Point of View: An easy way to improve lab meetings doi.org/10.7554/eLif...
I'm really happy to see this one out @elife.bsky.social. Awesome Cara Glynn and I describe and reflect on a year-long, low-cost practice that transformed our group meetings.
#researchculture #ECR #labmeetings
Few people are aware of how much progress has been made against cancers.
Leukemia is probably the most striking example.
Before the 1970s, most children affected by leukemia would soon die from it.
Now, most children in rich countries survive.
ourworldindata.org/childhood-le...
I wrote about why every lab should have AI use guidelines, and how to do it.
open.substack.com/pub/blekhman...
$2.45 billion NIH grant cuts and ~2300 terminated active research grants were DOGE'd in early 2025
Who were most affected?
www.pnas.org/doi/full/10....
Early career and women researchers
Fragmentomic liquid biopsy enables early breast cancer detection, molecular subtyping and lymph node assessment www.nature.com/articles/s4...
“Hiring, promotion, and funding decisions often still revolve around traditional journal publications.”
www.science.org/content/arti...
Figure 1.(A) Classical gel electrophoresis experiments showing mono-, di-, tri-, tetra-, and further multinucleosome bands upon chromatin digestion. (B) The nucleosome repeat length (NRL) is defined as the genomic distance between the centres of two neighbouring nucleosomes.
Figure 2.Nucleosome mapping using MNase-seq versus ATAC-seq. (A) In MNase-seq, nucleosomes in both open and tightly packed genomic regions are accessible to digestion. MNase preferentially cleaves DNA between nucleosomes and digests DNA until it encounters a histone octamer, which provides a footprint of nucleosome-protected DNA regions. (B) Bulk MNase-seq results in averaged maps across millions of cells, effectively capturing all possible nucleosome positioning configurations. (C) Single-cell MNase-seq (scMNase-seq) results in a noisier and sparser signal. The resulting footprints still represent nucleosome-protected regions, but not all nucleosomes are represented. (D) In ATAC-seq, open regions can be accessed by the enzyme Tn5 transposase, which can insert primers in regions free from the binding of nucleosomes and transcription factors (TFs). (E) For open chromatin regions, nucleosome maps can be obtained from ATAC-seq similar to MNase-seq. (F) Closed, tightly packed chromatin regions may be less represented in ATAC-seq nucleosome maps.
Figure 5.Molecular mechanisms affecting nucleosome spacing. (A) Linker histones H1 and nonhistone chromatin proteins which compete with H1s and modulate nucleosome spacing through structural and electrostatic mechanisms. (B) Chromatin remodellers actively reposition nucleosomes following context-dependent rules. (C) Cell state-dependent chromatin boundaries formed by CTCF and other structural proteins, as well as associated recruitment of chromatin remodellers which space nucleosomes. (D) Gene activity associated with remodeller action and RNA polymerases transcribing through the nucleosomes, leading to smaller distances between nucleosomes in regulatory regions and gene bodies. (E) DNA sequence repeats of different types.
![Figure 6. Examples of NRL changes in biological systems. (A) Cell differentiation leads to NRL changes between different cell types, e.g. mouse dorsal root ganglia neurons (NRL ∼165 bp) versus cortical astrocytes (NRL ∼183 bp) [175]. Schematic cell shapes are adapted from an image created in BioRender (https://BioRender.com/89trj2t). (B) Paired normal versus tumour breast tissues show NRL shortening in cancer (figure adapted from [36] under the CC BY 4.0 licence (https://creativecommons.org/licenses/by/4.0/)). (C) Nucleosome positioning derived from cfDNA of human volunteers shows NRL increase with age (figure reprinted from [79] under the CC BY 4.0 licence (https://creativecommons.org/licenses/by/4.0/)).](https://cdn.bsky.app/img/feed_thumbnail/plain/did:plc:7rjg5hcnnloxgwuvwi23aixu/bafkreihl7mkdtxojw23qoqxm7yt57frzc24mjjllszhbohbvb67ffguccy)
Figure 6. Examples of NRL changes in biological systems. (A) Cell differentiation leads to NRL changes between different cell types, e.g. mouse dorsal root ganglia neurons (NRL ∼165 bp) versus cortical astrocytes (NRL ∼183 bp) [175]. Schematic cell shapes are adapted from an image created in BioRender (https://BioRender.com/89trj2t). (B) Paired normal versus tumour breast tissues show NRL shortening in cancer (figure adapted from [36] under the CC BY 4.0 licence (https://creativecommons.org/licenses/by/4.0/)). (C) Nucleosome positioning derived from cfDNA of human volunteers shows NRL increase with age (figure reprinted from [79] under the CC BY 4.0 licence (https://creativecommons.org/licenses/by/4.0/)).
Nucleosome aficionados! Our new review "Nucleosome spacing across cell types, diseases, and ages" is out in NAR: academic.oup.com/nar/article/...
A huge effort to pull together what we’ve learned about nucleosome spacing in many systems. Enjoy!
@milena-bikova.bsky.social @chrsclrksn.bsky.social
‘No one quite like her’: meet the female colleagues who inspire these award-winning women in science
To mark International Women’s Day, Nature asked winners of its awards programmes to nominate a colleague who brings out the best in them.
www.nature.com/articles/d41...
1/ The hardest skill in bioinformatics?
It's not coding. It's not stats.
A hiring manager told me their biggest challenge: finding bioinformaticians who can talk to biologists. Here's why that matters:
The role of KRAB zinc-finger proteins in expanding the domestication potential of transposable elements
New study from Dr. Hansen Housheng He’s team, thrilled that we contributed, on functional mapping of m6A in cancer at scale with implications for novel target discovery and future therapeutic development. www.nature.com/articles/s43...
We are looking for a research associate with a working knowledge and interest in mass spectrometry of small molecules. If interested, please check this out! careers.miami.edu/us/en/job/R1...
Our new study found that, when prostate cancer cells spread, they adopt an “inflammatory-like” state and mimic immune cells, suggesting new ways to control cancer progression.
Co-led by @matlupien.bsky.social @uhn.ca @uhnresearch.ca with @dkfz.bsky.social:
doi.org/10.1038/s414...
Hot from the press: Using single-cell chromatin accessibility and gene expression across ~300,000 cells, we show that prostate cancer dissemination involves phenotypic plasticity over clonal selection, with malignant cells converging toward an inflammatory-like state during lymph node spread.
Cell-type deconvolution methods for spatial transcriptomics
rdcu.be/el1kC
ATCC's Cell Line Omics Data www.atcc.org/application...
Our lab website just got a major refresh to better present:
Our research philosophy: why chromatin is central to our work.
A snapshot of our culture: diverse, collaborative, impact-driven.
Our priorities: how we translate discoveries into clinical reality.
Check it out
We are looking for a postdoctoral fellow to work on induced proximity 🤜🤛 and functional genomics! Join our team in Toronto 🇨🇦 to tackle major challenges in oncology and neurodegeneration. www.nature.com/naturecareer...
This looks really cool! Would you consider including variable direct repeats, this should minimize homology between the interspersed repeats? >>> doi.org/10.1038/s415...
1/ You run ChIP-seq to find where your transcription factor binds. You run RNA-seq to see which genes change expression. Now, you ask a "simple" question, what are the "direct targets"?
Lunch today halfway around the world in Hangzhou and met a new asst professor who was very thankful for this resource. Please help out folks like them and other early career scientists with examples of job apps. Submit yours!
github.com/RILAB/statem...
Studying cancer evolution needs multi-region or single cell seq for phylogenetics, right? Amazingly (I think!) we found single-sample bulk methylation suffices, via analysis of "fluctuating methylation". In @nature.com today led by brilliant @calumgabbutt.bsky.social www.nature.com/articles/s41...
8 Resources to study Transcription factor binding, enhancers and histone modification distribution
1. ENCODE www.encodeproject.org/
Included in this is SickKids in Toronto, by the way. So Canadian kids with cancer will also be affected by this.
Imagine voting for kids with brain tumors to lose access to clinical trials.
“‘She uncovered the social experience of women in science’ — the lab assistants who never became managers, the geologists poring over data in government offices while their male peers were doing fieldwork, those who despite their advanced degrees didn’t get hired or promoted, or who were sidelined…”
Two PhD positions available in our lab to study #chromatin, #epigenetics and cancer
Thrilled to share our latest work, just published in @nature.com ⬇
www.nature.com/articles/s41...
We discovered that PARP inhibitors 💊 trigger histone eviction from the chromatin and this creates a hidden vulnerability in PARPi resistant tumors.
🧵 (1/8)
Image credit: @gloglita.bsky.social @lifescienceeditors.bsky.social captured DynaTag in action: a pA-Tn5 probe (multicoloured) binds an antibody (white), which binds p53 DNA-binding domain (green) on DNA (blue) within 2 nucleosomes
🧪Move over CUT&Tag, there’s a new #TranscriptionFactor mapping method in town.
Our newly developed DynaTag is faster, cleaner, more sensitive than #ChIPseq, #CUT&RUN and #CUT&Tag.
🔗 Our @natcomms.nature.com paper: www.nature.com/articles/s41...
🧵Let’s break down what makes DynaTag so powerful (1/7)
Please pread the word.
We have just launched the Hubrecht International PhD Program (HIPP).
Are you looking for a PhD position in molecular and developmental biology or related subject in an international, very supportive and collaborative environment?
Then apply to the HIPP!! 👇
