Contents

Bioinformatics

• MATCHER: manifold alignment reveals correspondence between single cell transcriptome and epigenome dynamics

Databases

• Evaluation of relational and NoSQL database architectures to manage genomic annotations

Epigenetics

• Interplay between the cancer genome and epigenome

• The diverse roles of DNA methylation in mammalian development and disease

• DNA methylation loss in late-replicating domains is linked to mitotic cell division

• Cell division drives DNA methylation loss in late-replicating domains in primary human cells

Cell type vs cell state

• Quantifying cell-state densities in single-cell phenotypic landscapes using Mellon

• Precise identification of cell states altered in disease using healthy single-cell references

• SEACells infers transcriptional and epigenomic cellular states from single-cell genomics data

• Transition states and cell fate decisions in epigenetic landscapes

• Defining cell types and states with single-cell genomics

• The evolving concept of cell identity in the single cell era

• What is a cell type and how to define it

• Epigenetic regulation of cell fate reprogramming in aging and disease: A predictive computational model

• Control of cell state transitions

• Cell Fate Decision as High-Dimensional Critical State Transition

• Dynamic Heterogeneity and DNA Methylation in Embryonic Stem Cells

• Transcriptome-wide noise controls lineage choice in mammalian progenitor cells

RNA velocity

• RNA velocity of single cells

• Generalizing RNA velocity to transient cell states through dynamical modeling

• RNA velocity—current challenges and future perspectives

• Multi-omic single-cell velocity models epigenome–transcriptome interactions and improves cell fate prediction

Lineage tracing

• Defining ancestry, heritability and plasticity of cellular phenotypes in somatic evolution

• Lineage tracing in human tissues

• Barcode-free prediction of cell lineages from scRNA-seq datasets

Cancer

• An Integrative Model of Cellular States, Plasticity, and Genetics for Glioblastoma

Fallopian tube

• The Notch and Wnt pathways regulate stemness and differentiation in human fallopian tube organoids

State space

• DREISS: Using State-Space Models to Infer the Dynamics of Gene Expression Driven by External and Internal Regulatory Networks

Transcriptomics

• The triumphs and limitations of computational methods for scRNA-seq

• Separating measurement and expression models clarifies confusion in single-cell RNA sequencing analysis

Single-nucleus RNA-seq

• Systematic comparison of single-cell and single-nucleus RNA-sequencing methods

• Single-Nucleus RNA-Seq Is Not Suitable for Detection of Microglial Activation Genes in Humans

Cancer

• Selective advantage of epigenetically disrupted cancer cells via phenotypic inertia

• Non-genetic determinants of malignant clonal fitness at single-cell resolution

Cancer stem cells

• Heterogeneity in Cancer: Cancer Stem Cells versus Clonal Evolution

Ovarian cancer

• Cellular heterogeneity of human fallopian tubes in normal and hydrosalpinx disease states identified using scRNA-seq

• A single-cell landscape of high-grade serous ovarian cancer

• The Repertoire of Serous Ovarian Cancer Nongenetic Heterogeneity Revealed by Single-Cell Sequencing of Normal Fallopian Tube Epithelial Cells

• Identifying an ovarian cancer cell hierarchy regulated by bone morphogenetic protein 2

• Clear cell and endometrioid carcinomas: are their differences attributable to distinct cells of origin?

• Both fallopian tube and ovarian surface epithelium are cells-of-origin for high-grade serous ovarian carcinoma

• Stem-Like Epithelial Cells Are Concentrated in the Distal End of the Fallopian Tube: A Site for Injury and Serous Cancer Initiation

• Developing ovarian cancer stem cell models: laying the pipeline from discovery to clinical intervention

Ageing

• Counteracting age-related VEGF signaling insufficiency promotes healthy aging and extends life span

Cellular Senescence

• Senescence-Associated Secretory Phenotypes Reveal Cell-Nonautonomous Functions of Oncogenic RAS and the p53 Tumor Suppressor

• Four faces of cellular senescence

• Inhibition of stress induced premature senescence in presenilin-1 mutated cells with water soluble Coenzyme Q₁₀

• Epigenetic Basis of Cellular Senescence and Its Implications in Aging

• Cellular senescence: Immunosurveillance and future immunotherapy

• Transcriptome signature of cellular senescence

• Cellular senescence: Defining a path forward

• Impaired immune surveillance accelerates accumulation of senescent cells and aging

• Astrocyte senescence promotes glutamate toxicity in cortical neurons

• A multidimensional systems biology analysis of cellular senescence in aging and disease

• Single-Cell Transcriptome Analysis Reveals Six Subpopulations Reflecting Distinct Cellular Fates in Senescent Mouse Embryonic Fibroblasts

• Cellular senescence and failure of myelin repair in MS

• Early onset senescence and cognitive impairment in a murine model of repeated mTBI

• An aged immune system drives senescence and ageing of solid organs

• The long non-coding RNA MIR31HG regulates the senescence associated secretory phenotype

Neuroscience

Neurodegeneration

• Cellular Senescence in Neurodegenerative Diseases

• Aging as a risk factor for neurodegenerative disease

• Genetically determined susceptibility to neurodegeneration is associated with expression of inflammatory genes

• Evidence of the Cellular Senescence Stress Response in Mitotically Active Brain Cells-Implications for Cancer and Neurodegeneration

• Neuroblast senescence in the aged brain augments natural killer cell cytotoxicity leading to impaired neurogenesis and cognition

• Dystrophic microglia are associated with neurodegenerative disease and not healthy aging in the human brain

Alzheimer’s Disease

• Inflammation, A beta deposition, and neurofibrillary tangle formation as correlates of Alzheimer’s disease neurodegeneration

• The Genetic Landscape of Alzheimer’s Disease

• Genetics of Alzheimer’s disease: where we are, and where we are going

• When does Alzheimer’s disease really start? The Role of Biomarkers

• Genetic meta-analysis of diagnosed Alzheimer’s disease

• The Cellular Phase of Alzheimers Disease

• Single-cell transcriptomic analysis of Alzheimer’s disease

• Alzheimer’s Patient Microglia Exhibit Enhanced Aging and Unique Transcriptional Activation

• Dysregulation of the epigenetic landscape of normal aging in Alzheimer’s disease

• Loss-of-function of p53 isoform Δ113p53 accelerates brain aging in zebrafish

• Telomere Attrition in Neurodegenerative Disorders

• Cerebrovascular Senescence Is Associated With Tau Pathology in Alzheimer’s Disease

• Molecular Mechanism for Age-Related Memory Loss: The Histone-Binding Protein RbAp48

• Big Data Analysis of Genes Associated With Neuropsychiatric Disorders in an Alzheimer’s Disease Animal Model

Cellular senescence and AD

• Vascular Cell Senescence Contributes to Blood–Brain Barrier Breakdown

• Cellular Senescence and Iron Dyshomeostasis in Alzheimer’s Disease

• Cellular senescence and Alzheimer disease: the egg and the chicken scenario

• Senescence as an Amyloid Cascade: The Amyloid Senescence Hypothesis

• Astrocyte Senescence and Alzheimer’s Disease: A Review