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| Name | Country | Summary | Techniques | Can host STSM? | ORCID |
|---|---|---|---|---|---|
| María Espinosa | Argentina | I am away from the experimental work now (scarcity of resources). I am interested in science and education about the interaction between genome and the environment because the risks of environmental contamination have for health. | Maybe | 0000-0003-3034-9302 |
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| Wim Vanden Berghe | Belgium | BisulfiteSeq, Transcriptomics (RNAseq, microarrays, etc.), Proteomics (mass spectrometry, etc.), Biochemistry, Nanopore sequencing, Pacbio sequencing, Bioinformatics, NGS data analysis, pathway enrichment analysiss | Yes | 0000-0003-0161-7355 |
|
| Shazie Yuein-Myahkova | Bulgaria | HMGB1 - a chromatin protein involved in cellular and extracellular signaling and its role in cancer; Mechanisms of synchronization between different processes taking place during replication, repair and transcription of DNA. | FISH (DNA, RNA), Superresolution Microscopy, Immunofluorescence, Transcriptomics (RNAseq, microarrays, etc.), Biochemistry, Live cell microscopy, FRAP, Flow cytometry, Bioinformatics, Image analysis | Maybe | 0000-0002-0573-5685 |
| Đurđica Ugarković | Croatia | FISH (DNA, RNA), Chip-Seq, Electron microscopy, Immunofluorescence, Transcriptomics (RNAseq, microarrays, etc.), Biochemistry, Biostatistics, Bioinformatics, NGS data analysis | Yes | 0000-0002-9450-3551 | |
| Željka Pezer Sakač | Croatia | FISH (DNA, RNA), Chip-Seq, Transcriptomics (RNAseq, microarrays, etc.), Biochemistry, Biostatistics, Bioinformatics, NGS data analysis | Yes | ||
| Jan Palecek | Czech Republic | Our lab studies assembly and functions of the Structure Maintenance of Chromosome (SMC) complexes (particularly, SMC5/6 complex). We use combination of genetic, biochemical and bioinformatic methods to get deep insights into their features. | Chip-Seq;Electron microscopy;Immunofluorescence;Genome engineering (CRISPR, TALEN, Cre-Lox, etc.);Proteomics (mass spectrometry, etc.);Structural Biology (NMR, X-ray);Biochemistry. protein-protein interaction, protein-DNA interaction. Bioinformatics;NGS data analysis;Visualization/graphics | Maybe | 0000-0002-6223-5169 |
| Barbora Kozlikova | Czech Republic | Our laboratory, Visitlab, at the Faculty of Informatics, specialized on the visualization and visual analysis of scientific data. We have a long-term experience in designing novel visual representations for biomolecular data. | Bioinformatics;Machine learning & AI;Molecular Dynamics;Software/pipeline development;Algorithmics;Visualization/graphics | Maybe | 0000-0003-0045-0872 |
| David Honys | Czech Republic | Bioinformatics, NGS data analysis, Image analysis | Chip-Seq, Genome engineering (CRISPR, TALEN, Cre-Lox, etc.), Transcriptomics (RNAseq, microarrays, etc.), Proteomics (mass spectrometry, etc.), Single-cell technologies. | Yes | |
| Daniel Jost | France | In close connection with experimentalists, our computational research aims at probing the universal principles driving chromatin folding and regulation, while contextualizing our approaches to fundamental, specific problems of 3D genomics. | Biological physics, Polymer modeling, Machine learning & AI, Deep learning/neural networks, Numerical simulations, Molecular Dynamics, Kinetic Monte-Carlo, Dynamical systems. Stochastic modeling, Polymer lattice models | Yes | 0000-0002-9877-6864 |
| Julie Chaumeil | France | Hi-C and similar 'C' techniques (3C, 4C, 5C, capture Hi-C, etc.), FISH (DNA, RNA), Immunofluorescence, Genome engineering (CRISPR, TALEN, Cre-Lox, etc.), Image analysis, | Maybe | 0000-0002-8976-2890 |
|
| Aurele Piazza | France | Hi-C and similar 'C' techniques (3C, 4C, 5C, capture Hi-C, etc.), Chip-Seq, Genome engineering (CRISPR, TALEN, Cre-Lox, etc.), NGS data analysis, DNA recombination, DNA repair | No | 0000-0002-7722-0955 |
|
| Marco Di Stefano | France | Hi-C and similar 'C' techniques (3C, 4C, 5C, capture Hi-C, etc.), Superresolution Microscopy, Biological physics, Biostatistics, Bioinformatics, Polymer modeling, Integrative/restraint-based modeling, Molecular Dynamics, Software/pipeline development | Maybe | 0000-0001-6195-4754 |
|
| Annick Lesne | France | My research focuses on the tole of physical mechanisms in genome organization and function, using modeling and analysis tools from theoretical physics. | Biological physics, Biomathematics, Biostatistics, Polymer modeling, Dynamical systems | Maybe | 0000-0002-6647-612X |
| Ana Pombo | Germany | We study mechanisms of gene expression from the local action of transcription factors, to long-range chromatin looping, to how whole chromosomes are positioned within cell nuclei, in mammalian cells and especially neurons. | GAM, FISH (DNA, RNA), Chip-Seq, ATAC-Seq, Immunofluorescence, Genome engineering (CRISPR, TALEN, Cre-Lox, etc.), Transcriptomics (RNAseq, microarrays, etc.), Single-cell technologies, Bioinformatics, Molecular Dynamics, NGS data analysis, Software/pipeline development | Yes | 0000-0002-7493-6288 |
| Argyris Papantonis | Germany | ChIP-seq, RNA-seq, Hi-C | Yes | ||
| Babis Spilianakis | Greece | Research in our laboratory focuses on the effect of the three-dimensional structure of chromatin on gene expression patterns in the innate and adaptive immune system. | Hi-C and similar 'C' techniques, HiChip, FISH (DNA, RNA), Chip-Seq, ATAC-Seq, BisulfiteSeq, Immunofluorescence, Genome engineering (CRISPR, TALEN, Cre-Lox, etc.), Transcriptomics, Proteomics, Biochemistry, NGS data analysis, Image analysis | Maybe | 0000-0003-0921-1923 |
| Endre Sebestyén | Hungary | We are studying the effect of transcriptional, post-transcriptional expression and chromatin structural variance on gene regulatory networks, and the role of this variance in the development of human disease. | Biostatistics, Bioinformatics, NGS data analysis, Software/pipeline development, Visualization/graphics | Maybe | 0000-0001-5470-2161 |
| Ranjith Padinhateeri | India | We do computational study of chromatin organization and dynamics using statistical mechanics and polymer physics. We also study study of kinetics of nucleosome and epigenetic modifications | Biological physics, Biomathematics, Biostatistics, Polymer modeling, Numerical simulations, Kinetic Monte-Carlo, Dynamics of chromatin, kinetics of nucleosomes | Yes | 0000-0001-5485-1474 |
| Ronan Murphy | Ireland | Transcriptomics (RNAseq, microarrays, etc.), Biochemistry, in vitro modelling of human diseases (Cardiovascular, Skin, and Lung), | Yes | 0000-0002-4579-8007 |
|
| Daniel Remondini | Italy | My group applies bioinformatics, network based-methods and stochastic approaches to study biological processes: cancer, metagenomics, properties of DNA structure in 1d and 3d. We are actually working on DNA methylation features at multi-organism level, application of network methods to chromatin 3D configuration characterization, metagenomics ecology (resistome), drug repurposing and novel target identification in oncology. | Data Analysis (Machine Learning, Statistics, Bioinformatics) on NGS and high-throughput data; Systems Biology with network-based approaches physical modelling of Biological Complex Systems (e.g. DNA sequences). Fluorescence and optical microscopy; electrophysiology at single-cell level (patch clamp), Biological physics, Biomathematics, Biostatistics, Bioinformatics, Machine learning & AI, Deep learning/neural networks, NGS data analysis, Image analysis, Software/pipeline development, Dynamical systems, Visualization/graphics. Network-based approaches (e.g. spectral and diffusion-based) | Yes | 0000-0003-3185-7456 |
| Francesco Ferrari | Italy | My group is interested in the role of chromatin 3D organization in regulating genome functionality. Our computational biology expertise is particularly focused on the use of genome-wide techniques based on high-throughput sequencing. | Hi-C and similar 'C' techniques (3C, 4C, 5C, capture Hi-C, etc.), Chip-Seq, ATAC-Seq,Biostatistics, Bioinformatics, NGS data analysis, Software/pipeline development | Yes | 0000-0002-9811-3753 |
| Mario Nicodemi | Italy | My group works on the Physics of Complex Systems and its applications to Molecular Biology, combining physics, computer simulations and data analysis. In particular, we investigate the 3D architecture of the genome and gene regulation. | Biological physics, Biomathematics, Bioinformatics, Polymer modeling, Machine learning & AI, Numerical simulations, Molecular Dynamics, Kinetic Monte-Carlo, NGS data analysis | Maybe | 0000-0002-8416-6416 |
| Alessio Zippo | Italy | We aim to dissect the molecular mechanisms through which chromatin players mediate the epigenetic responses to environmental signals in stem cells by using multidisciplinary approaches. | ATAC-Seq, CUT&RUN, Superresolution Microscopy, Genome engineering (CRISPR, TALEN, Cre-Lox, etc.), Transcriptomics, Bioinformatics, NGS data analysis, Image analysis | Yes | 0000-0002-3686-6151 |
| Jekaterina Erenpreisa | Latvia | Currently, we are involved in cancer cell biology research. Cell nucleus organisation is 'a second love", linked to the first (not funded). We are interested in the biophysical principles of genome regulation for differentiation. | Immunofluorescence, Transcriptomics (RNAseq, microarrays, etc.), Acridine orange DNA structural test, Bioinformatics, NGS data analysis, Image analysis | Maybe | 0000-0002-2870-7775 |
| Saulius Klimasauskas | Lithuania | Mechanistic studies of DNA methylation and engineering of methyltransferases and their cofactors for targeted derivatization of DNA and RNA, new methodologies for DNA epigenome analysis. | ATAC-Seq, BisulfiteSeq, Transcriptomics (RNAseq, microarrays, etc.), Proteomics (mass spectrometry, etc.), Bioinformatics, NGS data analysis | Maybe | 0000-0002-1395-2030 |
| Pernette Verschure | Netherlands | My research focus is to mechanistically understand dynamics of epigenetic gene regulation and how it affects cell behavior in (i) breast cancer resistance to treatment, (ii) UV-induced DNA damage/repair, (iii) forensic age determination. | FISH (DNA, RNA);Chip-Seq;BisulfiteSeq;Immunofluorescence;Genome engineering (CRISPR, TALEN, Cre-Lox, etc.);Transcriptomics (RNAseq, microarrays, etc.);Single-cell technologies; advanced micrsocopy analysis, 4SU pulse/chase sequencing, Bioinformatics, Image analysis, Software/pipeline development, Random Forest machine learning, stochastic simulation, transcription dynamics parameter analysis | Yes | 0000-0003-2922-4836 |
| Frank Dekker | Netherlands | Genome engineering (CRISPR, TALEN, Cre-Lox, etc.), Protein expression | Maybe | 0000-0001-7217-9300 | |
| Marianne Rots | Netherlands | We pioneered the concept of epigenetic editing to locally overwrite epigenetic signatures in order to achieve long-term gene expression reprogramming. In addition, we are interested in understanding mitochondrial epigenetics. | Genome engineering (CRISPR, TALEN, Cre-Lox, etc.), Biochemistry, pyrosequencing, mitochondrial epigenetics | Maybe | 0000-0002-7416-2788 |
| Jonas Paulsen | Norway | We use computational modeling, statistical analyses and machine learning to elucidate 3D genome structure-activity relationships across cell-types, tissues and species. | Bioinformatics, Integrative/restraint-based modeling, Machine learning & AI, Deep learning/neural networks, Numerical simulations, NGS data analysis, Image analysis, Software/pipeline development, Visualization/graphics | Yes | 0000-0002-0151-4279 |
| Dariusz Plewczynski | Poland | We perform computational studies, whose main objective is to analyze and predict the three-dimensional structure of the human genomes, and its relation with the genomic diversity of human populations, both natural and pathological. | Hi-C and similar 'C' techniques (3C, 4C, 5C, capture Hi-C, etc.), Micro-C, GAM, SPRITE, ChiA-PET, FISH (DNA, RNA), Chip-Seq, ATAC-Seq, Superresolution Microscopy, Electron microscopy, Immunofluorescence, Nanopore sequencing, Biostatistics, Bioinformatics, Polymer modeling, Integrative/restraint-based modeling, Machine learning & AI, Deep learning/neural networks, Molecular Dynamics, NGS data analysis, Image analysis, Software/pipeline development, Visualization/graphics, bioinformatics, computational biology, deep learning, biostatistics, chromatin loops | Yes | 0000-0002-3840-7610 |
| Alexandra Paulo | Portugal | We are a medicinal chemistry lab focused in the development of chemical tools (e.g. fluorescent probes) to discover new drug targets and in the discovery of small molecules to modulate oncogene expression by targeting DNA/RNA quadruplexes. | organic synthesis; FRET melting assay; PCR stop assay; Integrative/restraint-based modeling, Molecular Dynamics, Visualization/graphics | Yes | 0000-0003-1433-5402 |
| Joana Costa | Portugal | Main focus of research has been related to the development of DNA-based methods for the detection of allergenic foods, identification of plant/animal species, plant food supplement authentication and GMO. Starting to work on RNA editing. | Proteomics (mass spectrometry, etc.) real-time PCR, HRM analysis, PCR, LC-MS, Biostatistics, Image analysis, Visualization/graphics | Maybe | 0000-0002-8229-2902 |
| Carmen Jerónimo | Portugal | We work in the development of cancer epigenetic biomarkers based in liquid biopsies as well in epi-drug discovery. Moreover, we are tackling the contribution Post translational modifications and non-coding RNAs in malignant transformation. | RepliSeq, BisulfiteSeq, Immunofluorescence, Genome engineering (CRISPR, TALEN, Cre-Lox, etc.), Transcriptomics, QMSP, dPCR, Image analysis | Yes | 0000-0003-4186-5345 |
| Sorina Dinescu | Romania | We study the molecular mechanisms involved in stem cells differentiation (at transcriptional level (qPCR, microarrays), post-transcriptional control by ncRNAs and epigenetic changes) and stem cell potential for regenerative applications. | Immunofluorescence, Transcriptomics (RNAseq, microarrays, etc.), Biochemistry, Single-cell technologies, qPCR, single-cell qPCR, confocal microscopy, NGS, Visualization/graphics | Maybe | 0000-0001-7196-1712 |
| Yulii Shidlovskii | Russia | Our research focuses on the molecular mechanisms that regulate gene expression. | Hi-C and similar 'C' techniques (3C, 4C, 5C, capture Hi-C, etc.), FISH (DNA, RNA), Immunofluorescence, Genome engineering (CRISPR, TALEN, Cre-Lox, etc.), Transcriptomics (RNAseq, microarrays, etc.), Proteomics (mass spectrometry, etc.), Bioinformatics | Maybe | 0000-0002-3643-9889 |
| Melita Vidakovic | Serbia | “Epi-cure” for diabetic patients based on CRISPR/cas9 technology for a transdifferentiation of pancreatic alpha- to insulin-producing cell via targeted DNA methylation of genes essential for maintaining pancreatic cell identity. | ATAC-Seq, BisulfiteSeq, Immunofluorescence, biochemistry. MeFISH (5mC FISH) | Yes | 0000-0001-8410-6264 |
| Ksenija Taski-Ajdukovic | Serbia | Biochemistry, Biostatistics | Yes | 0000-0002-0149-9320 | |
| Marc A. Marti-Renom | Spain | Our research group employs the laws of physics and the rules of evolution to develop and apply computational methods for determining the 3D structures genomes and genomic domains. | Hi-C and similar 'C' techniques (3C, 4C, 5C, capture Hi-C, etc.), Biological physics, Biostatistics, Bioinformatics, Polymer modeling, Integrative/restraint-based modeling, Machine learning & AI, Deep learning/neural networks, Molecular Dynamics, Image analysis, Software/pipeline development, Algorithmics, Visualization/graphics, Integrative Modelng | Yes | 0000-0002-0151-4279 |
| Puri Fortes | Spain | Long noncoding RNAs related to hepatocellular carcinoma (HCC), inflammation and the antiviral response. | Immunofluorescence, Genome engineering (CRISPR, TALEN, Cre-Lox, etc.), Transcriptomics (RNAseq, microarrays, etc.). Setting up Cas-APEX labelling of RNA. Bioinformatics, Machine learning & AI, Deep learning/neural networks, NGS data analysis | Maybe | 0000-0001-7571-6220 |
| Peter Meister | Switzerland | Hi-C and similar 'C' techniques (3C, 4C, 5C, capture Hi-C, etc.), DamID, FISH (DNA, RNA), Chip-Seq, BisulfiteSeq, Immunofluorescence, Genome engineering (CRISPR, TALEN, Cre-Lox, etc.), Nanopore sequencing,Bioinformatics, NGS data analysis, Software/pipeline development | Yes | 0000-0002-6230-4216 | |
| Maria Cristina Gambetta | Switzerland | We address the question of how regulatory elements (like enhancers and silencers) find their target promoters and restrict their activity to their cognate targets. We study the molecular mechanisms of factors that organize regulatory interactions and assess their biological functions in Drosophila using genetics, genomics, biochemistry and imaging tools. | Hi-C and similar 'C' techniques (3C, 4C, 5C, capture Hi-C, etc.), FISH (DNA, RNA), Chip-Seq, ATAC-Seq, CUT&RUN, Immunofluorescence, Genome engineering (CRISPR, TALEN, Cre-Lox, etc.), Transcriptomics (RNAseq, microarrays, etc.), Proteomics (mass spectrometry, etc.), Biochemistry, Single-cell technologies, NGS data analysis | Maybe | 0000-0002-9450-3551 |
| Tuncay Baubec | Switzerland | We study the regulation of protein-genome interactions through combing genomics and proteomics. | Chip-Seq, ATAC-Seq, CUT&RUN, BisulfiteSeq, Immunofluorescence, Genome engineering (CRISPR, TALEN, Cre-Lox, etc.), Transcriptomics (RNAseq, microarrays, etc.), Proteomics (mass spectrometry, etc.), Single-cell technologies, ChromID, Bioinformatics, NGS data analysis | Yes | 0000-0001-8474-6587 |
| Célia Baroux | Switzerland | FISH (DNA, RNA), Superresolution Microscopy, Immunofluorescence, Biostatistics, Bioinformatics, Image analysis | Yes | 0000-0001-6307-2229 |
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| Ozlen Konu | Turkey | systems biology for cancer research, expression profiling in breast cancer cell lines exposed to drugs, comparative transcriptomics between mammals and zebrafish | Biochemistry, Biostatistics, Bioinformatics, NGS data analysis, Image analysis, Software/pipeline development, Visualization/graphics | Yes | |
| İkbal Agah İNCE WG 5 Chair | Turkey | Yes | |||
| Selcen Celik Uzuner | Turkey | I work on improvement of methodologies to detect DNA modifications, and intra-nuclear (co)localisation of cytosine modifications. I do also some research on the regulation of epigenetic markers in cancer after some natural compounds. | Immunofluorescence, Immunostaining, cell culture, PCR-based applications, Image analysis | Maybe | 0000-0002-9558-7048 |
| Bünyamin Akgül | Turkey | Investigation of genomewide lncRNA-chromatin interactions under apoptotic conditions | Electron microscopy, Immunofluorescence, Genome engineering (CRISPR, TALEN, Cre-Lox, etc.), Proteomics (mass spectrometry, etc.), Biochemistry, iMARGI, Bioinformatics, NGS data analysis | Maybe | 0000-0001-9877-9689 |
| Vladimir Teif | UK | We are interested in quantitative aspects of gene regulation in chromatin using approaches of biophysics, bioinformatics and next generation sequencing. We work on biomedical systems ranging from stem cell differentiation to cancer. | Chip-Seq, MNase-seq, Biological physics, Bioinformatics, Polymer modeling, NGS data analysis, Algorithmics, Lattice models, statistical mechanics, thermodynamics, nucleosome positioning, CTCF, chromatin, TF binding, DNA-protein interaction | Yes | 0000-0002-5931-7534 |
| Sara Buonomo | UK | My group is interested in understanding the molecular mechanisms coordinating DNA replication, transcription and chromatin architecture. We employ mouse embryonic stem cells to recapitulate the developmental dynamics of these pathways. | Hi-C and similar 'C' techniques (3C, 4C, 5C, capture Hi-C, etc.), FISH (DNA, RNA), Chip-Seq, RepliSeq, Immunofluorescence, embryoid bodies differentiation, Bioinformatics, NGS data analysis | Yes | 0000-0002-0177-2884 |