Next Generation Genomics 2018 Symposium + Workshops

Next Generation Genomics 2018 Symposium

University of Helsinki

The Next Generation Genomics Symposium takes place in Helsinki on October 23-24, 2018 targeting researchers in the field including PhD students and postdocs. The meeting is fifth in a series of successful symposia organized at two year intervals.

The symposium is part of a larger PhD course package organized by the Integrative Life Science (ILS) doctoral program. The PhD course package comprises a Pre-symposium Journal Club, an International Scientific Symposium, and three related Workshops where students have a chance to learn hands-on methods in genomics. The workshops are instructed by experts in the field. The course will be held in the University of Helsinki in October - November, 2018. The meeting will focus on state-of-the-art sequencing technologies and their applications.

Confirmed speakers

Mark Daly, University of Helsinki, FIMM - HiLIFE UNIT and Broad Institute
Steve Kelly, University of Oxford
Trevor Graham, Barts Cancer Institute, QMUL
Peter Kharchenko, Harvard Medical School
Riitta Lahesmaa, BioCity Turku, Finland
Tanja Slotte, Stockholm University and SciLifeLab
Nicolas Delhomme, Umeå University
Bernhard Blob, University of Cambridge
Stephan Schiffels, MPI Jena
Ville Pimenoff, IDIBELL Bellvitge Biomedical Research Institute, Barcelona, Spain
Nina Dombrowski, NIOZ (Netherlands Institute for Sea Research) and Uppsala University
Kimmo Palin, University of Helsinki
Juha Partanen, University of Helsinki
Taru Tukiainen, University of Helsinki
Teija Ojala, University of Helsinki
Timo Hytönen, University of Helsinki
Olli-Pekka Smolander, TalTech University
Alan Schulman, University of Helsinki
Petri Auvinen, University of Helsinki
Ari Löytynoja, University of Helsinki

Dates:

NGG2018 Symposium Tue - Wed 23.-24.10.2018
Pre-symposium journal club Mon 15.10. and Mon 22.10.2018
Workshop I (Computational methods to analyze human genetic variation, Stephan Schiffels) Thu – Fri 25.-26.10.2018
Workshop II (RNAseq data analysis, Nicolas Delhomme) Mon – Wed 29.-31.10.2018
Workshop III (ENSEMBL genome browser, Emily Perry) Thu 1.11.2018               

Venue: Please note the changed venue! Lecture hall 2041 (Biocenter 2, Viikki campus, Helsinki)

Tuesday 23.10.2018

Session 1  
9.30-10.00 Coffee & registration
10.00-10.15 Welcoming words
10.15-11.00 Keynote:
Mark Daly, University of Helsinki & Broad Institute

Beyond GWAS: Next steps in human genetics of complex disease
11.00-11.30 Trevor Graham, Barts Cancer Institute, QMUL
Measuring evolutionary dynamics within human cancers
11.30-12.00 Kimmo Palin, University of Helsinki
Applications of nanopore sequencing for cancer genetics
12.00-12.30 Taru Tukiainen, Unversity of Helsinki
Genomics approaches to study the human X chromosome inactivation from cells to population
12.30-14.00 Lunch
Session 2  
14.00-14.30 Peter Kharchenko, Harvard Medical School
Analysis of transcriptional dynamics with single-cell RNA-seq data
14.30-15.00 Riitta Lahesmaa, BioCity Turku, Finland
 New regulators of human immune response
15.00-15.30 Student presentations
15.30-16 Coffee
16.00-16.30 Bernhard Blob, University of Cambridge
Plant cell differentiation: Understanding phloem sieve element differentiation at single cell resolution
16.30-17.00 Liisa Holm, University of Helsinki
Large-scale sequence comparison

Wednesday 24.10.2018

Session 3  
9.30-10.15 Keynote:
Steve Kelly, University of Oxford

The Evolution of Photosynthetic Efficiency
10.15-10.45 Tanja Slotte, Stockholm University and SciLifeLab
Genomic analyses of cis-regulatory variation in Capsella (Brassicaceae)
10.45-11.15 Nicolas Delhomme, Umeå University
Transcriptomics post Differential Expression; approaches to look into the complex network and dynamics of transcriptome modulation
11.15-11.45 Ville Pimenoff, IDIBELL Bellvitge Biomedical Research Institute, Barcelona, Spain 
Exploring Host-Pathogen Co-Evolutionary Relationships in Deep time
11.45-13.15 Lunch
Session 4  
13.15-13.45 Nina Dombrowski, NIOZ (Netherlands Institute for Sea Research) and Uppsala University
How metagenomics has changed our view on archaeal diversity
13.45-14.15 Stephan Schiffels, MPI Jena
What genomes tell us about human history: New methods and insights from ancient and modern DNA
14.15-14.30 Teija Ojala, University of Helsinki
Metatranscriptomics of complex host-microbe samples
14.30-15.00

Coffee

15.00-15.30 Juha Partanen, University of Helsinki
Towards understanding the brainstem - one cell at a time
15.30-15.50 Timo Hytönen, University of Helsinki
Population genomics of woodland strawberry (Fragaria vesca L.) reveals population history and adaptation to different climates
15.50-16.10 Olli-Pekka Smolander, TalTech University
Silver birch genome – past, present and possibly the future
16.10-16.30 Marion Sinclair-Waters, University of Helsinki
Moving beyond single SNP approaches for understanding the genetic basis of complex traits: a case study in Atlantic salmon

NOTE!

  • REGISTRATION TO JOURNAL CLUB OR WORKSHOPS IS NOT ANYMORE POSSIBLE!
  • Symposia and journal club may include preliminary tasks (e.g. reading) and an on-line exam after the course. Both parts are required in addition to the presence at the course in order to receive the credits.
  • The workshops have traditionally been oversubscribed and we may not be able to accept all registered students to each workshop. Please indicate in the registration form which workshops (if any) you would like to attend and rank your choices (1=most interested, 3=least interested).
  • Please also note that Workshops I and II are relatively advanced and may require special computational skills. Workshop III is suitable to everyone.

Pre-Symposium Journal Club (ILS-104, 1 cr)

Monday 15.10. at 10-12 (Biocenter 2, room 2012)
and Monday 22.10.2018  at 10-16 (Biocenter 2, room 1015)

Workshop I, Computational methods to analyze human genetic variation, Stephan Schiffels (ILS-106, 2 cr)

Thu – Fri 25.-26.10.2018, 9:15-17:00
Room: B-building (Metsätieteiden talo), hall 106

Instructor: Stephan Schiffels

Course description: This course will consist of lectures and practical sessions on how to analyze genomic data to infer a population's history. The course is targeted at students of all disciplines who are interested in human population structure and demographic history. Basic experience with command line tools and a Unix environment are necessary. The course covers several software packages, including MSMC (Schiffels and Durbin, 2014), Eigensoft and Admixtools (Patterson et al. 2012), and python's matplotlib plotting framework. Participants are required to bring their own laptop. Software and Data will be provided through a virtual machine that is used through a web browser. No special software is needed.

Further reading:
Four articles suggested by Stephan Schiffels can be found in
https://drive.google.com/open?id=1Cu_xOFBAMuG1u4LECdTabVqpN9CV-OQd

Workshop II, RNAseq data analysis (ILS-107, 2 cr)    

Mon – Wed 29.-31.10.2018, 9:15-17:00
Room: C-building, hall K110 

Instructor: Nicolas DelHomme, Umeå University, Sweden

Target audience: This course is aimed at MSc students with suitable background studies as well as PhD students and post-doctoral researchers who are applying or planning to apply high throughput sequencing technologies and bioinformatics methods in their research.

Course content: Lectures will give insight into how biological knowledge can be generated from RNA seq experiments and illustrate different ways of analyzing such data. Practicals will consist of computer exercises that will enable the participants to apply statistical methods to the analysis of RNA-seq data under the guidance of the lecturers and teaching assistants. Familiarity with the technology and biological use cases of high throughput sequencing is required, as is some experience with R/Bioconductor. Participants can bring along and analyze their own RNA-seq data on the course.

Software and Data will be provided through a virtual machine that is used through a web browser. No special software is needed.

Please note! The workshop is intensive and it is recommended that all participants get familiar with central concepts before the course. Please read the seven articles (LINK) covering the different stages of RNAseq analysis. Material from these articles will be included in the exam that students need to pass to obtain the study credits.

Workshop III, ENSEMBL genome browser (ILS-120, 1 cr)                                                    

Thu 1.11.2018, 9:15-17:00
Room: Infocenter Korona, room 511

Instructor: Erin Haskell, EBI

This one-day browser workshop offers participants the possibility of gaining lots of hands-on experience in the use of the Ensembl genome browser, but also provides them with the necessary background information. The workshop is primarily targeted at wetlab researchers.

Content: The workshop consists of a series of modules (announced later).  Most modules consist of a presentation and a demonstration of the tools, followed by the opportunity to do exercises. Participants are encouraged to bring problems/questions about their research and we will try to tackle these during the workshop using Ensembl.

Feedback from previous courses:
“There are probably quite few people out there who all assume that Ensembl today is the same as it was years ago. It is not. With many new features and datasets incorporated/interlinked, it offers data exploration like never before. This course was a very useful update on what Ensembl has become” Browser workshop, CRUK, April 2016
“Very useful workshop, certainly one of the most informative and useful I have attended. Delivered by someone who was extremely familiar with the website and its capabilities, not someone who had used it a couple of times and proclaimed themselves to be an expert.” Browser workshop, Cardiff, March 2014

Learning outcomes
At the end of this course participants should be able to:

  • view genomic regions and manipulate the view to add features they are interested in.
  • explore information about genes and their sequences, and gene data in bulk using BioMart.
  • analyse genomic variants and associated phenotypes and their own variation data using the VEP.
  • view homologous genes and genomic regions, functional elements involved in gene regulation and their activity in different cell types.

Registration, full time participation and returning the required reports and/or other assignments are required for obtaining credits. ECTS credits can be earned according to the information below:

ILS-104 Pre-Symposium Journal Club Mondays 15.10. and 22.10.2018 (1 cr)
ILS-105 NGG Symposium (23.-24.10.), lecture hall 2041, Biocenter 2, Viikki campus
 - 1 cr full time attendance
 - 1 cr Write a report of 1 talk/day, 250-400 words/topic. Report will be returned in Moodle and checked for plagiarism in Urkund. Pass/fail.
-Instructions and returning of the reports: https://moodle.helsinki.fi/user/index.php?id=31071
ILS-106
Workshop I Thu – Fri 25.-26.10.2018 (2 cr)
ILS-107 Workshop II Mon – Wed 29.-31.10.2018 (2 cr)
ILS-120 Workshop III Thu 1.11.2018 (1 cr)                               

Please note that the registration to workshops and journal club ended on October 1st. You can still register to the main symposium.

The symposium and associated workshops are free of charge.
Registration to workshops and journal club is open 30.8. - 1.10.2018
Registration to Symposium is open until 15.10.2018
Registration through this link: https://elomake.helsinki.fi/lomakkeet/91313/lomake.html

The course will be organized at the University of Helsinki Viikki Campus.

Addresses of lecture halls

  • Biocenter 2, Viikinkaari 5, 00790 Helsinki
  • Infocenter Korona, Viikinkaari 11, 00790 Helsinki
  • B-buiding (Metsätieteiden talo), Latokartanonkaari 7, 00790 Helsinki
  • C-building, Latokartanonkaari 5, 00790 Helsinki

Helsinki, map link

Helsinki has an effective local transport and various possibilities for accommodation.

Local transport route planner

Tickets and fares

Accomodation possibilities    

Viikki map

The symposium is organized by the Integrative life Science (ILS) doctoral program in collaboration with the Research Program in Genome Biology, Institute of Biotechnology, University of Helsinki

Organizing Committee:

Mikko Frilander
Alan Schulman
Petri Auvinen
Susana Maria Garcia
Ari Löytynoja
Liisa Holm
Ari Pekka Mähönen
Yrjö Helariutta
Ville Mustonen
Craig Primmer