“Atf3 defines a population of pulmonary endothelial cells essential for lung regeneration” by Niethamer et al. 2022 doi.org/10.1101/2022.1… describes an important discovery in which reanalysis of data previously published by those researchers had a key role. Lung performance

Recent paper by Morrison et al. shows that gluten-free diet (GFD) can cause dysbiosis with consequences like intestinal inflammation, food allergies etc.  25-50% of people have genetic susceptibility to Celiac Disease (CeD) that in a minority of cases leads to this disease, and

YAP/TAZ can be a trigger in “marine mines” laid by tumors to create delayed metastasis.  This is but one of many cancer mechanisms involving YAP/TAZ (a central component of Hippo pathway) reviewed by Piccolo et al. in YAP/TAZ as master regulators in cancer, Nature Cancer, Dec

A new paper in Cancer Cell should be a great resource in future work on immunotherapy. Immunotherapy is currently the best method to treat many cancers, but its success is mixed, and long-term side effects occur too.  Investigating bulk data is hard without single cell reference

Interpreting gene expression and epigenetic data requires understanding heterochromatin assembly, regulatory mechanisms that can silence gene expression in wider chromosomal regions, and when those mechanisms are blocked, we can observe activation of gene expression.  Shiv Greval

To proliferate and self-renew, cells of glioblastoma (GBM) need significantly faster metabolism than their ancestral neuronal cells, and for that, they take mitochondria from glial cells, mostly from astrocytes.  This is achieved by “hijacking” the healthy mechanism of astrocyte

There is a big excitement about Nature paper by Lopera et al. published on May 15.  Development of Alzheimer disease and resulting dementia involves the emergence and growth of amyloid plaque that impedes the function of neurons.  After regulatory dysregulation leads to plaque

Manolis was my mentor but purely independently I don’t like bullying either.

An R-loop reorganizes a small section of a chromosome: DNA strands are separated and one of them is bound to its complementary RNA sequence.  They appear frequently during elongation, and for many genes, they are essential for their proper expression.  However, exposed single DNA

Standard methods sometimes produce nonsense.  In 2020, researchers of UC La Jolla published in Nature their discovery that microbiome present in cancer samples identifies their cancer identity and type, using authoritative TCGA data base, hg19 genome assembly and Kraken pipeline

Some cell cultures get more ❤️ than other, especially if they start with at least one ❤️

Hot new insights on pioneer transcription factors are reviewed by Barral and Zaret in the latest Trends in Genetics. Cells adopt new roles during cell differentiation or tumor disregulation, and it is well known that this change is guided by master transcription factors, known

Google AI scientists teamed up with Liverpool FC coaches to create a strategy for corner kicks during a football game. I wonder if Liverpool FC will test it in real life; that could be exciting. Imagine a match between Google-supported Liverpool FC and ChatGPT-supported Arsenal.

Mattei, Bailly, and Meissner provide an insightful review of CpG methylation in Trends in Genetics, tracing from its discovery in 1925 to current knowledge and outstanding questions. Originally a defense mechanism in bacteria against bacteriophages, DNA methylation has evolved

This year, RECOMB was held at MIT, within walking distance from my place, so I simply HAD to attend. I went to the satellite workshops this weekend. It was great to see new results in computational biology and potential future methods. Today's science can be tomorrow's

Gene regulatory networks: with cycles or without cycles? Inferring gene regulatory networks (GRNs) from data such as knockout screens or single-cell assays has many applications. In particular, it helps identify biological mechanisms and enhances the discovery power of GWAS

In a recent publication in Cell Report Medicine (November 19, 2024), the authors explore a novel strategy to prevent T-cell exhaustion in the context of immuno-oncology. While adoptive cell therapies involving in vitro modified T cells can avoid immune exhaustion, the