- BBClist - maillist.psb.ugent.be

Fwd: Master 2 internship (Brest, France)
by Lieven Sterck 09 Dec '19

09 Dec '19

Hi, colleagues in the Ifremer Centre in Brest are looking for a master 2 student to do an internship in genome assembly and annotation of the oyster genome. More info in the attached advert. with kind regards, lieven > From: "Alexandre Cormier" <cormieralexandre(a)gmail.com> > To: "Lieven Sterck" <lieven.sterck(a)psb.vib-ugent.be> > Sent: Friday, 6 December, 2019 16:01:40 > Subject: Master 2 internship

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Workshop CNRS Single-Cell 2020 (Roscoff, France)
by Morgane Thomas-Chollier 05 Dec '19

05 Dec '19

Training : Single-Cell Transcriptomics and Epigenetics: Theory and Practice (sincellTE) // Ecole thématique CNRS Single-Cell 2020 Date : 22 March 2020 – 27 March 2020 Place : Roscoff, France Deadline pre-registration: 15th January 2020 This one-week class focuses on the large-scale study of heterogeneity across individual cells from the genomic, transcriptomic and epigenomic points of view. New technological developments enable the characterization of molecular information at a single cell resolution for large numbers of cells. The high dimensional omics data that these technologies produce comes with novel methodological challenges for the analysis. In this regard, specific bioinformatics and statistical methods have been developed in order to extract robust information. This course is directed towards engineers and researchers who regularly need to undertake single-cell data analysis as well as PhD Student and Post Doc in computational biology or bioinformatics that are interested in the development of methods and pipelines for highly dimensional single-cell data analysis. A wide range of single-cell topics will be covered in lectures, demonstrations and practical classes. Among others, the areas and issues to be addressed will include the choice of the most appropriate single-cell sequencing technology, the experimental design and the bioinformatics and statistical methods and pipelines. Requirements : Understanding of bioinformatics tools and pipelines for next generation sequencing data (RNA-seq or Hi-C or ATAC-seq bulk). Participants must have prior experience on NGS data analysis with everyday use of R and good knowledge of Unix command line. It is not necessary to have personal single-cell data to analyse. All information and pre-registration: https://www.france-bioinformatique.fr/en/evenements/ecole-single-cell-2020 Share our leaflets: English : https://www.france-bioinformatique.fr/sites/default/files/Plaquette_sincell… French : https://www.france-bioinformatique.fr/sites/default/files/Plaquette_sincell…

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message for BBC mailing list
by Puck Knipscheer 04 Dec '19

04 Dec '19

Hi, The research groups of Juan Garaycoechea and Puck Knipscheer at the Hubrecht Institute in Utrecht have a position available for a bioinformatician. Attached you will find the advertisement. Would it be possible to post this on the BBC list? Many thanks, Puck -- Puck Knipscheer Group leader, Hubrecht Institute Oncode Institute Hubrecht Institute Uppsalalaan 8 3584 CT, Utrecht The Netherlands Phone: +31(0)30-2121 875 Email: p.knipscheer(a)Hubrecht.eu<applewebdata://B6A43367-B3E9-4EE4-9FAF-EDD3ECC44A9C/p.knipscheer@Hubrecht.eu>

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Postdoc position:
by Lodewyk Wessels 03 Dec '19

03 Dec '19

POSTDOC POSITION: Mapping cellular regulation from 130 genome-wide phenotype screens Are you a computational biologist with a fascination for cellular regulation? This project is a unique opportunity to unravel cellular regulation and discover new biology and therapeutic strategies. THE PROJECT Human cells perform highly complex tasks but the map of cellular regulation that controls these processes is surprisingly poorly known. In diseases, these processes are disturbed and targeted interference is required to rebalance disease. Such interference can only result in effective disease eradication with minimal side effects when the map of cellular regulation is known in sufficient detail. We will employ Phenosaurus, a large collection ~130 genome-wide haploid screens and advanced computational inference to reconstruct this map. Phenosaurus is a genotype to phenotype map that contains the strength of association between every gene and 130 (phopho)protein readouts in HAP1 cells. We envisage charting the regulatory map using two approaches. First, we will identify functional units. We will determine gene-gene similarity based on Phenosaurus phenotypic profiles and fuse these similarities with independent co-data sources such as protein-protein interaction maps, co-expression maps and gene ontologies to identify high confidence functional units (complexes and pathways). Second, we will identify regulatory interactions between functional units and genes. As many associations in Phenosaurus are indirect i.e. mediated by e.g. ‘master regulators’, we will employ network inference approaches, such as the PC algorithm, guided by co-data sources to identify (master) regulators and their associated interactions. High confidence predictions emerging from these analyses, such as protein complex or pathway membership (first approach) and new putative regulatory interactions with master regulators (second approach) will be validated experimentally. Importantly, this project provides the opportunity to develop novel computational approaches associated with data fusion, network inference and effective application of co-data. YOUR WORKING ENVIRONMENT You will research and benchmark the latest algorithms, develop new algorithms and help design validation and follow-up experiments. You will be working closely with fellow computational scientists of the Wessels group (ccb.nki.nl) experimentalists in the Brummelkamp group and scientists of Scenic Biotech BV (scenicbiotech.com) a biotech startup. You will be part of the Netherlands Cancer Institute (NKI), a world-class cancer research institute residing under the same roof as the Antoni van Leeuwenhoek cancer hospital in the vibrant city of Amsterdam. The NKI provides an open, lively and stimulating environment with access to top-notch facilities, including high-performance computing and with many opportunities to interact with colleagues at social events, attend high-quality seminars and perform translational research. WHAT WE ARE LOOKING FOR: Highly motivated postdocs with: - A degree or advanced skills in bioinformatics, or a related discipline - A degree or a high level of proficiency in (molecular) biology - Proficiency in R, Python and data base management - Experience in interacting with molecular biologists INTERESTED? Please send applications by email to Lodewyk Wessels and use “#application #postdoc” in the subject line. Include a CV, motivation letter and the names and contact information of at least two references in your application. DEADLINE: 20 January 2020

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VITO is hiring an OMICS DATA SCIENTIST!
by Bogaerts Elien 30 Nov '19

30 Nov '19

[cid:image001.jpg@01D5A756.B53D57E0] VITO is an independent Flemish research organisation in the area of cleantech and sustainable development. We are looking for an OMICS DATA SCIENTIST to help accelerate the transition to a sustainable world. Want to know more? Visit our jobsite: https://vito.be/en/jobs/rd-professional-omics-data-scientist! [cid:image003.jpg@01D5A756.B53D57E0] Kind regards, Elien Bogaerts HR business partner VITO NV | Boeretang 200 | 2400 Mol Phone tel:+3214335308 [vito_logo]<http://vito.be/> Vision on technology for a better world [cid:image002.png@01D35939.31B2DD90]<https://www.facebook.com/VITObelgium> [cid:image003.png@01D35939.31B2DD90] <https://twitter.com/VITObelgium> [cid:image004.png@01D35939.31B2DD90] <https://www.linkedin.com/company/vito> [cid:image005.png@01D35939.31B2DD90] <https://vimeo.com/vitovideo> Indien u VITO Mol bezoekt, hou aub er dan rekening mee dat de hoofdingang voortaan enkel bereikbaar is vanuit de richting Dessel-Retie, niet vanuit richting Mol, zie vito.be/route.<http://www.vito.be/route> If you plan to visit VITO at Mol, then please note that the main entrance can only be reached coming from Dessel-Retie and no longer coming from Mol, see vito.be/en/contact/locations.<http://www.vito.be/en/contact/locations> VITO Disclaimer: http://www.vito.be/e-maildisclaimer

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Try again! Sysadmin Vacancy at the University of Edinburgh, SBS
by MEDD Nathan 28 Nov '19

28 Nov '19

Sorry the link bellow does not work: please use this one instead! https://www.vacancies.ed.ac.uk/pls/corehrrecruit/erq_jobspec_version_4.jobs…<https://www.google.com/url?q=https%3A%2F%2Fwww.vacancies.ed.ac.uk%2Fpls%2Fc…> Thanks Nathan Medd On 28/11/2019 09:57, Nathan Medd wrote: Dear all Please share this vacancy for a systems administrator here at the University of Edinburgh's School of Biological Sciences to any relevant parties. https://www.vacancies.ed.ac.uk/pls/corehrrecruit/erq_jobspec_version_4.disp… Thank you! Nathan Medd -- Training and Outreach Manager - Edinburgh Genomics ======================================================== Edinburgh Genomics' Privacy Notice can be viewed at: http://genomics.ed.ac.uk/about-us/privacy-notice This email and any attachments are confidential and intended solely for the use of the recipient(s) to whom they are addressed. If you have received it in error, please destroy all copies and inform the sender. ======================================================== -- Training and Outreach Manager - Edinburgh Genomics ======================================================== Edinburgh Genomics' Privacy Notice can be viewed at: http://genomics.ed.ac.uk/about-us/privacy-notice This email and any attachments are confidential and intended solely for the use of the recipient(s) to whom they are addressed. If you have received it in error, please destroy all copies and inform the sender. ======================================================== The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336.

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Bioinformatics research scientist in Bordeaux, France - Single Cell RNAseq of innate immune cells
by Nikolski Macha 28 Nov '19

28 Nov '19

Dear colleagues, A post-doctoral position (18 months, extendable) is available to work jointly in the ImmunoConcept (UMR 5164) and the Bordeaux Bioinformatics Center in Bordeaux, France, under the supervision of Dr. Maya Saleh and Dr. Macha Nikolski. The research project consists in developing methods and analyzing human samples by single cell RNA sequencing for mapping of the innate immune cells associated with the response to immunotherapies and the functional microbiome linked to the control of cancers. Cover letter, CV and references contacts may be directed to Maya Saleh and Macha Nikolski, msaleh(a)immuconcept.org <mailto:msaleh@immuconcept.org> and macha.nikolski(a)u-bordeaux.fr <mailto:macha.nikolski@u-bordeaux.fr>. Best regards, Macha Nikolski -- Head of Bordeaux Bioinformatics Center Research Director IBGC / CNRS CBiB - Université Bordeaux 146, rue Léo Saignat, 33076 Bordeaux www : http://www.labri.fr/perso/macha/ <http://www.labri.fr/perso/macha/> tel : +33 (0)5 57 57 12 47

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"Making microscopy data FAIR: Why? What? How?" 10 December 2019, Delft
by Celia van Gelder 28 Nov '19

28 Nov '19

On behalf of Marta Teperek: --------------------- "Making microscopy data FAIR: Why? What? How?" by Katy Wolstencroft from the Leiden Institute of Advanced Computer Science and Bernd Rieger from TU Delft. Abstract Why would you want to share microscopy data? There are multiple reasons for this. First, storing and finding large image databases from a heterogeneous group of scientists can be very challenging, especially if they work at multiple locations. Second, to make research more efficient: if microscopy data was more findable and accessible, this could facilitate a broad range of scientists to make ground-breaking discoveries. So what do you need to this happen and how would you do it? The platform Wolstencroft and Rieger have in mind will not only provide coordinated access to cutting-edge imaging technologies but also solutions and training for FAIR data. They like also to discuss the challenges encountered and suggestions for other communities which would like to make their data more FAIR (Findable, Accessible, Interoperable, Re-usable). Date and location: * Tuesday 10 December, 16.00 - 17.30 * Hall 10, Pulse, TU Delft Read more and register: https://www.eventbrite.com/e/making-microscopy-data-findable-accessible-inte roperable-and-re-usable-why-what-how-tickets-77976663299 <https://urldefense.proofpoint.com/v2/url?u=https-3A__www.eventbrite.com_e_m aking-2Dmicroscopy-2Ddata-2Dfindable-2Daccessible-2Dinteroperable-2Dand-2Dre -2Dusable-2Dwhy-2Dwhat-2Dhow-2Dtickets-2D77976663299&d=DwMFAg&c=XYzUhXBD2cD- CornpT4QE19xOJBbRy-TBPLK0X9U2o8&r=hKqBgYpLFT3VvRo617g6QTQcQhJ57CCknXTWyYLImu 4&m=Gc8XUfkmsyU35ut6ErwEWkervuyvtcxEm93S76HQi7E&s=Yn_0o1jwr87mQve3IbvukSmtAI wi4qjlhWTpcvn3zJ4&e=> Best wishes, Marta, on behalf of all the organisers Marta Teperek, PhD TU Delft Library | Research Data Services | Data Stewardship Coordinator M +31 (0) 63 40 81 427 | m.teperek(a)tudelft.nl <mailto:m.teperek@tudelft.nl> | @martateperek <https://urldefense.proofpoint.com/v2/url?u=https-3A__twitter.com_martateper ek&d=DwMFAg&c=XYzUhXBD2cD-CornpT4QE19xOJBbRy-TBPLK0X9U2o8&r=hKqBgYpLFT3VvRo6 17g6QTQcQhJ57CCknXTWyYLImu4&m=Gc8XUfkmsyU35ut6ErwEWkervuyvtcxEm93S76HQi7E&s= 2JVgGCKBIueToxzMsHYbU8hMtp8AitLPhzSfqWOSzJU&e=> My calendar is <http://webmail.tudelft.nl/owa/calendar/M.Teperek@tudelft.nl/Calendar/calend ar.html> available online

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PhD Position Utrecht : Machine learning, genome, transcriptome, neurological disease
by Kenna, K.P. 25 Nov '19

25 Nov '19

Dear all, We are looking to a fill a 4year PhD position exploring new strategies to interpret large scale whole genome sequencing of patients afflicted by amyotrophic lateral sclerosis. Project Title: Machine learning to integrate genome, transcriptome and patient outcome in neurological disease. Brief description below with extended details in the attachment. Please feel free to forward my contact details to any interested parties. Many thanks! Kevin Kenna Description: Work to decode the genetics of amyotrophic lateral sclerosis (ALS), a devastating neurological disease that strikes 1 in 300 people. You will contribute to analyses of one of the largest genetic datasets in the world and combine the state of the art in machine learning, computational genetics and multi-omic profiling of human tissue. Kevin Kenna, PhD | assistant professor | University Medical Center Utrecht | UMC Utrecht Brain Center | Department of Neurology | room Str.5.227 | Universiteitsweg 100, 3584 CG Utrecht, The Netherlands | T +31 (0)88 75 68877 ------------------------------------------------------------------------------ De informatie opgenomen in dit bericht kan vertrouwelijk zijn en is uitsluitend bestemd voor de geadresseerde. Indien u dit bericht onterecht ontvangt, wordt u verzocht de inhoud niet te gebruiken en de afzender direct te informeren door het bericht te retourneren. Het Universitair Medisch Centrum Utrecht is een publiekrechtelijke rechtspersoon in de zin van de W.H.W. (Wet Hoger Onderwijs en Wetenschappelijk Onderzoek) en staat geregistreerd bij de Kamer van Koophandel voor Midden-Nederland onder nr. 30244197. Denk s.v.p aan het milieu voor u deze e-mail afdrukt. ------------------------------------------------------------------------------ This message may contain confidential information and is intended exclusively for the addressee. If you receive this message unintentionally, please do not use the contents but notify the sender immediately by return e-mail. University Medical Center Utrecht is a legal person by public law and is registered at the Chamber of Commerce for Midden-Nederland under no. 30244197. Please consider the environment before printing this e-mail.

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VIB Applied Bioinformatics Conference 2020 - deadline abstract 2-12-2019
by Alexander Botzki 25 Nov '19

25 Nov '19

Dear All, I would like to let you know that the deadline for the abstracts (2/12/2019) for our VIB Applied Bioinformatics Conference 2020 is approaching fast. More information and the submission details could be found here: https://www.vibconferences.be/events/applied-bioinformatics-in-life-science… Thanks a lot for your consideration. Best regards, Alex Alexander Botzki - Head of VIB Bioinformatics Core | Training Coordinator ELIXIR-BE VIB Bioinformatics Core Rijvisschestraat 126, 9052 GENT, Belgium | +32 9 248 16 00 www.bits.vib.be<http://www.bits.vib.be/> | @vibbioinfocore | https://corefacilities.vib.be<https://corefacilities.vib.be/<https://corefacilities.vib.be%3Chttps/corefacilities.vib.be/>> Alexander Botzki - Head of VIB Bioinformatics Core | Training Coordinator ELIXIR-BE VIB Bioinformatics Core Rijvisschestraat 126, 9052 GENT, Belgium | +32 9 248 16 00 www.bits.vib.be<http://www.bits.vib.be/> | @vibbioinfocore | https://corefacilities.vib.be<https://corefacilities.vib.be/> [signatureFooter (002)]

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