Action Calls

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Looking for a challenging and interesting PhD or post-doc position? Here are the latest young researcher job offers at Mye-Infobank’s partner institutions:

• Post-Doc Position for UMESciA Medical Scientist School, Brandau Lab, University Hospital Essen, DE

STSM CALL - Advancing in silico myeloid cell deconvolution from bulk transcriptomics - NOW CLOSED

Host Institution: Technical University of Munich, Germany

Supervisor/Coordinators: Markus List

Instructors: Markus List, Francesca Finotello, Javier De Las Rivas

Timeframe: 13^th February to 16^th February 2023

Attendees: On-site: 10x WG 1 members, Virtually: 5x WG 1 and/or WG 2 members

Purpose: Building on existing methods and software tools, we will investigate in how much detail myeloid cells can be differentiated (e.g. M1 and M2 macrophages) reliably using simulated pseudo-bulk data sets created from single-cell RNA-seq data, where we can systematically assess detection limits and spillover effects. Where available, we will also use experimental gold standard data sets (e.g. matched bulk RNA-seq and FACS data). For this STSM, we will focus on bulk data with varying difficulty, e.g. one example of PBMCs, cancer and auto-immune disease for which well-annotated single-cell data sets are available. As an outcome, we envision establishing best practices for the deconvolution of myeloid cells.

Tasks: It is our aim to identify the best computational strategy to quantify myeloid subsets in bulk transcriptomics data using in silico deconvolution.

Selection Criteria:

WG 1 members: Expertise in bioinformatics and/or bulk as well as single-cell RNA-seq data sets. Preferably prior experience with in silico cell type deconvolution

WG 2 members: Expertise in myeloid cell immunology in particular with the ability to assess the quality of cell-type specific gene signatures and the interpretation of cell subtypes corresponding to single-cell RNA clusters.

Requirements:

• Availability from February 13 at 14:00 h until February 16^th 13:00 h.
• Notebook / laptop and skills in R / python to engage in data processing and application of in silico cell type deconvolution tools, plotting of results.
• WG 1 members should have identified candidate data sets ready for analysis BEFORE the STSM.

Expected Outcome: Based on our work during the STSM we will write a white paper and possibly a manuscript on best practices for myeloid cell type deconvolution.

Application Deadline: 31^st December 2022

Workshop Call - Analysis and integration of scRNA-seq datasets - NOW CLOSED

Purpose: In this workshop, in session 1 we will give an overview of scRNA-seq data analysis steps such as quality control, preprocessing, normalization, cell annotation. Then we will move to the task of integrating multiple scRNA-seq datasets where we first show variations caused by batch effects or variations caused by biological factors. We will give an overview of existing scRNA-seq integration methods and provide an evaluation where we explain their advantages/disadvantages thoroughly. In session 2, for a few selected integration methods, we will provide a hands-on application to show how multiple scRNA-seq datasets can be integrated.

Selection Criteria: WG 1 or 2 members: Expertise in bioinformatics and/or OMICS data sets, preferentially with a focus on single-cell RNA-seq data analysis. Familiarity with R or Python is required.

Requirements:

• Availability on March 23th, from 10 AM till 5 PM
• Own notebook to download and run the required software

Expected Outcome: Publication of the course material on Github for future references.

Host Institution: Antalya Bilim University, Antalya, Turkey

Venue: Belek, Antalya, Turkey

Instructors: Hilal Kazan, Cesim Erten, Yasin Kaymaz, Aissa Houdjdedj, Mekan Myradov

Timeframe: 23^th March 2023 (whole day)

Attendees: On-site: 10x WG 1 members, 2x WG 2 members; Virtually: 10x WG 1 and/or WG 2 members (only for session 1)

Application deadline: 15^th January 2023

Send applications to: Dr. Hilal Kazan, e-mail: hilal.kazan@antalya.edu.tr or Dr. Cesim Erten, e-mail: cesim.erten@antalya.edu.tr (Workshop Coordinators)

Participant confirmation announcement: 23^rd January 2023

DOWNLOAD APPLICATION FORM here

As soon as these are released, announcements will appear here.