From cstorm at birc.au.dk  Thu Apr  3 11:26:25 2025
From: cstorm at birc.au.dk (=?utf-8?B?Q2hyaXN0aWFuIE7DuHJnYWFyZCBTdG9ybSBQZWRlcnNlbg==?=)
Date: Thu, 3 Apr 2025 09:26:25 +0000
Subject: [SocBiN] Open position: Tenure Track Assistant Professor or
 Associate Professor in bioinformatics at Aarhus University
Message-ID: <BB36CEA1-74EB-485F-B735-4B841DC8B17D@birc.au.dk>

Dear all,

We have an open position as Tenure-Track Assistant Professor or Associate Professor in bioinformatics at the Bioinformatics Research Centre (BiRC), Department of Molecular Biology and Genetics (MBG), Aarhus University, Denmark.

We seek a highly motivated researcher in bioinformatics to complement and expand our current research portfolio and teaching activities. We welcome applicants within all areas of bioinformatics with a strong focus on development of computational and statistical methods, particularly within machine learning and artificial intelligence. The applicant must have earned a PhD degree and have demonstrated excellence in research and scholarship within the field of interest.

https://international.au.dk/about/profile/vacant-positions/job/tenure-track-assistant-professor-associate-professor-in-bioinformatics-at-aarhus-university-denmark-1

Application deadline is June 1, 2025.

Please forward to anybody who might be interested.

Regards,
Christian

--
Christian Nørgaard Storm Storm Pedersen
Bioinformatics Research Center (BiRC), Aarhus University

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From arne.elofsson at gmail.com  Fri Apr  4 17:04:47 2025
From: arne.elofsson at gmail.com (Arne Elofsson)
Date: Fri, 4 Apr 2025 17:04:47 +0200
Subject: [SocBiN] Opening: Max Planck Research Group Leader (W2) in
 Molecular Design
In-Reply-To: <D618C81D-3728-46F4-9B4A-7428D08C48EE@mpip-mainz.mpg.de>
References: <D618C81D-3728-46F4-9B4A-7428D08C48EE@mpip-mainz.mpg.de>
Message-ID: <CAND8g_YJwQiWS-by7qSeHtrGfxxYN0iW2=GCN-uKpMjUeiPYOg@mail.gmail.com>

From: Frauke Graeter <fgraeter at mpip-mainz.mpg.de>
Date: Fri, 4 Apr 2025, 16:58
Subject: Opening: Max Planck Research Group Leader (W2) in Molecular Design
To: Frauke Graeter <graeter at mpip-mainz.mpg.de>


Dear friends and colleagues,



I am reaching out to you to let you know about an exciting opportunity for
early-career researchers to start an own research group at the MPI-P in
Mainz, Germany, which I hope you might share within your network.


https://www.mpip-mainz.mpg.de/1010939/202504_w2?c=944116


We are looking for enthusiastic candidates who are interested in starting
their own research group in the field of generative models for
(bio)molecular design. We offer a 6+3 year position with great research
freedom, excellent infrastructure for computational - and if desired also
experimental - work, and an inspiring and collaborative research
environment.


I believe this position will be particularly attractive to talented (early)
postdocs keen on embarking on their own research agenda without strings
attached.


Could you please pass the call to potentially interested young scientists
and/or distribute it in your network?



Thanks very much for your support!

Best,
Frauke

--

Prof. Dr. Frauke Gräter
Director
Max Planck Institute for Polymer Research
Department of Biomolecular Mechanics

e-mail: graeter at mpip-mainz.mpg.de
www: http://www.mpip-mainz.mpg.de

Ackermannweg 10
<https://www.google.com/maps/search/Ackermannweg+10+55128+Mainz,+Germany?entry=gmail&source=g>
 55128 Mainz,
<https://www.google.com/maps/search/Ackermannweg+10+55128+Mainz,+Germany?entry=gmail&source=g>
 Germany
<https://www.google.com/maps/search/Ackermannweg+10+55128+Mainz,+Germany?entry=gmail&source=g>
Tel +49 (0)6131 379180
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From arne.elofsson at gmail.com  Tue Apr  8 12:13:31 2025
From: arne.elofsson at gmail.com (Arne Elofsson)
Date: Tue, 8 Apr 2025 12:13:31 +0200
Subject: [SocBiN] Fwd: [3d-bioinfo-steering-committee] Webinar Today
 Activity 2
In-Reply-To: <CALoR5AJWqzJKQUc-N0OESJdUucRWb=4LPfENUj7QxT3RT0g3Dg@mail.gmail.com>
References: <CALoR5AJWqzJKQUc-N0OESJdUucRWb=4LPfENUj7QxT3RT0g3Dg@mail.gmail.com>
Message-ID: <CAND8g_ataF91WH3bbv2Z+poKAOKmzvARDy+kcor=5cyH5LNBww@mail.gmail.com>

---------- Forwarded message ---------
From: R. Gonzalo Parra via 3d-bioinfo-steering-committee <
3d-bioinfo-steering-committee at elixir-europe.org>
Date: Tue, 8 Apr 2025, 12:00
Subject: [3d-bioinfo-steering-committee] Webinar Today Activity 2
To: Nathalie Reuter via 3d-bioinfo-steering-committee <
3d-bioinfo-steering-committee at elixir-europe.org>


Dear all,

We will have a new webinar today from Activity 2!

Prof. Qian Cong
*Computing the Human interactome*
Protein-protein interactions (PPI) are essential for biological function.
Recent advances in coevolutionary analysis and Deep Learning (DL) based
protein structure prediction have enabled comprehensive PPI identification
in bacterial and yeast proteomes, but these approaches have limited success
to date for the more complex human proteome. Here, we overcome this
challenge by 1) enhancing the coevolutionary signals with 7-fold deeper
multiple sequence alignments harvested from 30 petabytes of unassembled
genomic data, and 2) developing a new DL network trained on augmented
datasets of domain-domain interactions from 200 million predicted protein
structures. These advancements allow us to systematically screen through
200 million human protein pairs and predict 18,316 PPIs with an expected
precision of 90%, among which 5,578 are novel predictions. 3D models of
these predicted PPIs nearly triple the number of human PPIs with accurate
structural information, providing numerous insights into protein function
and mechanisms of human diseases.

Here is the zoom link:
https://stockholmuniversity.zoom.us/my/arneelof/

Please join if you can and spread the word in your social circles.

Best,

Gonzalo
-----
Dr. R. Gonzalo Parra
Established Researcher (R3)
Life Sciences Department
Barcelona Supercomputing Center
Barcelona, Spain
https://www.bsc.es/discover-bsc/organisation/scientific-structure/computational-biology
You are on this mailing list because you registered to join an ELIXIR
group, and this is one of your group's mailing lists.

TO UNSUBSCRIBE: please email webmaster at elixir-europe.org. Put
"3d-bioinfo-steering-committee" as the subject and "Unsubscribe" as the
body text.

To view the groups you belong to, log in to the ELIXIR intranet:
https://www.elixir-europe.org/intranet

See also the website privacy statement:
https://www.elixir-europe.org/legal/privacy

3d-bioinfo-steering-committee mailing list
3d-bioinfo-steering-committee at elixir-europe.org
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From allison.hsiang at gmail.com  Wed Apr  9 14:47:11 2025
From: allison.hsiang at gmail.com (Allison Hsiang)
Date: Wed, 9 Apr 2025 14:47:11 +0200
Subject: [SocBiN] Two open PhD positions at Stockholm University
Message-ID: <67D3153B-437F-4163-93A5-7E116845857F@gmail.com>

Dear all,

We are advertising two PhD positions at Stockholm University, one in the Department of Ecology, Environment and Plant Sciences (DEEP) and the other in the Department of Zoology. The former position focuses on plant evolutionary genomics (including population genomics and transcriptomic analyses) while the latter focuses on macroevolutionary analyses, image analysis, and AI.

Both positions are part of a large interdisciplinary project titled “Harnessing evolutionary transitions, machine learning, and genomics to decode pollen evolution and unravel sexual selection mechanisms shared across kingdoms”, led by Prof. Tanja Slotte in close collaboration with co-investigators Prof. John Fitzpatrick, Prof. Catarina Rydin, and Dr. Allison Hsiang at Stockholm University.

The application deadline is 22 April 2025; links to the ads and application instructions below. We’d appreciate it if you could spread the ads in your networks — thanks!

DEEP: https://su.varbi.com/en/what:job/jobID:805144/where:4/
Zoology: https://su.varbi.com/what:job/jobID:805542/where:4/


Best,
Allison


------------------------------------------------
Allison Y. Hsiang, Ph.D. (she/her)
Early Career Researcher
Department of Geological Sciences
Stockholm University
allison.hsiang at geo.su.se <mailto:allison.hsiang at geo.su.se>
allisonhsiang.com <http://allisonhsiang.com/>



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From Fredrik.Ronquist at nrm.se  Thu Apr 10 18:24:43 2025
From: Fredrik.Ronquist at nrm.se (Fredrik Ronquist)
Date: Thu, 10 Apr 2025 16:24:43 +0000
Subject: [SocBiN] Researcher in insect phylogenomics
Message-ID: <62D33BCC-BD83-42DF-B32A-222FB7C0A0FA@nrm.se>

Researcher in insect phylogenomics

A four-year full-time position as researcher in insect phylogenomics is available in Stockholm. The successful candidate will be a joint member of the Ronquist lab at the Swedish Museum of Natural History (https://ronquistlab.github.io/) and the van der Valk lab at the Centre for Paleogenomics, Stockholm University / Swedish Museum of Natural History (https://www.scilifelab.se/researchers/tom-van-der-valk/).

We are looking for someone with a passionate interest in insect phylogeny and evolution, and with strong competence in de novo genome assembly and phylogenomic analysis. The successful candidate will be a key member of the DarkTree project, funded by the Knut and Alice Wallenberg Foundation. The project aims to fill the gaps in the genome-based insect tree of life using the unique global insect material from the Insect Biome Atlas (https://www.insectbiomeatlas.org/) and Lifeplan (https://www.helsinki.fi/en/projects/lifeplan) projects. The material consists of around 50,000 Malaise trap samples, containing some 50 million insects representing more than 1 million species, most of which are currently undescribed. The entire material has gone through DNA metabarcoding using mild lysis protocols, providing a detailed index to the taxonomic content of each sample.

In DarkTree, we will use this material to systematically target the species-rich insect radiations that are not covered properly (or at all) by previous and ongoing genome sequencing efforts. The aim is to generate the first reasonably unbiased view of the insect tree of life, based on a backbone of some 5,000 genomes ‘decorated’ with at least 1 million DNA barcodes. The project involves collaboration with a computer vision lab at Linköping University, focused on developing AI-assisted techniques for picking out specimens for genome sequencing, and with computer scientists at KTH in Stockholm, focused on developing scalable probabilistic machine learning techniques for online phylogenomic analysis and placement of DNA barcodes.

You will be responsible for setting up a high-throughput pipeline for de novo assembly of genomes from short-read Illumina sequencing, and processing of the assemblies to generate suitable datasets for phylogenomic analysis. Together with other team members, you will also be developing and implementing the evolutionary models used in the phylogenomic analyses, and in interpreting and publishing the results. There will be considerable freedom in developing your own research projects based on the data we generate in the project.

Qualification Requirements. We are looking for a candidate with a PhD and postdoctoral research experience in phylogenomics. You should have a strong background in bioinformatics, statistical phylogenetics and comparative genomics. Previous experience of working with de novo assemblies and insects would be meritorious.

About the employment. The employment is a temporary four-year position. Scope of employment 100%. Starting date September 1, or as agreed.

For further information about the position: please contact professor
Fredrik Ronquist, fredrik.ronquist at nrm.se<mailto:fredrik.ronquist at nrm.se>, or Dr Tom van der Valk, tom.vandervalk at nrm.se<mailto:tom.vandervalk at nrm.se>.

Please upload your written application no later than May 16, 2025.

For more information and to apply, please visit

https://recruit.visma.com/spa/public/apply?guidAssignment=12b46c01-9af4-4ec4-b181-9dc224be598c&description=True
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From coordinator at rth.dk  Mon Apr 14 09:29:47 2025
From: coordinator at rth.dk (Betina Wingreen Jensen)
Date: Mon, 14 Apr 2025 09:29:47 +0200
Subject: [SocBiN] 1st Announcement - Registration open for Summer School on
 Applied Deep Learning in Bioinformatics 2025 ( Aug 11-15)
Message-ID: <002101dbad0f$0013bd90$003b38b0$@rth.dk>

Dear All,

 

We are delighted to announce that we are again this year hosting the Summer School – Applied Deep Learning in Bioinformatics.

 

DATE: from Monday, August 11, 2025, to Friday, August 15, 2025 (incl)

 

VENUE: Summer School venue at University of Copenhagen (details TBA) and the symposium day at the Lundsgaard Auditorium, PANUM. BLEGDAMSVEJ 3B, 2200 Copenhagen N.

 

LECTURERS: Alberto Santos Delgado (DTU), Sampo Pyysalo (University of Turku), Arne Elofsson (Stockholm University), Stefano Roncelli, Lars Juhl Jensen, Christian Anthon, Simon Rasmussen & Jan Gorodkin (University of Copenhagen)

 

TOPICS: The summer school will for example cover the following topics:

 

Text mining & Transformers

Language models for biological sequences

Variational autoencoders

Graphs & networks

Practical Applications

 

The format will consist of an approximately equal mix of lectures and hands-on exercises. 

 

PARTICIPANTS: Max. 30 talented MSc students, PhDs and postdocs who are already comfortable in programming. 

 

PRICE: O DKK. There is no course fee, but you must cover your own travel, accommodation and meals (expect those meals included in the programme). The course is run and hosted by the CRISPRnet project granted by the Novo Nordic Foundation.

 

STIPENDS: A handful of travel and accommodation stipends are available for talented applicants, who could otherwise not afford to participate. 

 

SYMPOSIUM: On Friday, August 15, 2025, all summer school attendees will be attending the Symposium - on Applied Deep Learning in Bioinformatics being held at University of Copenhagen, the Lundsgaard Auditorium, PANUM. BLEGDAMSVEJ 3B, 2200 Copenhagen N. All summer school participants will automatically be signed up to the symposium.  

 

DEADLINES:

 

REGISTRATION DEADLINE - JUNE 15, 2025 - You will receive an email confirming your application to the course - this is NOT a confirmation of participation. All registrations received by the deadline will be evaluated by the course organisers and max 30 people will be selected for participation in the summer school. 

NOTIFICATION OF SUCCESSFUL PARTICIPANTS - JUNE 27, 2027 - Everyone approved for participation in the summer school and recipients of stipends will receive a confirmation email. If you do not hear back from us on June 27, your application has, unfortunately, not been successful.

 

For more information and registration go to: https://conferencemanager.events/2025-summerschool-applied-deep-learning-in-bioinformatics

 

Best wishes,

Betina

 

Betina Wingreen Jensen

Specialkonsulent

 

University of Copenhagen

Department of Veterinary and Animal Sciences

Ridebanevej 9

Frederiksberg C

 

DIR +45 35 33 47 04

MOB +45 21 51 09 32

 <mailto:bwj at sund.ku.dk> bwj at sund.ku.dk

 

  

 

 <https://informationssikkerhed.ku.dk/english/protection-of-information-privacy/privacy-policy/> How we protect personal data

 

 

 

 

 

 

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From vang at clin.au.dk  Thu Apr 17 23:59:34 2025
From: vang at clin.au.dk (=?Windows-1252?Q?S=F8ren_Vang?=)
Date: Thu, 17 Apr 2025 21:59:34 +0000
Subject: [SocBiN] Two post doc positions in generative AI and blood-based
 cancer detection, Aarhus University, Denmark.
Message-ID: <DB9PR01MB9342BACD2BF92A05C64A448AF7BC2@DB9PR01MB9342.eurprd01.prod.exchangelabs.com>

Dear all,

I have two open post doc positions in generative AI and blood-based cancer detection (application deadline: 25 May 2025). Please share with whomever you think may be interested.

  https://health.au.dk/en/about-health/vacant-positions/job/two-postdoctoral-positions-in-generative-ai-modeling-for-blood-based-cancer-detection

Brief description: We seek outstanding candidates to develop generative-AI-based statistical methods for blood-based cancer detection. You will apply the methods to unprecedented genome-wide circulating cell-free DNA data sets from cancer patients and healthy individuals. The data contains rich information on cancer presence, type, and epigenomic regulation. You will develop predictive statistical methods to improve our ability to detect and characterize cancer from blood and other liquid biopsies, characterize chromatin structure, and improve nucleosome maps.

The positions are part of the project: “Development and application of generative AI models for ctDNA detection and characterization,” supported by the Novo Nordic Foundation. You will join a vibrant research team led by Prof. Jakob Skou Pedersen that uses generative AI for cancer genomics and single-cell data analysis.

Best,
Jakob

---
Jakob Skou Pedersen, Professor
Department of Molecular Medicine & BiRC
Aarhus University

Office:   (+45) 7845 5360<tel:+4578455360>
Mobile: (+45) 3141 8132<tel:+4531418132>
Home:  (+45) 3543 3562<tel:+4535433562>

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From ingemar.andre at biochemistry.lu.se  Wed Apr 23 14:29:03 2025
From: ingemar.andre at biochemistry.lu.se (=?iso-8859-1?Q?Ingemar_Andr=E9?=)
Date: Wed, 23 Apr 2025 12:29:03 +0000
Subject: [SocBiN] Open position for PhD student in bioinformatics and
 machine learning
Message-ID: <GVYP280MB13066A1F36C061F13F8A2819DEBA2@GVYP280MB1306.SWEP280.PROD.OUTLOOK.COM>

Dear all,

I am seeking a highly motivated PhD student to join our team at Lund University to develop bioinformatics and machine learning methods to study codon evolution and co-translational folding. The position is funded by DDLS and the student will join the DDLS research school.

Application deadline: May 26th, 2025.
Apply: https://www.scilifelab.se/career/doctoral-student-in-bioinformatics-and-machine-learning/

I would greatly appreciate if you could spread this to talented individuals in your network.

Best regards,

Ingemar

Ingemar André
Biochemistry & Structural Biology
Lund University
PO Box 124
221 00 Lund
tel: +46 46 222 4470<tel:+46462224470>
email: ingemar.andre at biochemistry.lu.se<mailto:ingemar.andre at biochemistry.lu.se>


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From oliver.billker at umu.se  Fri Apr 25 08:48:48 2025
From: oliver.billker at umu.se (Oliver Billker)
Date: Fri, 25 Apr 2025 06:48:48 +0000
Subject: [SocBiN] =?iso-8859-1?q?Two_faculty_positions_at_Ume=E5_Universit?=
 =?iso-8859-1?q?y_--_1=2E_DDLS_Group_Leader_Infection_--__2=2E_Associate_P?=
 =?iso-8859-1?q?rofessor_Bioinformatics?=
Message-ID: <GVZP280MB07653E5539EA4BB58336537BFD842@GVZP280MB0765.SWEP280.PROD.OUTLOOK.COM>

Two attractive positions at Umeå University are closing in May.


  1.  Group Leader Position in data-driven infection research is available at the Swedish EMBL node, closing May 11.

  *   EMBL Group Leader type, research focussed.
  *   Part of a dynamic national programme for data-driven life science (SciLifeLab/KAW).
  *   Funded with the equivalent of up to 2 mio EUR over 9 years subject to mid-term review.
  *   Suits projects with strong computational element.
  *   Broad range of putative host departments depending on background from computing to life sciences.
  *   https://www.umu.se/en/mims/


  1.  Associate Professor in Bioinformatics, closing May 27.
     *   At our main host department for Molecular Biology.
     *   Note: no infection focus needed for this position.
     *   https://umu.varbi.com/en/what:job/jobID:818929/

Oliver Billker, PhD
Professor, Department of Molecular Biology
Director, Laboratory for Molecular Infection Medicine Sweden (MIMS)
Umeå University
S-90187 Umeå
Sweden
Phone: ++46 72 219 28 03


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From erik.sonnhammer at scilifelab.se  Mon Apr 28 17:12:39 2025
From: erik.sonnhammer at scilifelab.se (Erik Sonnhammer)
Date: Mon, 28 Apr 2025 17:12:39 +0200
Subject: [SocBiN] Bioinformatics PhD position in Stockholm:
 "Biology-informed Robust AI Methods for Inferring,
 Complex Gene Regulatory Networks"
Message-ID: <974d582f-21b4-4dc7-88a8-55ba0318c17f@scilifelab.se>

Dear colleagues,

There is an open PhD student position in the Sonnhammer group at Science 
for Life Laboratory in Stockholm, Sweden

The goal of the project is to develop new AI-based methods to improve 
biological realism in simulations which will lead to more accurately 
inferred GRNs from real data. The project will develop fundamental 
theory and tools that will be key for understanding biological 
mechanisms causing diseases that are due to gene dysregulation, such as 
cancer.

See ad at https://sonnhammer.org/download/ads/open.html Deadline May 13

Thanks for spreading to potentially interested persons.

Best Regards,
___________________________________
Erik Sonnhammer, Ph.D.
Professor of Bioinformatics
DBB, Stockholm University
Science for Life Laboratory <https://www.scilifelab.se/>
Stockholm, Sweden
Email: Erik.Sonnhammer at scilifelab.se
https://sonnhammer.org
https://x.com/eriksonnhammer
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