Researchers database

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NameCountrySummaryTechniquesCan host STSM?ORCID
Wim Vanden BergheBelgiumBisulfiteSeq, Transcriptomics (RNAseq, microarrays, etc.), Proteomics (mass spectrometry, etc.), Biochemistry, Nanopore sequencing, Pacbio sequencing, Bioinformatics, NGS data analysis, pathway enrichment analysissYes0000-0003-0161-7355
Shazie Yuein-MyahkovaBulgaria
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 analysisMaybe0000-0002-0573-5685
Đurđica UgarkovićCroatiaFISH (DNA, RNA), Chip-Seq, Electron microscopy, Immunofluorescence, Transcriptomics (RNAseq, microarrays, etc.), Biochemistry, Biostatistics, Bioinformatics, NGS data analysisYes0000-0002-9450-3551
Željka Pezer SakačCroatiaFISH (DNA, RNA), Chip-Seq, Transcriptomics (RNAseq, microarrays, etc.), Biochemistry, Biostatistics, Bioinformatics, NGS data analysisYes
Jan Palecek
Czech RepublicOur 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/graphicsMaybe0000-0002-6223-5169
Barbora Kozlikova Czech RepublicOur 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/graphicsMaybe0000-0003-0045-0872
David HonysCzech RepublicBioinformatics, NGS data analysis, Image analysisChip-Seq, Genome engineering (CRISPR, TALEN, Cre-Lox, etc.), Transcriptomics (RNAseq, microarrays, etc.), Proteomics (mass spectrometry, etc.), Single-cell technologies.Yes
Daniel Jost FranceIn 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 modelsYes0000-0002-9877-6864
Julie ChaumeilFranceHi-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, Maybe0000-0002-8976-2890
Ana Pombo GermanyWe 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 developmentYes0000-0002-7493-6288
Argyris Papantonis GermanyChIP-seq, RNA-seq, Hi-CYes
Endre Sebestyén
HungaryWe 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/graphicsMaybe0000-0001-5470-2161
Ronan MurphyIrelandTranscriptomics (RNAseq, microarrays, etc.), Biochemistry, in vitro modelling of human diseases (Cardiovascular, Skin, and Lung), Yes0000-0002-4579-8007
Daniel Remondini
ItalyMy 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)
Yes0000-0003-3185-7456
Francesco Ferrari ItalyMy 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 developmentYes0000-0002-9811-3753
Mario Nicodemi ItalyMy 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 analysisMaybe0000-0002-8416-6416
Jekaterina ErenpreisaLatviaCurrently, 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 analysisMaybe0000-0002-2870-7775
Saulius KlimasauskasLithuaniaMechanistic 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 analysisMaybe0000-0002-1395-2030
Pernette Verschure NetherlandsMy 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
Yes0000-0003-2922-4836
Frank DekkerNetherlandsGenome engineering (CRISPR, TALEN, Cre-Lox, etc.), Protein expression
Maybe0000-0001-7217-9300
Jonas PaulsenNorwayWe 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/graphicsYes0000-0002-0151-4279
Alexandra PauloPortugalWe 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/graphicsYes0000-0003-1433-5402
Joana Costa
PortugalMain 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
Maybe0000-0002-8229-2902
Sorina DinescuRomaniaWe 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/graphicsMaybe0000-0001-7196-1712

Yulii Shidlovskii
RussiaOur 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.), BioinformaticsMaybe0000-0002-3643-9889
Melita VidakovicSerbia“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, Genome engineering (CRISPR, TALEN, Cre-Lox, etc.), Biochemistry. MeFISH (5mC FISH) Yes0000-0001-8410-6264
Ksenija Taski-AjdukovicSerbiaBiochemistry, BiostatisticsYes0000-0002-0149-9320
Marc A. Marti-RenomSpainOur 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 ModelngYes0000-0002-0151-4279
Puri Fortes
SpainLong 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 analysisMaybe0000-0001-7571-6220
Peter Meister
SwitzerlandHi-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 developmentYes0000-0002-6230-4216
Maria Cristina GambettaSwitzerlandWe 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 analysisMaybe0000-0002-9450-3551
Tuncay Baubec SwitzerlandWe 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 analysisYes0000-0001-8474-6587
Ozlen Konu Turkeysystems biology for cancer research, expression profiling in breast cancer cell lines exposed to drugs, comparative transcriptomics between mammals and zebrafishBiochemistry, Biostatistics, Bioinformatics, NGS data analysis, Image analysis, Software/pipeline development, Visualization/graphicsYes
İkbal Agah İNCE
WG 5 Chair
TurkeyYes
Selcen Celik Uzuner
TurkeyI 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 analysisMaybe0000-0002-9558-7048
Bünyamin AkgülTurkey
Investigation of genomewide lncRNA-chromatin interactions under apoptotic conditionsElectron microscopy, Immunofluorescence, Genome engineering (CRISPR, TALEN, Cre-Lox, etc.), Proteomics (mass spectrometry, etc.), Biochemistry, iMARGI, Bioinformatics, NGS data analysisMaybe0000-0001-9877-9689

Vladimir TeifUKWe 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
Yes0000-0002-5931-7534
Sara BuonomoUKMy 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 differentiaton, Bioinformatics, NGS data analysisYes0000-0002-0177-2884