Mohamed Ghafoor
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View article: Cell–ECM Graphs: A Graph-Based Method for Joint Analysis of Cells and the Extracellular Matrix
Cell–ECM Graphs: A Graph-Based Method for Joint Analysis of Cells and the Extracellular Matrix Open
Spatial proteomics technologies enable in situ characterization of both cells and the extracellular matrix (ECM), yet methods to jointly analyse their interactions remain limited. Here, we present a computational framework for constructing…
View article: <i>CellPie</i> : a scalable spatial transcriptomics factor discovery method via joint non-negative matrix factorization
<i>CellPie</i> : a scalable spatial transcriptomics factor discovery method via joint non-negative matrix factorization Open
Spatially resolved transcriptomics has enabled the study of expression of genes within tissues while retaining their spatial identity. Most spatial transcriptomics (ST) technologies generate a matched histopathological image as part of the…
View article: Extracellular matrix phenotyping by imaging mass cytometry defines distinct cellular matrix environments associated with allergic airway inflammation
Extracellular matrix phenotyping by imaging mass cytometry defines distinct cellular matrix environments associated with allergic airway inflammation Open
The extracellular matrix (ECM) forms the scaffold in which cells reside and interact. The composition of this scaffold guides the development of local immune responses and tissue function. With the advent of multiplexed spatial imaging met…
View article: DeepARV: ensemble deep learning to predict drug-drug interaction of clinical relevance with antiretroviral therapy
DeepARV: ensemble deep learning to predict drug-drug interaction of clinical relevance with antiretroviral therapy Open
Drug-drug interaction (DDI) may result in clinical toxicity or treatment failure of antiretroviral therapy (ARV) or comedications. Despite the high number of possible drug combinations, only a limited number of clinical DDI studies are con…
View article: <i>CellPie</i>: a scalable spatial transcriptomics factor discovery method via joint non-negative matrix factorization
<i>CellPie</i>: a scalable spatial transcriptomics factor discovery method via joint non-negative matrix factorization Open
Spatially resolved transcriptomics has enabled the study of expression of genes within tissues while retaining their spatial identity. Most spatial transcriptomics technologies generate a matched histopathological image as part of the stan…
View article: DeepECMP: Predicting Extracellular Matrix Proteins using Deep Learning
DeepECMP: Predicting Extracellular Matrix Proteins using Deep Learning Open
Introduction: The extracellular matrix (ECM) is a networkof proteins and carbohydrates that has a structural and bio-chemical function. The ECM plays an important role in dif-ferentiation, migration and signaling. Several studies havepredi…