Osiel Recoder @OsRecoder

New book chapter: "How to Weigh a Cell." This chapter explains how scientists have weighed cells throughout history, often using simple equipment and back-of-the-envelope calculations. It has lots of interactives, so you can "repeat" the experiments directly in your browser.

Our paper is out in @ScienceMagazine Here we describe how stem cell retain epigenetic inflammatory memory long-term. Full text in the link below! Congratulations @chris_cowley14 @SairajSajjath @LFSoto12 and everyone else involved! science.org/doi/10.1126/sc…

The epigenome "remembers" inflammation and primes stem cells for cancer @snaga13 @Nature @JD_Buenrostro @Harvard nature.com/articles/s4158… nature.com/articles/d4158…

Jason Buenrostro @JD_Buenrostro

2 months ago

It’s well known that inflammation increases cancer risk, but how? The answer: the epigenome "remembers" inflammation and primes stem cells for cancer. Here is our paper: nature.com/articles/s4158… And a special shoutout to the lead author @snaga13 A 🧵

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Density transitions in the regulation of transcription dlvr.it/TR4V0h

New online! Global reorganization of genome architecture at the transition to gametogenesis dlvr.it/TR4WYw

Writing forces your brain to coordinate memory, reasoning, and meaning-making simultaneously. Every time you write, you rewire toward clearer thinking. Every time you let an LLM do it, you rewire toward consumption.

(1/8) Still wondering how low complexity intrinsically disordered regions (IDRs) guide transcription factors (TFs) to bind in genomes? Previous studies on sequence grammars; our new @molcell paper takes the next step: de novo design of functional TF IDRs! cell.com/molecular-cell…

Is there a formula for a competitive NIH grant application? This Perspective aims to provide an inclusive roadmap on the elements of NIH funding. Elements of successful NIH grant applications

New Online! Organization of replicated chromosomes by DNA loops and sister chromatid cohesion bit.ly/4jiRJV8

This is what amino acids look like if you let the side chains flop around on the page

New Online! Critical constituents and assembly principles of centriole biogenesis in human cells bit.ly/4pAu30v

Five years ago, researchers at Google DeepMind unveiled AlphaFold2 go.nature.com/4rpvkct

Here are 30 great essays about biology. I consider these to be my "personal canon," and think that they are all basically perfect in their own ways, despite being different in form and style. All have shaped my own writing considerably. I'm not including links here, but you can easily search and find these. 1. Diagnosing the decline in pharmaceutical R&D efficiency, Jack W. Scannell et al., 2012 2. Predictive validity in drug discovery: what it is, why it matters and how to improve it, Jack Scannell et al., 2022 3. Is the cell really a machine?, Daniel J. Nicholson, 2019 4. How academia and publishing are destroying scientific innovation: a conversation with Sydney Brenner, Elizabeth Dzeng, 2014 5. A Future History of Biomedical Progress, Adam Green (Markov), 2022 6. The pharma industry from Paul Janssen to today, Alex Telford, 2023 7. The Lives of a Cell, Lewis Thomas, 1974 8. The maddening saga of how an Alzheimer’s ‘cabal’ thwarted progress toward a cure for decades, Sharon Begley, 2019 9. The Scientific Virtues, Slime Mold Time Mold, 2022 10. First Clean Water, Now Clean Air, Fin Moorhouse, 2023 11. I should have loved biology, James Somers, 2020 12. The Baffling Intelligence of a Single Cell, James Somers & Edwin Morris, 2024 13. Biology is more theoretical than physics, Jeremy Gunawardena, 2013 14. Can a biologist fix a radio?, Yuri Lazebnik, 2002 15. Cells are very fast and crowded places, Ken Shirriff, 2011 16. Life at Low Reynolds Number, E.M. Purcell, 1976 17. Lena, qntm, 2021 18. Sequences and Consequences, Sydney Brenner, 2010 19. The NIH Report, Matt Faherty, 2022 (I edited this one) 20. Simplicity in biology, Uri Alon, 2007 21. A breakthrough from 60 years ago: “General nature of the genetic code for proteins” (1961), Matthew Cobb, 2021 22. Molecular “Vitalism”, Marc Kirschner, John Gerhart, Tim Mitchison, 2000 23. The Coming Technological Singularity, Vernor Vinge, 1993 24. Review of Scientific Self-Experimentation, Brian Hanley & William Bains & George Church, 2018 25. Coming full circle-from endless complexity to simplicity and back again, Robert Weinberg, 2014 26. Nothing in Biology Makes Sense Except in the Light of Evolution, Theodosius Dobzhansky, 1973 27. The Impersonator: The Fake Data Were Coming From Inside the Lab, Uri Simonsohn, 2024 28. The Longevity FAQ, José Luis Ricón (Nintil), 2020 29. The Perfect Human is Puerto Rican, Lior Pachter, 2014 30. No Evidence of Disease, Stephanie Bourque, 2012

New Online! Mechanistic insights into cargo sorting and export from the Golgi apparatus bit.ly/49FYldq

Enjoy! link.springer.com/book/10.1007/9…

In its first year tidyplots.org has become the go-to data viz for many life science researchers, got 620+ stars on Github, ~30K CRAN downloads, and 11 citations. Thank you for using, sharing, citing, and feedback! There is more to come 🤩 #rstats #dataviz #phd

Nature research paper: Adenosine signalling drives antidepressant actions of ketamine and ECT go.nature.com/4qPa53C

Scientists have created the most detailed maps yet of how our brains differentiate from stem cells during embryonic development and early life go.nature.com/3LsSpuj

The protein concentration in the cytoplasm is so high that the average protein has a water hydration shell of only ≈ 10 water molecules separating it from the adjacent protein hydration shell.

How are promoter interactions coordinated during cell differentiation? In our first paper, we investigate the temporal relationship between genome folding, transcription and histone modifications during ESC differentiation. (1)

Molecular Cell @MolecularCell

2 years ago

Online Now: Transient promoter interactions modulate developmental gene activation dlvr.it/TFrfM2

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