Mark Mendoza
@doctorshark.bsky.social
MCB PhD candidate studying (bad) blood and stem cells @FredHutch and UW | home means nevada | ¡no manches! | YNWA
Reposted by Mark Mendoza
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.)
(Please repost to reach a broad audience.)
November 12, 2025 at 4:49 AM
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.)
(Please repost to reach a broad audience.)
Reposted by Mark Mendoza
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
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
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...
rdcu.be
June 18, 2025 at 8:33 AM
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
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
Reposted by Mark Mendoza
Generation of a MYC-based gene circuitry that enhances immunotherapy response and tumor killing in bladder cancer. doi.org/10.1038/s414...
August 28, 2025 at 3:13 PM
Generation of a MYC-based gene circuitry that enhances immunotherapy response and tumor killing in bladder cancer. doi.org/10.1038/s414...
Reposted by Mark Mendoza
@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
Details below
careersearch.stanford.edu/jobs/computa...
Plz RT
August 19, 2025 at 12:29 AM
@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
Details below
careersearch.stanford.edu/jobs/computa...
Plz RT
Reposted by Mark Mendoza
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...
* 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...
February 9, 2025 at 6:56 PM
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...
* 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...
Reposted by Mark Mendoza
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...
I want to provide some context on what that means and why it matters.
grants.nih.gov/grants/guide...
NOT-OD-25-068: Supplemental Guidance to the 2024 NIH Grants Policy Statement: Indirect Cost Rates
NIH Funding Opportunities and Notices in the NIH Guide for Grants and Contracts: Supplemental Guidance to the 2024 NIH Grants Policy Statement: Indirect Cost Rates NOT-OD-25-068. OD
grants.nih.gov
February 8, 2025 at 12:18 AM
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...
I want to provide some context on what that means and why it matters.
grants.nih.gov/grants/guide...
Reposted by Mark Mendoza
@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...
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...
www.exphem.org
February 6, 2025 at 10:03 AM
@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...
Reposted by Mark Mendoza
Fascinating and timely thread.
THREAD
Weird and wrong beliefs that humanity held onto for way longer than we should have.
These days we enlightened denizens look back on those simpletons and giggling fools of old and tut-tut at their hilarious beliefs.
*Record Scratch*
Here's some stuff we got wrong until recently.
1/19
Weird and wrong beliefs that humanity held onto for way longer than we should have.
These days we enlightened denizens look back on those simpletons and giggling fools of old and tut-tut at their hilarious beliefs.
*Record Scratch*
Here's some stuff we got wrong until recently.
1/19
February 6, 2025 at 8:02 AM
Fascinating and timely thread.
Reposted by Mark Mendoza
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
January 28, 2025 at 6:34 AM
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
Reposted by Mark Mendoza
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...
Paper: www.nature.com/articles/s41...
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.
www.nature.com
January 23, 2025 at 2:11 AM
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...
Paper: www.nature.com/articles/s41...
Reposted by Mark Mendoza
Totally. But you come out much more dusty and with lab tape stuck to you.
January 16, 2025 at 12:18 AM
Totally. But you come out much more dusty and with lab tape stuck to you.
Reposted by Mark Mendoza
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 🎆 !
Happy 2025 everyone 🎆 !
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...
doi.org
January 6, 2025 at 2:05 PM
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 🎆 !
Happy 2025 everyone 🎆 !
Reposted by Mark Mendoza
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.
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.
December 30, 2024 at 9:43 PM
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.
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.
Reposted by Mark Mendoza
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.
If you’d like to support children with cancer, especially those in your area, consider donating to your local children’s hospital.
December 28, 2024 at 7:12 PM
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.
If you’d like to support children with cancer, especially those in your area, consider donating to your local children’s hospital.
Reposted by Mark Mendoza
Integrative analysis of the 3D genome and epigenome in mouse embryonic tissues. #3Dgenome #Epigenetics #ChromatinContacts #NatureStructuralAndMolecularBiology 🧬
www.nature.com/articles/s41...
www.nature.com/articles/s41...
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...
www.nature.com
December 19, 2024 at 11:29 PM
Integrative analysis of the 3D genome and epigenome in mouse embryonic tissues. #3Dgenome #Epigenetics #ChromatinContacts #NatureStructuralAndMolecularBiology 🧬
www.nature.com/articles/s41...
www.nature.com/articles/s41...
Reposted by Mark Mendoza
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
Terrific. Grants help you gain control over your career.
Here are 9 tips for writing fundable grants:
#AcademicSky #PhDSky
December 9, 2024 at 4:38 PM
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
Terrific. Grants help you gain control over your career.
Here are 9 tips for writing fundable grants:
#AcademicSky #PhDSky
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
#PhDSky
December 20, 2024 at 1:48 AM
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
#PhDSky
Reposted by Mark Mendoza
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...
@alexkschurer.bsky.social
@gritsmanlab.bsky.social
academic.oup.com/stcltm/advan...
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
academic.oup.com
December 4, 2024 at 3:20 AM
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...
@alexkschurer.bsky.social
@gritsmanlab.bsky.social
academic.oup.com/stcltm/advan...
Reposted by Mark Mendoza
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/🧵
nature.com/articles/s41588-024-01945-x
In it, we show that epigenetic DNA methylation causes errors during DNA replication!
#epigenetics #mutations
1/🧵
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...
nature.com
December 2, 2024 at 12:12 PM
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/🧵
nature.com/articles/s41588-024-01945-x
In it, we show that epigenetic DNA methylation causes errors during DNA replication!
#epigenetics #mutations
1/🧵
Reposted by Mark Mendoza
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...
www.cell.com/molecular-ce...
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...
www.cell.com
December 3, 2024 at 2:51 AM
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...
www.cell.com/molecular-ce...
Reposted by Mark Mendoza
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 🧪
December 1, 2024 at 1:36 PM
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 🧪
Reposted by Mark Mendoza
🚀 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
November 26, 2024 at 1:40 PM
🚀 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
Reposted by Mark Mendoza
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
‘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.
nyti.ms
November 25, 2024 at 4:19 PM
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
Reposted by Mark Mendoza
Here’s the updated Computational Biology Starter Pack! Let me know if you'd like to be included.
go.bsky.app/QVPoZXp
go.bsky.app/QVPoZXp
November 24, 2024 at 4:33 PM
Here’s the updated Computational Biology Starter Pack! Let me know if you'd like to be included.
go.bsky.app/QVPoZXp
go.bsky.app/QVPoZXp
Reposted by Mark Mendoza
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.
November 23, 2024 at 7:53 PM
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.