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Physalia courses

SPECIATION GENOMICS

OVERVIEW

    This course will provide a thorough introduction to the growing field of speciation genomics. The course aims to take students from the initial steps required for handling raw sequencing data to demographic modelling and inference of genome-wide signatures of selection and introgression. Through a combination of lectures covering key theoretical and conceptual topics, alongside hands-on exercises, participants will learn the most important computational approaches used in speciation genomics. This will include a heavy emphasis on data visualization and intepretation. After completing of the course, the participants should be able to begin using NGS data to shed light on the genomic aspects of speciation in their study system of choice.

    FORMAT

      This course is designed for researchers and graduate students with strong interests in applying novel high-throughput DNA sequencing technologies to study the population genomic basis of speciation. The course will mainly focus on the analysis of NGS data for study systems for which a reference genome is available. We will provide theoretical lectures and hands-on exercises drawing on examples of whole-genome resequenced and RAD-sequencing data. Participants will make use of the UNIX command line and R.

       

       

      ASSUMED BACKGROUND

        The participants should have some basic background in evolution and genomics. No programming or scripting expertise is required. Previous experience in UNIX-based command line and R is an advantage. Because we will only provide a very brief introduction, we would like to ask participants without previous experience in R to go through this tutorial and participants without previous knowledge in the unix command line to go through this tutorial before the course. All hands-on exercises will be run in a Linux environment on remote servers. Statistical analyses will be run in R using RStudio.

         

         

        LEARNING OUTCOMES

        1)      Handling NGS data from raw reads to genetic variants

         

        2)      Applying basic population genetic statistics

         

        3)      Visualizing the genetic structure

         

        4)      Inferring demographic history

         

        5)      Identifying regions under divergent selection or barriers to gene flow

         

        6)      Understanding the potential and limitations of different methods to detect regions under selection

         

         

        PROGRAM

        Day 1 - 2 -9 pm Berlin time

         

        • Introduction to Unix

         

        • Introduction to NGS data

         

        • Mapping NGS reads to a reference genome

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        New York University Abu Dhabi

        Center for Genomics and Systems Biology Symposium XI

        About the Event 

        System biology aims to identify and understand the mechanisms that transform genomic information into cellular and organismal behavior using a holistic perspective. In their own research programs, the organizers of this symposium apply cutting-edge genomic technology and systems-level approaches to areas including Environmental Adaptation and Sustainability, and Biomedicine and Health. The internationally distinguished speakers invited for this year's symposium reflect the diverse research areas. This is the eleventh NYUAD Center for Genomics and Systems Biology's Symposium and one of the region's leading symposia on modern biology.

        Email nyuad.cgsb.conferenceXI@nyu.edu for more details.

        Organized by

        Stéphane Boissinot
        , Professor of Biology; Global Network Professor of Biology, Faculty of Arts and Science, NYU and Director of the Center for Genomics and Systems Biology
        Kristin Gunsalus, Professor of Biology, Center for Genomics and Systems Biology, NYU New York; Faculty Director of Bioinformatics, and co-director of Center for Genomics and Systems Biology, NYU Abu Dhabi
        Claude Desplan, Silver Professor; Professor of Biology and Neural Science, NYU New York, and co-director of Center for Genomics and Systems Biology, NYU Abu Dhabi
        Enas Qudeimat, Head of CGSB Administration and Outreach, NYU Abu Dhabi

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        Arsss

        International Conference on Physics (ICP)

        About Conference

        The key intention of ICP is to provide opportunity for the global participants to share their ideas and experience in person with their peers expected to join from different parts on the world. In addition this gathering will help the delegates to establish research or business relations as well as to find international linkage for future collaborations in their career path. We hope that ICP outcome will lead to significant contributions to the knowledge base in these up-to-date scientific fields in scope.

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        METABARCODING IN MICROBIAL ECOLOGY

        OVERVIEW

          This course will provide a thorough introduction to the application of metabarcoding techniques in microbial ecology. The topics covered by the course range from bioinformatic processing of next-generation sequencing data to the most important approaches in multivariate statistics. Using a combination of theoretical lectures and hands-on exercises, the participants will learn the most important computational steps of a metabarcoding study from the processing of raw sequencing reads down to the final statistical evaluations. After completing the course, the participants should be able to understand the potential and limitations of metabarcoding techniques as well as to process their own datasets to answer the questions under investigation.

           

           

          FORMAT

          This course is designed for researchers and students with strong interests in applying novel high-throughput DNA sequencing technologies to answer questions in the area of community ecology and biodiversity. The course will mainly focus on the analysis of phylogenetic markers to study bacterial, archaeal and fungal assemblages in the environment, but the theoretical concepts and computational procedures can be equally applied to any taxonomic group or gene of interest.

           

           

          ASSUMED BACKGROUND

          The participants should have some basic background in biology and understand the central role of DNA for biodiversity studies. No programming or scripting expertise is required and some basic introduction to UNIX-based command line applications will be provided on the first day. However, some basic experience with using command line and/or R is clearly an advantage as not all the basics can be thoroughly covered in that short amount of time.

           

          No previous knowledge of computer science is required but a basic knowledge of “bash” would allow to focus more on the microbial analysis.

           

           

          LEARNING OUTCOMES

          1) Understanding the concept, potential and limitation of microbial metabarcoding techniques.

           

           

          2) Learning how to process raw sequencing reads to obtain meaningful information.

           

           

          3) Obtaining experience on how to statistically evaluate and visualize your data.

           

           

          4) Being able to make informed decisions on best practices for your own data.

           

           

          PROGRAM

          Monday - Classes from 2 to 8 pm Berlin time

           

          Lecture 1 – Introduction to NGS in microbial ecology

           

           

          •    Key concepts (metabarcoding, metagenomics, single-cell sequencing)

           

          •    Sequencing platforms (core concepts, read length, read numbers, error rates)

           

          •    In-depth example of sequencing with Illumina platforms (over-and under-loading, sequencing process)

           

          •    Genetic markers for metabarcoding (markers, primer selection & evaluation)

           

          •    Experimental design (library preparation, replication, multiplexing, coverage, costs)

           

          •    Understanding data formats (FASTQ, FASTA, others)

           

          •    Core concept of computational pipeline for amplicons

           

          •    Introduction of the QIIME2 suite

           

           

           

          Lab 1 – Introduction to compute lab

           

           

           

          •    Introduction to the BASH command line (e.g. basic UNIX commands, batch processing)

           

          •    Check functionality of computational environment with demo data

           

          •    Checking basic characteristics of datasets (number of reads, read length, read quality)

           

           

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          World Research Society

          International Congress On Cell Science And Molecular Biology (IC-CSMB)

          About Event

          The conference provides a platform for professionals involved in Cell Science and Molecular Biology to exchange knowledge and gain an insight into the state of the art in the current technology, techniques and solutions in Cell Science and Molecular Biology as they have been developed and applied in different countries. Participants include a wide variety of stakeholders from research and academia, to industrial sectors as well as government organizations.

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          Inderscience

          International Conference on Astronomy, Astrophysics, Space Science (ICAASS)

              About Conference
              International Conference on Astronomy, Astrophysics and Space Science aims to bring together leading academic scientists, researchers and research scholars to exchange and share their experiences and research results on all aspects of Astronomy, Astrophysics and Space Science. It also provides a premier interdisciplinary platform for researchers, practitioners and educators to present and discuss the most recent innovations, trends, and concerns as well as practical challenges encountered and solutions adopted in the fields of Astronomy, Astrophysics and Space Science.
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          Eurasia Web

          International Conference on Environment and Life Science (EUCELS)

          About Event:

          The conference provides a platform for professionals involved in Environment and Life Science to exchange knowledge and gain an insight into the state of the art in the current technology, techniques and solutions in Environment and Life Science as they have been developed and applied in different countries. Participants include a wide variety of stakeholders from research and academia, to industrial sectors as well as government organizations.

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          Physalia courses

          SEX CHROMOSOME EVOLUTION

          OVERVIEW

          This course will introduce attendees to how genomic and transcriptomic data can be used to detect homomorphic/heteromorphic sex chromosomes and inform the cause and consequences of sex chromosome differentiation. The instructors will guide students through study design, genomic/transcriptomic data collection methods, handling of raw genomic/transcriptomic data, and methods to identify sex chromosomes. Then, we will work through a suite of analyses looking at the molecular evolution of sex chromosomes, particularly the timing and patterns of recombination suppression, gene gain/loss, gene expression differentiation, and genome divergence. We will provide background on the theory and hands-on exercises, running analysis, and interpreting results. After completing the course, the participants should be able to manipulate, visualize and interpret genomic data and patterns of sex chromosome evolution.

          TARGET AUDIENCE AND ASSUMED BACKGROUND

          The course is aimed at graduate students and researchers who are interested in using genomic/transcriptomic data to explore the mode of sex chromosome evolution. Participants should have some basic background in evolutionary biology, genetics, bioinformatics, or other relevant disciplines. Basic experience in UNIX-based command line and R is an advantage. Hands-on exercises will be run in a Linux environment on remote servers and data analysis and visualization will be run in R using RStudio.

          TEACHING FORMAT

          The course will be delivered fully online over 5 half-day (6 hours) sessions, with a combination of lectures and practical exercises that will be live (synchronous). Discussions among participants and with the instructors on concepts and data analysis will be possible through video conferencing and a dedicated Slack workspace.

           

           

           

          LEARNING OUTCOMES

          1. Conduct computational analysis to detect homo/heteromorphic sex chromosomes.
          2. Searching for signals of early stages of sex chromosome differentiation.
          4. Detect the timing and patterns of recombination suppression.
          5. Conduct computational analysis to detect sex chromosome gene expression differentiation and genome divergence.
          6. Study of dosage compensation.
          7. Interpret these in the light of evolution.

           

          PROGRAM

          Monday. 2 -8 pm Berlin time

           

          We will introduce different sex determination systems and explore types of sex chromosomes (X0, XY, ZW, UV). We will then discuss the typical workflows from study design, sample collection, through NGS data to sex chromosome identification.
          We will start the practical sessions with an introduction to Unix, manipulation of the NGS data, mapping sequencing reads to reference genomes, and finally, we will use coverage-based methods to identify sex-linked genomic regions.

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          transmitting science

          INTRODUCTION TO MACROEVOLUTIONARY ANALYSES USING PHYLOGENIES

          Phylogenetic trees have changed the way we study and understand life on Earth. Taking phylogenetic information into account in our analyses is critical to account for the non-independence of biological data. Also, phylogenies allow us to get a deep-time perspective of the processes that have shaped the evolutionary history of groups, including diversification and trait evolution.

          This course will introduce participants to the use, modification and representation of phylogenetic trees. Also, we will focus on the use of phylogenetic information to reconstruct ancestral characters and biogeographic histories, using different phylogenetic comparative methods.

          This course will also tackle trait evolution modelling and the assessment of phylogenetic signal. Finally, we will learn about the shape of phylogenetic trees and its evolutionary causes, and how to estimate the rates of diversification throughout the history of groups. Participants are encouraged to bring their data sets to use in the practical classes.

          The course includes an optional first introductory day to basic R.

          Important note: Please bear in mind that this course is not about reconstructing (building) phylogenetic trees.

          Software: Mesquite, FigTree, R (ape, TreeSim, TreePar, Geiger, OUwie, BioGeoBEARS).

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          World Research Society

          International Congress on Cell Science and Molecular Biology (IC-CSMB)

          About Event:

          The conference provides a platform for professionals involved in Cell Science and Molecular Biology to exchange knowledge and gain an insight into the state of the art in the current technology, techniques and solutions in Cell Science and Molecular Biology as they have been developed and applied in different countries. Participants include a wide variety of stakeholders from research and academia, to industrial sectors as well as government organizations.

          Read More
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