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

VIB Bioinformatics Conference - last chance to register by 30th of January 2020
by Alexander Botzki 22 Jan '20

22 Jan '20

Dear all, Last chance to join your bioinformatics colleagues at ABLS20 | February 13-14, 2020 | Leuven The third edition of Applied Bioinformatics in Life Sciences will feature recent developments in bioinformatics research and highlight the power of computational biology. The selection of scientific topics are of a great interest to a large audience of researchers. VIB conference's goals are to bring together a diverse international group of upcoming and renowned scientists to present and exchange break-through ideas relating to how bioinformatics is applied broadly in life sciences and shed light on the future perspectives of their research. Read more: https://www.vibconferences.be/events/applied-bioinformatics-in-life-science… Best regards, Alex Alexander Botzki - Head of VIB Bioinformatics Core, ELIXIR Belgium Training Coordinator VIB Bioinformatics Core Rijvisschestraat 126 9052 Zwijnaarde Belgium + 32 9 248 16 00 https://corefacilities.vib.be/bic | @vibbioinfocore [cid:image002.jpg@01D5D13C.5519E120]

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Bioinformaticus MSc/PhD bij de Metabole Diagnostiek
by Deutekom-3, H.W.M. van 21 Jan '20

21 Jan '20

De sectie Metabole Diagnostiek in het UMCU is op zoek naar een bioinformaticus (MSc of PhD). Als bio-informaticus participeer jij in ons team van bio-informatici, laboratoriumspecialisten, analisten, promovendi en postdocs. Samen implementeren wij untargeted metabolomics in de diagnostiek van erfelijke stofwisselingsziekten, waarbij jij verantwoordelijk bent voor het opzetten en ontwikkelen van de bioinformatische pipeline. Daarnaast ben je betrokken bij de integratie metabolomics & whole exome sequencing, waar je samenwerkt met de collega’s van de sectie genoomdiagnostiek. https://www.werkenbijumcutrecht.nl/vacatures/Paginas/bio-informaticus%20(20… Met vriendelijke groet, Hanneke van Deutekom [Universitair Medisch Centrum Utrecht] Hoofd Bioinformatica | Divisie Laboratoria, Apotheek en Biomedische Genetica, Genoomdiagnostiek Universitair Medisch Centrum Utrecht | Kamernummer STR.0.308 | Huispostnummer STR.1.305 T: +31 88 75 68116 | www.umcutrecht.nl<http://www.umcutrecht.nl> | Werkdagen: ma,di,do,vr 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. P Denk s.v.p. aan het milieu voor u deze e-mail afdrukt.

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PhD student Digital Twinning for a Serious and Personalized Diabetes Game
by Riel, N.A.W. van 21 Jan '20

21 Jan '20

Position for a PhD student in Biomedical Systems Biology at Eindhoven University of Technology: https://jobs.tue.nl/en/vacancy/phd-student-digital-twinning-for-a-serious-a… . The PhD candidate will develop and apply dynamic models of human metabolic physiology to develop 'Digital Twins' of patients with diabetes. Digital twins are virtual copies of human metabolic physiology that enable simulations based on data collected from the patient and artificial intelligence. The models are expected to perform realistic simulation of glucose and insulin dynamics in response to the intake of food, the effect of medication, physical activity and mental stress and should allow for large differences between individuals. The PhD position is part of the NWO funded project 'DiaGame: serious and personalized game for self-management of diabetes.' The DiaGame project applies learning systems and biomedical simulations to develop a data-driven, personalized serious game that empowers individuals with diabetes to manage the disease they are facing. In order to personalize the game, we will integrate our expertise on processing of personal data collected from health-related smartphone apps into our game platform. The information that this approach yields will be used to personalize the simulation that drives the game. Together, this will allow the use of patient-gathered health data to make the diabetes game a realistic representation of the condition of the gamer. Hence, the goal is to obtain a personalized simulator for a person's metabolism. In this way, DiaGame will change the approach to diabetes care by using data sciences in support of a data-driven personal diabetes games for learning to manage their own disease. Ultimately, this will improve the quality of life for patients and lighten the socio-economic and medical burden that diabetes has. The partners in the project include the Department of Industrial Engineering & Innovation Sciences of TU/e and Maxima Medical Centre in Eindhoven Kind regards Prof. dr. ir. Natal A.W. van Riel Professor of Biomedical Systems Biology Head of Systems Biology and Metabolic Disease (SBMD) Computational Biology group Department of Biomedical Engineering Eindhoven University of Technology T +31 40 247 5506 (5537) n.a.w.v.riel(a)tue.nl www.tue.nl/en/research/researchers/natal-van-riel/ | www.tue.nl/cbio Professor of Computational Modelling Amsterdam University Medical Centers University of Amsterdam

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Postdoctoral Fellow in Computational Systems Biology at the Luxembourg Centre for Systems Biomedicine
by Venkata Pardhasaradhi SATAGOPAM 20 Jan '20

20 Jan '20

Dear all Computational Biology Unit at LCSB, University of Luxembourg headed by Prof. Dr. Antonio del Sol is looking for a highly skilled and motivated Postdoctoral fellow to work on an exciting project that aims at developing a computational framework to design cellular conversion strategies for Regenerative Medicine purposes. This framework will be applied to obtain in vitro limbal stem cells, which will be later used for clinical transplantation to treat patients who have lost their vision. In particular, the selected candidate shall develop a computational methodology based on information and graph theories, using single-cell transcriptomics data, to model cell populations dynamics and design strategies for cellular conversion. In addition, he/she will participate in the project management and planning, including the supervision of one Ph.D. student. This is a collaborative project with Professor Michele de Luca’s group at the Center for Regenerative Medicine “Stefano Ferrari”, University of Modena, where the experimental validation of the computational predictions will be conducted. Please refer the attached job advert for more details and please distribute in your circles. Thanks & Regards, Venkata — Dr. Venkata Satagopam Bioinformatics Core Luxembourg Centre For Systems Biomedicine (LCSB) University of Luxembourg Campus Belval, House of Biomedicine II 6, avenue du Swing L-4367 Belvaux T +352-466-644-6421 F +352-466-644-36421 venkata.satagopam(a)uni.lu<mailto:venkata.satagopam@uni.lu> http://lcsb.uni.lu LCSB is turning 10! We’ve come a long way since launching our activities in 2009. Today, nearly 250 talented people work together to accelerate biomedicine! Stay tuned for a year full of new collaborations, exciting research projects and a unique exhibition! 15 research groups | 56 graduated PhDs | 745 scientific papers | 24 patents | over 400 collaborative projects ----- This message is confidential and may contain privileged information. It is intended for the named recipient only. If you receive it in error please notify me and permanently delete the original message and any copies. -----

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PostDoc position (evolutionary genomics) in Roscoff, France
by Lieven Sterck 16 Jan '20

16 Jan '20

Note that three postdocs and one PhD studentship in evolutionary genetics/genomics/epigenetics will be advertise this Spring for a start from September 2020 (in the context of a recently awarded ERC Consolidator grant). > BIOINFORMATICS POSTDOC IN EVOLUTIONARY GENOMICS > Roscoff Marine Station, France > A postdoctoral position (1 year with possible renewal for 3 years) is available > immediately in the Algal Genetics group at the Roscoff Marine Station, > Brittany, France ( [ http://www.sb-roscoff.fr/en/team-algal-genetics | > http://www.sb-roscoff.fr/en/team-algal-genetics ] ). > We are seeking highly qualified and enthusiastic applicants with strong skills > in computational biology/bioinformatics, ideally also with experience in data > mining and comparative or evolutionary genome analyses. > We have been interested in a range of topics related to the evolution of sexual > reproduction across the brown algal group. In the framework of our research, > and together with collaborators at Genoscope (Paris) we have generated full > genomes of 48 lines of brown algae and comprehensive sets of RNA-seq data for a > range of life cycle stages from representatives of all major brown algal > lineages and evolutionary outgroups. We perform integrated analyses to study > the evolution of brown algal genomes across lineages, life cycle stages, > chromosomes and sexes. > The postdoctoral fellow will be funded by an awarded ERC Starting Grant (SEXSEA) > and perform integrated evolutionary/bioinformatics analyses based on data > produced in our lab and available genomic data. The project will focus on > analyses of the ‘omics’ datasets generated in the framework of the ERC Grant > and Phaeoexplorer (France Genomique), including high quality genomes, HiC > datasets, genetic maps, transcriptomes, etc. More precisely the postdoc will > use bioinformatics and comparative evolutionary genomic approaches to identify > sex chromosomes and investigate their evolution. > The language of the institute is English and its members form a highly > international group. The Roscoff Marine Station is located in Britany at the > sea Front, and Roscoff is a picturesque city close to Brest, 3h away from > Paris. > Please submit a CV, statement of research interest, and names of three > references to: Susana Coelho ( [ mailto:Coelho@sb-roscoff.fr | > Coelho(a)sb-roscoff.fr ] ). > We are always interested in applications from highly qualified and motivated > bioinformatics postdocs, experimental (genomics/molecular/ developmental > biology) postdocs and bioinformatics PhD students. Please send applications and > other requests to Susana Coelho ( [ mailto:Coelho@sb-roscoff.fr%29 | > Coelho(a)sb-roscoff.fr) ] . > Note that three postdocs and one PhD studentship in evolutionary > genetics/genomics/epigenetics will be advertise this Spring for a start from > September 2020 (in the context of a recently awarded ERC Consolidator grant). > Susana Coelho > Algal Genetics Group > Integrative Biology of Marine Organisms Department (UMR8227) > Station Biologique CNRS UPMC > Place Georges Teissier CS 90074 > 29688 Roscoff cedex > France > tel: +33 (0)2 98 29 23 60 > [ http://www.sb-roscoff.fr/en/algal-genetics-0 | > http://www.sb-roscoff.fr/en/algal-genetics-0 ] > [ https://www.embo-embl-symposia.org/symposia/2020/EES20-09/index.html | > https://www.embo-embl-symposia.org/symposia/2020/EES20-09/index.html ]

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Bioinformatician (m/f/d) | Max Planck Institute of Immunobiology and Epigenetics
by Lieven Sterck 15 Jan '20

15 Jan '20

[ https://www.ie-freiburg.mpg.de/5197180/job_full_offer_14345720 | https://www.ie-freiburg.mpg.de/5197180/job_full_offer_14345720 ] The Max Planck Institute of Immunobiology and Epigenetics in Freiburg, Germany has an opening for a Bioinformatician (m/f/d) to start as soon as possible for an initial period of two years with the possibility of subsequent permanency. L. Lieven Sterck - Senior Postdoctoral Scientist Bioinformatics VIB Department of Plant Systems Biology Ghent University Technologiepark-Zwijnaarde 71 - 9052 Ghent - Belgium Tel. +32(0)9 331 38 21 [ http://bioinformatics.psb.ugent.be/ | http://bioinformatics.psb.ugent.be ] "Facts are meaningless. You could use facts to prove anything that's even remotely true" - H. Simpson

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CFP META'2020 @Marrakech
by El-ghazali Talbi 14 Jan '20

14 Jan '20

Dear colleagues, please distribute the CFP of META'2020 in your networks. Thanks for your collaboration. Apologies for cross-posting. Appreciate if you can distribute this CFP to your network. ********************************************************************** META'2020 International Conference on Metaheuristics and Nature Inspired Computing 27-31 Oct 2020 Marrakech, Morocco http://meta2020.sciencesconf.org/ ********************************************************************** META is one of the main event focusing on the progress of the area of metaheuristics and their applications. As in previous editions, META’2020 will provide an opportunity to the international research community in metaheuristics to discuss recent research results, to develop new ideas and collaborations, and to meet old friends and make new ones in a friendly and relaxed atmosphere. All selected long papers will be published in the Springer (SCOPUS, ISI, DBLP) conference proceedings. At least, 2 special special issues in ISI and SCOPUS journals are also confirmed. META'2020 welcomes presentations that cover any aspects of metaheuristic research such as new algorithmic developments, high-impact applications, new research challenges, theoretical developments, implementation issues, and in-depth experimental studies. META'2020 strives for a high-quality program that will be completed by a number of invited talks, tutorials, workshops and special sessions. The scope of the META’2020 conference includes, but is not limited to: * Local search, tabu search, simulated annealing, VNS, ILS, … * Evolutionary algorithms, swarm optimization, bio-inspired algorithms, … * Emergent nature inspired algorithms: quantum computing, artificial immune systems, bee colony, DNA computing, … * Quantum computing * Parallel and distributed algorithms * Hybrid methods with machine learning, game theory, mathematical programming, constraint programming, co-evolutionary, … * Application to: logistics and transportation, networks, scheduling, data mining, engineering design, energy, cloud, bio-medical, … * Theory of metaheuristics, landscape analysis, convergence, problem difficulty, very large neighbourhoods, … * Multi-objective optimization, bi-level optimization * Dynamic optimization, problems with uncertainty, … * Parameter tuning (static, dynamic, adaptive, self-adaptive) * Hyper-heuristics, cross-domain metaheuristics * Software frameworks for metaheuristics and nature inspired computing Submission of papers: ____________________ - Submission of papers via the website S1) Short papers: Extended abstracts of work-in-progress and position papers of a maximum of 3 pages. S2) Long papers: Original research contributions of a maximum of 10 pages. S3) Journal papers: High-quality manuscripts that have recently, within the last year, been submitted or accepted for journal publication. For this special case, the submission should have the same title that the accepted work, the abstract AND the complete reference of the work. - Proceedings of the conference will be provided. Selected papers of type S2 will be published in a Springer book (SCOPUS, ISI, DBLP). - Predefined styles are available on the website http://meta2020.sciencesconf.org/ - Proposals for invited sessions, workshops and tutorials: Deadline 30th March 2020, contact meta2020(a)sciencesconf.org Important dates _______________ - Submission deadline: April 24, 2020 - Notification of acceptance: May 30, 2020 -- *********************************************************************** META'2020 International Conference on Metaheuristics and Nature Inspired Computing 28-31 Oct 2020, Marrakech, Morocco http://meta2020.sciencesconf.org *********************************************************************** Prof. El-ghazali TALBI Polytech'Lille, University Lille - INRIA CRISTAL - CNRS

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IEEE/ACM SPECIAL ISSUE ANNOUNCEMENT
by PietroHiram Guzzi 14 Jan '20

14 Jan '20

(APOLOGIZE FOR MULTIPLE POSTING) CALL FOR PAPERS IEEE Transactions on IEEE/ACM Transactions on Computational Biology and Bioinformatics Special Issue/Section on Deep Learning and Graph Embeddings for Network Biology GUEST EDITORS: Pietro Hiram Guzzi Associate Professor, University of Catanzaro, Department of Surgical and Medical Sciences hguzzi(a)unicz.it Marinka Zitnik Assistant Professor, Harvard University, Department of Biomedical Informatics marinka(a)hms.harvard.edu TOPIC SUMMARY: Biological Networks are powerful resources for modelling, analysis, and discovery in biological systems, ranging from molecular to epidemiological levels. In recent years, network models and algorithms have been used to represent and analyse the whole set of associations and interactions among biologically relevant molecules inside cells, (e.g., proteins, genes, transcription factors and more recently the big class of non-coding genes), supporting the elucidation of the molecular mechanisms as well as the development of precision medicine for many relevant diseases (e.g., cancers or brain disorders). Mathematical machinery that is central to this area of research is graph theory and machine learning on graph-structured data. Recent research efforts have introduced methods and tools that can model biological phenomena and learn and reason about them through networks. Such data and models are typically stored in various databases of experimental data and repositories of biomedical knowledge. Network data extracted from these databases are often mined for knowledge about a biological system of interest (e.g., using network statistics or community detection algorithms) and to compare two or more networks (e.g., using network alignment algorithms). Current approaches may present limitations in some applications since they can fail to generalize from observed network structure to new biological phenomena, are unable to include prior knowledge in the analysis, rely on user-defined heuristics and painstaking manual feature engineering to extract features from biological networks, or fail to support researchers when limited biological data is available (e.g., small datasets with low coverage). Recent years have seen a surge in approaches, such as deep learning, that have shown broad utility in uncovering new biology and contributing to new discoveries in wet laboratory experiments. In particular, in biological and biomedical area, deep learning have evidenced an efficient way to deal with data generated from modern high-throughput technologies. In parallel, the field of network science has been influenced by the development of methods that automatically learn to encode network structure into low-dimensional embeddings, using data transformation techniques based on matrix factorization, deep learning, nonlinear dimensionality reduction, and complex non-linear models. The key idea of these methods (or graph representation learning) is to automatically learn a function able to map nodes in the graph (or other graph structures) to points in a compact vector space, whose geometry is optimized to reflect topology of the input graph. The relevance and potential of graph representation learning are evidenced by the rise of approaches that are beginning to effect on the way network biology is performed today at the fundamental level. Therefore, there is strong need to discuss and foster these advances in a systematic way to give support both to researchers and practitioners. The goal of this special issue is to collect both surveys and papers describing novel methods and applications in computational biology and bioinformatics. Papers presenting applications in medicine and healthcare are also welcome. The topics of interest for this special issue include, but are not limited to: * Deep learning and graph neural networks for network biology * Learning meaningful representations for biomedical networks * Learning node, edge, higher-order, and graph-level embeddings for biological networks * Next-generation graph embedding techniques for important problems, including node classification, link prediction, graph classification, network alignment and beyond * Graph representation learning for visualizing and interpreting interaction data * Next-generation network science through network embeddings * Relevant benchmark datasets, initial solutions for new challenges and new directions in network biology * Applications of network embeddings broadly in computational biology, genomics, medicine, and health IMPORTANT DATES: Abstract submission: Jan-Feb 2020 Open for submissions in ScholarOne Manuscripts: February 28 2020 Closed for submissions: July 30, 2020 Results of first round of reviews: September 15, 2020 Submission of revised manuscripts: October 15, 2020 Results of second round of reviews: November 15, 2020 Publication materials due: December 15, 2020 SUBMISSION GUIDELINES: Prospective authors are invited to submit their manuscripts electronically after the Òopen for submissionsÓ date, adhering to the IEEE/ACM Transactions in Computational Biology and Bioinformatics guidelines (http://www.computer.org/portal/web/tcbb-cs/author) Please submit your papers through the online system (https://mc.manuscriptcentral.com/tcbb-cs) and be sure to select the special issue or special section name. Manuscripts should not be published or currently submitted for publication elsewhere. Please submit only full papers intended for review, not abstracts, to the ScholarOne portal. If requested, abstracts should be sent by e-mail to the Guest Editors directly. GUEST EDITORS BIOGRAPHIES: Pietro Hiram Guzzi Pietro H. GuzziÊis an Associate Professor of Computer Science and Bioinformatics at the University ÔMagna Gr¾ciaÕ of Catanzaro, Italy, since 2008. He received his PhD in Biomedical Engineering in 2008, from Magna Gr¾cia University of Catanzaro. He received his Laurea degree in Computer Engineering in 2004 from the University of Calabria, Rende, Italy. His research interests comprise bioinformatics, network analysis. In network analysis, in particular, Pietro has worked on local alignment of biological networks providong some tools for network alignment. Actually is working on novel approaches of alignment that merge together both local and global alignment and on the development of novel methods of analysis based on the integration of heterogeneous networks thorugh embedding. Pietro is an ACM member and serves the scientific community as reviewer for many conferences. He is associate editor of IEEE/ACM TCBB, and of SIGBioinformatics Record. Marinka Zitnik Marinka Zitnik is an Assistant Professor at Harvard University. Her research investigates artificial intelligence and machine learning to advance science, medicine, and health. Her methods have had a tangible impact in biology, genomics, and drug discovery, and are used by major biomedical institutions, including Baylor College of Medicine, Karolinska Institute, Stanford Medical School, and Massachusetts General Hospital. Before Harvard, she was a postdoctoral scholar in Computer Science at Stanford University and a member of the Chan Zuckerberg Biohub at Stanford. She received her Ph.D. in Computer Science from University of Ljubljana while also researching at Imperial College London, University of Toronto, Baylor College of Medicine, and Stanford University. Her work received several best paper, poster, and research awards from the International Society for Computational Biology. She has recently been named a Rising Star in EECS by MIT and also a Next Generation in Biomedicine by The Broad Institute of Harvard and MIT, being the only young scientist who received such recognition in both EECS and Biomedicine.

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GSK Data Science/Bioinformatics positions
by Fernando Ulloa Montoya 13 Jan '20

13 Jan '20

We have 3 exciting positions at GSK Vaccines in Rixensart, take a look at: Data Scientist: https://jobs.gsk.com/nl-be/jobs/236345?lang=en-us&previousLocale=nl-BE Senior Data Scientist: https://jobs.gsk.com/nl-be/jobs/223722?lang=en-us&previousLocale=nl-BE Senior Manager Data Science: https://jobs.gsk.com/nl-be/jobs/236342?lang=en-us&previousLocale=nl-BE Best regards, Fernando GSK monitors email communications sent to and from GSK in order to protect GSK, our employees, customers, suppliers and business partners, from cyber threats and loss of GSK Information. GSK monitoring is conducted with appropriate confidentiality controls and in accordance with local laws and after appropriate consultation.

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Postdoc: Computational Biology
by Lodewyk Wessels 12 Jan '20

12 Jan '20

[image: New CellCircuits Graphic Add Jan2020 V2.jpg]

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