November 2018 - BBClist - maillist.psb.ugent.be

Bioinformatics position available at the Erasmus MC Cancer Computational Biology Center
by Harmen van de Werken 04 Oct '19

04 Oct '19

A bioinformatics position is currently available at the Erasmus MC Cancer Computational Biology Center. http://www.erasmusmc.nl/vacature/?num=21578 Please apply, if you are enthusiastic and eager to improve our knowledge on cancer biology. Harmen van de Werken

2 1

COMPUTATIONAL BIOLOGIST - TUMOR IMMUNOLOGY
by Lodewyk Wessels 25 Jul '19

25 Jul '19

VACANCY COMPUTATIONAL BIOLOGIST - TUMOR IMMUNOLOGY YOUR ROLE WITHIN THE INSTITUTE The research groups of Dr Karin de Visser, dr Marleen Kok and Prof dr Lodewyk Wessels, are looking for a motivated and talented Computational Biologist to join their teams at the Netherlands Cancer Institute (NKI). The Inflammation and Cancer group of dr. Karin de Visser is studying the impact of the immune system on metastatic breast cancer utilizing sophisticated mouse tumor models and state-of-the art ex vivo and in vitro immunological and molecular assays. The lab of de Visser closely collaborates with the translational research group of medical oncologist dr Marleen Kok. The mission of this team is to discover novel mechanisms underlying the crosstalk between breast cancer and the immune system, to optimize immunotherapy for breast cancer patients using novel combination treatments in clinical trials and the discovery of predictive biomarkers. The Computational cancer biology group of Prof dr Lodewyk Wessels is focused on quantifying and understanding treatment response in model systems and patients. To this end we develop bespoke and novel computational methods focusing on data integration and tailored to new technologies. We actively collaborate with many research groups in the NKI and strongly believe in the power of 'team science'. PROJECTS You will be involved in the following projects: 1. MOUSE MODELS FOR METASTATIC ESCAPE FROM IMMUNE CONTROL. To study the causal relationship between immune cells and metastatic breast cancer, we utilize state-of-the art genetically engineered mouse tumor models. We have extensive RNA-sequencing datasets of isolated immune cell populations, as well as RNA-sequencing and exome sequencing data of primary breast tumors and organ-specific metastases from these mouse models. You will be responsible for the computational analyses of the data, and to extract candidate pathways/genes from these datasets that can subsequently be tested in follow up experiments in the lab. Moreover, you will link these pre-clinical data to human datasets. 2. SYSTEMIC AND INTRA-TUMORAL IMMUNOMONITORING FOR PRECISION IMMUNE-MODULATION. We are performing extensive immunomonitoring studies in human breast cancer patients treated with immune checkpoint blockade, with the ultimate aim to validate hypotheses derived from our preclinical research in human cancer patients, and to stratify breast cancer patients for immunomodulatory therapies. We are setting-up multiplex immunohistochemistry with antibody panels that audit intratumoral lymphoid and myeloid cell populations and their functional state. In parallel, we have established an extensive multiplex flow cytometry pipeline to monitor the systemic immune landscape of breast cancer patients and healthy controls. These analyses generate a substantial amount of data which require thorough computational analyses. 3. MAPPING IMMUNO-GENOMIC INTERACTIONS. We are interested in dissecting the impact of the genetic make-up of breast tumors on the intra-tumoral and systemic immune landscape. You will be responsible for the identification and validation of genotype-immunophenotype associations by connecting DNA exome sequencing data, RNA sequencing data and immune profiles derived from our mouse tumor models and cancer patients. You will use both publicly available datasets and newly generated datasets. You will be embedded in the collaborative and enthusiastic international research groups of dr. Karin de Visser, dr Marleen Kok and Prof. dr. Lodewyk Wessels, providing a unique environment that combines computational cancer biology with pre-clinical and translational research into immune-oncology. YOUR PROFILE We seek to recruit an ambitious postdoc, capable of independent thinking, with a strong commitment to translational research. Candidates should hold a degree in bioinformatics, computer science or a related discipline, have experience in statistics and/or machine learning and be proficient in bioinformatics programming languages (e.g. R, Python). We expect candidates to be highly self-motivated, creative, and a team-player with strong communication skills. General background knowledge in biology and immunology is essential, and experience with projects involving the use of genomics and immune profiling data to identifying candidate targets and biomarkers is a plus. WANT MORE INFORMATION? Please visit our home pages https://www.nki.nl/divisions/tumor-biology-immunology/de-visser-k-group/ https://ccb.nki.nl or contact Karin de Visser: k.d.visser(a)nki.nl Marleen Kok: m.kok(a)nki.nl Lodewyk Wessels: l.wessels(a)nki.nl

1 2

Tenure track: ASSISTANT PROFESSOR BIOINFORMATICS - VU Amsterdam
by Sanne Abeln 11 Dec '18

11 Dec '18

Dear colleagues, The Vrije Universiteit Amsterdam has an open tenure track position in Bioinformatics or Statistical Machine Learning. We seek a new colleague who will actively contribute to the research in the Bioinformatics research group and will be responsible for teaching various Bioinformatics elements in the MSc Bioinformatics & Systems Biology. We look for an active researcher with a specific interest to apply research in the *biomedical domain*, while *using statistics, machine learning* and/or sequence analysis as underlying methodology. The successful applicant will receive a well-structured tenure track appointment. For more details, see: https://www.vu.nl/en/employment/vacancies/2018/18405ASSISTANTPROFESSORBIOIN… Applications need to be received by 19 December 2018. It would be nice if you could share this position with potential candidates, Many thanks, Sanne -- -- Sanne Abeln Assistant Professor Bioinformatics - VU University Amsterdam s.abeln(a)vu.nl +31 20 59 87816 www.few.vu.nl/~abeln <http://www.few.vu.nl/%7Eabeln>

1 1

Bioinformatics Data Analyst position in Dresden, Germany
by Alexander Botzki 29 Nov '18

29 Nov '18

Dear All, On behalf of Ian Henry: We are currently looking to hire a bioinformatician to work as part of the MPI-CBG Scientific Computing Facility Team here in Dresden. Specific information regarding the position can be found here: https://www.scionics.com/jobs.html#bioinformatics_data_analyst If you know of any suitable interested candidates for such a position, please feel free to pass this information on to them. Best regards, Ian Dr. Ian Henry Scientific Computing Facility Leader (Bioinformatics, Scientific Software Development & BioImage Informatics) MPI-CBG Dresden Pfotenhauerstrasse 108 01307 Dresden Germany phone: +49 351 210 2638 email: henry(a)mpi-cbg.de<mailto:henry@mpi-cbg.de> twitter:@IanHenry1982 web: http://people.mpi-cbg.de/henry wiki: https://wiki.mpi-cbg.de/scicomp/

1 0

Postdoctoral Fellow in Computational Systems Biology at the Luxembourg Centre for Systems Biomedicine
by Venkata Pardhasaradhi SATAGOPAM 27 Nov '18

27 Nov '18

Dear all We are looking for a postdoc to work on an exciting project that aims at developing a computational framework to design cellular reprogramming strategies. This framework will be applied to establish novel protocols for dopaminergic neuron development in consonance with the interest of our Center in the study of neurodegenerative diseases, especially Parkinson’s disease. In particular, the selected candidate shall develop a network-based computational approach, using single-cell transcriptomics data, to model cell populations dynamics and design strategies for cellular reprogramming. In addition, he/she will participate in the project management and planning, including the supervision of one Ph.D. student and one master student. This is a collaborative project with Karolinska Institute, where the experimental validation of the computational predictions will be conducted. Please refer the below URL for more details: http://recruitment.uni.lu/en/details.html?id=QMUFK026203F3VBQB7V7VV4S8&nPos… Best regards, Venkata — 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. -----

1 0

bioinformatics-molecular biologist position AZ Delta General Hospital, Roeselaere, Belgium
by Alexander Botzki 23 Nov '18

23 Nov '18

Dear all, On behalf of Geert Martens: The Geert MARTENS lab at AZ Delta General Hospital (Roeselare, Belgium) is currently recruiting a bioinformatician-molecular biologist. The candidate will work partly in clinical diagnostics on tumor sequencing and NIPT, and partly on various research projects in collaboration with academia. We prefer an entrepreneurial personality who wants to do high-level work, but is seeking more job stability than often available in academia. Nice salary too! Attached the pdf job descriptions in English and Dutch. Best wishes, Dr. Geert Martens, Geert MARTENS <Geert.Martens(a)vub.be> Laboratory for Molecular Diagnostics at AZ Delta General Hospital ________________________________ Van: bbclist-bounces(a)psb.vib-ugent.be<mailto:bbclist-bounces@psb.vib-ugent.be> <bbclist-bounces(a)psb.vib-ugent.be<mailto:bbclist-bounces@psb.vib-ugent.be>> namens Alexander Botzki <Alexander.Botzki(a)vib.be<mailto:Alexander.Botzki@vib.be>> Verzonden: maandag 19 november 2018 19:41:27 Aan: bbclist(a)psb.ugent.be<mailto:bbclist@psb.ugent.be> Onderwerp: [BBC] [Postdoc-ad] Three postdoc positions in Computational Sysgtems Biology of Cancer at institut Curie, Paris Dear All, On behalf of Emmanuel Barillot Currently we have three available post-doc positions in my group, one on application of multi-scale modeling to tumor microenvironment and two data analyst-type positions (one focused on working with single-cell data and one focused on application of machine learning methods to multi-level omics data). Can you please spread the word as much as possible? Here are the advertisements: http://sysbio.curie.fr/texts/Curie_SysBio_Multiscale_modeling2018.pdf http://sysbio.curie.fr/texts/CurieSysBio-PostDoc_DataAnalyst2018.pdf http://sysbio.curie.fr/texts/CurieSysBio-PostDoc_DataAnalyst_SingleCell2018… Best regards, Emmanuel

1 0

[Postdoc-ad] Three postdoc positions in Computational Sysgtems Biology of Cancer at institut Curie, Paris
by Alexander Botzki 19 Nov '18

19 Nov '18

Dear All, On behalf of Emmanuel Barillot Currently we have three available post-doc positions in my group, one on application of multi-scale modeling to tumor microenvironment and two data analyst-type positions (one focused on working with single-cell data and one focused on application of machine learning methods to multi-level omics data). Can you please spread the word as much as possible? Here are the advertisements: http://sysbio.curie.fr/texts/Curie_SysBio_Multiscale_modeling2018.pdf http://sysbio.curie.fr/texts/CurieSysBio-PostDoc_DataAnalyst2018.pdf http://sysbio.curie.fr/texts/CurieSysBio-PostDoc_DataAnalyst_SingleCell2018… Best regards, Emmanuel

1 0

Vacancy for Senior Software Engineer - Genetwister Technologies B.V.
by Andrzej Czech 19 Nov '18

19 Nov '18

Dear all, We are looking for an experienced Software Engineer to join our software development team in Wageningen, The Netherlands. If you want to build software solutions to analyze and visualize complex genomic data but also contribute to develop an environment in which pipelines and tools from other departments of the company can be integrated, take a look at the detailed job description in the attachment or visit our website: https://www.genetwister.nl/jobs/ Best, Andrzej S. Czech. [andrzej]<http://www.genetwister.nl/> Disclaimer This e-mail and any files transmitted with it are confidential and intended solely for the use of the individual or entity to whom/which they are addressed. If you have received this e-mail in error please notify the sender immediately, delete this e-mail from your system and do not disseminate, distribute or copy this e-mail. This e-mail shall not constitute a binding agreement unless expressly confirmed in writing by one of the Directors of Genetwister. Please note that any views or opinions presented in this e-mail are solely those of the author and do not necessarily represent those of Genetwister. Finally, the recipient should check this e-mail and any attachments for the presence of viruses. Genetwister accepts no liability for any damage caused by any virus transmitted by this e-mail or damage caused by the use of the information contained in this e-mail. / Chamber of Commerce Arnhem, The Netherlands no.: 11043533

1 0

Bioinformatics scientist / IT positions open at Inivata - A liquid biopsy company
by Frank de Kievit 19 Nov '18

19 Nov '18

Dear readers, Inivata, a liquid cancer diagnostics company spin-off from Cancer Research UK is rapidly expanding and hiring in several key positions: - Bioinformatics scientist - Statistical Genomics https://www.inivata.com/jobs/bioinformatics-scientist-statistical-elements/ - Bioinformatics scientist - Algorithm & Assay Development https://www.inivata.com/jobs/bioinformatics-scientist-algorithm-assay-devel… - Senior QA Testing Engineer https://www.inivata.com/jobs/senior-qa-testing-engineer/ If any of these positions are of interest to you, please contact me at frank.dekievit(a)inivata.com or apply directly and add me as a referal. Kind regards, Frank de Kievit Computational Scientist Inivata 01223 790748 Granta Park, Cambridge, UK inivata.com<http://www.inivata.com/> | Follow us on Twitter<http://www.twitter.com/inivata> and LinkedIn<https://www.linkedin.com/company/inivata-limited> [cid:image002.jpg@01D2AD74.8F2F9EC0] All information contained in this e-mail, including the information contained in any attachments, is strictly private and belongs to Inivata Limited. It is to be treated as being marked "Proprietary and Confidential" and is intended only for the recipient(s) to whom it has been sent by us. Further dissemination, or forwarding of this e-mail, is prohibited without Inivata's written consent. If you are not the intended recipient, we hereby give you notice that any reproduction or dissemination of its contents in any manner or format whatsoever is strictly prohibited. If you have received this e-mail in error or without authority, please contact us immediately. Inivata Limited is a limited company registered in England and Wales with registered number 09144647. The registered office of Inivata Limited is The Portway Granta Park, Cambridge, CB21 6GS. UK VAT No. GB 197 2211 03. Inivata Inc. is a Delaware corporation headquartered in Research Triangle Park, NC.

1 0

Edinburgh Genomics R for Genomics Workshop - Final two spaces!
by TRAIN edgenomics-training 08 Nov '18

08 Nov '18

To all budding bioinformaticians Two last-minute spaces have become available for 'R for Genomics' workshop at Edinburgh Genomics, Monday 26th and Tuesday 27th November 2018. This two-day workshop, taught by experienced Edinburgh Genomics' Bioinformaticians, is aimed at complete beginners so don't worry if you have no experience, we'll get you up to speed! By the end of the workshop, you will be comfortable with the basics of R, knowing how to manipulate basic data sets and apply various useful functions. We will introduce you to genomic annotation data and show you how to turn those data into beautiful plots for your next publication! This is a great introduction for researchers planning to use R for the analysis of genomic data or for those wanting to increase their R literacy in general. Instructors: Dr Katie Emelianova ( Edinburgh Genomics Bioinformatician) Nathan Medd (Training and Outreach Manager) Cost: £400 So if you need an introduction into the potentially bewildering world of bioinformatics SIGN UP NOW! To register or for more information please visit our training page at https://genomics.ed.ac.uk/services/training Kind Regards Nathan Medd 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 0