My colleague Joachim Wistuba is looking for a for his fully funded
@dfg_public project on Deadline for application 27th December. More information on the position and how to apply here: jobs-sf.ukmuenster.de/job/UKM-

Congratulations to member Hubert Schorle for his two recent publications:
Actl7b deficiency leads to mislocalization of LC8 type dynein light chains and disruption of murine spermatogenesis doi.org/10.1242/dev.201593
Cylicins are a structural component of the sperm calyx being indispensable for male fertility in mice and human elifesciences.org/articles/861
this last one having multiple Andronet members in the author list.

Such a stimulating session this morning on male infertility, I loved how many unexpected points of contact there were between the different speakers and what great company I was in. Thank you to Don Conrad and Maris Laan for the invitation to present my work on male reproductive ageing here.

Really enjoyed the session on genome interpretation and functional studies. Lots of great work on splicing changes, an ongoing (side) interest of mine, including new validation strategies.

Really interesting selected talk by Christina Falugi about use of "natural" vs traditional photos of patients to showcase phenotypes. Perception is more positive with natural ones without difference in educational value. Time to retire some awful photos from textbooks?

Random 1st impressions of the :
🧬It's not a large meeting, it's absolutely gigantic
🧬Conference ribbons are a thing
🧬Opening address included security advices for participants
🧬Closed captions, I assume automatic/AI, are getting some words very, very wrong

Great to see the consequences of advanced paternal age given attention by The Guardian.
If anyone is attending next week and wants to hear more, I'm giving a talk about this (and more).

"But problems pile up as a man gets older. Stem cells acquire more mutations. Epigenetic marks get modified. Experiences in the man’s life, including environmental exposures, cause oxidative stress and damage. These things, and more, may act in concert to cause the effects researchers are seeing in children born to older fathers.

What’s clear is that paternal age matters – and that more men are becoming older fathers. As Robaire and Chan write, a number of factors including delayed marriages, second marriages, assisted reproduction, treatments such as Viagra for erectile dysfunction, and celebrity men modelling older fatherhood “have provided elements for a perfect storm”."

theguardian.com/science/2023/o

Call to action on male infertility research
Several members are co-authors of this Expert Recommendation on @NatRevUrol

"Frequency, morbidity and equity - the case for increased research on male fertility"
lnkd.in/eHQvVZ2s

Did you know that most men with don't receive a causal diagnosis? This is caused by a lack of knowledge around the factors responsible for male infertility. What is more, treatment options are limited and not individualised. Often, the burden of male infertility is simply transferred to the female partner during medically assisted reproduction. On the other hand, lack of rigorous research into male fertility also results in a relative lack of male contraceptives. In this article the authors identify the most pressing questions currently facing and make specific recommendations for action. Congratulations to the authors on this important piece of work 👏

3rd Virtual Symposium on Male Reproductive Immunology organised by the colleagues from Giessen will take place 29th-30th November. Great program and attendance is free!

The seminar series “Human Reproduction: Researching the Secrets of Life” will take place from Monday, 25 September until Thursday, 28 September 2023, every day 1:00 - 1:50 pm (CEST).
The seminar will be live-streamed via ZOOM (link to follow).

“So how long am I going to do this? Until indoor air is safe for all, until vaccines prevent transmission, until there’s a cure for long covid. Until I’m not risking my family’s future on a grocery run. The truth is that however immortal we feel, we are all just one infection away from a new life.”

Please read this key piece by Madeline Miller. The pandemic isn’t over until we can prevent Long COVID. washingtonpost.com/opinions/20

Our new work was just published on BMC Bioinformatics
OGRE: calculate, visualize, and analyze overlap between genomic input regions and public annotations
bmcbioinformatics.biomedcentra
OGRE is a tool that calculates the overlap between a set of genes or regions (e.g. coming from RNA-seq) and publically available annotations (e.g. TFBSs). It was developed to be easy to use and with scientists without computational training in mind.
It's available on @bioconductor bioconductor.org/packages/deve and on
@GitHub github.com/svenbioinf/OGRE

OGRE: calculate, visualize, and analyze overlap between genomic input regions and public annotations - BMC Bioinformatics

Background Modern genome sequencing leads to an ever-growing collection of genomic annotations. Combining these elements with a set of input regions (e.g. genes) would yield new insights in genomic associations, such as those involved in gene regulation. The required data are scattered across different databases making a manual approach tiresome, unpractical, and prone to error. Semi-automatic approaches require programming skills in data parsing, processing, overlap calculation, and visualization, which most biomedical researchers lack. Our aim was to develop an automated tool providing all necessary algorithms, benefiting both bioinformaticians and researchers without bioinformatic training. Results We developed overlapping annotated genomic regions (OGRE) as a comprehensive tool to associate and visualize input regions with genomic annotations. It does so by parsing regions of interest, mining publicly available annotations, and calculating possible overlaps between them. The user can thus identify location, type, and number of associated regulatory elements. Results are presented as easy to understand visualizations and result tables. We applied OGRE to recent studies and could show high reproducibility and potential new insights. To demonstrate OGRE’s performance in terms of running time and output, we have conducted a benchmark and compared its features with similar tools. Conclusions OGRE’s functions and built-in annotations can be applied as a downstream overlap association step, which is compatible with most genomic sequencing outputs, and can thus enrich pre-existing analyses pipelines. Compared to similar tools, OGRE shows competitive performance, offers additional features, and has been successfully applied to two recent studies. Overall, OGRE addresses the lack of tools for automatic analysis, local genomic overlap calculation, and visualization by providing an easy to use, end-to-end solution for both biologists and computational scientists.

bmcbioinformatics.biomedcentral.com

The Andronet co-organised European Testis Workshop is underway! Until Thursday there will be a lot of science and interaction between researchers studying testis.

On this day in 1902: Barbara McClintock born, won 1938 #NobelPrize for showing how chromosomes change #ThisDayInBiotech #WomenInBiotech

RT @MaleGermCells
Great opportunity for aspiring young scientists working in the field of reproductive research! Co-headed by speaker @JorgGromoll. Don‘t be shy and apply! twitter.com/repro_forschung/st

RT @Repro_Forschung
❗️Only six weeks to go❗️The deadline for applications for the @dfg_public Junior Research Academy is approaching fast!
Check out the program and the requirements on our websites and get your application ready!
➡️reproduktionsforschung.de/dfg-

RT @matthewcobb
70 years ago, 3 papers appeared in @Nature under the title ‘Molecular structure of nucleic acids’. In an article in Nature today (link at end) @nccomfort and I shed new light on ‘what Watson and Crick really took from Rosalind Franklin’. This thread summarises our findings. 1/23

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