@James Fellows Yates has joined the channel
@Katerina Guschanski has joined the channel
@Linda Armbrecht has joined the channel
@Antonio Fernandez-Guerra has joined the channel
Draft programme for 'Ancient Biomolecules of Plants, Animals and Microbes'
Sessions of interest:
Featuring @Lucy van Dorp, @Christina Warinner and @Katerina Guschanski
@Christina Warinner has joined the channel
@Sterling Wright has joined the channel
If anyone is interested in contributing or learning about nf-core pipelines, there is an upcoming Hackathon in march: https://nf-co.re/events/2021/hackathon-march-2021
You can use the time to write your own pipelines with support from a lot of nextflow/nf-core developers, or if you're interested in learning but unsure what to do you can help out contributing to existing pipelines (e.g. nf-core/eager for aDNA processing, or nf-core/mag for de Novo assembly of bacterial genomes, or bacass for bacterial genome assembly and annotation)
Registration is open for the early career researcher-targeted conference “The Bioinformatics Virtual Coordination Network presents: Holistic Bioinformatic Approaches used in Microbiome Research” https://biovcnet.github.io/_pages/conference-2021/ (with @Miriam Bravo as a speaker!)
And I think @Antonio Fernandez-Guerra’s student in the Env. Microbio?
yes, Chiara is presenting our work with the unknowns https://www.biorxiv.org/content/10.1101/2020.06.30.180448v5 https://merenlab.org/2020/07/01/dark-side/
https://docs.google.com/forms/d/e/1FAIpQLSfIITJ5qAdxi1vFce5LGnDx3xCX9ikBwOi6Xy0DTzJmtmISZQ/viewform
Hey for those interested in environmental aDNA, there is this webinar activity on April 8th that may be nice…
Environmental Genomics network webinars : DNA et al. in paleoenvironments
See you on Monday @Markella Moraitou @Nikolay Oskolkov 😅 !
*Thread Reply:* And @Jaelle Brealey presenting on Tuesday
could someone share the full program/abstract book of the “Ancient Biomolecules of Plants, Animals and Microbes” conference here? I can’t find it online.
I dont think ti's publically avaliable. The links I have all have the programms/abstract books embedded in non-downloadable PDF viewer
I guess there might be some embargoed stuff there or something
Here's the program but I guess access is only available for registered participants
Hello everyone, I was wondering which microbial genomics& microbiome conferences& trainings are you attending this year?
ISBA https://isba9.sciencesconf.org
☝️ that's for archaeological sciences in general.
@Başak Uysal do you mean specific aDNA or generalised ones?
@ivelsko probably can suggest a few
As much as I enjoy aDNA and worked on it for my bachelors thesis, now I work with vaginal microbiome so more general would be appreciated
Hi @Başak Uysal I suggest you check out the conferences offered by the American Society for Microbiology (https://asm.org/Events) and the conferences offered by the Microbiology Society (https://microbiologysociety.org/events.html)
Thanks a lot! @ivelsko! they seem to have a couple of good ones, cheers!
https://www.pathlms.com/ashg/courses/18113/webinars/19963
If anyone is interested in learning how to set up institutional-level config files for their cluster for nf-core pipelines (such as nf-core eager), I'm giving a 15m talk plus Q/A session tomorrow at. 13:00 CEST
YouTube link: https://nf-co.re/events/2021/bytesize-10-institutional-profiles
Annnnd another one: https://twitter.com/nf_core/status/1397100121750482949
This time it will be @Zandra Fagernäs TODAY talking about the importance of making good images for documentation!
*correction* I originally wrote tomorrow for ☝️ it's actually TODAY (I thought it was monday today 🤦 )
*Thread Reply:* happy people don't observe the clock (Russian proverb)
*Thread Reply:* Way to go @Zandra Fagernäs!
Next week, on Thursday, November 4th, the Genome and Genetics Department from Institut Pasteur will host a symposium on ancient DNA, entitled “A Journey to Ancient DNA: from Humans to Human Pathogens and Microbiomes”. https://research.pasteur.fr/en/event/ancient-dna-journey-from-humans-to-human-pathogens-and-microbiomes/ KEYNOTES: Johannes Krause, Ludovic Orlando INVITED SPEAKERS: Christina Warinner, Barbara Bramanti, Flora Jay, Simon Rasmussen, Lluis Quintana-Murci, Nicolás Rascovan The event will be held at Institut Pasteur and also broadcasted live via teams. You can register to the event by sending an email to aDNA@pasteur.fr. Registration is mandatory in all cases.
Registration on site is already closed (the quota is already reached) There is a limited number of seats available in the auditorium. We therefore strongly recommend registering as soon as possible to secure your seat.
*Thread Reply:* @Nico Rascovan is the deadline correct?
*Thread Reply:* That was yesterday 😬
*Thread Reply:* Or is that just for in person attending?
*Thread Reply:* hahaha, good point. That was for attending in person. Sorry.
*Thread Reply:* @Nico Rascovan will the symposium be recorded and available online at a later date? I would like to attend (and have sent a sign-up email), but I have several meetings already booked for that day and will have to miss some of the talks
*Thread Reply:* Hey Ash! I already registered you. I am not sure about the recording, but possibly yes
Great event @Nico Rascovan! Thank you so much for organizing and live streaming it! 🎉
*Thread Reply:* Yes!! Thank you @Nico Rascovan it was awesome (also thanks for your talks both!)
Thank you @Christina Warinner for coming! It wouldn’t have been so nice if it wasn’t for awesome speakers like you! Everybody was delighted with your talk. I hope you had a good trip back!
*Thread Reply:* @Nico Rascovan Thanks for a magical time in Paris! It was my first in-person conference since the pandemic, and it was so nice to see and talk to people! I know it must have been a lot of work to host the conference, but we all appreciated it so much - thank you!
*Thread Reply:* thanks Tina! It was actually much easier than I thought, and as you said a great pleasure to meet with colleagues in person again!
🧬💀 If you want to learn how to identify the "true maker" of Illumina sequenced 💩Coprolites/Paleofaeces by checking the microbiome composition and the endogenous DNA, listen to @Maxime Borry today at 13:00! Details 👇
https://nf-co.re/events/2021/bytesize-29-nf-core-coproid
I share here the following colloquium taking place next year in May in Majorca. The event is free. I think that the participation of many people in SPAM working with ancient pathogens and plague in particular would be very welcomed.
Plague and Plagues. Transdisciplinary and diachronic perspectives on the history of plague. International Colloquium 2022 May 19th-21th Majorca (Spain)
Excellent online and free course starting in 4 days (registration still possible) for those wanting to get a first approximation to Human Poop Gen from great referents in the field: https://www.fun-mooc.fr/en/courses/human-population-and-evolutionary-genetics/
For #TeamDirt
perhaps too grant specific (it focuses a lot of Horizon Europe requirements) for some of you but this might be of interest to either yourselves or colleagues/collaborators https://dans.knaw.nl/en/agenda/dans-data-trail-workshop-data-management-tools-for-archaeologists/
Hi! Maybe some of you are interested in this conference happening in Girona: https://www.congresopaleopatologia.com/en/home . It also happens to be that Vanessa Villalba and myself are organising a round table to discuss palaeogenetics within the context of palaeopathology! We will love to have people in the palaeogenetics community involved in this discussion! If you want to submit an abstract (they have a session in zoonosis!) the deadline is the 15th of March!
*Thread Reply:* You should also send to the mailing list, there might be extra people who could be interested
Hi folks — because of COVID I haven’t had a chance to go to any conferences yet so I’m just wondering if anyone has recommendations for ones they like (or don’t like 😉 ) that I should look into!
Good question... Off the top of my head In our department people normally go to:
SMBE (international, Evo bio), EAA (Europe, archaeology but lots of aDNA/ArchSci normally), ISBA (international but mostly Europe, Biomolecular archaeology), AAPA/SAA etc (n. Amèrica, anthropology but lots of palaeoanthropology?
But it depends what you are looking for (more archaeology? More biology? More microbiology/microbiomes? Palaeopathology?)
*Thread Reply:* Thank you! I’m gonna look at these.
If anyone is interested to apply: We invite submissions to MLMG 2022, the ECML-PKDD 2022 workshop on machine learning for microbial genomics to be held virtually, on September 23rd. Submission deadline: June 20th 2022.
The improvement and increasing accessibility of Next Generation Sequencing data calls for innovative data analysis strategies to extract meaningful and actionable information. Machine learning approaches are more and more popular in this context, offering alternative and complementary tools beyond bioinformatics to analyze genomic data. However, despite the recent advances, their application remains challenging and new approaches that are robust, scalable to large-scale high-dimensional data and interpretable are needed.
This workshop aims to bring together interdisciplinary researchers working at the interface of machine learning and computational biology for the study of microbial genomic data to discuss recent advances in this field. We will also have the privilege of hosting two distinguished speakers from this community to discuss and present their current research.
Typical topics of interest include:
Key dates:
Meriem El Azami Laurent Jacob Flora Jay Pierre Mahé https://mlmg2022.github.io/
In case someone is interested to join EBAME https://twitter.com/LoiMai/status/1534463409495867392 Here is the program from last year: https://maignienlab.gitlab.io/ebame6/ebame6_program.html This year I will have a session where we will go through all the new tools and methods we have developed for ancient metagenomics
From an email sent to the mailing list:
```Dear SedaDNA Community,
we are delighted to host the SedaDNA Meeting, co-organized with the PaleoEcoGen PAGES working group, in Potsdam next year.
We are currently in the planning phase, but for now we would like to ask you to save the date - 07.-09.06.2023.
All meeting details will be stored and regularly updated here: https://docs.google.com/document/d/13tvQSsiWDWVYNwo638D9ByT3cKc1HLZsXTSC_3GRtSY/edit?usp=sharing
We are looking forward to seeing you in Potsdam,
the local organizing committee
(Ulrike Herzschuh, Kathleen Stoof-Leichsenring and Liv Heinecke) ``` Please email Kathleen if you have any further questions: Kathleen.Stoof-Leichsenring@awi.de
Hi all! Is anyone attending to ISME? https://isme18.isme-microbes.org I was wondering if there would be people coming, maybe we could meet.
Hi SPAAM organizers! I missed the registration and was wondering if the talks will be made available for streaming later?
*Thread Reply:* I am wondering the same thing. I did sign up but the time difference killed me 🦘
*Thread Reply:* Same here. I missed the registration.
Hi folks — the SPAAM 5 organizers are trying to figure out a date which doesn’t conflict with other conferences that are scheduled for 2023. If you could please respond in a thread with the name of conferences you are considering going to (don’t have to be attending!) that would be super helpful for us 🙂 I can look up the dates, you don’t need to do that part.
*Thread Reply:* EMBO The human microbiome (https://www.embl.org/about/info/course-and-conference-office/events/ees23-08/)
*Thread Reply:* World of microbiome (https://microbiome.kenes.com/)
*Thread Reply:* SMBE 2023 (July 23-27) http://www.smbe.org/smbe/MEETINGS/SMBE2023.aspx
*Thread Reply:* Are you guys not planning to try and do it same week as ISBA?
If not,
• ISBA: 13-16th Sept (https://www.isbarch.org/meetings) • ESHE sometime mid-to-end sept (https://www.eshe.eu/past/)
*Thread Reply:* And a niche one for me:
• Nextflow summit: first/second week October
Last minute, but if anyone wants to hear about a new pipeline for simultaneous taxonomic classification with multiple tools and databases (incdlues MALT, Kraken2, KrakenUniq, MetaPhlAn2 and more!), there is a 15minute talk on Zoom *today at 13:00 CET* about if you're interested:
https://nf-co.re/events/2023/bytesize_nf-core-taxprofiler
Starting now!
Hello SPAAM people, I got a suggestion to advertise here our EAA 2023 session (661: Pathogenic Disease in the Past), in case you here are interested in a little bit more archaeological meeting this year! (Abstract submission DL next Monday, February 13th at 23:59 CET)
So warm welcome to everyone working on ancient diseases, with genetics, proteomics, etc. More info in the docx attached!
*Thread Reply:* You can also post to the SPAAM and ISBA mailing lists:
https://www.listserv.dfn.de/sympa/info/spaam-community https://www.jiscmail.ac.uk/ISBARCH
*Thread Reply:* Cool! Shevan's taking care of the mail lists, will tell her!
Hello @channel!
We would like to invite you to submit an abstract to our SMBE 2023 symposium, "Host-pathogen co-evolutionary dynamics through the lens of paleogenomics." The SMBE 2023 will be held in beautiful Ferrara, Italy, from July 23 to July 27.
The aim of this symposium is to assemble findings from the field of Paleogenomics addressing the interactions between pathogens and their hosts throughout human history, such as pathogen origins and spread, the genetic processes involved in the emergence of epidemics among past human populations, and the evolutionary mechanisms underlying human adaptation to infectious disease exposure.
During this symposia, two outstanding invited speakers will be featured: @Maria Spyrou with a title talk, "Investigating the genomic history of plague, from the Neolithic to the present" and Gaspard Kerner presenting "A time-series aDNA approach detects genetic adaptation to pathogens in post-Neolithic Europe".
The deadline for abstract submission will be on the 15th of March. See the website for more details https://www.smbe2023.org/abstractsubmission.
Please, feel free to forward this to colleagues and students that might be interested !!
Let us know if you have any further questions.
Dr. Federica Pierini (Max Planck Institute for Evolutionary Anthropology) Dr. Linda Ongaro (Trinity College Dublin) Dr. Marco Rosario Capodiferro (Trinity College Dublin) Dr. Miriam Bravo (LIIGH-UNAM)
The ISBA10 programme is out!
https://www.jiscmail.ac.uk/cgi-bin/wa-jisc.exe?A2=ISBARCH;bc7bc4e0.2306
Note you need to sign up to the ISBA society mailing list to see it 😬
It will be sent out through other means as well. Due to ongoing website issues, we decided to go the pdf route for now, but it will be available everywhere in due course.
(but please also join the society mailing list 🙂 )
Hello @channel! If you came to the SMBE2023 at Ferrara, I hope to see you in the symposium "Host-pathogen co-evolutionary dynamics through the lens of paleogenomics" at 4 pm in the AD2 building!! 🦠🧬😄
*Thread Reply:* For people at the SMBE2023, is there any plan for a dinner togheter tonight to meet each other?
*Thread Reply:* that will be great! We can chat after the simposium to pick a place!
*Thread Reply:* yes of course
*Thread Reply:* People interested for tonight write here so that, basing on the number, I can find a place for all of us (which is not so easy these days in Ferrara) ;)
*Thread Reply:* We’re going to https://maps.app.goo.gl/7bMdaDU7QMxikBNj9 at 7.30 pm to have a beer 🍺
Hi @channel, We are very excited to announce a new event: Speed networking between PIs and young researchers! We will group PIs and young researchers into pairs/small groups in breakout rooms to share a bit about their background, all within a limited amount of time. We have planned this event to replicate the informal networking that happens in a conference but from the comfort of your own house ;).
The first date for this event series would be the 17th of July at 16:00 CEST (Paris time)! Come to talk with: • Prof. Anne Stone (Arizona State University, https://stone.lab.asu.edu/). Topics: ancient pathogens, mycobacteria, primate variation, human population history, forensics. • Associate Prof. Dr. Christina Warinner (Ph.D.) (Harvard University, Max Planck Institute for Evolutionary Anthropology, https://christinawarinner.com/ ). Topics: oral microbiome, gut microbiome, food culture through microbes, proteomics, human adaptation to extreme environments • Dr. Nicolás Rascovan (Institut Pasteur, https://research.pasteur.fr/en/team/microbial-paleogenomics/). Topics: oral microbiome, ancient pathogens, human population genetics, evolution • Dr. Katerina Guschanski (The University of Edinburgh, Uppsala University, https://www.uu.se/en/contact-and-organisation/staff?query=N14-1484). Topics: microbiome, evolution, ecology, nonhuman primates, biological diversity This is your chance to get to talk to them in an informal setting, to ask them any questions and see if they may be a good fit for your future career! If you are interested in participating, please fill out the registration form by July 10th.
Please note -- slots are going to be given on a first-come-first serve basis! so please sign up soon if you are interested!
Hi everyone! We are pleased to announce that the next International Symposium on Biomolecular Archaeology will be held in Turin, Italy, from the 26th to the 29th of August 2025. Stay tuned for updates by following our social media channels: Instagram: @isba11turin X: @ISBA11Torino Website: www.isba11.com We look forward to welcoming many of you next summer!