From haja.kadarmideen at iscb.org Thu Apr 2 19:38:33 2020 From: haja.kadarmideen at iscb.org (Haja Kadarmideen) Date: Thu, 2 Apr 2020 19:38:33 +0200 Subject: [SocBiN] =?utf-8?q?Job_Vacancy_=E2=80=93_Bioinformatician_at_Syno?= =?utf-8?q?mics?= Message-ID: Job Vacancy – Bioinformatician (Senior/Junior) Location: Oxford, UK or Copenhagen, Denmark Type: Full-time, permanent Job Ref Nr: SYN-BI- 02/20 Synomics aims to transform the efficiency of the agri-food industry by improving animal and crop production efficiency, and the economics and sustainability of the entire production value chain for multiple species. Our platform is a revolutionary advance in the analysis of high-throughput genotypic, phenotypic and environmental data to accurately measure and analyse protein production efficiency, health, accelerate genetic progress, and deliver more sustainable protein production from animals and plants. We’re rapidly growing AI enabled genomics, breeding and precision agriculture company with global ambition and partnerships with some of the largest international livestock breeding companies and research institutes. We’re located near Oxford, UK and near Copenhagen, Denmark. We have a fantastic opportunity for a Senior or Junior Bioinformatician (with a focus on Animal/Plant sciences) to join our team at Synomics, reporting to our CTO, Professor Haja Kadarmideen. We are looking for someone who is comfortable working with one or more livestock species (e.g., dairy & beef cattle, pig, companion animal and poultry breeding) datasets both commercial and academic. The ideal candidate will have relevant expertise and experience in bioinformatics, data science and computational (systems) biology. The main responsibilities will involve identifying and interpreting novel associations within large, multi-dimensional animal/crop phenotypic, pedigree and genetic / genomic datasets. The ideal candidate will have a keen interest in creating insight and value from complex data from animal/crop breeding organizations and experiments, a good knowledge of animal/crop biology and a passion for identifying and answering questions that help us solve real-world problems and build the best products. This is an exciting opportunity to help shape the direction of the business as a key member of the team. Please go to: https://github.com/Synomics/jobvacancies to download the full job description matching with job title / reference ID. To apply, please submit cover letter, your CV, and publication list (if relevant) to: jobs at synomics.ai DEADLINE FOR APPLICATIONS: 27 April 2020 Synomics is a new portfolio company of Wheatsheaf Group Ltd and has a close collaboration with PrecisionLife Ltd. Prof.Haja Kadarmideen CTO Synomics Ltd & Director Synomics ApS Professor, Technical University of Denmark From haja.kadarmideen at iscb.org Thu Apr 2 19:42:31 2020 From: haja.kadarmideen at iscb.org (Haja Kadarmideen) Date: Thu, 2 Apr 2020 19:42:31 +0200 Subject: [SocBiN] Job Vacancy - Quantitative Geneticist at Synomics Message-ID: Job Vacancy: Quantitative Geneticist (Senior/Junior) Location: Oxford, UK or Copenhagen, Denmark Type: Full-time, permanent Job Ref Nr: SYN-QG-01/20 Synomics aims to transform the efficiency of the agri-food industry by improving animal and crop production efficiency, and the economics and sustainability of the entire production value chain for multiple species. Our platform is a revolutionary advance in the analysis of high-throughput genotypic, phenotypic and environmental data to accurately measure and analyse protein production efficiency, health, accelerate genetic progress, and deliver more sustainable protein production from animals and plants. We’re rapidly growing AI enabled genomics, breeding and precision agriculture company with global ambition and partnerships with some of the largest international livestock breeding companies and research institutes. We’re located near Oxford, UK and near Copenhagen, Denmark. We have a fantastic opportunity for a Senior or Junior Quantitative Geneticist to join our team, reporting to our Chief Technology Officer, Professor Haja Kadarmideen. We are looking for someone who is comfortable working with one or more livestock species (e.g., dairy & beef cattle, pigs, companion animals and poultry) datasets both commercial and academic. The ideal candidate will have strong expertise and experience in quantitative genetics, statistical genetics, genomic breeding value estimation, genomic selection in animal / plant breeding and large-scale genome-phenotype association studies using standard as well as new computational tools (e.g. AI/machine learning). The main responsibilities will involve identifying and interpreting novel associations within large, multi-dimensional animal/crop phenotypic, pedigree and genetic / genomic datasets. The ideal candidate will have a keen interest in creating insight and value from complex data from animal/crop breeding organizations and experiments, a good knowledge of animal/crop biology and a passion for identifying and answering questions that help us solve real-world problems and build the best products.This is an exciting opportunity to help shape the direction of the business as a key member of the team. Please go to: https://github.com/Synomics/jobvacancies to download the full job description matching with job title / reference ID. To apply, please submit cover letter, your CV, and publication list (if relevant) to: jobs at synomics.ai DEADLINE FOR APPLICATIONS: 27 April 2020 Synomics is a new portfolio company of Wheatsheaf Group Ltd and has a close collaboration with PrecisionLife Ltd. Prof.Haja Kadarmideen CTO Synomics Ltd & Director Synomics ApS Professor, Technical University of Denmark From jondelius at gmail.com Thu Apr 2 20:39:40 2020 From: jondelius at gmail.com (Ulf Jondelius) Date: Thu, 2 Apr 2020 20:39:40 +0200 Subject: [SocBiN] Postdoc position: Phylogenomics in Stockholm Message-ID: In view of the current situation we have extended the closing date for applications and delayed the staring date for this position. Postdoctoral position in phylogenomics A two-year postdoctoral position is available in the Department of Zoology, Swedish Museum of Natural History, Stockholm. The position is supervised by Prof. Ulf Jondelius, as a part of the project "Evolution of Xenacoelomorpha, an ancient animal group " funded by the Swedish Reseach Council. The goal of this project is to perform an analysis of phylogeny, evolutionary rates and gene content of the marine animal group Xenacoelomorpha using transcriptomic and genomic data. The successful candidate will manage and analyse transcriptome and genome sequencing data, perform phylogenomic analyses and write papers. There will be opportunities to participate in undergraduate teaching and supervision of students. Qualifications Postdoctoral positions are appointed primarily for purposes of research. Applicants are expected to hold a Swedish doctoral degree or an equivalent degree from another country. The degree should have been completed no more than three years before the deadline for applications. In the appointment process, special attention will be given to research skills. We are looking for candidates with primarily dry-lab skills in the fields of genomics, transcriptomics and phylogenomics including experience with managing, processing and analysing next-generation sequencing data. Specific experience with metazoan evolution and microscopic invertebrates constitutes an advantage, but is not strictly necessary. The candidate must be highly motivated, creatively thinking with a collaborative attitude, have strong writing skills and a record of high-quality scientific publications. Excellent English language skills both written and spoken, are a requisite. Terms of employment The position involves full-time employment for a maximum of two years, Start date 2020-08-01 or as per agreement. The Swedish Museum of Natural History strives to be a workplace free from discrimination and with equal opportunities for all. Application deadline 1 May 2020 Informal queries may be directed to ulf.jondelius at nrm.se FURTHER INFORMATION AND HOW TO APPLY (in English): https://www.nrm.se/en/ommuseet/jobbahososs/ledigatjanster.9005019.html Ulf Jondelius, PhD Professor of Invertebrate Zoology, Swedish Museum of Natural History Box 50007 SE-104 05 Stockholm, Sweden From arne at bioinfo.se Fri Apr 3 20:32:47 2020 From: arne at bioinfo.se (Arne Elofsson) Date: Fri, 3 Apr 2020 20:32:47 +0200 Subject: [SocBiN] Fwd: Urgent need, Region Stockholm In-Reply-To: <15B7AA42-CFA2-4893-A81F-296462848B6E@mech.kth.se> References: <68CB6305-2D7A-4DBE-A556-574D48AB1404@kth.se> <15B7AA42-CFA2-4893-A81F-296462848B6E@mech.kth.se> Message-ID: ---------- Forwarded message --------- From: Olivia Eriksson Date: Fri, 3 Apr 2020, 19:05 Subject: Fwd: Urgent need, Region Stockholm To: Olivia Eriksson Cc: Hedvig Kjellström Dear SeRC PIs, I believe this call might be of interest so some of you? Contact Tobias Oechtering (below): All the best, /Hedvig Kjellström Vidarebefordrat mejl: *Från: *Tobias Oechtering *Ämne: **Urgent need, Region Stockholm* *Datum: *3 april 2020 15:34:23 CEST *Till: *Joakim Jaldén , Saikat Chatterjee , Hedvig Kjellström , Danica Kragic Jensfelt , Alexandre Proutiere , Carlo Fischione , Patric Jensfelt , Jonas Beskow , Ragnar Thobaben , Christian Smith , Petter Ögren < petter at kth.se>, Atsuto Maki , Martin Monperrus < martin.monperrus at csc.kth.se>, Benoit Baudry , Seif Haridi < haridi at kth.se>, Henrik Boström , Magnus Boman , Sarunas Girdzijauskas , Henrik Hult , Gabriel Skantze , Ozan Öktem , Aristides Gionis < argioni at kth.se> *Kopia: *Johan Blaus Dear all Region Stockholm approached KTH since they are in an urgent need of an experienced data scientist related to Covid-19. Please see the description below. Here the request forwarded by Johan: Däremot en sak de har behov av med mkt kort varsel är en resurs/person med den kompetens som finns beskriven i bifogat dokument. Fundera gärna igenom om det finns någon sådan person i ert nätverk, antingen inom akademin eller industrin och återkom till mig och Mikael Östling så kan vi sammanställa för dialog med Region Stockholm. Helst vill de ha en sådan resurs på plats nästa vecka, så vi skulle uppskatta om ni skyndsamt kan komma med uppslag. Please forward names if you know people that could be help here. Best, Tobias Begin forwarded message: *From: *Johan Blaus *Subject: **FW: Region Stockholm idag* *Date: *3 April 2020 at 11:50:05 CEST *To: *Tobias Oechtering , Peter Savolainen , Gert Svensson , Patrick Norman , Pontus Johnson < pontusj at kth.se>, Mats Danielsson , Daniel Jonsson < daniel.jonsson at abe.kth.se> *Cc: *Mikael Östling ----------------------------------------------- Hedvig Kjellström (née Sidenbladh) Professor, KTH EECS RPL http://people.kth.se/~hedvig/ +46-8-790 69 06 Through, Olivia Eriksson Coordinator, SeRC KTH Mechanics Phone:+46-8-790-84-82 Cell:+46-730-710031 -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: Data Scientist.docx Type: application/vnd.openxmlformats-officedocument.wordprocessingml.document Size: 14854 bytes Desc: not available URL: From hiller at mpi-cbg.de Fri Apr 3 20:49:05 2020 From: hiller at mpi-cbg.de (Michael Hiller) Date: Fri, 3 Apr 2020 20:49:05 +0200 Subject: [SocBiN] Urgent need, Region Stockholm In-Reply-To: References: <68CB6305-2D7A-4DBE-A556-574D48AB1404@kth.se> <15B7AA42-CFA2-4893-A81F-296462848B6E@mech.kth.se> Message-ID: <8F426FC4-A59B-4E4A-89EF-5EA13DD4B1CC@mpi-cbg.de> Hi all, I contacted Florian Jug from our institute and he recommended to post the request in english to https://forms.gle/D4KmuTfRmqBk2pos6 and https://discourse.data-against-covid.org which is a forum where a whole bunch of data scientists have gathered and would be happy to help. - Michael > On 3. Apr 2020, at 20:32, Arne Elofsson wrote: > > > ---------- Forwarded message --------- > From: Olivia Eriksson > > Date: Fri, 3 Apr 2020, 19:05 > Subject: Fwd: Urgent need, Region Stockholm > To: Olivia Eriksson > > Cc: Hedvig Kjellström > > > > Dear SeRC PIs, > > I believe this call might be of interest so some of you? Contact Tobias Oechtering (below): > > All the best, > /Hedvig Kjellström > >> Vidarebefordrat mejl: >> >> Från: Tobias Oechtering > >> Ämne: Urgent need, Region Stockholm >> Datum: 3 april 2020 15:34:23 CEST >> Till: Joakim Jaldén >, Saikat Chatterjee >, Hedvig Kjellström >, Danica Kragic Jensfelt >, Alexandre Proutiere >, Carlo Fischione >, Patric Jensfelt >, Jonas Beskow >, Ragnar Thobaben >, Christian Smith >, Petter Ögren >, Atsuto Maki >, Martin Monperrus >, Benoit Baudry >, Seif Haridi >, Henrik Boström >, Magnus Boman >, Sarunas Girdzijauskas >, Henrik Hult >, Gabriel Skantze >, Ozan Öktem >, Aristides Gionis > >> Kopia: Johan Blaus > >> >> Dear all >> >> Region Stockholm approached KTH since they are in an urgent need of an experienced data scientist related to Covid-19. Please see the description below. Here the request forwarded by Johan: >> >> Däremot en sak de har behov av med mkt kort varsel är en resurs/person med den kompetens som finns beskriven i bifogat dokument. >> Fundera gärna igenom om det finns någon sådan person i ert nätverk, antingen inom akademin eller industrin och återkom till mig och Mikael Östling så kan vi sammanställa för dialog med Region Stockholm. Helst vill de ha en sådan resurs på plats nästa vecka, så vi skulle uppskatta om ni skyndsamt kan komma med uppslag. >> >> Please forward names if you know people that could be help here. >> >> Best, Tobias >> >> >>> Begin forwarded message: >>> >>> From: Johan Blaus > >>> Subject: FW: Region Stockholm idag >>> Date: 3 April 2020 at 11:50:05 CEST >>> To: Tobias Oechtering >, Peter Savolainen >, Gert Svensson >, Patrick Norman >, Pontus Johnson >, Mats Danielsson >, Daniel Jonsson > >>> Cc: Mikael Östling > >>> > > >> > > ----------------------------------------------- > Hedvig Kjellström (née Sidenbladh) > Professor, KTH EECS RPL > http://people.kth.se/~hedvig/ > +46-8-790 69 06 > > > Through, > Olivia Eriksson > Coordinator, SeRC > KTH Mechanics > Phone:+46-8-790-84-82 > Cell:+46-730-710031 > _______________________________________________ > SocBiN mailing list > SocBiN at lists.su.se > https://lists.su.se/mailman/listinfo/socbin-at-sbc.su.se -- Michael Hiller, PhD Senior Research Group Leader Max Planck Institute of Molecular Cell Biology and Genetics& Max Planck Institute for the Physics of Complex Systems Dresden, Germany https://www.mpi-cbg.de/hiller/ -------------- next part -------------- An HTML attachment was scrubbed... URL: From lukas.kall at scilifelab.se Tue Apr 7 09:38:49 2020 From: lukas.kall at scilifelab.se (=?UTF-8?Q?Lukas_K=C3=A4ll?=) Date: Tue, 7 Apr 2020 09:38:49 +0200 Subject: [SocBiN] Tenure Track position in Computational Biology at the Center for Computational Biology (Mines ParisTech) In-Reply-To: References: Message-ID: The Centre for Computational Biology (CBIO) of Mines ParisTech (PSL University) and Institut Curie in Paris is opening a *tenure-track *position at the intersection of *machine learning / statistics and biological or health *applications. For details please see our website at http://cbio.mines-paristech.fr/ and the offer at http://cbio.mines-paristech.fr/pdf-files/job-offer-junior-researcher-in-computational-biology and do not hesitate to contact me at chloe-agathe.azencott [at] mines-paristech.fr or Thomas Walter at thomas.walter [at] mines-paristech.fr . Applications are open until May 15. -------------- next part -------------- An HTML attachment was scrubbed... URL: From dirk.repsilber at oru.se Thu Apr 9 09:21:06 2020 From: dirk.repsilber at oru.se (Dirk Repsilber) Date: Thu, 9 Apr 2020 09:21:06 +0200 Subject: [SocBiN] Permanent position: Database manager/Data Engineer with AI / Machine Learning Expertise Message-ID: <06043807-3871-9bc5-4009-ac362fba050a@oru.se> Dear Bioinformaticians, we offer a permanent (tillsvidare) position as Database manager / Data Engineer with AI / Machine Learning Expertise at Örebro University. https://www.oru.se/jobba-hos-oss/lediga-jobb/jobbannons/?jid=20200130 Deadline: April 26th Glad Påsk! Sincerely Dirk -- _________________________________________________________ Dirk Repsilber Professor Functional Bioinformatics School of Medical Sciences (MV) University of Örebro S - 701 82 Örebro Sweden phone: +46 19 30 1256 web: http://www.oru.se/English/Employee/dirk_repsilber/ _________________________________________________________ From torognes at ifi.uio.no Wed Apr 15 17:47:42 2020 From: torognes at ifi.uio.no (=?utf-8?Q?Torbj=C3=B8rn_Rognes?=) Date: Wed, 15 Apr 2020 17:47:42 +0200 Subject: [SocBiN] Three bioinformatics postdoctoral positions (Scientia Fellows) in Oslo Message-ID: <1D13BCE5-E69B-4381-97AD-34B6CBCEB539@ifi.uio.no> Three bioinformatics postdoctoral positions (Scientia Fellows) are available at the Centre for Bioinformatics, University of Oslo, Norway. All 3 positions are open/independent projects related to broad thematic areas. Project description has to be defined and written together with the host before the application deadline (30 April 2020). Duration of positions: 3 years (fully funded) Thematic areas: Precision Medicine, 3D/4D Genome Dynamics, Microbiome Bioinformatics Skills required: Bioinformatics, computational sciences, molecular biology, physics, modeling, and/or programming Salary offered: 52,400 - 55,300 EUR/year (approximately 515,200 NOK/year) Latest starting date: 1 March 2021 Application deadline: 30 April 2020 How to apply: Email as soon as possible to ehovig at ifi.uio.no (Precision Medicine), jonas.paulsen at ibv.uio.no (3D/4D genome) or torognes at ifi.uio.no (Microbiome Bioinformatics) Short description of positions & thematic areas: Position 1 (Precision Medicine): development and application of novel classification algorithms, tools for precise molecular and patient stratification in cancer studies. Deep learning and novel machine learning methods are keywords. Position 2 (3D/4D Genome dynamics): development of novel computational methods and tools to explore dynamics of 3D genomes in time, essentially providing a 4D view of the genome. These will be used to study cancer and immune regulation processes. Position 3 (Microbiome Bioinformatics): development of new or improved algorithms, tools, and analysis pipelines for holistic microbiome bioinformatics on data from both amplicon and metagenomic sequencing, as well as metabolomics. For further details, please visit https://www.mn.uio.no/sbi/english/scientia-fellows/index.html -------------- next part -------------- An HTML attachment was scrubbed... URL: From xianjun.dong.umass at gmail.com Wed Apr 15 17:52:30 2020 From: xianjun.dong.umass at gmail.com (Xianjun Dong) Date: Wed, 15 Apr 2020 11:52:30 -0400 Subject: [SocBiN] Research scientist in bioinformatics position in Harvard Medical School & Brigham and Women's Hospital Message-ID: <0D104269-85AD-4A86-B3E8-311375818C60@gmail.com> Position: Research Scientist in Bioinformatics Location: Genomics and Bioinformatics Hub, Department of Neurology, Brigham and Women’s Hospital, Harvard Medical School We are looking for a bioinformatician or computational biologist to work with data from a wide variety of experimental platforms, with a focus on next-generation sequencing technologies. This role provides a unique opportunity to collaborate with world-class researchers who are working to understand and treat a wide range of diseases, including Alzheimer’s, Parkinson’s, multiple sclerosis, glioblastoma, and others. About us The Genomics and Bioinformatics Hub (http://bioinformatics.bwh.harvard.edu ) is a newly established program for bioinformatics research, services, and training in the Department of Neurology at Brigham and Women’s Hospital (BWH), a world-leading center of excellence in academic medicine and research. Jointly supported by the Program for Interdisciplinary Neuroscience and the Precision Neurology Program, the goal of the Genomics and Bioinformatics Hub is to bridge the gap between neuroscientists and computational scientists to their mutual benefit, and to advance the application of cutting-edge computational methods for brain disorders research. The hub will develop bioinformatics tools, data resources, infrastructure, and will provide training and collaborative support to the neuro research community (including neurology, neuro-oncology, neurosurgery, neuropathology, and basic neuroscience) at BWH, Harvard, and potentially with our industry collaborators. About you You have a background in biomedical or quantitative science and a strong interest in working with medical and/or biological researchers. You enjoy solving scientific questions with computational skills. You are an active user in biostars.org. You like to collaborate with an interdisciplinary team. You can integrate your knowledge of biology, genetics and cell biology with your computational knowledge to excel at communicating with programmers and wet-lab scientists alike. You are an independent learner, are keen to learn and apply new methods, and are motivated to continually expand your skills. You have good coding and data management habits that enable reproducible research. You are time-sensitive and able to simultaneously work on different projects and deadlines. The position is for two years with the possibility of further extension. The position is based at the new Hale Building for Transformative Medicine (HBTM) at Brigham and Women’s Hospital. The successful candidate will be appointed to the BWH Medical Staff as a Research Associate, and the Department of Neurology will propose that s/he be appointed as a Research Associate at the Harvard Medical School (HMS); however, final approval of this appointment rests with HMS. Responsibilities and Duties Reporting to the Hub director, and coordinating closely with other Hub members, the applicant will work on all aspects of the hub mission, providing expert bioinformatics support and promoting the hub within the BWH research community. S/he will be expected to develop collaborations and connections to researchers across multiple departments, to become informed about their work, and to contribute to the overall development of the hub strategy. Specific duties will include the following: Using existing bioinformatics tools to perform standard next-generation sequencing (NGS) data analysis, incl. genomic, transcriptomic, epigenomic, and other data; Developing or adapting new algorithms and pipeline to support customized data analysis; Documenting all work thoroughly, and providing manuscript-level reporting of final analyses and results; Providing project-based collaborative support in bioinformatics to investigators in different areas, including neurology, neuro-oncology, neurosurgery, neuropathology, and basis neuroscience; Coordinating with collaborating Research Computing groups to ensure consistent computing resources and data storage; Providing basic and advanced bioinformatics training to students and researchers in BWH, building on the success of our existing Bioinformatics Club. The research scientist is expected to assist the Director to maintain the training environment. We also have access to a sequencing platform (NextSeq and 10x Genomics) and the Research Scientist will manage the sequencing data stored on the server. Qualifications We are looking for a candidate with the following skills and experience: Master’s or doctoral degree in a related field (Bioinformatics, Statistics, Engineering, Computer Science etc.) Strong computational genomics experience in one of the following fields: Bulk RNA-Seq, single-cell sequencing data analysis, small RNA-Seq, ChIP-Seq, ATAC-Seq, whole-genome sequencing, target sequencing, exome-sequencing, CAGE, Hi-C. Fluent programming skills in R, Linux/Bash, and one or more scripting languages (Python, Perl, C or C++) Good spoken and written communication skills in English. At least one first-authored or co-authored paper, submitted, accepted or published in an English-language journal. Research experience in neuroscience is a plus. Github or other version control experience is a plus Cloud computing experience is a plus Statistics background is a plus Informal inquiries may be directed to Xianjun Dong, PhD, Director of Genomics and Bioinformatics Hub (xdong at rics.bwh.harvard.edu), or to Charles Jennings, PhD, Executive Director, Program for Interdisciplinary Neuroscience (cgjennings at bwh.harvard.edu). For consideration for this position, please send a cover letter explaining your background and motivation, detailing how you feel your skills can enrich the group’s activities, three (3) references and a full CV including contact details as a combined PDF to Xianjun Dong, Ph.D. by email (xdong at rics.bwh.harvard.edu) or by mail (60 Fenwood Road, Boston, MA 02115, USA). Brigham and Women’s Hospital is an Equal Opportunity Employer. All qualified applicants will receive consideration for employment without regard to race, color, religion, creed, sex, sexual orientation, gender identity, national origin, ancestry, age, veteran status, disability unrelated to job requirements, genetic information, military service, or other protected status. -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: Brigham+WomensMedCtr_Thea+JamesMStonemanCentennialPark_PP1001_lg.jpeg Type: image/jpeg Size: 119679 bytes Desc: not available URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: e3d29fa9-cacf-4be2-acf4-834400f16af9.jpeg Type: image/jpeg Size: 328918 bytes Desc: not available URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: 6817f6ffabcea547ff306b5896b69b10.jpeg Type: image/jpeg Size: 133565 bytes Desc: not available URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: bwh-us-news-2016-700x400.jpeg Type: image/jpeg Size: 54060 bytes Desc: not available URL: From xianjun.dong.umass at gmail.com Wed Apr 15 19:24:14 2020 From: xianjun.dong.umass at gmail.com (Xianjun Dong) Date: Wed, 15 Apr 2020 13:24:14 -0400 Subject: [SocBiN] Research scientist in bioinformatics position in Harvard Medical School & Brigham and Women's Hospital Message-ID: <8E30325A-5CA5-4C48-86EB-EA18FC5F9EB9@gmail.com> Position: Research Scientist in Bioinformatics Location: Genomics and Bioinformatics Hub, Department of Neurology, Brigham and Women’s Hospital, Harvard Medical School We are looking for a bioinformatician or computational biologist to work with data from a wide variety of experimental platforms, with a focus on next-generation sequencing technologies. This role provides a unique opportunity to collaborate with world-class researchers who are working to understand and treat a wide range of diseases, including Alzheimer’s, Parkinson’s, multiple sclerosis, glioblastoma, and others. About us The Genomics and Bioinformatics Hub (http://bioinformatics.bwh.harvard.edu ) is a newly established program for bioinformatics research, services, and training in the Department of Neurology at Brigham and Women’s Hospital (BWH), a world-leading center of excellence in academic medicine and research. Jointly supported by the Program for Interdisciplinary Neuroscience and the Precision Neurology Program, the goal of the Genomics and Bioinformatics Hub is to bridge the gap between neuroscientists and computational scientists to their mutual benefit, and to advance the application of cutting-edge computational methods for brain disorders research. The hub will develop bioinformatics tools, data resources, infrastructure, and will provide training and collaborative support to the neuro research community (including neurology, neuro-oncology, neurosurgery, neuropathology, and basic neuroscience) at BWH, Harvard, and potentially with our industry collaborators. About you You have a background in biomedical or quantitative science and a strong interest in working with medical and/or biological researchers. You enjoy solving scientific questions with computational skills. You are an active user in biostars.org . You like to collaborate with an interdisciplinary team. You can integrate your knowledge of biology, genetics and cell biology with your computational knowledge to excel at communicating with programmers and wet-lab scientists alike. You are an independent learner, are keen to learn and apply new methods, and are motivated to continually expand your skills. You have good coding and data management habits that enable reproducible research. You are time-sensitive and able to simultaneously work on different projects and deadlines. The position is for two years with the possibility of further extension. The position is based at the new Hale Building for Transformative Medicine (HBTM) at Brigham and Women’s Hospital. The successful candidate will be appointed to the BWH Medical Staff as a Research Associate, and the Department of Neurology will propose that s/he be appointed as a Research Associate at the Harvard Medical School (HMS); however, final approval of this appointment rests with HMS. Responsibilities and Duties Reporting to the Hub director, and coordinating closely with other Hub members, the applicant will work on all aspects of the hub mission, providing expert bioinformatics support and promoting the hub within the BWH research community. S/he will be expected to develop collaborations and connections to researchers across multiple departments, to become informed about their work, and to contribute to the overall development of the hub strategy. Specific duties will include the following: Using existing bioinformatics tools to perform standard next-generation sequencing (NGS) data analysis, incl. genomic, transcriptomic, epigenomic, and other data; Developing or adapting new algorithms and pipeline to support customized data analysis; Documenting all work thoroughly, and providing manuscript-level reporting of final analyses and results; Providing project-based collaborative support in bioinformatics to investigators in different areas, including neurology, neuro-oncology, neurosurgery, neuropathology, and basis neuroscience; Coordinating with collaborating Research Computing groups to ensure consistent computing resources and data storage; Providing basic and advanced bioinformatics training to students and researchers in BWH, building on the success of our existing Bioinformatics Club. The research scientist is expected to assist the Director to maintain the training environment. We also have access to a sequencing platform (NextSeq and 10x Genomics) and the Research Scientist will manage the sequencing data stored on the server. Qualifications We are looking for a candidate with the following skills and experience: Master’s or doctoral degree in a related field (Bioinformatics, Statistics, Engineering, Computer Science etc.) Strong computational genomics experience in one of the following fields: Bulk RNA-Seq, single-cell sequencing data analysis, small RNA-Seq, ChIP-Seq, ATAC-Seq, whole-genome sequencing, target sequencing, exome-sequencing, CAGE, Hi-C. Fluent programming skills in R, Linux/Bash, and one or more scripting languages (Python, Perl, C or C++) Good spoken and written communication skills in English. At least one first-authored or co-authored paper, submitted, accepted or published in an English-language journal. Research experience in neuroscience is a plus. Github or other version control experience is a plus Cloud computing experience is a plus Statistics background is a plus Informal inquiries may be directed to Xianjun Dong, PhD, Director of Genomics and Bioinformatics Hub (xdong at rics.bwh.harvard.edu ), or to Charles Jennings, PhD, Executive Director, Program for Interdisciplinary Neuroscience (cgjennings at bwh.harvard.edu ). For consideration for this position, please send a cover letter explaining your background and motivation, detailing how you feel your skills can enrich the group’s activities, three (3) references and a full CV including contact details as a combined PDF to Xianjun Dong, Ph.D. by email (xdong at rics.bwh.harvard.edu ) or by mail (60 Fenwood Road, Boston, MA 02115, USA). Brigham and Women’s Hospital is an Equal Opportunity Employer. All qualified applicants will receive consideration for employment without regard to race, color, religion, creed, sex, sexual orientation, gender identity, national origin, ancestry, age, veteran status, disability unrelated to job requirements, genetic information, military service, or other protected status. -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: Brigham+WomensMedCtr_Thea+JamesMStonemanCentennialPark_PP1001_lg.jpeg Type: image/jpeg Size: 119679 bytes Desc: not available URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: e3d29fa9-cacf-4be2-acf4-834400f16af9.jpeg Type: image/jpeg Size: 328918 bytes Desc: not available URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: 6817f6ffabcea547ff306b5896b69b10.jpeg Type: image/jpeg Size: 133565 bytes Desc: not available URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: bwh-us-news-2016-700x400.jpeg Type: image/jpeg Size: 54060 bytes Desc: not available URL: From Karin.Lagesen at vetinst.no Thu Apr 16 10:11:00 2020 From: Karin.Lagesen at vetinst.no (Lagesen, Karin) Date: Thu, 16 Apr 2020 08:11:00 +0000 Subject: [SocBiN] Permanent position, Research Software Engineer/Sysadmin, Norwegian Veterinary Institute, Norway Message-ID: Hi all! The Norwegian Veterinary Institute, Oslo/Ås, Norway, has a permanent position out as a research software engineer/systems administrator. The closing deadline for this posting is the 3rd of May. The person employed will work on modernizing infrastructure and digitalization of the Institute's work processes, and as such will have a high impact on how the Norwegian Veterinary Institute will operate in future. This person will be employed in the IT section, and will collaborate closely with the inhouse bioinformatics team and other data focused research teams. If anybody would like to discuss further about this job, feel free to contact me directly. Here is the full ad: https://vetinst.easycruit.com/vacancy/2497515/41906 Karin -- Karin Lagesen, PhD Bioinformatician, Section for Epidemiology Norwegian Veterinary Institute From arne at bioinfo.se Thu Apr 16 16:13:41 2020 From: arne at bioinfo.se (Arne Elofsson) Date: Thu, 16 Apr 2020 16:13:41 +0200 Subject: [SocBiN] Fwd: Research scientist in bioinformatics position in Harvard Medical School & Brigham and Women's Hospital In-Reply-To: <34675410-9B55-4C5D-8EE2-C0A7B608A321@gmail.com> References: <8E30325A-5CA5-4C48-86EB-EA18FC5F9EB9@gmail.com> <34675410-9B55-4C5D-8EE2-C0A7B608A321@gmail.com> Message-ID: Begin forwarded message: *From: *Xianjun Dong *Subject: **Research scientist in bioinformatics position in Harvard Medical School & Brigham and Women's Hospital* *Date: *April 15, 2020 at 1:24:14 PM EDT *To: *socbin-at-sbc.su.se at lists.su.se *Position*: Research Scientist in Bioinformatics *Location*: Genomics and Bioinformatics Hub, Department of Neurology, Brigham and Women’s Hospital, Harvard Medical School We are looking for a bioinformatician or computational biologist to work with data from a wide variety of experimental platforms, with a focus on next-generation sequencing technologies. This role provides a unique opportunity to collaborate with world-class researchers who are working to understand and treat a wide range of diseases, including Alzheimer’s, Parkinson’s, multiple sclerosis, glioblastoma, and others. *About us* The Genomics and Bioinformatics Hub (http://bioinformatics.bwh.harvard.edu) is a newly established program for bioinformatics research, services, and training in the Department of Neurology at Brigham and Women’s Hospital (BWH), a world-leading center of excellence in academic medicine and research. Jointly supported by the Program for Interdisciplinary Neuroscience and the Precision Neurology Program, the goal of the Genomics and Bioinformatics Hub is to bridge the gap between neuroscientists and computational scientists to their mutual benefit, and to advance the application of cutting-edge computational methods for brain disorders research. The hub will develop bioinformatics tools, data resources, infrastructure, and will provide training and collaborative support to the neuro research community (including neurology, neuro-oncology, neurosurgery, neuropathology, and basic neuroscience) at BWH, Harvard, and potentially with our industry collaborators. *About you* You have a background in biomedical or quantitative science and a strong interest in working with medical and/or biological researchers. You enjoy solving scientific questions with computational skills. You are an active user in biostars.org. You like to collaborate with an interdisciplinary team. You can integrate your knowledge of biology, genetics and cell biology with your computational knowledge to excel at communicating with programmers and wet-lab scientists alike. You are an independent learner, are keen to learn and apply new methods, and are motivated to continually expand your skills. You have good coding and data management habits that enable reproducible research. You are time-sensitive and able to simultaneously work on different projects and deadlines. The position is for two years with the possibility of further extension. The position is based at the new Hale Building for Transformative Medicine (HBTM) at Brigham and Women’s Hospital. The successful candidate will be appointed to the BWH Medical Staff as a Research Associate, and the Department of Neurology will propose that s/he be appointed as a Research Associate at the Harvard Medical School (HMS); however, final approval of this appointment rests with HMS. *Responsibilities and Duties* Reporting to the Hub director, and coordinating closely with other Hub members, the applicant will work on all aspects of the hub mission, providing expert bioinformatics support and promoting the hub within the BWH research community. S/he will be expected to develop collaborations and connections to researchers across multiple departments, to become informed about their work, and to contribute to the overall development of the hub strategy. Specific duties will include the following: - Using existing bioinformatics tools to perform standard next-generation sequencing (NGS) data analysis, incl. genomic, transcriptomic, epigenomic, and other data; - Developing or adapting new algorithms and pipeline to support customized data analysis; - Documenting all work thoroughly, and providing manuscript-level reporting of final analyses and results; - Providing project-based collaborative support in bioinformatics to investigators in different areas, including neurology, neuro-oncology, neurosurgery, neuropathology, and basis neuroscience; - Coordinating with collaborating Research Computing groups to ensure consistent computing resources and data storage; - Providing basic and advanced bioinformatics training to students and researchers in BWH, building on the success of our existing Bioinformatics Club. The research scientist is expected to assist the Director to maintain the training environment. - We also have access to a sequencing platform (NextSeq and 10x Genomics) and the Research Scientist will manage the sequencing data stored on the server. *Qualifications* We are looking for a candidate with the following skills and experience: - Master’s or doctoral degree in a related field (Bioinformatics, Statistics, Engineering, Computer Science etc.) - Strong computational genomics experience in one of the following fields: Bulk RNA-Seq, single-cell sequencing data analysis, small RNA-Seq, ChIP-Seq, ATAC-Seq, whole-genome sequencing, target sequencing, exome-sequencing, CAGE, Hi-C. - Fluent programming skills in R, Linux/Bash, and one or more scripting languages (Python, Perl, C or C++) - Good spoken and written communication skills in English. - At least one first-authored or co-authored paper, submitted, accepted or published in an English-language journal. - Research experience in neuroscience is a plus. - Github or other version control experience is a plus - Cloud computing experience is a plus - Statistics background is a plus Informal inquiries may be directed to Xianjun Dong, PhD, Director of Genomics and Bioinformatics Hub (xdong at rics.bwh.harvard.edu), or to Charles Jennings, PhD, Executive Director, Program for Interdisciplinary Neuroscience (cgjennings at bwh.harvard.edu). For consideration for this position, please send a cover letter explaining your background and motivation, detailing how you feel your skills can enrich the group’s activities, three (3) references and a full CV including contact details as a combined PDF to Xianjun Dong, Ph.D. by email ( xdong at rics.bwh.harvard.edu) or by mail (60 Fenwood Road, Boston, MA 02115, USA). *Brigham and Women’s Hospital is an Equal Opportunity Employer. All qualified applicants will receive consideration for employment without regard to race, color, religion, creed, sex, sexual orientation, gender identity, national origin, ancestry, age, veteran status, disability unrelated to job requirements, genetic information, military service, or other protected status.* [image: enter image description here] [image: enter image description here] [image: enter image description here] [image: enter image description here] -------------- next part -------------- An HTML attachment was scrubbed... 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Name: bwh-us-news-2016-700x400.jpeg Type: image/jpeg Size: 54060 bytes Desc: not available URL: From ovidiu.radulescu at umontpellier.fr Fri Apr 17 13:44:34 2020 From: ovidiu.radulescu at umontpellier.fr (Ovidiu Radulescu) Date: Fri, 17 Apr 2020 13:44:34 +0200 Subject: [SocBiN] 2 phD openings in mathematical and systems biology in Montpellier Message-ID: <72d6fae0-69fc-5c84-cd1e-b32a9cfbd6ff@umontpellier.fr> Dear All, We are offering 2 phD positions in mathematical and systems biology at the University of Montpellier, France, funded under the U Chicago-CNRS Collaboration program and LabMuse EPIGENMED training network. The students will be trained in two interdisciplinary training networks involving four labs in Montpellier and one lab at the University of Chicago. Our research combines mathematical modelling and cutting-edge biological experiments to understand the impact of stochastic fluctuations in two relevant problems in HIV-1 infection and developmental biology. We are seeking motivated students holding a master degree in a field relevant to the project: biology, mathematics, physics, engineering. The students will contribute to all the aspects of the project: theoretical, mathematical and experimental. A high level of interest for interdisciplinary research is therefore compulsory for successful candidates. More details can be found at https://ovidiu-radulescu.yj.fr/stages/PhD_CNRS_CHICAGO_long.pdf https://ovidiu-radulescu.yj.fr/stages/PhD_MUSE_long.pdf Kind regards, Ovidiu Radulescu  -- Prof. Ovidiu Radulescu Université de Montpellier ------------------------------------------------------------------- LPHI - UMR 5235 CNRS/UM1/UM2   Phone: +33-(0)4-6714-9221 Pl. E. Bataillon - Bat. 24      Fax:   +33-(0)4-6714-4286 Université de Montpellier        email: ovidiu.radulescu at univ-montp2.fr CP 107 34095 Montpellier Cedex 5 FRANCE -------------- next part -------------- An HTML attachment was scrubbed... URL: From Ola.Spjuth at farmbio.uu.se Tue Apr 21 16:32:46 2020 From: Ola.Spjuth at farmbio.uu.se (Ola Spjuth) Date: Tue, 21 Apr 2020 14:32:46 +0000 Subject: [SocBiN] Postdoc position: 'AI methods for large-scale microscopy imaging' at Uppsala University Message-ID: <4F35B849-738F-453D-95B2-62DD6D7CA69E@farmbio.uu.se> Postdoc position available: AI methods for large-scale microscopy imaging [https://pharmb.io/img/continuous-ai.png] In my team at Uppsala University we are currently looking for an ambitious, highly motivated Postdoc with a good background in AI and imaging to join our research group where we have built up a robotized cell profiling system with high-content microscopy imaging as primary readout. The successful candidate will join an interdisciplinary team of researchers and participate in a project aiming to develop autonomous laboratories with applications in systems pharmacology and systems toxicology. For more information on the group, see https://pharmb.io and the automation project: https://pharmb.io/project/ai-automated-laboratory/. This is a 2-year postdoc position. Assignments include development and application of methods for large-scale analysis of microscopy images using AI / Machine Learning within the framework of the HASTE project. The project focuses on AI / machine learning with quantifiable confidence or probability, based on methods such as Active Learning, Conformal Prediction, Probabilistic (Venn) Prediction, and Deep Learning. Applicants are expected to collaborate with other project members and participate in regular research visits with industry partners AstraZeneca and Vironova. Qualifications PhD degree or a foreign degree equivalent to a PhD degree in a relevant field. The PhD degree must have been obtained no more than three years prior to the application deadline. The three year period can be extended due to circumstances such as sick leave, parental leave, duties in labour unions, etc. Documented experience with AI / ML methods and / or computerized image analysis. Experience in programming in eg Python is a requirement. Applicants should have excellent communication skills and be keen to actively interact with other team members including biologists, systems developers and researchers in AI / ML. Furthermore, applicants should be curious and creative, take initiatives and build relationships. Applicants should have good organizational ability, be able to structure work with multiple projects and solve anticipated and unexpected problems. The applicant must be able to express themselves very well in written and oral English More information: https://pharmb.io/blog/postdoc-pos-ai-haste-2020/ -- Ola Spjuth, PhD, Docent Associate Professor, Department of Pharmaceutical Biosciences Director of Studies, Pharmaceutical Bioinformatics Box 591, Uppsala University, Uppsala, Sweden Email: ola.spjuth at farmbio.uu.se Ph: +46 (0)70 425 06 28 Web: https://pharmb.io N?r du har kontakt med oss p? Uppsala universitet med e-post s? inneb?r det att vi behandlar dina personuppgifter. F?r att l?sa mer om hur vi g?r det kan du l?sa h?r: http://www.uu.se/om-uu/dataskydd-personuppgifter/ E-mailing Uppsala University means that we will process your personal data. For more information on how this is performed, please read here: http://www.uu.se/en/about-uu/data-protection-policy -------------- next part -------------- An HTML attachment was scrubbed... URL: From clements at galaxyproject.org Tue Apr 28 00:34:57 2020 From: clements at galaxyproject.org (Dave Clements) Date: Mon, 27 Apr 2020 15:34:57 -0700 Subject: [SocBiN] Bioinformatics Community Conference: Abstract submission and registration are open Message-ID: 2020 Bioinformatics Community Conference (BCC2020) Online, July 17-26 https://urlproxy.sunet.se/canit/urlproxy.php?_q=aHR0cHM6Ly9iY2MyMDIwLmdpdGh1Yi5pby8%3D&_s=ZGVmYXVsdA%3D%3D&_c=6b7a5e41&_r=c3Utc2U%3D The 2020 Bioinformatics Community Conference (BCC2020) will be online, global, affordable, and accessible. Key Dates: May 8: Deadline for submitting talk/poster/demo abstracts (this will not be extended) June 6: Authors notified about talk/poster/demo acceptance July 10: Early registration ends July 17-19: BCC2020 Training sessions July 19-22: BCC2020 Main meeting July 22-24, 24-26: CollaborationFest Core and Encore BCC2020 BCC2020 is a joint event bringing together the Bioinformatics Open Source Conference (BOSC) and Galaxy Communities. If you are working in data intensive life science research then there is no better event for sharing your work, and learning from other researchers addressing the challenges of modern data driven biology. BCC2020 will be held July 17-26 , and offer 2 days of training , a 3 day meeting , and a 4 day CollaborationFest . BOSC is organized by the Open Bioinformatics Foundation (OBF) , a non-profit group dedicated to promoting the practice and philosophy of open source software development and open science within the biological research community. Galaxy is an open source data integration and analysis platform for the life sciences that is used, deployed, maintained and extended by a worldwide community of researchers, students, software engineers, and infrastructure providers. BCC2020 is Online All BCC2020 events will be held online . Training will be live and interactive. The meeting will feature keynotes, accepted talks, lightning talks, posters, demos, and birds-of-a-feather and other networking opportunities. Talks (with the possible exception of keynotes) will be pre-recorded. Posters, demos, and BoFs will be live and interactive. The CoFest will also be live and interactive. BCC2020 is Global BCC2020 events will be held twice : once in the originally scheduled Toronto time zone (BCC West) , and then again 12 hours later in the Eastern hemisphere (BCC East) . Training will differ between East and West, with enrollment open to all, regardless of where you are. The main conference content will be presented in both East and West. We are striving to have the CoFest run continuously , with participants from every part of the world. BCC2020 is Affordable We have slashed registration rates for BCC2020 , and are offering even larger discounts to participants based in low and lower-middle income countries. Pricing starts at US$3 per training session, and $12 for the 3 day meeting. The CoFest is free. BCC2020 is Accessible Going online and global, combined with the low registration rates this enables, makes this the most accessible Galaxy or BOSC conference ever. If you work in open source bioinformatics then this is 2020’s best opportunity to share your work and learn from others. Abstracts Due May 8 BCC2020 is seeking oral presentations, lightning talks, posters, and demos, from researchers working in bioinformatics, and all over the world. Abstracts are due May 8 (and that deadline will not be extended). Please submit your work today. Register Now BCC2020 registration is now open . Registering early saves 50% off of the full rates. We hope to see you in July at BCC2020, BCC2020 Organizers -- https://galaxyproject.org/ -------------- next part -------------- An HTML attachment was scrubbed... URL: From Rolf.I.Skotheim at rr-research.no Tue Apr 28 13:34:01 2020 From: Rolf.I.Skotheim at rr-research.no (Rolf I. Skotheim) Date: Tue, 28 Apr 2020 11:34:01 +0000 Subject: [SocBiN] Postdoc position in cancer genomics In-Reply-To: <53884856FB6613478340EBDBA97D8B010DA6ED17@RHS-EXCHANGE-01.ad.medicalresearch.no> References: <53884856FB6613478340EBDBA97D8B010DA6ED17@RHS-EXCHANGE-01.ad.medicalresearch.no> Message-ID: <53884856FB6613478340EBDBA97D8B010DA6ED38@RHS-EXCHANGE-01.ad.medicalresearch.no> Dear all, We have a vacant position as postdoctoral fellow at the Genome Biology Group, Dept. Mol. Oncology, Institute for Cancer Research, Oslo University Hospital. The group’s projects are directed towards improvement of cancer diagnosis and management by utilization of genome technologies. Particular emphasis is on translational research of prostate cancer. The work will involve analysis of multiple omics and clinical data. Particularly the analyses will concern high-throughput DNA and RNA-sequencing data. It will involve database work, machine learning, and scripting, etc., both to develop and establish new analytical flow for genomics using existing software, and it will be needed to develop new ones. The candidate will contribute at all phases of the project, including planning, implementation, discussion of implications of the results, and presentation of the project, orally and manuscript preparation. Please see attached announcement. Best regards, Rolf Skotheim - - Group leader Genome Biology Group Department of Molecular Oncology Institute for Cancer Research Oslo University Hospital-Radiumhospitalet P. O. Box 4953 Nydalen, 0424 Oslo, Norway Tel: +47 2278 1727 http://www.ous-research.no/molecularoncology Professor II Biomedical Informatics, Section for Machine Learning Department of Informatics University of Oslo http://www.mn.uio.no/ifi/english/research/groups/bmi NCMM Associate Investigator Centre for Molecular Medicine Norway, University of Oslo https://www.med.uio.no/ncmm/english/about/collaborations/associate-investigators/ -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: 20200428_Postdoc_announcement.pdf Type: application/pdf Size: 656800 bytes Desc: 20200428_Postdoc_announcement.pdf URL: