methods

Jul 28, 2026

Intratumor Heterogeneity

Jul 28, 2026

Subclonal Architecture

Jul 18, 2026

FFPE Pre-Analytical Variables

Jul 18, 2026

Sequencing Library Artifacts

Jul 18, 2026

Subclonal Reconstruction

Jul 18, 2026

Variant Allele Fraction

methods

Jul 18, 2026

Zavala, E. I., Aximu-Petri, A., Richter, J., Nickel, B., Vernot, B., & Meyer, M. (2022). Quantifying and reducing cross-contamination in single- and multiplex hybridization capture of ancient DNA. Molecular Ecology Resources, 22, 2196–2207.

Jul 17, 2026

Cancer Evolution Olog

Jul 17, 2026

Cross-Domain Functors

Jul 17, 2026

Ecology Invasion Olog

Jul 16, 2026

Nova, A., Keten, S., Pugno, N. M., Redaelli, A., & Buehler, M. J. (2010). Molecular and nanostructural mechanisms of deformation, strength and toughness of spider silk fibrils. Nano Letters, 10(7), 2626–2634.

Jul 12, 2026

Cancer Cell Fraction

methods

Jul 12, 2026

Copy Number Alteration

Jul 12, 2026

Flores Bueso, Y., Walker, S. P., & Tangney, M. (2020). Characterization of FFPE-induced bacterial DNA damage and development of a repair method. Biology Methods and Protocols, 5(1), bpaa015.

Jul 12, 2026

Dahlmann, H. A., Vaidyanathan, V. G., & Sturla, S. J. (2009). Investigating the biochemical impact of DNA damage with structure-based probes: Abasic sites, photodimers, alkylation adducts, and oxidative lesions. Biochemistry, 48(40), 9347–9359.

Jul 12, 2026

Do, H., & Dobrovic, A. (2015). Sequence artifacts in DNA from formalin-fixed tissues: Causes and strategies for minimization. Clinical Chemistry, 61(1), 64–71.

Jul 12, 2026

Greytak, S. R., Engel, K. B., Bass, B. P., & Moore, H. M. (2015). Accuracy of molecular data generated with FFPE biospecimens: Lessons from the literature. Cancer Research, 75(8), 1541–1547.

Jul 12, 2026

Pignatta, S., Tazzari, M., Indio, V., Tumedei, M. M., Limarzi, F., Tauceri, F., Tebaldi, M., Fanelli, D., & Bulgarelli, J. (2025). Comparative analysis of library preparation approaches for FFPE gene expression profiling and related recommendations. Scientific Reports, 15, 12992.

Jul 12, 2026

Steiert, T. A., Fuß, J., Franke, A., & Forster, M. (2023). A critical spotlight on the paradigms of FFPE-DNA sequencing. Nucleic Acids Research, 51(14), 7143–7158.

Jul 12, 2026

Zhu, Y., Weiss, T., Zhang, Q., Sun, R., Wang, B., Yi, X., Wu, Z., Gao, H., Cai, X., Ruan, G., Zhu, T., Pockley, A. G., Witzens-Harig, M., Wild, P. J., Aebersold, R., & Guo, T. (2019). High-throughput proteomic analysis of FFPE tissue samples facilitates tumor stratification. Molecular Oncology, 13(11), 2305–2328.

Jul 11, 2026

Crossing Rule

Jul 11, 2026

Phylogenetic Tree

Jul 11, 2026

Chavarriaga (2025) — ASCO GU 2025: Evolution of ctDNA Detection with Next Generation Technology

Jul 11, 2026

Bian (2025) — LLM-Empowered Knowledge Graph Construction: A Survey

Jul 11, 2026

Life in the Lab Staff. (2025, January 23). Cell-Free DNA (cfDNA) vs. Circulating Tumor DNA (ctDNA) Explained. Life in the Lab Blog. Thermo Fisher Scientific.

Jul 11, 2026

Building a Local Knowledge Base in Google's Open Knowledge Format (OKF) — Extended Brain (2026)

Jul 11, 2026

Satas, Zaccaria, El-Kebir, & Raphael (2021) — DeCiFering the Elusive Cancer Cell Fraction in Tumor Heterogeneity and Evolution

Jul 11, 2026

Yuan et al. (2026) — Knowledge-to-Verification: Exploring RLVR for LLMs in Knowledge-Intensive Domains

Jul 06, 2026

Compression Progress Olog

Jul 06, 2026

Representing Knowledge and Querying Data using Double-Functorial Semantics (Lambert & Patterson, 2024)

Jul 05, 2026

Abbosh et al. (2017) — Phylogenetic ctDNA Analysis Depicts Early-Stage Lung Cancer Evolution

Jul 05, 2026

Stejskal, Goodarzi, Srovnal, Hajdúch, van 't Veer, & Magbanua (2023) — Circulating Tumor Nucleic Acids: Biology, Release Mechanisms, and Clinical Relevance

Jul 05, 2026

Wander, Weipert, Cabel, et al. (2026) — Real-World Cell-Free ctDNA Analysis Identifies CDK4/6 Inhibitor Resistance and Tumor Evolution in HR+ Advanced Breast Cancer

Jul 03, 2026

Giesa, Spivak, & Buehler (2011) — Reoccurring Patterns in Hierarchical Protein Materials and Music: The Power of Analogies

Jul 03, 2026

Schmidhuber (2009) — Driven by Compression Progress: A Simple Principle Explains Essential Aspects of Subjective Beauty, Novelty, Surprise, Interestingness, Attention, Curiosity, Creativity, Art, Science, Music, Jokes

Jun 27, 2026

Molecular Clock

Jun 17, 2026

Clonal Evolution

Explorer

methods

Intratumor Heterogeneity

Subclonal Architecture

FFPE Pre-Analytical Variables

Sequencing Library Artifacts

Subclonal Reconstruction

Variant Allele Fraction

Zavala, E. I., Aximu-Petri, A., Richter, J., Nickel, B., Vernot, B., & Meyer, M. (2022). Quantifying and reducing cross-contamination in single- and multiplex hybridization capture of ancient DNA. Molecular Ecology Resources, 22, 2196–2207.

Cancer Evolution Olog

Cross-Domain Functors

Ecology Invasion Olog

Nova, A., Keten, S., Pugno, N. M., Redaelli, A., & Buehler, M. J. (2010). Molecular and nanostructural mechanisms of deformation, strength and toughness of spider silk fibrils. Nano Letters, 10(7), 2626–2634.

Cancer Cell Fraction

Copy Number Alteration

Flores Bueso, Y., Walker, S. P., & Tangney, M. (2020). Characterization of FFPE-induced bacterial DNA damage and development of a repair method. Biology Methods and Protocols, 5(1), bpaa015.

Dahlmann, H. A., Vaidyanathan, V. G., & Sturla, S. J. (2009). Investigating the biochemical impact of DNA damage with structure-based probes: Abasic sites, photodimers, alkylation adducts, and oxidative lesions. Biochemistry, 48(40), 9347–9359.

Do, H., & Dobrovic, A. (2015). Sequence artifacts in DNA from formalin-fixed tissues: Causes and strategies for minimization. Clinical Chemistry, 61(1), 64–71.

Greytak, S. R., Engel, K. B., Bass, B. P., & Moore, H. M. (2015). Accuracy of molecular data generated with FFPE biospecimens: Lessons from the literature. Cancer Research, 75(8), 1541–1547.

Pignatta, S., Tazzari, M., Indio, V., Tumedei, M. M., Limarzi, F., Tauceri, F., Tebaldi, M., Fanelli, D., & Bulgarelli, J. (2025). Comparative analysis of library preparation approaches for FFPE gene expression profiling and related recommendations. Scientific Reports, 15, 12992.

Steiert, T. A., Fuß, J., Franke, A., & Forster, M. (2023). A critical spotlight on the paradigms of FFPE-DNA sequencing. Nucleic Acids Research, 51(14), 7143–7158.

Crossing Rule

Phylogenetic Tree

Chavarriaga (2025) — ASCO GU 2025: Evolution of ctDNA Detection with Next Generation Technology

Bian (2025) — LLM-Empowered Knowledge Graph Construction: A Survey

Life in the Lab Staff. (2025, January 23). Cell-Free DNA (cfDNA) vs. Circulating Tumor DNA (ctDNA) Explained. Life in the Lab Blog. Thermo Fisher Scientific.

Building a Local Knowledge Base in Google's Open Knowledge Format (OKF) — Extended Brain (2026)

Satas, Zaccaria, El-Kebir, & Raphael (2021) — DeCiFering the Elusive Cancer Cell Fraction in Tumor Heterogeneity and Evolution

Yuan et al. (2026) — Knowledge-to-Verification: Exploring RLVR for LLMs in Knowledge-Intensive Domains

Compression Progress Olog

Representing Knowledge and Querying Data using Double-Functorial Semantics (Lambert & Patterson, 2024)

Abbosh et al. (2017) — Phylogenetic ctDNA Analysis Depicts Early-Stage Lung Cancer Evolution

Stejskal, Goodarzi, Srovnal, Hajdúch, van 't Veer, & Magbanua (2023) — Circulating Tumor Nucleic Acids: Biology, Release Mechanisms, and Clinical Relevance

Wander, Weipert, Cabel, et al. (2026) — Real-World Cell-Free ctDNA Analysis Identifies CDK4/6 Inhibitor Resistance and Tumor Evolution in HR+ Advanced Breast Cancer

Giesa, Spivak, & Buehler (2011) — Reoccurring Patterns in Hierarchical Protein Materials and Music: The Power of Analogies

Schmidhuber (2009) — Driven by Compression Progress: A Simple Principle Explains Essential Aspects of Subjective Beauty, Novelty, Surprise, Interestingness, Attention, Curiosity, Creativity, Art, Science, Music, Jokes

Molecular Clock

Measuring Cancer Evolution from the Genome