Chris Bakal

Pheno-MYCN maps the morphological footprint of MYCN amplification in paediatric neuroblastoma

Pheno-MYCN links slide-level MYCN prediction to interpretable morphological sub-populations in neuroblastoma, revealing a continuous gradient of MYCN-associated features.

Multi-Site Reproducibility Study of 3D High-Content Analysis with Dual-View Oblique Plane Microscopy

This study assesses the reproducibility of a 3D spheroid-based assay across four institutes using dual-view oblique plane microscopy and finds high consistency in treatment effects with low technical noise.

Structural Identification of Major Molecular Determinants for Phosphotyrosine Recognition in Tyrosine Kinases Reveals Tumour Promoting and Suppressive Functions

The paper identifies molecular determinants for phosphotyrosine recognition in tyrosine kinases and shows their roles in tumor promotion and suppression.

Actin nucleators safeguard replication forks by limiting nascent strand degradation

The paper identifies actin nucleators as essential for protecting replication forks by modulating RPA activity and preventing ssDNA degradation during replicative stress.

A rare genetic disorder provides insights into mechanisms of early-onset neurodegeneration

This study investigates neurodegeneration in Xeroderma pigmentosum using stem cell-derived neurons, identifying endoplasmic reticulum stress and UPS dysfunction as key factors and developing an early detection assay.

Characterization of proteome-size scaling by integrative omics reveals mechanisms of proliferation control in cancer

The paper uses multi-omic data to show how protein and mRNA scaling with cell size regulates proliferation in melanoma cells, revealing mechanisms of growth and division coupling.

3D single-cell shape analysis using geometric deep learning

The paper uses geometric deep learning to analyze 3D cell shapes from melanoma cells, identifying morphological signatures and predicting small molecule mechanisms.

Identification of phenotype-specific networks from paired gene expression-cell shape imaging data

The paper integrates gene expression and cell shape imaging data to identify phenotype-specific gene networks and signaling pathways involved in breast cancer cell morphology.

Epithelial-Mesenchymal Plasticity is regulated by inflammatory signalling networks coupled to cell morphology.

The paper shows that epithelial-mesenchymal plasticity is regulated by inflammatory signalling networks linked to cell morphology through changes in microtubule and nuclear organization.

Membrane voltage fluctuations in human breast cancer cells

This study characterizes membrane voltage fluctuations in human breast cancer and non-cancerous cells, identifying distinct dynamic patterns linked to cellular transformation.

Multiplexed quantitative screens of single cell shape and YAP/TAZ localisation identify DOCK5 as a coincident detector of polarity and adhesion during migration.

The paper identifies DOCK5 as a regulator of YAP/TAZ localization and cell shape during migration, showing its role in maintaining polarity through interactions with CDC42, RAC, and RHOA.

Wdr5, Brca1 and Bard1 link the DNA damage response to the mesenchymal-to-epithelial transition during early reprogramming.

The paper identifies Brca1, Bard1, and Wdr5 as factors linking DNA damage response to MET during reprogramming, using siRNA screening and colony morphology analysis.

Specificity of RNAi, LNA and CRISPRi as loss-of-function methods in transcriptional analysis

This study compares the off-target effects of RNAi, antisense oligonucleotides, and CRISPRi in transcriptomic analyses, showing that all methods have non-negligible off-target effects and recommend using multiple LOF methods for functional validation.