Lausanne Workshop

When 19 March, 2019 - This activity is over

Short description:

The Lausanne workshop will take place on the 19th and 20th of March 2019. In it we will focus on how the nucleotide sequence is recognised by proteins, putting our attention to the status and quality of the current annotations and curation guidelines for annotating protein-nucleotide interactions. More details will be provided once the agenda is updated.

Local organiser(s):

Philipp Bucher

Agenda:

18th of March:

Social activities:

19:00: Dinner.

19th of March:

Morning session:

08:45 – 10:45: Opening Symposium – session 1 (Room SV1717)
- 08:45 – 09:00: Opening (Philipp Bucher and Martin Kuiper).
- 09:00 – 09:35: Completing the collection of human TF motifs (Tim Hughes).
- 09:35 – 10:10: A flexible algorithm for fitting accurate biophysical models of protein-DNA interaction directly to SELEX data (Harmen Bussemaker).
- 10:10 – 10:45: A comprehensive Drosophila melanogaster transcription factor interactome (Sachi Inukai).
10:45 – 11:15: Coffee break.
11:15 – 13:00: Symposium – session 2 (Room SV1717)
- 11:15 – 11:50: Predicting regulatory interactions from transcription factor ChIP-seq data (Tim Bailey).
- 11:50 – 12:25: Fitting complementary motif sets to ChIP-seq data and dinucleotide weight tensors for TF specificities (Erik van Nimwegen).
- 12:25 – 13:00: Use of variability across individuals to identify gene regulatory elements (Judith Zaugg).
13:00 – 14:00: Lunch break.

Afternoon session:

14:00 – 15:45: Symposium – session 3 (Room SV1717)
- 14:00 – 14:35: From automated to curated annotation of regulatory elements and interactions in Ensembl (Daniel Zerbino).
- 14:35 – 15:10: Characterising mammalian regulatory elements in the light of evolution (Maša Roller).
- 15:10 – 15:45: Articulating the high throughput (epi)genomics data knowledge commons (Colin Logie).
15:45 – 16:15: Coffee break.
16:15 – 18:00: Break-out sessions:
- TF specificity models break-out 1 – Predicting the precise location of TF binding at regulatory DNA (Moderators: Philipp Bucher and Ivan Kulakovskiy) (Room SV17171):
  - Part 1 (20 min): TFBS as a component of DNA-centric annotation: what is unclear. Ljubljana keypoints revisited.
  - Part 2 (15 min): TFBS prediction and annotation: performance measures and descriptive quality criteria.
  - Part 3 (10 min):(TFBS BE-IN 1) TFBS models open benchmarking initiative: current status (Ivan Kulakovskiy).
  - Part 4 (30 min): (TFBS BE-IN 2) Benchmarking protocols: which are there and which are missing (Philipp Bucher).
  - Part 5 (10 min): (TFBS BE-IN 3) Ensuring benchmarking re-usability by containerization of protocols (Ivan Kulakovskiy and Ilya Vorontsov).
  - Part 6 (15 min): Proposed deliverables for DNA-centric annotation, and questions to DNA-centric group.
- DNA-centric annotation 1 – Regulatory elements for GREEKC (Moderators: Astrid Lægrid and Martin Kuiper) (Room AI153):
  - Part 1 (15 min): How do regulatory elements fit in the main GREEKC use cases/cartoons?
  - Part 2 (30 min): Review of available ontologies and proposed terms (GO/MSO/GRAO).
  - Part 3 (45 min): Develop a short list of needed terms.
  - Part 4 (15 min): Broad Yes/No proposals are voted upon and dissent is noted.

Social activities:

20:00: Dinner.

20th of March:

Morning session:

09:00 – 10:45: Break-out sessions:
- TF-specificity models break-out 2 -From the experimental data to TF binding models and TFBS annotations (Moderators: Vsevolod Makeev and Tim Hughes) (Room INR219):
  - Part 1 (15 min): Introducing the table of DNA-protein interaction data (basing on https://doi.org/10.1016/j.cell.2018.01.029). Possible additions after one year?
  - Part 2 (10 min): (TFBS BE-IN 4) TF and data selection: the strategy and key sources of experimental data (Oriol Fornes, Skype).
  - Part 3 (35 min): Motif discovery. Model selection depending on the availability of the experimental data. Can we formulate guidelines for prudent use of models of appropriate complexity?
  - Part 4 (30 min):Motif finding / Pattern matching. TFBS occupancy as a function of site accessibility, TF concentration, and TF affinity. Competition between TF. What is to annotate?
  - Part 5 (15 min): Which TFBS model and prediction descriptors should be included in TFBS prediction ontology?
- DNA-centric annotation 2 – Biochemical properties of regulatory elements. (Moderators: Judith Zaug, Maša Roller and Colin Logie) (Room DIA004).
10:45 – 11:00: Coffee break.
11:00 – 12:30: Joint session (Room INR219).
12:30 – 13:30: Lunch.

Afternoon session:

13:30 – 15:00: Break-out session:
- TF-specificity models break-out 3 (Moderators: Vsevolod Makeev and Anthony Mathelier) (Room INR219):
  - Part 1 (45 min): (TFBS BE-IN 5) Roadmap: setting the stage for the open challenge (deadlines, key participants, invitation emails). Subtopics: standard representation of basic TFBS models (file formats, etc), and other technical questions.
  - Part 2 (30 min): Lessons from joint sessions. TFBS annotation viewed as a part of DNA-centric annotation.
  - Part 3 (15 min): Future plans + wrap-up for the final joint session.
- DNA-centric annotation 3 – Measurable properties of regulatory elements. (Moderators: Daniel Zerbino, Camille Berthelot and Tim Hughes) (Room DIA004):
  - Part 1 (45 min): What are the measurable properties of a regulatory element, and what assays are available to measure them?
  - Part 2 (30 min): What are the existing data sets? Which data types are linked to which WG1 terms defined in this workshop?
  - Part 3 (15 min): Data sets to benchmark the GRAO.
15:00 – 15:15: Coffee break.
15:15 – 17:00: Wrap-up session, action points (Room INR219).

Social activities:

19:00: Dinner.