#bioRxiv : Bioinformatics

[evoldir]

Fwd: PostDoc: GenoscopeCEA_Evry_France.MarinePlankton

Begin forwarded message: > From: evoldir@evol.biology.mcmaster.ca > Subject: PostDoc: GenoscopeCEA_Evry_France.MarinePlankton > Date: 14 November 2024 at 06:32:27 GMT > To: rdmpage@gmail.com > > > Two years Postdoctoral position on Marine Plankton Communities Metabolic > Modelling > > > Marine plankton encompass highly diverse species assemblages across > various environmental conditions, and is pivotal to key ecosystem > services, ranging from biological carbon pump, marine food web or impact > on major biogeochemical cycles. > > Throughout more than 15 years of expeditions, the Tara Ocean Consortium > gathered a unique collection of samples covering a wide diversity > of marine environments to describe composition and biological > activities of marine plankton communities, and already contributed > to significant breakthroughs in understanding this set of living > organisms (cf. Tara Ocean Foundation et al. 2023. Nature Microbiology > [https://ift.tt/loth4GC] for recent a review and > prospective). > > What are the biological functions that shape the building of plankton > communities? What are the metabolic interactions within a given > community? What is the metabolic impact of viral infection? Can > we decipher the impact of environmental parameters (e.g. nutrients > availability) on biological functions, and vice versa? These are some > of the research questions that are addressed in our group. > > In this context, we propose a 2 years post-doc position at CEA/Genoscope, > near Paris (France), to model metabolic interactions within marine > plankton communities (from viruses to unicellular eukaryotes) sampled > in the context of the Tara Oceans campaigns, and their intertwining > with environment. > > This project will take advantage of a new top-down metabolic modelling > system for unicellular phototroph eukaryotes (PhotoEukStein, Burel et > al. 2023. BiorXiv [https://ift.tt/i46Vhz0]) combined > with existing methods and resources for prokaryotes, and metabolic > niche modelling techniques (Régimbeau et al. 2022. Ecology Letters > [https://ift.tt/VQBthN5]; Régimbeau et al. 2023. BiorXiv > [https://ift.tt/rAMBIJx]). > > Research will take place within the Ocean EuKaryotes SYstems biology > and GENomics (OEKSYGEN) group of the Metabolic Genomics research unit > at Genoscope (CEA �" CNRS �" Université Paris Saclay) in Evry, France. > > Salary ranges from 32 to 35k€ net per year, including health coverage. > > Position is to start as soon as possible. > > Required qualifications: > -     Ph.D. by the time of start date in metabolic modelling, > bioinformatics, genomics, or some equivalent. > -     Excellent communication (verbal and written) and > organizational skills. > -     Positive attitude and desire to work as part of a > dynamic, multi-disciplinary team. > -     Strong expertise in bioinformatics, metabolic > modelling, genomics. > > Preferred qualifications: > -     Fluency in Python or Perl, and R. > -     Expertise in metabolic modelling. > > The application should contain a short letter of motivation, a CV with a > short description of prior research experience, copy of transcripts, and > contact information for 2-3 references. > > Informal inquiries prior to application are welcome. > Contact and application to be sent to: Eric Pelletier > (eric.pelletier@genoscope.fr) > > > > > Eric Pelletier - Research Director - CEA / Genoscope > Ocean EuKaryotes SYstems biology and Genomics - OEKSYGEN > +33 160 872 519 > via Email February 08, 2025 at 02:53PM

[biopractify]

"How to stay updated with the latest research in bioinformatics?

Bioinformatics is evolving rapidly, with new discoveries, algorithms, and datasets emerging every day. Whether you're a student, researcher, or professional, staying updated is crucial for growth in this interdisciplinary field. But with the overwhelming amount of information out there, how can you keep track of the latest research?

Here’s a step-by-step guide to staying informed about bioinformatics advancements:

📚 1. Follow Peer-Reviewed Journals

Leading journals publish cutting-edge bioinformatics research. Consider subscribing to:

Bioinformatics (Oxford Journals)

BMC Bioinformatics

Nucleic Acids Research (NAR)

Genome Biology

PLoS Computational Biology

Nature Biotechnology

📝 Pro Tip: Set up Google Scholar alerts for specific keywords like "machine learning in bioinformatics" or "single-cell RNA sequencing" to receive relevant papers directly in your inbox.

📰 2. Leverage Preprint Servers

Not all groundbreaking research is published in journals immediately. Many researchers upload their work to preprint servers:

bioRxiv (Preprints in biology and bioinformatics)

arXiv (Computational biology & AI in bioinformatics)

🧠 Why use preprints? They help you access fresh research before peer review, giving you a competitive edge.

💻 3. Follow Top Bioinformatics Blogs & Websites

Several platforms curate the latest developments in bioinformatics:

OMGenomics (Personal insights from bioinformatics professionals)

Bits of DNA (Exploring genomics and computational biology)

Biostars (Community-driven discussions on bioinformatics challenges)

SEQC Blog (Sequencing and bioinformatics trends)

🎙️ 4. Listen to Bioinformatics Podcasts

If you prefer learning on the go, podcasts are a great way to absorb new knowledge: 🎧 Best Bioinformatics Podcasts:

The Bioinformatics Chat

Genomics in 5 Minutes

The OmicsCast

🧑‍🤝‍🧑 5. Engage with the Bioinformatics Community

Joining discussions and interacting with experts helps you stay informed: 🔹 Reddit: r/bioinformatics, r/genomics 🔹 Twitter/X: Follow researchers and hashtags like #Bioinformatics, #ComputationalBiology 🔹 LinkedIn Groups: Bioinformatics Discussion Forum, AI in Bioinformatics 🔹 Slack & Discord: Join bioinformatics-specific communities for direct interaction

🎓 6. Take Online Courses & Webinars

Platforms like Coursera, edX, and BioPractify frequently update their courses to reflect the latest techniques in bioinformatics. Also, keep an eye out for:

Workshops by EMBL-EBI

Online tutorials from Galaxy Project & Bioconductor

📅 Tip: Many universities and conferences offer free webinars. Sign up for event notifications!

🔬 7. Attend Conferences & Hackathons

Networking at events helps you learn from researchers and industry leaders. Some key conferences include:

ISMB (Intelligent Systems for Molecular Biology)

RECOMB (Research in Computational Molecular Biology)

Genome Informatics Conference

BioHackathons (Hands-on experience with the latest tools)

🌍 Virtual & Hybrid Options: Many conferences now offer remote participation—take advantage of them!

🚀 8. Stay Hands-On with Open-Source Projects

Following GitHub repositories for bioinformatics tools and frameworks keeps you engaged with real-world applications. Some trending repositories:

Bioconductor (for R-based bioinformatics analysis)

Nextflow (for scalable data analysis workflows)

DeepVariant (AI-powered genome sequencing analysis by Google)

💡 Bonus: Contributing to open-source projects is a great way to learn while building your portfolio.

🔎 Final Thoughts

Bioinformatics is a dynamic field that blends biology, data science, and AI. Staying updated requires a multi-pronged approach—reading journals, engaging in online discussions, participating in hackathons, and continuously learning. By following these strategies, you’ll remain ahead in this ever-evolving domain.

📢 What’s your go-to method for staying updated in bioinformatics? Share your insights below! ⬇️✨

[virusevolution]

StrainHub: A phylogenetic tool to construct pathogen transmission networks is available online at strainhub.io and the preprint can be accessed online at bioRxiv 

[didanawisgi]

Abstract

This manuscript concisely reports an in-silico study on the potential impact of the Spike protein mutations on immuno-escape ability of SARS-CoV-2 lambda variant. Biophysical and bioinformatics data suggest that a combination of shortening immunogenic epitope loops and generation of potential N-glycosylation sites may be a viable adaptation strategy potentially allowing this emerging viral variant escaping host immunity.

Introduction

A number of SARS-CoV-2 variants termed variants of interest (VOI) or concern (VOC) have attracted investigators’ attention to elucidate the mechanisms underlying their enhanced transmission and/or resistance to neutralization by immune sera and monoclonal antibodies [1,2]. Among more recently identified VOI, the lambda variant, which has emerged in Peru and has rapidly spread to South American regions and US remains poorly investigated, particularly regarding the effects of mutations on the thermodynamic parameters affecting the stability of the Spike protein and its Receptor Binding Domain (RBD). Variations in these parameters, if consistent, have been shown to predict relevant changes in SARS-CoV-2 contagiousness and immunoescape ability [3,4]....

....Overall, our in-silico analysis suggests that the point mutations characterizing the lambda variant do not seem to directly influence RBD affinity for ACE2 receptor, thus making it uncertain a relevant impact on virus transmission, unless the mutations in the S2 domain have a long-distance allosteric effect on conformational flexibility and ACE2 affinity. The most evident and likely functionally impacting change of the lambda variant is represented by the 246-252 deletion since they could confer to the virus an enhancing capacity to escape the host immune response by two theoretic though likely and already reported strategies; shortening epitopes located in the loops and exploiting increased glycosylation. variations in spike cell epitopes and glycosylation profile during virus transmission have been already described [16].

While this manuscript was being prepared for submission, we came across a pre-print published in BioRxiv by Izumi Kimura and collaborators (bioRxiv doi: https://doi.org/10.1101/2021.07.28.454085;) where the N-terminus 7 amino acids deletion is described and discussed for its potential relevance in conferring to the lambda variant of SARS-CoV-2 resistance to antiviral immunity. Though with different approach, the data by Kimura and collaborators are in total agreement with our own from in silico methods.

[bioinfoacronym-blog]

BURRITO: Browser Utility for Relating micRobiome Information on Taxonomy and functiOn

Yet another bad, food-related bioinformatics acronym. H/t Roberto Olivares-Amaya.

bioRxiv: https://www.biorxiv.org/content/early/2017/11/15/217315?rss=1

[naivelocus]

EpiSAFARI: Sensitive detection of valleys in epigenetic signals for enhancing annotations of functional elements [NEW RESULTS]

The genomewide signal profiles from functional genomics experiments are dense information sources for annotating the regulatory elements. These profiles measure epigenetic activity at the nucleotide resolution and they exhibit distinct patterns along the genome. Most notable of these patterns are the valley patterns that are prevalently observed in many epigenetic assays such as ChIP-Seq and bisulfite sequencing. Valleys mark locations of cis-regulatory elements such as enhancers. Systematic identification of the valleys provides novel information for delineating the annotation of regulatory elements using epigenetic data. Nevertheless, the valleys are generally not reported by analysis pipelines. Here, we describe EpiSAFARI, a computational method for sensitive detection of valleys from diverse types of epigenetic profiles. EpiSAFARI employs a novel smoothing method for decreasing noise in signal profiles and accounts for technical factors such as sparse signals, mappability, and nucleotide content. In performance comparisons, EpiSAFARI performs favorably in terms of accuracy. The histone modification and DNA methylation valleys detected by EpiSAFARI exhibit high conservation, transcription factor binding, and they are enriched in nascent transcription. In addition, the large clusters of histone valleys are found to be enriched at the promoters of the developmentally associated genes. — bioRxiv : Bioinformatics

[evoldir]

Fwd: Postdoc: Barcelona.Bioinformatics

Begin forwarded message: > From: evoldir@evol.biology.mcmaster.ca > Subject: Postdoc: Barcelona.Bioinformatics > Date: 27 January 2025 at 05:11:51 GMT > To: rdmpage@gmail.com > > > > > The Evolutionary and Functional Genomics Lab at the Institut Botànic > de Barcelona (CSIC) is looking for a bioinformatics postdoctoral > researcher. The postdoctoral researcher will be part of a team carrying > out a research project that aims at understanding the genomic basis of > adaptation to natural environments. The selected candidate will analyze > -omics data to discover and annotate transposable element insertions and > to understand what determines their abundance, diversity, activity, and > functional effects on gene expression and transcriptome diversification > across species. Genomic sequences are already available and more -omics > data sets will be generated within the project. > > Desired Skills and Expertise > > Experience with computing programming > Experience with modeling, statistical analysis and/or machine learning. > Experience with high-performance computing or use of clusters (SLURM). > Knowledge on evolutionary processes is desirable. > Knowledge on transposable element biology is desirable. > Strong organizational skills. Good scientific writing and oral > communication skills. Ability to work as part of a team > > Contract duration and benefits > 2 year contract. Full time: 37,5 hours/week. > Position available immediately, starting date is negotiable. > The candidate will join a research team that has expertise > both in experimental and bioinformatics methodologies > (www.gonzalezlab.eu). Several projects are currently ongoing in the > laboratory which allows for collaborative opportunities. The Evolutionary > and Functional Genomics lab also offers extensive networking opportunities > as we are co-leaders of the European Drosophila Population Genomics > Consortium (https://droseu.net) that brings together 74 research > labs across 28 countries. We are also co-leading the CSIC Genomics Hub > (https://ift.tt/7wKGb64) that brings together 156 research groups > based in Spain. We are also members of the Spanish excellence network > in Adaptation Genomics (https://adaptnet.es), the CSIC LifeHub network > (https://lifehub.csic.es), and the TE hub initative (http://tehub.org/). > > Required Information and Contact > Send your CV and a brief letter of motivation explaining > qualifications and interest in the position to Dr. Josefa González > at josefa.gonzalez@csic.es. Please include “Bioinformatics postdoc > position” in your e-mail subject. Deadline: 28 February 2025. > > > Josefa González | CSIC Research Scientist > Institut Botànic de Barcelona, IBB, CSIC-CMCNB > Passeig del Migdia s/n. 08038, Barcelona. Spain. > www.gonzalezlab.eu | > > @GonzalezLab_BCN > > Co-organizer of the European Drosophila Population > Genomics Consortium(DrosEU) > Coordinator of CSIC GENOME Hub > Vice President of the European Society for Evolutionary Biology > Associate Editor for GBE > Science Outreach La Ciència Al Teu Món > > melanogaster.eu > > Most recent > preprints/publications: > Gene-TE chimeras Genome Res | > TEs context dependent effects Mol Biol Evol | > TE library curation Genome Res | > TE & Epigenetics bioRxiv > > "GONZALEZ PEREZ, JOSEFA"

[scienceblogtumbler]

Age Reduction Breakthrough

If you eschew hyperbole and hang in for the long haul, maintaining a discipline of understatement in the midst of a flashy neon world, you may be offered a modicum of credence when you make an extraordinary announcement. No one is entitled to this courtesy twice. If the news that you trumpet to the moon does not pan out, your readers will be justified in discounting everything you say thereafter.  

Here goes.

I believe major rejuvenation has been achieved in a mammal, using a relatively benign intervention that shows promise of scaling up to humans. I’m going to stake my reputation on it.

Cartoon by Maddy Ballard

In the race to effect substantial, system-wide rejuvenation, Harold Katcher is a dark horse. He has the right academic credentials and a solid history of research. In fact, in earlier life he was part of a team that discovered the breast cancer gene, brca1. I asked Harold for a biographical sketch, and have printed it in a box at the end of this posting.

But Katcher has no research grants or university lab or venture capital funding, no team of grad students mining databases and screening chemicals in the back room.

One thing Katcher has going for him is the correct theory. Most of the explosion in aging research (and virtually all the venture capital startups) are looking to treat aging at the cellular level. Their paradigm is that aging is an accumulation of molecular damage, and they see their job as engineering of appropriate repair mechanisms.

The truth, as Katcher understands it, is that, to a large extent, aging is coordinated system-wide via signal molecules in the blood. It was our common realization of this vision that brought Katcher and me together more than a decade ago. Katcher briefly describes his 2009 epiphany below. It was the source of his 2013 essay (it took a few years to get it into print) on the significance of parabiosis experiments for the future of aging science.

Of course, Katcher was not the only one to get the message about the power of signal molecules in the blood to reprogram tissues to a younger state throughout the body. The problem is that there are thousands of constituents represented in tiny concentrations in blood plasma, but conveying messages that cells read. Which of these are responsible for aging? A small number of labs, including the Conboys at Berkeley, Amy Wager at Harvard, and Tony Wyss-Coray at Stanford have been searching for the answer over the last decade and more.

Katcher has been able to guess or intuit or experimentally determine the answer to this question. With seed funding from Akshay Sanghavi, he set up a lab in Bangalore two years ago, and tried to rejuvenate old lab rats, using a fraction extracted from the blood of younger rats. The first round of experiments were encouraging, published in this space a year ago. He obtained the next round of funding from a reader of this blog, and had enough rats to titrate dosages experimentally, and to see if treated rats who aged again over time could be re-treated successfully.

There is a hole in this story that awaits the resolution of intellectual property rights. Katcher and Sanghvi have not applied for patents and have not yet found a suitable partner to provide financing for human trials. They have not revealed any details of the treatment, besides the fact that it is in four intravenous doses, and that it is derived from a fraction of blood plasma. Katcher thinks that the molecules involved will not be difficult to manufacture, so that when a product is eventually commercialized, it will not require extraction from the blood of live subjects, rodent or human.

We’re still waiting for longevity curves of these treated rats. In the meantime, the best available surrogate measure of age comes from methylation clocks, as developed by Steve Horvath at UCLA, and other scientists as well. Crucially, Katcher found an ally in Horvath, who didn’t just test his rejuvenated rats, but did the needed statistical analysis to develop a set of six methylation clocks specialized to rats. FIve of the clocks are optimized for different tissues, and one is calibrated across species, so that it can measure age in humans as well as corresponding age in “rat years” (about 1/40 human year). The two-species clock was a significant innovation, a first bridge for translating results from an animal model into their probable equivalent in humans.

In a paper posted to BioRxiv on Friday, Katcher and Horvath report results of the methylation measurements in rejuvenated rats. “Crucially, plasma treatment of the old rats [109 weeks] reduced the epigenetic ages of blood, liver and heart by a very large and significant margin, to levels that are comparable with the young rats [30 weeks]….According to the final version of the epigenetic clocks, the average rejuvenation across four tissues was 54.2%. In other words, the treatment more than halved the epigenetic age.”

Human-rat clock measure of relative age defined as age/maximum species lifespan.

Besides the methylation clock, the paper presents evidence of rejuvenation by many other measures. For example:

IL-6, a marker of inflammation, was restored to low youthful levels

Glutathione (GSH), superoxide dismutase (SOD), and other anti-oxidants were restored to youthful levels

In tests of cognitive function (Barnes maze), treated rats scored better than old rats, but not as well as young rats.

Blood triglycerides were brought down to youthful levels

HDL cholesterol rose to youthful levels

Blood glucose fell toward youthful levels

A major question in blood plasma rejuvenation experiments has been how often the cure must be administered. Many of the components of blood plasma are short-lived, secreted into the blood and absorbed continuously throughout the day. The good news from Katcher’s results is that it seems only four injections are needed in order to achieve rejuvenation.

A second question which these experiments resolve is whether rejuvenation requires both adding and removing molecular species from the blood plasma. For example, pro-inflammatory cytokines are found in old blood at much higher levels. Irina and Mike Conboy, people who I regard as most credible in the field, have said that removing bad actors from the blood is probably more important than restoring youthful levels of beneficial signals. They were grad students at Stanford 15 years ago, when the modern wave of parabiosis science was initiated, and have pursued the subject continuously ever since. Katcher’s experiments have achieved their results only by adding blood components, not by removing or even neutralizing others.

In Katcher‘s experiments, molecular species were added, but nothing was removed. This suggests that he has found the necessary formula for re-programming epigenetics, so that lower levels of the bad actors occur as a result. But it remains to be seen whether even better results can be obtained if some plasma constituents are removed.

A question that remains unresolved concerns the location and mechanism of the aging clock. I have been undecided over the years between two models:

There is a central aging clock, perhaps in the hypothalamus, which keeps its own time and transmits signals throughout the body that coordinate methylation state of dispersed tissues

Information about epigenetic age is dispersed through the body, and the body’s clock is a feedback loop that is continually updating methylation age locally in response to signals received about the methylation age globally.

There is a suggestion in the data that the hypothalamus may be more difficult to rejuvenate than other tissues. Does it play a more important role than other tissues in coordinating the age of the entire body? Horvath (personal communication) counsels caution in drawing this inference until measurements are corroborated and more experiments are done.

The Bottom Line

These results bring together three threads that have been gaining credibility over the last decade. Mutually reinforcing, the three have a strength that none of them could offer separately.

The root cause of aging is epigenetic progression = changes in gene expression over a lifetime.

Methylation patterns in nuclear DNA are not merely a marker of aging, but its primary source. Thus aging can be reversed by reprogramming DNA methylation.

Information about the body’s age state is transmitted system-wide via signal molecules in the blood. Locally, tissues respond to these signals and adopt a young or an old cellular phenotype as they are directed.

Harold Katcher, Biographical Sketch

So, you might consider me a late bloomer.  While I have thousands of citations in the literature, with publications ranging from the discovery of the human ‘breast cancer gene’, to protein structure, bacteriology, biotechnology, bioinformatics, and biochemistry, there was no center or direction to my work as I had given up my personal goal of solving/curing aging when I learned that ‘wear and tear’ was the cause of it.  Yet something happened in year 1985 when I was in California working with Michael Waterman and Temple Smith (fathers of bioinformatics) that is inexplicable: I found myself in Intensive Care with a tube inserted into my trachea and the knowledge that I might not live.   And then I had a dream: I dreamed that somehow in the far future (and on another world), I was being feted for ‘bringing immortality to mankind’. Clearly, I survived that incident (started with an infected tooth).    I lived a wonderful life – becoming a computer programmer (which I loved), leaving that for the University of Maryland’s Asian division, becoming a full professor and then the Academic Director for the Sciences, in Tokyo, Japan.  By the time I left Japan in 2004, (my daughter Sasha was a fourth-grader, (yonensei), in the Japanese school system), I was teaching for U of M online – somewhat retired, and looking forwards to writing computer programs for fun and profit. Yet I never ever forgot that dream. It was clearly impossible; I had no lab – and really, there was no way to repair all damaged cells – it’d be like sweeping back the ocean. And then, in 2009, I read an old paper from 2005, a paper written by the Conboys, (Michael and Irina), Tom Rando and others, coming from Irv Weisman’s lab, that completely changed my life; that showed me that everything I believed about aging was wrong – that aging occurred at the organismic level, not at the cellular level and could be reversed. Well, the rest of the story is about persistence and the blessed intervention of Akshay Sanghvi who too saw there was another way and provided the structural, monetary, and emotional support (and some good ideas) that had me start a new career at age 72 in Mumbai, India.  I feel twenty years younger than I did three years ago, I guess that’s another hint about aging. Now the ‘mystical’ dream?  It wouldn’t be the first time in history that that happened – take that as a datum.

source https://joshmitteldorf.scienceblog.com/2020/05/11/age-reduction-breakthrough/

[makingscipub]

Astrogenomics: Integration and inspiration

I should have blogged about embryo editing in Russia. I should have blogged about Netflix’s ‘Unnatural selection’ series on CRISPR and genome editing. I should have blogged about prime editing, but life is getting in the way at the moment.

That doesn’t mean I don’t look at twitter once in a while (au contraire!). So, while idly browsing my twitter stream, I saw a tweet from Christopher Mason saying “Slides from my talk today at the #HGNYC conference about our lab’s work on astro-genomics and other genomics plans”.

I thought: astrogenomics, what next! I more or less tweeted that exclamation and a tweet came back from John Greally, an expert on clinical genomics and my go-to person for epigenetics, saying: “We used the term in a fun perspective paper.” Interestingly #HGNYC in Mason’s tweet stands for “Eighth human genetics at NYC conference”, and I think both Greally and Mason were there. Astrogenomics can be quite localised it seems!

Anyway, I downloaded the paper Greally referred to and was quite surprised by what I found. It was about using astronomy as an inspiration for how to deal with big data in genomics.

When reading the term astrogenomics, I had expected to find something like astrobiology with a new genomic twist. I googled a bit and found that there are indeed a few instances where people advocate an integration of genomics with astrobiology in order to study life on earth, especially microbial life “as a surrogate for understanding how life could have emerged elsewhere in the universe” on the one hand and for using synthetic biology to tailor-make microbes that could function in extra-terrestrial environments.

The field also deals with how humans function in such environments, physiologically, genetically and otherwise (what I call space biology) and the powerpoint presentation by Christopher Mason deals with that, referencing for example the somewhat contested twin study that was recently in the news.

So we have two uses of ‘astrogenomics’, one where genomics takes inspiration from astronomy and another were genomics is integrated with astrobiology and/or space biology. (Other uses are emerging, one inevitably related, as with epigenetics and microbiomics, to ‘woo‘…)

Astronomically big data

I shall focus here on the first use of astrogenomics, as that was the more surprising one.

The paper Greally referred to in his tweet was by Aaron Goldon S. George Djorgovski and John M. Greally published in Genome Biology in 2013 and entitled “Astrogenomics: Big data, old problems, old solutions?” The article should still be of interest to genomics people as the issue of big data is not getting any smaller. It was also interesting to me, as it contained some nice metaphors.

The paper advocates that the genomics and epigenomics communities take inspiration from astronomy in how to deal with big data. I became aware of the big data issue in 2012 and started to explore some of the metaphors used then in a blog post. The 2013 paper on astrogenomics uses some of them, namely ‘data deluge’, ‘data avalanche’ and ‘data tsunami’. They all refer to a huge ‘data universe’ that has been emerging in astronomy and is now emerging in genomics.

In one case the advent of new digital imaging detectors and more and more sophisticated telescopes and observatories brought about this explosion in data; in the other case it was the advent of high-throughput DNA sequencing, advances in bioinformatics etc., which has led to a ‘big data predicament’.

Astronomy tackled these issues through setting image standards, using metadata, and establishing a Virtual Observatory framework. This dealt not only with the data deluge but also with the human beings that had to cope with that deluge. The new way of dealing with data assured interoperability, flexibility and community engagement. This is called metaphorically a ‘federated data ecosystem’ or a ‘common cyberecosystem’.

The article ends by appealing to funding agencies to step in and fund such a new open, interactive and integrative approach to big data in genomics. It says (bringing the main metaphors structuring the article together): “With the creation of a cyberecosystem in which evolutionarily convergent software development can take place, the risk of developing dead end software is diminished, the security of highly sensitive sample data is enhanced, and the big data deluge can be stemmed, to the benefit of all.”

My impression is that not a lot has happened in this respect since 2013, but I might be wrong! It would be a shame.

Astro-Brexit

When writing this post, my hope was that I’d get away for a bit from life and Brexit. However, that hope is, as we all know, astronomically small, indeed non-existent. When looking through Mason’s slides on genomics and astrogenomics, I came across one slide that said “Chromosome 3 and Brexit” – which startled me. It turns out that it refers to an article published un-peer-reviewed in 2018 on bioRxiv entitled “Genetic consequences of social stratification in Britain”. This working paper was immediately ‘peer-reviewed’ online – openness is good! If I am not wrong, it has just been published in a peer-reviewed journal now, namely Nature Human Behaviour. Have look!

Conclusion

When thinking about what needs to be done about big data in genomics and epigenomics as laid out in the 2013 paper, I fear that nothing much will be done, as, at this very moment, our eyes are glued inexorably to the drama of daily politics wherever we are in the world. This leaves no time, really, to look at the stars or indeed to look across disciplines for inspiration on how to advance science in society.

Image: Pixabay – Milky Way

The post Astrogenomics: Integration and inspiration appeared first on Making Science Public.

via Making Science Public https://ift.tt/2NzMdyU

[ribosome-papers]

A flexible pipeline combining bioinformatic correction tools for prokaryotic and eukaryotic metabarcoding

bioRxiv: http://dlvr.it/R9VTs7

[netmyname-blog]

Jacquely Hsin-li IN

New Post has been published on https://nerret.com/netmyname/jacquely-hsin-li/jacquely-hsin-li-in/

Jacquely Hsin-li IN

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web.bii.a-star.edu.sg The Loo lab @ Bioinformatics Institute The overall goal of our research is to develop next-generation assays for predicting the toxicity and/or efficacy of chemical compounds. We develop and use …

[evoldir]

Fwd: Graduate position: Montpellier.AdaptationCropWildRelatives

Begin forwarded message: > From: evoldir@evol.biology.mcmaster.ca > Subject: Graduate position: Montpellier.AdaptationCropWildRelatives > Date: 9 July 2024 at 05:11:12 BST > To: rdmpage@gmail.com > > > > Applications are invited for a fully funded 3-year PhD fellowship based > at INRAE Montpellier (France), aiming at characterizing the genetic > bases of adaptation in wheat wild relatives. > > Studying the molecular and evolutionary mechanisms underlying species > response to selection is crucial to understand how biodiversity and > agroecosystems may adapt to current global changes. There is evidence > that the probability that the same genetic variants are mobilized in > response to selection depends on populations and species divergence > (e.g. Bohutínská/et al./, 2021). A relevant strategy to quantify to > which extent different species adapt through the same genes/alleles is > to investigate the signatures of selection in a multispecies comparative > setting. > > This PhD proposal addresses this question using as model system > the Triticeae, a family of grasses that includes worldwide staples > wheat, barley and rye, and their wild relatives (Glémin/et al./, > 2019; Burgarella/et al./2023). We will leverage transcriptomic and > genomic data to investigate the molecular signatures of selection > at two evolutionary scales, i.e. phylogenetic and within-species > levels, with approaches of molecular evolution, population genomics > and bioinformatics.  The PhD student will be hosted by the team GE2pop > (/Evolutionary genomics and population management/), UMR AGAP Institut > (https://ift.tt/PDkpU5G). Supervisors will be Concetta Burgarella > (population geneticist, INRAE), Nathalie Chantret (evolutionary > genomicist, INRAE) and Vincent Ranwez (molecular phylogeneticist, > Institut Agro Montpellier). > > We are looking for applicant holding a MSc. Degree and with expertise > in evolutionary biology and genomic data analysis. Interested > candidates should provide: (1) a motivation letter with a statement of > research interests, skills and experience relevant to the position, > (2) a CV, (3) contact details of two referees, (4) copies of > previous degrees and transcripts of records and (5) a copy of the > master thesis.  Candidatures or informal queries should be emailed > to concetta.burgarella@inrae.fr,nathalie.chantret@inrae.fr and > vincent.ranwez@supagro.fr. > > The deadline to apply is August 25th. > > The start date is flexible during autumn 2024.  A more > detailed version of the proposal is available here: > https://ift.tt/P18qGvr > > Bohutínská, M., Vlček, J., Yair, S., Laenen, B., Konečná, V., > Fracassetti, M., et al. (2021) Genomic basis of parallel adaptation > varies with divergence in Arabidopsis and its relatives. Proceedings of > the National Academy of Sciences, 118, e2022713118. > Burgarella, C., Brémaud, M.-F., Hirschheydt, G.V., Viader, V., Ardisson, > M., Santoni, S.,/et al./(2023) Mating systems and recombination > landscape strongly shape genetic diversity and selection in wheat > relatives. bioRxiv doi: 10.1101/2023.03.16.532584 > Glémin, S., Scornavacca, C., Dainat, J., Burgarella, C., Viader, V., > Ardisson, M.,/et al./(2019) Pervasive hybridizations in the history of > wheat relatives./Science Advances/,*5*, eaav9188. > > > Best regards, > > Concetta Burgarella > > > Concetta Burgarella > INRAe, Equipe Genomique Evolutive et Gestion des Populations > UMR AGAP > Batiment Arcad > 10 rue Arthur Young > 34090 Montpellier > concetta.burgarella@inrae.fr > www.inrae.fr > > > > Concetta Burgarella

[evoldir]

Fwd: Postdoc: MaxPlanck_Cologne.Genomics

Begin forwarded message: > From: evoldir@web.rhpcs.mcmaster.ca > Subject: Postdoc: MaxPlanck_Cologne.Genomics > Date: 15 February 2022 at 05:44:43 GMT > To: rdmpage@gmail.com > > > Location: > > Max Planck Institute for Plant Breeding Research, Cologne, Germany > > Institute: > > LMU Munich, Faculty of Biology, Munich, Germany > > Group: > Prof. Korbinian Schneeberger > > Starting date: > April 2022 (to be negotiated) > > Apply until: > February 28th, 2022 (position remains open until filled) > > Duration: > 3 years > > Postdoctoral position in Bioinformatics (m/f/d) > > The Ludwig-Maximilians University Munich is one of the largest and most > renowned universities in Germany. > > Working environment: > > The established group "Genome Plasticity and Computational > Genetics" managed by Korbinian Schneeberger is focused on plant > genomics, specifically on the development of novel computational and > biotechnological methods for the analysis of genome sequences. The group > is located at the Faculty of Biology at the LMU in Munich, with a part > of the group working at the Max Planck Institute for Plant Breeding > Research in Cologne, Germany. We are currently searching for a postdoc > for our location at the MPI in Cologne. > > Our group analyzes genomic changes on different levels. We compare > the genomes between species, populations and artificial crosses. We > do this using latest technologies (including third generation as well > as single-cell genomic technology) to get insights into how and why > genomes change over time. Current projects include genetic experiments > and the establishment of computational methods for the analysis of > multidimensional genome data to study the natural diversity of mutations > and recombination. > > We are a multi-disciplinary group including bioinformaticians, biologists > and biotechnologists (schneebergerlab.org). Our approach to science > is curiosity-driven, and is closely aligned to our interests in new > genomic technologies. Scientific support comes from a wide range of > facilities (genomics, microscopy, high performance compute clusters) > and lab technicians. Salaries will be based on previous experience > according to TV-L guidelines. > > > Project Description > > We have recently developed a new method to assemble the individual > haplotypes of tetraploid genomes based on the combination of long-read > sequencing and the analysis of single pollen genomes (Sun et al, 2021, > biorxiv). We applied this method for the reconstruction of the first > fully haplotype-resolved assembly of a cultivated potato genome. > > Following up on this work we now would like to make use of the individual > haplotypes and develop genotyping methods for a simplified analysis of > even more complex genomes. The method should then be applied to genotyping > recombinant pollen genomes (which will allow us to analyze the inheritance > on the individual haplotypes) as well as other potato cultivars. While > applied in the context of plant genomics, such haplotype-type based > genotyping would be applicable across many different species including > even humans. > > Qualifications > > We are searching for highly motivated applicants with a PhD in > bioinformatics or a similar field in computational biology. Applicants > should be proficient in scripting e.g. Python and should have experiences > in the analysis of next-generation sequencing data and in the use of a > high-performance compute cluster. Good oral and writing skills in English > are essential. We are particularly looking for open-minded, creative > and critical minded candidates who like to work in an international team. > > Disabled people with the appropriate qualifications will be considered > preferably. > > Have we raised your interest? Please submit your application to Finni > H�u�ler (finni.haeussler@lmu.de). In case of questions, please directly > email Korbinian Schneeberger (k.schneeberger@lmu.de). > > > Postdoctoral Researcher > Division of Evolutionary Biology > Faculty of Biology > LMU Munich > Grosshaderner Str. 2 > 82152 Planegg-Martinsried > Germany > > > > Sergio Tusso > via IFTTT

[evoldir]

Fwd: Postdoc: MaxPlanck_Cologne.Genomics

Begin forwarded message: > From: evoldir@web.rhpcs.mcmaster.ca > Subject: Postdoc: MaxPlanck_Cologne.Genomics > Date: 22 January 2022 at 05:18:28 GMT > To: rdmpage@gmail.com > > > Location: > > Max Planck Institute for Plant Breeding Research, Cologne, Germany > > Institute: > > LMU Munich, Faculty of Biology, Munich, Germany > > Group: > > Prof. Korbinian Schneeberger > > > > Starting date: > > April 2022 (to be negotiated) > > > > Apply until: > > February 28th, 2022 (position remains open until filled) > > > > Duration: > > 3 years > > > > Postdoctoral position in Bioinformatics (m/f/d) > > The Ludwig-Maximilians University Munich is one of the largest and most > renowned universities in Germany. > > > > Working environment: > > The established group “Genome Plasticity and Computational Genetics” > managed by Korbinian Schneeberger is focused on plant genomics, > specifically on the development of novel computational and biotechnological > methods for the analysis of genome sequences. The group is located at the > Faculty of Biology at the LMU in Munich, with a part of the group working > at the Max Planck Institute for Plant Breeding Research in Cologne, > Germany. We are currently searching for a postdoc for our location at the > MPI in Cologne. > > Our group analyzes genomic changes on different levels. We compare the > genomes between species, populations and artificial crosses. We do this > using latest technologies (including third generation as well as > single-cell genomic technology) to get insights into how and why genomes > change over time. Current projects include genetic experiments and the > establishment of computational methods for the analysis of multidimensional > genome data to study the natural diversity of mutations and recombination. > > We are a multi-disciplinary group including bioinformaticians, biologists > and biotechnologists (schneebergerlab.org). Our approach to science is > curiosity-driven, and is closely aligned to our interests in new genomic > technologies. Scientific support comes from a wide range of facilities > (genomics, microscopy, high performance compute clusters) and lab > technicians. Salaries will be based on previous experience according to > TV-L guidelines. > > > Project Description > > We have recently developed a new method to assemble the individual > haplotypes of tetraploid genomes based on the combination of long-read > sequencing and the analysis of single pollen genomes (Sun et al, 2021, > biorxiv). We applied this method for the reconstruction of the first fully > haplotype-resolved assembly of a cultivated potato genome. > > Following up on this work we now would like to make use of the individual > haplotypes and develop genotyping methods for a simplified analysis of even > more complex genomes. The method should then be applied to genotyping > recombinant pollen genomes (which will allow us to analyze the inheritance > on the individual haplotypes) as well as other potato cultivars. While > applied in the context of plant genomics, such haplotype-type based > genotyping would be applicable across many different species including even > humans. > > > Qualifications > > We are searching for highly motivated applicants with a PhD in > bioinformatics or a similar field in computational biology. Applicants > should be proficient in programming (Java, C/C++ etc.) or scripting and > should have experience in the analysis of next-generation sequencing data > and in the use of a high-performance compute cluster. Good oral and writing > skills in English are essential. We are particularly looking for > open-minded, creative and critical minded candidates who like to work in an > international team. > > Disabled people with the appropriate qualifications will be considered > preferably. > > Have we raised your interest? Please submit your application to Finni > Häußler (finni.haeussler@lmu.de). In case of questions, please directly > email Korbinian Schneeberger (k.schneeberger@lmu.de). > > > > Postdoctoral Researcher > Division of Evolutionary Biology > Faculty of Biology > LMU Munich > Grosshaderner Str. 2 > 82152 Planegg-Martinsried > Germany > > Sergio Tusso > via IFTTT

[evoldir]

Fwd: Graduate position: Earlham_RBGKew.RiceGenDiversityAdaptation

Begin forwarded message: > From: evoldir@web.rhpcs.mcmaster.ca > Subject: Graduate position: Earlham_RBGKew.RiceGenDiversityAdaptation > Date: 20 January 2022 at 07:22:45 GMT > To: rdmpage@gmail.com > > > Characterising rice genetic diversity in the Mekong Delta to sustain > future crops > > This project is based in the Jose De Vega Group at the Earlham Institute > and the Rafal Gutaker Group at Royal Botanic Gardens, Kew. > > Project Summary > Rice is a versatile carbohydrate essential to diets worldwide and a > staple for over 50% of the human population. Rice production in Vietnam > is of enormous value, both as an export commodity and a daily food staple > for more than 96 million people in Vietnam. However, climate change is > threatening rice’s wide availability. In Vietnam, the highest rice > production areas are in the low-lying deltas of the Mekong and Red rivers > which are particularly exposed to drought and increased salinity from > seawater due to climate change. > > Plant genetic resources provide the reservoir of adaptive and productive > genes free of deleterious mutations needed to develop the improved > cultivars that help ensure future crop production. Vietnam’s rice > diversity constitutes a significant and precious genetic resource. The > highly productive Mekong Delta is a cultural and agricultural > hotspot in Southeast Asia, where a unique and rich diversity of rice > landraces developed through centuries (Gutaker et al. 2020; Higgins et > al. 2021a). These locally adapted and inherited rice varieties constitute > a highly valuable genetic resource for breeders to address increasing > threats from climate change in the Mekong Delta. However, the growing > adoption for high-yielding rice varieties in the Mekong Delta in the > last five decades has driven the progressive replacement of locally > adapted landraces. > > This PhD aims to understand better the changes in rice genetic diversity > in the region and the extent of potential genetic erosion from the > loss of adapted local landraces. The student will quantify the genetic > diversity in local landraces and admixed accessions, investigate their > genetic make-up, and quantify deleterious mutations that hinder the > further improvement of rice and its adaptation to future climates. The > introduction and later widespread displacement of local landraces left us > with a limited understanding of the extent of loss in genetic diversity > and adaptive potential available to breeders in admixed elite varieties > that retain local adaption. > > The project will be based at De Vega's lab at the Earlham Institute > (Y1 and Y2) and Gutaker's group at RBG Kew (Y3 and Y4). The combined > expertise across the team will provide mentorship and guidance in > genomic and bioinformatic approaches to the study of plant diversity > and evolution. The student will have access to Earlham Institute's > and RGB Kew's state-of-art high-performance computing, horticultural > infrastructure, herbarium and seed collections. > > Apply here: > https://ift.tt/3rxzW20 > > Related Reading: > > - Gutaker et al. (2020) Genomic history and ecology of the geographic >  spread of rice. Nature Plants 6: 492-502. > - Latorre et al. (2020) Isolation, Library Preparation, and >  Bioinformatic Analysis of Historical and Ancient Plant DNA. Curr >  Protocols Plant Biol 5(4): e20121. > - Higgins et al. (2021) Resequencing of 672 Native Rice Accessions >  to Explore Genetic Diversity and Trait Associations in Vietnam. >  Rice, 14: 52. > - Higgins et al. (2021) Identifying genomic regions and candidate genes >  selected during the breeding of rice in Vietnam. bioRxiv, >  2021.08.04.455072v1 > > Further Information > Please note that all international awards have been made for our > programme for 2022 so we will not be accepting applications from > international candidates, as defined by UKRI’s guidance on International > Eligibility criteria for UKRI funded studentships.  This project is a > Joint-Studentship with Royal Botanical Gardens, Kew.  You can also visit: > https://ift.tt/3BnHVS3 > > > > The Royal Botanic Gardens, Kew is a non-departmental public body with > exempt charitable status, whose principal place of business is at Royal > Botanic Gardens, Kew, Richmond, Surrey TW9 3AE, United Kingdom. > > > > Rafal Gutaker > via IFTTT

[evoldir]

Fwd: Postdoc: Basel_Switzerland.HostParasitePopGenomics

Begin forwarded message: > From: evoldir@web.rhpcs.mcmaster.ca > Subject: Postdoc: Basel_Switzerland.HostParasitePopGenomics > Date: 22 September 2021 at 07:49:35 BST > To: rdmpage@gmail.com > > > Postdoc position in host-parasite population genetics and genomics at > University of Basel, Switzerland > > A postdoc position is available in the research group of Dieter Ebert, > at Basel University in Switzerland. I am looking for a highly motivated > post-doc with interest in the genetics/genomics of host-parasite > interactions. This position is funded to work on the Daphnia - > microparasite system. A background in evolutionary genetics, molecular > genetics and bioinformatics skills is welcome. Excellent written, > verbal, and interpersonal skills, a superb work ethic, and the ability > to think creatively and critically are desired. Here are 4 recent > publications related to this project: > - Bento et al 2017. PLoS Genetics, DOI:10.1371/journal.pgen.1006596). > - Ebert, D. & Fields, P.D. 2020. Host-parasite coevolution and >   its genomic signature. Nature Reviews Genetics 21: 754-768. >   doi: 10.1038/s41576-020-0269-1 > - Ameline, C., Voegtli, F., Andras, J., Dexter, E., Engelstaedter,J. & >   Ebert, D. Genetic slippage after sex maintains diversity for parasite >   resistance in a natural host population. bioRxiv 2021.07.11.451958; >   doi: https://ift.tt/3CAbgtM > - Ameline,C., Bourgeois,Y., Voegtli, F., Savola, E., Andras, J., >   Engelstaedter, J. & Ebert, D. 2021. A two-locus system with strong >   epistasis underlies rapid parasite-mediated evolution of host >   resistance. Molecular Biol. and Evol. 38: 1512-1528. >   https://ift.tt/3lLTnRU > > The starting date for the position is negotiable. The working language > in the group is English. Speaking German is helpful in everyday life in > Basel, but is not a requirement. A PhD degree is required. The position > is initially for 2 years, but can be extended. > > Please send your application by E-mail (all material in one PDF please) > to Dieter Ebert. Applications should include a motivation letter, a CV, > a list of publications and a 1-page statement about research interests. > Please give names and email addresses of two persons who are willing to > write a letter of recommendation. Application deadline is 15. October 2021. > > Further information and address for application: > Prof. Dr. Dieter Ebert, University of Basel, > Department of Environmental Sciences, Zoology, > Basel, Switzerland > Email: dieter.ebert@unibas.ch > Web:  https://ift.tt/3hRNelW > > Dieter Ebert > via IFTTT