MEDICC2: whole-genome doubling aware copy-number phylogenies for cancer evolution
Kaufmann, Tom L, Petkovic, Marina, Watkins, Thomas B K, Colliver, Emma C, Laskina, Sofya, Thapa, Nisha, Minussi, Darlan C, Navin, Nicholas, Swanton, Charles, Van Loo, Peter, Haase, Kerstin, Tarabichi, Maxime, Schwarz, Roland F
Published in Genome Biology (14.11.2022)
Published in Genome Biology (14.11.2022)
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Refphase: Multi-sample phasing reveals haplotype-specific copy number heterogeneity
Watkins, Thomas B K, Colliver, Emma C, Huska, Matthew R, Kaufmann, Tom L, Lim, Emilia L, Duncan, Cody B, Haase, Kerstin, Van Loo, Peter, Swanton, Charles, McGranahan, Nicholas, Schwarz, Roland F
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Published in PLoS computational biology (23.10.2023)
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SMITH: spatially constrained stochastic model for simulation of intra-tumour heterogeneity
Streck, Adam, Kaufmann, Tom L, Schwarz, Roland F
Published in Bioinformatics (Oxford, England) (01.03.2023)
Published in Bioinformatics (Oxford, England) (01.03.2023)
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Antibodies against endogenous retroviruses promote lung cancer immunotherapy
Ng, Kevin W, Boumelha, Jesse, Enfield, Katey S S, Almagro, Jorge, Cha, Hongui, Pich, Oriol, Karasaki, Takahiro, Moore, David A, Salgado, Roberto, Sivakumar, Monica, Young, George, Molina-Arcas, Miriam, de Carné Trécesson, Sophie, Anastasiou, Panayiotis, Fendler, Annika, Au, Lewis, Shepherd, Scott T C, Martínez-Ruiz, Carlos, Puttick, Clare, Black, James R M, Watkins, Thomas B K, Kim, Hyemin, Shim, Seohee, Faulkner, Nikhil, Attig, Jan, Veeriah, Selvaraju, Magno, Neil, Ward, Sophia, Frankell, Alexander M, Al Bakir, Maise, Lim, Emilia L, Hill, Mark S, Wilson, Gareth A, Cook, Daniel E, Birkbak, Nicolai J, Behrens, Axel, Yousaf, Nadia, Popat, Sanjay, Hackshaw, Allan, Hiley, Crispin T, Litchfield, Kevin, McGranahan, Nicholas, Jamal-Hanjani, Mariam, Larkin, James, Lee, Se-Hoon, Turajlic, Samra, Swanton, Charles, Downward, Julian, Kassiotis, George
Published in Nature (London) (20.04.2023)
Published in Nature (London) (20.04.2023)
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Lung adenocarcinoma promotion by air pollutants
Hill, William, Lim, Emilia L, Weeden, Clare E, Lee, Claudia, Augustine, Marcellus, Chen, Kezhong, Kuan, Feng-Che, Marongiu, Fabio, Evans, Jr, Edward J, Moore, David A, Rodrigues, Felipe S, Pich, Oriol, Bakker, Bjorn, Cha, Hongui, Myers, Renelle, van Maldegem, Febe, Boumelha, Jesse, Veeriah, Selvaraju, Rowan, Andrew, Naceur-Lombardelli, Cristina, Karasaki, Takahiro, Sivakumar, Monica, De, Swapnanil, Caswell, Deborah R, Nagano, Ai, Black, James R M, Martínez-Ruiz, Carlos, Ryu, Min Hyung, Huff, Ryan D, Li, Shijia, Favé, Marie-Julie, Magness, Alastair, Suárez-Bonnet, Alejandro, Priestnall, Simon L, Lüchtenborg, Margreet, Lavelle, Katrina, Pethick, Joanna, Hardy, Steven, McRonald, Fiona E, Lin, Meng-Hung, Troccoli, Clara I, Ghosh, Moumita, Miller, York E, Merrick, Daniel T, Keith, Robert L, Al Bakir, Maise, Bailey, Chris, Hill, Mark S, Saal, Lao H, Chen, Yilun, George, Anthony M, Abbosh, Christopher, Kanu, Nnennaya, Lee, Se-Hoon, McGranahan, Nicholas, Berg, Christine D, Sasieni, Peter, Houlston, Richard, Turnbull, Clare, Lam, Stephen, Awadalla, Philip, Grönroos, Eva, Downward, Julian, Jacks, Tyler, Carlsten, Christopher, Malanchi, Ilaria, Hackshaw, Allan, Litchfield, Kevin, DeGregori, James, Jamal-Hanjani, Mariam, Swanton, Charles
Published in Nature (London) (06.04.2023)
Published in Nature (London) (06.04.2023)
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Tracking early lung cancer metastatic dissemination in TRACERx using ctDNA
Abbosh, Christopher, Frankell, Alexander M, Harrison, Thomas, Kisistok, Judit, Garnett, Aaron, Johnson, Laura, Veeriah, Selvaraju, Moreau, Mike, Chesh, Adrian, Chaunzwa, Tafadzwa L, Weiss, Jakob, Schroeder, Morgan R, Ward, Sophia, Grigoriadis, Kristiana, Shahpurwalla, Aamir, Litchfield, Kevin, Puttick, Clare, Biswas, Dhruva, Karasaki, Takahiro, Black, James R M, Martínez-Ruiz, Carlos, Bakir, Maise Al, Pich, Oriol, Watkins, Thomas B K, Lim, Emilia L, Huebner, Ariana, Moore, David A, Godin-Heymann, Nadia, L'Hernault, Anne, Bye, Hannah, Odell, Aaron, Roberts, Paula, Gomes, Fabio, Patel, Akshay J, Manzano, Elizabeth, Hiley, Crispin T, Carey, Nicolas, Riley, Joan, Cook, Daniel E, Hodgson, Darren, Stetson, Daniel, Barrett, J Carl, Kortlever, Roderik M, Evan, Gerard I, Hackshaw, Allan, Daber, Robert D, Shaw, Jacqui A, Aerts, Hugo J W L, Licon, Abel, Stahl, Josh, Jamal-Hanjani, Mariam, Birkbak, Nicolai J, McGranahan, Nicholas, Swanton, Charles
Published in Nature (London) (20.04.2023)
Published in Nature (London) (20.04.2023)
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The evolution of lung cancer and impact of subclonal selection in TRACERx
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
Published in Nature (London) (20.04.2023)
Published in Nature (London) (20.04.2023)
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The evolution of non-small cell lung cancer metastases in TRACERx
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
Published in Nature (London) (20.04.2023)
Published in Nature (London) (20.04.2023)
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Genomic-transcriptomic evolution in lung cancer and metastasis
Martínez-Ruiz, Carlos, Black, James R M, Puttick, Clare, Hill, Mark S, Demeulemeester, Jonas, Larose Cadieux, Elizabeth, Thol, Kerstin, Jones, Thomas P, Veeriah, Selvaraju, Naceur-Lombardelli, Cristina, Toncheva, Antonia, Prymas, Paulina, Rowan, Andrew, Ward, Sophia, Cubitt, Laura, Athanasopoulou, Foteini, Pich, Oriol, Karasaki, Takahiro, Moore, David A, Salgado, Roberto, Colliver, Emma, Castignani, Carla, Dietzen, Michelle, Huebner, Ariana, Al Bakir, Maise, Tanić, Miljana, Watkins, Thomas B K, Lim, Emilia L, Al-Rashed, Ali M, Lang, Danny, Clements, James, Cook, Daniel E, Rosenthal, Rachel, Wilson, Gareth A, Frankell, Alexander M, de Carné Trécesson, Sophie, East, Philip, Kanu, Nnennaya, Litchfield, Kevin, Birkbak, Nicolai J, Hackshaw, Allan, Beck, Stephan, Van Loo, Peter, Jamal-Hanjani, Mariam, Swanton, Charles, McGranahan, Nicholas
Published in Nature (London) (20.04.2023)
Published in Nature (London) (20.04.2023)
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Evolutionary characterization of lung adenocarcinoma morphology in TRACERx
Karasaki, Takahiro, Moore, David A, Veeriah, Selvaraju, Naceur-Lombardelli, Cristina, Toncheva, Antonia, Magno, Neil, Ward, Sophia, Bakir, Maise Al, Watkins, Thomas B K, Grigoriadis, Kristiana, Huebner, Ariana, Hill, Mark S, Frankell, Alexander M, Abbosh, Christopher, Puttick, Clare, Zhai, Haoran, Gimeno-Valiente, Francisco, Saghafinia, Sadegh, Kanu, Nnennaya, Dietzen, Michelle, Pich, Oriol, Lim, Emilia L, Martínez-Ruiz, Carlos, Black, James R M, 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
Published in Nature medicine (12.04.2023)
Published in Nature medicine (12.04.2023)
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Using DNA sequencing data to quantify T cell fraction and therapy response
Bentham, Robert, Litchfield, Kevin, Watkins, Thomas B K, Lim, Emilia L, Rosenthal, Rachel, Martínez-Ruiz, Carlos, Hiley, Crispin T, Bakir, Maise Al, Salgado, Roberto, Moore, David A, Jamal-Hanjani, Mariam, Swanton, Charles, McGranahan, Nicholas
Published in Nature (London) (23.09.2021)
Published in Nature (London) (23.09.2021)
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Body composition and lung cancer-associated cachexia in TRACERx
Al-Sawaf, Othman, Weiss, Jakob, Skrzypski, Marcin, Lam, Jie Min, Karasaki, Takahiro, Zambrana, Francisco, Kidd, Andrew C, Frankell, Alexander M, Watkins, Thomas B K, Martínez-Ruiz, Carlos, Puttick, Clare, Black, James R M, Huebner, Ariana, Bakir, Maise Al, Sokač, Mateo, Collins, Susie, Veeriah, Selvaraju, Magno, Neil, Naceur-Lombardelli, Cristina, Prymas, Paulina, Toncheva, Antonia, Ward, Sophia, Jayanth, Nick, Salgado, Roberto, Bridge, Christopher P, Christiani, David C, Mak, Raymond H, Bay, Camden, Rosenthal, Michael, Sattar, Naveed, Welsh, Paul, Liu, Ying, Perrimon, Norbert, Popuri, Karteek, Beg, Mirza Faisal, McGranahan, Nicholas, Hackshaw, Allan, Breen, Danna M, O'Rahilly, Stephen, Birkbak, Nicolai J, Aerts, Hugo J W L, Jamal-Hanjani, Mariam, Swanton, Charles
Published in Nature medicine (01.04.2023)
Published in Nature medicine (01.04.2023)
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Author Correction: The evolution of lung cancer and impact of subclonal selection in TRACERx
Dietzen, Michelle, Lim, Emilia L., Ward, Sophia, Veeriah, Selvaraju, Colliver, Emma, Moore, David A., Thol, Kerstin, Salgado, Roberto, Wilson, Gareth A., Martínez-Ruiz, Carlos, Hessey, Sonya, Lee, Claudia, Prymas, Paulina, Toncheva, Antonia, Middleton, Gary, Fennell, Dean A., Forster, Martin D., Lee, Siow Ming, Lim, Eric, Benafif, Sarah, Krebs, Matthew G., Lester, Jason F., Dive, Caroline, Blackhall, Fiona H., Schwarz, Roland F., Birkbak, Nicolai J., Hiley, Crispin T., Van Loo, Peter, Nakas, Apostolos, Tufail, Mohamad, Chowdhry, Mohammed Fiyaz, Scotland, Molly, Rathinam, Sridhar, Wilson, Claire, Marrone, Domenic, Shaw, Jacqui A., Cheyne, Heather, Richardson, Shirley, Gilbert, Kayleigh, Patel, Akshay J., Lacson, Christer, Djearaman, Madava, Leek, Angela, Novasio, Juliette, Joseph, Leena, Carter, Mathew, Chaturvedi, Anshuman, Priest, Lynsey, Lindsay, Colin R., Rothwell, Dominic G., Aerts, Hugo J. W. L., Szallasi, Zoltan, Kisistok, Judit, Karamani, Angeliki, Campbell, Brittany B., Nye, Emma, Gimeno-Valiente, Francisco, Lowe, Helen L., Rane, Jayant K., Lam, Jie Min, Hartley, John A., Enfield, Katey S. S., Selvaraju, Kayalvizhi, Litchfield, Kevin, Ng, Kevin W., Dijkstra, Krijn, Thakkar, Krupa, Shah, Mansi, Werner Sunderland, Mariana, Escudero, Mickael, Sivakumar, Monica, Pawlik, Piotr, Stone, Richard Kevin, Vendramin, Roberto, Gamble, Samuel, Ung, Seng Kuong Anakin, Barbè, Vittorio, Veiga, Catarina, Royle, Gary, Borg, Elaine, Wilson, James, Taylor, Magali N., Nair, Arjun, Martinoni Hoogenboom, Emilie, Monk, Fleur, Khiroya, Reena, Leslie, Rachel, Zhang, Hanyun, AbdulJabbar, Khalid, Pan, Xiaoxi, Chee, Serena, Ingram, Papawadee, Austin, Silvia, Jordan, Simon, Devaraj, Anand, Chavan, Hema, Kaniu, Daniel, Malima, Mpho, Robinson, Lily, Bilancia, Rocco
Published in Nature (London) (25.07.2024)
Published in Nature (London) (25.07.2024)
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Representation of genomic intratumor heterogeneity in multi-region non-small cell lung cancer patient-derived xenograft models
Hynds, Robert E, Huebner, Ariana, Pearce, David R, Hill, Mark S, Akarca, Ayse U, Moore, David A, Ward, Sophia, Gowers, Kate H C, Karasaki, Takahiro, Al Bakir, Maise, Wilson, Gareth A, Pich, Oriol, Martínez-Ruiz, Carlos, Hossain, A S Md Mukarram, Pearce, Simon P, Sivakumar, Monica, Ben Aissa, Assma, Grönroos, Eva, Chandrasekharan, Deepak, Kolluri, Krishna K, Towns, Rebecca, Wang, Kaiwen, Cook, Daniel E, Bosshard-Carter, Leticia, Naceur-Lombardelli, Cristina, Rowan, Andrew J, Veeriah, Selvaraju, Litchfield, Kevin, Crosbie, Philip A J, Dive, Caroline, Quezada, Sergio A, Janes, Sam M, Jamal-Hanjani, Mariam, Marafioti, Teresa, McGranahan, Nicholas, Swanton, Charles
Published in Nature communications (31.05.2024)
Published in Nature communications (31.05.2024)
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A local human Vδ1 T cell population is associated with survival in nonsmall-cell lung cancer
Wu, Yin, Biswas, Dhruva, Usaite, Ieva, Angelova, Mihaela, Boeing, Stefan, Karasaki, Takahiro, Veeriah, Selvaraju, Czyzewska-Khan, Justyna, Morton, Cienne, Joseph, Magdalene, Hessey, Sonya, Reading, James, Georgiou, Andrew, Al-Bakir, Maise, McGranahan, Nicholas, Jamal-Hanjani, Mariam, Hackshaw, Allan, Quezada, Sergio A, Hayday, Adrian C, Swanton, Charles
Published in Nature cancer (01.06.2022)
Published in Nature cancer (01.06.2022)
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Copy-number dosage regulates telomere maintenance and disease-associated pathways in neuroblastoma
Burkert, Martin, Blanc, Eric, Thiessen, Nina, Weber, Christiane, Toedling, Joern, Monti, Remo, Dombrowe, Victoria M., Stella de Biase, Maria, Kaufmann, Tom L., Haase, Kerstin, Waszak, Sebastian M., Eggert, Angelika, Beule, Dieter, Schulte, Johannes H., Ohler, Uwe, Schwarz, Roland F.
Published in iScience (01.09.2024)
Published in iScience (01.09.2024)
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The artificial intelligence-based model ANORAK improves histopathological grading of lung adenocarcinoma
Pan, Xiaoxi, AbdulJabbar, Khalid, Coelho-Lima, Jose, Grapa, Anca-Ioana, Zhang, Hanyun, Cheung, Alvin Ho Kwan, Baena, Juvenal, Karasaki, Takahiro, Wilson, Claire Rachel, Sereno, Marco, Veeriah, Selvaraju, Aitken, Sarah J, Hackshaw, Allan, Nicholson, Andrew G, Jamal-Hanjani, Mariam, Swanton, Charles, Yuan, Yinyin, Le Quesne, John, Moore, David A
Published in Nature cancer (01.02.2024)
Published in Nature cancer (01.02.2024)
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Refphase: Multi-sample reference phasing reveals haplotype-specific copy number heterogeneity
Watkins, Thomas Bk, Colliver, Emma C, Huska, Matthew R, Kaufmann, Tom L, Lim, Emilia L, Haase, Kerstin, Peter Van Loo, Swanton, Charles, Mcgranahan, Nicholas, Schwarz, Roland F
Published in bioRxiv (17.10.2022)
Published in bioRxiv (17.10.2022)
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