We are looking for a postdoctoral researcher to work on modeling of protein complexes as networks.
Please see the details here
drive.google.com/file/d/1tATn37…
Please fill the application form for applying - forms.office.com/r/YzSg0Jw57n
Areejit Samal Mohit Kumar Jolly Ragothaman Yennamalli Anshu Bhardwaj, Ph.D.

Human Pathomap. Now in Bioinformatics. academic.oup.com/bioinformatics…

scPRAM accurately predicts single-cell gene expression perturbation response based on attention mechanism academic.oup.com/bioinformatics…

HelixFold-Multimer: Elevating Protein Complex Structure Prediction to New Heights
HelixFold extends to Multimer case. They showed better performance against AlphaFold and RoseTTAFold

Check out our website 'Clocks Around and Within Us': follow dolphins sleeping with one side of the brain, how circadian clocks are wired, why roses can bloom in winter, and how, during evolution, life on earth has adapted to the day/night environment:

buff.ly/3U0xY8K

Evaluation and optimization of sequence-based gene regulatory deep learning models biorxiv.org/content/10.110…

and the answer is: still not sure yet. Close to 20,000 protein-coding genes but more like 100,000 different protein isoforms. And noncoding RNAs? Who knows?

Our review is now online! We discuss what we know (and what we don't know) about 'Mechanistic drivers of chromatin organization into compartments'. See our discussion of compartment interval sizes and our proposed multiple compartment 'flavor' model. sciencedirect.com/science/articl…

Transcriptional rewiring of an evolutionarily conserved circadian clock:
Luis Larrondo Luis F. Larrondo and collaborators show that basic circuit topology can be dramatically changed, while still yielding a functional semi-synthetic clock
embopress.org/doi/full/10.10…

Traditional economics has failed. Meet the disruptive economist applying chaos theory and complexity science to make more accurate predictions. newscientist.com/article/mg2623…

Happy to share preprint from our group on understanding the binding pocket dynamics of nuclear receptor REV-ERB. Shriyansh led the work.
biorxiv.org/content/10.110…

How intermittent fasting can change fat cells to affect energy use. elifesciences.org/digests/91060/….

How do animals regulate what time of day they are active? @rosmalenlaura et al show gene expression dynamics in tissues and brain regions differ in nocturnal and diurnal mice, especially in the habenula, suggesting a particular role:

buff.ly/3vU9g1F

You can use ConservFold (by Rodrigues lab: rodrigueslab.com/resources) to assign a conservation score instead of b_factor. Then render model as worms and use a coloring scheme (twitter.com/miangoar/statu…) and voila! Now you has the most conserved positions! (pdb: 1zg4)

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Rapid and Sensitive Protein Complex Alignment with Foldseek-Multimer biorxiv.org/cgi/content/sh… #biorxiv_bioinfo

Protein–ligand structure prediction | Nature Methods nature.com/articles/s4159…

Predictomes: A classifier-curated database of AlphaFold-modeled protein-protein interactions
Interesting PPI virtual screening work based on AlphaFold-Multimer.
- SPOC (Structure Prediction and Omics informed Classifier) is a random forest-based classifier that accurately…

In Silico Generation of Gene Expression profiles using Diffusion Models biorxiv.org/content/10.110…

Lol

The scales, mechanisms, and dynamics of the genome architecture

Lizana and Schwartz, Sci. Adv. (April 10, 2024)

science.org/doi/pdf/10.112…