- BBClist - maillist.psb.ugent.be

1 Phd position available - Deep learning/Computer vision/Bioimaging (Belgium)
by Raphaël Marée 26 Sep '18

26 Sep '18

Dear colleagues, The Montefiore Institute (http://www.montefiore.uliege.be) at the University of Liège, Belgium has an opening for a PhD candidate to work on the development of novel deep/machine learning algorithms for quantitative multimodal biomedical image analysis. More specifically, this PhD project entails the development of novel algorithms to automatically locate, measure, and classify elements in multimodal biomedical images with a specific focus on skeletal development applications. These algorithms will be disseminated to a wide audience through the open-source Cytomine web-based software platform (http://uliege.cytomine.org) The ideal candidate should have a Master in Computer Science or Biomedical Engineering, with a taste for deep/machine learning and modern software programming. The candidate will be supervised by senior scientific staff with a background in computer science (Prof. Wehenkel, Prof. Geurts, Dr. Raphaël Marée) in collaboration with biomedical researchers (Dr. Marc Muller) and other project partners. The candidate will actively participate in PhD training activities within the BioMedaqu consortium. It is a Marie Sklodowska-Curie Innovative Training Network (MCSA-ITN) with the primary research aim to create an innovative expertise combining research in skeletal biology of aquaculture fish species with that in biomedical models and humans. In total, 15 Early Stage Researchers (ESRs) will be appointed by the BioMedaqu consortium for 36 months each. There are strict eligibility requirements for the ESR PhD positions in MSCA-ITN. Please ensure that you qualify before applying, as ineligible candidates cannot be considered. See more details here: http://www.giga.uliege.be/cms/c_279692/en/biomedaqu-open-positions https://euraxess.ec.europa.eu/jobs/315826 The position starts before January 2019. Interested and eligible candidates should send their résumé and application letter to Dr. Raphaël Marée (raphael.maree(a)uliege.be) and Dr. Marc Muller (m.muller(a)uliege.be) as soon as possible. Best regards, Raphaël. -- Raphaël Marée (PhD) http://www.montefiore.ulg.ac.be/~maree/ http://www.cytomine.org/ Tél.: +32 4 366 26 44

1 0

Assistant Professor Bioinformatics for personalized Medicine, Nijmegen, The Netherlands
by Celia van Gelder 26 Sep '18

26 Sep '18

On behalf of Peter-Bram ‘t Hoen please find this interesting job opening below: Do you have the ambition to build your own bioinformatics research group and are you passionate about personalised medicine? If so, consider the vacancy in the Centre for Molecular and Biomolecular Informatics (CMBI) at Radboudumc Nijmegen, The Netherlands. https://www.radboudumc.nl/en/vacancies/60641-assistant-professor-bioinforma… Best regards Celia Dr. Celia W.G. van Gelder Programme Manager DTL Learning Training Coordinator ELIXIR-NL ELIXIR Training Platform Leader tel. +31613375327 e-mail: celia.van.gelder(a)dtls.nl <mailto:celia.van.gelder@dtls.nl> websites: <http://www.dtls.nl/> www.dtls.nl, <http://www.biosb.nl/> www.biosb.nl skype: celia.van.gelder Office: DTL | Jaarbeurs Innovation Mile (JIM) | 6th floor Beatrixgebouw | Jaarbeursplein 6 | 3521 AL Utrecht Postal address: Postbus 8500 | 3503 RM Utrecht While I may be sending this email outside my normal office hours, I have no expectation to receive a reply outside yours.

1 0

Postdoctoral position - Mathematical modeling in network biology
by REMY Elisabeth 25 Sep '18

25 Sep '18

Please find hereafter a job offer for a 2 years interdisciplinary post-doc position in Marseille (France). ------- Project The aim of the project is to characterize molecular pathways deregulated in myelofibrosis development and define predictive factors of disease evolution. Hematopoietic tissue is sensitive to aging, which results in senescence and haematological age-related diseases like myelofibrosis. We propose an interdisciplinary approach focused on the understanding of the hematopoietic stem cell (HSC)/stromal cell cross-talk that evolves during aging and favors myelofibrosis. The applicant will be in charge of the establishment and analysis of mathematical models centered on bone marrow and HSC aging in order to better understand haematological age-related disease onset. We have developed a unique mouse model, which recapitulates physiological and pathological aging that will be used to generate single cell transcriptomic data. The generated data, together with an extensive literature study, will be the base to address the complexity of the network deregulated upon HSC/stromal cell aging by mathematical modeling approaches. Environment The successful applicant will work in the Mathematics and Algorithms for Systems Biology (Mabios, http://mabios.math.cnrs.fr/index.html) group in the Marseille Institute of Mathematics (I2M, Aix-Marseille University) an interdisciplinary team of mathematicians and computational biologists, in close collaboration with the E. Duprez team (http://crcm.marseille.inserm.fr/en/researchteams/estelle-duprez) specialised in Epigenetic Factors in Normal and Malignant Hematopoiesis in the Centre de Recherche en Cancérologie de Marseille (CRCM). Expected profile The applicant should have a formation (PhD) in Computer Science, Applied Mathematics, Computational Biology (or related fields). He/she should have a strong interest in biology and interdisciplinary approaches to decipher biological processes. Skills in programming/scripting and/or bioinformatics (for *-seq data processing) would be an advantage. Offer Fully-funded position for 2 years in Marseille. The starting date is expected in January 2019. Application can be sent directly to “elisabeth.remy(a)univ-amu.fr<mailto:elisabeth.remy@univ-amu.fr>” and “estelle.duprez(a)inserm.fr<mailto:estelle.duprez@inserm.fr>”. Please make sure your application includes a letter of motivation, a list of publications, a detailed CV and the contact information of 2 references (including email addresses and phone numbers). Keywords: Mathematical modeling, Single cell, Data Analysis, Systems Biology --------- --------------------------------------------------------------------- Élisabeth REMY Institut de Mathématiques de Marseille (I2M) Campus de Luminy- Case 907 13288 Marseille cedex 09 +33 (0)4 91 26 95 65 http://mabios.math.cnrs.fr/index.html

1 0

Job: lecturer bioinformatics at Hogeschool van Arnhem en Nijmegen (Dutch)
by Bruggen Martijn van der 25 Sep '18

25 Sep '18

Dear all, We have an opening for a lecturer bioinformatics/informatics and for an instructor bioinformatics. Note: vacancies are only for Dutch-speaking candidates. Please also forward to any potentially interested candidates you might know. https://www.han.nl/start/corporate/werken-bij-de-han/vacatures/_detail/inde… https://www.han.nl/start/corporate/werken-bij-de-han/vacatures/_detail/inde… Martijn. Drs. M.H.H. van der Bruggen Docent bioinformatica / Opleidingscoördinator bioinformatica Hogeschool van Arnhem en Nijmegen (HAN) Instituut voor Toegepaste Biowetenschappen en Chemie Postadres: postbus 6960 | 6503 GL NIJMEGEN | Nederland Bezoekadres: Laan van Scheut 2 | Kamer 0.07 | 6525 EM NIJMEGEN | Nederland | +31-6-55206344 Aanwezig: maandag – dinsdag – woensdag – donderdag - vrijdag [1512978560569_PastedImage] [cid:c8979e1a-6e02-48b0-9801-f1d99ff2285e]

1 0

PhD position: Metabolic modeling of bacterial interactions
by Karoline Faust 24 Sep '18

24 Sep '18

PhD position: Metabolic modeling of bacterial interactions The Laboratory of Microbial Systems Biology (http://tinyurl.com/MicrobialSysBio) is looking for a motivated PhD candidate who is interested in investigating microbial communities through metabolic modeling. The young lab, started in 2016, is part of the Molecular Bacteriology unit at the Rega Institute and aims at improving our understanding of microbial community structure and dynamics. The PhD position is funded through an ERC starting grant. Project While metabolic models have been successfully applied to describe the behavior of bacteria grown in mono-culture, their extension to several interacting bacterial strains is a field of active research. The goal of this PhD is to develop and evaluate approaches based on metabolic modeling to predict bacterial interactions. In addition, we want to apply metabolic modeling to predict the behavior of bacterial communities growing in well-defined conditions. Profile The candidate should have a solid background in systems biology. Knowledge of metabolic modeling or metabolic network analysis is a plus. Applicants should have a Master degree in systems biology, bioinformatics or equivalent with at least a distinction, obtained in January 2019 at the latest. A proof of proficiency in English is a requirement. Offer -full-time 4-year contract -enrolment at one of the top universities in Europe -exciting research environment -competitive salary Interested? Please submit a cover letter, a CV including obtained grades, and a list with at least two references (with name, function, email, address and phone number) through the online application tool (https://www.kuleuven.be/personeel/jobsite/jobs/54798210) You can apply for this position no later than 1st December, 2018. The PhD will start in January 2019. For more information, please contact Karoline Faust at: karoline.faust(a)kuleuven.be

1 0

Invitation: Life Sciences with Industry Workshop 2018 @ Lorentz Center, Leiden
by Gokhan Ertaylan 19 Sep '18

19 Sep '18

********************************************************************************************** Invitation to participate in the Life Sciences with Industry 2018 Lorentz workshop: Leiden, November 19 – 23, 2018 ********************************************************************************************** We invite researchers (especially PhD students and postdocs) from all branches of the life sciences to participate in the one-week* Lorentz workshop* *Life Sciences with Industry 2018* in Leiden: November 19 – 23, 2018. During the workshop, 24 participants will tackle, three *scientifically challenging* and *commercially important* problems formulated by the following three companies. *Heineken* *Selective recovery of ethanol and aroma compounds from alcoholic solutions* *Solynta* *Quality Matters: how to monitor frying quality of potato tubers?* *VITO* *A Serious Game on Preventive Health* For a full description of these challenges https://www.lorentzcenter.nl/lc/web/2018/1055/info.php3?wsid=1055&venue=Sne… The workshop will take place in Leiden in the building of the Lorentz Center, an organisation that is specialised in organising scientific workshops (http://www.lorentzcenter.nl/) To create multi-disciplinary teams, participants will be selected based on their (i) specific background, (ii) motivation to participate, and (iii) date of registration (*first come first served).* *Register on the workshop website*: https://www.lorentzcenter.nl/lc/web/2018/1055/info.php3?wsid=1055&venue=Sne… *Deadline: Friday October 19, 2018. * Participation is free of charge, including hotel accommodation, lunches and two dinners during the workshop. The workshop is sponsored by the Lorentz Center, the Research School BioSB (http://biosb.nl/) and the three companies involved. Need for more information? Contact (Carey Batenburg-Einthoven <batenburg(a)lorentzcenter.nl>) at the Lorentz Center (phone +31 715 275 578). We hope to welcome you on November 19th 2018. *Scientific organizers:* Dennis Botman, Vrije Universiteit Amsterdam Em. prof. dr. Roel van Driel, Universiteit van Amsterdam Dr. Gökhan Ertaylan, VITO, Mol, Belgium Eunice van Pelt-KleinJan, Vrije Universiteit Amsterdam Klara Scupakova, Maastricht University Prof. dr. Bas Teusink, Vrije Universiteit Amsterdam *Organizers (NWO): * Dr. Ansa Baykus-Fiaz, NWO-Domain Science, Den Haag Dr. Margot Beukers, NWO-Domain Applied and Engineering Sciences, Utrecht Drs. Lisette Krul, NWO-Domain Applied and Engineering Sciences, Utrecht **********************************************************************************************

1 0

byteMAL2018 Bioinformatics conference for young researchers
by Loïc 18 Sep '18

18 Sep '18

Dear all, We are pleased to announce that byteMAL2018 (Bioinformatics for Young inTernational researchers Maastricht - Aachen - Liège) will take place on the 5th of October 2018 at the University of Liège, in Belgium. This conference aims to provide an opportunity for young researchers in the fields of bioinformatics and computational biology to meet and network together. The keynote speaker list is available on the website (http://www.bytemal.org/2018/) Information desks will also be provided, where PIs/representatives of Bioinformatics and related fields are open to answer questions about research opportunities or potential vacancies for the master’s/PhD students. The subscription is free but mandatory, please subscribe before the 4th of October on our website (http://www.bytemal.org/2018/#Registration) Also a poster session and flash talks (selected among poster abstracts) will be organized! Date: October 5th, 9.30 AM Location: B22, Chemin de la Vallée 4 (Sart Tilman Campus) 4000 Liège https://www.campus.uliege.be/cms/c_5799509/en/b22-institut-de-botanique We are looking forward to welcoming you! The Liège byteMAL team

1 0

Registration Open for ELIXIR-NL Course Bioinformatics for Translational Medicine using Galaxy - 17- 19 October 2018, Amsterdam
by Celia van Gelder 17 Sep '18

17 Sep '18

ELIXIR-NL Course: Bioinformatics for Translational Medicine using Galaxy Please circulate this email to those who might be interested. Date: 17-19 October, 2018 Location: VU Amsterdam ( <https://goo.gl/maps/CphwJEFDegt> O|2 Lab Building, Gustav Mahlerlaan 665, 1082 MK, 1082 MK Amsterdam) Organizers: Chao (Cico) Zhang (VU), Sanne Abeln (VU), Anton Feenstra (VU), Saskia Hiltemann (ErasmusMC), Mateusz Kuzak (DTL) and Celia van Gelder (DTL). Course page: <https://www.biosb.nl/education/course-portfolio/bioinformatics-for-translat ional-medicine-using-galaxy/> https://www.biosb.nl/education/course-portfolio/bioinformatics-for-translati onal-medicine-using-galaxy/ Application form: <https://www.biosb.nl/education/course-portfolio/bioinformatics-for-translat ional-medicine-using-galaxy/enrollment-galaxy-workshop-2018/> https://www.biosb.nl/education/course-portfolio/bioinformatics-for-translati onal-medicine-using-galaxy/enrollment-galaxy-workshop-2018/ TARGET AUDIENCE This course consists of two parts, each of which you could register separately in the <https://www.biosb.nl/education/course-portfolio/bioinformatics-for-translat ional-medicine-using-galaxy/enrollment-galaxy-workshop-2018/> application form. Part 1 (Day 1 and 2): biomedical & translational medicine researchers/students who are keen on bioinformatics Part 1 and 2 (Day 1, 2 and 3): educators in the bio domain who would like to start using Galaxy in their courses as an introduction to bioinformatics. COURSE DESCRIPTION Analysing molecular data in translational medicine involves a multitude of computational steps. Here, we introduce the basics of how to design and run these steps within Galaxy, a free and easy-to-use web platform that enables users to connect bioinformatics tools into a workflow without any prior programming expertise. This course consists of two parts, each of which you could register separately. Part 1 will let you get familiar with Galaxy; it will introduce some bioinformatics workflows used for RNAseq, variant detection and metagenomics; and how to easily connect different computational steps in Galaxy. Part 2 will focus on how to teach bioinformatics with Galaxy and to design bioinformatics courses using Galaxy. Participants can register for both parts separately. This course is also interspersed with a few keynotes, from recognized researchers in the fields of biomedicine, bioinformatics education, and Galaxy workflows. The confirmed speakers include Remond Fijneman (Day 1), a scientist in oncology from NKI; Björn Grüning (Day 2), the leader of Galaxy training network, who is also actively involved in Bioconda, and Jaap Heringa (Day 3), the scientific director of the Netherlands Bioinformatics Centre. PREREQUISITE KNOWLEDGE The attendees of Part I are assumed to have the basic knowledge of biomedicine (molecular biology and genomics) and be interested in analyzing patient-derived sequencing data. The attendees of Part II are assumed to have some teaching experience in the relevant field (e.g., bioinformatics, computational biology, systems biology, quantitative biology, etc.) COURSE SCHEDULE The course consists of six modules, as the table below shows, covering a list of topics as follows: * Introduction to Galaxy. Run bioinformatics tools and workflows in Galaxy without the need for any programming expertise. * Reference-based RNA-Seq data analysis * Module detection in differential gene expression in meta transcriptomics samples. * Microbiota Analysis: 16S rRNA sequencing analysis in Galaxy * How to teach bioinformatics workflows. * How to prepare training material development. Day 1 - Wed Oct 17 Day 2 - Thu Oct 18 Day 3 - Fri Oct 19 Morning <http://galaxyproject.github.io/training-material/topics/introduction/> Introduction to Galaxy <https://www.ncbi.nlm.nih.gov/pubmed/26342232> Network analysis with microbiota metatranscriptome Teaching bioinformatics workflows <https://shiltemann.github.io/> Saskia Hiltemann <https://hi-it.org/> Chao Zhang <http://www.few.vu.nl/~feenstra/> Anton Feenstra Keynote I: About bioinformatics workflows II: About Galaxy and ELIXIR III: About bioinformatics teaching <https://www.nki.nl/people/fijneman-remond/> Remond Fijneman <https://galaxyproject.org/people/bjoern-gruening/> Björn Grüning <https://www.cs.vu.nl/~heringa/> Jaap Heringa Afternoon <http://galaxyproject.github.io/training-material/topics/transcriptomics/> RNAseq <http://galaxyproject.github.io/training-material/topics/metagenomics/> 16S rRNA sequencing with mothur <http://galaxyproject.github.io/training-material/> Galaxy training material development <https://galaxyproject.org/people/bjoern-gruening/> Björn Grüning <https://shiltemann.github.io/> Saskia Hiltemann <https://shiltemann.github.io/> Saskia Hiltemann Evening Social dinner About the instructor: Each session is led by one instructor listed in the table above but strongly supported by multiple co-instructors, including, but not limited to, Saskia Hiltemann (ErasmusMC), Björn Grüning, Chao Zhang (VU), Leon Mei (LUMC), Ruben Vorderman (LUMC) and Sanne Abeln (VU). Correction: An earlier version of this announcement mentioned that you dont need to bring your own laptop, this is NOT TRUE. We regret the error. You do need to bring your own laptop. COURSE FEE Course participation is free of charge. A workshop dinner will be organized on Thursday (at participants own expenses) Should you have any question about this course, please contact Celia van Gelder ( <mailto:celia.van.gelder@dtls.nl> celia.van.gelder(a)dtls.nl) Dr. Celia W.G. van Gelder Programme Manager DTL Learning Training Coordinator ELIXIR-NL ELIXIR Training Platform Leader tel. +31613375327 e-mail: <mailto:celia.van.gelder@dtls.nl> celia.van.gelder(a)dtls.nl websites: <http://www.dtls.nl/> www.dtls.nl, <http://www.biosb.nl/> www.biosb.nl skype: celia.van.gelder Office: DTL | Jaarbeurs Innovation Mile (JIM) | 6th floor Beatrixgebouw | Jaarbeursplein 6 | 3521 AL Utrecht Postal address: Postbus 8500 | 3503 RM Utrecht While I may be sending this email outside my normal office hours, I have no expectation to receive a reply outside yours.

2 1

OLA'2018 @Thailand on Optimization and Learning
by El-Ghazali Talbi 16 Sep '18

16 Sep '18

Apologies for cross-posting. Appreciate if you can distribute this CFP to your network. **************************************************************************************** OLA'2019 International Conference on Optimization and Learning: Challenges and Applications 29-31 Jan 2019 Bangkok Thailand http://ola2019.sciencesconf.org/ **************************************************************************************** OLA is a conference focusing on the future challenges of optimization and learning methods and their applications. The conference OLA'2019 will provide an opportunity to the international research community in optimization and learning to discuss recent research results and to develop new ideas and collaborations in a friendly and relaxed atmosphere. OLA'2019 welcomes presentations that cover any aspects of optimization and learning research such as optimization for learning, learning for optimization, optimization and learning under uncertainty, new high-impact applications, parameter tuning, 4th industrial revolution, hybridization issues, optimization-simulation, meta-modeling, high-performance computing, parallel and distributed optimization and learning, surrogate modeling, multi-objective optimization ... Submission papers: We will accept submissions in two different formats: - S1: Extended abstracts of work-in-progress and position papers of a maximum of 3 pages - S2: Original research contributions of a maximum of 10 pages Important dates: =============== Submission deadline Oct 19 2018 Notification of acceptance Nov 9, 2018 Proceedings: Accepted papers in categories S1 and S2 will be published in the proceedings that will be available at the conference. In addition, a post-conference indexed Springer book and special issue of Journal (ITOR International Transaction on Operational Research) is planned to be published. Participants will be invited to submit extended versions of their work for consideration.

1 0

Fwd: I'm looking for a new colleague
by Stephane Rombauts 12 Sep '18

12 Sep '18

JOB > From: "Dauchot, Nicolas" <nicolas.dauchot(a)thermofisher.com> > To: "stephane rombauts" <stephane.rombauts(a)ugent.vib.be> > Sent: Wednesday, September 12, 2018 10:47:19 AM > Subject: I'm looking for a new colleague > Dear Stephane, > I hope you’re doing fine. > Find bellow a job offer that might interest some of your contacts. > [ > http://jobs.thermofisher.com/ShowJob/Id/350126/Field%20Applications%20Speci… > | > http://jobs.thermofisher.com/ShowJob/Id/350126/Field%20Applications%20Speci… > ] > Thermo Fisher Scientific is currently looking for a talented scientist to > support ABi capillary electrophoresis (sequencing and fragment analysis) and > Ion Torrent NGS platform. > That person would replace my current colleague (Dutch/English speaking, > currently based in Amsterdam) who moved to a new position within Thermo. > If you think that this job offer could interest some of your contacts, do not > hesitate to share the link or forward this email. > I’m also always available if he/she needs further information. > Have a nice day, > Cheers, > Nicolas > Nicolas Dauchot, PhD > Field Application Scientist > Next Generation & Capillary Electrophoresis Sequencing Solutions > Thermo Fisher Scientific > Guldensporenpark 26 | 9820 Merelbeke | Belgium > T 00 800 5345 5345 • F 00 32 (0) 2 582 1886 > [ mailto:Nicolas.Dauchot@thermofisher.com | Nicolas.Dauchot(a)thermofisher.com ] | > [ http://www.thermofisher.com/ | www.thermofisher.com ] > [ > https://www.thermofisher.com/uk/en/home/life-science/sequencing/next-genera… > ] > For any support inquery being answered swiftly, please submit them through (in > English) to [ http://www.thermofisher.com/askaquestion | > http://www.thermofisher.com/askaquestion ] > This email and its attachments are confidential. If you received this email in > error, please notify the sender and delete.

1 0