Search Results - "Kaufmann, Tom L"

MEDICC2: whole-genome doubling aware copy-number phylogenies for cancer evolution by 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

“…Aneuploidy, chromosomal instability, somatic copy-number alterations, and whole-genome doubling (WGD) play key roles in cancer evolution and provide…”
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Electrostatic and bending energies predict staggering and splaying in nonmuscle myosin II minifilaments by Kaufmann, Tom L, Schwarz, Ulrich S, Alber, Mark, Vavylonis, Dimitrios

“…Recent experiments with super-resolution live cell microscopy revealed that nonmuscle myosin II minifilaments are much more dynamic than formerly appreciated,…”
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Refphase: Multi-sample phasing reveals haplotype-specific copy number heterogeneity by 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

“…Most computational methods that infer somatic copy number alterations (SCNAs) from bulk sequencing of DNA analyse tumour samples individually. However, the…”
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Improved identification of cancer mutational processes by Kaufmann, Tom L., Schwarz, Roland F.

“…Mutational signatures help to deconvolve the different processes that shape cancer genomes. A new tool now alleviates some of the persistent challenges in the…”
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SMITH: spatially constrained stochastic model for simulation of intra-tumour heterogeneity by Streck, Adam, Kaufmann, Tom L, Schwarz, Roland F

“…Abstract Motivation Simulations of cancer evolution are highly useful to study the effects of selection and mutation rates on cellular fitness. However, most…”
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Antibodies against endogenous retroviruses promote lung cancer immunotherapy by 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

“…B cells are frequently found in the margins of solid tumours as organized follicles in ectopic lymphoid organs called tertiary lymphoid structures (TLS) 1 , 2…”
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MHC Hammer reveals genetic and non-genetic HLA disruption in cancer evolution by Puttick, Clare, Jones, Thomas P., Leung, Michelle M., Galvez-Cancino, Felipe, Liu, Jiali, Varas-Godoy, Manuel, Rowan, Andrew, Pich, Oriol, Martinez-Ruiz, Carlos, Bentham, Robert, Dijkstra, Krijn K., Black, James R. M., Rosenthal, Rachel, Kanu, Nnennaya, Litchfield, Kevin, Salgado, Roberto, Moore, David A., Van Loo, Peter, Jamal-Hanjani, Mariam, Quezada, Sergio A., Swanton, Charles, McGranahan, Nicholas

“…Disruption of the class I human leukocyte antigen (HLA) molecules has important implications for immune evasion and tumor evolution. We developed major…”
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Representation of genomic intratumor heterogeneity in multi-region non-small cell lung cancer patient-derived xenograft models by 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

“…Patient-derived xenograft (PDX) models are widely used in cancer research. To investigate the genomic fidelity of non-small cell lung cancer PDX models, we…”
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A local human Vδ1 T cell population is associated with survival in nonsmall-cell lung cancer by 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

“…Murine tissues harbor signature γδ T cell compartments with profound yet differential impacts on carcinogenesis. Conversely, human tissue-resident γδ cells are…”
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Copy-number dosage regulates telomere maintenance and disease-associated pathways in neuroblastoma by 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.

“…Telomere maintenance in neuroblastoma is linked to poor outcome and caused by either telomerase reverse transcriptase (TERT) activation or through alternative…”
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