ALBERT

Description: The widespread adoption of high-throughput next-generation sequencing (NGS) technology among the Australian life science research community is highlighting an urgent need to up-skill biologists in tools required for handling and analysing their NGS data. There is currently a shortage of cutting-edge bioinformatics training courses in Australia as a consequence of a scarcity of skilled trainers with time and funding to develop and deliver training courses. To address this, a consortium of Australian research organizations, including Bioplatforms Australia, the Commonwealth Scientific and Industrial Research Organisation and the Australian Bioinformatics Network, have been collaborating with EMBL-EBI training team. A group of Australian bioinformaticians attended the train-the-trainer workshop to improve training skills in developing and delivering bioinformatics workshop curriculum. A 2-day NGS workshop was jointly developed to provide hands-on knowledge and understanding of typical NGS data analysis workflows. The road show–style workshop was successfully delivered at five geographically distant venues in Australia using the newly established Australian NeCTAR Research Cloud. We highlight the challenges we had to overcome at different stages from design to delivery, including the establishment of an Australian bioinformatics training network and the computing infrastructure and resource development. A virtual machine image, workshop materials and scripts for configuring a machine with workshop contents have all been made available under a Creative Commons Attribution 3.0 Unported License. This means participants continue to have convenient access to an environment they had become familiar and bioinformatics trainers are able to access and reuse these resources.

Description: Blood cells derive from hematopoietic stem cells through stepwise fating events. To characterize gene expression programs driving lineage choice, we sequenced RNA from eight primary human hematopoietic progenitor populations representing the major myeloid commitment stages and the main lymphoid stage. We identified extensive cell type-specific expression changes: 6711 genes and 10,724 transcripts, enriched in non-protein-coding elements at early stages of differentiation. In addition, we found 7881 novel splice junctions and 2301 differentially used alternative splicing events, enriched in genes involved in regulatory processes. We demonstrated experimentally cell-specific isoform usage, identifying nuclear factor I/B (NFIB) as a regulator of megakaryocyte maturation-the platelet precursor. Our data highlight the complexity of fating events in closely related progenitor populations, the understanding of which is essential for the advancement of transplantation and regenerative medicine.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4254742/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4254742/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Chen, Lu -- Kostadima, Myrto -- Martens, Joost H A -- Canu, Giovanni -- Garcia, Sara P -- Turro, Ernest -- Downes, Kate -- Macaulay, Iain C -- Bielczyk-Maczynska, Ewa -- Coe, Sophia -- Farrow, Samantha -- Poudel, Pawan -- Burden, Frances -- Jansen, Sjoert B G -- Astle, William J -- Attwood, Antony -- Bariana, Tadbir -- de Bono, Bernard -- Breschi, Alessandra -- Chambers, John C -- BRIDGE Consortium -- Choudry, Fizzah A -- Clarke, Laura -- Coupland, Paul -- van der Ent, Martijn -- Erber, Wendy N -- Jansen, Joop H -- Favier, Remi -- Fenech, Matthew E -- Foad, Nicola -- Freson, Kathleen -- van Geet, Chris -- Gomez, Keith -- Guigo, Roderic -- Hampshire, Daniel -- Kelly, Anne M -- Kerstens, Hindrik H D -- Kooner, Jaspal S -- Laffan, Michael -- Lentaigne, Claire -- Labalette, Charlotte -- Martin, Tiphaine -- Meacham, Stuart -- Mumford, Andrew -- Nurnberg, Sylvia -- Palumbo, Emilio -- van der Reijden, Bert A -- Richardson, David -- Sammut, Stephen J -- Slodkowicz, Greg -- Tamuri, Asif U -- Vasquez, Louella -- Voss, Katrin -- Watt, Stephen -- Westbury, Sarah -- Flicek, Paul -- Loos, Remco -- Goldman, Nick -- Bertone, Paul -- Read, Randy J -- Richardson, Sylvia -- Cvejic, Ana -- Soranzo, Nicole -- Ouwehand, Willem H -- Stunnenberg, Hendrik G -- Frontini, Mattia -- Rendon, Augusto -- 082961/Wellcome Trust/United Kingdom -- 082961/Z/07/Z/Wellcome Trust/United Kingdom -- 084183/Z/07/Z/Wellcome Trust/United Kingdom -- 095908/Wellcome Trust/United Kingdom -- 100140/Wellcome Trust/United Kingdom -- C45041/A14953/Cancer Research UK/United Kingdom -- FS/12/27/29405/British Heart Foundation/United Kingdom -- MC_UP_0801/1/Medical Research Council/United Kingdom -- MR/J011711/1/Medical Research Council/United Kingdom -- MR/K006584/1/Medical Research Council/United Kingdom -- MR/K023489/1/Medical Research Council/United Kingdom -- RG/09/012/28096/British Heart Foundation/United Kingdom -- RG/09/12/28096/British Heart Foundation/United Kingdom -- RP-PG-0310-1002/British Heart Foundation/United Kingdom -- RP-PG-0310-1002/Department of Health/United Kingdom -- WT091310/Wellcome Trust/United Kingdom -- WT098051/Wellcome Trust/United Kingdom -- Medical Research Council/United Kingdom -- New York, N.Y. -- Science. 2014 Sep 26;345(6204):1251033. doi: 10.1126/science.1251033.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK. Department of Haematology, University of Cambridge, Cambridge Biomedical Campus, Cambridge CB2 0PT, UK. National Health Service (NHS) Blood and Transplant, Cambridge Biomedical Campus, Cambridge CB2 0PT, UK. ; Department of Haematology, University of Cambridge, Cambridge Biomedical Campus, Cambridge CB2 0PT, UK. European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK. National Health Service (NHS) Blood and Transplant, Cambridge Biomedical Campus, Cambridge CB2 0PT, UK. ; Department of Molecular Biology, Radboud University, 6525 GA Nijmegen, Netherlands. ; Department of Haematology, University of Cambridge, Cambridge Biomedical Campus, Cambridge CB2 0PT, UK. National Health Service (NHS) Blood and Transplant, Cambridge Biomedical Campus, Cambridge CB2 0PT, UK. ; Sanger Institute-EBI Single-Cell Genomics Centre, Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, UK. ; Department of Haematology, University of Cambridge, Cambridge Biomedical Campus, Cambridge CB2 0PT, UK. National Health Service (NHS) Blood and Transplant, Cambridge Biomedical Campus, Cambridge CB2 0PT, UK. Medical Research Council Biostatistics Unit, Cambridge Biomedical Campus, Cambridge CB2 0SR, UK. ; Department of Haematology, University College London Cancer Institute, London WC1E 6DD, UK. The Katharine Dormandy Haemophilia Centre and Thrombosis Unit, Royal Free NHS Trust, London NW3 2QG, UK. ; CHIME Institute, University College London, Archway Campus, London NW1 2DA, UK. Auckland Bioengineering Institute, University of Auckland, Auckland 1010, New Zealand. ; Centre for Genomic Regulation and University Pompeu Fabra, 08002 Barcelona, Spain. ; Imperial College Healthcare NHS Trust, DuCane Road, London W12 0HS, UK. Ealing Hospital NHS Trust, Southall, Middlesex UB1 3HW, UK. ; European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK. ; Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK. ; Pathology and Laboratory Medicine, University of Western Australia, Crawley, Western Australia 6009, Australia. ; Department of Laboratory Medicine, Laboratory of Hematology, Radboud University Medical Center, 6525 GA Nijmegen, Netherlands. ; Assistance Publique-Hopitaux de Paris, INSERM U1009, 94805 Villejuif, France. ; Biomedical Research Centre, Norwich Medical School, University of East Anglia, Norwich NR4 7TJ, UK. ; Center for Molecular and Vascular Biology, University of Leuven, 3000 Leuven, Belgium. ; The Katharine Dormandy Haemophilia Centre and Thrombosis Unit, Royal Free NHS Trust, London NW3 2QG, UK. ; Department of Haematology, University of Cambridge, Cambridge Biomedical Campus, Cambridge CB2 0PT, UK. National Health Service (NHS) Blood and Transplant, Cambridge Biomedical Campus, Cambridge CB2 0PT, UK. Cambridge University Hospitals NHS Foundation Trust, Cambridge Biomedical Campus, Cambridge B2 0QQ, UK. ; Department of Haematology, Hammersmith Campus, Imperial College Academic Health Sciences Centre, Imperial College London, London W12 0HS, UK. ; Department of Haematology, University of Cambridge, Cambridge Biomedical Campus, Cambridge CB2 0PT, UK. National Health Service (NHS) Blood and Transplant, Cambridge Biomedical Campus, Cambridge CB2 0PT, UK. Department of Twin Research & Genetic Epidemiology, Genetics and Molecular Medicine Division, St Thomas' Hospital, King's College, London SE1 7EH, UK. ; School of Cellular and Molecular Medicine, University of Bristol, Bristol BS8 1TD, UK. ; Department of Oncology, Addenbrooke's Cambridge University Hospital NHS Trust, Cambridge Biomedical Campus, Cambridge CB2 0RE, UK. Cancer Research UK, Cambridge Institute, Cambridge Biomedical Campus, Cambridge CB2 0RE, UK. ; National Health Service (NHS) Blood and Transplant, Cambridge Biomedical Campus, Cambridge CB2 0PT, UK. ; School of Clinical Sciences, University of Bristol, Bristol BS2 8DZ, UK. ; European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK. Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK. ; European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK. Genome Biology and Developmental Biology Units, European Molecular Biology Laboratory, 69117 Heidelberg, Germany. Wellcome Trust-Medical Research Council Stem Cell Institute, University of Cambridge, Cambridge CB2 1QR, UK. ; Department of Haematology, Cambridge Institute for Medical Research, University of Cambridge, Cambridge Biomedical Campus, Cambridge CB2 0XY, UK. ; Medical Research Council Biostatistics Unit, Cambridge Biomedical Campus, Cambridge CB2 0SR, UK. ; Department of Haematology, University of Cambridge, Cambridge Biomedical Campus, Cambridge CB2 0PT, UK. Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK. ; Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK. Department of Haematology, University of Cambridge, Cambridge Biomedical Campus, Cambridge CB2 0PT, UK. ; Department of Haematology, University of Cambridge, Cambridge Biomedical Campus, Cambridge CB2 0PT, UK. National Health Service (NHS) Blood and Transplant, Cambridge Biomedical Campus, Cambridge CB2 0PT, UK. Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK. ; Department of Haematology, University of Cambridge, Cambridge Biomedical Campus, Cambridge CB2 0PT, UK. National Health Service (NHS) Blood and Transplant, Cambridge Biomedical Campus, Cambridge CB2 0PT, UK. ar506@cam.ac.uk mf471@cam.ac.uk. ; Department of Haematology, University of Cambridge, Cambridge Biomedical Campus, Cambridge CB2 0PT, UK. National Health Service (NHS) Blood and Transplant, Cambridge Biomedical Campus, Cambridge CB2 0PT, UK. Medical Research Council Biostatistics Unit, Cambridge Biomedical Campus, Cambridge CB2 0SR, UK. ar506@cam.ac.uk mf471@cam.ac.uk.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/25258084" target="_blank"〉PubMed〈/a〉

Description: Ensembl ( www.ensembl.org ) is a database and genome browser for enabling research on vertebrate genomes. We import, analyse, curate and integrate a diverse collection of large-scale reference data to create a more comprehensive view of genome biology than would be possible from any individual dataset. Our extensive data resources include evidence-based gene and regulatory region annotation, genome variation and gene trees. An accompanying suite of tools, infrastructure and programmatic access methods ensure uniform data analysis and distribution for all supported species. Together, these provide a comprehensive solution for large-scale and targeted genomics applications alike. Among many other developments over the past year, we have improved our resources for gene regulation and comparative genomics, and added CRISPR/Cas9 target sites. We released new browser functionality and tools, including improved filtering and prioritization of genome variation, Manhattan plot visualization for linkage disequilibrium and eQTL data, and an ontology search for phenotypes, traits and disease. We have also enhanced data discovery and access with a track hub registry and a selection of new REST end points. All Ensembl data are freely released to the scientific community and our source code is available via the open source Apache 2.0 license.