Mark Mendoza

Join us in congratulating Elana Thieme and Mark Mendoza, fourth-year graduate students in the Molecular and Cell Biology program, on receiving prestigious graduate awards from @ash.hematology.org! #ASH25

Read more: https://bit.ly/4rLo3UA

Start #ASH2025 off with a bang and come to the Myeloid Workshop, OCCC 314 3pm.

Are you an early-stage graduate student (2nd or 3rd year) or early-stage postdoc based in the US or Canada, working primarily in Drosophila? Would you like to help improve the experience of all trainees working in Drosophila research? If so, read on.

(Please repost to reach a broad audience.)

A checklist for designing and improving the visualization of scientific data Nature Cell Biology - Creating clear and engaging scientific figures is crucial to communicate complex data. In this Comment, I condense principles from design, visual perception and data...

I gave in! After students asking for it, I now made a simple figure design checklist.
To help all scientists w/o graphic skills create clear, accessible, and truthful charts!
-> Out in @nature Cell Biology: rdcu.be/erwl4

#DataVisualization #PhD #SciComm

Thx for review @bethcimini.bsky.social + 2

Generation of a MYC-based gene circuitry that enhances immunotherapy response and tumor killing in bladder cancer. doi.org/10.1038/s414...

@jengreitz.bsky.social l & my lab want to co-hire a computational biologist/biostatistician with project management expertise to help map the regulatory code of the human genome and discover genetic mechanisms of disease.

Details below
careersearch.stanford.edu/jobs/computa...

Plz RT

Here's just a smattering of examples of things that indirects fund

* STARTUP COSTS. It's hard to get your first grants. Why should an agency bet its limited & competitive money on you before you have a track record? You make it less risky for them to bet on you by...

1. Today the NIH director issued a new directive slashing overhead rates to 15%.

I want to provide some context on what that means and why it matters.

grants.nih.gov/grants/guide...

Methodological Considerations on How to Identify Human Hematopoietic Stem Cells The hematopoietic system is highly regenerative and is organized hierarchically with hematopoietic stem cells (HSCs) sitting at the apex. Despite being some of the most widely studied stem cells, ques...

@isehsociety.bsky.social community: if you’re interested in HSC research in humans then this is a must read from leaders in the field. www.exphem.org/article/S030...

Fascinating and timely thread.

It’s been a week and it’s about as bad I was expecting. And it will continue to be bad, but whatever you are doing in your work or your community, you need to keep showing up, keep contributing to the foundation of something new and better, out of solidarity and love for each other and those to come

Multiscale footprints reveal the organization of cis-regulatory elements - Nature We developed PRINT, a computational method that identifies footprints of DNA–protein interactions from bulk and single-cell chromatin accessibility data across multiple scales of protein size.

Super excited to share our new study from the @jbuenrostro.bsky.social Lab in @nature.com! We developed a computational method for tracking transcription factor and nucleosome binding using single-cell ATAC-seq and deep learning.
Paper: www.nature.com/articles/s41...

Totally. But you come out much more dusty and with lab tape stuck to you.

ChromatinHD connects single-cell DNA accessibility and conformation to gene expression through scale-adaptive machine learning - Nature Communications Functional chromatin changes occur at different scales. Here, the authors introduce ChromatinHD, a method that characterises differential and predictive chromatin accessibility changes in a scale-adap...

Superb work by Wouter @Zouters & @OlgaPushkarev developing ChromatinHD, two scale-adaptive #machinelearning models & interpretation tools that use #scRNAseq + #scATACseq data to better understand how chromatin accessibility relates to gene expression doi.org/10.1038/s414...

Happy 2025 everyone 🎆 !

The 3 hardest things to learn as a scientist:
1. Trust the data, even when it’s not what you expected,
2. Trust the data, allowing it to change your direction,
3. Trust the data, but not too much: test with new data at every turn.

Many pediatric oncology programs rely on philanthropy and have just a small fraction of the resources that St Jude has.

If you’d like to support children with cancer, especially those in your area, consider donating to your local children’s hospital.

Integrative analysis of the 3D genome and epigenome in mouse embryonic tissues - Nature Structural & Molecular Biology The authors here show that chromatin interactions during mouse fetal development are spatiotemporally dynamic. Integrating interactomes with other datasets predicts target genes for candidate enhancer...

Integrative analysis of the 3D genome and epigenome in mouse embryonic tissues. #3Dgenome #Epigenetics #ChromatinContacts #NatureStructuralAndMolecularBiology 🧬
www.nature.com/articles/s41...

Scholars, want to write a fundable grant in 2024?

Terrific. Grants help you gain control over your career.

Here are 9 tips for writing fundable grants:

#AcademicSky #PhDSky

A few things I learned along the way

1) organizing citations with detailed tags is a game changer
2) setting boundaries (still a work in progress) creates more time
3) routines like going to the gym are grounding
4) I probably drink too much coffee

Hard to believe it’s been one week since I passed my general exam! It was a grind to get the proposal written and presentation completed but it’s done. I’m excited to get my experiments under way in the new year

#PhDSky

Targeting chromatin modifying complexes in acute myeloid leukemia Abstract. Acute myeloid leukemia (AML) is a devastating hematologic malignancy with high rates of relapse, which can, in part, be attributed to the dysregu

Overwhelmed by all of the exciting new research on chromatin modifiers in AML? Find it hard to keep track of all the new menin inhibitors? Well good news, we’ve just published the perfect review for you in SCTM!

@alexkschurer.bsky.social
@gritsmanlab.bsky.social

academic.oup.com/stcltm/advan...

Human DNA polymerase ε is a source of C>T mutations at CpG dinucleotides - Nature Genetics A new method called polymerase error rate sequencing (PER-seq) can measure the nucleotide misincorporation rate of DNA polymerases. DNA polymerase ε mutants produce an excess of CpG<TpG errors duri...

I'm going to repost a #thread here about a recent #paper from my group together with the labs of Marketa Tomkova and Skirmantas Kriaucionis:

nature.com/articles/s41588-024-01945-x

In it, we show that epigenetic DNA methylation causes errors during DNA replication!

#epigenetics #mutations
1/🧵

Long-range regulation of transcription scales with genomic distance in a gene-specific manner Jensen et al. show that targeting dCas9-VPR using a multiplexed array of RNA guides results in effective activator recruitment to promoter-distal, previously inaccessible genomic sites, allowing for l...

Today in Molecular Cell the work of one of my favorite (ex)PhD students in the Wysocka Lab: Dr. Christina Jensen. I saw this project develop throughout the years and it has kept me engaged in hypothesizing scenarios in every lab meeting. Congratulations to the authors!
www.cell.com/molecular-ce...

Diagram of our internal organs https://en.wikipedia.org/wiki/Organ_%28biology%29

We learn in school about the distinctive shapes of each of our body’s organs, but how did that arise? Organs self-assemble, as individual cells change shape and move in coordinated ways, sometimes with multiple cell /tissue types shaping one another 1/n 🧪

🚀 New preprint from our lab, Ekaterina Krymova, and @fabiantheis.bsky.social: UniversalEPI, an attention-based method to predict enhancer-promoter interactions from DNA sequence and ATAC-seq🌟 Read the full preprint: www.biorxiv.org/content/10.1... by @aayushgrover.bsky.social, L. Zhang & I.L. Ibarra

‘DNA Typewriters’ Can Record a Cell’s History Labs around the world are trying to turn cells into autobiographers, tracking their own development from embryos to adults.

Imagine a mouse in which all 10 billion cells keep a diary from fertilization. Imagine sentinel cells recording your experiences and sending out dispatches in the form of DNA. Here's a story I wrote about cell recorders 🧪 Gift link: nyti.ms/3Z3Mqza

Here’s the updated Computational Biology Starter Pack! Let me know if you'd like to be included.

go.bsky.app/QVPoZXp

What would Plato say about systems biology? In his Allegory of the Cave, prisoners can only see shadows on a wall and so they have a distorted reality. Also our measurements of genes, RNAs, proteins & metabolites are the shadows, not the reality of the complex biological systems.

In this episode of the Epigenetics Podcast, we talked with Yadira Soto-Feliciano from MIT about her work on the Menin-MLL complex and the effect of small molecules on its stability in leukemia. #podcast #epigenetics #chromatin

Listen here: https://buff.ly/3Ojf3nc

@mjafreeman.bsky.social's encyclopedia of Bluesky starter packs for 'mechanistic' biologists

People in need of specific bio content — check out this spreadsheet 🧫🔬🥼🧪