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Extra R2 workshop December 9th 2019
by r2-support 14 Oct '19

14 Oct '19

Dear Researcher, Since the next R2 workshop on Monday October 28th is overbooked, we are organizing another R2 introduction workshop on Monday the 9h of December 2019 (09:30-17:30). R2 is a free, publicly accessible web-based genomics analysis and visualization platform (http://r2.amc.nl<http://r2.amc.nl/>) allowing biomedical researchers, without bioinformatics training, to integrate clinical and genomics data. The workshop will cover the essentials of working with genomics data in R2 and will be an excellent opportunity to learn how to use this versatile tool. If you are: Studying a specific pathway in disease Trying to find biomarkers in specific tissue Investigating the function of a specific protein Involved in any kind of molecular biology Then this workshop may be of interest to you. Every participant will receive a printed tutorial book. Coffee / tea and a simple lunch will be provided during the workshop. If you are interested in participating in the workshop then please visit the R2 website for more information and registration (http://hgserver1.amc.nl/cgi-bin/r2/main.cgi?option=about_intro_workshop ). The workshop is provided free of charge, however, we will have to charge 25 euro (for administation, lunch, printing costs) in case of a no show on the workshop. Best regards, R2-support r2-support(a)amc.nl<mailto:r2-support@amc.nl> r2.amc.nl<http://r2.amc.nl/> Department of Oncogenomics, M1-132 Amsterdam UMC Location AMC Meibergdreef 9 1105 AZ Amsterdam the Netherlands ________________________________ AMC Disclaimer : https://www.amc.nl/disclaimer ________________________________

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Job offer part time teaching in bioinformatics in Mons / Bergen
by SAND Olivier 11 Oct '19

11 Oct '19

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Helis Academy Course: FAIR Data Stewardship - digital data scholarship for life scientists, 4-6 November 2019, Utrecht, the Netherlands
by Celia van Gelder 08 Oct '19

08 Oct '19

Dear colleague, >From 4-6th November, 2019, we will give another round of the Helis Academy - FAIR Data Stewardship course: FAIR Data Stewardship - digital data scholarship for life scientists The target audience is life scientists - from industry and academia - and graduate students in the Life Sciences who wish to improve their digital scholarship on data handling. Some basic experience with programming and scripting languages like python, perl, R, matlab, etc. are an advantage, but not needed. The course is also relevant for Data Stewards who are supporting the life science researchers. The course will introduce the trainees to important concepts of data stewardship. We start with a general introduction covering the data life cycle, the FAIR principles and a definition of data stewardship and data stewards. The course will introduce the trainees to important concepts of data stewardship <https://www.dtls.nl/fair-data/research-data-management/research-data-manage ment/> . We start with a general introduction covering the data life cycle, the FAIR principles <https://doi.org/10.1038%2Fsdata.2016.18> and a definition of data stewardship and data stewards. We will pass the stages of the data life cycle in more detail in the training modules of this 3 day course. * Day 1: Why use a data management plan and what for? On day one trainees will investigate data management plans, which types are there and how they should be used. * Day 2: Mastering the data chaos during the research phase. On day two the course highlights how to work with data during the research phase, explaining how to create well formatted data which helps in the second module of day two to make data interoperable already during the active research phase. * Day 3: Boost your visibility and get cited for your data! On day three trainees will have an in-depth at persistent identifiers, different use cases and types of identifiers. Finally we are closing the data life cycle by making data fit for sharing, archiving and publishing. The training is organised by <http://www.dtls.nl/> DTL and delivered as a joint effort by DTL partners. You can find all the information, including the full programme and registration possibilities here: https://www.aanmelder.nl/helis-fair-data-stewardship-course This course is part of the Data Analysis and Stewardship theme of Helis Academy <https://www.helisacademy.com/en> and is organised by DTL and DTL collaborators. Info about other courses in the theme of Data Analysis and Stewardship can be found on the Helis Academy website <https://www.helisacademy.com/en/data-analysis-stewardship> and on the Helis Academy page on the DTL website <https://www.dtls.nl/training-and-education/helis-academy/> . Please spread this announcement in your organisation as you see fit. Best regards, Celia van Gelder 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: <https://www.dtls.nl/> https://www.dtls.nl/, <https://www.elixir-europe.org/platforms/training> https://www.elixir-europe.org/platforms/training 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.

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postdoc position in Bordeaux on Cancer Bioinformatics
by Nikolski Macha 04 Oct '19

04 Oct '19

Dear all, We are looking for a post-doctoral scientist interested in Cancer Bioinformatics to work in our institute at the University of Bordeaux. The primary focus will be set upon analysis of RNA-seq data by both bulk and single-cell, to elucidate the invasive processes in glioblastoma. -- 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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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

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SDM 2020 Call for Papers
by Alfredo Cuzzocrea 02 Oct '19

02 Oct '19

20th SIAM International Conference on Data Mining May 7 - May 9, 2020, Cincinnati, OH, USA ======================================== SDM 2020 - http://www.siam.org/meetings/sdm20 Last Call for Papers Scope ===== Data mining is the computational process for discovering valuable knowledge from data - the core of modern Data Science. It has enormous application in numerous fields, including science, engineering, healthcare, business, and medicine. Typical datasets in these fields are large, complex, and often noisy. Extracting knowledge from these datasets requires the use of sophisticated, high-performance, and principled analysis techniques and algorithms, which are based on sound theoretical and statistical foundations. These techniques in turn require implementations on high performance computational infrastructure that are carefully tuned for performance. Powerful visualization technologies along with effective user interfaces are also essential to make data mining tools appealing to researchers, analysts, data scientists and application developers from different disciplines, as well as usable by stakeholders. The SDM conference provides a venue for researchers who are addressing these problems to present their work in a peer-reviewed forum. It also provides an ideal setting for graduate students and others new to the field to learn about cutting-edge research by hearing outstanding invited speakers and attending presentations and tutorials (included with conference registration). A set of focused workshops is also held on the last day of the conference. The proceedings of the conference are published in archival form and are also made available on the SIAM web site. Topics of Interest ================== *Methods and Algorithms -Anomaly & Outlier Detection -Big Data & Large-Scale Systems -Classification & Semi-Supervised Learning -Clustering & Unsupervised Learning -Data Cleaning & Integration -Deep Learning & Representation Learning -Frequent Pattern Mining -Feature Extraction, Selection and Dimensionality Reduction -Mining Data Streams -Mining Graphs & Complex Data -Mining on Emerging Architectures & Data Clouds -Mining Semi Structured Data -Mining Spatial & Temporal Data -Mining Text, Web & Social Media -Online Algorithms -Optimization Methods -Parallel and Distributed Methods -Probabilistic & Statistical Methods -Scalable & High-Performance Mining -Other Novel Methods *Applications -Astronomy & Astrophysics -Automation & Process Control -Climate / Ecological / Environmental Science -Customer Relationship Management -Data Science -Drug Discovery -Finance -Genomics & Bioinformatics -Healthcare Management -High Energy Physics -Intelligence Analysis -Internet of Things -Intrusion & Fraud detection -Logistics Management -Recommendation -Risk Management -Social Network Analysis -Supply Chain Management -Other Emerging Applications *Human Factors and Social Issues -Ethics of Data Mining -Intellectual Ownership -Interestingness & Relevance -Privacy and Fairness Models -Privacy Preserving Data Mining -Risk Analysis and Risk Management -Transparency and Algorithmic Bias -User Interfaces and Visual Analytics -Other Human and Social Issues Submission URL ============== https://cmt3.research.microsoft.com/SDM2020 Workshop and Tutorials ====================== The conference will feature workshops and tutorials on several special topics. Please see the SDM 2020 website for submission requirements. Examples of workshops and tutorials are available through the SDM 2019 website, http://www.siam.org/meetings/sdm19/ Organization ============ GENERAL CO-CHAIRS Nitesh Chawla, University of Notre Dame, USA Carlotta Domeniconi, George Mason Univeristy, USA PROGRAM CO-CHAIRS Yan Liu, University of Southern California, USA Sriraam Natarajan, University of Texas at Dallas, USA WORKSHOPS CO-CHAIRS Yuxiao Dong, Microsoft Research, USA Gregor Stiglic, University of Maribor, Slovenia TUTORIALS CHAIR Danai Koutra, University of Michigan, USA DOCTORAL FORUM CHAIRS Matteo Riondato, Amherst College, USA Brandeis Marshall, Spelman College, USA PANELS CHAIR Zhenhui Jessie Li, Penn State University, USA PUBLICITY CHAIRS Xiang Ren, University of Southern California, USA Alfredo Cuzzocrea, University of Calabria, Italy Sourangshu Bhattacharya, IIT, Kharagpur, India AWARDS CHAIR TBA STEERING COMMITTEE CHAIR Zoran Obradovic, Temple University, USA LOCAL CHAIR Ping Zhang, Ohio State University, USA Important Dates (tentative) =========================== Abstract Submission: October 4, 2019 11:59pm (US Eastern Time) Paper Submission: October 11, 2019 11:59pm (US Eastern Time) Workshop Proposals: October 4, 2019 11:59pm (US Eastern Time) Tutorial Proposals: October 4, 2019 11:59pm (US Eastern Time)

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Senior academic staff (ZAP vacature) on SINGLE CELL OMICS
by Stein Aerts 02 Oct '19

02 Oct '19

FYI: we have an open PI position at the Center for Human Genetics in Leuven to start your own research group focused on single-cell omics and bioinformatics ! Deadline: 21st of October. https://www.kuleuven.be/personeel/jobsite/jobs/55322305?hl=en&lang=en Cheers, Stein SINGLE CELL OMICS (ref. ZAP-2019-123) A full-time Senior Academic position in the domain of Single cell genomics is available in the Department of Human Genetics at the University of Leuven. Biological and biomedical research is shifting from multicellular analyses to single cell analyses. This type of research requires new computational and artificial intelligence-based methods for the analysis of large datasets. We seek to appoint a new Senior Academic staff member in this area. The candidate will also be affiliated with and play an important role in the newly established Single Cell Omics Institute. It is the mission of the Department of Human Genetics, within the areas of human genetics, neurogenetics and cancer genetics, to diagnose, treat and counsel patients, to conduct excellent research and to offer an up-to-date education curriculum. It is the aim of every staff member to use the newest genetic and molecular technologies in order to improve our understanding of human disorders, at the service of our patients and society as a whole. We aspire to be an international centre of excellence within the field of molecular genetics, and to offer a platform of genetic technologies that can support clinical and fundamental, both national and international research groups. We put our clinical services and scientific knowhow at the disposal of our patients, by making diagnoses and by giving them (therapeutic) advice and treatment. We also reflect on the societal, ethical, and psychological impact of new knowledge and clinical practices in the field of human genetics on individuals and on our society Duties Research The research is situated in the domain of human genetics/genomics. The candidate will be an expert in the development and implementation of innovative computational and artificial intelligence-based methods for the analysis of large ‘omics’ datasets from individual cells. The research aims to understand the biology of human cells during normal development, ageing and/or diseases. • You strive for excellence in your research and thus contribute to the further scientific development of the department. • You will start a new research group to further expand. • You will be a motor in the consolidation of the Single Cell Institute of the University of Leuven (KU Leuven). • You supervise PhD students at an international level. • You work closely together with other research teams inside and outside the department. • You contribute to the further development of novel national and international collaborations of the Department of Human Genetics. Education The candidate will be appointed at the Faculty of Medicine and takes up teaching assignments (in English or in Dutch) in this or other faculties. You ensure high-quality education, with a clear commitment for the quality of the programme as a whole.You also contribute to the pedagogic project of the university through the supervision of Msc. theses and as a promoter of PhD students. Profile • You are holder of a PhD degree on a topic related to the research domain eg. molecular biology, cell biology, (bio) medical sciences and with a clear focus on computational biology and bioinformatics during the PhD or Postdoctoral research. • You have a strong research record in a relevant field of study. The quality of your research is evident from publications in prominent, international journals in the domains of genetics & genomics, development of computational methods or applications for single cell omics and/or spatial (single cell) data analyses. • International experience is an important asset. • You have already proven that you are capable of acquiring competitive funding. • You have good teaching and training skills. Experience in an academic teaching environment, as lecturer or as supervisor of MSc. and PhD students is recommended. • You have a cooperative attitude and you are a strong communicator, to a specialized and lay public alike. • You possess organizational skills and leadership (management) capacities within an academic context. • You have a thorough knowledge of spoken and written English. • The official administrative language used at KU Leuven is Dutch. If you do not speak Dutch (or do not speak it well) at the start of employment, KU Leuven will provide language training to enable you to take part in meetings. • Before teaching courses in Dutch or English, you will be given the opportunity to learn Dutch resp. English to the required standard. Offer We have a full-time position available in an intellectually challenging environment. KU Leuven is a research-intensive, internationally oriented university that carries out both fundamental and applied scientific research.It is highly inter- and multidisciplinary focused and strives for international excellence. In this regard, it actively works together with research partners in Belgium and abroad. It provides its students with an academic education that is based on high-quality scientific research. You will work in Leuven, a historic, dynamic and lively city located in the heart of Belgium, within 20 minutes from Brussels, the capital of the European Union, and less than two hours from Paris, London and Amsterdam. Depending on your record and qualifications, you will be appointed to or tenured in one of the grades of the senior academic staff: assistant professor,associate professor, professor or full professor. In the case of a postdoctoral fellowship, you can be asked to finish your fellowship first. For this period, you will be appointed as a part-time assistant professor. KU Leuven is well set to welcome foreign professors and their family and provides practical support with regard to immigration & administration, housing, childcare, learning Dutch, partner career coaching, … To facilitate scientific onboarding and accelerate research in the first phase a starting grant of 100.000 euro is offered to new professors without substantial other funding, appointed for at least 50%. Interested? For more information please contact Prof. dr. Joris Vermeesch, tel.: +3216345941, mail: joris.vermeesch(a)kuleuven.be<mailto:joris.vermeesch@kuleuven.be>. For problems with online applying, please contact solliciteren(a)kuleuven.be<mailto:solliciteren@kuleuven.be>. You can apply for this job no later than October 21, 2019 via the online application tool <https://webwsp.aps.kuleuven.be/esap/public/ui5_ui5/sap/zh_erc_esol_go/index…>

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Postdoc Position in Berlin on Human Evolution
by Katja Nowick 27 Sep '19

27 Sep '19

*Dear all,* *We are looking for a postdoc who is interested in Human Evolution. The position can be for a bioinformatician:* *Our group “Human Biology and primate Evolution“ investigates the molecular evolution of humans using state-of-the art experimental and computational methods. Our focus is on differences in gene regulation, evolution of transcription factors and non-coding RNAs and their influence on the evolution of the human brain, its development and functions. * *The postdoc position is fully funded. The applicant is expected to propose and develop a research project that fits to the general interests of the group. Requirements for the position are a Dr. rer. nat. or PhD in Biology or Bioinformatics or another relevant field. The ideal candidate would have a strong interest in human evolution and expertise within multiple of the following areas: conducting research with induced pluripotent stem cells, differentiation into neuronal cells, CRISPR/Cas9, functional investigation of transcription factors and non-coding RNAs, ChIP-Seq, ChIRP-Seq, RNA-Seq, gene regulatory networks, computational analysis of –omics data, R, Python, network analysis.* *She/he will participate in teaching “Human Biology” (in German) as well as in “Human Evolution” and/or “Bioinformatics for Biologists” (in English). The position allows for supervising Bachelor and Master students as well as for applying for own funding, and is thus a good opportunity for acquiring necessary experience for applying for faculty positions afterward. It is initially for three years but can be extended to up to six years. Scientific communication within the group is in English.* *If interested, please send a motivation letter including your project idea along with your CV and two reference letters to *katja.nowick(a)fu-berlin.de <mailto:katja.nowick@fu-berlin.de>*.* *Best wishes,* *Katja * -- Dr. Katja Nowick Professorin für Humanbiologie Freie Universität Berlin Institut für Zoologie Königin-Luise-Straße 1-3 14195 Berlin Phone: +49 30 83863761

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European Bioconductor meeting 2019, 9 - 10 December in Brussels, Belgium
by Laurent Gatto 27 Sep '19

27 Sep '19

The European Bioconductor meeting is aimed at biologists, bioinformaticians, statisticians, programmers and software engineers who use or contribute to the Bioconductor project, or are interested in using Bioconductor. The goals are to: - foster the exchange of technical expertise - keep contributors up to speed with the latest developments - coordinate any related efforts The main conference will be on Monday 9 and Tuesday 10 December 2019 at the Brussels campus of the UCLouvain. An optional developer/user day is scheduled on the 11 December. The conference will feature 10 invited speakers and contributed flashlight talks and poster sessions. For details and abstract submissions, see http://eurobioc2019.bioconductor.org/index

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IBIP19 Integrative Biological Interpretation using Proteomics - Course announcement / reminder
by Pedro L Fernandes 27 Sep '19

27 Sep '19

> Course Announcement / Reminder > > IBIP19 > Integrative Biological Interpretation using Proteomics > with Veit Schwämmle, Marc Vaudel and David Bouyssié > > IMPORTANT DATES for this Course > Deadline for applications: October 30th 2019 > Course date: November 04th - November 07th 2019 > > Course description > Quantitative proteomics by mass spectrometry has become an essential tool for multi-omics studies aiming at answering important biological questions in a system-wide perspective. Proteomics data contain rich and deep information that can become challenging to extract, interpret, and interface with other experimental outcomes. > This training course is aimed at researchers who are not expert in proteomics and want to integrate quantitative proteomics results into wider biomedical experiments. We will focus on quality control from an end-user perspective, link to the underlying genomic context, multivariate analysis, protein complexes investigation, and compare different platforms for biological interpretation. > After the training, participants will be able to critically interpret results, troubleshoot analyses, and will be ready to successfully attend more specialized training e.g. in proteogenomics or biological network analysis. > > For more information, including details about meeting the pre-requisites and how to apply, please visit: > > http://gtpb.igc.gulbenkian.pt/bicourses/2019/IBIP19/ > > Hoping that this course meets your interests, > > Pedro Fernandes > GTPB Coordinator > Biionformatics Training Coordinator, Bioidata.pt (Elixir-Portugal) > -- > The Gulbenkian Training Programme in Bioinformatics > Pedro L. Fernandes, Organiser > Instituto Gulbenkian de Ciência > Rua da Quinta Grande, 6 > 2780-156 OEIRAS > Portugal

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