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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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Workshop on biological data visualisation
by Jan Aerts 26 Sep '19

26 Sep '19

Dear all, We are again organising the workshop on biological data visualisation at the EBI in March 2020. Participants of this workshop will get acquainted with the fundamentals of data visualisation, be introduced to visual design, and practise coding these visualisations (depending on their background: in vega or D3). For more information and registration, see here: https://www.ebi.ac.uk/training/events/2020/data-visualisation-biology-pract… Jan Aerts

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Job: Bioconductor infrastructure for the integration of genomics, transcriptomics and proteomics data
by Laurent Gatto 26 Sep '19

26 Sep '19

A position for a PhD student or post-doctoral research is open in the group of Prof Laurent Gatto at the UCLouvain (Brussels, Belgium) in collaboration with Prof Vince Carey at Harvard University (Boston, MA, USA) to develop the necessary infrastructure and statistical software to integrate genomic, mass spectrometry-based quantitative proteomics and transcriptomics expression data. The promise of omics integrative approaches is that the whole will become more than the sum of its parts and will thus reveal new insights into the comprehension of the underlying biology. Natural candidates for such integration are proteomics and transcriptomics. Both approaches aim, among other things, at measuring differences in expression of genes, albeit measuring different biological entities. Different studies have recorded diverging observations about the correlation of the measurements. The goal of this project is to develop and expand the Bioconductor infrastructure into an integrative proteogenomics framework to ensuring explicit and robust integration of quantitative proteomics, transcriptomics and genomics data. The successful candidate will be able to demonstrate experience in the following areas: - You have a master's degree or a PhD in computational biology/bioinformatics, computer science, data science, statistics, computer/electrical engineering, physics, or other related fields. - You have hands-on experience in analysing and interpreting omics data. - You have created/maintained/used software to address research problems in high throughput biology. - You are committed to open research best practices and know how to adapt these to biomedical research contexts. The ideal candidate will be able to demonstrate at least some of the following skills: - Experience with the processing and analysis of omics data (important). - Good knowledge of the R programming language and the Bioconductor infrastructure (important). - Experience in open and reproducible research, open source software and open data (important). - Experience in high performance computing (desirable). - Experience in C/C++ (desirable). - Experience with code versioning and collaborative tools such as, for example, git, and GitHub/GitLab (desirable). - Experience with other languages commonly used in computational biology and bioinformatics like Python or Julia (optional). - Knowledge of French and English is desirable. The contract is full time for a duration of 3 years (for the post-doctoral position) or 4 years (for the PhD position) and is available immediately. Candidates must be in a situation of “international mobility”, i.e. they should not have resided or carried out their main activity (work, studies, etc.) in Belgium for more than 12 months in the 3-year period before submission of their application. We value equality, diversity and an open, collaborative and welcoming work environment. To apply, please send your application by email to Laurent Gatto referencing this position, including a CV with publications and software outputs, a 1-page statement of research interests and names and email addresses of three references. Do not hesitate to contact Laurent Gatto (laurent.gatto(a)uclouvain.be) for additional information.

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2nd ATCR meeting on T-cell receptor sequencing advances
by Pieter Meysman 26 Sep '19

26 Sep '19

Dear all, On the 9th&10th of December 2019 the second Antwerp T-cell Receptor (TCR) Meeting will be organised, following the success of last year’s edition. This two-day international meeting aims to offer a venue for researchers working on TCR sequencing, analysis and applications to present their data and discuss their views on this quickly evolving field. We have assembled a list of leading researchers in the field to provide keynotes for the meeting, including Dr. Victor Greiff (University of Oslo), Dr. Aridaman Pandit (University Medical Center Utrecht), Dr. Sarina Ravens (Hannover Medical School), Dr. Mikhail Shugay (Skoltech Faculty), and Dr. Paul Thomas (St. Jude Children's Research Hospital). Thanks to sponsorship from the University of Antwerp, Research Foundation Flanders and Adaptive Biotechnologies, we are able to provide registration at a reduced rate. For more information on the programme and registration: https://www.uantwerpen.be/en/projects/audacis/antwerp-tcr-meeting/ . Our beautiful venue is limited to 140 visitors, thus we advise you to register on time if you are planning to come. We welcome researchers to present their latest TCR related work via an oral or poster presentation. If you are interested, submit your abstract before the 19th of October: https://easychair.org/conferences/?conf=atcr2019 We hope that you will join us in December! Best wishes, Benson Ogunjimi & Pieter Meysman ATCR2019 chairs https://www.uantwerpen.be/en/projects/audacis/

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VIB Applied Bioinformatics in Life Sciences - February 13-14, 2020 Leuven - registration is open
by Alexander Botzki 26 Sep '19

26 Sep '19

Dear all, We would like to invite you warmly to our VIB Applied Bioinformatics Conference early next year. You could find more details here: https://vibconferences.be/event/applied-bioinformatics-in-life-sciences-3rd… Registration is open. Best regards, Alex Click here https://email.vibconferences.be/t/r-e-jdyhuylk-l-g/ Dear colleague, After two sold out meetings the third edition of Applied Bioinformatics in Life Sciences will host internationally renowned speakers. These including Diafeng Wang, Roser Vento, Klaus Mayer and many more, who will shed light on the future perspectives of their research in the following plenary sessions: Microbial & plant genomics: from simple to complexProteomics Structural and BioinformaticsData integration, machine learning and networksSingle Cell Bioinformatics This conference is organized by VIB, a non-profit life sciences research institute, and will take place on February 13-14, 2020 in the beautiful historic city of Leuven. Find out more [https://vibconferences.be/event/applied-bioinformatics-in-life-sciences-3rd…] Packed program offers new insight in Bioinformatics research We are honored to showcase the following academic world leaders: Roser Vento, Sanger Institute, UKKlaus Mayer, Helmholtz Zentrum München, DEThijs Ettema, Wageningen University, NLRohit Pappu, Washington University, USPatrick Aloy, IRB Barcelona, ESHelen Parkinson, EMBL-EBI, UKNick Loman, University of Birmingham, UKDaifeng Wang, University of Wisconsin-Madison, USSushmita Roy, University of Wisconsin, USOlga Vitek, Northeastern University, USNikolai Slavov, Northeastern University, USEvangelia Petsalaki, EMBL-EBI, UKAedin Culhane, Dana-Farber Cancer Institute & Harvard TH Chan School of Public Health, USAshley Lu, VIB-KU Leuven Center for Brain & Disease Research, BESofia Forslund, Experimental and Clinical Research Centre (ECRC), DELaurent Gatto, De Duve Institute - UC Louvain, BEErik Garrison, UC Santa Cruz, US For more information about the speakers and the program please visit the website: Visit the conference website [https://vibconferences.be/event/applied-bioinformatics-in-life-sciences-3rd…] Submit your abstract before 2 December To support junior researchers, VIB offers PhD students a special rate when registering before the Early Bird deadline. We also encourage young scientists to show their own research to the international research community during the poster sessions at the conference. The best four abstracts will be selected for a short talk in the plenary program. Submit your abstract [https://vibconferences.be/event/applied-bioinformatics-in-life-sciences-3rd…] Apply for a travel Grant VIB offers 5 travel grants to international attendees, which will reimburse travel costs up to 400 Euros. Are you interested in attending ABLS20 and want to have a chance on a travel grant? Submit your motivation by clicking on the 'Apply for a grant' button before 15 November. The organizing committee will notify you of your travel grant acceptance on 22 November 2019. No registration is needed before submitting a travel grant proposal. When you're awarded with a travel grant you will receive a practical email containing the next steps. Note that being awarded a travel grant does not mean being registered for the conference. Find out more [https://vibconferences.be/event/applied-bioinformatics-in-life-sciences-3rd…] We look forward to welcoming you in Leuven on 13 -14 February 2020! With kind regards, Evy Vierstraete Organizing committee: Alex Botzki, VIB Bioinformatics Core, BE Klaas Vandepoele, VIB-UGent Center for Plant Systems Biology, BE Peter Tompa, VIB-VUB Center for Structural Biology, BE Vera van Noort, Centre of Microbial and Plant Genetics, BE Laurent Gatto, de Duve Institute - UC Louvain, BE Evy Vierstraete, VIB Science Events Manager, BE To stop receiveiving our invitations please click below. Tweet https://email.vibconferences.be/t/r-tw-jdyhuylk-l-w/ Share [https://email.vibconferences.be/t/r-li-jdyhuylk-l-c/] Unsubscribe https://email.vibconferences.be/t/r-u-jdyhuylk-l-yd/ Alexander Botzki - Head of VIB Bioinformatics Core | Training Coordinator ELIXIR-BE VIB Bioinformatics Core Rijvisschestraat 126, 9052 GENT, Belgium | +32 9 248 16 00 www.bits.vib.be<http://www.bits.vib.be/> | @vibbioinfocore | https://corefacilities.vib.be<https://corefacilities.vib.be/> [signatureFooter (002)]

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Post-doctoral researcher in Computational Cancer Epigenomics, German Cancer Research Center (DKFZ)
by Pavlo Lutsik 26 Sep '19

26 Sep '19

Dear all, We are looking for a post-doc to strengthen our computational team within the Cancer Epigenomics Division at the DKFZ in Heidelberg. The successful candidate will help expand and bring to maturity our portfolio of best-practice workflows for epigenomic data. To enable this work we are actively employ and create infrastructure for the Common Workflow Language (http://commonwl.org) The primary focus will be set upon workflows for DNA methylation profiling by whole-genome bisulfite sequencing, both bulk and single-cell, for which we are currently running a large-scale benchmarking study supported by external funding (see this talk for details: https://www.youtube.com/watch?v=eGUO_d-xaIE) The candidate will take active part in finalising and publishing results of the initial phase of the study. Furthermore, the candidate will participate in downstream and integrative analyses of these data types, contributing to several exciting projects in cancer epigenomics. Further details and the application portal are available here: https://jobs.dkfz.de/en/jobs/31521/postdoctoral-researcher-in-the-field-of-… We would be happy to see applicants from your community, please spread the word. Best regards, Pavlo

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SDM 2020 Call for Papers
by Alfredo Cuzzocrea 25 Sep '19

25 Sep '19

20th SIAM International Conference on Data Mining May 7 - May 9, 2020, Cincinnati, OH, USA ======================================== SDM 2020 - http://www.siam.org/meetings/sdm20 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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