Federico Ansaloni

Interested in repetitive elements, single-cell omics, multiple sclerosis and developmental biology

[Federico Ansaloni @fansalon64]

Happy to see this out!

Here we suggest a transcriptional antagonism between ERVs and LINE-1s during the minor wave of the murine ZGA.

https://t.co/dQfSihnMIO

@remosanges @SGustincich

[Eunjung Alice Lee @EAliceLee2]

Excited to share a new call for papers from Genome Research on somatic mosaicism. If you're working on something exciting in this area, consider submitting your work! The deadline is September 15, 2025. Looking forward to seeing your great science featured there.

[Federico Ansaloni @fansalon64]

The magic world of R....

[Donald McKnight @donaldmcknight2]

The informal poll results are in, & as I feared, most people are running ANOVAs in #R with functions that can give highly misleading (or flat out wrong) results. Follow along to see why using anova() and aov() is usually inadvisable & why you should be using car::Anova() 🧵

[Rainer Melzer @UCDflowerpower]

GWAS for Nobel prize laureates.

[Magdalena Zernicka-Goetz @ZernickaGoetz]

What is the origin of our body? Our paper @CellCellPress shows that when a human embryo is one day old and comprises just two cells, only one cell will create most of the fetus in addition to placenta, while the other cell will create placenta.
https://t.co/88l48YezzA

[Piero Carninci @carninci]

Warmly recommend to candidates interested in repeats, retrotransposons etc to consider this PhD position. Remo also collaborating with the Fantom.
SISSA works in English. Trieste is a beautiful city and not so expensive.

[Martina Nigri @NigriMartina]

Extremely happy to see this out!

Here we suggested that male mice can have a disadvantage relative to females in mastering difficult, appetitively-motivated learning tasks, likely due to sex differences in value-based decision-making!

https://t.co/I2EPXjdx10

[Michael 英泉 Eisen @mbeisen]

Disturbing visual similarities aside, which is worse? A laughably flawed AI anatomical hallucination that nobody took seriously, or a massive NIH project misusing UMAP hallucinations that wildly exaggerate genetic differences between races?

[Federico Ansaloni @fansalon64]

Extremely happy to have contributed to this!

[Qiaolin Deng @QiaolinDeng]

Excited to announce this symposium that I organized with two amazing co-organizors Amanda Sferruzzi-Perri and Susana Chuva de Sousa Lopes. A great line of speakers and it is free registration thanks to StratRegen KI initiative by @ChristianGoritz @fredrik_lanner

[Kieran Samuk @ksamuk]

PSA, since I've now seen problems arising from this: As of Sept 2023, GATK no longer makes missing genotypes explicit in VCFs (i.e. "./." as in the VCF spec). Missing genotypes are instead coded as "0/0" with a DP=0 format field. See attached for examples.

[Federico Ansaloni @fansalon64]

Interested in simultaneously profiling chromatin accessibility and two histone marks at single-cell resolution?
The single-cell nanoCUT&Tag protocol + computational workflow for data analysis is now out!
https://t.co/D0zkodaACB

@marekbartosovic @GoCasteloBranco

[Miguel Branco @BrancoLab]

"Herpesviruses mimic zygotic genome activation to promote viral replication" 😯
https://t.co/p0Xdm13Bg0

[bioRxiv Genomics @biorxiv_genomic]

A single-cell transposable element atlas of human cell identity https://t.co/xbKfoHzO3Q #biorxiv_genomic

[𝕐 @nomad421]

Did @10xGenomics just make newer versions of Cell Ranger open source? https://t.co/5aGEEN9dL8 (cc @sjackman, @luizirber). This is a huge win for open, transparent, and reproducible science if it’s the case!

[Stefano Gustincich @SGustincich]

Pleased to see the principles described in “Internal Ribosome Entry Site sequences act as Effector Domain in linear and circular antisense long non-coding SINEUP RNA” https://t.co/sNyH5Pl4DE are independently validated in https://t.co/uXc7Xl6aUK SINEUP technology works worldwide!

[Cedric🧬➰🧬Feschotte @CedricFeschotte]

💥Excited to unleash ENCOTE: Encyclopedia of Transposable Elements with cis-regulatory activity in the human genome!
Collab w @twang5 for #ENCODE led by🔥trio Alan Du, Jason Chobirko & @XiaoyuZhuo
TEs = 25% of all cCREs = 200,000+ elements!!
Deep dive! 1/n https://t.co/t9xacOAOAQ

[Federico Ansaloni @fansalon64]

Finally out! Happy to have contributed to this:

LINE-1 regulates cortical development by acting as long non-coding RNAs

https://t.co/izV1ZMIV9A

[Biozentrum, University of Basel @biozentrum]

We are mourning the death of Prof. em. John Nicholls, who passed away on July 13, 2023. We bid farewell to a pioneer in neurobiological research and a dedicated and passionate scientist who played an important role in shaping the @biozentrum. https://t.co/qrOxHltBRe

[Tartaglia Lab @tartaglialab]

Do you know that protein-RNA interactions can be predicted from single cell transcriptomics? Here is a new exciting story by Johnny, Alex and Alessio!
https://t.co/ZPKXEMGzWi

[Federico Ansaloni @fansalon64]

Lastly: proper characterization of LINE-1 transcriptional dynamic was possible only by integrating transcriptomic, chromatin accessibility and Pol-II binding dataset. Data integration is great, and sometimes needed, for accurate quantification of repeat transcriptional dynamics.

[Federico Ansaloni @fansalon64]

Happy to see this out!

Here we suggest a transcriptional antagonism between ERVs and LINE-1s during the minor wave of the murine ZGA.

https://t.co/dQfSihnMIO

@remosanges @SGustincich

[Federico Ansaloni @fansalon64]

This would make sense with previous evidence showing how LINE-1 mRNAs are required to switch-off the 2C transcriptional program allowing embryos to develop beyond the 2-cell stage: i.e., antagonist pathways are activated/regulated from spatially separated genomic compartments