This page summarises the active projects I am working on.

1 Lung Cancer irAE analysis

Collaboration with Margarida Souto-Carneiro

Project website: https://www.huber.embl.de/users/jlu/irAE_report/index.html

2 Phospho-/Full-proteomic analysis of drug perturbed lung cancer cell lines

Collaboration with Sotillo and Klingmüller groups

Project website: https://www.huber.embl.de/users/jlu/LungCancer_SotilloLab/index.html

3 EMBL2016 analysis

Collaboration with Jarno Kivioja

Project website: https://www.huber.embl.de/users/jlu/newEMBL/docs/index.html

4 CD38 and ZAP70 expression in CLL samples

Collaboration with Alexander Ring

Manuscript link
html report:
CD38/ZAP70 expression analysis: https://www.huber.embl.de/users/jlu/CD38_ZAP70/CD38_ZAP70.html
NRIP1/ZAP70 expression analysis: https://www.huber.embl.de/users/jlu/CD38_ZAP70/NRIP1_ZAP70.html
Analysis of the cluster defined by four genes (ZAP70, PLD1, ZNF667, ZNF471): https://www.huber.embl.de/users/jlu/CD38_ZAP70/clusterAnalysis.html
Source code: https://git.embl.de/jlu/CLLproject_jlu/-/blob/master/analysis/CD38_ZAP70/

5 CLL transcriptomics

Collaboration with Almut

Manuscript link
Source code: https://git.embl.de/aluetge/Transcriptome_CLL

6 CLL BH3 profiling data analysis and manuscript writing

Collaboration with Rebecca Valentine

html reports: https://www.huber.embl.de/users/jlu/BH3profiling/index.html
Link to manuscript

7 1000CPS data analysis and manuscript writing

Collaboration with Sebastian Scheinost

html reports: link to CLLwiki
Source code: https://git.embl.de/jlu/CLLproject_jlu/-/tree/master/analysis/Phenotype1000
Link to manuscript

8 Function of DDX3X mutations in B-cell lymphomas

Collaboration with Ester Cannizzaro

html reports
Expression analysis: https://www.huber.embl.de/users/jlu/DDX3X/DDX3X_RNAseq.html
Splicing analysis: https://www.huber.embl.de/users/jlu/DDX3X/DDX3_Splicing.html
Source code:

9 Single-cell ATACseq in Follicular Lymphoma

Raw data and prelimiary reports are at: /g/huber/projects/nct/cll/RawData/ATACseq (EMBL server)

10 Finished projects

10.1 CLL proteomic data analysis and manuscript writing

Collaboration with Fabienne Meier-Abt

html reports (old version): https://www.huber.embl.de/users/jlu/Proteomics/index.html
html reports (new version for revision): https://www.huber.embl.de/users/jlu/Proteomics/batch13Combine/index.html
Source code: https://git.embl.de/jlu/Proteomics
Link to manuscript
Link to rebuttal letter

11 Target importance inference (DepInfeR)

Collaboration with Alina Batzilla

Manuscript: https://docs.google.com/document/d/1A2RiOnKxkuxehSZYaoHYGNj3ZCcZWQNeJ8zikl5b21w/edit?ts=60dc469a
Source code: https://git.embl.de/jlu/targetimportance