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Associate professor at SciLifeLab Genomics, Uppsala University. Computational biology and new sequencing technologies with focus on human/medical applications
Check out our new paper on long-read single-cell WGS! Here we show that SNVs, SVs and TRs can be analyzed in individual human T-cells and present results of de novo assembly https://www.nature.com/articles/s41467-023-40898-3
Long-read whole-genome analysis of human single cells - Nature Communications

Here the authors introduce a new method to study DNA in single cells by long-read sequencing. Their method gives a more complete view of the genomic structure of individual cells and allows to study genetic differences at the single-cell level.

Nature

The saddest part of the already sad story at https://www.science.org/content/article/paleontologist-accused-faking-data-dino-killing-asteroid-paper

"After trying to discuss the matter with editors at Scientific Reports for nearly a year, During recently decided to make her suspicions public."

I have no idea whether During's complains are legitimate or not. But the part where she gets stonewalled by the journal rings terribly true.

Paleontologist accused of faking data in dino-killing asteroid paper

Scientist who oversees famed extinction-day site denies claims he made up data to scoop a former collaborator

We're soon about to start our first single cell MAS-Iso-Seq run on
@PacBio Sequel II. Anyone who knows what bioinfo tool & version is state-of-the-art? And what we could expect in terms of throughput?

#Introduction
Hi all, I am Elisabeth Bik, @microbiomdigest on Twitter. I am a Dutch/American microbiologist with a PhD from Utrecht University (not an MD).

In 2019 I started working for myself. I specialize in #ImageForensics, i.e. searching for image problems in published scientific papers, #ResearchIntegrity and #ScienceMisconduct.

Hope to meet and discuss problems in science papers with you here!

I mostly post #ImageForensics challenges or rant about #SciencePublishing.

#CRISPRpapers hashtag?

Let's start with detection of large CRISPR edits.

https://www.science.org/doi/10.1126/sciadv.abo7676

Why care:
Often first questions after #CRISPR editing is: What mutations do I have? Unfortunately, that can be hard to answer. Target sites are typically PCR amplified and sequenced, but that has a strong survivor bias. PCR favors some sequences, creates chimeras and fails if primer site is deleted. This paper presents a workflow to mitigate some of these issues and get a more complete picture.

@adameur I completely agree w you wrt amplification-free is the true way here.
Let's get the ball rolling here. First proper toot: How to identify artifacts in cDNA-seq, a case study

Hey everyone. Just making sure everyone knows that direct messages on here are not end-to-end encrypted. They work more like a post, with visibility set to the person/people you tag.

This means an admin (like me), can read these by looking at the database/in backups.

I promise never to do this.

If that's not good enough (which is fine, obviously), please use something like signal for DMs

p.s. Twitter DMs are also not encrypted and anyone there can read them too.

@adameur good question.
In the explore page there will be some in the last tab.

As admin I can scroll everyone. Maybe try searching for them? It works across instances too.
Otherwise use one of the automated tools. If someone could post the ones they've been using to help out?

Is there some way to browse the users of genomic.social? I think there might be lots of familiar faces here but don't know how to find them.