From arne.elofsson at gmail.com Tue Dec 3 02:34:28 2024 From: arne.elofsson at gmail.com (Arne Elofsson) Date: Tue, 3 Dec 2024 02:34:28 +0100 Subject: [SocBiN] Fwd: Early registration is February 1st! CGSI 2025 In-Reply-To: <4dada5071380a1bffc57a5e22.ef10470c82.20241203011111.d68305a8d3.3069582e@mail27.atl261.mcdlv.net> References: <4dada5071380a1bffc57a5e22.ef10470c82.20241203011111.d68305a8d3.3069582e@mail27.atl261.mcdlv.net> Message-ID: ---------- Forwarded message --------- From: Computational Medicine | UCLA Date: Mon, 2 Dec 2024, 21:30 Subject: Early registration is February 1st! CGSI 2025 To: Arne Elofsson *July 9 - August 1, **2025 | Computational Genomics Summer Institute | UCLA* CGSI brings together mathematical and computational scientists working in genomics, medical imaging, and electronic health record analysis. The program fosters interactions between researchers at all career stages and advances the mathematical foundations of this exciting field. We are now accepting applications for the Computational Genomics Summer Institute 2025! Please follow the application link HERE . The preliminary CGSI 2025 speakers will be announced in the winter and updated as they confirm. *CGSI alumni, did you publish an article as a result of CGSI?* *Please tell us about it! * NIH Grant GM112625 *July 9 - July 12* - Opening Retreat in Palos Verdes *July 14 - July 18* - First Short Program Computational Genomics - Workshops in Popgen/Statgen, Computational Methods in Genomics and Computational Methods *July 21 - 25* - Middle Week Long Program *July 28 - August 1* - Second Short Program Computational Medicine - Workshops in Genomic Biobanks, Machine Learning in Health *Long program participants attend the entire program. *Short program participants attend one of the two short programs. *2025 CGSI Registration Deadlines* *Early Bird* February 1st, 2025 - $550 *Regular* March 15th, 2025 - $650 *Late* May 1st, 2025 - $750 *Very Late* After May 1st, 2025 - $850 (space permitting) Apply Now *CGSI Co-Founders* Eleazar Eskin, UCLA Eran Halperin, UCLA John Novembre, University of Chicago Ben Raphael, Princeton University This email was sent to arne at bioinfo.se *why did I get this?* unsubscribe from this list update subscription preferences Computational Medicine Department | UCLA · 404 Westwood Plaza · Los Angeles, CA 90095-0001 · USA -------------- next part -------------- An HTML attachment was scrubbed... URL: From jacques.dainat at gmail.com Wed Dec 4 17:11:12 2024 From: jacques.dainat at gmail.com (Jacques Dainat) Date: Wed, 4 Dec 2024 17:11:12 +0100 Subject: [SocBiN] Internship Opportunity: Pipeline Development for Epitranscriptomics Message-ID: Dear SocBiN community, I am offering a Master's internship in bioinformatics at IRD, Montpellier, France (https://en.ird.fr). The project focuses on developing a Nextflow pipeline for RNA editing analysis. Details about the internship and application process are provided below. Please feel free to share with interested students! Best regards, Jacques Dainat Ph.D. Research engineer in Bioinformatics at IRD UMR (IRD 224-CNRS 5290-UM) MIVEGEC ---------------------------------- *In Brief* *What: *Internship *How long*: >= 6 Month *When*: Beginning of 2025 *Where*: IRD Montpellier France *Gratification*: ~600 euro/month Subject *Development of a Pipeline for the Analysis of Epitranscriptomic Modifications* Context RNA editing is a key post-transcriptional mechanism that modifies the genetic information carried by the RNA molecule and influences the diversity of the transcriptional signal. In more concrete cases, this process leads to nonsynonymous mutations at the codon level, which can affect protein function. In most cases, these mutations occur outside of translated regions but can still impact the regulation of gene expression. Despite the importance of this phenomenon, it remains understudied due to the challenges associated with using existing tools (portability, reproducibility, parallelization). In this context, we propose an internship aimed at developing a bioinformatics pipeline using Nextflow, to integrate and automate the use of various existing relevant tools and to combine their outputs into a “meta-editome.” Objective of the Internship The main goal of this internship is to develop a complete pipeline in Nextflow that will facilitate the analysis of RNA sequencing data to detect RNA editing events. This pipeline must be reproducible, portable, and easy to execute on various computing platforms (local or HPC). It will integrate commonly used bioinformatics tools for: • Preparation and quality control of RNA sequencing data. • Alignment of RNA reads to the reference genome. • Identification of editing sites from RNA-seq data. • Annotation and interpretation of identified editing sites, with options for cross-species and cross-condition comparisons. • Testing and validating the pipeline on public datasets. • Documenting the pipeline, including configuration, workflow steps, and execution instructions. Candidate Profile • Master’s student in their second year (bioinformatics, computational biology, or related field). • Skills in bioinformatics, especially in RNA sequencing data analysis. • Prior experience with bioinformatics workflows (e.g., Nextflow, Snakemake) is a plus. • Good proficiency in one or more scripting languages (e.g., Bash, Python, Perl, R). • Familiarity with RNA-seq analysis tools and biological databases. Supervision Jacques Dainat, Ph.D. - Research Engineer in Bioinformatics Location French National Research Institute for Sustainable Development (IRD), MiVEGEC Laboratory, Montpellier. Duration Six-month internship starting in January, with potential for extension. ApplicationPlease send your CV, cover letter, transcript of records, and names of referees to jacques.dainat at ird.fr -------------- next part -------------- An HTML attachment was scrubbed... URL: From henrik.lantz at nbis.se Mon Dec 9 11:31:45 2024 From: henrik.lantz at nbis.se (Henrik Lantz) Date: Mon, 9 Dec 2024 11:31:45 +0100 Subject: [SocBiN] Bioinformatician position in pipeline development at NBIS (Uppsala, Sweden) Message-ID: Dear all, The bioinformatics infrastructure NBIS (National Bioinformatics Infrastructure Sweden; a part of SciLifeLab) is hiring a bioinformatician with focus on pipeline development. The position is in Uppsala, Sweden, and it is a permanent position as staff scientist (not a post doc). The work focuses on supporting Swedish researchers with Nextflow development. We require experience of pipeline development (with examples of own developed pipelines available in an online repository like GitHub), but do not require Nextflow experience specifically. If you for example have experience in Snakemake and have a keen interest to learn Nextflow, we encourage you to apply! There are experienced Nextflow developers in NBIS that you can learn from. Also, NBIS is an infrastructure of 120 staff, with around half of them bioinformaticians (average 10 years post PhD experience), which means there are plenty of experienced colleagues to discuss with in general. Find more information and how to apply here (email applications not accepted): https://www.uu.se/en/about-uu/join-us/jobs-and-vacancies/job-details?query=778701 Best, Henrik ———————————— Henrik Lantz Support manager, NBIS/SciLifeLab Uppsala, Sweden -------------- next part -------------- An HTML attachment was scrubbed... URL: From sampsa.hautaniemi at helsinki.fi Fri Dec 13 09:58:06 2024 From: sampsa.hautaniemi at helsinki.fi (Hautaniemi, Sampsa) Date: Fri, 13 Dec 2024 08:58:06 +0000 Subject: [SocBiN] PhD/Post-doc position in mathematical modeling of cancer Message-ID: Dear colleagues, I would greatly appreciate if you could spread the word that there is a super exciting PhD/post-doc position available on mathematical modeling of cancer in my group. This project is a collaborative project with Orion Pharmaceuticals, so also those students fancying an industry career might be interested in this one. The idea is to make a digital twin model using multi-modal sequencing, imaging and clinical data from our observational DECIDER trial (https://www.deciderproject.eu/). The position advertisement is available here:https://jobs.helsinki.fi/job-invite/3720/. I wish you all smooth end of the year and Happy Holidays! Best, Sampsa -- Sampsa Hautaniemi, DTech Professor of Systems Biology Director, Research Program in Systems Oncology (ONCOSYS) & EU Horizon 2020 consortium DECIDER Room B316a PO Box 63 (Haartmaninkatu 8) Faculty of Medicine 00014, University of Helsinki, Finland Tel: +358503364765 URL: https://www.mv.helsinki.fi/home/shautani/ -------------- next part -------------- An HTML attachment was scrubbed... URL: From benjamin.ulfenborg at his.se Mon Dec 16 11:02:02 2024 From: benjamin.ulfenborg at his.se (Benjamin Ulfenborg) Date: Mon, 16 Dec 2024 10:02:02 +0000 Subject: [SocBiN] =?utf-8?q?Bioinformatics_lecturer_position_in_Sk=C3=B6vd?= =?utf-8?q?e?= Message-ID: Dear colleagues, The Department of Biology and Bioinformatics at University of Skövde has an open 1-year lecturer position Bioinformatics. The position as a lecturer primarily involves teaching in bioinformatics and associated administration tasks. Additional duties may also be included in the position. Please spread the word and apply here: https://www.his.se/en/about-us/job-opportunities/available-positions/?rmpage=job&rmjob=941&rmlang=UK Application deadline: 6st January 2025 Merry Christmas and Happy New Year from Skövde! Best regards, Benjamin ———————————————— Benjamin Ulfenborg, PhD Docent in bioinformatics Systems Biology Research Environment School of Bioscience University of Skövde, Sweden Contact: email: benjamin.ulfenborg at his.se phone: +46 (0)500 44 86 83 webpage: https://www.his.se/en/ulfb -------------- next part -------------- An HTML attachment was scrubbed... URL: From arne at bioinfo.se Thu Dec 19 16:04:11 2024 From: arne at bioinfo.se (Arne Elofsson) Date: Thu, 19 Dec 2024 16:04:11 +0100 Subject: [SocBiN] Two PhD or Postdoc positions in computational off-target analysis of siRNA and small peptides Message-ID: https://jobportal.ku.dk/videnskabelige-stillinger/?show=162883 Two PhD or Postdoc positions in computational off-target analysis of siRNA and small peptides We have two positions each as either a three-year PhD or a three-year postdoc available in the Gorodkin lab (https://ivh.ku.dk/bioinformatics), Center for non-coding RNA in Technology and Health (RTH), (http://rth.dk) at Department of Veterinary and Animal Sciences (https://ivh.ku.dk/english), Faculty of Health and Medical Sciences at University of Copenhagen. The projects concern safety when siRNAs and small peptides are applied as pesticides in plants and the aim is to develop the computational tools and analyses that will contribute to an environmental risk assessment framework for new bio-based plant protection products (PPPs). The project is part of the Novo Nordic Foundation Challenge project ENSAFE: “ENvironmental SAFEty of biotechnological plant protection products based on short interfering RNA and peptides” headed by Professor Nina Cedergreen. The title of the two positions are: Computational methods to predict and analyze siRNA off-targets and their effects Computational methods to predict and analyze small peptide off-targets and their effects Start date is February or March 2025 or as soon as possible thereafter. The project The vision of ENSAFE is to develop the in silico and experimental methods and tools needed to underpin an efficient evidence-based risk assessment framework for new bio-based plant protection products (PPPs) based on short double stranded RNA (dsRNA) or peptides. The two positions will be filled as PhD students or postdocs working with each their model compound of newly commercialised dsRNA or peptide-based products: Position 1: Data analysis and computational tools for siRNA-RNA interactions of the target and off-target organisms will be developed with outset in established and in-house methods such as RIsearch2. Position 2: Data analysis and computational tools for small peptide interactions to proteins will be developed with outset in predicting interactions between the peptides and the proteins of the target and off-target organisms. The methodological framework will take outset in a combination of sequence motif detection algorithms and 3D folding with Alphafold for predicting the interactions. In both projects data structures or efficient initial omics-wide searches will be constructed. The data obtained from the public domain and from within the ENSAFE project will be used to build the search tools, test its quality and guide the design of novel experiments. To the extent data allows for it, the projects will further explore the possibilities for modelling with machine/deep learning techniques. The two positions will work close with collaborators of the Gorodkin lab on computational elements and with the project partners of ENSAFE in general. If a position is offered as a PhD, your key tasks as a PhD student at SUND are: Carrying through an independent research project under supervision. Completing PhD courses or other equivalent education corresponding to approximately 30 ECTS points. Participating in active research environments including a stay at another research team. Obtaining experience with teaching or other types of dissemination related to your PhD project Teaching and disseminating your knowledge. Writing a PhD thesis on the grounds of your project Who are we looking for We are looking for highly motivated and enthusiastic candidates with a strong technical background and experience in programming, algorithms, data structures, machine learning and data analysis, in particular omics, who are familiar and have experience with either RNA structure and RNA-RNA interactions or protein structure and interactions. You will work in a cross-disciplinary environment and collaborate with other researchers internally in the group and with external groups working on the experimental aspects. You will be an excellent and emphatic team player and pleasant to work with. You will be highly dedicated, work with great excitement and be a key person in the project essential for obtaining successful results. Essential experience and skills: For postdoc applicants: You have completed PhD degree in bioinformatics, computer science or in a similar area For PhD applicants: You have completed MSc degree in bioinformatics, in computer science or in a similar area. Please note that your master’s degree must be equivalent to a Danish master’s degree (two years) You are highly experienced in Python You have strong experience with the Linux/Unix environment, command lines and shell scripting You are well familiar with machine learning algorithms both theoretically and practical implementation You are proficient communication skills You have excellent English skills, written and spoken You have good people skills and is a strong team player Desirable experience and skills: Knowledge about RNA and / or protein structure and interactions Knowledge about algorithms for RNA and/or protein structure and interaction prediction Knowledge about omics e.g., transcriptomics / proteomics data analysis Knowledge and experience with machine/deep learning Knowledge with analysis of biological networks beyond basic applications through GUIs. For postdoc applicants we expect a general higher level of expertise relative to PhD applicants, including (but not limited to) higher experience research, programming, theoretical thinking and writing of scientific articles. This higher experience for postdocs should be reflected in having at least three additional years of experiences in their scientific career including published and amount code written. Key selection criteria for both PhD-student and postdoc: Publications Professional qualifications relevant for the position Relevant work experience Language skills Creativity Our research group Our research group Computational Biology and Bioinformatics ( https://ivh.ku.dk/bioinformatics) work with computational algorithms and methods for molecular structure and interactions. We have excellent computational infrastructure and further access to supercomputing when needed. The research group is working on a range of bioinformatical aspects both algorithm, data and omics-wise. The research group is located on Frederiksberg Campus. Our research environment is highly international and stimulating. We frequently organize seminars, workshops, summer schools with international speakers and have retreats with our international collaborators. Terms of employment The average weekly working hours are 37 hours per week. The position is a fixed-term position limited to a period of 3 years both as PhD-student and as postdoc. The starting date is February 1st, 2025, or as soon as possible thereafter. Salary, pension and other conditions of employment are set in accordance with the Agreement between the Ministry of Taxation and AC (Danish Confederation of Professional Associations) or another relevant organisation. Currently, the monthly salary for Postdocs starts at 35,000 DKK/approx. 4,700 EUR (October 2021 level). For PhD, the monthly salary starts at 27,800 DKK/approx.. 3,700 EUR (October 2021 level). Depending on qualifications, a supplement for both PhD-student and postdoc may be negotiated. The employer will pay an additional 17.1 % to your pension fund. Foreign and Danish applicants may be eligible for tax reductions, if they hold a PhD degree and have not lived in Denmark the last 10 years. The position either as PhD-student or as postdoc is covered by the Job Structure for Academic Staff at Universities 2020. Questions For further information about the scientific content of the position please contact Professor Jan Gorodkin, email gorodkin at sund.ku.dk, phone +45 23375667 or for application procedure and formalities, please contact HR Officer, email sund-hr-ivh at sund.ku.dk / www.sund.ku.dk Foreign applicants may find this link useful: www.ism.ku.dk (International Staff Mobility). Application procedure Your online application must be submitted in English by clicking ‘Apply now’ below. Furthermore, your application must include the following documents/attachments – all in PDF format: Motivation letter of application. In this letter you must briefly detail, one by one, how you meet the requirements for each item listed under “Essential experience and skills” and “Desirable experience and skills”. CV incl. education, work/research experience, language skills and other skills relevant for the position. A certified/signed copy of: a) For the postdoc position: PhD certificate. If the PhD is not completed, a written statement from the supervisor will do. b) For the PhD position: Certified copy of original Master of Science diploma and transcript of records in the original language, including an authorized English translation if issued in other language than English or Danish. If not completed, a certified/signed copy of a recent transcript of records or a written statement from the institution or supervisor is accepted. As a prerequisite for a PhD fellowship employment, your master’s degree must be equivalent to a Danish master’s degree. We encourage you to read more in the assessment database: https://ufm.dk/en/education/recognition-and-transparency/find-assessments/assessment-database. Please note that we might ask you to obtain an assessment of your education performed by the Ministry of Higher Education and Science 4. List of publications. 5. Personal Recommendations. If none, please explain why it has not been possible to obtain. Deadline for applications: 3 January 2025, 23.59pm CET We reserve the right not to consider material received after the deadline, and not to consider applications that do not live up to the abovementioned requirements. The further process After the expiry of the deadline for applications, the authorized recruitment manager selects applicants for assessment on the advice of the hiring committee. All applicants are then immediately notified whether their application has been passed for assessment by an unbiased assessor. The assessor makes a non-prioritized assessment of the academic qualifications and experience with respect to the above-mentioned area of research, techniques, skills and other requirements listed in the advertisement. Once the assessment work has been completed each applicant has the opportunity to comment on the part of the assessment that relates to the applicant him/herself. You find information about the recruitment process at: https://employment.ku.dk/faculty/recruitment-process/ The applicants will be assessed according to the Ministerial Order no. 242 of 13 March 2012 on the Appointment of Academic Staff at Universities. The University of Copenhagen wish to reflect the diversity of society and encourage all qualified candidates to apply regardless of personal background. Københavns Universitet giver sine knap 10.000 medarbejdere muligheder for at udnytte deres talent fuldt ud i et ambitiøst, uformelt miljø. Vi sikrer traditionsrige og moderne rammer om uddannelser og fri forskning på højt internationalt niveau. Vi søger svar og løsninger på fælles problemer og gør ny viden tilgængelig og nyttig for andre. Info -------------- next part -------------- An HTML attachment was scrubbed... URL: From arne.elofsson at gmail.com Mon Dec 30 08:00:00 2024 From: arne.elofsson at gmail.com (Arne Elofsson) Date: Mon, 30 Dec 2024 08:00:00 +0100 Subject: [SocBiN] Professor in bioinformatics Message-ID: https://www.slu.se/en/about-slu/work-at-slu/jobs-vacancies/ Professor of Bioinformatics Reference number SLU.ua.2024.2.5.1-4167 Faculty of Veterinary Medicine and Animal Science The Department of Animal Biosciences The Department of Animal Biosciences is part of the Faculty of Veterinary Medicine and Animal Science and is responsible for education and research in several basic and applied areas. These areas include anatomy, physiology, biochemistry, pathology, pharmacology, toxicology, genetics, breeding, immunology, bacteriology, virology, parasitology, epizootology, comparative medicine, food safety, bioinformatics, and One Health. Our research covers everything from production animals to sport and companion animals, laboratory animals, and wild animals. The department's researchers work on the entire scale, from molecular mechanisms and microbiology to the structure, function, and behaviour of animals and how these are affected by breeding, physical activity, care, production, stress, environmental factors, and diseases. The current employment in bioinformatics is placed in the research group of bioinformatics. Our research is focused on developing methods for analysing and understanding the code that governs life, from DNA sequences to complex biological processes. By understanding these processes, we can improve the quality of life for many by offering better food, more precise diagnoses of diseases, and improved treatments Read more about our activities and infrastructure here. Read more about our benefits and what it is like to work at SLU via the following link. Subject description The subject of the employment is bioinformatics. It comprises developing methods for analysing biological data, such as DNA, RNA, proteins, and metabolites, focusing on farmed animals, sport and companion animals, and microorganisms from their internal or external environment. Duties The applicant will be expected to: develop and lead internationally successful research develop, lead, and participate in teaching at first, second, and third cycle levels primarily teach bioinformatics, in addition to other components at first, second, and third cycle levels covering the subject develop and maintain national and international networks with academia, the relevant public authorities, industry, organizations, and society at large collaborate with other SLU research teams to strengthen interdisciplinary activities at the university apply for external research funding from both national and international sources supervise doctoral students contribute to the strategic development of the department, faculty, and SLU communicate research findings and other relevant information to society at large perform administrative duties within the department, faculty, and university possibly have a managerial role be able to use Swedish as the working language within four years. The department uses Swedish and English in parallel. The professor should be able to perform the majority of their tasks in English. However, as a public authority, the university has Swedish as its main language according to the requirements of the Language Act, and the professor must be able to use Swedish as their working language within four years of beginning the position. The department will provide support with language learning. Eligibility The applicant must have successfully completed a doctoral degree with a focus on bioinformatics, as well as hold the qualifications required for appointment as an associate professor (docent) within a subject relevant to the position demonstrate research expertise in the subject demonstrate teaching expertise and have the ability to integrate research and a scientific approach into their teaching have demonstrated the ability to lead and develop a successful, internationally recognized research team have demonstrated the ability to compete for substantial external research funding have good knowledge of English. Grounds of assessment As assessment criteria for employment, the degree of such proficiency required for eligibility for employment shall primarily apply. The assessment of research expertise will be based on: completed and ongoing research and its relevance and development potential for the faculty and department the ability to independently initiate and run successful and internationally recognised research the ability to successfully compete for external research funding experience in the role of principal supervisor for third-cycle study programmes. As a principal supervisor, the applicant should have supervised doctoral students throughout their studies until they are awarded their doctoral degree. The following will be taken into consideration when assessing teaching expertise: planning, implementation, examination, and assessment of teaching and education the ability to integrate research and scientific approaches into teaching work supervision and examination of first, second, and third cycle courses training in teaching and learning in higher education or the equivalent knowledge pedagogic vision and reflection. The following abilities will also be assessed: developing and leading activities and staff within academia communicating and collaborating internally collaborating with external stakeholders and society at large communicating research and development work. The appointment will be offered to the applicant who, following a qualitative comprehensive assessment, is deemed to have the best skill set to conduct and develop the duties in question and contribute to the positive development of the organisation. This position offers the vibrant research climate at SLU. The benefits of the position include Swedish family health care provisions, parenting support including generous paid leave of absence policies that allow both parents to care for newborns and toddlers. Additionally Sweden has a well-established pre-school structure as well as an educational system that provides no-cost education through university studies. Find out more facts and stories about Sweden at www.sweden.se Located in the greater Stockholm region, the city of Uppsala has a rich history and culture, and is a true academic and cultural hub. Find out more about moving, living and working here at https://internationalhub.uppsala.se/ Application deadline: 2025-04-28 Place of work: Uppsala Extent: 100% Form of employment: Permanent employment Starting date: By agreement. Application: For the guidance of your application, there is SLU's appointment procedure for teachers at SLU and General assessment criteria for the appointment of teachers, which you can read here. Please apply by clicking the apply-button below. Academic union representatives: https://internt.slu.se/min-anstallning/facket/kontaktpersoner/ The Swedish University of Agricultural Sciences (SLU) has a key role in the development for sustainable life, based on science and education. Through our focus on the interaction between humans, animals and ecosystems and the responsible use of natural resources, we contribute to sustainable societal development and good living conditions on our planet. Our main campuses are located in Alnarp, Umeå and Uppsala, however, the university also operates at research stations, experimental forests and teaching sites throughout Sweden. SLU has around 3,000 employees, 5,000 students and doctoral students and a turnover of over SEK 3 billion. We are investing in attractive environments on all of our campuses. We strive to provide a work environment characterised by inclusivity and gender equality, where different experiences generate conversations between people and pave the way for science, creativity and development. Therefore, we welcome applications from people with diverse backgrounds and perspectives. Contact person Sarah Hedenskog Faculty Administrative Officer sarah.hedenskog at slu.se Anna Jansson Head of Department, Professor anna.jansson at slu.se Apply Back -------------- next part -------------- An HTML attachment was scrubbed... URL: