Lisanne Mout

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

METTL3-based epitranscriptomic editing screening identifies functional m6A sites in cancers - Nature Cancer He and colleagues develop a METTL3-based RNA base-editing screening strategy to identify functional N6-methyladenosine (m6A) sites that are important for prostate cancer cells and validate the role of...

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...

Research Associate 1 in Miami, Florida, United States of America | Research at University of Miami Apply for Research Associate 1 job with University of Miami in Miami, Florida, United States of America. Research at University of Miami

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...

Prostate cancer cells converge to an inflammatory-like state upon metastatic dissemination - Nature Communications Understanding tumor heterogeneity and its impact on prostate cancer progression remains elusive. Here, single nucleus snATAC and snRNA sequencing of a multi-loci sampled cohort of advanced prostate ca...

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.

Genetic and Epigenetic Reprogramming of Transposable Elements Drives ecDNA-Mediated Metastatic Prostate Cancer Extrachromosomal DNAs (ecDNAs), which replicate and segregate in a non-Mendelian manner, serve as vectors for accelerated tumor evolution. By integrating chromatin accessibility, whole-genome sequenci...

www.biorxiv.org/content/10.1...

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

POSTDOCTORAL FELLOW - Toronto (City), Ontario (CA) job with Taipale Lab, Donnelly Centre, University of Toronto | 12849004 The Taipale lab in the Donnelly CCBR and University of Toronto is looking for a highly motivated Postdoctoral Fellow

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...

Optimization of AsCas12a for combinatorial genetic screens in human cells - Nature Biotechnology Improved Cas12a variants and sgRNA design rules enhance genome-wide screens.

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"?

GitHub - RILAB/statements: Successful Job Applications and Grants Successful Job Applications and Grants. Contribute to RILAB/statements development by creating an account on GitHub.

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...

Fluctuating DNA methylation tracks cancer evolution at clinical scale - Nature Cancer evolutionary dynamics are quantitatively inferred using a method, EVOFLUx, applied to fluctuating DNA methylation.

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

NASP modulates histone turnover to drive PARP inhibitor resistance - Nature PARP inhibitor treatment triggers histone release from the chromatin in cancer cells; consequently, targeting the histone chaperone NASP renders cells vulnerable to PARP inhibition.

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!! 👇

Range extender mediates long-distance enhancer activity - Nature The REX element is associated with long-range enhancer–promoter interactions.

Our paper describing the Range Extender element which is required and sufficient for long-range enhancer activation at the Shh locus is now available at @nature.com. Congrats to @gracebower.bsky.social who led the study. Below is a brief summary of the main findings www.nature.com/articles/s41... 1/

Transcriptional and post-transcriptional regulation of transposable elements and their roles in development and disease - Nature Reviews Molecular Cell Biology Transposable elements (TEs) comprise nearly half of the human genome. This Review discusses transcriptional and post-transcriptional mechanisms that repress TE activity, how TEs escape this suppressio...

We wrote a review on Transposable Elements (TEs) and almost all aspects of TE silencing and their roles in biological processes & disease.
www.nature.com/articles/s41...

1/ Working with big data in R?
Your wrangling just got a massive upgrade.
duckplyr is now in the tidyverse—and it’s fast. Really fast. 🧵

Applications are now open! We are recruiting 20 Assistant Professors in a wide range of subject areas. We're looking for early-career researchers with strong scientific merits and future potential.
🔗 All positions: ki.se/en/about-ki/...

Postdoctoral Associate – Nima Sharifi Laboratory - Miami, Florida (US) job with University of Miami Desai Sethi Urology Institute | 12840300 The Nima Sharifi Laboratory is seeking to recruit outstanding postdoctoral associates with a primary interest in the fundamental mechanisms of huma...

Do you have a primary interest in fundamental mechanisms of human biology, biochemistry, metabolism, genetics, or medicinal and analytical chemistry and looking for a postdoctoral fellowship? 🧪 www.nature.com/naturecareer...

@saramostafavi.bsky.social (@Genentech) & I (@Stanford) r excited to announce co-advised postdoc positions for candidates with deep expertise in ML for bio (especially sequence to function models, causal perturbational models & single cell models). See details below. Pls RT 1/

Are you @ the late stages of your postdoc ? Want to pursue a PI career ?

Then this 👇👇 is for you ! Apply for a spot @ our Talent Forum
www.helmholtz-munich.de/en/stem-cell...

Peer-networking / Career orientation and more !!!

Please distribute :) 🙂

How a discovery in Yellowstone National Park led to the development of PCR - Richmond Scientific A discovery in Yellowstone National Park led to the development of PCR, the gold-standard COVID-19 tests used to fight the global pandemic.

Reminder: Nobel-prize winning PCR (1983), used in basically all genetic tech today, was only possible because of extremophile bacterium discovered in 1964 in Yellowstone funded by a small ~$80k NSF grant with no obvious application at the time. #science 🧪
www.richmondscientific.com/how-a-discov...