September 2020 - 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

2 1

NERC Bursaries for Edinburgh Genomics Courses
by TRAIN edgenomics-training 02 Mar '22

02 Mar '22

Dear All We are pleased to announce we have a number of bursaries available to cover up-to the full fees of any of our upcoming bioinformatics courses. These bursaries are available to UK based students or researchers funded by the NERC or working on research that falls under the remit of the NERC (https://nerc.ukri.org/research/portfolio/remit/) Bursaries are available for any of our courses (see below) but are available for a LIMITED TIME ONLY: They are available for any course booked BEFORE 27th MARCH. So please don't wait to sign up! Our upcoming courses: Linux for Genomics, 13th March - An introduction to working on the command line, running commands and handling data relevant to bioinformatics. https://genomics.ed.ac.uk/services/linux-genomics R for Genomics, 14-15th March - An introduction to the statistical environment R, taking you from the very basics to writing basic functions and creating beautiful figures with ggplot2 https://genomics.ed.ac.uk/services/r-genomics Introduction to Python for Biologists, 18-22 March - This introductory course gives an overview of the language with an emphasis on practical problem-solving, using examples and exercises drawn from various aspects of bioinformatics work. https://genomics.ed.ac.uk/services/introduction-python-biologists-0 Data Manipulation and Visualisation with Python, 08 - 12 April - Python has a many high-quality libraries for working with scientific data. In this workshop we will see how to leverage these libraries to efficiently work with and visualise large volumes of data. https://genomics.ed.ac.uk/services/data-manipulation-and-visualisation-pyth… Introduction to RNA-seq Data Analysis, 9-10th May - This two-day course takes you through a tried-and-tested workflow for analysing RNA-seq data, from read mapping and QC to differential expression and result visualisation. https://genomics.ed.ac.uk/services/introduction-rna-seq-data-analysis If you think you are provably eligible for one of these bursaries, sign up to your desired course through the link provided and we will be in contact regarding fees. Kind Regards Nathan Medd Training and Outreach Manager - Edinburgh Genomics G.06, Ashworth Laboratories, Charlotte Auerbach Road, The King's Buildings, The University of Edinburgh, EH9 3FL, Edinburgh, Scotland 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.

1 24

Invitation to Lunch seminar Compelling visualisations of your data
by Alexander Botzki 30 Sep '20

30 Sep '20

Dear all, Have a little time after lunch? Learn about creating compelling visualisations of your data with Matthias Stahl @h_i_g_s_c_h<https://twitter.com/h_i_g_s_c_h> in the first of a series of #RSeng<https://twitter.com/hashtag/RSeng?src=hashtag_click> seminars. Save the date for the first seminar: 14 October (https://be-rse.org/seminars<https://t.co/vHrzfUbbyH?amp=1>)! Best regards, Alex on behalf of RSE BE, supported by VIB Bioinformatics Core and ELIXIR Belgium Alexander Botzki - Head of VIB Bioinformatics Core, ELIXIR Belgium Training Coordinator VIB Bioinformatics Core Technologiepark-Zwijnaarde 75 9052 Zwijnaarde Belgium https://vib.be/labs/vib-bioinformatics-core/research | https://www.bits.vib.be | @vibbioinfocore [cid:image002.jpg@01D69770.3A9FA280]

1 0

SW engineer positions available in Agilent Technologies (Ghent)
by michael.vyverman＠agilent.com 30 Sep '20

30 Sep '20

Dear all, Agilent technologies currently has several open positions for the software team in their Ghent office. We are developing a range of innovative, cloud-based software products for the analysis and interpretation of genetic data generated by the company’s test kits. Full stack developer https://recruiting.adp.com/srccar/public/nghome.guid?c=2167807&d=External&p… or https://www.linkedin.com/jobs/view/2011646106 Senior full stack developer https://recruiting.adp.com/srccar/public/nghome.guid?c=2167807&d=External&p… or https://www.linkedin.com/jobs/view/2151288802/ Bioinformatician https://recruiting.adp.com/srccar/public/nghome.guid?c=2167807&d=External&p… or https://www.linkedin.com/jobs/view/2011647046 Best regards, Michaël Vyverman Michaël Vyverman [signature_2132868848]<http://www.agilent.com/home> Software Engineer DGG - Genomics Ghent Agilent Technologies T: +32 9 277 77 13 | www.agilent.com<http://www.agilent.com/>

1 0

FW: Post-doc/PhD position advert - clinical cancer epigenomics - Charite, Berlin
by Lutsik, Pavlo 27 Sep '20

27 Sep '20

Dear all, Please see below an opening for a computational postdoc/PhD student at Berlin Institute of Health and Charite. Best regards, Pavlo From: "Ishaque, Naveed" <naveed.ishaque(a)charite.de> Date: Friday, 25. September 2020 at 10:10 To: "Ishaque, Naveed" <naveed.ishaque(a)charite.de> Subject: Post-doc/PhD position advert - clinical cancer epigenomics - Charite, Berlin Dear all, I hope this email finds you and your families well and healthy. I was hoping that you could reach out to your groups/networks to advertise a position for clinical cancer epigenomics at the Charite in Berlin: https://www.charite.de/service/stellenangebot/angebot/detailinfo/cc04_bih_3… It is a 3 year post-doc (or 4 year PhD) position which will be supporting the software development and maintenance for the nanoDX trail – a Europe wide multi-centric trial for using ultra rapid (<24 hrs), low throughput (<1x genome coverage) to profile the DNA methylome and CNVs of cancer genomes as a basis to diagnose the tumour type. The basis of using DNA methylation for identifying cell or origin is well established, with the most prominent work for cancer being published by Prof David Capper in collaboration with the group of Prof Stephan Pfister (Capper et al, Nature 2018, https://doi.org/10.1038/nature26000) This methodology was further adapted by using nanopore profiling instead of methylation arrays as the profiling assay, reducing the pipeline time from weeks to hours (Euskirchen et al, Acta Neuropath. 2017, https://doi.org/10.1007/s00401-017-1743-5) This adaptation has shown promise for use in clinical routine and a Europe wide multi-centric trial has just started. This position is shared between the department of Prof Roland Eils (Computational Oncology group, led by Naveed Ishaque) and Dr Philipp Euskirchen at Charite, with a focus on bioinformatics. The major expectation is to maintain and further develop the existing software used in the clinic, with strong prospects for research potential. Further details can be found in the link, and candidates should enquire for further details and/or submit applications to Naveed.ishaque(a)charite.de<mailto:Naveed.ishaque@charite.de> or Philipp.euskirchen(a)charite.de<mailto:Philipp.euskirchen@charite.de>. Kind regards and all the best, Naveed

1 0

PhD position in BIOINFORMATIC ANALYSIS OF WHOLE-GENOME DATA FOR PERSONAL HEALTH
by Gokhan Ertaylan 23 Sep '20

23 Sep '20

Dear All, We are looking for a suitable Ph.D. candidate for the position "*BIOINFORMATIC ANALYSIS OF WHOLE-GENOME DATA FOR PERSONAL HEALTH*". The Ph.D. candidate will join our group consisting of other PhDs and data scientists with complementary backgrounds. The position is part of a joined applied research project between the University of Hasselt and VITO. https://vito.be/en/jobs/phd-position-bioinformatic-analysis-whole-genome-da… Please feel free to distribute this in your networks. Best Regards, -- Gökhan Ertaylan, PhD

1 0

MEIJER POTATO ZOEKT EEN BIOINFORMATICUS / DATA- EN ANALYSE-EXPERT
by Han Rauwerda 23 Sep '20

23 Sep '20

MEIJER POTATO ZOEKT EEN BIOINFORMATICUS / DATA- EN ANALYSE-EXPERT We zijn als familiebedrijf sinds 1920 actief in aardappelen, wereldwijd één van de meest genuttigde voedingsgewassen. De gevolgen van wereldtrends als bevolkings- en welvaartsgroei en klimaatverandering geven richting aan ons veredelingsprogramma. Dat zet in op versnelde groei in opbrengst, kwaliteit en duurzame teelt. Daarbij gebruiken we de nieuwste technologie en kennis. Ons gefocuste assortiment bestaat uitsluitend uit hoogwaardige aardappelrassen die specifieke segmenten of behoeften aanspreken. We werken samen met de Genomics Service en Support Provider van de Universiteit van Amsterdam (UvA) op het gebied van bioinformatica analyse. Gezamenlijk onderzoeken we genomische markers voor fenotypische eigenschappen zoals opbrengst of droogtetolerantie. Kruisingsexperimenten, grootschalige DNA en RNA sequencing technologieën en innovatieve bioinformatica methodes combineren we in toegepast onderzoek. Binnen deze unieke samenwerking zoeken wij een: Bioinformaticus / Data- en analyse-expert (32-40 uur) Jij wordt de verbindende schakel tussen Meijer Potato, waar je in dienst treedt, en de UvA Genomics Service en Support Provider. Je R&D collega's bij Meijer Potato maken je wegwijs binnen de organisatie, ons werkveld en onze sector. Experts in bioinformatica methode ontwikkeling en data-analyse van de UvA Genomics Service en Support Provider begeleiden je in jouw dagelijks werk. Jouw standplaats wordt Amsterdam, Genomics Service en Support Provider, Science Park 904 te Amsterdam. Wat ga je doen? * Ontwikkelen van toegepaste bioinformatica methoden. * Uitvoering van complexe bioinformatica analyses. * Organisatie van dry-lab experimenten. * Informatie-uitwisseling tussen beide organisaties. Wat heb je hier voor nodig? * Een MSc/BSc bioinformatica opleiding (HBO/WO) of werkervaring op een vergelijkbaar niveau. * Ervaring met Linux/command line. * Voldoende inzicht in toegepaste statistiek en/of machine learning. * Affiniteit met plantenveredeling. * Goede communicatieve eigenschappen. Wat hebben wij jou te bieden? Jij draagt je eigen steentje bij in een sector die ertoe doet wereldwijd. Wij bieden je een marktconform salaris, goede secundaire voorwaarden en uitstekende opleidings- of specialisatiemogelijkheden. Je krijgt een aanstelling voor 2 jaar. Daarna heb je zicht op een vaste aanstelling bij Meijer Potato. Meer informatie Voor meer informatie over deze functie kun je contact opnemen met manager R&D Guus Heselmans, via tel 0113-760100. Jouw sollicitatie kun je mailen naar Kim van Walsum<mailto:kimvanwalsum@meijerpotato.com>. Bekijk deze vacature in het Engels / View this vacancy in English: https://www.meijerpotato.com/en/vacancies-/data-and-analysis-expert/

1 0

CFP: AIHA 2020 – International Workshop on Artificial Intelligence for Healthcare Applications
by Nicole Dalia CILIA 23 Sep '20

23 Sep '20

[image: logoAHIA.PNG] *CALL FOR PAPERS* International Workshop on Artificial Intelligence for Healthcare Applications (AIHA 2020) http://lia.unicas.it/AIHA2020 The workshop will be held on *January 10*, *2021* in conjunction with *ICPR 2020* <https://www.micc.unifi.it/icpr2020/> (25th International Conference on Pattern Recognition, Milan, Italy, January 10-15, 2021). 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 *INVITED SPEAKER * Nico Karssemeijer <http://lia.unicas.it/AIHA2020/invited.html>, Co-chair of DIAG <http://diagnijmegen.nl/index.php/Home> at Radboud UMC, Founder of ScreenPoint <https://screenpoint-medical.com/> Co-founder of Volpara <https://www.matakina.com/> Professor of Computer-Aided Diagnosis, Radboud University Nijmegen, Netherlands. *DATES * - Paper Submission: October 1, 2020 - Notification of Acceptance: November 10, 2020 - Camera-ready Submission: November 15, 2020 *SUBMISSIONS * Submissions must be formatted in accordance with the Springer's Computer Science Proceedings guidelines (Guidelines <https://www.springer.com/gp/computer-science/lncs/conference-proceedings-gu…>). Two types of contribution will be considered: - Full papers (12-15 pages, including references) - Short papers (6-8 pages, including references) Accepted manuscripts will be included in the ICPR 2020 Workshop Proceedings Springer volume. Once accepted, at least one author is expected to attend the event and orally present the paper. Submission instructions are available here <http://lia.unicas.it/AIHA2020/submission.html>. The submission platform is available here: EasyChair <https://easychair.org/conferences/?conf=aiha2020> *CHAIRS * Alessandro Bria, Nicole Dalia Cilia, Francesco Fontanella, Claudio Marrocco University of Cassino and Southern Lazio, Italy *PROCEEDINGS AND SPECIAL ISSUE* Accepted papers will be published by Springer in the Lecture Notes in Computer Science series (LNCS). We are negotiating with major international journals the publication of a special issue for selected papers presented at the workshop. Contact Information: Nicole Dalia Cilia, nicoledalia.cilia(a)unicas.it

1 0

Bioinformatics job position
by bram.slabbinck＠agilent.com 23 Sep '20

23 Sep '20

Dear all, Agilent Technologies is currently hiring a bioinformatician to strengthen its software team in Ghent, Belgium. If you are interested, please go to https://be.linkedin.com/jobs/view/2011647046 or https://careers.agilent.com/ Best regards Bram Slabbinck

1 0

Postdoc opening at Weill Cornell
by A.Mahfouz＠lumc.nl 23 Sep '20

23 Sep '20

Dear All, Tilgner Lab is currently seeking a highly motivated computational postdoc/research associate to join our collaborative lab at WCMC (the Medical School of Cornell University) in New York City. The work is geared towards algorithm development and data analysis revolving around healthy and diseased brain using single-cell and spatial long-read sequencing. A few representative papers include: 1. https://www.biorxiv.org/content/10.1101/2020.08.27.268730v1 (bioinformatic development of sample comparison using single-cell long-read sequencing and development of slide-isoform sequencing (Sl-ISO-Seq)) 2. https://www.nature.com/articles/nbt.4259 (development of single-cell long-read sequencing using 10x + PacBio/Nanopore applied to early postnatal mouse brain; 2018) 3. https://www.nature.com/articles/nbt.3242 (wetlab and bioinformatic development of Illumina-based long-read sequencing applied to human and mouse adult brain; 2015) 4. https://www.pnas.org/content/111/27/9869.long (bioinformatic development of allele-specific splicing detection from long reads in lymphoblastoid cell lines; 2014) 5. https://www.nature.com/articles/nbt.2705 (development of PacBio for transcriptomics … applied to transcriptome sequencing in multiple human organs; 2013) They are located at Weill Cornell Medical College on Manhattan’s Upper East Side. The university has a nearby postdoc housing program for easier rental in New York City. If you are interested, please send a CV and contact information for referees to tilgnerlab(a)gmail.com. We are eager to talk to you as soon as possible! On behalf of Hagen Tilgner, Cheers, Ahmed Ahmed Mahfouz, PhD | Assistant Professor, Department of Human Genetics Leiden University Medical Center | Dept. of Human Genetics | P.O. Box 9600, 2300 RC Leiden | Postal zone S4-P Room R-04-022 | Phone +31 71 52 69513

1 0