, Hayley C., Dunning, Mark J., Lamb, Alastair D., Ramos-Montoya, Antonio, Brewer, Daniel, Cooper, Colin, Eeles, Rosalind A., Warren, Anne Y., Tavaré, Simon, Neal, David E. and Lynch, Andy G. (2015) HES5 silencing is an early and recurrent change in prostate tumourigenesis. Endocrine-Related Cancer (ERC), 22 (2). pp. 131-144. ISSN 1351-0088

Cooper, Colin S., Eeles, Rosalind A., Wedge, David C., Van Loo, Peter, Gundem, Gunes, Alexandrov, Ludmil B., Kreymer, Barbara, Butler, Adam, Lynch, Andrew, Edwards, Sandra E., Camacho, Niedzica, Massie, Charlie E., Kote-Jarai, Zsofia, Dennis, Nening, Merson, Sue, Leongamornlert, Daniel A., Zamora, Jorge, Kay, Jonathan, Luxton, Hayley J., Corbishley, Cathy, Thomas, Sarah, Nik-Zainal, Serena, Ramakrishna, Manasa, O'Meara, Sarah, Matthews, Lucy, Clark, Jeremy, Hurst, Rachel, Mithen, Richard, Bristow, Robert G., Boutros, Paul C., Fraser, Michael, Cooke, Susanna, Raine, Keiran, Jones, David, Menzies, Andrew, Stebbings, Lucy, Hinton, Jon, Teague, Jon, McLaren, Stuart, Mudie, Laura, Hardy, Claire, Anderson, Elizabeth, Joseph, Olivia, Goody, Victoria, Robinson, Ben, Maddison, Mark, Gamble, Stephen J., Greenman, Christopher, Berney, Dan, Hazell, Steven, Livni, Naomi, Fisher, Cyril, Ogden, Christopher, Kumar, Pardeep, Thompson, Alan, Woodhouse, Christopher J., Nicol, David, Mayer, Erik, Dudderidge, Tim, Shah, Nimish, Gnanapragasam, Vincent, Voet, Thierry, Campbell, Peter, Futreal, P. Andrew, Easton, Douglas F., Warren, Anne Y., Foster, Christopher S., Stratton, Michael R., Whitaker, Hayley C., McDermott, Ultan, Brewer, Daniel S. and Neal, David E. and the ICGC Prostate Group (2015) Analysis of the genetic phylogeny of multifocal prostate cancer identifies multiple independent clonal expansions in neoplastic and morphologically normal prostate tissue. Nature Genetics, 47. 367–372. ISSN 1061-4036

Manson-Bahr, David, Ball, Richard, Gundem, Gunes, Mills, Robert, Rochester, Mark, Goody, Victoria, O'Meara, Sarah, Flather, Marcus, Keeling, Matthew, Yazbek Hanna, Marcelino, Hurst, Rachel, Curley, Helen, Clark, Jeremy, Brewer, Daniel, Mcdermott, Ultan and Cooper, Colin (2015) Mutation detection in formalin-fixed prostate cancer biopsies taken at the time of diagnosis using next generation DNA sequencing. Journal of Clinical Pathology, 68. pp. 212-217. ISSN 0021-9746

Wu, Ping, Walker, Brian A, Broyl, Annemiek, Kaiser, Martin, Johnson, David C, Kuiper, Rowan, van Duin, Mark, Gregory, Walter M, Davies, Faith E, Brewer, Daniel, Hose, Dirk, Sonneveld, Pieter and Morgan, Gareth J (2015) A gene expression based predictor for high risk myeloma treated with intensive therapy and autologous stem cell rescue. Leukemia & Lymphoma, 56 (3). pp. 594-601. ISSN 1042-8194

Zuo, Jie, Brewer, Daniel, Arlt, Volker M, Cooper, Colin and Phillips, David H (2014) Benzo[a]pyrene-induced DNA adducts and gene expression profiles in target and non-target organs for carcinogenesis in mice. BMC Genomics, 15. ISSN 1471-2164

Ju, Young Seok, Alexandrov, Ludmil B., Gerstung, Moritz, Martincorena, Inigo, Nik-Zainal, Serena, Ramakrishna, Manasa, Davies, Helen R., Papaemmanuil, Elli, Gundem, Gunes, Shlien, Adam, Bolli, Niccolo, Behjati, Sam, Tarpey, Patrick S., Nangalia, Jyoti, Massie, Charles E., Butler, Adam P., Teague, Jon W., Vassiliou, George S., Green, Anthony R., Du, Ming-Qing, Unnikrishnan, Ashwin, Pimanda, John E., Teh, Bin Tean, Munshi, Nikhil, Greaves, Mel, Vyas, Paresh, El-Naggar, Adel K., Santarius, Tom, Collins, V. Peter, Grundy, Richard, Taylor, Jack A., Hayes, D. Neil, Malkin, David, Foster, Christopher S., Warren, Anne Y., Whitaker, Hayley C., Brewer, Daniel, Eeles, Rosalind, Cooper, Colin, Neal, David, Visakorpi, Tapio, Isaacs, William B., Bova, G. Steven, Flanagan, Adrienne M., Futreal, P. Andrew, Lynch, Andy G., Chinnery, Patrick F., McDermott, Ultan, Stratton, Michael R. and Campbell, Peter J. and ICGC Breast Cancer Group (2014) Origins and functional consequences of somatic mitochondrial DNA mutations in human cancer. eLife, 3. ISSN 2050-084X

Tubio, Jose M. C., Li, Yilong, Ju, Young Seok, Martincorena, Inigo, Cooke, Susanna L., Tojo, Marta, Gundem, Gunes, Pipinikas, Christodoulos P., Zamora, Jorge, Raine, Keiran, Menzies, Andrew, Roman-Garcia, Pablo, Fullam, Anthony, Gerstung, Moritz, Shlien, Adam, Tarpey, Patrick S., Papaemmanuil, Elli, Knappskog, Stian, Van Loo, Peter, Ramakrishna, Manasa, Davies, Helen R., Marshall, John, Wedge, David C., Teague, Jon W., Butler, Adam P., Nik-Zainal, Serena, Alexandrov, Ludmil, Behjati, Sam, Yates, Lucy R., Bolli, Niccolo, Mudie, Laura, Hardy, Claire, Martin, Sancha, McLaren, Stuart, O'Meara, Sarah, Anderson, Elizabeth, Maddison, Mark, Gamble, Stephen, Foster, Christopher, Warren, Anne Y., Whitaker, Hayley, Brewer, Daniel, Eeles, Rosalind, Cooper, Colin, Neal, David, Lynch, Andy G., Visakorpi, Tapio, Isaacs, William B., van't Veer, Laura and Caldas, Carlos and ICGC Breast Cancer Group (2014) Mobile DNA in cancer. Extensive transduction of nonrepetitive DNA mediated by L1 retrotransposition in cancer genomes. Science, 345 (6196). ISSN 0036-8075

Merson, S, Yang, Z H, Brewer, D, Olmos, D, Eichholz, A, McCarthy, F, Fisher, G, Kovacs, G, Berney, D M, Foster, C S, Møller, H, Scardino, P, Cuzick, J, Cooper, C S and Clark, Jeremy and Transatlantic Prostate Group (2014) Focal amplification of the androgen receptor gene in hormone-naive human prostate cancer. British Journal of Cancer, 110 (6). pp. 1655-1662. ISSN 0007-0920

Wu, Ping, Agnelli, Luca, Walker, Brian A, Todoerti, Katia, Lionetti, Marta, Johnson, David C, Kaiser, Martin, Mirabella, Fabio, Wardell, Christopher, Gregory, Walter M, Davies, Faith E, Brewer, Daniel, Neri, Antonino and Morgan, Gareth J (2013) Improved risk stratification in myeloma using a microRNA-based classifier. British Journal of Haematology, 162 (3). pp. 348-59. ISSN 0007-1048

Cuzick, J, Yang, Z H, Fisher, G, Tikishvili, E, Stone, S, Lanchbury, J S, Camacho, N, Merson, S, Brewer, D, Cooper, C S, Clark, J, Berney, D M, Møller, H, Scardino, P and Sangale, Z and Transatlantic Prostate Group (2013) Prognostic value of PTEN loss in men with conservatively managed localised prostate cancer. British Journal of Cancer, 108 (12). pp. 2582-2589. ISSN 0007-0920

Olmos, David, Brewer, Daniel, Clark, Jeremy, Danila, Daniel C, Parker, Chris, Attard, Gerhardt, Fleisher, Martin, Reid, Alison Hm, Castro, Elena, Sandhu, Shahneen K, Barwell, Lorraine, Oommen, Nikhil Babu, Carreira, Suzanne, Drake, Charles G, Jones, Robert, Cooper, Colin S, Scher, Howard I and de Bono, Johann S (2012) Prognostic value of blood mRNA expression signatures in castration-resistant prostate cancer:a prospective, two-stage study. The Lancet Oncology, 13 (11). pp. 1114-24. ISSN 1470-2045

Reid, Alison H. M., Attard, Gerhardt, Brewer, Daniel, Miranda, Susana, Riisnaes, Ruth, Clark, Jeremy, Hylands, Lucy, Merson, Sue, Vergis, Roy, Jameson, Charles, Høyer, Søren, Sørensen, Karina Dalsgaard, Borre, Michael, Jones, Chris, de Bono, Johann S. and Cooper, Colin S. (2012) Novel, gross chromosomal alterations involving PTEN cooperate with allelic loss in prostate cancer. Modern Pathology, 25 (6). pp. 902-10. ISSN 1530-0285

Wu, Ping, Walker, Brian A, Brewer, Daniel, Gregory, Walter M, Ashcroft, John, Ross, Fiona M, Jackson, Graham H, Child, Anthony J, Davies, Faith E and Morgan, Gareth J (2011) A gene expression-based predictor for myeloma patients at high risk of developing bone disease on bisphosphonate treatment. Clinical Cancer Research, 17 (19). pp. 6347-55. ISSN 1078-0432

Bee, Alix, Brewer, Daniel, Beesley, Carol, Dodson, Andrew, Forootan, Shiva, Dickinson, Timothy, Gerard, Patricia, Lane, Brian, Yao, Sheng, Cooper, Colin S., Djamgoz, Mustafa B. A., Gosden, Christine M., Ke, Youqiang and Foster, Christopher S. (2011) siRNA knockdown of ribosomal protein gene RPL19 abrogates the aggressive phenotype of human prostate cancer. PLoS One, 6 (7). ISSN 1932-6203

Suwaki, Natsuko, Vanhecke, Elsa, Atkins, Katelyn M, Graf, Manuela, Swabey, Katherine, Huang, Paul, Schraml, Peter, Moch, Holger, Cassidy, Amy Mulick, Brewer, Daniel, Al-Lazikani, Bissan, Workman, Paul, De-Bono, Johann, Kaye, Stan B, Larkin, James, Gore, Martin E, Sawyers, Charles L, Nelson, Peter, Beer, Tomasz M, Geng, Hao, Gao, Lina, Qian, David Z, Alumkal, Joshi J, Thomas, Gary and Thomas, George V (2011) A HIF-regulated VHL-PTP1B-Src signaling axis identifies a therapeutic target in renal cell carcinoma. Science Translational Medicine, 3 (85). 85ra47. ISSN 1946-6242

Yao, Sheng, Bee, Alix, Brewer, Daniel, Dodson, Andrew, Beesley, Carol, Ke, Youqiang, Ambroisine, Laurence, Fisher, Gabrielle, Møller, Heinrich, Dickinson, Tim, Gerard, Patricia, Lian, Lu-Yu, Risk, Janet, Lane, Brian, Smith, Paul, Reuter, Victor, Berney, Daniel, Gosden, Christine, Scardino, Peter, Cuzick, Jack, Djamgoz, Mustafa B A, Cooper, Colin and Foster, Christopher S (2010) PRKC-ζ expression promotes the aggressive phenotype of human prostate cancer cells and is a novel target for therapeutic intervention. Genes & Cancer, 1 (5). pp. 444-464. ISSN 1947-6027

Reid, A H M, Attard, G, Ambroisine, L, Fisher, G, Kovacs, G, Brewer, D, Clark, J, Flohr, P, Edwards, S, Berney, D M, Foster, C S, Fletcher, A, Gerald, W L, Møller, H, Reuter, V E, Scardino, P T, Cuzick, J, de Bono, J S and Cooper, C S and Transatlantic Prostate Group (2010) Molecular characterisation of ERG, ETV1 and PTEN gene loci identifies patients at low and high risk of death from prostate cancer. British Journal of Cancer, 102 (4). pp. 678-684. ISSN 0007-0920

Santarius, Thomas, Shipley, Janet, Brewer, Daniel, Stratton, Michael R. and Cooper, Colin S. (2010) A census of amplified and overexpressed human cancer genes. Nature Reviews, 10 (1). pp. 59-64.

Jhavar, Sameer, Brewer, Daniel, Edwards, Sandra, Kote-Jarai, Zsofia, Attard, Gerhardt, Clark, Jeremy, Flohr, Penny, Christmas, Timothy, Thompson, Alan, Parker, Matthew, Shepherd, Christopher, Stenman, Ulf-Hakan, Marchbank, Tania, Playford, Raymond J, Woodhouse, Christopher, Ogden, Christopher, Fisher, Cyril, Kovacs, Gyula, Corbishley, Cathy, Jameson, Charles, Norman, Andy, De-Bono, Johann, Bjartell, Anders, Eeles, Rosalind and Cooper, Colin S (2009) Integration of ERG gene mapping and gene-expression profiling identifies distinct categories of human prostate cancer. BJU International, 103 (9). pp. 1256-69. ISSN 1464-4096

Hockley, Sarah L., Mathijs, Karen, Staal, Yvonne C. M., Brewer, Daniel, Giddings, Ian, van Delft, Joost H. M. and Phillips, David H. (2009) Interlaboratory and interplatform comparison of microarray gene expression analysis of HepG2 cells exposed to benzo(a)pyrene. OMICS, 13 (2). pp. 115-25. ISSN 1557-8100

Barenco, M, Papouli, E, Shah, S, Brewer, D, Miller, C J and Hubank, M (2009) rHVDM: an R package to predict the activity and targets of a transcription factor. Bioinformatics, 25 (3). pp. 419-420. ISSN 1460-2059

Barenco, Martino, Brewer, Daniel, Papouli, Efterpi, Tomescu, Daniela, Callard, Robin, Stark, Jaroslav and Hubank, Michael (2009) Dissection of a complex transcriptional response using genome-wide transcriptional modelling. Molecular Systems Biology, 5. p. 327. ISSN 1744-4292

Jhavar, S, Bartlett, J, Kovacs, G, Corbishley, C, Dearnaley, D, Eeles, R, Khoo, V, Huddart, R, Horwich, A, Thompson, A, Norman, A, Brewer, D, Cooper, C S and Parker, C (2009) Biopsy tissue microarray study of Ki-67 expression in untreated, localized prostate cancer managed by active surveillance. Prostate Cancer and Prostatic Diseases, 12 (2). pp. 143-147. ISSN 1476-5608

Knight, J F, Shepherd, C J, Rizzo, S, Brewer, D, Jhavar, S, Dodson, A R, Cooper, C S, Eeles, R, Falconer, A, Kovacs, G, Garrett, M D, Norman, A R, Shipley, J and Hudson, D L (2008) TEAD1 and c-Cbl are novel prostate basal cell markers that correlate with poor clinical outcome in prostate cancer. British Journal of Cancer, 99 (11). pp. 1849-1858. ISSN 0007-0920

Shepherd, Christopher J, Rizzo, Siân, Ledaki, Ioanna, Davies, Melissa, Brewer, Daniel, Attard, Gerhardt, de Bono, Johann and Hudson, David L (2008) Expression profiling of CD133+ and CD133- epithelial cells from human prostate. The Prostate, 68 (9). pp. 1007-24. ISSN 0270-4137

Brewer, Daniel, Barenco, Martino, Callard, Robin, Hubank, Michael and Stark, Jaroslav (2008) Fitting ordinary differential equations to short time course data. Philosophical Transactions of the Royal Society A: Mathematical, Physical and Engineering Sciences, 366 (1865). pp. 519-544. ISSN 1364-503X

Jhavar, Sameer, Reid, Alison, Clark, Jeremy, Kote-Jarai, Zsofia, Christmas, Timothy, Thompson, Alan, Woodhouse, Christopher, Ogden, Christopher, Fisher, Cyril, Corbishley, Cathy, De-Bono, Johann, Eeles, Rosalind, Brewer, Daniel and Cooper, Colin (2008) Detection of TMPRSS2-ERG translocations in human prostate cancer by expression profiling using GeneChip Human Exon 1.0 ST arrays. Journal of Molecular Diagnostics, 10 (1). pp. 50-7. ISSN 1525-1578

Hockley, Sarah L, Arlt, Volker M, Brewer, Daniel, Te Poele, Robert, Workman, Paul, Giddings, Ian and Phillips, David H (2007) AHR- and DNA-damage-mediated gene expression responses induced by benzo(a)pyrene in human cell lines. Chemical Research in Toxicology, 20 (12). pp. 1797-810. ISSN 0893-228X

Hockley, Sarah L, Arlt, Volker M, Brewer, Daniel, Giddings, Ian and Phillips, David H (2006) Time- and concentration-dependent changes in gene expression induced by benzo(a)pyrene in two human cell lines, MCF-7 and HepG2. BMC Genomics, 7. ISSN 1471-2164

Barenco, Martino, Stark, Jaroslav, Brewer, Daniel, Tomescu, Daniela, Callard, Robin and Hubank, Michael (2006) Correction of scaling mismatches in oligonucleotide microarray data. BMC Bioinformatics, 7. ISSN 1471-2105

Barenco, Martino, Tomescu, Daniela, Brewer, Daniel, Callard, Robin, Stark, Jaroslav and Hubank, Michael (2006) Ranked prediction of p53 targets using hidden variable dynamic modeling. Genome Biology, 7 (3). ISSN 1474-760X

Stark, J, Brewer, D, Barenco, M, Tomescu, D, Callard, R and Hubank, M (2003) Reconstructing gene networks: what are the limits? Biochemical Society Transactions, 31 (6). pp. 1519-1525. ISSN 0300-5127

Book Section

Gihawi, Abraham, Cardenas, Ryan, Hurst, Rachel and Brewer, Daniel S. (2023) Quality Control in Metagenomics Data. In: Metagenomic Data Analysis. Methods in Molecular Biology . Springer, New York, pp. 21-54. ISBN 978-1-0716-3071-6

Barenco, Martino, Brewer, Daniel, Callard, Robin and Hubank, Michael (2011) Modelling Transcription Factor Activity. In: Handbook of Statistical Systems Biology. UNSPECIFIED.

Conference or Workshop Item

Cardenas, Ryan, Prinsley, Peter, Philpott, Carl, Bhutta, Mahmood F., Wilson, Emma, Brewer, Daniel and Jennings, Barbara (2024) Loss of function variants and locus heterogeneity in familial cholesteatoma. In: 56th European Society of Human Genetics (ESHG) Conference, 2023-06-10 - 2023-06-13.