The advent of immune stimulating CAFs in cancer
M Tsoumakidou - Nature Reviews Cancer, 2023 - nature.com
The theory that cancer-associated fibroblasts (CAFs) are immunosuppressive cells has
prevailed throughout the past decade. However, recent high-throughput, high-resolution …
prevailed throughout the past decade. However, recent high-throughput, high-resolution …
Cellular barcoding to decipher clonal dynamics in disease
Cellular barcodes are distinct DNA sequences that enable one to track specific cells across
time or space. Recent advances in our ability to detect natural or synthetic cellular barcodes …
time or space. Recent advances in our ability to detect natural or synthetic cellular barcodes …
Single-cell lineage capture across genomic modalities with CellTag-multi reveals fate-specific gene regulatory changes
Complex gene regulatory mechanisms underlie differentiation and reprogramming.
Contemporary single-cell lineage-tracing (scLT) methods use expressed, heritable DNA …
Contemporary single-cell lineage-tracing (scLT) methods use expressed, heritable DNA …
Map** human adult hippocampal neurogenesis with single-cell transcriptomics: reconciling controversy or fueling the debate?
The notion of exploiting the regenerative potential of the human brain in physiological aging
or neurological diseases represents a particularly attractive alternative to conventional …
or neurological diseases represents a particularly attractive alternative to conventional …
CellOracle: Dissecting cell identity via network inference and in silico gene perturbation
Cell identity is governed by Gene Regulatory Networks (GRNs), a complex system of
molecular interactions resulting in the precise spatial and temporal regulation of gene …
molecular interactions resulting in the precise spatial and temporal regulation of gene …
Single-cell analysis of neonatal HSC ontogeny reveals gradual and uncoordinated transcriptional reprogramming that begins before birth
Fetal and adult hematopoietic stem cells (HSCs) have distinct proliferation rates, lineage
biases, gene expression profiles, and gene dependencies. Although these differences are …
biases, gene expression profiles, and gene dependencies. Although these differences are …
Gene regulatory network reconfiguration in direct lineage reprogramming
In direct lineage conversion, transcription factor (TF) overexpression reconfigures gene
regulatory networks (GRNs) to reprogram cell identity. We previously developed CellOracle …
regulatory networks (GRNs) to reprogram cell identity. We previously developed CellOracle …
Topological and geometric analysis of cell states in single-cell transcriptomic data
T Huynh, Z Cang - Briefings in Bioinformatics, 2024 - academic.oup.com
Single-cell RNA sequencing (scRNA-seq) enables dissecting cellular heterogeneity in
tissues, resulting in numerous biological discoveries. Various computational methods have …
tissues, resulting in numerous biological discoveries. Various computational methods have …
Targeting the Tumor-Tumor microenvironment crosstalk
Introduction Cancer development and progression is a complex process influenced by co-
evolution of the cancer cells and their microenvironment. However, traditional anti-cancer …
evolution of the cancer cells and their microenvironment. However, traditional anti-cancer …
Lmo4 synergizes with Fezf2 to promote direct in vivo reprogramming of upper layer cortical neurons and cortical glia towards deep-layer neuron identities
T Felske, C Tocco, S Péron, K Harb, C Alfano… - PLoS …, 2023 - journals.plos.org
In vivo direct neuronal reprogramming relies on the implementation of an exogenous
transcriptional program allowing to achieve conversion of a particular neuronal or glial cell …
transcriptional program allowing to achieve conversion of a particular neuronal or glial cell …