July 2022 - BBClist - maillist.psb.ugent.be

PhD position in Integrating of multiple -omics datasets
by Claesen Jürgen 04 Jun '24

04 Jun '24

Dear all, SCK CEN and UHasselt are looking for candidates for a PhD project with the title: "Integromics - Towards integration of big biomolecular data to enable systems biology" Description The last decades, development of high-throughput technologies such as next-generation sequencing, microarrays and mass spectrometry has led to a paradigm shift in biology and life sciences. Where previously one biomolecule (for example, a gene, or a protein) was studied as a single entity, these experimental techniques allow to study a set of biomolecules (for example, the genome or the proteome) in one go and in a limited amount of time. While, at first, experiments were analyzed independently from each other, combining information of several experimental techniques, and correlating them with environmental and/or clinical parameters, is, nowadays, of great interest. As a consequence, novel statistical and computational methodologies for the analysis of multi-omics datasets have to be developed, allowing a multi-dimensional view on complex biological processes. In this PhD project, we aim at the development of computational methods for the analysis of multi-omics datasets, that are commonly generated by the three biology units of SCK*CEN, which will improve the understanding and valorization of the data, and which will keep the biology units up to date with current developments in biology and bioinformatics. Profile and diploma As a doctorate researcher you will join the dynamic bioinformatics team at SCK CEN and CenStat (UHasselt). A successful candidate should have : * A master degree in biostatistics/applied statistics/bioinformatics/statistical bioinformatics. * You are acquainted with statistical methodologies and had exposure to computer programming in SAS/R/Winbugs/Python. * You can work independently and within a team. * You have excellent communication skills. * You are interested to develop new methodology from both theoretical and applied aspects. * You enjoy working in a multidisciplinary and multicultural environment. * You are willing to closely collaborate with biologists/biostatisticians. * You speak and write English fluently. * You have work experience with at least two different "omics" platforms. For more information contact: Dr. Claesen Jürgen (SCK-CEN), jclaesen(a)sckcen.be<https://academy.sckcen.be/en/Mailform?contactid=b22040b5-cf18-496f-a82a-3bc…> Prof. Shkedy Ziv (Hasselt University), ziv.shkedy(a)uhasselt.be<https://academy.sckcen.be/en/Mailform?contactid=51ae7733-8006-4347-b211-9a4…> Link to the project in SCK-CEN: https://academy.sckcen.be/en/Your_thesis_internship/AllTopics/Integromics--… Kind Regards, Jürgen

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Permanent position of Scientist in Modelling and Systems biology at Gencovery
by Karoline Faust 10 Aug '22

10 Aug '22

Permanent position of Scientist in Modelling and Systems biology * Company: Gencovery SAS * Website: https://gencovery.com * Starting date: Sept 2022 * Contact: D. A. Ouattara, douattara(a)gencovery.com<mailto:douattara@gencovery.com> Description of the company GENCOVERY is a software company based in Lyon (France) which develops a collaborative AI software to accelerate bioengineering and bioproduction processes of biotechnology and pharmaceutical companies. The developments of the company are focused on two axes: * - a collection of algorithms for the construction and simulation of cell metabolic models, and * - a collaborative software suite, ConstellabTM, designed to handle complex omics data and analytical pipelines. Generated in silico models, called digital twins of cell metabolism, can be used to simulate experiments, and assess biological hypothesis, thereby significantly shortening time and cost of in vivo and in vitro experiments. The company is looking today for a talented scientist in systems biology and cell metabolism modelling to develop and manage its modeling pipelines. Required qualifications * You have a PhD in systems biology and/or bioinformatics * You have a strong expertise in the modelling of cell metabolism, modelling of the metabolism of microbial communities (e.g. whole-genome metabolic modelling, metabolic network reconstruction, flux balance/variability analysis, cell metabolic interactions, keystone species analysis, etc.). Gencovery, SAS – 47 Boulevard du 11 Novembre 1918, 69100 Villeurbanne, https://gencovery.com Connecting people through innovation [page2image38214352] * You have a good experience in the analysis of omics data (e.g. genomics, transcriptomics, proteomics, metabolomics data). * You have a good experience on standard bioinformatics tools and databases: o Python, R, Jupyter lab, o Biopython, Scikit-learn, Pandas, o Reference Fluxomics / FBA toolboxes (e.g. OpenCobra) o NCBI databases, EMBL-EBI databases, Kegg, BioCyc, etc. o BioModels, BiGG, Agora databases, etc. Missions * You will be in charge of developing the in-house bioinformatics and modeling pipelines that will feed our portfolio of analytics methods. * You will be accountable of the execution and delivery of the bioinformatics analyses to our clients (data integration and curation, modelling and simulation, reporting). * Your will be in charge of the supervision of bioinformaticians and students. Working place Gencovery technologies are designed for collaborative remote work. This is important for next-generation research and development with the COVID-19 pandemic. Gencovery has therefore decided to encourage and develop remote work for its own employees. The recruited candidate must be autonomous and committed to quality reporting. She/He will have the opportunity to be based outside Lyon during the first 3 months but is expected to move to Lyon after. Closing application date: 31 Aug. 2022 Position type: Permanent position Salary: Attractive with career evolution opportunities To apply for this position, please send a resume and cover letter to: douattara(a)gencovery.com<mailto:douattara@gencovery.com>

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Postdoc position in Ireland available
by Claesson, Marcus 28 Jul '22

28 Jul '22

Hi all, A PostDoc position is available in my lab to investigate the role of the microbiome in inflammatory bowel disease. Search 058831 on http://ore.ucc.ie for full details. Closing date 1st Sept. Regards, Marcus -- Marcus J. Claesson, PhD Associate Professor in Bioinformatics School of Microbiology & APC Microbiome Ireland University College Cork Western Road, Cork, Ireland Tel: +353-(0)21-4901390 Email: m.claesson(a)ucc.ie<mailto:m.claesson@ucc.ie> http://orcid.org/0000-0002-5712-0623

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Postdoctoral postion bioinformatics in Brussels
by Tom Lenaerts 28 Jul '22

28 Jul '22

We are recruiting a postdoctoral researcher to develop, in collaboration with the Oligogenic Team at (IB)2, novel methods to predict the effect of combinations of variants in disease phenotypes, and more precisely discerning pathogenic modifications associated with known disease-causing genes. This research builds 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/>). The position would be 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. The position will be closed as soon as a suitable candidate is found. Detailed information via EurAxess: https://euraxess.ec.europa.eu/jobs/697360 <https://euraxess.ec.europa.eu/jobs/697360> More information, contact Tom.Lenaerts(a)ulb.be <mailto:Tom.Lenaerts@ulb.be>

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INSPIRE Postdoctoral Fellowship Programme
by Thinnes, Cyrille 26 Jul '22

26 Jul '22

Dear all, At the Molecular Systems Physiology group<https://www.thielelab.eu/> at NUI Galway we hereby present an opportunity for talented postdoctoral fellows to conduct biocomputational research in human-microbiome interactions in the context of food systems and health for societal impact. INSPIRE is a Horizon 2020 Marie Skłodowska-Curie Actions (MSCA) postdoctoral fellowship programme for intersectoral training, career development, and mobility. INSPIRE will offer 20 fellowship positions for incoming postdocs to focus on Microbiome and the Sustainable Development Goals aimed at tackling global societal challenges related to food systems and health. INSPIRE will fund 20 two-year prestigious postdoctoral fellowships for incoming mobility at APC Microbiome Ireland and participating host institutions, also including NUI Galway. Linked are more information about the INSPIRE programme<https://www.ucc.ie/en/inspire/> and application process<https://www.ucc.ie/en/inspire/apply/>. Best wishes, Cyrille Cyrille Thinnes, MBA, DPhil Engagement Manager for the Virtual Metabolic Human<https://vmh.life/> Research Fellow Molecular Systems Physiology Group University of Galway | Ryan Institute | APC Microbiome Ireland School of Medicine Orbsen Building | Galway, Ireland https://www.thielelab.eu

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Postdoc position @ Aertslab
by Stein Aerts 25 Jul '22

25 Jul '22

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WIVACE 2022 - Paper submission DEADLINE APPROACHING (25 July, 2022)
by Francesco FONTANELLA 22 Jul '22

22 Jul '22

*WIVACE 2022* *XVI International Workshop on Artificial Life and Evolutionary Computation * *Gaeta (LT), Italy* *14-16 **September** 2022* Web site: http://wivace2022.unicas.it/ The International Workshop on Artificial Life and Evolutionary Computation aims at bringing together researchers working in Artificial Life and Evolutionary Computation to present and share their research in a multidisciplinary context. The workshop provides a forum for the discussion of new research directions and applications in these fields, where different disciplines could effectively meet. It was first held in 2007 in Sampieri (Ragusa), as the incorporation of two previously separately running workshops (WIVA and GSICE). After the success of the first edition, the workshop was organized in the following years in Venice (2008), Naples (2009), Parma (2012), Milan (2013), Vietri (2014), Bari (2015), Salerno (2016), Venice (2017) and Parma (2018). Interested authors are invited to contribute papers on theory and applications of Artificial Life, Evolutionary Computation, and complex smart systems. Contributions solicited cover a variety of topics including but not limited to: - Bioinspired Algorithms - Bioinspired Robotics - Coevolution and Collective Behavior - Complex Systems - Data-driven Self-regulating Systems - Evolutionary Computation - Evolutionary Approaches to Big Data and Big Data Streams - Evolutionary Learning Systems - Evolutionary Agents - Modeling and Simulation of Artificial and Biological Systems - Modeling and Simulation of Social and Economical Systems - Modeling of Business Intelligence Systems - Neural Computers - Neuroevolution: Improving Deep Learning with Evolutionary Computation - Self-organizing Cyber-Physical Systems - Socio-inspired Swarm Intelligence Algorithms - Synthetic and Systems Biology - Systems Chemistry - Theories and Applications of Artificial Life *SUBMISSION DETAILS* Contributions may be submitted in one of the following forms: - Full research papers (up to 12 pages). - Simple Abstracts (1-4 pages). Full research papers should present original unpublished work. Simple abstracts should describe original work in progress or a summary of a full paper. The submissions will be peer-reviewed by at least three members of the program committee. The authors of accepted papers or abstracts will have to improve their papers on the basis of reviewers’ comments and will be asked to send a camera-ready version of their manuscripts. At least one author of each accepted work has to register for the conference, attend the conference and present his work. We have contacted Springer to publish the proceedings of Wivace 2022 in Springer's Communications in Computer and Information Science (CCIS) proceedings series, which is abstracted/indexed in DBLP, Google Scholar, EI-Compendex, Mathematical Reviews, SCImago, Scopus. Accepted abstracts describing unpublished work will be considered for publication of extended versions (up to 12 pages) in the same volume. Submission instructions can be found here: http://wivace2022.unicas.it/submission.html *IMPORTANT DATES* Abstract/paper submission deadline: 25 July 2022 (*extended*) Notification of acceptance: 12 August 2022 Early Registration: 22 August 2022 *GENERAL CHAIRS* Claudio De Stefano (University of Cassino and Southern Lazio) - destefano(a)unicas.it Francesco Fontanella (University of Cassino and Southern Lazio) - fontanella(a)unicas.it *CONTACTS* Francesco Fontanella (fontanella(a)unicas.it)

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Researcher Novel Genomics Techologies
by Han Rauwerda 21 Jul '22

21 Jul '22

Dear all, The Dutch Genomics Service & Support Provider (MAD) of the University of Amsterdam, Swammerdam Institute for Life Sciences (SILS) is looking for a Researcher Novel Genomics Techologies: Faculteit/Dienst: Faculteit der Natuurw., Wiskunde & Informatica Opleidingsniveau: Gepromoveerd Functie type: Wetenschappelijk Personeel Sluitingsdatum: 10 augustus 2022 Vacaturenummer: 9860 Introductie Ben jij gefascineerd door de nieuwste DNA en RNA technologieën die aan de basis liggen van de grote wetenschappelijke doorbraken in de Life Sciences? Houd je ervan om deze genomics technologieën op te zetten, te verbeteren en toe te passen in gezamenlijke onderzoeksprojecten met levenswetenschappers? Dan past de positie als onderzoeker Novel Genomics Technologies bij het Swammerdam Institute for Life Sciences (SILS) van de Universiteit van Amsterdam wellicht goed bij jou en gaan we graag met je in gesprek. Binnen het SILS verzorgt de “Dutch Genomics Service & Support Provider (MAD)<http://www.dutchgenomics.nl>” met 9 multidisciplinaire experts sinds 2000 genomics/transcriptomics technologie en bioinformatica implementatie en toepassing voor het onderzoek van wetenschappers binnen en buiten het instituut. De MAD heeft een eigen Illumina DNA/RNA-sequencing systeem plus Oxford Nanopore MinIon platform en beheert een geavanceerde high-performance computing infrastructuur. Recentelijk zijn er belangrijke nieuwe genomics technologieën ontwikkeld zoals eDNA applications, single-cell sequencing, spatial gene expression en image-based in-situ transcriptomics. De MAD is bezig deze revolutionaire technologieën te implementeren en beschikbaar te maken. Wat ga je doen Je gaat een belangrijke rol spelen bij het introduceren van de genoemde genomics technologieën en het toepassen hiervan in genomics/transcriptomics projecten met een externe partij en met onderzoekers van het SILS. Taken en verantwoordelijkheden * Optimaliseren en implementeren van innovatieve genomics technologieën; * Toepassen genomics technologieën via samenwerking in wetenschappelijke projecten; * Samenwerken met analisten en begeleiden van stagestudenten bij lab-experimenten. Wat neem je mee Jouw profiel Je kiest bewust voor een technologie positie in een academische setting. Je bent een teamplayer met een flexibele en sociale instelling. Daarnaast ben je accuraat, zelfstandig en weet je prioriteiten te stellen. Je hebt je zaken altijd goed op orde, ook als het soms tegenzit. Ervaring * Een PhD met aantoonbare praktische genomics/transcriptomics technologie componenten; * Ervaring of affiniteit met de optimalisatie van laboratorium protocollen; * Uitstekende communicatieve vaardigheden in woord en geschrift (Nederlands en Engels); Wat bieden we jou We bieden een tijdelijke arbeidsovereenkomst voor 30-38 uur per week voor een periode van 12 maanden. De gewenste startdatum is 1 oktober 2022. Een verlenging van 12 maanden is mogelijk indien we je functioneren positief beoordelen. Je salaris bedraagt, afhankelijk van relevante werkervaring bij aanvang van het dienstverband, €2.960 tot €4.670 bruto per maand op basis van een volledige werkweek van 38 uur. Dit is exclusief 8 % vakantie- en 8.3 % eindejaarsuitkering. De Cao Nederlandse Universiteiten<http://vsnu.nl/nl_NL/cao-universiteiten.html> is van toepassing. Over ons De Universiteit van Amsterdam<https://www.uva.nl/over-de-uva/over-de-universiteit/over-de-universiteit.ht…> is de grootste universiteit van Nederland, met het breedste opleidingsaanbod. Een intellectueel knooppunt met 30.000 studenten, 6.000 medewerkers en 3.000 PhD kandidaten verbonden door een cultuur van nieuwsgierigheid. Medewerkers van de Faculteit der Natuurwetenschappen, Wiskunde en Informatica<https://www.uva.nl/faculteit/faculteit-der-natuurwetenschappen-wiskunde-en-…> (FNWI) worden gedreven door een gedeelde passie om uit te vinden hoe de wereld in elkaar zit. Onze acht onderzoeksinstituten beslaan de hele breedte van de bètawetenschappen: van astronomie en natuurkunde, tot levens- en aardwetenschappen, moleculaire wetenschappen, wiskunde en de informatiewetenschappen. Of we nu bezig zijn de oorsprong en bouwblokken van het leven te ontrafelen of aan de basis staan van de technologie voor de toekomst, we vinden elkaar in een onbegrensde nieuwsgierigheid. Met zo’n 1.800 medewerkers zetten we ons dagelijks in om onze kennis en nieuwsgierigheid over te brengen aan de ruim 8.000 studenten in de bachelor- en masteropleidingen die we aanbieden op onze Amsterdam Science Park campus. Zo leiden we de volgende generatie van wetenschappers op en inspireren we hen aan de start van hun eigen ontdekkingstocht. Wil je meer weten over werken bij de UvA? Lees meer over werken bij<https://www.uva.nl/over-de-uva/werken-bij-de-uva/werken-bij-de-uva> de Universiteit van Amsterdam. Vragen Voor vragen over de functie kun je tijdens kantooruren contact opnemen met: * Dr. Timo Breit<mailto:t.breit@uva.nl> * T: 020-5257058 Sollicitatie Herken je je in het profiel en ben je geïnteresseerd in de functie, dan zien we je sollicitatie graag tegemoet. Je kunt via onderstaande link online solliciteren. Alle documenten naast je cv ontvangen we graag in één .pdf bestand voor 24 juli 2022. Een cv met weergave in maanden (niet alleen jaren) met betrekking tot opleiding en ervaring; * motivatiebrief; * namen en emailadressen van twee referenten. Als werkgever handhaaft de UvA een beleid van gelijke kansen. We vinden diversiteit belangrijk en zetten ons volledig in om een plek te zijn waar iedereen zich thuis voelt. We koesteren de onderzoekende geest en het doorzettingsvermogen en laten de ruimte om door te vragen. Bij ons vormen nieuwsgierigheid en creativiteit de heersende cultuur. Wij stellen acquisitie niet op prijs ============================================================= Dr. Han Rauwerda, bioinformatician +31 (0)6 50 999 438 MAD - Dutch Genomics Service & Support Provider RB&AB - RNA Biology & Applied Bioinformatics Swammerdam Institute for Life Sciences University of Amsterdam Postbox 94215 1090 GE Amsterdam The Netherlands www.dutchgenomics.nl<http://www.dutchgenomics.nl> www.rnabiology.nl<http://www.rnabiology.nl> Visiting address: Science Park 904, room C2.201 1098 XH Amsterdam The Netherlands =============================================================

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BSC: New vacancies Life Sciences
by Laura Delshams Munoz 21 Jul '22

21 Jul '22

Hello, My name is Laura Delshams, I am part of the HR team at the Barcelona Supercomputing Center - Centro Nacional de Supercomputación. I am contacting you because we have opened four new vacancies in the Life Sciences department, and we would be grateful if you could share these opportunities with your contacts: * Research Engineer - Text Mining (RE2) <https://www.bsc.es/join-us/job-opportunities/27322lstmre2> : 2 vacancies - Deadline 16/09 * Junior Research Engineer - Bioinformatician in Transcriptomics (RE1): <https://www.bsc.es/join-us/job-opportunities/10522lstfgre1> Deadline 16/09 * Team Leader - Health Data Research (R/RE3): <https://www.bsc.es/join-us/job-opportunities/28922lsinbr3>Deadline 16/09 Thank you! -- Laura Delshams /Human Resources - Talent & Development Officer/ *Barcelona Supercomputing Center – Centro Nacional de Supercomputación* <mailto:anais.delastre@bsc.es>Tel. +34- 93 413 40 72<mailto:anais.delastre@bsc.es> <mailto:anais.delastre@bsc.es>laura.delshams(a)bsc.es <mailto:laura.delshams@bsc.es><http://www.bsc.es/> <http://www.bsc.es/>www.bsc.es <http://www.bsc.es/>

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Team Leader - Health Data Research unit
by Eva Alloza 19 Jul '22

19 Jul '22

Dear colleagues, The Barcelona Supercomputing Center (BSC <https://www.bsc.es>) seeks a *team leader to establish a new team on Health Data Research within the **Life Sciences Dept <https://www.bsc.es/discover-bsc/organisation/scientific-structure/life-scie…>* that will collaborate closely with the INB/ELIXIR-ES <https://inb-elixir.es/> units at the BSC. The selected candidate will work on the *acquisition, normalisation and standardisation of Health Research Data*, potentially incorporate new members to the team in the near future, *and drive projects in the area in close collaboration with domain experts in the clinic* (collaborators). The candidate will implement a project to accelerate the potential of biomedical research to advance human health, scaling up and further bringing together two initiatives: (i) at the international data-stewardship level, the European Genome-phenome Archive (EGA); and (ii) at the local health research level, a unique pilot on shared computational infrastructures –known as StarLife– shared between three flagship research centres (BSC, CRG and IRB Barcelona). *Female candidates are especially encouraged to apply.* *Deadline: *The vacancy will remain open until suitable candidate has been hired. Applications will be regularly reviewed and potential candidates will be contacted. Further information on the Job vacancy: https://www.bsc.es/join-us/job-opportunities/28922lsinbr3 Please share as you see fit. Best regards, -- -- Eva Alloza Spanish National Bioinformatics Institute (INB/ELIXIR-ES) coordination node mail:eva.alloza@bsc.es web:http://inb-elixir.es Barcelona Supercomputing Center (BSC-CNS) Pl. Eusebi Güell, 1-3. E-08034 Barcelona, Spain

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