Dimitrios Kyriakis, PhD
Bioinformatics consultant for single-cell neurogenomics
I turn single-nucleus and bulk sequencing data from the human brain into results you can defend in review: from raw counts and cell-type annotation to disease signatures and the figures that go in the paper.
Currently consulting for the Roussos Lab at Icahn School of Medicine at Mount Sinai.
About
I'm a computational biologist working on neurodegenerative and neuropsychiatric disease. My PhD at the Luxembourg Centre for Systems Biomedicine used single-cell transcriptomics to follow Parkinson's disease through iPSC-derived neuronal differentiation and to map microglial heterogeneity in the brain.
Since 2022 I've worked with Panos Roussos's group at Mount Sinai, first as a visiting researcher and postdoc and now as a consultant, on population-scale single-nucleus data from the human brain and on human brain tissue models.
Before that I trained in biology at Aristotle University of Thessaloniki and in bioinformatics at the University of Crete, working on population genetics and transcriptomics in fish. That background still shows in how I approach study design and genetic data.
I also take on independent projects through EvoDecode BioInsights, my consultancy based in Thessaloniki.
Services
Single-cell and single-nucleus RNA-seq
QC, doublet and ambient-RNA handling, integration across batches and donors, clustering and annotation that holds up at the donor level.
Reference mapping and label transfer
Projecting new datasets onto large brain atlases with scVI/scANVI, with seed-robust consensus labels and checks you can show a reviewer.
Disease and differential expression
Pseudo-bulk models with the right covariates, cell-type composition analysis, and pathway and network interpretation.
Bulk RNA-seq
Differential expression, alternative splicing and functional enrichment, from FASTQ to publication figures.
Genetics
GWAS, genetic mapping of traits and variant-level analyses that connect risk loci to cell types.
Reproducible pipelines
Snakemake workflows on HPC, version-controlled code and documentation your team can rerun after I leave.
Skills
Programming
- R (Bioconductor, tidyverse)
- Python (scanpy, AnnData, pandas)
- Bash
- rpy2 and anndata2ri for mixed R/Python workflows
Single-cell and single-nucleus RNA-seq
- Cell Ranger
- Seurat
- scanpy
- Pegasus
- ambient RNA removal (SoupX)
- doublet detection (scDblFinder)
- SCTransform
Integration and annotation
- scVI and scANVI (scvi-tools)
- Harmony
- LIGER
- Conos
- reference mapping and label transfer
- SingleR
- Garnett
- UCell
Statistics and differential expression
- pseudo-bulk mixed models (dreamlet, variancePartition, lme4)
- muscat
- DESeq2
- compositional analysis (crumblr)
- meta-analysis (metafor)
Trajectories and dynamics
- Monocle
- Slingshot
- tradeSeq
- time-series single-cell analysis
Gene regulation and networks
- pySCENIC
- WGCNA and hdWGCNA
- GENIE3
- Bayesian networks (bnlearn)
- STRING
- Cytoscape (RCy3)
Cell–cell communication
- CellChat
- LIANA
- ligand–receptor analysis
Pathways and interpretation
- clusterProfiler
- fgsea
- ReactomePA
- MSigDB
- zenith
- decoupler
Genetics and translation
- GWAS integration with single-cell data (scDRS)
- ddRAD-seq and genetic mapping
- computational drug repurposing (CMap)
Reproducibility
- Snakemake
- conda
- Docker and Singularity
- Git and GitHub
- versioned code releases with Zenodo DOIs
Visualization
- ggplot2
- ComplexHeatmap
- matplotlib and seaborn
- publication-ready figures
Data and biology
- human post-mortem brain
- iPSC-derived neurons
- brain organoid and miBrain models
- peripheral immune cells
- mouse microglia
Experience
- 2024 – now
Bioinformatics Consultant
Icahn School of Medicine at Mount Sinai, Roussos Lab
Computational biology for neurodegenerative disease.
- 2023 – 2024
Postdoctoral Researcher
Icahn School of Medicine at Mount Sinai, Roussos Lab
Computational biology for neurodegenerative disease.
- 2022 – 2023
Postdoctoral Researcher
University of Luxembourg, Skupin group
Single-cell analysis of Parkinson's disease models.
- 2022
Visiting Researcher
Icahn School of Medicine at Mount Sinai, Roussos Lab
- 2017
Assistant Researcher
Computational Biology Lab, IMBB-FORTH, Heraklion
Modelling mossy cells in the hippocampus.
- 2015 – 2016
Erasmus Intern
Wageningen UR, Animal Breeding and Genomics
Transcriptome assembly and annotation of yellowtail kingfish.
- 2014
Intern
Hellenic Centre for Marine Research, Heraklion
Genetic differentiation of pikeperch; introduction to RNA-seq analysis.
Education
- 2018 – 2022
PhD, Computational Biology
Luxembourg Centre for Systems Biomedicine, University of Luxembourg
Single-cell biology of neurodegenerative disease. Supervisor: Alexander Skupin.
- 2016 – 2018
MSc, Bioinformatics
School of Medicine, University of Crete
Genetic mapping of phenotypic traits in gilthead seabream from ddRAD-seq.
- 2010 – 2016
BSc, Biology
Aristotle University of Thessaloniki
Publications
Decoding immune landscapes and therapeutic targets in intracerebral hemorrhageKyriakis D, Wang X, Pavlopoulos A, Vicari J, Kleopoulos SP, et al., Roussos PManuscript in preparation
Cholesterol-mediated lysosomal dysfunction in APOE4 astrocytes promotes α-synuclein pathology in miBrains, a human brain microphysiological systemMesentier-Louro LA, Goldman C, Gaese S, Buonfiglioli A, Kyriakis D, et al.bioRxiv, preprint
Multi-omics integration of scRNA-seq time series data predicts new intervention points for Parkinson's diseaseMihajlović K, Ceddia G, Malod-Dognin N, Novak G, Kyriakis D, Skupin A, Pržulj NScientific Reports
Glioblastoma-instructed microglia transit to heterogeneous phenotypic states with phagocytic and dendritic cell-like features in patient tumors and patient-derived orthotopic xenograftsYabo YA, Moreno-Sanchez PM, Pires-Afonso Y, Kaoma T, Kyriakis D, et al., Golebiewska AGenome Medicine
Early-to-mid stage idiopathic Parkinson's disease shows enhanced cytotoxicity and differentiation in CD8 T-cells in femalesCapelle CM, Ciré S, Hedin F, Hansen M, Pavelka L, Grzyb K, Kyriakis D, et al., Hefeng FQNature Communications
Rac1 and Rac3 GTPases and TPC2 are required for axonal outgrowth and migration of cortical interneuronsKounoupa Z, Tivodar S, Theodorakis K, Kyriakis D, Denaxa M, Karagogeos DJournal of Cell Science
Single-cell transcriptomics of human iPSC differentiation dynamics reveal a core molecular network of Parkinson's diseaseNovak G, Kyriakis D, Grzyb K, Bernini M, Skupin ACommunications Biology
Assessing genetic variation in wild and domesticated pikeperch populations: implications for conservation and fish farmingTsaparis D, Lecocq T, Kyriakis D, Oikonomaki K, Fontaine P, Tsigenopoulos CSAnimals
Single-cell transcriptomics and in situ morphological analyses reveal microglia heterogeneity across the nigrostriatal pathwayUriarte O, Kyriakis D, Heurtaux T, Grzyb K, Pires-Afonso Y, et al., Michelucci AFrontiers in Immunology
Scanning of genetic variants and genetic mapping of phenotypic traits in gilthead seabream through ddRAD sequencingKyriakis D, Kanterakis A, Manousaki T, Tsakogiannis A, Tsagris M, et al., Tsigenopoulos CSFrontiers in Genetics
Muscle and liver transcriptome characterization and genetic marker discovery in the farmed meagre, Argyrosomus regiusTsigenopoulos CS, Manousaki T, Tsakogiannis A, Lagnel J, Kyriakis D, Duncan N, Estevez AMarine Genomics
In vivo effects of lipopolysaccharide on peroxisome proliferator activated receptor expression in the gilthead seabream (Sparus aurata)Antonopoulou E, Kaitetzidou E, Castellana B, Panteli N, Kyriakis D, Vraskou Y, Planas JVBiology
The full, current list is on Google Scholar.
Code
- scMyeloids_ICH
Single-cell RNA-seq of myeloid cells from 30 patients with intracerebral hemorrhage: outcome-linked activation states, cell–cell signalling, regulatory networks and drug repurposing. Reproduces all main and supplementary figures.
- miBrain-snRNAseq-APOE4-aSynuclein
Single-nucleus RNA-seq pipeline for APOE4 miBrain models: Cell Ranger, QC and annotation, concordance with a reference atlas, pseudo-bulk differential expression and enrichment.
- IPSCs_PINK1
Snakemake workflow for single-cell time series of PINK1-mutant iPSC differentiation into dopaminergic neurons, with network analysis of Parkinson's disease genes.
- CoPImmunoPD
Single-cell analysis of peripheral CD8 T cells in early-to-mid stage Parkinson's disease.
- microglia-heterogeneity
Regional heterogeneity of mouse microglia across the nigrostriatal pathway, from QC to figures.
Off the clock
Contact
Have a dataset or a project in mind? Send a short description and I'll reply with how I'd approach it.
- Emailkyriakds@gmail.com
- LinkedIndimitrios-kyriakis
- GitHubKyriakisDimitrios
- Google ScholarPublication profile
- ConsultancyEvoDecode BioInsights
- Based inThessaloniki, Greece