From nicosia at dmi.unict.it Tue Jan 7 15:22:34 2020 From: nicosia at dmi.unict.it (Giuseppe Nicosia) Date: Tue, 7 Jan 2020 15:22:34 +0100 Subject: [SocBiN] Call for Participation, 7th International Synthetic & Systems Biology Summer School - SSBSS 2020, Scuola Normale Superiore di Pisa, Tuscany, Italy June 8-12 Message-ID: 7th International Synthetic & Systems Biology Summer School - SSBSS 2020 June 8-12, 2020 - Scuola Normale Superiore di Pisa, Tuscany, Italy https://urlproxy.sunet.se/canit/urlproxy.php?_q=aHR0cHM6Ly9zc2JzczIwMjAuaWNhcy54eXo%3D&_s=ZGVmYXVsdA%3D%3D&_c=5b00b0ec&_r=c3Utc2U%3D ssbss at icas.xyz * Our sincere apologies if you receive multiple copies of this announcement * * Please help us distributing in your circles (emails, blogs, and social networks) the call for participation and call for oral talks/posters for SSBSS 2020. Together we will make SSBSS 2020 a great Summer School! * The Synthetic and Systems Biology Summer School (SSBSS) is a full-immersion five-day residential summer school at the Scuola Normale Superiore di Pisa, on cutting-edge advances in systems and synthetic biology with lectures delivered by world-renowned experts. The school provides a stimulating environment for students (from Master students to PhD students), Post-Docs, early career researches, academics and industry leaders. Participants will also have the chance to present their results (with Oral Talks and Posters), and to interact with their peers, in a friendly and constructive environment. Keynote Speakers: * JOEL S. BADER, Department of Biomedical Engineering, Johns Hopkins University, USA Topics: Cancer, Systems Biology, Synthetic Biology, Synthetic Chromosomes, Genome-wide association studies * JEF D. BOEKE, Institute for Systems Genetics - New York University Langone Health, USA Topics: Humane Genome Project - Write, Genomics, Genetics, Retrotransposons, Synthetic Biology * FRANCESCA BUFFA, Department of Oncology, University of Oxford, UK Topics: Systems Biology, Functional Genomics, Transcriptomics, Biostatistics, Integrative Genomics & Metabolism * YVONNE CHEN, Department of Chemical and Biomolecular Engineering, UCLA, USA Topics: Mammalian Synthetic Biology, Cell-based therapies for intractable diseases, chimeric antigen receptor (CAR)-T cells. * VIRGINIA CORNISH, Department of Chemistry, Columbia University, USA Topics: Synthetic Biology, Chemical Complementation & Ribosome Chemistry * TOM ELLIS, Department of Bioengineering, Imperial College London, UK Topics: Synthetic Genomics, Synthetic Biology, Genome Engineering, Biotechnology * RODRIGO LEDESMA-AMARO, Department of Bioengineering, Imperial College London, UK Topics: Metabolic Engineering, Synthetic and Systems Biology * NICOLA PATRON, Synthetic Biology Group, Earlham Institute, UK Topics: Synthetic Biology, Engineering Plant Biology, Recoding Regulation, Recoding Plant Metabolism * GUIDO SANGUINETTI, School of Informatics, University of Edinburgh, UK Topics: Systems Biology, Biomedical Artificial Intelligence, Probabilistic Modeling of Biological systems. More Speakers TBA soon! DEADLINES: Application: February 20, 2020 Oral Presentation/Poster Submission: February 20, 2020 Notification of Decision for Oral/Poster Presentation: March 12, 2020 https://urlproxy.sunet.se/canit/urlproxy.php?_q=aHR0cHM6Ly9zc2JzczIwMjAuaWNhcy54eXovcmVnaXN0cmF0aW9uLw%3D%3D&_s=ZGVmYXVsdA%3D%3D&_c=5521d982&_r=c3Utc2U%3D CALL FOR POSTER & ORAL PRESENTATIONS: During the Registration Process we accept abstract submissions for posters and oral presentations to be presented during the poster sessions and the talk sessions. https://urlproxy.sunet.se/canit/urlproxy.php?_q=aHR0cHM6Ly9zc2JzczIwMjAuaWNhcy54eXovcmVnaXN0cmF0aW9uLw%3D%3D&_s=ZGVmYXVsdA%3D%3D&_c=5521d982&_r=c3Utc2U%3D Early registration deadline: February 20, 2020 See you in Tuscany in July! JOEL S. BADER, Johns Hopkins University, USA JEF D. BOEKE, New York University, USA ANTONINO CATTANEO, Scuola Normale Superiore di Pisa, Tuscany, Italy MASSIMO GULISANO, University of Catania, Italy GIUSEPPE NICOSIA, University of Cambridge, UK & University of Catania, Italy STEVE OLIVER, University of Cambridge, UK GIOVANNI STRACQUADANIO, University of Edinburgh, UK the SSBSS 2020 Directors. ssbss at icas.xyz https://urlproxy.sunet.se/canit/urlproxy.php?_q=aHR0cHM6Ly9zc2JzczIwMjAuaWNhcy54eXo%3D&_s=ZGVmYXVsdA%3D%3D&_c=5b00b0ec&_r=c3Utc2U%3D https://www.facebook.com/ssbss.school/ SSBSS - Synthetic & Systems Biology Summer School Group: https://www.facebook.com/groups/238417586492061/ Computational Synthetic Biology Group: https://www.facebook.com/groups/1014624245288596/ * Apologies for multiple copies. Please forward to anybody who might be interested * -------------- next part -------------- An HTML attachment was scrubbed... URL: From news at bioclues.org Wed Jan 8 08:51:06 2020 From: news at bioclues.org (Virtual Post Bioclues) Date: Wed, 8 Jan 2020 13:21:06 +0530 Subject: [SocBiN] Fwd: CfP: Indian conference on Bioinformatics 2020 (Inbix'20) in NEHU SHillong In-Reply-To: References: Message-ID: FYKI ---------- Forwarded message --------- From: Virtual Post Bioclues Date: Wed, Jan 8, 2020 at 1:20 PM Subject: CfP: Indian conference on Bioinformatics 2020 (Inbix'20) in NEHU SHillong To: Dear All We are pleased to call for participation for our yet another Inbix event in North Eastern Hills, this time organised by Devendra Biswal and Team NEHU during April 16-18, 2020. We have great speakers lined up along with call for submissions for video abstracts, ideation challenge etc. All submissions are open even as the registrations are fast filling up! Please join us at www.inbix.bioclues.org. Bioclues members have huge discounts, so hurry up! Attached is the flyer for your perusal. Questions? You're welcome to contact us at www.inbix.bioclues.org or email inbix at bioclues.org Thank you and looking forward to seeing you in Shillong Regards Devendra Biswal, PhD Secretary, Bioclues.org for Team Inbix PS: Apologies for cross post, if any -- http://www.bioclues.org Join Bioclues. Reach us at Linkedin: http://www.linkedin.com/groups?gid=1339327 Googlegroups: http://groups.google.com/group/bioclues Bioclues is an affiliate of International Society for Computational Biology (ISCB) -- For www.bioclues.org. Bioclues is an affiliate of International Society for Computational Biology (ISCB). -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: Inbix'20_poster.jpeg Type: image/jpeg Size: 135831 bytes Desc: not available URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: inbix2020_logo.png Type: image/png Size: 89491 bytes Desc: not available URL: From Joana.Goncalves at tudelft.nl Fri Jan 10 13:03:59 2020 From: Joana.Goncalves at tudelft.nl (=?utf-8?B?Sm9hbmEgR29uw6dhbHZlcyAtRVdJ?=) Date: Fri, 10 Jan 2020 12:03:59 +0000 Subject: [SocBiN] PhD and Postdoc positions Message-ID: <02AF1964-253E-4F56-99E5-F863CBFBC0E0@tudelft.nl> Dear All, We have new vacancies for a PhD candidate and two postdoc positions: * PhD candidate (4-year contract) on learning algorithms for cancer therapeutic target discovery leveraging heterogeneous molecular data and large-scale loss-of-function screens. Opportunity to pursue machine learning challenges such as learning across different domains, and/or delve into topics like causal inference. Application at https://www.academictransfer.com/en/288752/phd-learning-algorithms-for-drug-target-prediction/. * Postdoc positions (2-year contract) in a flagship collaboration between the TU Delft, the Erasmus MC, and the Holland Proton Therapy Center: on single-cell discovery of biomarkers for targeted proton therapy of head and neck cancer. The position at Erasmus MC will have an experimental focus on using single-cell DNA and RNA sequencing and photoselection for phenotypic labeling of DNA repair dynamics to characterize (un)treated tumor cell line and patient samples. The position at the TU Delft is computational and focuses on the modelling of single-cell response to treatment and discovery of molecular and phenotypic biomarkers conferring resistance to therapy. Application at https://convergence.healthandtechnology.nl/square/position/37. The application deadline for the PhD position is 9 February 2020. For the postdoc positions, recruitment will take place until the positions are filled. Please feel free to contact me for additional information, or to send the vacancies around to potentially interested candidates. Kind regards, Joana -- Joana Gonçalves Assistant Professor TU Delft Faculty EEMCS, Dept. Intelligent Systems Van Mourik Broekmanweg 6, 2628 XE Delft Building 28, Office E05.060 http://joanagoncalves.org -------------- next part -------------- An HTML attachment was scrubbed... URL: From juho.rousu at aalto.fi Thu Jan 9 15:18:21 2020 From: juho.rousu at aalto.fi (Rousu Juho) Date: Thu, 9 Jan 2020 14:18:21 +0000 Subject: [SocBiN] PhD position in AI for Synthetic Biology open Message-ID: <7FAF899C-577A-4E5D-98CE-3D6C8F2F28E9@aalto.fi> PhD position in AI for synthetic biology open KEPACO research group (research.cs.aalto.fi/kepaco/) in Aalto university (www.aalto.fi) is looking or a PhD student in the field of Artificial intelligence for Synthetic Biology. Synthetic biology has a large potential to tackle the issues of circular economy, from converting waste to useful products to carbon-neutral industrial production, through the use of synthetically engineered microbes. These engineering efforts can potentially be expedited with AI-assisted design processes, however, this potential still largely unharnessed. We envision a AI system facilitating the DBTL cycle (Design, Build, Test, Learn), where the strain is designed (D), built in a laboratory (B), measured and tested (T), to learn (L) a model on the current strain to be exploited for the next cycle design phase (D) again. Automatic operation of the DBTL loop has so far been been demonstrated only in selected settings. In this project, we propose to develop new AI approaches to tackle the problem of accelerating the design of synthetic microbial strains. In short, we propose learning a model to suggest modifications to an existing design by a reinforcement learning approach, where the feedback from the testing of a design is used to propose new, improved designs. Such a model has been recently shown to be promising approach for finding genetic modifications that maximise the productivity of synthetic microbial strain. The project will be conducted in collaboration with Synthetic biology team at VTT Technical Research Center of Finland. The ideal background for the student is an MSc in computer science, mathematics or statistics, with strong experience in machine learning. Experience in reinforcement learning, robotics, control systems engineering, synthetic biology or systems biology is considered as an advantage. To apply, fill in an application form at https://www.hict.fi/spring2020 by the call deadline Mon, 27.01.2020 Questions about the position: email juho.rousu at aalto.fi -------------- next part -------------- An HTML attachment was scrubbed... URL: From lodewykwessels at gmail.com Thu Jan 16 09:54:56 2020 From: lodewykwessels at gmail.com (Lodewyk Wessels) Date: Thu, 16 Jan 2020 09:54:56 +0100 Subject: [SocBiN] Postdoc Computational Biology Message-ID: Dear all We have a postdoc position open at the Netherlands Cancer Institute in collaboration with Scenic Biotech on reconstructing maps of cellular regulation. See ccb.nki.nl/open-positions/ Best wishes Lodewyk Wessels [image: New CellCircuits Graphic Add Jan2020 V2.jpg] -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: New CellCircuits Graphic Add Jan2020 V2.jpg Type: image/jpeg Size: 523637 bytes Desc: not available URL: From oliver.sohnlein at ki.se Thu Jan 23 09:07:18 2020 From: oliver.sohnlein at ki.se (=?iso-8859-1?Q?Oliver_S=F6hnlein?=) Date: Thu, 23 Jan 2020 08:07:18 +0000 Subject: [SocBiN] Post-Doc position on circadian rhythms at Karolinska Institute in Stockholm Message-ID: Dear Colleagues, I am looking for a skilled Post-Doc with expertise in bioinformatics and an interest in connecting vascular inflammation and circadian rhythms. The 3-year position is in my lab in Stockholm, details can be found here: https://ki.varbi.com/se/what:job/jobID:311728/ I would much appreciate if you could forward this link to potential candidates. Kind regards. Oliver När du skickar e-post till Karolinska Institutet (KI) innebär detta att KI kommer att behandla dina personuppgifter. Här finns information om hur KI behandlar personuppgifter. Sending email to Karolinska Institutet (KI) will result in KI processing your personal data. You can read more about KI's processing of personal data here. -------------- next part -------------- An HTML attachment was scrubbed... URL: From par.engstrom at scilifelab.se Tue Jan 28 13:02:49 2020 From: par.engstrom at scilifelab.se (=?utf-8?B?UMOkciBFbmdzdHLDtm0=?=) Date: Tue, 28 Jan 2020 13:02:49 +0100 Subject: [SocBiN] Two bioinformatician positions at Karolinska Institutet, Stockholm References: <6304A236-A8A0-4C22-9459-4B2636F8998B@ki.se> Message-ID: > Begin forwarded message: > > From: Goncalo Castelo-Branco > Subject: two bioinformatician positions > Date: 27 January 2020 at 16:52:35 CET > To: Goncalo Castelo-Branco > > Hi all, > > Would you mind spreading the word of these 2 bioinformatician positions in my lab and at Ana Falcao’s? > > Thanks! > All the best, > Gonçalo > > > https://ki.varbi.com/en/what:job/jobID:313855/ > > Applications for two bioinformatician positions are welcome at the unit of Molecular Neurobiology (MBB), at Karolinska Institutet, Stockholm, Sweden. One position will be as a core bioinformatician at the Gonçalo Castelo-Branco research group and the other position will be for a post-doctoral project, joint with Ana Mendanha Falcao’s group (also at University of Minho , Portugal). > > Your mission > > The successful candidates will be actively working in specific projects with single-cell and bulk transcriptomics and epigenomics, and will be integrated in a multidisciplinary team comprising computational, molecular and cellular biologists. The core bioinformatician will also work on web development, data curation, handling of data integration and visualization frameworks, among other tasks. > > Your profile > > We are looking for highly motivated, driven, inquisitive, enthusiastic persons interested in our area of research, and ready to explore new avenues in science. The candidates should have a collaborative approach to research, working productively in a team and contributing to a good social environment in the laboratory. > > The applicants must have at least a Master in bioinformatics and computational biology (for the core bioinformatician position) or PhD degree (for the post-doctoral bioinformatician position), and strong programming skills (R and/or Python and/or others), UNIX and LINUX systems knowledge, familiarity with data science a big data. Research experience and expertise in analysis of sequencing data is highly desirable. Wet lab experience is not required but it is an advantage for the postdoctoral bioinformatician position. > > Note: qualification to be employed for the postdoctoral position is a doctoral degree or equivalent scientific competence. Applicants who have not completed a doctorate at the end of the application period may also apply, provided that all requirements for a completed degree are met before the (intended) date of employment. This must be substantiated by the applicant's main supervisor, director or equivalent. > > What do we offer? > > A creative and inspiring environment full of expertise and curiosity. Karolinska Institutet is one of the world's leading medical universities. Our vision is to pursue the development of knowledge about life and to promote a better health for all. At Karolinska Institutet, we conduct successful medical research and hold the largest range of medical education in Sweden. Karolinska Institutet is a state university, which entitles to several benefits such as extended holiday and generous occupational pension. Employees also have access to our modern gym for free and receive reimbursements for medical care. > > The Unit of Molecular Neurobiology has presently seven research groups, focused on several aspects of development, stem cell biology, neuroscience and cancer, providing a unique critical mass and expertize, and vibrant scientific environment. > > The Castelo-Branco research group is interested in the molecular mechanisms defining the epigenetic state of cells of the oligodendrocyte lineage. We are focused on how interplay between transcription factors, non-coding RNAs and chromatin modifying enzymes contribute to the transition between states within the oligodendrocyte lineage, with the aim to design epigenetic based-therapies to induce regeneration (remyelination) in demyelinating diseases, such as multiple sclerosis. Our research group has performed single nuclei/cell RNA-Seq and identified several cell states within the oligodendrocyte lineage in development and disease (Science 2016, Dev Cell 2018, Nature Medicine 2018, Nature 2019). Our findings suggest that oligodendrocyte lineage cells might present other functional properties than previously thought. > > Dr. Ana Mendanha Falcão has recently established her research group, which is focusing on the role of the choroid plexus in diseases such as multiple sclerosis. Her team aims to investigate the choroid plexus as a source of biologically active molecules to the central nervous system, in order to influence disease dynamics. The choroid plexus will be studied as an alternative target for disease therapies since it can be modulated by peripheral blood and it can substantially alter the brain composition both in terms of biologically active molecules and immune cell content. > > Location: Biomedicum, Solna (Stockholm, Sweden) > > https://ki.se/en/mbb/goncalo-castelo-branco-group > http://www.icvs.uminho.pt/about-icvs/people/analuisafalcao > > > _____________________________ > > Gonçalo Castelo-Branco > Associate Professor of Neurobiology > Senior Researcher in Neuroepigenetics > > Laboratory of Molecular Neurobiology > Department of Medical Biochemistry and Biophysics > Karolinska Institutet, Stockholm, Sweden > > address: Biomedicum, C6073,17177 Stockholm, Sweden > e-mail: Goncalo.Castelo-Branco at ki.se > Phone: +46(0)8 524 879 36 > Mobile: +46 (0)700 91 59 22 > > Skype: gcastb > Twitter: @GoCasteloBranco > website: http://ki.se/en/mbb/goncalo-castelo-branco-group > > > > > > När du skickar e-post till Karolinska Institutet (KI) innebär detta att KI kommer att behandla dina personuppgifter. Här finns information om hur KI behandlar personuppgifter . > > Sending email to Karolinska Institutet (KI) will result in KI processing your personal data. You can read more about KI’s processing of personal data here . -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: image001.png Type: image/png Size: 8372 bytes Desc: not available URL: From evdh at sniprbiome.com Thu Jan 30 12:16:42 2020 From: evdh at sniprbiome.com (Eric van der Helm) Date: Thu, 30 Jan 2020 11:16:42 +0000 Subject: [SocBiN] Microbiome Bioinformatician position in Copenhagen Message-ID: <37C7D13E-0C19-4E15-8EBB-B4A1C430966A@sniprbiome.com> Dear all, We have a position open at SNIPR BIOME in Copenhagen for a Microbiome Bioinformatician. We are looking for an experienced bioinformatician with fundamental skills in biological data analysis. The ideal candidate must have significant and proven experience handling next-generation sequencing data and working with large datasets. Please see https://www.jobindex.dk/vis-job/h957951?lang=en for the full job ad. Best regards, Eric Eric van der Helm, PhD Head of Synthetic Biology & Bioinformatics SNIPRBIOME Lersø Parkallé 44, 5.floor 2100 Copenhagen Denmark -------------- next part -------------- A non-text attachment was scrubbed... Name: image001.png Type: image/png Size: 12585 bytes Desc: image001.png URL: