Discover and read the best of Twitter Threads about #biorxiv

Most recents (19)

Are you interested in performing splice-aware quantification of your #scrnaseq data, obtaining unspliced, spliced, and ambiguous UMI counts quickly & in <3GB of RAM? If so, check out the new manuscript by @DongzeHe, @CSoneson and me on #bioRxiv bit.ly/3vJr0Ji. 1/🧵
Understanding the origin of sequencing reads — the molecules from which they arise, the "gene" with which those molecules are associated, and the splicing status of those molecules — is a key task in single-cell RNA-seq quantification.
The short, (effectively) single-end nature of the reads used in popular technologies leads to situations in which it can be difficult or impossible to predict if a read was sequenced from an unspliced (nascent) or spliced (mature) RNA; these reads are designated as "ambiguous."
Read 20 tweets
So excited to finally share our paper, now available as a #bioRxiv preprint!

We found that enhancing #mtDNA replication can be highly deleterious, causing #Ferroptosis and neonatal 🫀#HeartDisease. 🧵thread coming soon..

biorxiv.org/content/10.110…

#newpublication #mitochondria
This project would not have been possible without the fantastic work from many people, so thank you all! @ASW_lab, @Kivela_lab, @WickstromLab, @JMitophile, @AWartiovaara et twitterless al.
@HelsinkiUniMed @helsinkiuni @HelsinkiUniMed @MitoResearch @uniofjyvaskyla @UniEastFinland
Recent years have brought several promising approaches to treat different kinds of #mitochondrial dysfunction, and increasing #mtDNA amount has been proposed to be beneficial for certain defects.
Read 11 tweets
Our preprint presenting the #genome of the most #endangered #seabird in Europe #Balearic #shearwater is out in #biorxiv

Cristian Cuevas Caballé @VizuetaJoel @meritxellgeno @SeabirdEcology @RiutortLab @JRozasUB

See 🧵👇 1/7
The Balearic shearwater is a Critically Endangered #IUCNRedlist #seabird endemic of the Balearic Islands affected by #introduced mammals and #bycatch in longline #fisheries. Previous studies predict their extinction by 2070! doi.org/10.1111/1365-2…

2/7
Combining #Illumina & #Nanopore data, we present the first high-quality reference genome for the species.

3/7
Read 8 tweets
Unlike traditional pharmacological inhibition, targeted protein degradation (TPD) induces ubiquitin-dependent degradation of proteins. However, it’s poorly understood which/why certain proteins are susceptible to TPD. We developed a machine learning model to answer this question.
Our paper is now available on #bioRxiv biorxiv.org/content/10.110…. This work couldn’t be accomplished without help from @ssroyburman, Jiaye Chen, @kdonovan1008 and other co-authors. Appreciate the great support and supervision from @XShirleyLiu, @ctokheim and @eric_fischer.
Donovan et al. previously mapped kinase degradability based on a library of multi-kinase degraders. Here, by modeling features intrinsic to protein targets, we classified highly- and lowly- degradable kinases, which show similar drug-target engagement, but different degradation.
Read 11 tweets
Absolutely thrilled to share our VASA-seq pre-print on #biorxiv today: Droplet-based single-cell total RNA-seq reveals differential non-coding expression and splicing patterns during mouse development 🧵
biorxiv.org/content/10.110…
VASA-seq captures most parts of the transcriptome (total RNA) of a #singlecell rather than just a portion. It was expertly developed by Fredrik Salmen, a postdoc in @AlexandervanOu1's lab at the @_Hubrecht and partner in crime for this project 🕵️ (1/n).
The method fragments the entire RNA payload of a cell and polyadenylates each fragment which makes them compatible with all poly(T) based barcoding methods, enabling UMI-tagging and retaining strand-specificity (2/n) 🧑‍🔬👨‍🔬
Read 14 tweets
After a year since #biorxiv, I am glad that this story found its home at @Dev_journal. Huge thanks to my colleagues @GurdonInstitute @MarioniLab, and people who reached out after #biorxiv submission! Here is the lengthy Tweetorial and some notes.
journals.biologists.com/dev/article/do…
We want to know why mammals fail at regen their arms or legs. However, we do not even know if we have cell types to perform such a feat.
To answer this, we use pre-metamorphic frogs/tadpoles. Gladly, my leg doesn’t look like a frog leg, but tadpoles are the most similar lab animal developing their limbs like mammals and can regen limbs + older they get, they fail at regen. So, what`s going different?
Read 16 tweets
#new paper in SARS-CoV-2 innate immunity
Pre-print in #bioRxiv

We found, SARS2 viral load and antiviral responses in nasal epithelium wane with advancing age, but Viral load alone is unlikely to explain differences in IFN induction observed.
biorxiv.org/content/biorxi…
thread/
1/
We infected differentiated nasal epithelium cultures derived from healthy children (1-12 y/o), young adults (26-34 y/o) and older adults (56-62 y/o) with SARS2 to identify age-related cell-intrinsic differences that may influence viral entry, replication and host response
2/
We integrated imaging, transcriptomics, proteomics and biochemical assays revealing age-related changes
in transcriptional regulation that impact viral replication, effectiveness of host responses and therapeutic
drug targets
Read 9 tweets
1/ Hark, a #tweeprint! Our new paper is up on #bioRxiv! It’s the results from our #OpenScope project with the @AllenInstitute about learning from unexpected events in the neocortical microcircuit!

Here's a thread with more details...

biorxiv.org/content/10.110…
2/ In this paper, we show that unexpected events drive different changes in the responses of somata and distal apical dendrites in primary visual cortex pyramidal neurons. Schematic figure of a pyramidal neuron with a long apical tr
3/ Previous research has shown that neurons in sensory areas respond to unexpected events. It’s hypothesized that these responses guide our brain in learning a predictive, hierarchical model of the world in an unsupervised (or self-supervised) manner.
Read 20 tweets
2.

"We must move on from Neoliberalism in the post-COVID era. The 'Great Reset' offers an opportunity to re-evaluate sacred cows, defining the pre-pandemic era: the coming #Industry40 and the digitization of countless economic activities."

weforum.org/agenda/2020/10…
3.

"The #COVID19 crisis is going to accelerate a number of changes and transformations in human society. Notably, the pandemic is expected to significantly accelerate the Fourth Industrial Revolution."

weforum.org/agenda/2020/10…
Read 26 tweets
Today, HHMI is announcing a new open access publishing policy:bit.ly/3iiC3jF
We’ve invited Bodo Stern, HHMI’s Chief of Strategic Initiatives, to explain the key points and offer perspective.
HHMI’s new open access publishing policy will go into effect on January 1, 2022. Articles with major contributions from HHMI labs will be freely available immediately upon publication. You can read the policy here: bit.ly/3jjGI6g
The policy includes options for all types of journals: open access journals and transformative journals can publish HHMI articles under @CreativeCommons CC BY in exchange for open access fees...
Read 14 tweets
Identifying hard and soft sweeps has been basically a solved problem for almost 15 years. This is because loci drifting (a) in the population have very different frequency histories than loci being swept to fixation (b).
However, selection on complex, quantitative traits does not leave signatures of sweeps. When selecting quantitative traits, the trait changes rapidly, but this is due to hundreds or thousands of loci having small changes in allele frequency (c).
This has made it difficult to identify polygenic selection loci. However, in our recent preprint, we report results which basically solve this problem.
1) We have large datasets. 2) We use appropriate models.
Read 20 tweets
So, some positive news. I’m excited to announce that I will step in as Editor-in-Chief of the journal Chemical Senses as of April 1. So, here are a few reasons you should consider submitting your manuscript to #ChemicalSenses, as well as some new initiatives. (Please RT) 1/
#ChemicalSenses is the leading journal focused on research in all areas of chemosensation in humans and other vertebrate and invertebrate animals, including #olfaction, #taste, #chemesthesis, internal chemosensation and chemical ecology. 2/
#ChemicalSenses is the official journal of @AChemsinfo, @ECRO_online, the Japanese Association for the Study of Taste & Smell (JASTS), the Australasian Association for ChemoSensory Science (AACSS), and the Korean Society for Chemical Senses & Ingestive Behaviour (KSCSIBF). 3/
Read 15 tweets
#neurotwitter🎶welcome to the #natverse - we’ve got tools for brains!🎶Open software to analyse neurons, connections, brains #bioRxiv biorxiv.org/content/10.110… Others are using it, why should you? natverse.org: @gsxej lab @MRC_LMB @flyconnectome @CamZoology #rstats 1/10
The natverse allows you to easily plot neurons and neuroanatomical volumes, measure features and implement interesting algorithms, e.g. flow centrality @csdashm and NBLAST @martamcosta2 natverse.org/gallery/. We give lots of examples: github.com/natverse/nat.e… 2/10
Read 11 tweets
1/n Fresh on #bioRxiv: a simple and ultra-low-cost #openhardware approach to upgrade an out-of-the-box two-photon system to reach a 3.5(xy) x 0.6 (z) mm field of view for mesoscale 3D random access scans. /w @FilipKJaniak et al. bit.ly/2BRTrJq
2/n Our ‘diverging beam optics’ (DBO) approach exploits the fact that in 2P microscopy there is no traditional collection plane. This means the images does not get blurry if the incoming laser beam is not parallel as it would in 1P microscopy.
3/n using DBO, we can flexibly set our field of view and excitation volume to match the structural properties of different biological samples. This is critical, as different species have vastly different size and density neural processes...
Read 14 tweets
I always liked personal journals as framing devices for Romantic or Gothic horror novels like in Dracula and Frankenstein. I decided to write a satirical thread using this same device but for a common #scientific #journey:
Personal Journal of Dr. Nicholas Gladman
-Day 1-
Our scientific voyage began this afternoon. I am excited for what we shall discover and observe. #Manuscript first draft almost complete. Weird dark clouds on the horizon but sure it is normal.
-Day 2-
Manuscript sent to co-authors for initial thoughts and edits. Am hopeful for quick turnover and minimal comments. Anderson died of freak roof collapse but I’m sure that doesn’t portend anything sinister.
Read 15 tweets
Unrealistic assumptions (baseline scenario: random disease distribution, random sampling) overestimate the detection probability (~ confidence in detecting #CWD). Agent-based framework for wildlife disease surveillance Belsare et. al ow.ly/6U7M30mQFTc #bioRxiv #gganimate
The model was simulated for Franklin County Missouri deer population. Alternate scenario simulates clustering of cases and non-random sampling. Very low prevalence thresholds reflect recent CWD introduction. User-friendly-sliders to set age-sex class specific harvest and testing.
Can be used to calculate region-specific sample sizes for efficient and sustainable CWD surveillance. Also facilitates inferring negative surveillance outcomes. #AdaptiveManagementApproach
Read 6 tweets
So so so so excited to share this!
This preprint summarizes my journey of trying to engineer the brain parasite Toxoplasma gondii to deliver therapeutic proteins into neurons, together with @OdedRechavi and @SheinerLab 1/n biorxiv.org/content/early/… #bioRxiv
You probably heard of Toxoplasma because of the way it cycles between cats and their prey. However, Toxoplasma also infects people. 2/n
Toxoplasmosis can be dangerous in people with weakened immune systems, but in most people infections are asymptomatic, and aren’t even noticed. In fact, it is estimated that a third of the human population are chronically infected with Toxoplasma. 3/n
Read 15 tweets
The water in the pipeline cannot fix the leaks. Contrary to the advice #WomenInSTEM & #POCinSTEM receive, we cannot actually #leanin to solving the problem of #genderbias & #racialbias in #STEM & #academia. Thanks to @NatureEcoEvo & @RoinnAnLuisigh for this chance to say this. 1/
A few months ago, @Nature published a piece with advice on how senior women can confront #genderbias. While the advice contained therein was useful, the title was enraging. nature.com/articles/d4158…. 2/
It led me to rage tweet a thread of statistics on #genderbias in #STEM, and that thread blew up And then I got incredibly lucky when @RoinnAnLuisigh offered me the opportunity to turn it into a column. Working with her was AMAZING! 1000% fantastic 3/
Read 51 tweets
Congrats to Jason (and the rest of the team) on this awesome IgA-deficiency story! biorxiv.org/content/early/… @YaleIBIO #Immunology #Microbiota #IgA #ASAPbio #bioRxiv
It’s been awesome watching this story develop over the last couple years. Truly fantastic effort by the whole group on this intriguing patient cohort, complete with some exciting and new longitudinal data on stability of the microbiota in IgA-deficient patients.
I’ll let the story speak for itself (go read it!) - important work on human immunology and the role of IgA in shaping the gut microbiota. Way to go Jason!
Read 3 tweets

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