Leukemia

Deep Learning links TP53 genotype to expression-defined transcriptional program in Acute Myeloid Leukemia

Acute myeloid leukemia (AML) is a hematological cancer characterized by genetic diversity and poor clinical outcomes. Among various genetic mutations in AML, TP53 mutations have relatively low prevalence and present very dismal survival rates. While the genetic features of AML are well understood, the transcriptional programs associated with TP53 dysfunction are less clear, especially across diffe...

Multiplex imaging combined to machine learning enable automated profiling of cortical malformations: applications in tuberous sclerosis complex

Malformations of cortical development such as tuberous sclerosis complex arise within a heterogeneous cellular landscape that conventional histopathology only partially resolves. Here, we combined a 19-marker multiplex immunofluorescence panel with a machine learning-driven image analysis pipeline to map and quantify over 365 000 cells from paediatric surgical cortex, defining the single-cell arch...

Single recipient cell tracking of tellurium-labeled extracellular vesicle proteomes (TeLEV) identifies EV-driven immunomodulation

Extracellular vesicles (EVs) mediate tumor-immune cell communication by carrying protein cargo that can immediately modulate signaling and antigen pre...

Beyond one-size-fits-all: single-cell transcriptomic signatures predict drug efficacy and reveal responder subgroups in endometriosis

Endometriosis affects ∼10% of reproductive-age women, yet targeted non-hormonal therapies remain unavailable, and treatment response is highly variabl...

A comprehensive bulk and single-cell transcriptional atlas of pediatric leukemias

Advancements in understanding the molecular factors driving pediatric leukemias have led to an ever-increasing volume and diversity of data being gene...

Social isolation upregulates takeout expression in female Drosophila melanogaster to promote sucrose feeding

Drosophila melanogaster provides a model system to examine how environmental stress interacts with sex to induce changes in brain function and behavio...

Classpose: foundation model-driven whole slide image-scale cell phenotyping in H&E

Cell segmentation and phenotyping in histopathology samples are essential techniques applied across diagnostic and research workflows. However, annota...

TASC: A transcriptome-driven machine learning classifier to explore molecular heterogeneity and relapse-associated programs in T-cell Acute Lymphoblastic Leukemia

T-cell acute lymphoblastic leukemia is a biologically heterogeneous malignancy characterized by diverse transcriptional and genomic alterations. Recen...

OmniCell: Unified Foundation Modeling of Single-Cell and Spatial Transcriptomics for Cellular and Molecular Insights

Single-cell RNA sequencing (scRNA-seq) enables characterization of cellular heterogeneity but lacks spatial context, while Spatially Transcriptomics m...

Deep learning inference of universal dormancy pseudotime reveals the cellular targets of anti-cancer therapies

Controlled exit from and re-entry into the cell cycle is essential for multi-cellular life, while aberrant quiescent and senescent cell states have be...

scCotag: Diagonal integration of single-cell multi-omics data via prior-informed co-optimal transport and regularized barycentric mapping

Recent advances in high-throughput single-cell technologies have enabled characterization of cellular states across distinct omics layers, yielding co...

High throughput quantitative tracking of single parasite in Plasmodium falciparum

New systematic profiling of drug effects is in urgent demand due to limitations in existing drug assessment approaches to evaluate comprehensive drug ...

BCL-XL Dependence is a Subtype Agnostic Actionable Feature of Difficult-to-Treat Kidney Cancers

The BCL-XL anti-apoptotic protein is a clear cell Renal Cell Carcinoma (ccRCC) dependency; however, the mechanism of this dependence and its relevance...

Spatially distinct chromatin compaction states predict neoadjuvant chemotherapy resistance in Triple Negative Breast Cancer

Organisation and dynamics of chromatin play a key role in regulation of cell state and function. In cancer, chromatin plasticity is known to be import...

A Druggable Tumor Suppressor and Leukemic Stem Cell Marker

Acute myeloid leukemia (AML) often enters remission after chemotherapy but frequently relapses due to chemotherapy-resistant leukemic stem cells (LSCs...

lncAPNet enables the deciphering of lncRNA–mRNA connections in patient transcriptomic data

Long non-coding RNAs (lncRNAs) regulate gene expression through chromatin remodeling, transcriptional control, and post-transcriptional modulation, in...

A large-scale dataset of functional mouse ganglion cell layer responses

We present the All-GCL dataset, a large-scale resource of functional two-photon Ca2+-imaging recordings with rich meta-data information from more than...

WAD: a wavelet-based linear programming method using L1-minimal reconstruction loss for accessible chromatin data deconvolution

Bulk tissue-based accessible chromatin studies provide summary annotations across all cell types within the tissue. These annotations can be skewed by...

Image-based Explainable Artificial Intelligence Accurately Identifies Myelodysplastic Neoplasms Beyond Conventional Signs of Dysplasia

Evaluation of bone marrow morphology by experienced hematologists is key in the diagnosis of myeloid neoplasms, especially to detect subtle signs of d...

Integrating Multidimensional Data Analytics for Precision Diagnosis of Chronic Low Back Pain

Low back pain (LBP) is a leading cause of disability worldwide, with up to 25% of cases become chronic (cLBP). Optimal diagnostic tools for cLBP remai...