From arne at bioinfo.se  Tue Nov 18 14:07:49 2025
From: arne at bioinfo.se (Arne Elofsson)
Date: Tue, 18 Nov 2025 14:07:49 +0100
Subject: [SocBiN] Online seminar
Message-ID: <CAND8g_YuhEeNk4qdS1H1j1eAXD+wHFCSZrskK9xjYkjN1-riHg@mail.gmail.com>

https://elixir-europe.org/events/modern-cells-ancient-proteins-and-complexes


Modern cells, ancient proteins and complexes
Registration
Date: Tue 25 Nov 2025 - 16:00 to 17:00
GMT

You are invited to join this webinar with Pro. Edward M. Marcotte of
University of Austin, Texas.

We will describe how our interest in deeply conserved human genes and
pathways led us to attempt to systematically determine the core
multi-protein assemblies that are shared more generally across
eukaryotes—many dating back to the last common eukaryotic ancestor—by
directly detecting protein complexes using thousands of mass spectrometry
experiments to define their composition and interactions, and how these
data inform us about their functions and 3D molecular assemblies..

This webinar is part of the 3D-BioInfo and will be moderated by Prof. Arne
Elofsson (Stockholm University) supported by Dr Gonzalo Parra.

Yours

Arne

-----------------------------------------
  Arne Elofsson                  Science for Life Laboratory
  Tel:+46-(0)70 695 1045   Stockholm University
  http://bioinfo.se/               Box 1031,
  Email: arne at bioinfo.se   17121 Solna, Sweden
Bluesky: @bioinfo.se
Twitter/X: @arneelof
  Mastodon: @arneelof at fediscience.org
  Zoom: https://stockholmuniversity.zoom.us/my/arneelof/
  Scholar: http://scholar.google.se/citations?user=s3OCM3AAAAAJ
  ORCID: 0000-0002-7115-9751 <https://orcid.org/0000-0002-7115-9751>

Yours

Arne

-----------------------------------------
  Arne Elofsson                  Science for Life Laboratory
  Tel:+46-(0)70 695 1045   Stockholm University
  http://bioinfo.se/               Box 1031,
  Email: arne at bioinfo.se   17121 Solna, Sweden
Bluesky: @arneelof.bsky.social
Twitter/X: @arneelof
  Mastodon: @arneelof at fediscience.org
  Zoom: https://stockholmuniversity.zoom.us/my/arneelof/
  Scholar: http://scholar.google.se/citations?user=s3OCM3AAAAAJ
  ORCID: 0000-0002-7115-9751 <https://orcid.org/0000-0002-7115-9751>
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From e.roohparvar at modares.ac.ir  Thu Nov 20 12:51:44 2025
From: e.roohparvar at modares.ac.ir (Esmaeil Roohparvar)
Date: Thu, 20 Nov 2025 15:21:44 +0330
Subject: [SocBiN] [Unknown URLs]   Online seminar
In-Reply-To: <CAND8g_YuhEeNk4qdS1H1j1eAXD+wHFCSZrskK9xjYkjN1-riHg@mail.gmail.com>
References: <CAND8g_YuhEeNk4qdS1H1j1eAXD+wHFCSZrskK9xjYkjN1-riHg@mail.gmail.com>
Message-ID: <WC20251120115144.652256@modares.ac.ir>

Dear Arne,
Thank you very much for the invitation.
I am the CEO and founder of a bioinformatics company in Iran and Australia, 
and I have shared the link to this event across our social media channels.
If you have future events or announcements you would like to promote, please 
feel free to send them to us, we will be happy to share them as well.
Best,
Esmaeil Roohparvar Basmenj
From: Arne Elofsson <arne at bioinfo.se>
To: casp-zoom at googlegroups.com, socbin at socbin.org
Date: Tue, 18 Nov 2025 14:07:49 +0100
Subject: [Unknown URLs]  [SocBiN] Online seminar

https://elixir-europe.org/events/modern-cells-ancient-proteins-and-complexes 
[https://elixir-europe.org/events/modern-cells-ancient-proteins-and-complexes]


Modern cells, ancient proteins and complexes
Registration
Date: Tue 25 Nov 2025 - 16:00 to 17:00
GMT

You are invited to join this webinar with Pro. Edward M. Marcotte of 
University of Austin, Texas.

We will describe how our interest in deeply conserved human genes and 
pathways led us to attempt to systematically determine the core 
multi-protein assemblies that are shared more generally across 
eukaryotes—many dating back to the last common eukaryotic ancestor—by 
directly detecting protein complexes using thousands of mass spectrometry 
experiments to define their composition and interactions, and how these data 
inform us about their functions and 3D molecular assemblies..

This webinar is part of the 3D-BioInfo and will be moderated by Prof. Arne 
Elofsson (Stockholm University) supported by Dr Gonzalo Parra.
Yours

Arne
-----------------------------------------
Arne Elofsson                  Science for Life Laboratory
Tel:+46-(0)70 695 1045   Stockholm University
http://bioinfo.se/ [http://bioinfo.se/]Box 1031,
Email:arne at bioinfo.se [mailto:arne at bioinfo.se]17121 Solna, Sweden
Bluesky: @bioinfo.se [http://bioinfo.se/]
Twitter/X: @arneelof
Mastodon: @arneelof at fediscience.org [mailto:arneelof at fediscience.org]
Zoom:https://stockholmuniversity.zoom.us/my/arneelof/ 
[https://stockholmuniversity.zoom.us/my/arneelof/]
Scholar:http://scholar.google.se/citations?user=s3OCM3AAAAAJ 
[http://scholar.google.se/citations?user=s3OCM3AAAAAJ]
ORCID:0000-0002-7115-9751 [https://orcid.org/0000-0002-7115-9751]
Yours

Arne
-----------------------------------------
Arne Elofsson                  Science for Life Laboratory
Tel:+46-(0)70 695 1045   Stockholm University
http://bioinfo.se/ [http://bioinfo.se/]Box 1031,
Email:arne at bioinfo.se [mailto:arne at bioinfo.se]17121 Solna, Sweden
Bluesky: @arneelof.bsky.social
Twitter/X: @arneelof
Mastodon: @arneelof at fediscience.org [mailto:arneelof at fediscience.org]
Zoom:https://stockholmuniversity.zoom.us/my/arneelof/ 
[https://stockholmuniversity.zoom.us/my/arneelof/]
Scholar:http://scholar.google.se/citations?user=s3OCM3AAAAAJ 
[http://scholar.google.se/citations?user=s3OCM3AAAAAJ]
ORCID:0000-0002-7115-9751 [https://orcid.org/0000-0002-7115-9751]
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From daniele.raimondi at igmm.cnrs.fr  Thu Nov 20 18:36:23 2025
From: daniele.raimondi at igmm.cnrs.fr (Daniele Raimondi)
Date: Thu, 20 Nov 2025 18:36:23 +0100
Subject: [SocBiN] postdoctoral position in machine learning and
 bioinformatics in Montpellier
In-Reply-To: <f2749528-6508-4178-a7cd-8c1ccfc6c110@igmm.cnrs.fr>
References: <f2749528-6508-4178-a7cd-8c1ccfc6c110@igmm.cnrs.fr>
Message-ID: <92e09bb3-05e6-4c35-9fb2-4caad876fbfc@igmm.cnrs.fr>


*Postdoctoral Position – Mixed Effects Neural Networks for Genome 
Interpretation*

*

We are looking for a motivated postdoctoral researcher to join the AI 
for Genome Interpretation (AI4GI 
<https://www.igmm.cnrs.fr/team/ia-pour-linterpretation-du-genome/>) 
group at the IGMM (CNRS, Montpellier) for 18 months. The project is a 
collaboration between IGMM and IMAG, at the interface of genetics, 
bioinformatics, statistics, machine learning and deep learning.

The projectInterpreting the genome means modeling the relationship 
between genotype and phenotype, which is the fundamental goal of 
biology. Achieving this could revolutionize genetics, medicine, and 
agricultural technology, leading for example to the development of 
better crops, able to face the challenges posed by global 
warming._Objectives:_ This project is an interdisciplinary effort at the 
frontier between Biology (Genetics, Genomics), Bioinformatics, 
Artificial Intelligence (Neural Networks) and Statistics (LMMs). The aim 
is to join the Bioinformatics expertise of Dr. Raimondi on the 
development of GI NN methods and their application to relevant 
biological problems with the expertise of Dr. Bry and Dr. Trottier on 
the statistical inference of Linear Mixed Models (LMMs).

The project’s goal is to develop a new breed of Mixed Effects Neural 
Networks (MENN) for Genome InterpretationI that take the best from both 
worlds, merging the flexibility and power of NNs with the ability of 
LMMs to robustly learn from structured and noisy (non i.i.d.) data, 
applying them on the prediction of both plantsand humanphenotypes.

These models will combine the flexibility of neural networks with the 
statistical robustness of linear mixed models to tackle one of biology’s 
most fundamental questions: how do genetic variants determine phenotypes?

The postdoc will:

  *

    Start by familiarizing with existing research and methods for genome
    interpretation (GI NNs, LMMs, GWAS).

  *

    Familiarize with the sequencing data

  *

    Develop and benchmark MENN prototypes on sequencing datasets
    (WES/WGS), starting first from model organisms and then working on
    disease risk prediction in humans.

_Candidate profile:_We are looking for a motivatedand curious candidate, 
with a strong passion for scienceand for scientific discovery through 
the use and creation of new neural networks and machine learning methods.

Bioinformatics and Genome Interpretation are multi-disciplinary and 
rapidly evolving fields. Therefore, the candidate is expected to 1) be 
eager to continuously learnnew skills, methods and concepts, and 2) to 
enjoy finding new solutionsin the face of new and unforeseen difficulties.

The ideal candidate has very good 1) python programming skills, 2) 
understanding of the mathematical foundations and principles of Machine 
Learning, Linear Algebra(vectorial and matricial operations, 
optimization), with a particular focus on Neural Networks, 3) problem 
solving skills, 4) familiarity with GNU/Linuxenvironment.

A good understanding of the basic concepts of Bioinformatics is not 
necessary but welcome. The project will consist in developing 
un-orthodox Neural Network models with Pytorch.

At least the B2 level of English is required.

Skills requiredWe are looking for someone with:

  *

    Strong backgroundin neural networks, machine learning, linear
    algebra and an understanding of statistics.

  *

    Solid programming skills in Pythonand in scientific
    computing(PyTorch, scikit-learn, numpy, etc).

  *

    Familiarity with GNU/Linux.

  *

    Problem solving skills.

  *

    Good communication and teamwork skills.

  *

    Knowledge of linear/mixed models is a plus.

  *

    Familiarity with GWAS, population genetics, or bioinformatics
    pipelines are a plus.

  *

    Experience with the processing of genomic biological data (whole
    exome or genome sequencing) is a plus

_Practical details_

  *

    Location: IGMM, Montpellier (with joint supervision at IMAG).

  *

    Duration: 18 months.

  *

    Starting date: flexible, but the candidate must be selected
    beforethe end of 2025.

If you’re interested in working at the crossroads of AI, statistics, and 
genomics—and in developing new methods rather than just applying 
existing ones—we’d like to hear from you.

You can apply from this link

*

emploi.cnrs.fr

Portail Emploi CNRS - Offre d'emploi - Postdoctoral Researcher – 
Mixed-Effects Neural Networks for Genome Interpretation (M/F)

🔗 
https://emploi.cnrs.fr/Offres/CDD/UMR5535-SARADE-091/Default.aspx?lang=EN 
<https://emploi.cnrs.fr/Offres/CDD/UMR5535-SARADE-091/Default.aspx?lang=EN>



On 9/29/25 12:55, Matteo Pallocca wrote:
>
> caro Daniele
>
> puoi usare la funzione submit news del sito
> o mandarci l'annuncio a questa mail provvederemo alla pubblicazione
> grazie
> MP
>
> Il giorno gio 25 set 2025 alle ore 14:09 Daniele Raimondi 
> <daniele.raimondi at igmm.cnrs.fr> ha scritto:
>
>     Gent Bits,
>
>     mi chiamo Daniele Raimondi e ho recentemente aperto il mio gruppo di
>     bioinformatica all'istituto di genetica molecolare di Montpellier
>     (IGMM). Vorrei sapere come posso pubblicizzare le offerte di lavoro
>     (phd, postdocs) che saranno disponibili nel mio gruppo sul vostro
>     sito.
>
>     Al momento, per esempio, sto cercando un postdoc per 18 mesi.
>
>     grazie,
>
>     Daniee
>
>     -- 
>     Daniele Raimondi, PhD
>     Chaire de Professeur Junior CNRS
>     AI for Genome Interpretation group
>     Institut de Génétique Moléculaire de Montpellier (IGMM)
>     1919 Route de Mende
>     34090 Montpellier, France
>
>     -obscurum per obscurius-
>
-- 
Daniele Raimondi, PhD
Chaire de Professeur Junior CNRS
AI for Genome Interpretation group
Institut de Génétique Moléculaire de Montpellier (IGMM)
1919 Route de Mende
34090 Montpellier, France

-obscurum per obscurius-
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From bartoszekkj at gmail.com  Wed Nov 26 23:14:36 2025
From: bartoszekkj at gmail.com (Krzysztof Bartoszek)
Date: Wed, 26 Nov 2025 23:14:36 +0100
Subject: [SocBiN] Stochastic differential equations with R workshop at
 Linkoping University, Sweden
Message-ID: <CADP6=aXQ=3=24bq6zxG-yQ6tTphtmMAcYskcGpRBbntVysffXQ@mail.gmail.com>

At the Division of Statistics and Machine Learning, Department of
Computer and Information Science, Linköping University, Sweden,
17th-20th March 2026, we will be hosting a workshop concerning
stochastic differential equations and the YUIMA R package (Simulation
and Inference for SDEs and Other Stochastic Processes,
https://cran.r-project.org/web/packages/yuima/index.html ). The
lectures will be given by members of the YUIMA team. The dates are
fixed.
A similar event took place in summer 2019:
https://yuimaproject.com/yss2019/ and in March 2023 in Linkoping.

Please feel free to spread information about the event around. If
anyone would be interested in coming, they should e-mail Krzysztof
Bartoszek (krzysztof.bartoszek at liu.se) directly. The registration
deadline is 28th February 2026. However, we might end registration
early if the number of interested participants exceeds our capacity.

PhD-students can choose to take an examination to obtain 3credits for
the event. Examination will be through a hand-in assignment. Please
let us know if you would be interested in this option.

We assume the participants are familiar with R. We are finalizing the
programme but it will include:
Introduction to stochastic calculus (stochastic processes, Brownian
motion, stochastic integral and SDE),
Simulation of diffusion processes I (Euler-Maruyama approximation and
introduction to YUIMA: yuima object, simulation, plot,
Black-Scholes model), Poisson process and Compound Poisson processes,
Inference for diffusion processes
(QMLE, quasi-Bayes estimation), Model selection for diffusion
processes, YUIMA GUI, Levy processes and Levy driven SDE.
The final programme will be announced in due course of time.

The contents will include basic facts, laboratory sessions
(participants work on their own laptops),
and more advanced research-oriented talks. If you have a related
research topic and would be interested in presenting, then please let
us know.

More information on the workshop will be made available at
https://www.ida.liu.se/~krzba67/include/YUIMA_2026LiU.html .

Kind regards
Krzysztof Bartoszek, PhD,
Senior Assoc. Prof. in Statistics
Department of Computer and Information Science (IDA)
Linköping University, Sweden
Phone: +46 (0)13-28 18 85
krzysztof.bartoszek at liu.se