November 2020 - BBClist - maillist.psb.ugent.be

New plugin available for ImageJ / FIJI (microscopy / histology)
by Yves Sucaet 13 Nov '20

13 Nov '20

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job opening for a BSc/MSc_Bioinformatics
by Vos-3, H.R. 12 Nov '20

12 Nov '20

Dear All, We have a job opening for a BSc/MSc_Bioinformatics We offer: We are offering a position in bioinformatics (BSc/MSc) in proteomics, in an excellent research environment at the Center for Molecular Medicine, with innovative technology, and high-quality research and support. We ask: You are a recently graduated Bachelor/Master in Bioinformatics, motivated to work in a collaborative academic environment in fundamental biomedical research. Department The Center for Molecular Medicine is a research center that focuses on understanding the molecular and cellular basis of disease. More than 160 researchers perform multidisciplinary fundamental and translational research in relation to various diseases, including cancer and genetic disorders. The aim of the CMM is to train the next generation of biomedical scientists by performing internationally leading, fundamental biomedical research and by offering stimulating and excellent education. Within the CMM there are several core facilities, providing scientists access to high end technologies, among which is the facility for (single cell) proteomics. Job description You will work in an interdisciplinary team, with experts in nano-LC, mass spectrometry, flow cytometry, tissue culture and signaling in cancer. You will work together with wet-lab team members to design proteomics experiments for clients, processes mass spectrometry based data and help the client to interpret those data using bioinformatic analysis methods that are in-house but also which you have developed. Requirements You are motivated to work in a collaborative academic research environment in a facilitatory role in the field of proteomics. You are a creative, outgoing person, and enjoy working in a team. You have recently obtained your Bachelor/Master degree in bioinformatics, and would like to develop and implement innovative analysis methods for (single cell) proteomics in a multi-disciplinary team. You have experience in collaborating with wet-lab researchers, from whom you are eager to learn some wet-lab skills. This job is based on a temporary position, starting for 2.5 years, and option for extension upon positive evaluation. Starting date is January 1st, 2021. Contact: Harmjan Vos, H.R.Vos-3 at umcutrecht.nl ------------------------------------------------------------------------------ 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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Vacancy for a structural bioinformatician at Radboudumc Nijmegen
by Hanka.Venselaar＠radboudumc.nl 11 Nov '20

11 Nov '20

Dear all, we would like to draw your attention to this vacancin our structural bioinformatics group at Radboudumc Nijmegen. Full tekst and details can be foud here: https://www.radboudumc.nl/en/vacancies/89341-postdoc-diagnostics-in-3d GRTZ from Nijmegen, Hanka "Job description The increasing pace at which genomes are being sequenced and at which protein 3D structures are being solved opens the possibilities to predict the effect of mutations on the functioning of a protein at an unprecedented scale. Furthermore, advances in Artificial Intelligence (AI) allow us to efficiently exploit that information to make reliable predictions about disease causing mutations. Such predictions can be applied in diagnostics, solving the many variants in patients' genomes for which we do not know whether they are responsible for disease. The project, named Diagnostics-in-3D, will therewith have a significant impact on diagnosis of (rare disease) patients. Your role in this project is to investigate how to optimally exploit protein 3D structure information in an AI framework that discriminates between benign and damaging mutations in human genomes. For that you will use our protein 3D modeling project HOPE, our deep learning platform for 3D protein structures DeepRank and our expertise in deep learning approaches to protein structures, comparative genomics and diagnostic classifiers. You will be working with a scientific programmer to turn your solutions into professional software. You will furthermore be collaborating with two companies, one from which you will to obtain relevant 3D data and sequence alignments and one with which we will implement parallel/distributed CPU/GPU computing solutions for this data and computation intensive project. Your job thus entices both scientific research into the effect of protein 3D structures and regular communication with the scientific and industrial partners. Tasks and responsibilities Obtain relevant data and find the best representation of 3D structure data for deep learning. Modeling effects of mutations on protein 3D structure. Extend DeepRank to work with single protein structures. Developing and training classifiers using DeepRank to predict the effect of mutations on protein function. Communicate with a scientific programmer about implementation of software. Reporting your results in the form of publications and presentation. Profile You either have a PhD in computational structural biology, with a strong computational background in modeling and interpreting 3D structures, or you have a PhD in machine learning and AI with a proven interest in protein 3D structures and biochemistry. Furthermore, you are enthusiastic about genetics and biomedical research. Lastly, you have strong communication skills and you have a collaborative mindset. " De informatie in dit bericht is uitsluitend bestemd voor de geadresseerde. Aan dit bericht en de bijlagen kunnen geen rechten worden ontleend. Heeft u deze e-mail onbedoeld ontvangen? Dan verzoeken wij u het te vernietigen en de afzender te informeren. Openbaar maken, kopiëren en verspreiden van deze e-mail of informatie uit deze e-mail is alleen toegestaan met voorafgaande schriftelijke toestemming van de afzender. Het Radboudumc staat geregistreerd bij de Kamer van Koophandel in het handelsregister onder nummer 41055629. The content of this message is intended solely for the addressee. No rights can be derived from this message or its attachments. If you are not the intended recipient, we kindly request you to delete the message and inform the sender. It is strictly prohibited to disclose, copy or distribute this email or the information inside it, without a written consent from the sender. Radboud university medical center is registered with the Dutch Chamber of Commerce trade register with number 41055629.

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a postdoc vacancy for computational structural biology and genetics
by Li Xue 10 Nov '20

10 Nov '20

Dear all, We have a postdoc vacancy for computational structural biology ad genetics: https://www.radboudumc.nl/en/vacancies/89341-postdoc-diagnostics-in-3d Could you help us to distribute the vacancy to anyone interested in or via your preferred communication channels? Thanks. Best, Li Assistant Professor Center for Molecular and Biomolecular Informatics Radboud University Medical Center Nijmegen the Netherlands

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Opening for a data scientist/bioinformatician at Princess Maxima Center for Pediatric Oncology
by Kemmeren-2, P.P.C. 05 Nov '20

05 Nov '20

Dear all, We have an opening for a data scientist/bioinformatician within the Princess Maxima Center for Pediatric Oncology! Interested in contributing to our efforts in providing state-of-the-art precision oncology for pediatric cancer patients as well as contribute to our whole-genome driven biobanking efforts, please apply using the link below. https://werkenbijprinsesmaximacentrum.nl/vacature/data-scientist-bioinforma… Regards, Patrick -- Patrick Kemmeren, PhD Principal Investigator & head Big Data Core T +31 (0)88 972 90 00 | M +31 (0)6 53 11 25 53 [signature_902055192] Princess Máxima Center for Pediatric Oncology Heidelberglaan 25 | 3584 CS Utrecht | T +31 (0)88 972 90 00 | > Website<https://research.prinsesmaximacentrum.nl/en/research-groups/kemmeren-group>

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Training on Visual Analytics for Life Sciences & Health
by Marques Neves, A.R. 05 Nov '20

05 Nov '20

Helis Academy: Training on Visual Analytics for Life Sciences & Health On the 1st of December 2020, Helis Academy and TU/e will organize an online course on Visual Analytics for Life Sciences & Health. This online program provides the opportunity to get insights on theory, current practice in industry and expected possible future Practice in industry within just one day, right from behind your own PC. More information and registration is available here: https://helisacademy-trainingonvisualanalytics.eventbrite.nl [A picture containing text Description automatically generated] Kind regards, [Eindhoven University of Technology] Rita Neves, M.Sc. Researcher | Eindhoven University of Technology | Department of Mathematics and Computer Science M: +351 914 878 562 | +31 (0)6 838 33 047<tel:+351%20914%20878%20562%20|%20+31%20(0)6%20838%2033%20047> E: a.r.m.marques.neves(a)tue.nl<mailto:a.r.m.marques.neves@tue.nl> A: Eindhoven University of Technology, P.O. Box 513, 5600 MB Eindhoven [https://img.mysignature.io/s/v3/0/d/a/0da47aae-d980-5ecc-919d-f6cbbc5bd6e2.…]<https://www.linkedin.com/in/rita-neves/>

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postdoc in machine learning for structure-based virtual screening
by Pedro Ballester 02 Nov '20

02 Nov '20

Dear all, I will like to inform you that a postdoc position in machine learning for structure-based virtual screening is available in my lab. Further information and how to apply at https://doctorat.campusfrance.org/en/CF202018350 Best regards, Pedro -- ©¤©¤©¤©¤©¤©¤©¤©¤©¤©¤©¤©¤©¤©¤©¤©¤©¤©¤©¤©¤© Dr. Pedro J. Ballester Group Leader at the Cancer Research Centre of Marseille (CRCM) Research scientist at INSERM <http://crcm.marseille.inserm.fr/en/researchteams/pedro-ballester/> http://crcm.marseille.inserm.fr/en/researchteams/pedro-ballester/ <https://publons.com/researcher/975063/pedro-j-ballester/> https://publons.com/researcher/975063/pedro-j-ballester/ ©¤©¤©¤©¤©¤©¤©¤©¤©¤©¤©¤©¤©¤©¤©¤©¤©¤©¤©¤©¤©

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BSC: Life Sciences vacancy
by BSC Human Resources 02 Nov '20

02 Nov '20

Dear all, We would like to inform you about a new job opportunitiy offered by Barcelona Supercomputing Center: - Post-doc Researchers in Computer Science and Bioinformatics (R2). Deadline: 16 December, 2020 Link here <https://www.bsc.es/join-us/job-opportunities/35720lsiconbir2> We would appreciate that you share the information with your contacts. Sincerely, /Human Resources/* Barcelona Supercomputing Center – Centro Nacional de Supercomputación* Tel. +34- 934137745 <mailto:anais.delastre@bsc.es>www.bsc.es <http://www.bsc.es/> http://bsc.es/disclaimer

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PhD Candidate Tumor Heterogeneity in Acute Myeloid Leukemia
by Erik van den Akker 02 Nov '20

02 Nov '20

THE POSITION We are looking for a highly motivated candidate for a PhD project in Computational Oncology at the department of Biomedical Data Sciences. This project focusses on modelling tumor heterogeneity and discerning drivers of clonal evolution and therapy resistance by analyzing single-cell data on material derived from patients with acute myeloid leukemia. IN SHORT • You will work on integrative computational methods to discern, characterize and trace different clonal lines present within tumors • You will work in a multi-disciplinary environment ranging from data science to translational oncology within the recently established Leiden Center for Computational Oncology • You will disseminate your work by writing scientific manuscripts and presenting your research at international conferences. The combination of this work will lead to a PhD title WHAT YOU WILL DO Acute myeloid leukemia (AML) is a cancer of the myeloid immune lineage and represents about 1.2% of all new cancer cases. AML typically affects elderly patients, with only 5-15% of the patients above age 60 achieving a durable remission. Promising treatments are steadily released, with yet unknown resistance mechanisms. Hence, within this project, you will conduct integrative analyses using various types of single-cell molecular data sources to identify mechanisms driving clonal evolution and therapy resistance. Within the newly established Leiden Center for Computational Oncology, acute myeloid leukemia was chosen as one of the projects to spearhead the development of novel computational tools that provide more insight into tumor heterogeneity and tumor evolution under therapeutic pressure. The activities of the PhD candidate are purely computational and will be embedded within the Leiden Computational Biology Center (prof. M. Reinders), and the department of Hematology (prof. H. Veelken, MD). WHAT WE ASK You hold a MSc degree in Bioinformatics, Statistics, Life Sciences, or a similar area. You possess a strong background in data analytics, have hands-on experience with applying machine learning methods, and you are familiar with scripting languages such as R or Python. Knowledge of genetic analyzation and transcriptomic studies are favored but not required. You enjoy the pursuit of knowledge across multiple field, and you have an optimistic and kind nature. INTERESTED? Please send your CV and motivation letter (deadline November 15th) to: https://lumc.recruitee.com/l/en/o/phd-candidate-tumor-heterogeneity-in-acut… Kind regards, Erik van den Akker Leiden University Medical Centre Molecular Epidemiology <http://www.molepi.nl/en/people/people_item/t/erik_van_den_akker> Einthovenweg 20, 2333 ZC, Leiden, The Netherlands Building 2 [Research], Room S5-38 tel: +31 (0)71 526 85 57 Delft University of Technology Delft Bioinformatics Lab <https://www.tudelft.nl/ewi/over-de-faculteit/afdelingen/intelligent-systems…> Van Mourik Broekmanweg 6, 2628 XE, Delft, The Netherlands Building 28 [WI], Room W5.820 tel: +31 (0)15 278 55 17

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PhD Candidate Patient Sub-stratification in Acute Myeloid Leukemia
by Erik van den Akker 02 Nov '20

02 Nov '20

THE POSITION We are looking for a highly motivated candidate for a PhD project in Computational Oncology at the department of Biomedical Data Sciences. This project focuses on the integrative analysis of multiple types of omics data to improve diagnosis, prognosis and predicted treatment outcomes of patients with acute myeloid leukemia. IN SHORT • You will work on the deep molecular characterization of acute myeloid leukemia, to identify clinically relevant sub-entities of the disease, actionable determinants of treatment resistance and potential targets for immuno-therapy • You will work in a multi-disciplinary environment ranging from data science to translational oncology within the recently established Leiden Center for Computational Oncology • You will disseminate your work by writing scientific manuscripts and presenting your research at international conferences. The combination of this work will lead to a PhD title WHAT YOU WILL DO Acute myeloid leukemia (AML) is a cancer of the myeloid blood lineage that typically affects elderly patients. Current efforts for a personalized prognosis and treatment focus on the detection of just a few genetic aberrations, thereby ignoring the overwhelming evidence that AML is mostly driven by epigenetic and metabolic factors. Within the newly established Leiden Center for Computational Oncology, acute myeloid leukemia was chosen as one of the projects to spearhead the development of novel computational tools that support personalized medicine beyond the 'one-mutation one-drug' paradigm. Hence, within this project, you will be employing molecular data created from clinical material to capture multiple regulatory levels (genetics, transcriptomics, metabolomics, proteomics) to improve patient stratification, prediction of treatment responses and identification of novel therapeutic targets. The activities of the PhD candidate are purely computational and will be embedded within the Leiden Computational Biology Center (prof. M. Reinders), and the department of Hematology (prof. H. Veelken MD). WHAT WE ASK You hold a MSc degree in Bioinformatics, Statistics, Life Sciences, or a similar area. You possess a strong background in data analytics, have hands-on experience with applying machine learning methods, and you are familiar with scripting languages such as R or Python. Knowledge of genetic analysis and transcriptomic studies are favored but not required. You enjoy the pursuit of knowledge across multiple fields, and you have an optimistic and kind nature. INTERESTED? Please send your CV and motivation letter (deadline November 15th) to: https://lumc.recruitee.com/l/en/o/phd-candidate-patient-substratification-i… Kind regards, Erik van den Akker Leiden University Medical Centre Molecular Epidemiology <http://www.molepi.nl/en/people/people_item/t/erik_van_den_akker> Einthovenweg 20, 2333 ZC, Leiden, The Netherlands Building 2 [Research], Room S5-38 tel: +31 (0)71 526 85 57 Delft University of Technology Delft Bioinformatics Lab <https://www.tudelft.nl/ewi/over-de-faculteit/afdelingen/intelligent-systems…> Van Mourik Broekmanweg 6, 2628 XE, Delft, The Netherlands Building 28 [WI], Room W5.820 tel: +31 (0)15 278 55 17

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