Publications by authors named "Thomas Watkins"

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DNA methylation cooperates with genomic alterations during non-small cell lung cancer evolution.
Francisco Gimeno-Valiente, Carla Castignani, Elizabeth Larose Cadieux, Nana E Mensah, Xiaohong Liu, Thomas B K Watkins

Nat Genet· September 2025

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A Guide to Extrachromosomal DNA: Cancer's Dynamic Circular Genome.
Natasha E Weiser, Thomas B K Watkins, Howard Y Chang, Paul S Mischel

Cancer Discov· June 2025

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Learning to estimate sample-specific transcriptional networks for 7,000 tumors.
Caleb N Ellington, Benjamin J Lengerich, Thomas B K Watkins, Jiekun Yang, Abhinav K Adduri

Proc Natl Acad Sci U S A· May 2025

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ImmuneLENS characterizes systemic immune dysregulation in aging and cancer.
Robert Bentham, Thomas P Jones, James R M Black, Carlos Martinez-Ruiz, Michelle Dietzen, Thomas B K Watkins

Nat Genet· March 2025

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Clonal driver neoantigen loss under EGFR TKI and immune selection pressures.
Maise Al Bakir, James L Reading, Samuel Gamble, Rachel Rosenthal, Imran Uddin, Thomas B K Watkins

Nature· March 2025

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Origins and impact of extrachromosomal DNA.
Chris Bailey, Oriol Pich, Kerstin Thol, Thomas B K Watkins, Jens Luebeck

Nature· November 2024

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Author Correction: The evolution of lung cancer and impact of subclonal selection in TRACERx.
Alexander M Frankell, Michelle Dietzen, Maise Al Bakir, Emilia L Lim, Takahiro Karasaki, Thomas B K Watkins

Nature· July 2024

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Mixed responses to targeted therapy driven by chromosomal instability through p53 dysfunction and genome doubling.
Sebastijan Hobor, Maise Al Bakir, Crispin T Hiley, Marcin Skrzypski, Alexander M Frankell, Thomas B K Watkins

Nat Commun· June 2024

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Novel method for determining when a field-collected donor unit is sufficiently full.
Mark H Yazer, Kendall Werneiwski, Patrick Thompson, Kjell Titlestad, Thomas Watkins

Transfusion· May 2024

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Integrative temporal multi-omics reveals uncoupling of transcriptome and proteome during human T cell activation.
Harshi Weerakoon, Ahmed Mohamed, Yide Wong, Jinjin Chen, Bhagya Senadheera, Thomas S Watkins

NPJ Syst Biol Appl· February 2024

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Quantifying the impact of immunotherapy on RNA dynamics in cancer.
Ieva Usaite, Dhruva Biswas, Krijn Dijkstra, Thomas Bk Watkins, Oriol Pich

J Immunother Cancer· November 2023

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Refphase: Multi-sample phasing reveals haplotype-specific copy number heterogeneity.
Thomas B K Watkins, Emma C Colliver, Matthew R Huska, Tom L Kaufmann, Emilia L Lim

PLoS Comput Biol· October 2023

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Evolutionary characterization of lung adenocarcinoma morphology in TRACERx.
Takahiro Karasaki, David A Moore, Selvaraju Veeriah, Cristina Naceur-Lombardelli, Antonia Toncheva, Thomas B K Watkins

Nat Med· April 2023

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Body composition and lung cancer-associated cachexia in TRACERx.
Othman Al-Sawaf, Jakob Weiss, Marcin Skrzypski, Jie Min Lam, Takahiro Karasaki, Thomas B K Watkins

Nat Med· April 2023

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Genomic-transcriptomic evolution in lung cancer and metastasis.
Carlos Martínez-Ruiz, James R M Black, Clare Puttick, Mark S Hill, Jonas Demeulemeester, Thomas B K Watkins

Nature· April 2023

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Antibodies against endogenous retroviruses promote lung cancer immunotherapy.
Kevin W Ng, Jesse Boumelha, Katey S S Enfield, Jorge Almagro, Hongui Cha, Thomas B K Watkins

Nature· April 2023

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The evolution of non-small cell lung cancer metastases in TRACERx.
Maise Al Bakir, Ariana Huebner, Carlos Martínez-Ruiz, Kristiana Grigoriadis, Thomas B K Watkins

Nature· April 2023

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The evolution of lung cancer and impact of subclonal selection in TRACERx.
Alexander M Frankell, Michelle Dietzen, Maise Al Bakir, Emilia L Lim, Takahiro Karasaki, Thomas B K Watkins

Nature· April 2023

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Tracking early lung cancer metastatic dissemination in TRACERx using ctDNA.
Christopher Abbosh, Alexander M Frankell, Thomas Harrison, Judit Kisistok, Aaron Garnett, Thomas B K Watkins

Nature· April 2023

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Robust Copper-Based Nanosponge Architecture Decorated by Ruthenium with Enhanced Electrocatalytic Performance for Ambient Nitrogen Reduction to Ammonia.
Kui Li, Lei Ding, Zhiqiang Xie, Gaoqiang Yang, Shule Yu, Thomas R Watkins

ACS Appl Mater Interfaces· March 2023

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MEDICC2: whole-genome doubling aware copy-number phylogenies for cancer evolution.
Tom L Kaufmann, Marina Petkovic, Thomas B K Watkins, Emma C Colliver, Sofya Laskina

Genome Biol· November 2022

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Clonal somatic copy number altered driver events inform drug sensitivity in high-grade serous ovarian cancer.
Filipe Correia Martins, Dominique-Laurent Couturier, Ines de Santiago, Carolin Margarethe Sauer, Maria Vias, Thomas B K Watkins

Nat Commun· October 2022

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Soluble RAGE Prevents Type 1 Diabetes Expanding Functional Regulatory T Cells.
Sherman S Leung, Danielle J Borg, Domenica A McCarthy, Tamar E Boursalian, Justen Cracraft, Thomas Watkins

Diabetes· September 2022

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Classifying cGAS-STING Activity Links Chromosomal Instability with Immunotherapy Response in Metastatic Bladder Cancer.
Mateo Sokač, Johanne Ahrenfeldt, Kevin Litchfield, Thomas B K Watkins, Michael Knudsen

Cancer Res Commun· August 2022

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The translational challenges of precision oncology.
Oriol Pich, Chris Bailey, Thomas B K Watkins, Simone Zaccaria, Mariam Jamal-Hanjani

Cancer Cell· May 2022

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