From joshbaskaran at gmail.com Tue Nov 2 13:42:57 2021 From: joshbaskaran at gmail.com (Joshua Baskaran) Date: Tue, 2 Nov 2021 13:42:57 +0100 Subject: [SocBiN] Special engineer position available at the Bioinformatics Core Facility, OUS, Norway Message-ID: <36E23619-20ED-4E4A-878C-0BA88D371F02@gmail.com> Hi all, The Bioinformatics Core Facility at the Oslo University Hospital, Norway is looking for a special engineer. The position is for 2 years with possibility of extension. For more information, check-out the finn.no listing below: https://www.finn.no/job/fulltime/ad.html?finnkode=236969287 Best regards, Joshua -------------- next part -------------- An HTML attachment was scrubbed... URL: From felipe.cava at umu.se Tue Nov 2 14:02:33 2021 From: felipe.cava at umu.se (Felipe Cava) Date: Tue, 2 Nov 2021 14:02:33 +0100 Subject: [SocBiN] =?utf-8?q?Postdoc_position_in_data-driven_antimicrobial-?= =?utf-8?q?resistance_research_at_Ume=C3=A5_University?= Message-ID: Dear All, We are looking for a highly motivated postdoc who would like to join a multidisciplinary team with complementing expertise in molecular infection biology, systems biology, and machine learning. For more information about the project, the team, and how to apply, please see the attachment and here: https://icelab.se/opportunities/postdoctoral-fellowship-bacteria-cell-wall-systems-biology/ Best, Felipe -- Felipe Cava Associate Professor (Lektor) in Infection Biology Department of Molecular Biology, Umeå University (Affiliated) MIMS - Laboratory for Molecular Infection Medicine Sweden Laboratory 6k-42. Office 6K-26B SE-901 87 Umeå. Sweden https://thecavalab.com/ telephone: +46-090-7856755 Fax: +46(0)90-77 26 30 -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: Postdoc Data driven AMR 2021.pdf Type: application/pdf Size: 75287 bytes Desc: not available URL: From shilpa.garg2k7 at gmail.com Thu Nov 4 07:51:53 2021 From: shilpa.garg2k7 at gmail.com (shilpa) Date: Thu, 4 Nov 2021 07:51:53 +0100 Subject: [SocBiN] International course cum summer school 2022 - Copenhagen In-Reply-To: References: Message-ID: Hello, I am Shilpa Garg, an assistant professor at the University of Copenhagen. I am delighted to announce the course cum summer school on “Topics in Computational Biology” in the beautiful city of Copenhagen, July 11-24, 2022. Here is the form: https://forms.gle/5jMnvhepPHphJDi36. The deadline is Nov 26, 2021. If this will be helpful to any relevant students/departments/groups, please feel free to share. -- Regards, Shilpa From laurent.guyon at cea.fr Thu Nov 4 14:06:19 2021 From: laurent.guyon at cea.fr (GUYON Laurent 217719) Date: Thu, 4 Nov 2021 13:06:19 +0000 Subject: [SocBiN] Virtual seminar on microRNA targets welcoming Herve Seitz Message-ID: Dear all, In the framework of the small non-coding RNA bioinformatics club (https://smallrna-bioinformatics.eu/), we are happy to announce the virtual seminars of Sophie Mockly and Hervé Seitz about functional microRNA targets, and microRNA degradation. The club will propose seminars every two months. Start Monday November 8th at 4pm (CET, Berlin/Paris) (3 pm London/Lisbon, 10am New-York, 7am San Francisco, 5pm Tel Aviv) More information here: https://smallrna-bioinformatics.eu/Pages/Seminars/Seminar-Seitz.aspx Tweet for easy re-transmission: https://twitter.com/Laurent_Guyon/status/1450381126032371713 Link to the Zoom conference: https://univ-grenoble-alpes-fr.zoom.us/j/96875973366?pwd=SlB3eGtaUVovK2dDeEpEWDROVVJsUT09 Alternate link if you don't plan to ask questions (comments are authorized in YouTube): https://www.youtube.com/watch?v=Vyz9Gp6C7FM Main Speaker: Hervé Seitz, Research Director at CNRS, IGH, Montpellier, France *Title: A functional definition of "microRNA targets": current issues, biological implications, perspectives for improvement* Abstract: MicroRNAs (miRNAs) guide repressive proteins onto specific target RNAs. Targets are recognized by sequence complementarity, and the biochemical rules for target recognition are well described, allowing precise computational predictions of molecular miRNA targets. Consequently, high-throughput molecular biology and computational predictions now largely agree on the lists of miRNA targets, and it may seem that the biological impact of miRNA-guided regulation could be faithfully predicted and modeled. Yet these results are contradicted by the observed in vivo phenotypes: while current molecular biology and bio-informatics identify hundreds of targets for each miRNA (suggesting that miRNAs control many biological processes), in vivo genetics shows that miRNA mutants tend to exhibit subtle, discrete phenotypes (usually specific to a given organ and a given biological pathway). We will discuss the reasons for such a discrepancy, their practical implications in terms of miRNA biology, and potential improvements in the functional assignment of miRNAs. Short session speaker (8 minutes long): Sophie Mockly (PhD student) *Title: Computational prediction of microRNA degradation inducers* Abstract: MicroRNAs constitute a large family of ~21-nt-long RNAs loaded by AGO proteins to form the miRISC complex, which silences specific target mRNAs. In metazoans, the miRISC complex binds to perfectly or imperfectly complementary sequences, present most commonly in the 3 ́ UTRs of target mRNAs, causing mRNA translational repression or deadenylation. The spatial and temporal distribution of microRNAs in organisms is tightly regulated, and aberrant microRNA expression leads to disease. Up to now, the regulation of microRNA levels has been mainly explained by the regulation of microRNA biogenesis alone, neglecting microRNA turnover pathways. However, recent studies have described an endogenous mechanism of microRNA degradation based on binding specific target RNAs to microRNAs with extensive complementarity. This emerging pathway, named TDMD for Target-Directed MicroRNA Degradation, enables highly specific microRNA decay subsequently to the proteolysis of AGO by the ubiquitin-proteasome pathway, and in this way, provides a new layer of microRNA regulation. To date, in vivo examples have been observed mainly in some viruses and only three TDMD events have been characterized in metazoans. Based on published data about target RNA patterns leading to TDMD and phylogenetic conservation, we developed a computational tool for the in silico identification of RNA sites that induce microRNA degradation through TDMD. Supplemented with published RNA-seq and small-RNA-seq data, our workflow allows focusing on cell-specific TDMD inducer candidates. Our search uncovered several convincing candidates in mouse neurons and their molecular characterization has been initiated. References • microRNA target prediction programs predict many false positives, by Natalia Pinzón, Blaise Li, Laura Martinez, Anna Sergeeva, Jessy Presumey, Florence Apparailly, and Hervé Seitz Genome Research, published on 2017 (https://genome.cshlp.org/content/27/2/234.full) • On the Number of Functional microRNA Targets, by Hervé Seitz Molecular Biology and Evolution, published on 2019 (https://academic.oup.com/mbe/article/36/7/1596/5372676) • A rationalized definition of tumor suppressor microRNAs excludes miR-34a, by Sophie Mockly, Élisabeth Houbron, and Hervé Seitz bioRxiv, pre-print published on 2021 (https://www.biorxiv.org/content/10.1101/2021.02.11.430795v4) ____________________________ Laurent GUYON, PhD – Bioinformatics CEA IRIG (Interdisciplinary Research Institute of Grenoble) BioHealth Department BCI (Biology of Cancer and Infection laboratory) UMR 1292 CEA/Inserm/Université Grenoble Alpes CEA Grenoble - Bât C3 – Bureau 224 17 rue des Martyrs 38054 GRENOBLE Cedex 9 Tél : (+33)4.38.78.04.53 Fax : (+33)4 38 78 50 58 Email : laurent.guyon at cea.fr http://laurent.guyon.phd.free.fr/ Happy to share miRViz (free to use website to analyze your microRNA datasets): http://mirviz.prabi.fr/ Article: https://doi.org/10.1093/nar/gkaa259 Messages of the paper: https://twitter.com/Laurent_Guyon/status/1255487510563651586 -------------- next part -------------- An HTML attachment was scrubbed... URL: From tony.handstad at usit.uio.no Tue Nov 9 10:43:21 2021 From: tony.handstad at usit.uio.no (Tony =?utf-8?Q?H=C3=A5ndstad?=) Date: Tue, 09 Nov 2021 10:43:21 +0100 Subject: [SocBiN] Position available at Department of Microbiology, Oslo University Hospital References: Message-ID: A new position is now available at Department of Microbiology at Oslo University Hospital https://www.finn.no/job/fulltime/ad.html?finnkode=237761605 The candidate will have a key role in establishing the diagnostic offering at the department while also partaking in research within areas such as metagenomics, antibiotic resistance and virology. On behalf of Department of Microbiology, OUS Tony Håndstad From jenni.e.hamalainen at helsinki.fi Wed Nov 10 08:13:42 2021 From: jenni.e.hamalainen at helsinki.fi (=?utf-8?B?SMOkbcOkbMOkaW5lbiwgSmVubmkgRQ==?=) Date: Wed, 10 Nov 2021 07:13:42 +0000 Subject: [SocBiN] Call for postdoc/bioinformatician in computational cancer and autoimmunity research, University of Helsinki Message-ID: Open postdoctoral researcher/bioinformatician position at the University of Helsinki, Finland Professor Satu Mustjoki’s lab Hematology Research Unit (www.Helsinki.fi/hematology) at the University of Helsinki and Helsinki University Hospital Comprehensive Cancer Center has an opening for a POSTDOCTORAL RESEARCHER / BIOINFORMATICIAN in computational cancer and autoimmunity research. The new researcher / bioinformatician will play a critical role in the computational analysis and statistical modelling of large-size WES, WGS, lncRNA-seq, and scRNA-seq datasets and integration of these data with clinical information. The aim of the research is to further advance our understanding on the pathogenesis of cancer and autoimmunity diseases and builds upon the group’s previous successful work on the topic (please see our webpage and the latest publication list at https://pubmed.ncbi.nlm.nih.gov/?term=mustjoki+s%5Bau%5D&) See more and apply: https://www2.helsinki.fi/en/open-positions/postdoctoral-researcher-bioinformatician-in-computational-cancer-and-autoimmunity-research Best regards, Jenni Hämäläinen -- Jenni Hämäläinen Projektikoordinaattori / Project Coordinator Translational Immunology Program (TRIMM) Hematology Research Unit University of Helsinki jenni.e.hamalainen at helsinki.fi 0294126613 (+358504524919) -------------- next part -------------- An HTML attachment was scrubbed... URL: From iwona.zielinska at mimuw.edu.pl Wed Nov 17 21:17:55 2021 From: iwona.zielinska at mimuw.edu.pl (=?iso-8859-2?Q?Iwona_Zieli=F1ska?=) Date: Wed, 17 Nov 2021 21:17:55 +0100 Subject: [SocBiN] Post-doc Position in Computational Oncology and Machine Learning Message-ID: <019a01d7dbf0$35d78630$a1869290$@mimuw.edu.pl> Dear All, We invite applications for a Post-doc position, within a research collaboration between Merck Healthcare KGaA and the University of Warsaw. The Principal Investigator at Merck Healthcare is Dr Eike Staub, head of Oncology Bioinformatics and Dr Ewa Szczurek at the University of Warsaw. The project title is: "Machine learning methods for characterizing the tumour and its microenvironment from multidimensional molecular profiling data of tumours." All details can be found in the attached announcement and "Information on personal data processing". best regards, Iwona Zielińska _______________ Iwona Zielińska project manager University of Warsaw www.uw.edu.pl www.mimuw.edu.pl -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: 2021_11_17_PostdocPosition_Merck2.pdf Type: application/pdf Size: 113151 bytes Desc: not available URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: Inf. on personal data processing EN.pdf Type: application/pdf Size: 588699 bytes Desc: not available URL: From iwona.zielinska at mimuw.edu.pl Wed Nov 17 21:36:17 2021 From: iwona.zielinska at mimuw.edu.pl (=?iso-8859-2?Q?Iwona_Zieli=F1ska?=) Date: Wed, 17 Nov 2021 21:36:17 +0100 Subject: [SocBiN] Post-doc Position in project "Mapping tumor subclones ..." (Computational Biology and Machine Learning) Message-ID: <01bf01d7dbf2$c5b9b690$512d23b0$@mimuw.edu.pl> Dear All, We invite applications for a Post-doc position in the project: "TUMORMAP: Mapping tumour subclones and their immune microenvironment in ultra-high spatial and molecular resolution", led by Dr Ewa Szczurek at the Institute of Informatics at the Faculty of Mathematics, Informatics, and Mechanics of the University of Warsaw. All details can be found in the attached announcement and "Information on personal data processing". best regards, Iwona Zielińska _______________ Iwona Zielińska project manager University of Warsaw www.uw.edu.pl www.mimuw.edu.pl -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: Postdoc_TUMORMAP - SocBiN.pdf Type: application/pdf Size: 700807 bytes Desc: not available URL: From janina.bocksch at senckenberg.de Mon Nov 22 09:01:23 2021 From: janina.bocksch at senckenberg.de (Janina Bocksch) Date: Mon, 22 Nov 2021 09:01:23 +0100 (CET) Subject: [SocBiN] PostDoc Position in Comparative Genomics at Senckenberg Frankfurt / Application deadline December 12th 2021 Message-ID: <1417726444.524365.1637568083381@office.mailbox.org> The Hiller Lab at the LOEWE Center for Translational Biodiversity Genomics (TBG) in Frankfurt, Germany is looking for two ambitious Postdocs to investigate the genomic basis of phenotypic differences between vertebrates. The Project We offer several projects that range from the development of new comparative genomic methods to accurately detect relevant genomic changes in big datasets to applying existing and new approaches to link phenotypic adaptations to genomic differences, which is a central goal in the genomics era. The postdoc is expected to capitalize on a powerful repertoire of Forward Genomics and other methods such as TOGA (Tool to infer Orthologs from Genome Alignments) as well as available genome alignments and comparative data for hundreds of mammals and birds. A large list of interesting adaptations including metabolic, physiological and morphological traits in bats, dolphins, other mammals and vertebrates is available to be studied, and choices can be influenced by the preference of the postdoc. Our lab The mission of our group is to understand how nature's fascinating phenotypic diversity has evolved and how it is encoded in the genome. Work in the lab includes sequencing and assembly of reference-quality genomes, genome alignment and annotation, development and application of comparative genomic methods to discover differences in genes and cis-regulatory elements, and the use of statistical approaches to link phenotypic to genomic changes [1-9]. Our lab is part of TBG (https://tbg.senckenberg.de/) and Senckenberg Research Society, and is based near the city center of Frankfurt am Main, Germany. TBG provides access to cutting-edge computational (HPC clusters, genome browser) and lab infrastructure to sequence genomes. English is the working language in our lab. Senckenberg and TBG provide flexible working hours, an annual special payment, a company pension scheme, the Senckenberg badge for free entry in museums, the zoo, botanical garden and Palmengarten, a leave of 30 days per year, and a subsidy job ticket for public transport. Frankfurt is a vibrant and highly-international city at the heart of Europe that combines a skyscraper skyline with ample park and green areas. Requirements Applicants should have a degree in bioinformatics/computational biology, genomics or a related area, and a strong publication record. Solid programming skills in a Linux environment and experience with shell scripting and Unix tools are required. Previous experience in large-scale comparative genomic data analysis is an advantage. Place of employment: Frankfurt am Main Working hours: full time (40 hours/week) Type of contract: initially for 2 years, but funding is available to extend it further Salary and benefits: according to the collective agreement of the State of Hesse (pay grade E13 100%) The position is fully funded and should ideally start as soon as possible. The employer is the Senckenberg Gesellschaft für Naturforschung who supports equal opportunity of men and women and therefore strongly invites women to apply. Equally qualified handicapped applicants will be given preference. How to apply Please send your application, mentioning the reference of this job offer (ref.#12-21006), by e-mail to Michael Hiller (michael.hiller at senckenberg.de) and recruiting at senckenberg.de. Alternatively use our online application form on https://www.senckenberg.de/en/career/apply-online/. The application should include a CV with publication list and contact information for at least two references, and a summary of previous research experience (max 1 page), and copies of certificates, transcripts and grades. The initial application deadline is December 12th, 2021, but the search will continue until the position has been filled. For more information please contact Prof. Dr. Michael Hiller, michael.hiller at senckenberg.de or use the following link: https://tbg.senckenberg.de/personen/hiller/ https://tbg.senckenberg.de/personen/hiller/ Recent publications [1] Blumer et al., Gene losses in the common vampire bat illuminate molecular adaptations to blood feeding. bioRxiv, 2021.2010.2018.462363 (2021). [2] Jebb et al. Six reference-quality genomes reveal evolution of bat adaptations. Nature, 583, 578–584, 2020 [3] Huelsmann et al. Genes lost during the transition from land to water in cetaceans highlight genomic changes associated with aquatic adaptations. Science Adv, 5(9), eaaw6671, 2019 [4] Hecker et al. Convergent gene losses illuminate metabolic and physiological changes in herbivores and carnivores. PNAS, 116(8), 3036-3041, 2019 [5] Roscito et al. Phenotype loss is associated with widespread divergence of the gene regulatory landscape in evolution. Nature Communications, 9:4737, 2018 [6] Langer et al. REforge associates transcription factor binding site divergence in regulatory elements with phenotypic differences between species. MBE, 35(12), 3027–3040, 2018 [7] Lee et al. Molecular parallelism in fast-twitch muscle proteins in echolocating mammals. Science Adv, 4(9), eaat9660, 2018 [8] Sharma et al. A genomics approach reveals insights into the importance of gene losses for mammalian adaptations. Nature Communications, 9(1), 1215, 2018 [9] Nowoshilow et al. The axolotl genome and the evolution of key tissue formation regulators. Nature, 554(7690), 50-55, 2018 -------------- next part -------------- An HTML attachment was scrubbed... URL: From janina.bocksch at senckenberg.de Mon Nov 22 09:04:22 2021 From: janina.bocksch at senckenberg.de (Janina Bocksch) Date: Mon, 22 Nov 2021 09:04:22 +0100 (CET) Subject: [SocBiN] PhD Position in Comparative Genomics at Senckenberg Frankfurt / Application deadline December 12th 2021 Message-ID: <1350204129.524758.1637568262580@office.mailbox.org> The Hiller Lab at the LOEWE Center for Translational Biodiversity Genomics (TBG) in Frankfurt, Germany is looking for an ambitious PhD student to investigate the genomic basis of phenotypic differences between vertebrates. The Project We offer several projects that range from the development of new comparative genomic methods to accurately detect relevant genomic changes in big datasets to applying existing and new approaches to link phenotypic adaptations to genomic differences, which is a central goal in the genomics era. The PhD student is expected to capitalize on a powerful repertoire of Forward Genomics and other methods such as TOGA (Tool to infer Orthologs from Genome Alignments) as well as available genome alignments and comparative data for hundreds of mammals and birds. A large list of interesting adaptations including metabolic, physiological and morphological traits in bats, dolphins, other mammals and vertebrates is available to be studied, and choices can be influenced by the preference of the PhD student. Our lab The mission of our group is to understand how nature's fascinating phenotypic diversity has evolved and how it is encoded in the genome. Work in the lab includes sequencing and assembly of reference-quality genomes, genome alignment and annotation, development and application of comparative genomic methods to discover differences in genes and cis-regulatory elements, and the use of statistical approaches to link phenotypic to genomic changes [1-9]. Our lab is part of TBG (https://tbg.senckenberg.de/) and Senckenberg Research Society, and is based near the city center of Frankfurt am Main, Germany. TBG provides access to cutting-edge computational (HPC clusters, genome browser) and lab infrastructure to sequence genomes. English is the working language in our lab. Senckenberg and TBG provide flexible working hours, an annual special payment, a company pension scheme, the Senckenberg badge for free entry in museums, the zoo, botanical garden and Palmengarten, a leave of 30 days per year, and a subsidy job ticket for public transport. Frankfurt is a vibrant and highly-international city at the heart of Europe that combines a skyscraper skyline with ample park and green areas. Requirements Applicants should have a degree in bioinformatics/computational biology, genomics or a related area, and a strong publication record. Solid programming skills in a Linux environment and experience with shell scripting and Unix tools are required. Previous experience in large-scale comparative genomic data analysis is an advantage. Place of employment: Frankfurt am Main Working hours: part-time (30 hours/week) Type of contract: initially for 3 years, but funding is available to extend it further Salary and benefits: according to the collective agreement of the State of Hesse (pay grade E13 TV-H, 75%) The position is fully funded and should ideally start as soon as possible. The employer is the Senckenberg Gesellschaft für Naturforschung who supports equal opportunity of men and women and therefore strongly invites women to apply. Equally qualified handicapped applicants will be given preference. How to apply Please send your application, mentioning the reference of this job offer (ref.#12-21009), by e-mail to Michael Hiller (michael.hiller at senckenberg.de) and recruiting at senckenberg.de. Alternatively use our online application form on https://www.senckenberg.de/en/career/apply-online/. The application should include a CV with publication list and contact information for at least two references, and a summary of previous research experience (max 1 page), and copies of certificates, transcripts and grades. The initial application deadline is December 12th, 2021, but the search will continue until the position has been filled. For more information please contact Prof. Dr. Michael Hiller, michael.hiller at senckenberg.de or use the following link: https://tbg.senckenberg.de/personen/hiller/ Recent publications [1] Blumer et al., Gene losses in the common vampire bat illuminate molecular adaptations to blood feeding. bioRxiv, 2021.2010.2018.462363 (2021). [2] Jebb et al. Six reference-quality genomes reveal evolution of bat adaptations. Nature, 583, 578–584, 2020 [3] Huelsmann et al. Genes lost during the transition from land to water in cetaceans highlight genomic changes associated with aquatic adaptations. Science Adv, 5(9), eaaw6671, 2019 [4] Hecker et al. Convergent gene losses illuminate metabolic and physiological changes in herbivores and carnivores. PNAS, 116(8), 3036-3041, 2019 [5] Roscito et al. Phenotype loss is associated with widespread divergence of the gene regulatory landscape in evolution. Nature Communications, 9:4737, 2018 [6] Langer et al. REforge associates transcription factor binding site divergence in regulatory elements with phenotypic differences between species. MBE, 35(12), 3027–3040, 2018 [7] Lee et al. Molecular parallelism in fast-twitch muscle proteins in echolocating mammals. Science Adv, 4(9), eaat9660, 2018 [8] Sharma et al. A genomics approach reveals insights into the importance of gene losses for mammalian adaptations. Nature Communications, 9(1), 1215, 2018 [9] Nowoshilow et al. The axolotl genome and -------------- next part -------------- An HTML attachment was scrubbed... URL: From vignesh.bioinfo at gmail.com Mon Nov 22 23:56:52 2021 From: vignesh.bioinfo at gmail.com (vigneshwari subramanian) Date: Mon, 22 Nov 2021 23:56:52 +0100 Subject: [SocBiN] Senior Computational Biologist - Astrazeneca Message-ID: Dear all, Our extended team is looking for an enthusiastic senior scientist / Associate Director in Bioinformatics. It's an excellent opportunity for those interested in working in a collaborative environment. If you want to know more about this position, please check the link below. https://lnkd.in/eaE94nhZ Please feel free to distribute this information among your contacts. Thanks in advance, Vignesh -------------- next part -------------- An HTML attachment was scrubbed... URL: