[HTML][HTML] Incorporating biological structure into machine learning models in biomedicine
J Crawford, CS Greene - Current opinion in biotechnology, 2020 - Elsevier
In biomedical applications of machine learning, relevant information often has a rich
structure that is not easily encoded as real-valued predictors. Examples of such data include …
structure that is not easily encoded as real-valued predictors. Examples of such data include …
Cancer phylogenetic inference using copy number alterations detected from DNA sequencing data
B Lu - Cancer Pathogenesis and Therapy, 2024 - mednexus.org
Cancer is an evolutionary process involving the accumulation of diverse somatic mutations
and clonal evolution over time. Phylogenetic inference from samples obtained from an …
and clonal evolution over time. Phylogenetic inference from samples obtained from an …
Reconstructing tumor clonal lineage trees incorporating single-nucleotide variants, copy number alterations and structural variations
Motivation Cancer develops through a process of clonal evolution in which an initially
healthy cell gives rise to progeny gradually differentiating through the accumulation of …
healthy cell gives rise to progeny gradually differentiating through the accumulation of …
Tumor heterogeneity assessed by sequencing and fluorescence in situ hybridization (FISH) data
Motivation Computational reconstruction of clonal evolution in cancers has become a crucial
tool for understanding how tumors initiate and progress and how this process varies across …
tool for understanding how tumors initiate and progress and how this process varies across …
Semi-deconvolution of bulk and single-cell RNA-seq data with application to metastatic progression in breast cancer
Motivation Identifying cell types and their abundances and how these evolve during tumor
progression is critical to understanding the mechanisms of metastasis and identifying …
progression is critical to understanding the mechanisms of metastasis and identifying …
Determining Optimal Placement of Copy Number Aberration Impacted Single Nucleotide Variants in a Tumor Progression History
CH Wu, S Joshi, W Robinson, PF Robbins… - … on Research in …, 2024 - Springer
Intratumoral heterogeneity arises as a result of genetically distinct subclones emerging
during tumor progression. These subclones are characterized by various types of somatic …
during tumor progression. These subclones are characterized by various types of somatic …
Clonal reconstruction from time course genomic sequencing data
Background Bacterial cells during many replication cycles accumulate spontaneous
mutations, which result in the birth of novel clones. As a result of this clonal expansion, an …
mutations, which result in the birth of novel clones. As a result of this clonal expansion, an …
Sc-TUSV-ext: Single-cell clonal lineage inference from single nucleotide variants (SNV), copy number alterations (CNA) and structural variants (SV)
Clonal lineage inference (" tumor phylogenetics") has become a crucial tool for making
sense of somatic evolution processes that underlie cancer development and are …
sense of somatic evolution processes that underlie cancer development and are …
Joint clustering of single-cell sequencing and fluorescence in situ hybridization data for reconstructing clonal heterogeneity in cancers
Aneuploidy and whole genome duplication (WGD) events are common features of cancers
associated with poor outcomes, but the ways they influence trajectories of clonal evolution …
associated with poor outcomes, but the ways they influence trajectories of clonal evolution …
Robust and accurate deconvolution of tumor populations uncovers evolutionary mechanisms of breast cancer metastasis
Motivation Cancer develops and progresses through a clonal evolutionary process.
Understanding progression to metastasis is of particular clinical importance, but is not easily …
Understanding progression to metastasis is of particular clinical importance, but is not easily …