The Life History of 21 Breast Cancers

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2. Punctuated evolution of canonical genomic aberrations in uveal melanoma
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3. Optimizing Cancer Genome Sequencing and Analysis
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4. Haplotype-resolved genome sequencing: experimental methods and applications
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5. Phylogenetic analyses of melanoma reveal complex patterns of metastatic dissemination
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6. C. eleganswhole-genome sequencing reveals mutational signatures related to carcinogens and DNA repair deficiency
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7. Convergent somatic mutations in metabolism genes in chronic liver disease
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8. Transmissible Dog Cancer Genome Reveals the Origin and History of an Ancient Cell Lineage
   Elizabeth P. Murchison, David C. Wedge, Ludmil B. Alexandrov, Beiyuan Fu, Iñigo Martincorena, Zemin Ning, José M. C. Tubío, Emma Werner, Jan Allen, Andrígo Barboza De Nardi et al. · 2014 · Science
9. Spatial genomics maps the structure, nature and evolution of cancer clones
   Artem Lomakin, Jessica Svedlund, Carina Strell, Milana Gatarić, Artem Shmatko, Gleb D. Rukhovich, Jun Sung Park, Young Seok Ju, Stefan C. Dentro, Vitalii Kleshchevnikov et al. · 2022 · Nature
10. Expanding the computational toolbox for mining cancer genomes
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11. Evolution and dynamics of pancreatic cancer progression
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12. A practical guide to cancer subclonal reconstruction from DNA sequencing
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13. Integrated RNA and DNA sequencing reveals early drivers of metastatic breast cancer
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14. Acute myeloid leukaemia: a paradigm for the clonal evolution of cancer?
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15. The genomic landscape of 2,023 colorectal cancers
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16. Geographic and age variations in mutational processes in colorectal cancer
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17. Haplotype-aware analysis of somatic copy number variations from single-cell transcriptomes
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18. Triple-Negative Breast Cancer and the Need for New Therapeutic Targets
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19. Multi-region exome sequencing reveals genomic evolution from preneoplasia to lung adenocarcinoma
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20. Detecting repeated cancer evolution from multi-region tumor sequencing data
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21. PureCN: copy number calling and SNV classification using targeted short read sequencing
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22. Reconstructing metastatic seeding patterns of human cancers
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23. High-Definition Reconstruction of Clonal Composition in Cancer
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24. APOBEC3-dependent kataegis and TREX1-driven chromothripsis during telomere crisis
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25. Phylogenetic Quantification of Intra-tumour Heterogeneity
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26. TP53Mutations in Breast and Ovarian Cancer
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27. Tackling the Diversity of Triple-Negative Breast Cancer
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28. Clonal evolution in hematological malignancies and therapeutic implications
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29. A practical guide for mutational signature analysis in hematological malignancies
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30. Measuring cancer evolution from the genome
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31. The complex genetic landscape of familial breast cancer
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32. Deep whole-genome analysis of 494 hepatocellular carcinomas
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33. High-resolution lineage tracking reveals travelling wave of adaptation in laboratory yeast
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34. A systematic CRISPR screen defines mutational mechanisms underpinning signatures caused by replication errors and endogenous DNA damage
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35. Characterizing allele- and haplotype-specific copy numbers in single cells with CHISEL
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36. Circulating tumor cells and circulating tumor DNA for precision medicine: dream or reality?
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37. Cyclin A2/E1 activation defines a hepatocellular carcinoma subclass with a rearrangement signature of replication stress
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38. Tracking Cancer Evolution through the Disease Course
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39. Between-region genetic divergence reflects the mode and tempo of tumor evolution
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40. Heterogeneity within molecular subtypes of breast cancer
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41. Immunohistochemical Surrogates for Molecular Classification of Breast Carcinoma: A 2015 Update
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42. Embryonal precursors of Wilms tumor
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43. Subclonal variant calling with multiple samples and prior knowledge
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44. Advances in understanding tumour evolution through single-cell sequencing
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45. Clonal fitness inferred from time-series modelling of single-cell cancer genomes
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46. Mechanosensitive pannexin-1 channels mediate microvascular metastatic cell survival
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47. Multiregion Sequencing Reveals the Genetic Heterogeneity and Evolutionary History of Osteosarcoma and Matched Pulmonary Metastases
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48. Mutational Landscape and Patterns of Clonal Evolution in Relapsed Pediatric Acute Lymphoblastic Leukemia
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49. The molecular diversity of Luminal A breast tumors
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50. Validating the concept of mutational signatures with isogenic cell models
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51. The evolutionary landscape of colorectal tumorigenesis
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52. Evolution of DNA Methylation Is Linked to Genetic Aberrations in Chronic Lymphocytic Leukemia
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53. Glycoprotein non-metastatic b (GPNMB): A metastatic mediator and emerging therapeutic target in cancer
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54. Extensive phylogenies of human development inferred from somatic mutations
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55. Evolving cancer–niche interactions and therapeutic targets during bone metastasis
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56. Inferring the Mutational History of a Tumor Using Multi-state Perfect Phylogeny Mixtures
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57. SF3B1 mutations in chronic lymphocytic leukemia
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60. Principles of Reconstructing the Subclonal Architecture of Cancers
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61. Concurrent Whole-Genome Haplotyping and Copy-Number Profiling of Single Cells
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62. Evolutionary predictability of genetic versus nongenetic resistance to anticancer drugs in melanoma
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64. Exploiting Tumor Neoantigens to Target Cancer Evolution: Current Challenges and Promising Therapeutic Approaches
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65. Combined landscape of single-nucleotide variants and copy number alterations in clonal hematopoiesis
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66. Tumor Mutation Burden Forecasts Outcome in Ovarian Cancer with BRCA1 or BRCA2 Mutations
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67. Prediction of plasma ctDNA fraction and prognostic implications of liquid biopsy in advanced prostate cancer
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68. Tumor heterogeneity and cancer stem cell paradigm: Updates in concept, controversies and clinical relevance
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69. Dancing with the DNA damage response: next-generation anti-cancer therapeutic strategies
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70. Establishing community reference samples, data and call sets for benchmarking cancer mutation detection using whole-genome sequencing
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71. Detection of early seeding of Richter transformation in chronic lymphocytic leukemia
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72. Navigating cancer network attractors for tumor-specific therapy
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73. EXPANDS: expanding ploidy and allele frequency on nested subpopulations
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74. Concordance of Genomic Alterations by Next-Generation Sequencing in Tumor Tissue versus Circulating Tumor DNA in Breast Cancer
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75. Somatic mosaicism: on the road to cancer
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76. Mutational Signatures in Breast Cancer: The Problem at the DNA Level
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77. High-resolution clonal mapping of multi-organ metastasis in triple negative breast cancer
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78. Subclonal reconstruction of tumors by using machine learning and population genetics
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79. Maftools: Efficient analysis, visualization and summarization of MAF files from large-scale cohort based cancer studies
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80. Intra-tumor genetic heterogeneity and alternative driver genetic alterations in breast cancers with heterogeneous HER2 gene amplification
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81. Molecular Pathology of Breast Cancer
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82. Whole-genome single-cell copy number profiling from formalin-fixed paraffin-embedded samples
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83. Genomic landscape and evolution of metastatic chromophobe renal cell carcinoma
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84. Single‐Cell Transcriptome Analysis Uncovers Intratumoral Heterogeneity and Underlying Mechanisms for Drug Resistance in Hepatobiliary Tumor Organoids
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85. In silico saturation mutagenesis of cancer genes
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86. Understanding mutagenesis through delineation of mutational signatures in human cancer
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87. TrAp: a tree approach for fingerprinting subclonal tumor composition
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88. Biopsies: next-generation biospecimens for tailoring therapy
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89. Next generation sequencing in cancer research and clinical application
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90. Cell‐free circulating tumour DNA as a liquid biopsy in breast cancer
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91. SPhyR: tumor phylogeny estimation from single-cell sequencing data under loss and error
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92. Accurate quantification of copy-number aberrations and whole-genome duplications in multi-sample tumor sequencing data
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93. Computational analysis of cancer genome sequencing data
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94. Combined KIT and FGFR2b Signaling Regulates Epithelial Progenitor Expansion during Organogenesis
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95. Portrait of a cancer: mutational signature analyses for cancer diagnostics
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96. Going with the Flow: From Circulating Tumor Cells to DNA
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97. Quantifying tumor heterogeneity in whole-genome and whole-exome sequencing data
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98. Intratumour Heterogeneity in Urologic Cancers: From Molecular Evidence to Clinical Implications
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99. Single cell analysis of cancer genomes
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100. Somatic POLE mutations cause an ultramutated giant cell high-grade glioma subtype with better prognosis
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