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

Permanent opening in Germany: Data Management Scientist
by Erick Antezana 12 Apr '22

12 Apr '22

** Apologies for cross-posting ** YOUR TASKS AND RESPONSIBILITIES - Construction and maintenance of (biological) ontologies using semantic web technologies, methods and standards - Adaptation and application of checking and editing tools for ontologies - Automation of ontology maintenance tasks in a master data management environment, taking into account the company-wide framework for control and responsibility for data - Carrying out training courses for data stewards with regard to processes and the relevant tools for editing master data - Support for biological data integration, e.g. of genes, traits and organisms, through the design and implementation of algorithms and data models - Support of the data management organization through “insourcing” of external knowledge and standards - Building and maintaining knowledge of external public data sources WHO YOU ARE - Scientific university degree in bioinformatics, computational biology, engineering or any analytical field - Experience in building and maintaining (bio-)ontologies as well as in automatizing ontology maintenance tasks (e.g. using scripts) - Experience with master data management (data stewardship and governance), biological data integration as well as algorithms design and implementation - Experience in semantic web technologies and standards, e.g. with OBO, RDF, OWL, SHACL, ShEx, SPARQL, SKOS - Familiar with graph-based data systems (e.g. triple stores) - Good understanding of ontology editing tools as well as of public resources as gene ontology, plant ontology, traits ontology - High ability to solve problems and to structure and simplify complex tasks and ability to contribute in an international and dynamic research and development team - Fluent in English, both written and spoken https://karriere.bayer.de/en/job/data-management-scientist-m-f-d--SF585221_…

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CFP: AIHA (ICPR2022 workshop) - DEADLINE EXTENDED!
by Nicole Dalia CILIA 12 Apr '22

12 Apr '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). *// S U B M I S S I O N D E A D L I N E \\ \\ E X T E N D E D T O 1 5 MAY !!! **//* 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: May 15th, 2022 (*EXTENDED*) - Notification of Acceptance: June 15th, 2022 - Camera-ready Submission: July 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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ISCB Academy tutorial
by Venkata Pardhasaradhi SATAGOPAM 11 Apr '22

11 Apr '22

ISCB Academy is part of the International Society for Computational Biology (ISCB), which aims to provide training and workshops worldwide. We 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 “Integrating gene expression and biological knowledge for drug discovery and repurposing”, which will be held on the 22nd of April at 8:00am EDT. Description of the Tutorial: Screening for potential cancer therapies using existing large datasets of drug perturbations requires expertise and resources not available to all. This is often a barrier for lab scientists to tap into these valuable resources. To address these issues, one can take advantage of prior knowledge especially those coded in standard formats such as causal biological networks (CBN). Large datasets can be converted into appropriate structures, analyzed once and the results made freely available in easy-to-use formats. In these three parts tutorial, we will give a full description of one large scale analysis of using this approach, one case study of building a network of metastasis suppressors from scratch, and a walkthrough example code to perform and adapt these tools for different use cases. * Part One: a talk describing the construction of a database for cancer-cell-specific perturbations of biological networks (LINPS). We pre-computed cancer-cell-specific perturbation amplitudes of several biological networks and made the output available in a database with an interactive web interface. * Part Two: a talk describing the building of a functional network model of the metastasis suppressor RKIP and its regulators in breast cancer cells. In this case study, we applied text mining and a manual literature search to extract known interactions between several metastasis suppressors and their regulators. Then we adopted a reverse causal reasoning approach to evaluate and prioritize pathways that are most consistent and responsive to drugs that inhibit cell growth. We further validated some of the predicted regulatory links in the breast cancer cell line MCF7 experimentally and highlighted the points of uncertainty in our model. * Part Three: a code walkthrough encoding directed interactions into the biological expression language (BEL), computing the network perturbation amplitudes (NPA), and interpreting the output. Pre-requisites: ● Knowledge of the mechanisms of transcriptional regulation ● Familiarity with high-throughput gene expression data ● Basic knowledge of R and Bioconductor ● Familiarity with Docker and Git (This is only required to execute the code on a local machine) Register 👉 https://www.iscb.org/iscbacademy — Dr. Venkata Satagopam Bioinformatics Core Luxembourg Centre For Systems Biomedicine (LCSB) University of Luxembourg Campus Belval, House of Biomedicine II 6, avenue du Swing L-4367 Belvaux T +352-466-644-6421 F +352-466-644-36421 venkata.satagopam(a)uni.lu<mailto:venkata.satagopam@uni.lu> http://lcsb.uni.lu ----- This message is confidential and may contain privileged information. It is intended for the named recipient only. If you receive it in error please notify me and permanently delete the original message and any copies. -----

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metagenomics postdoc
by Falk Hildebrand (QIB) 11 Apr '22

11 Apr '22

Dear all, We are currently looking for a bioinformatician working on strain resolved metagenomics in Norwich, UK. This post requires an experienced bioinformatician with an interest to study reconstructed microbial genomes in metagenomes (bacterial, archaeal, fungal). The post-holder will be involved in conceptualizing & implementing bioinformatic pipelines to analyse large time-series metagenomes (human gut, soil, …), based on data from 2nd and 3rd gen sequencing platforms, such as illumina, PacBio, ONT, Hi-C & single cell sequencing data. Vacancy: Bioinformatician (earlham.ac.uk)<https://www.earlham.ac.uk/bioinformatician> Kind regards, Dr Falk Hildebrand PI Earlham / Quadram Institute Ext.: 2629 (EI), 5359 (QIB), +44 1603 255359 Norwich Research Park www.falk.science<https://eur01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.falk.s…>

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ECCB2022 | Last days to submit your Proceedings and Highlight Papers | Check out the preliminary programme!
by Eva Alloza 11 Apr '22

11 Apr '22

Dear BBC list, On behalf of the ECCB2022 <https://eccb2022.org> Organising Committee, don't miss this final deadline to submit your manuscript to the Proceedings track, and recently published papers to the Highlight Papers track. Find out more information about the deadlines and calls in the website: https://eccb2022.org/calls Best regards, -- Eva Alloza Training coordinator and support officer 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 ------------------------------------------------------------------------ 21st European Conference on Computational Biology 21st European Conference on Computational Biology <http://mail.eventsairmail.com/ls/click?upn=EU9ggqWL9UGtw-2FWRLoBKrtd8JsjWfs…> The extended submission dedline for Proceedings and Highlight pepers is Thu, 14 April 2022 <http://mail.eventsairmail.com/ls/click?upn=vTVo9WAROVynOTbDemV86EueByyahnvg…> *Thu, 14 April 2022* *Proceedings*: *manuscripts *for publication in the *ECCB2022 proceedings*. The accepted submissions will be published in the journal /Bioinformatics/ and will be presented in conference talks. Read the call <http://mail.eventsairmail.com/ls/click?upn=vTVo9WAROVynOTbDemV86EueByyahnvg…> *Highlight Papers:* submission of*recently published articles* that have generated ground-breaking results. The papers and possible related work will be presented in highlighted talks during the conference. Read the call <http://mail.eventsairmail.com/ls/click?upn=vTVo9WAROVynOTbDemV86EueByyahnvg…> The preliminary programme is out! <http://mail.eventsairmail.com/ls/click?upn=vTVo9WAROVynOTbDemV86IJA1tIvlCbg…> The *preliminary programme is now published* and will be updated regularly. ECCB2022 will include workshops and tutorials within the New Trends in Bioinformatics programme, talks from top keynotes and from delegates submissions, onsite poster sessions and the industry and institutional exhibition. Which sessions are you looking forward to the most? Check the preliminary programme <http://mail.eventsairmail.com/ls/click?upn=vTVo9WAROVynOTbDemV86IJA1tIvlCbg…> Visit our website for more information *ECCB2022.org <http://mail.eventsairmail.com/ls/click?upn=EU9ggqWL9UGtw-2FWRLoBKrtd8JsjWfs…>* #ECCB2022 <http://mail.eventsairmail.com/ls/click?upn=vTVo9WAROVynOTbDemV86I9M5CnW9VF-…> #ECCB2022 <http://mail.eventsairmail.com/ls/click?upn=vTVo9WAROVynOTbDemV86IIhk8LA29p1…> *Organised by:* BSC <http://mail.eventsairmail.com/ls/click?upn=vTVo9WAROVynOTbDemV86NN8S7iAhePN…> INB <http://mail.eventsairmail.com/ls/click?upn=vTVo9WAROVynOTbDemV86ITKzm0FTLx7…> ELIXIR Spain <http://mail.eventsairmail.com/ls/click?upn=vTVo9WAROVynOTbDemV86ITKzm0FTLx7…> Bco Congresos <http://mail.eventsairmail.com/ls/click?upn=vTVo9WAROVynOTbDemV86IZ8Vkhn8oIW…> Facebook <http://mail.eventsairmail.com/ls/click?upn=vTVo9WAROVynOTbDemV86JXpdeYbu-2F…> Twitter <http://mail.eventsairmail.com/ls/click?upn=vTVo9WAROVynOTbDemV86EaVGS8wj4kB…> LinkedIn <http://mail.eventsairmail.com/ls/click?upn=vTVo9WAROVynOTbDemV86LjbR4s-2BPd…> Instagram <http://mail.eventsairmail.com/ls/click?upn=vTVo9WAROVynOTbDemV86FV50uhrxSD-…> Web Site <http://mail.eventsairmail.com/ls/click?upn=vTVo9WAROVynOTbDemV86IZ8Vkhn8oIW…> E-Mail <mailto:congresos@bcocongresos.com> *TECHNICAL SECRETARIAT* Plaza Europa 17-19, 1st floor 08908 L'Hospitalet del Llobregat, Barcelona (Spain) +34 93 882 38 78 eccb2022(a)bcocongresos.com Policy Privacy <http://mail.eventsairmail.com/ls/click?upn=vTVo9WAROVynOTbDemV86IZ8Vkhn8oIW…> | View Browser <http://mail.eventsairmail.com/ls/click?upn=vTVo9WAROVynOTbDemV86F-2F6kFiVgu…>

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Postdoctoral position at the Sanger Institute (near Cambridge, UK) in genetics of autism/neurodevelopmental disorders; Closing Date: 21 April 2022
by Hilary Martin 11 Apr '22

11 Apr '22

Computational postdoctoral fellow in medical genomics https://jobs.sanger.ac.uk/vacancy/computational-postdoctoral-fellow-in-medi… [eur03.safelinks.protection.outlook.com]<https://urldefense.proofpoint.com/v2/url?u=https-3A__eur03.safelinks.protec…> We are seeking a highly motivated postdoctoral fellow to join the Martin group [eur03.safelinks.protection.outlook.com]<https://urldefense.proofpoint.com/v2/url?u=https-3A__eur03.safelinks.protec…> at the Wellcome Sanger Institute, to work on the genetics of autism and developmental disorders. The group investigates the genetic basis of rare and common diseases, as well as population genetic processes that influence the distribution of genetic variation. We currently have projects in the following areas: * The role of both rare and common variants in rare disorders, using data from the Deciphering Developmental Disorders [eur03.safelinks.protection.outlook.com]<https://urldefense.proofpoint.com/v2/url?u=https-3A__eur03.safelinks.protec…> study and the Genomics England 100,000 Genomes project [eur03.safelinks.protection.outlook.com]<https://urldefense.proofpoint.com/v2/url?u=https-3A__eur03.safelinks.protec…> * The genetics of cognitive and behavioral traits, using sequence and genotype data from UK Biobank and from large UK birth cohorts, the Avon Longitudinal Study of Parents and Children [eur03.safelinks.protection.outlook.com]<https://urldefense.proofpoint.com/v2/url?u=https-3A__eur03.safelinks.protec…> , the Millenium Cohort Study, and Born in Bradford [eur03.safelinks.protection.outlook.com]<https://urldefense.proofpoint.com/v2/url?u=https-3A__eur03.safelinks.protec…> * Population genetics and the genetic basis of complex diseases and traits in British South Asian populations, using data from the Genes & Health project [eur03.safelinks.protection.outlook.com]<https://urldefense.proofpoint.com/v2/url?u=https-3A__eur03.safelinks.protec…> This postdoc position is funded through a grant from the Simons Foundation Autism Research Initiative, as part of a large collaborative project investigating the causes of sex differences in autism. The postdoctoral fellow will collaborate closely with colleagues at the Autism Research Centre in Cambridge (Simon Baron-Cohen and Varun Warrier), the Hurles group at the Sanger, and the Autism Sequencing Consortium. The project will entail analysing large-scale exome/genome-sequencing data and genotype data from autism and developmental disorder cohorts (including a new UK-based study, Spectrum10K) and from population-based studies such as ALSPAC and UK Biobank. Salary per annum: £33,272 - £41,709 Contract Length: 2.5 years with possibility of extension Closing Date: 21 April 2022 -- The Wellcome Sanger Institute is operated by Genome Research Limited, a charity registered in England with number 1021457 and a company registered in England with number 2742969, whose registered office is 215 Euston Road, London, NW1 2BE. -- The Wellcome Sanger Institute is operated by Genome Research Limited, a charity registered in England with number 1021457 and a company registered in England with number 2742969, whose registered office is 215 Euston Road, London, NW1 2BE.

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Vacancies: Scientist Bioinformatics & Biostatistician at SkylineDx
by Domenico Bellomo 08 Apr '22

08 Apr '22

Dear All, we are currently looking for a Scientist Bioinformatics, and for a Biostatistician to expand our bioinformatics team at SkylineDx, a molecular diagnostic biotech, based in Rotterdam, Both post holders will be working on discovering new molecular signatures, and translating them into clinically relevant and commercially viable molecular assays, for diagnosis, prognosis and drug effectiveness prediction. More information is available here: https://www.skylinedx.com/jobs/scientist-bioinformatics https://www.skylinedx.com/jobs/biostatistician Best, regards, Domenico Bellomo PhD Director of Bioinformatics [/Users/mariekespaan/Library/Containers/com.microsoft.Outlook/Data/Library/Caches/Signatures/signature_801919664] SkylineDx BV Brainpark II – Building XI Lichtenauerlaan 40 3062ME Rotterdam The Netherlands +31 (0)10 – 72 00 316 [/Users/mariekespaan/Library/Containers/com.microsoft.Outlook/Data/Library/Caches/Signatures/signature_1707320200]<http://skylinedx.com/> [/Users/mariekespaan/Library/Containers/com.microsoft.Outlook/Data/Library/Caches/Signatures/signature_865269257] <https://www.linkedin.com/company/skylinedx-bv/> [/Users/mariekespaan/Library/Containers/com.microsoft.Outlook/Data/Library/Caches/Signatures/signature_604425005] <https://twitter.com/skylinedx>

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CFP: AIHA (ICPR2022 workshop) - DEADLINE EXTENDED!
by Nicole Dalia Cilia 01 Apr '22

01 Apr '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). *// S U B M I S S I O N D E A D L I N E \\ \\ E X T E N D E D T O 1 5 MAY !!! **//* 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: May 15th, 2022 (*EXTENDED*) - Notification of Acceptance: June 15th, 2022 - Camera-ready Submission: July 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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Vacancy: PhD student biomedical data science at Maastricht University
by Adriaens, Michiel (MACSBIO) 01 Apr '22

01 Apr '22

Dear all, We have an opening for a PhD candidate at Maastricht University, on a collaborative project between the department of Human Biology and The Maastricht Centre for Systems Biology: https://www.academictransfer.com/en/310585/phd-candidate-at-fhml-school-nut… The PhD candidate will study liver metabolism in relation to the development of obesity and diabetes by performing analyses on large human datasets. Hence, we are looking for someone with a MSc in biomedical sciences, biomedical engineering, bioinformatics/systems biology or equivalent, with proven interest in the biochemical and functional aspects of nutrition and metabolism, and with experience in statistical data analysis. Please share and forward! Best wishes, Michiel Adriaens [macsbio-logo] [UM-logo] Dr. ir. Michiel E. Adriaens, PhD Assistant Professor Maastricht Centre for Systems Biology - MaCSBio Paul-Henri Spaaklaan 1, 6229 EN Maastricht, The Netherlands T +31433881123 E michiel.adriaens(a)maastrichtuniversity.nl<mailto:michiel.adriaens@maastrichtuniversity.nl>

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