From arne.elofsson at gmail.com  Sun Jun  1 14:39:32 2025
From: arne.elofsson at gmail.com (Arne Elofsson)
Date: Sun, 1 Jun 2025 14:39:32 +0200
Subject: [SocBiN] Fwd: ELIXIR 3D-BioInfo Implementation Study application
 for integration of protein annotations in PDBe-KB
In-Reply-To: <AM7PR01MB6564F6C05F9CB69D91FC37D9CF63A@AM7PR01MB6564.eurprd01.prod.exchangelabs.com>
References: <AM7PR01MB6564F6C05F9CB69D91FC37D9CF63A@AM7PR01MB6564.eurprd01.prod.exchangelabs.com>
Message-ID: <CAND8g_Y2nCBzFPKkkQjrzu2qL_AfhATXY5hpwcCDchOXtJ5i7w@mail.gmail.com>

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>

---------- Forwarded message ---------
From: Orengo, Christine <c.orengo at ucl.ac.uk>
Date: Sun, 1 Jun 2025, 12:49
Subject: ELIXIR 3D-BioInfo Implementation Study application for integration
of protein annotations in PDBe-KB
To: 3d-bioinfo at elixir-europe.org <3d-bioinfo at elixir-europe.org>
Cc: Sameer Velankar <sameer at ebi.ac.uk>, Jennifer Fleming <jfleming at ebi.ac.uk>,
R. Gonzalo Parra <gonzalo.parra at bsc.es>, Vincent Zoete
<vincent.zoete at sib.swiss>, arne.elofsson at gmail.com <arne.elofsson at gmail.com>,
Bohdan Schneider <bohdan at ibt.cas.cz>


Dear 3D-BioInfo Community

Thanks to those of you who attended our conference in Barcelona this March.
It was a great meeting with nearly 120 participants and very exciting talks.

At the conference we held an ELIXIR panel session when we discussed a
possible application for funding for an ELIXIR Implementation Study by the
3D-BioInfo community.

The ELIXIR call for these studies is now live and 3D-BioInfo will be
applying.

As mentioned in the Barcelona session, our study will be based on a series
of workshops to increase the interaction of groups developing protein
annotations (e.g. prediction of protein structural characteristics like
functional sites, disorder, PTs, etc) with the PDBe knowledge base
(PDBeKB).

The workshops will train researchers in building NextFlow workflows and
APIs to export their predicted data to the PDBe-KB where their annotations
will be widely disseminated via a web portal that integrates multiple
annotations for protein structures. More details are given in the links
below.

If you are interested in participating in this study and attending one or
more of the workshops, which will be held at the EBI in Hinxton, UK, please
check the links below and add your name. The links include the planned
application for funding, to which you can add comments, together with
background information.

Expression of Interest (EOI) for Implementation Study Funding
*https://docs.google.com/document/d/1D7_p8CM832yK8HmZ3LKhceXhbCWcc20nP9o31-zgj70/edit?tab=t.0#heading=h.30rc0e6z3ov7
<https://docs.google.com/document/d/1D7_p8CM832yK8HmZ3LKhceXhbCWcc20nP9o31-zgj70/edit?tab=t.0#heading=h.30rc0e6z3ov7>*

Background
*https://docs.google.com/document/d/1o0i_7gpAmOirDT9h8RFwMt7-TcBDHMsBYX1dvx3JE2E/edit?usp=sharing
<https://docs.google.com/document/d/1o0i_7gpAmOirDT9h8RFwMt7-TcBDHMsBYX1dvx3JE2E/edit?usp=sharing>*

Ideas
*https://docs.google.com/document/d/1If6mTJb2_2p31BD88qgkqK6JcnwEpbLwkIwtYbBGp8w/edit?tab=t.0
<https://docs.google.com/document/d/1If6mTJb2_2p31BD88qgkqK6JcnwEpbLwkIwtYbBGp8w/edit?tab=t.0>*

Participants list:
*https://docs.google.com/document/d/1SMoMb6X1Fvyn7aJ_YUaPFE19uytENUVigJ6u6AgR8s4/edit?tab=t.0
<https://docs.google.com/document/d/1SMoMb6X1Fvyn7aJ_YUaPFE19uytENUVigJ6u6AgR8s4/edit?tab=t.0>*

*Please add your name and details to the participant list in the google
docs.*

*We need to submit the application to the hub by June 15th* so please add
your name by then to help increase the chance this study will be funded.

It will also be possible to join the study after that date by adding your
name.

Thanks very much
Christine

On behalf of 3D-BioInfo coordinating team
Sameer Velankar, Arne Elofsson, Vincent Zoete, Bohdan Schneider, Gonzalo
Parra
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From arne.elofsson at gmail.com  Tue Jun  3 15:08:04 2025
From: arne.elofsson at gmail.com (Arne Elofsson)
Date: Tue, 3 Jun 2025 15:08:04 +0200
Subject: [SocBiN] Phd position in Stockholm
Message-ID: <CAND8g_YpA-LvAEn1pH1dtqEZKsWFm8LkifwT0NensXXVU63Dow@mail.gmail.com>

PhD Position at Stockholm University in "Using Deep Learning to Understand
Protein Structure Evolution".


https://su.varbi.com/en/what:job/jobID:830925/


[image: Logo for Stockholms universitet] <https://su.varbi.com/>
PhD student in Bioinformatics
To apply you must first logout from your company account

*The Department of Biochemistry and Biophysics*
SciLifeLab (SciLifeLab <https://www.scilifelab.se/>) is a national center
for molecular biosciences with a focus on health and environmental
research. The center combines frontline technical expertise with advanced
knowledge of translational medicine and molecular bioscience. SciLifeLab is
a national resource hosted by Karolinska Institutet, KTH Royal Institute of
Technology, Stockholm University and Uppsala University. The center
also collaborates with several other universities.

The employment will be placed at the Department of biochemistry and
biophysics, at Stockholm university.

More information about us, please visit: the Department of Biochemistry and
Biophysics <http://www.dbb.su.se/>.
Project description

Your studies in Bioinformatics will be in the project: "Using Deep Learning
to Understand Protein Structure Evolution”.

We have studied domain evolution and observed that structural change is
roughly linear with sequence change. However, larger structural changes
might also occur within a domain during evolution, particularly within
transporters3.  Further, domains can be combined to create multi-domain
proteins. Most domain architectures arise from adding or removing a single
domain at the N- or C-terminal regions, while certain repeat-domain
families undergo more internal duplications. We also demonstrated that
eukaryotic proteins harbour substantially more disordered and linker
regions, which expand more rapidly than globular domains. Most phylogenetic
studies of proteins, including ours, have primarily focused on changes in
the amino-acid sequences. Today, accurate structural models from AlphaFold
make it possible to integrate structure into large-scale phylogenetic and
sequence analyses. Therefore, in this application, we propose revisiting
earlier studies, scaling them up, and adding structural information to the
analysis. This study will provide a detailed structural understanding of
changes within domains, how novel protein architectures emerge, and why
certain domains and architectures continue expanding and diversifying in
specific lineages. We believe this study will provide fundamental insights
into protein structure evolution and how evolutionary mechanisms and
selective pressures have shaped proteins. Together, the three aims of this
project will reveal how domain changes their structure and how
rearrangements shape structural protein diversity across the tree of life.

The Elofsson group is located at the Science for Life Laboratory. Elofsson
has worked on protein structure predictions and evolution for over two
decades. He has worked on various techniques using machine learning and
other computational techniques. Our most important contributions to this
work are the methods he has developed to identify the quality of protein
models, Pcons, and various versions of ProQ. The group comprises 5 PhD
students, one postdoc, and one senior researcher.
Qualification requirements

In order to be admitted to postgraduate education, the applicant must have
the general and specific entry requirements. The qualification requirements
must be met by the deadline for applications.

You meet *general entry requirements* if you have completed a second-cycle
degree, or completed courses equivalent to at least 240 higher education
credits, of which 60 credits must be in the second cycle, or have otherwise
acquired equivalent knowledge in Sweden or elsewhere.

In order to meet *the specific entry requirements*, for acceptance in the
Biochemistry, especially Bioinformatics, program the applicant must have
passed courses within the first and second cycles of at least 90 credits in
either, a) Chemistry/Molecular Biology/Biotechnology, or b) Computer
Science/Mathematics/Physics and at the second cycle level, 60 credits in
Life Science, Computer Science Mathematics, Physics or Bioinformatics
including a 30 credit Degree Project (thesis).
Selection

The selection amongst the eligible candidates will be based on their
capacity to successfully complete the program. Important criteria when
assessing this capacity are; documented knowledge and skill in the field of
the thesis project, written and oral proficiency in English, the capacity
for analytical thinking, the ability to collaborate, as well as creativity,
initiative, and independence. The assessment will be based on previous
experience and grades, the quality of the degree project, references,
relevant experience, interviews and the candidate’s written motivation for
seeking the position.

Admission Regulations for Doctoral Studies at Stockholm University.
<https://medarbetare.su.se/en/our-su/governance/rules--regulations/education/admission-regulations-for-third-cycle-study-programmes>
About the post

We offer a fixed-term employment as a doctoral student according to Chapter
5 of the Higher Education Ordinance (1993:100). The period of employment
may not be longer than what corresponds to full-time doctoral education for
four years. As a doctoral student, you should primarily devote yourself to
your own doctoral education, but the employment may include work with
education, research and administration to a limited extent (maximum 20 %).

A new employment as a doctoral student is for a maximum of one year, the
employment is then renewed for a maximum of two years at a time.

Stockholm University strives to be a workplace free from discrimination and
with equal opportunities for all.
Contact

For more information, please contact Professor Arne Elofsson,
arne.elofsson at dbb.su.se.
Application

Apply for the PhD student position at Stockholm University's recruitment
system. Attach a personal letter and CV as well as the attachments
requested in the application form. It is the responsibility of the
applicant to ensure that the application is complete in accordance with the
instructions in the job advertisement, and that it is submitted before the
deadline.

The instructions for applicants are available at: How to apply for a
position
<https://www.su.se/english/about-the-university/work-at-su/how-to-apply-for-a-position>
.

Stockholm University contributes to the development of sustainable
democratic society through knowledge, enlightenment and the pursuit of
truth.
Type of employment Temporary position
Contract type Full time
Salary Fixed salary
Number of positions 1
Full-time equivalent 100 %
City Stockholm
County Stockholms län
Country Sweden
Reference number SU FV-2178-25
Union representative

   - ST/OFR, st at st.su.se
   - Saco-S, saco at saco.su.se
   - Seko, seko at seko.su.se

Published 23.May.2025
Last application date 13.Jun.2025
To apply you must first logout from your company account


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: @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>
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From evdh at sniprbiome.com  Wed Jun 11 13:01:18 2025
From: evdh at sniprbiome.com (Eric van der Helm)
Date: Wed, 11 Jun 2025 11:01:18 +0000
Subject: [SocBiN] open position for a Bioinformatician/Data Scientist in
 Copenhagen
Message-ID: <AS2P194MB2070FE24A7A15FD863D74B0BB075A@AS2P194MB2070.EURP194.PROD.OUTLOOK.COM>

We have an open position for a Bioinformatician/Data Scientist in the field of bacterial genetics and microbiome science at SNIPR BIOME in Copenhagen. More details here https://www.linkedin.com/jobs/view/4244498813

Best,

Eric


Eric van der Helm, PhD
VP of Scientific Affairs, Bioinformatics & Automation

SNIPRBIOME
Lersø Parkallé 44, 5.floor
2100 Copenhagen
Denmark
Mail: evdh at sniprbiome.com<mailto:evdh at sniprbiome.com>

[cidimage001.png at 01D68B7C.A5684D10]

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From ansikuso at gmail.com  Fri Jun 20 05:59:14 2025
From: ansikuso at gmail.com (s.sudhanshu@iitb.ac.in)
Date: Fri, 20 Jun 2025 09:29:14 +0530
Subject: [SocBiN] open position for a Bioinformatician/Data Scientist in
 Copenhagen
In-Reply-To: <AS2P194MB2070FE24A7A15FD863D74B0BB075A@AS2P194MB2070.EURP194.PROD.OUTLOOK.COM>
References: <AS2P194MB2070FE24A7A15FD863D74B0BB075A@AS2P194MB2070.EURP194.PROD.OUTLOOK.COM>
Message-ID: <CAL24LEonhV0DH8p4XqA8-UGh8mfYXxsnLuMMvke1BJZA3Cam3g@mail.gmail.com>

Respected Sir,
Thanks for helping. PFA as CV.
Regards.

On Wed, 11 Jun, 2025, 4:31 pm Eric van der Helm via SocBiN, <
socbin-at-sbc.su.se at lists.su.se> wrote:

> We have an open position for a Bioinformatician/Data Scientist in the
> field of bacterial genetics and microbiome science at SNIPR BIOME in
> Copenhagen. More details here
> https://www.linkedin.com/jobs/view/4244498813
>
>
>
> Best,
>
>
>
> Eric
>
>
>
>
>
> *Eric van der Helm, PhD*
>
> *VP of Scientific Affairs, Bioinformatics & Automation*
>
>
>
> *SNIPR*BIOME
>
> Lersø Parkallé 44, 5.floor
>
> 2100 Copenhagen
>
> Denmark
>
> Mail: evdh at sniprbiome.com
>
>
>
> [image: cidimage001.png at 01D68B7C.A5684D10]
>
>
> _______________________________________________
> SocBiN mailing list
> SocBiN at lists.su.se
> https://lists.su.se/mailman/listinfo/socbin-at-sbc.su.se
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From praharshit1 at mail.com  Sat Jun 21 16:44:24 2025
From: praharshit1 at mail.com (Praharshit Sharma)
Date: Sat, 21 Jun 2025 16:44:24 +0200
Subject: [SocBiN] REGISTER FOR 100 HOURS NGS ANALYSIS GENOMIC DATA SCIENCE
 UPSKILLING PROGRAM
Message-ID: <trinity-62bbc9bf-a61a-4384-a39e-2670c817f0cd-1750517064888@3c-app-mailcom-lxa11>

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From praharshit1 at mail.com  Sat Jun 21 16:44:24 2025
From: praharshit1 at mail.com (Praharshit Sharma)
Date: Sat, 21 Jun 2025 16:44:24 +0200
Subject: [SocBiN] REGISTER FOR 100 HOURS NGS ANALYSIS GENOMIC DATA SCIENCE
 UPSKILLING PROGRAM
Message-ID: <trinity-62bbc9bf-a61a-4384-a39e-2670c817f0cd-1750517064888@3c-app-mailcom-lxa11>

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From recruitment at embl.org  Mon Jun 23 09:36:23 2025
From: recruitment at embl.org (HR Recruitment)
Date: Mon, 23 Jun 2025 07:36:23 +0000
Subject: [SocBiN] open position for a Bioinformatician/Data Scientist in
 Copenhagen
In-Reply-To: <CAL24LEonhV0DH8p4XqA8-UGh8mfYXxsnLuMMvke1BJZA3Cam3g@mail.gmail.com>
References: <AS2P194MB2070FE24A7A15FD863D74B0BB075A@AS2P194MB2070.EURP194.PROD.OUTLOOK.COM>
 <CAL24LEonhV0DH8p4XqA8-UGh8mfYXxsnLuMMvke1BJZA3Cam3g@mail.gmail.com>
Message-ID: <942a56016c744177b65570de93e6e1aa@embl.org>

Hallo,

Many thanks for your message and sending us your application! Great to hear you’re interested in joining EMBL.

Keep an eye on our vacancies online embl.org/jobs where you can apply to a specific position but also register your profile under the job alert function.

We kindly ask you to please apply through our online recruitment system as indicated on the web as we do not accept applications outside the system.

To learn more about the working conditions at EMBL have a look on our web. Any questions just ask!

With best wishes
EMBL recruitment team

From: SocBiN <socbin-at-sbc.su.se-bounces at lists.su.se>
Sent: 20 June 2025 05:59
To: Eric van der Helm <evdh at sniprbiome.com>
Cc: socbin at socbin.org
Subject: Re: [SocBiN] open position for a Bioinformatician/Data Scientist in Copenhagen

Respected Sir,
Thanks for helping. PFA as CV.
Regards.

On Wed, 11 Jun, 2025, 4:31 pm Eric van der Helm via SocBiN, <socbin-at-sbc.su.se at lists.su.se<mailto:socbin-at-sbc.su.se at lists.su.se>> wrote:
We have an open position for a Bioinformatician/Data Scientist in the field of bacterial genetics and microbiome science at SNIPR BIOME in Copenhagen. More details here https://www.linkedin.com/jobs/view/4244498813

Best,

Eric


Eric van der Helm, PhD
VP of Scientific Affairs, Bioinformatics & Automation

SNIPRBIOME
Lersø Parkallé 44, 5.floor
2100 Copenhagen
Denmark
Mail: evdh at sniprbiome.com<mailto:evdh at sniprbiome.com>

[cidimage001.png at 01D68B7C.A5684D10]

_______________________________________________
SocBiN mailing list
SocBiN at lists.su.se<mailto:SocBiN at lists.su.se>
https://lists.su.se/mailman/listinfo/socbin-at-sbc.su.se
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From ansikuso at gmail.com  Mon Jun 23 11:53:55 2025
From: ansikuso at gmail.com (s.sudhanshu@iitb.ac.in)
Date: Mon, 23 Jun 2025 15:23:55 +0530
Subject: [SocBiN] open position for a Bioinformatician/Data Scientist in
 Copenhagen
In-Reply-To: <942a56016c744177b65570de93e6e1aa@embl.org>
References: <AS2P194MB2070FE24A7A15FD863D74B0BB075A@AS2P194MB2070.EURP194.PROD.OUTLOOK.COM>
 <CAL24LEonhV0DH8p4XqA8-UGh8mfYXxsnLuMMvke1BJZA3Cam3g@mail.gmail.com>
 <942a56016c744177b65570de93e6e1aa@embl.org>
Message-ID: <CAL24LEoyA79xsqmE1bFCnF6FigEqncB90NEgxLxrn3K-4nKnaQ@mail.gmail.com>

Thanks sure

On Mon, 23 Jun, 2025, 1:06 pm HR Recruitment, <recruitment at embl.org> wrote:

> Hallo,
>
>
>
> Many thanks for your message and sending us your application! Great to
> hear you’re interested in joining EMBL.
>
> Keep an eye on our vacancies online embl.org/jobs where you can apply to
> a specific position but also register your profile under the job alert
> function.
>
> We kindly ask you to please apply through our online recruitment system as
> indicated on the web as we do not accept applications outside the system.
>
> To learn more about the working conditions at EMBL have a look on our web.
> Any questions just ask!
>
> With best wishes
>
> EMBL recruitment team
>
>
>
> *From:* SocBiN <socbin-at-sbc.su.se-bounces at lists.su.se>
> *Sent:* 20 June 2025 05:59
> *To:* Eric van der Helm <evdh at sniprbiome.com>
> *Cc:* socbin at socbin.org
> *Subject:* Re: [SocBiN] open position for a Bioinformatician/Data
> Scientist in Copenhagen
>
>
>
> Respected Sir,
>
> Thanks for helping. PFA as CV.
>
> Regards.
>
>
>
> On Wed, 11 Jun, 2025, 4:31 pm Eric van der Helm via SocBiN, <
> socbin-at-sbc.su.se at lists.su.se> wrote:
>
> We have an open position for a Bioinformatician/Data Scientist in the
> field of bacterial genetics and microbiome science at SNIPR BIOME in
> Copenhagen. More details here
> https://www.linkedin.com/jobs/view/4244498813
>
>
>
> Best,
>
>
>
> Eric
>
>
>
>
>
> *Eric van der Helm, PhD*
>
> *VP of Scientific Affairs, Bioinformatics & Automation*
>
>
>
> *SNIPR*BIOME
>
> Lersø Parkallé 44, 5.floor
>
> 2100 Copenhagen
>
> Denmark
>
> Mail: evdh at sniprbiome.com
>
>
>
> [image: cidimage001.png at 01D68B7C.A5684D10]
>
>
>
> _______________________________________________
> SocBiN mailing list
> SocBiN at lists.su.se
> https://lists.su.se/mailman/listinfo/socbin-at-sbc.su.se
>
>
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From henrik.lantz at nbis.se  Tue Jun 24 11:29:26 2025
From: henrik.lantz at nbis.se (Henrik Lantz)
Date: Tue, 24 Jun 2025 11:29:26 +0200
Subject: [SocBiN] Bioinformatician positions in NBIS/SciLifeLab, Uppsala,
 Sweden
Message-ID: <5344A887-9D22-4091-9864-97C822AEC9A7@nbis.se>

Dear all,

National Bioinformatics Infrastructure Sweden (NBIS), a part of SciLifeLab, have several bioinformatician positions out in Uppsala, Sweden. These are permanent staff scientist positions focusing on support to Swedish researchers. They are NOT post doc positions. Please see the links below for more information and how to apply. We only accept applications through the application system, not in email.

1-2 positions focusing on spatial transcriptomics and/or biostatistics/machine learning:
https://www.uu.se/en/about-uu/join-us/jobs-and-vacancies/job-details?query=838183
Deadline Aug 29.

1 position focusing on scripting/development/pipelines, placed in the Evolution and Biodiversity team:
https://www.uu.se/en/about-uu/join-us/jobs-and-vacancies/job-details?query=838223
Note that you need to supply a link to a GitHub repo with own-developed scripts/pipelines for this position. Deadline Aug 18.

Best regards,
Henrik
—————————
Henrik Lantz
Support manager, NBIS/SciLifeLab
Uppsala, Sweden
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From rishi.dasroy at helsinki.fi  Wed Jun 25 10:28:00 2025
From: rishi.dasroy at helsinki.fi (Das Roy, Rishi)
Date: Wed, 25 Jun 2025 08:28:00 +0000
Subject: [SocBiN] A multi-omics oriented bioinformatician position in the
 University of Helsinki
Message-ID: <AS8PR07MB9397BA0FAA7F7AF6FA334C13997BA@AS8PR07MB9397.eurprd07.prod.outlook.com>

Hi,

Apply here https://jobs.helsinki.fi/job/Helsinki-Bioinformatician/823615802/

About the job
The University of Helsinki is seeking a highly motivated and service-oriented

Bioinformatician

to join the newly established HiLIFE Biodata unit. The unit supports life scientists by transforming complex high-throughput data into actionable scientific insights.

Position overview:

We are looking for an experienced and collaborative bioinformatician to join the Biodata Meilahti team, located at the Institute for Molecular Medicine Finland (FIMM), on the Meilahti biomedical campus. This is a service-driven position in a core facility environment.

Your primary role will be to provide high-quality data analysis services to life scientists, with a focus on single-cell, spatial and multiomics data. You will work closely with researchers, provide support through consultation and training, and contribute to the development of reproducible analysis workflows and pipelines.

You have a PhD in bioinformatics, computational biology, data science, computer science, genetics or other relevant field. You have successfully completed projects involving high-throughput life science data, and have knowledge in the relevant bioinformatics methods and tools.

Key Responsibilities:


  *   Collaborate with life science researchers to understand their goals, and guide experiment design and data analysis accordingly
  *   Deliver high-quality, reproducible data analysis solutions for single-cell, spatial and multiomics data
  *   Support the unit's training activities and contribute to the development of shared tools and pipelines
  *   Engage with other core facilities and promote best practices in research data management and analysis



Qualifications and experience:


  *   PhD in bioinformatics, computational biology, data science, computer science, genetics or other relevant field
  *   Demonstrated experience in analyzing high-throughput life science data
  *   Proficiency in analyzing single-cell and spatial omics data (e.g., scRNA-seq, scATAC-seq, Visium, Xenium, scMultiome, long-read data)
  *   Fluent in working with Linux/Unix systems and HPC environments (e.g., Slurm)
  *   Strong programming skills in Python and/or R, with experience using notebooks (Jupyter, RStudio) and Git
  *   Familiarity with workflow managers such as Nextflow or Snakemake is a plus
  *   Ability to communicate complex concepts clearly in both oral and written English (our team is international)
  *   A genuine interest in collaborative science, service-mindedness and a proactive approach to problem-solving



What We Offer


  *   An opportunity to work at the interface of cutting-edge research and high-quality bioinformatics service
  *   A dynamic, multidisciplinary, and international environment in one of Europe’s leading life science campuses
  *   Support for professional development and contributions to impactful scientific projects



The salary will be commensurate with qualifications based on the Finnish university salary (YPJ) system on previous qualifications, experience and performance in the position. The contract will initially be offered for two years, and may be extended.

To apply, please submit the application together with your CV (including a github profile is encouraged) and a cover letter highlighting your relevant experience through the University of Helsinki electronic recruitment system by clicking on Apply for job.

Applications are welcomed as soon as possible - the call will be open until 15th of August, 2025, and may be extended until the hiring decision is made.

For further information please visit www.helsinki.fi/en/infrastructures/biodata-analytics-unit or contact Dr. Esa Pitkänen (esa.pitkanen at helsinki.fi).


With regards,
Rishi Das Roy
University researcher
Biodata Analytics Unit
Institute of Biotechnology
Room no 4013, Biocenter 2
P.O. Box 56 (Viikinkaari 9)
FIN-00014 University of Helsinki, FINLAND
https://dasroy.github.io/
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From leena.salmela at cs.helsinki.fi  Sat Jun 28 10:00:58 2025
From: leena.salmela at cs.helsinki.fi (Leena Salmela)
Date: Sat, 28 Jun 2025 11:00:58 +0300 (EEST)
Subject: [SocBiN] Doctoral researcher and postdoctoral researcher positions
 in algorithmsand computational biology at University of Helsinki
Message-ID: <92a05eaf-a9c3-5c40-6ebf-77e2cc3e466d@email.helsinki.fi>

Dear all,

I have open positions for a doctoral researcher and a postdoctoral 
researcher in algorithms and computational biology here in the Department 
of Computer Science at the University of Helsinki. My research group 
develops models, algorithms and data structures for high throughput 
sequencing data with a main emphasis on genome assembly. The research 
group is part of the Algorithmic Bioinformatics lab at University of 
Helsinki. In particular, these positions focus on developing novel models 
for estimating the correctness of genome and metagenome assembly and 
algorithms and data structures for computing such correctness estimates.

For more information see

https://jobs.helsinki.fi/job/Helsinki-Doctoral-Researcher-in-Algorithms-and-Computational-Biology/823908702/
https://jobs.helsinki.fi/job/Helsinki-Postdoctoral-Researcher-in-Algorithms-and-Computational-Biology/823910502/

Best regards,

D.Sc.(Tech) Leena Salmela
University Lecturer
leena.salmela at cs.helsinki.fi