Together these techniques will provide participants with a useful toolkit for designing new strategies to extract relevant information and understanding from large-scale biological data. This course is currently under construction and so details are subject to change. Salehi S, Kabeer F, Ceglia N, Andronescu M, Williams MJ, Campbell KR, Masud T, Wang B, Biele J, Brimhall J, Gee D, Lee H, Ting J, Zhang AW, Tran H, OFlanagan C, Dorri F, Rusk N, de Algara TR, Lee SR, Cheng BYC, Eirew P, Kono T, Pham J, Grewal D, Lai D, Moore R, Mungall AJ, Marra MA, IMAXT Consortium, McPherson A, Bouchard-Ct A, Aparicio S, Computational Genomics for Surgical Oncology | Sanchez-Vega, Germline-Somatic Interaction | Carrot-Zhang, Ovarian cancer mutational processes drive site-specific immune evasion. Hybrid options are not currently available. This cross-disciplinary meeting will bring together scientists using cellular, molecular, ecological, physiological, and theory-based approaches to explore the evolution of intimate species-species interactions. This course covers the use of computational tools to extract biological insight from omics datasets. Registration is not yet open for this event. Introduction to EMBL-EBI for teachers and trainers, Computing skills for reproducible research: data carpentry, Data-driven modelling of intercellular interactions in the tumour microenvironment, Accessing fine-grained Molecular Interactions data with IntAct, EuroFAANG GENE-SWitCH workshop: utilisation of GENE-SWitCH data in Ensembl and beyond, Exploring reproducible and reusable systems biology models with BioModels, Single-cell RNA-seq analysis using Galaxy, In situ structural biology: from cryo-EM to multi-scale modelling, In situ CLEM at room temperature and in cryo, Introduction to RNA-seq and functional interpretation, Analysis and integration of transcriptome and proteome data, Introduction to multiomics data integration and visualisation, Extracellular vesicles: from biology to biomedical applications, Measuring translational dynamics by ribosome profiling, EuroFAANG AQUA-FAANG workshop: methods to use and reuse the AQUA-FAANG data and Ensembl resources to advance science, Brain genome: regulation, evolution, and function, Bioinformatics resources for protein biology, Microscopy data analysis: machine learning and the BioImage Archive, BioMalPar XIX: biology and pathology of the malaria parasite, The ageing genome: from mechanisms to disease, Quantitative proteomics: strategies and tools to probe biology, Life at the periphery: mechanobiology of the cell surface, Computational modelling of multicellular systems, Bioinformatics for principal investigators, Terra incognita: navigating ethical boundaries in the life sciences, PerMedCoE summer school: from pathway modelling tools to cell-level simulations, New approaches and concepts in microbiology, Plasticity in developing systems: time, space, and environment, Protein synthesis and translational control, Developmental metabolism: flows of energy, matter, and information, Genome engineering: CRISPR/Cas from cells to mice, Single-cell RNA-seq analysis using Python, Seeing is believing: imaging the molecular processes of life, Organoids: modelling organ development and disease in 3D culture, FISHing for RNAs: classical to single molecule approaches, Systems biology: from large datasets to biological insight, Proteomics in cell biology and disease mechanisms, Preparation of genomic libraries for an emerging next-gen sequencing platform, Solution scattering from biological macromolecules, The mobile genome: genetic and physiological impacts of transposable elements. During this course, participants will gain theoretical insight in the structure of sequencing and proteomic data, and they will receive training in data analysis for the annotation, quantification, and statistical Martin Jechlinger, Rene van Amerongen, Mara dM Vivanco. The course content will also cover predicting function, and exploring interactions with other macromolecules. Be able to interpret statistical output and work independently as well as collaboratively. [2](https://doi.org/10.1016/j.bdr.2020.100178) Ren, Xiaoli, et al. To work with other trainees, staff, and faculty in the preparation of new and ongoing investigator-led funding proposals, To work with other trainees, staff, and faculty in the preparation of new and ongoing manuscript submissions, To provide strategic advice regarding individual research directions and emerging research projects. The cover letter should include a statement summarizing past research experience and future research interests, and a brief explanation of your interest in and qualification for the position. This workshop aims at disseminating and discussing expansion microscopy protocols and is intended for cell biologists, parasitologists, etc, with applications ranging from tissue to cells. The Proteomics in Cell Biology and Disease Mechanisms conference will provide attendees with a program that provides the current state-of-affairs in proteomics including a future perspective. The format allows processing of hundreds to thousands of samples per week with a 3-day workflow for population-scale studies. Lnnberg, T. et al. Non-parametric modelling of temporal and spatial counts data from RNA-seq experiments. Please be aware that we are continually evaluating the ongoing pandemic situation and, as Barbora Kozlikova, Marc A. Marti-Renom, Andrea Schafferhans, Nico Scherf, Michelle Scott, Srigokul Upadhyayula. Postdoctoral Position - Division of Gynecologic Oncology (Santin Lab), Postdoctoral Associate - Early Psychosis Research (Srihari Lab), Postdoctoral Associate - SEL For All Team, Postdoctoral Associate - Dermatology (Dr. Brett King), Postdoctoral Fellow - Cancer Prevention and Control Training Program T32, Postdoctoral Position - Molecular Biophysics and Biochemistry (Kabeche Lab), Postdoc Positions (2) - Pathology (Yan Lab), Postdoctoral Associate Positions (2) Human Evolutionary Genomics (Tucci Lab), Postdoc Positions - Immunology (Lucas Lab), Interested candidates should send their CV to, Postdoctoral Position - Wild Immunology and Disease Ecology (Ezenwa Lab), Postdoctoral Position Engineering translation enhancers for therapeutic mRNAs (Thoreen Lab), A postdoctoral position is immediately available in the laboratory of Carson Thoreen in the Department of Cellular and Molecular Physiology at Yale School of Medicine. Single cell RNA sequencing is highly important, particularly in cancer as it allows exploration of heterogenous tumor sample, obstructing therapeutic targeting which leads to poor survival. Doctoral degree in pathogen genomics, bioinformatics, or a closely related discipline, Excellent written and oral communication skills, Ability to work within an interdisciplinary team of researchers. Advisors: Pekka Parviainen, Ahmad Hemmati. This conference is assembling world leading experts from diverse fields including genomics epigenetics structural biology developmental biology immunology cancer biology and neurobiology to discuss the broad impacts of TEs on organismal biology OverviewSpeakersPreliminary programmePractical informationSponsorsMedia kit Overview This conference will take place at EMBL Heidelberg, with the option to attend virtually. As leading databases such as ClinVar continue to rapidly add new variants, Illumina is dedicated to ensuring the variants interrogated on the GSA remain updated and relevant. Please see EMBLs COVID-19 safety policy for testing and other requirements if attending the on-site event. To limit them, one can define rules that a neural network should follow and devise strategies to verify whether the rules are obeyed. This symposium will cover a broad range of topics in microbiology including antibiotic related research bacterial communities and microbiome cell biology regulation signalling pathogenesis and evolution Emphasis will be placed on novel approaches and technologies from systems based to single cell that drive each field or have the potential to revolutionise future research in microbiology OverviewSpeakersPreliminary programmePractical informationSponsorsMedia kit Overview This conference will take place at EMBL Heidelberg, with the option to attend virtually. In-person course We Overview Overview This conference will take place at EMBL Heidelberg with the option to attend virtually Please see EMBL s COVID 19 safety policy for testing and other requirements if attending the on site event Registration is not yet open for this event If you are interested in receiving more information please register your interest What past participants say about the conference Overview Overview This conference will take place at EMBL Heidelberg, with the option to attend virtually. Sequence Hub, BaseSpace The question is how to deal with such failures. We plan to deliver this course Vladimir Benes, Giuseppe DAuria, Jos Eduardo Gonzlez-Pastor, Elisabeth Zielonka. WebDownload scientific diagram | KRASG12V activation and tracking in a small group of cells within a live zebrafish embryo. How is neural activity regulated by and how does it affect genome output? During this course, we will focus on a specific method that has been developed at EMBL that enables the localisation of fluorescent proteins with high accuracy at the ultrastructural level. Do you want to know more about the sequence of your protein and its functions? However, often the function is unknown and we have only access to some (possibly noisy) values of the function. The R package Monocle 41 (v2.8) was applied to construct single-cell and single-nuclei pseudo-temporal trajectories of human imGCs, human mGCs, mouse imGCs, and mouse mGCs across ages. It will additionally provide guidance on strategies for managing data, the importance of data sharing; how to work with computational collaborators and what resources are available across the life sciences to support such work. These studies involve mouse organoids, sc-RNA-seq, knock down of genes, human intestinal organoids, swelling assays, fluorescence staining and imaging of organoids, and tissues, myosin studies (knock down), biochemistry, paraffin staining, cell culture. Software Suite, BaseSpace Single-cell RNA sequencing can reveal RNA abundance with high quantitative accuracy, sensitivity and throughput1. OverviewSpeakersPractical InformationSponsors Overview This conference will take place at EMBL Heidelberg with the option to attend virtually Please see EMBL s COVID 19 safety policy for testing and other requirements if attending the on site event Registration is not yet open for this event If you are interested in receiving more information please register your interest Conference OverviewSpeakersPractical InformationSponsors Overview This conference will take place at EMBL Heidelberg, with the option to attend virtually. Nature. Previous research experience in CPC is desirable but not required. We are interested in the major questions which underpin the cellular dynamics of cancer. The course combines interactive theoretical discussions that have been successfully used to train generations of Drosophila researchers for nearly 30 years combined with cutting edge experimental approaches taught by experts in the field OverviewSpeakersPreliminary programmePractical informationSponsors Overview Please see EMBLs COVID-19 safety policy for testing and other requirements to attend this on-site course. Group projects A major element of this course is a group project, where participants will be placed in small groups to work together on a challenge set by trainers from EMBL-EBI and external institutes. This means patients need to try several until they find one that is effective at the cost of side effects associated with every treatment. Thus, the Roberto Bonasio, Matthieu Boulard, Magdalena Gtz, Kyung-Min Noh. Use cases for surrogate models include model predictions where speed is favoured over accuracy and exploration of parameter space. While Knowledge Graphs are becoming increasingly popular, one persistent issue concerns the quality of data. This course covers the analysis of scRNA-seq data. AlphaFold, a program based on Artificial Intelligence (AI), has transformed the structural modeling of proteins and protein complexes by reaching accuracy similar to experimental structures. Interested persons should send a CV, a brief statement of research interests, and 2-3 letters of recommendation to Engin Deniz, MD, exclusively at the following address: or Lisa Palmieri, Department of Pediatrics, 333 Cedar Street, PO Box 208064, New Haven, CT 06520-8064. to phenocopy patient phenotype, then expand our analyses to evaluate the cell and molecular mechanisms linked to these novel hydrocephalus genes. In the project Machine Teaching for XAI (seehttps://xai.w.uib.no)a master thesis in collaborationbetween UiB and Equinor. The Spatial Transcriptomics spots are 100 m in diameter and are spaced 100 m apart, meaning they are not small enough or densely enough packed to achieve single-cell resolution. The focus will be on new technologies that empower studies of cell wall, cytoskeleton, and membrane biology, such as advanced imaging inin vitroandin vivosystems, as well as approaches combining molecular biology with computational and biophysical approaches. 2021 Jul;595(7868):585590. Participants will receive training on how to use search engines and post-processing software, quantitative approaches, MS data repositories, the use of public databases for protein analysis, annotation of subsequent protein lists, and incorporation of information from molecular interaction and pathway databases. Moncada, R. et al. In this project, you will design and train deep neural networks using actual weather prediction data, which are essentially ensemble of time series. We do this using Angluin's L*algorithm as a learner and the trained RNN as an oracle. This virtual course will show how public bioimaging data resources, centred around the BioImage Archive, enable and enhance machine learning based image analysis. Applicants should have a doctoral degree in epidemiology, biostatistics, environmental health sciences, social and behavioral sciences, health policy, medicine, or other areas in life or data sciences, as well as a strong interest in CPC. If you are interested in receiving more information please register your interest. Symposium overview Human microbiota the collection of microbes living in and on our body have a significant impact on human health and well-being. Monocyte derived macrophages help maintain tissue homeostasis and defend the organism against pathogens In tumours recent studies have uncovered complex macrophage populations including tumour associated macrophages which support tumorigenesis through cancer hallmarks such as immunosuppression angiogenesis or Research experience with mathematical and/or statistical models. It is now well established that genetic mutations cause cancer growth and spreading and importantly, these mutations are different in individual patients. Previous experience using Medicare claims data is highly desirable. Further instruction will be offered using applications such as ZeroCostDL4Mic, ilastik, ImJoy, the BioImage Model Zoo, and CellProfiler. Approximately 1.8M markers are included on the BeadChip for high exonic coverage in regions of disease relevance, providing highly accurate copy number variation calls, and an average resolution of 1.5Mb. If you are interested in receiving more information please register your interest. Spatio-temporal evolution of ovarian cancer at single cell resolution McPherson et al. This webinar will provide an introduction to molecular interactions and how to find these through the molecular interaction database IntAct. Immunol. https://doi.org/10.1186/s13059-018-1406-4, Removal of Batch Effects using Distribution-Matching Residual Networks, https://www.nature.com/articles/s41598-017-13665-w, A comparison of single-cell trajectory inference methods: towards more accurate and robust tools, A descriptive marker gene approach to single-cell pseudotime inference, Characterization of cell fate probabilities in single-cell data with Palantir, Inferring population dynamics from single-cell RNA-sequencing time series data, Supervised Classification Enables Rapid Annotation of Cell Atlases, Harmonization and Annotation of Single-cell Transcriptomics data with Deep Generative Models, Cell type classification and discovery across diseases, technologies and tissues reveals conserved gene signatures and enables standardized single-cell readouts, Reference-based analysis of lung single-cell sequencing reveals a transitional profibrotic macrophage. M3Drop - [R] - Michaelis-Menten Modelling of Dropouts for scRNASeq. Registration is not yet open for this event. Persistent homology is becoming a standard method for analyzing data. This approach provides multiple advantages: the user does not need to install all the software on its local server, the results generated by different containers can be organised in pipelines and reproducible research is guarantee by the possibility of sharing Niccolo Banterle, Gautam Dey, Paul Guichard, Virginie Hamel, Marine Laporte. Excellent statistics skills, including experience with multi-level modeling, meta-analysis and working with qualitative data. OverviewSpeakersProgrammePractical informationSponsorsMedia kit Overview Please see EMBL s COVID 19 safety policy for testing and other requirements to attend this on site course Course overview The mammary epithelium is a unique organ in that the majority of its development occurs postnatally This combined with ease of experimental access and a stereotypical growth pattern make it OverviewSpeakersProgrammePractical informationSponsorsMedia kit Overview Please see EMBLs COVID-19 safety policy for testing and other requirements to attend this on-site course. Please see EMBLs COVID-19 safety policy for testing and other requirements if attending the on-site event. Moreover, the diversity of imaging modalities, analysis algorithms and software solutions is growing so rapidly Alexander Aulehla, Heidi Lempradl, Jonathan Rodenfels. This one and a half day workshop will provide detailed training on the utilisation of the wealth of data generated by the EuroFAANG GENE-SWitCH projectthat is delivering new underpinning knowledge for pig and chicken agriculture. 2021 Jul;595(7868):585590. Nat Rev Cancer 2021 Oct 18; doi.org/10.1038/s41568-021-00408-3 PMID: 34663944, Salehi S, Kabeer F, Ceglia N, Andronescu M, Williams MJ, Campbell KR, Masud T, Wang B, Biele J, Brimhall J, Gee D, Lee H, Ting J, Zhang AW, Tran H, OFlanagan C, Dorri F, Rusk N, de Algara TR, Lee SR, Cheng BYC, Eirew P, Kono T, Pham J, Grewal D, Lai D, Moore R, Mungall AJ, Marra MA, IMAXT Consortium, McPherson A, Bouchard-Ct A, Aparicio S, Shah SP. For 1-dimensional signals, this can translate into looking at the birth/death persistence diagram, i.e. Throughout the week, more advanced topics will introduce the creation of pipelines, automation, and the scaling-up of analysis experiments. 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