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Mohamed Nadhir Djekidel, PhD

Mohamed Nadhir Djekidel, PhD

  • Bioinformatics Research Scientist, Epigenetics


Postdoctoral Fellow - Harvard Medical School, Boston, MA
PhD (Bioinformatics) - Tsinghua University, Beijing, China
MS (Computer Science/Bioinformatics) - Central South University, Changsha, China
BIng (Computer Science) - École nationale supérieure d'informatique, Algiers, Algeria


Dr. Mohamed Nadhir Djekidel is a Bioinformatics researcher in the epigenetic group of the Center of Applied Bioinformatics. He enjoys tackling challenging bioinformatics problems and likes to develop new and effective approaches to deal with them. He has experience in working  with different next generation sequencing data ranging from transcriptome (RNA-Seq), epigenome (ChIP-Seq, ATAC-Seq, CUT&RUN, WGBS, RRBS), chromatin structure (Hi-C, ChIA-PET) and single-cell sequencing data. He has also developed several publicly available computational methods and visualization tools.

Research Interests

  • Development of new computational/Statistical analysis methods and optimized NGS pipelines.
  • Epigenetic regulation of gene expression.
  • Integrative analysis of multi-omics data. 
  • Single-cell omics.
  • Biology of human diseases

Selected Publications

Fu, X.*, Djekidel, M. N.* & Zhang, Y. A transcriptional roadmap for 2C-like–to–pluripotent state transition. Science Advances 6, eaay5181 (2020).

Bhattacherjee, A*., Djekidel, M.N.*, Chen, R.* et al. Cell type-specific transcriptional programs in mouse prefrontal cortex during adolescence and addiction. Nat Commun 10, 4169 (2019.

Fu, X.*, Wu, X.*, Djekidel, M.N.* et al. Myc and Dnmt1 impede the pluripotent to totipotent state transition in embryonic stem cells. Nat Cell Biol 21, 835–844 (2019).

Tuesta, L.M., Djekidel, M.N., Chen, R. et al. In vivo nuclear capture and molecular profiling identifies Gmeb1 as a transcriptional regulator essential for dopamine neuron function. Nat Commun 10, 2508 (2019).

Djekidel, M. N.* et al. Reprogramming of Chromatin Accessibility in Somatic Cell Nuclear Transfer Is DNA Replication Independent. Cell reports 23, 1939–1947 (2018).

Djekidel, M. N., Chen, Y. & Zhang, M. Q. FIND: difFerential chromatin INteractions Detection using a spatial Poisson process. Genome research (2018).

Li, Y., He, Y., Liang, Z., Wang, Z., Cheng, F., Djekidel, M. N. et al. Alterations of specific chromatin conformation affect ATRA-induced leukemia cell differentiation. Cell Death Dis 9, 200 (2018).

Liang, Z., Li, G., Wang, Z., Djekidel, M. N. et al. BL-Hi-C is an efficient and sensitive approach for capturing structural and regulatory chromatin interactions. Nat Commun 8, 1622 (2017).

Djekidel, M.N., Wang, M., Zhang, M.Q. et al. HiC-3DViewer: a new tool to visualize Hi-C data in 3D space. Quant Biol 5, 183–190 (2017).

Djekidel, M.N., Liang, Z., Wang, Q. et al. 3CPET: finding co-factor complexes from ChIA-PET data using a hierarchical Dirichlet process. Genome Biol 16, 288 (2015).  

Full list of publications

Last update: September 2020