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ISMB 2022 CompMS - Save the date & call for proposals
by Bittremieux, Wout 28 Mar '22

28 Mar '22

— ISMB 2022 CompMS – Save the date & call for proposals — Dear colleagues, We are excited to announce that ISMB 2022 is returning with an in-person conference in Madison, WI, USA on July 10–14, 2022. Please join us for the Computational Mass Spectrometry (CompMS) COSI session on Monday July 11, 2022. The ISMB conference is the world's largest bioinformatics/computational biology conference. Every year it brings together scientists from computer science, molecular biology, mathematics, statistics, and related fields and provides an intense multidisciplinary forum for disseminating the latest developments in bioinformatics/computational biology. The conference fosters fresh dialogues, collaboration and learning opportunities, and is a gathering which shapes the future of the field. At the heart of the scientific program are ISCB’s Communities of Special Interest (COSIs), enabling community involvement and bolstering ISMB’s reputation as the leading conference in the field. The CompMS COSI promotes the efficient, high-quality analysis of mass spectrometry data through dissemination and training in existing approaches and discussion of new, innovative approaches. The CompMS initiative aims to exploit synergies between different mass spectrometry-based application domains, in particular proteomics, metabolomics, and lipidomics. A strong scientific and technical program showcases the best international developments in bioinformatics and computational biology, making ISMB 2022 a must attend event. Virtual participation options are also available. Date: July 11, 2022 (CompMS COSI) / July 10–14, 2022 (ISMB) Venue: Monona Terrace Convention Center, Madison, WI, USA / virtual Website: https://www.iscb.org/ismb2022 Key dates April 21, 2022: Abstract submission deadline May 12, 2022: Talk/poster acceptance notifications May 19, 2022: Late poster submission deadline May 26, 2022: Late poster acceptance notifications July 10–14, 2022: ISMB conference Call for proposals Abstract submission for ISMB 2022 is now open! Submit your abstract to ISMB to present your work at the leading bioinformatics/computational biology conference. Attend the CompMS session to learn about the latest algorithmic advances in computational mass spectrometry. Please remember to select the CompMS COSI as your session of interest upon submitting your abstract. Call for abstracts: https://www.iscb.org/ismb2022-submissions/abstracts We look forward to seeing you at ISMB! The CompMS organizing committee. Wout Bittremieux Isabell Bludau Lindsay Pino Timo Sachsenberg

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ELIXIR Belgium: FAIR data for Life Sciences research - Program available - Registration open
by Kim DE RUYCK 23 Mar '22

23 Mar '22

Dear, We are pleased to invite you for the ELIXIR Belgium meeting: FAIR data for Life Sciences Research which takes place on 18 May 2022 in Brussels . We have put together a programme touching on Open and FAIR science, demonstrating how infrastructure enables research, and mapping the different initiatives to share sensitive data across Europe. Next to the presentations, the event also includes panel discussions, an ask-me-anything session and ample networking time. [ https://www.eventbrite.co.uk/e/elixir-belgium-fair-data-for-life-sciences-r… | Link to the program and registration ] . The registration deadline is 3 May 2022. Kind regards, Kim De Ruyck Kim De Ruyck PhD Coordinator ELIXIR Belgium VIB-UGent Center for Plant Systems Biology Technologiepark 71, 9052 Ghent, Belgium [ http://www.elixir-belgium.org/ | www.elixir-belgium.org ] [ https://twitter.com/ELIXIRnodeBE | @ELIXIRnodeBE ] [ http://eepurl.com/cl-xOX | Subscribe to our mailing list ]

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VIB VUB webinar series "Quantitative biology at the molecular and cellular levels: leveraging the power of AI" up-coming
by Alexander Botzki 21 Mar '22

21 Mar '22

Hi all, Together with @ELIXIREurope @ELIXIRnodeBE #3DbioInfo and IDP communities and @vibbioinfocore, the VIB-VUB Center for Structure Biology presents a new webinar series: "Quantitative biology at the molecular and cellular levels: leveraging the power of AI" @structbiolbxl @VIBLifeSciences For more info, please visit: https://webinarseries.sites.vib.be/en Best regards, Alex Alexander Botzki – Head of VIB Bioinformatics Core, ELIXIR Belgium Training Coordinator VIB Bioinformatics Core Technologiepark-Zwijnaarde 75 9052 Zwijnaarde Belgium tel +32 9 224 9870 https://vib.be/labs/vib-bioinformatics-core/research | https://www.bits.vib.be | @vibbioinfocore [signature_1392704337]

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Open vacancy bacterial/phage genomics @Sciensano
by Kevin Vanneste 21 Mar '22

21 Mar '22

Dear all, The Bioinformatics Platform at the Belgian Institute of Health (www.sciensano.be<http://www.sciensano.be>) currently has an open vacancy for a bioinformatician to work in the field of bacterial and phage genomics. The initial contract duration is for 18 months. Please see the job description in attachment. Applications are possible using our job site: https://jobs.sciensano.be/content/jobpage.asp?a=DETAIL&jdkid=921&l=DUTCH Sincerely, K Kevin Vanneste, PhD Senior scientist - Responsible Bioinformatics Platform Transversal activities in Applied Genomics (TAG) T + 32 2 642 50 65 [cid:image001.jpg@01D4595B.6D6E05D0] Rue Juliette Wytsmanstraat 14 * 1050 Brussels www.sciensano.be<http://www.sciensano.be/> P Please consider the environment before printing this e-mail

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Vacancy: Bioinformatics developer at ENPICOM B.V.
by Henk-Jan van den Ham 21 Mar '22

21 Mar '22

Dear all, ENPICOM B.V., a scaleup company in The Netherlands, is looking for a bioinformatics developer (MSc/PhD) who loves combining cutting edge software engineering and bioinformatics to solve concrete challenges in the immunogenomics field. Interested? Take a look at the job description & requirements: https://enpicom.com/vacancies/bioinformatics-developer/ Please share this vacancy with anyone interested. Regards, Henk-Jan -- Dr. H.J. van den Ham Senior Scientist Bioinformatics & Immunology Research Team Lead [A picture containing text, clipart Description automatically generated] Sint Janssingel 88 | 5211 DA ‘s-Hertogenbosch | The Netherlands CoC 69524084 | T +31 627 578 895 | www.enpicom.com<https://enpicom.com/>   Disclaimer: The information contained in this communication is confidential and intended solely for the use of the individual or entity to whom it is addressed. If you are not the intended recipient, you are hereby requested to inform the sender and destroy the original and all copies unread. Publication, distribution, and provision of this information to third parties are prohibited and are unlawful. No rights may be attached to this message. ENPICOM B.V. is not responsible for the proper and complete transmission of the information contained in this communication nor for any delay in its receipt. Terms & Conditions: All offers and agreements are governed by the General Terms & Conditions<https://enpicom.com/terms-and-conditions/> of ENPICOM B.V. Privacy: This business communication is sent to you as it contains information that we consider of interest to you and/or your organization. In case you prefer not to be contacted anymore by anyone within our organization, just let us know and we will delete all your records immediately. All details on the personal data we collect, for what purposes, and your rights with respect to the foregoing are available in our Privacy Policy<https://enpicom.com/privacy-policy/>.

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CFP: AIHA 2022 – 2nd International Workshop on Artificial Intelligence for Healthcare Applications
by Nicole Dalia CILIA 16 Mar '22

16 Mar '22

[image: Cattura.JPG] *CALL FOR PAPERS* 2nd International Workshop on Artificial Intelligence for Healthcare Applications (AIHA 2022) https://aida.unicas.it/AIHA2022/ <http://lia.unicas.it/AIHA2022> The workshop will be held on August *21-25*, *2022* in conjunction with ICPR 2022 <https://www.icpr2022.com/> (26th International Conference on Pattern Recognition, Montréal, Canada, August 21-25, 2022). The increased availability of medical data collected from healthcare systems has enabled a number of artificial intelligence applications. Specifically, machine learning can generate insights to improve the discovery of new therapeutic tools, to support diagnostic decisions, to help in the rehabilitation process, just to name a few. Bringing together the advances of this wide and multidisciplinary subject, the aim of this workshop is to present recent advances in artificial intelligence techniques for healthcare applications. *TOPICS* Topics include but are not limited to the following: - Biomedical image analysis - Data analytics for healthcare - Automatic disease prediction - Automatic diagnosis support systems - Genomic and proteomic data analysis - Artificial intelligence for personalized medicine - Machine Learning as a tool to support medical diagnosis and decisions - Machine learning on handwriting and eye-tracking traces for diagnosis and rehabilitation - Decoding of neural signals for diagnosis assistance - Physiological signals processing - Gait analysis - Therapy selection - Brain-computer interface for healthcare - Biomechatronics for medicine - Neuromotor rehabilitation *DATES * - Paper Submission: April 4th, 2022 - Notification of Acceptance: May 25th, 2022 - Camera-ready Submission: June 1st, 2022 *SUBMISSIONS * Accepted papers will be included in the *ICPR 2022 Workshop Proceedings*, which will be published according to the publication rules of ICPR conference. Once accepted, at least one author is expected to attend the event and orally present the paper. Papers can be submitted using the EasyChair <https://easychair.org/account/signin_timeout?l=DBD94UdXygdTEPjELT3LxJ>. Both *source (latex/word) and pdf* files are required. *CHAIRS * Nicole Dalia Cilia, University of Enna Kore, Francesco Fontanella, Claudio Marrocco University of Cassino and Southern Lazio, Italy Contact Information: Nicole Dalia Cilia, nicoledalia.cilia(a)unikore.it

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Programmer/Bioinformatician contract at the Structural Genomics Group
by Karoline Faust 16 Mar '22

16 Mar '22

Centro Nacional de Análisis Genómico (CNAG-CRG) The Institute The Centro Nacional de Análisis Genómico (CNAG-CRG) is one of the largest Genome Sequencing Centers in Europe. CNAG-CRG researchers participate in major International Genomic Initiatives such as the International Cancer Genome Consortium (ICGC), the International Human Epigenome Consortium (IHEC), the International Rare Diseases Research Consortium (IRDiRC) and the European Infrastructure for life-science information (ELIXIR), as well as in several EU-funded projects. It is integrated with the Centre for Genomic Regulation (CRG), an international biomedical research institute of excellence, based in Barcelona, Spain, with more than 400 scientists from 44 countries. The CRG is composed by an interdisciplinary, motivated and creative scientific team which is supported both by a flexible and efficient administration and by high-end and innovative technologies. In April 2021, the Centre for Genomic Regulation (CRG) received the renewal of the 'HR Excellence in Research' logo from the European Commission. This is a recognition of the Institute's commitment to developing an HR Strategy for Researchers, designed to bring the practices and procedures in line with the principles of the European Charter for Researchers and the Code of Conduct for the Recruitment of Researchers (Charter and Code). Please, check out our Recruitment Policy The role Currently, we are looking for candidates with a minimum of a master in Bioinformatics or Computational- related sciences who can demonstrate codding experience and knowledge. The candidate will need to have experience in analysis of NGS and creating user interface and data visualizations for large datasets. Knowledge of computational approaches and use of R and/or Python coding is a must. This position will be funded by a fellowship associated to our research project H2020 3D’Omics (GA 101000309) entitled “Three-dimensional holo’omic landscapes to unveil host-microbiota interactions shaping animal production”. Please, visit our web site at http://marciuslab.org to grasp similar projects you could be involved by joining our Team. For all publications from the group please visit http://marciuslab.org/www/publications. About the team In a nut-shell, our group at the National Center for Genomic Analysis - Centre for Genomic Regulation (CNAG-CRG) develops and uses experimental and computational approaches for characterizing the molecular regulation of cells by studying the structure of macromolecules and their complexes. In particular, we focus on chromatin and tissues. Our group (http://marciuslab.org/www/people) is very interdisciplinary (the team has been composed by biologists, biochemists, physicists, architects, mathematicians, statisticians, pharmacists, molecular biologists, and geneticists, among others), young (http://marciuslab.org/www/people/?lab_pics) international and dynamic. We strive to make our people's stay as fun as possible while enjoying science. If you like such environment, apply to this position! [page1image464735424] [page1image464734656] [page1image464741376] [page1image464741760] [page1image464739840] [page1image464733696] [page1image464742528] [page1image464734464] Whom would we like to hire? Professional experience Must Have • You have previous experience in databases and data visualization Desirable but not required/ Nice to have • You have experience in NGS analysis Education and training * You hold a Master degree in Bioinformatics or Computational-related Sciences Languages * You are fluent in English Technical skills • You have knowledge of Python and/or R language programming Competences * You are proactive * You are a dynamic person * You are a team worker * You have highly developed organizational skills The Offer – Working Conditions * Contract duration: Long term position subject to external funding * Estimated annual gross salary: Salary is commensurate with qualifications and consistent with our pay scales * Target start date: 15 April 2022. We provide a highly stimulating environment with state-of-the-art infrastructures, and unique professional career development opportunities. To check out our training and development portfolio, please visit our website in the training section. We offer and promote a diverse and inclusive environment and welcomes applicants regardless of age, disability, gender, nationality, ethnicity, religion, sexual orientation or gender identity. The CRG is committed to reconcile a work and family life of its employees and are offering extended vacation period and the possibility to benefit from flexible working hours. Application Procedure All applications must include: 1. 2. 3. All applications must be addressed to Dr. Marc A. Marti-Renom and be submitted online on the CRG Career site - http://www.crg.eu/en/content/careers/job-opportunities Selection Process * − Pre-selection: The pre-selection process will be based on qualifications and expertise reflected on the candidates CVs. It will be merit-based. * − Interview: Preselected candidates will be interviewed by Dr. Marc A. Marti-Renom. * − Offer Letter: Once the successful candidate is identified the Human Resources department will send a Job Offer, specifying the start day, salary, working conditions, among other important details. Deadline: Please submit your application by 3rd April, 2022 [page3image465512768] A motivation letter addressed to Dr. Marc A. Marti-Renom. [page3image465513728] A complete CV including contact details.  [page3image465514112] Contact details of two referees. [page3image465514496] Suggestions: The CRG believes in ongoing improvement and promotes a culture of feedback. This is one of the reasons we have in place, at your disposal as a candidate, a mechanism to gather your suggestions/complaints concerning your candidate experience in our recruitment processes. Your feedback really matters to us in our aim at creating a positive candidate journey. You can make a difference and help us improve by letting us know your suggestions through the following form.

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Fwd: ISCB Academy Tutorial Series - 18 March - Spinning a semantic web of protein information
by Celia van Gelder 16 Mar '22

16 Mar '22

For your information > Van: Russell Schwartz <russell.s.schwartz(a)gmail.com> > Datum: 16 maart 2022 om 02:20:50 CET > Aan: Education COSI <education.cosi(a)iscb.org> > Onderwerp: ISCB Academy Tutorial Series > > > > ISCB Academy has recently started a new tutorial series in October 2021 to provide hands-on experience accessing and using newly developed bioinformatics tools while ensuring best practices for rigour and reproducibility. The next tutorial is under the title “Spinning a semantic web of protein information”, which will be held on the 18th of March at 11:00 am UTC (This Friday). > > > Short description of the Tutorial: > > Life science is the most demanding research field in terms of data quantity and complexity, with many relevant reference databases. To generate knowledge, heterogeneous data from various sources must often be combined. Semantic Web technologies, and in particular RDF and its companion query language SPARQL, provide a common framework allowing data to be shared and reused between resources. Many life science databases have recently turned to RDF to model their data, developed SPARQL endpoints and joined the Linked (Open) Data cloud. This tutorial will introduce neXtProt (www.nextprot.org/) one of the major public knowledge bases on human proteins, its comprehensive RDF data model, and its large collection of reusable example queries, including federated queries to other resources. > > At the end of the tutorial, the participants are expected to: > > • Describe the neXtProt data model > • Run example queries that answer biological questions > • Search for data by modifying existing SPARQL queries > • Understand how federated queries are constructed > > Instructor: > > Monique Zahn is the Quality Manager of the CALIPHO group which develops neXtProt. She is responsible for testing user interfaces and the contents of each release. She has established quality control procedures involving SPARQL queries carried out at each data release. She has taught biology in undergraduate degree programs in Switzerland and is also a Training Manager at the SIB. > > > Register https://www.iscb.org/cms_addon/academy/events#6 > > (posted on behalf of Batool Almarzouq <batool(a)liverpool.ac.uk>) > > -- > To unsubscribe from this group and stop receiving emails from it, send an email to education.cosi+unsubscribe(a)iscb.org.

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Re: [BBC] postdoctoral scientist in Bioinformatics for Systems Immunology of Critical Illness
by BOGAERT Debby 14 Mar '22

14 Mar '22

Dear people, I would like to ask whether you can share below position that is available within our Center for Inflammation Research of the University of Edinburgh with suitable candidates. It is a wonderful 3 year full-time post for a postdoctoral scientist, at the Centre for Inflammation Research/Institute for Regeneration and Repair/Deanery of Clinical Sciences/Medical School, University of Edinburgh. Principal Investigator: Professor Manu Shankar-Hari Deadline; March 16, 2022 This post is an excellent opportunity for a talented and ambitious individual to work as part of a multidisciplinary team characterising the immune responses in adult critically ill patients. The Shankar-Hari group focuses on combining deep immune phenotyping of clinical cohorts and targeted biological experiments to better understand immune networks of critical illness, with the goal of translating immune network insights into treatments. Professor Shankar is positioned in the Center for Inflammation Research (CIR), where a large number of researchers apply peer-reviewed interdisciplinary research programmes in a strong collaborative multidisciplinary environment, to characterise and manipulate key control points in inflammation across the spectrum of acute and chronic inflammation. The CIR aims to characterise what promotes health and resilience in order to prevent the harmful consequences of inflammation in clinical medicine. For details see (link to advert); https://elxw.fa.em3.oraclecloud.com/hcmUI/CandidateExperience/en/sites/CX_1… Perhaps it is also possible to add Prof. Shanhar to the bbc list for future communication? Thanks upfront! Debby Bogaert, CIR, University of Edinburgh The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336. Is e buidheann carthannais a th’ ann an Oilthigh Dhùn Èideann, clàraichte an Alba, àireamh clàraidh SC005336.

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Vacancy IB2 in Brussels
by Tom Lenaerts 14 Mar '22

14 Mar '22

Postdoctoral bioinformatics position at the Interuniversity institute of Bioinformatics in Brussels We are recruiting a postdoctoral researcher to join our Oligogenic Group at the Interuniversity Institute of Bioinformatics in Brussels (IB)2. The researcher will work on the development and application of statistical and machine learning methods relevant to whole genome analysis to detect pathogenic modifiers associated with oligogenic diseases. This research continues the work conducted in the oligogenic team on the Variant Combinations Pathogenicity Predictor work (https://doi.org/10.1073/pnas.1815601116 <https://doi.org/10.1073/pnas.1815601116>), as well as its associated developments, like ORVAL (http://orval.ibsquare.be <http://orval.ibsquare.be/>). Specific research directions in this context can be discussed yet certain deliverables need to be reached within the context of the project (G4BXL, funded by Innoviris) on which this position is opened. The postdoc position in this project concerns the detection of pathogenic modifiers in Marfan syndrome using a cohort of patients. One of the responsibilities is also to collaborate with technical support staff on the transfer of the ORVAL platform to a professional cloud environment hosted by the company FairGX and the Foundation 101 Genomes (http://f101g.org <http://f101g.org/>). The position is in the context of the Interuniversity Institute of Bioinformatics in Brussels (http://www.ibsquare.be <http://www.ibsquare.be/>) and the ULB Machine Learning group (http://mlg.ulb.ac.be <http://mlg.ulb.ac.be/>), under the supervision of professor Tom Lenaerts and in collaboration with Dr. Sofia Papadimitriou (Université Libre de Bruxelles), the PhDs working on this topic and the other partners of the G4BXL project, including the company FairGX. The position is available for 2 years. The position will be closed as soon as a suitable candidate is found. How to apply Persons interested in this position should send a CV, publication list, motivation letter and 3 reference letters to Tom.Lenaerts(a)ulb.be <mailto:Tom.Lenaerts@ulb.be>. We kindly ask to make it explicitly clear in the motivation letter which of the skills listed below fit your profile. Requested profile The ideal candidate has a PhD degree in computer science or related field, with prior expertise in data science, machine learning, bioinformatics or genetics to be a plus. The candidate has: · The analytical and critical mindset to help design novel machine learning algorithms · Understanding of genetics and their relation to disease · Practical knowledge of machine learning and techniques to make the methods explainable · Familiarity with bioinformatics resources, formats, and general concepts · Experience in writing and maintaining scientific papers · Interest in open-source tools The following skills are a plus: · Familiarity with container technologies such as Docker · Familiarity with Cloud computing architecture The candidate should have the following soft skills: · Good communication and presentation skills · Capable of working independently but with a good team spirit · Good organisational skills · Good knowledge of English is needed to interact with the team · Interest to work in an international environment

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