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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 |
|
Jan Smrek | Austria | Polymer physics | Biological physics, Polymer modeling, Numerical simulations, Molecular Dynamics, Kinetic Monte-Carlo | Yes | |
| 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 |
Loucif Remini | France | Modelling the multi scale organisation of polycomb domains | Biological physics;Biomathematics;Biostatistics;Polymer modeling;Numerical simulations;Kinetic Monte-Carlo;Dynamical systems | Maybe | |
Jean-Charles Walter | France | Biophysical modeling of DNA organization in bacteria and drosophila | Biological physics;Polymer modeling;Numerical simulations;Molecular Dynamics;Kinetic Monte-Carlo;Visualization/graphics | Yes | 0000-0002-7313-0100 |
Krister Swenson | France | I develop mathematical models and combinatorial algorithms for whole genome synteny comparison through large-scale rearrangement. I study the links between rearrangement breakpoints and Hi-C contacts/spacial proximity. | Biomathematics;Bioinformatics;Algorithmics | Maybe | 0000-0001-8690-1261 |
Ralf Everaers | France | Biological physics;Polymer modeling;Numerical simulations;Molecular Dynamics;Kinetic Monte-Carlo;Algorithmics | Yes | 0000-0002-6843-2753 |
|
Benjamin Audit | France | We are a computational lab interested in DNA replication and chromatin-mediated genome evolution. The latter involves the modelling of sequence-encoded nucleosome positioning and the analysis of its impacts on genome sequence dynamics. | Biological physics;Bioinformatics;Machine learning & AI;Deep learning/neural networks;Numerical simulations;NGS data analysis | Yes | 0000-0003-2683-9990 |
Christophe Zimmer | France | DNA/RNA FISH, Superresolution Microscopy, Immunofluorescence, Genome engineering, Polymer modeling;Machine learning & AI;Deep learning/neural networks;Numerical simulations;Molecular Dynamics;Image analysis;Software/pipeline development | Maybe | 0000-0001-9910-1589 |
|
Antoine Coulon | France | We study how the physical organization of the genome in the nucleus relates to the regulation of its expression at multiple spatio-temporal scales, with approaches combining single-molecule imaging and physical modeling. | DNA/RNA FISH, Superresolution Microscopy, Biological physics;Polymer modeling;Kinetic Monte-Carlo;Image analysis | Maybe | 0000-0003-4003-6043 |
Nicolas Destainville | France | I work in the Statistical Physics group of the Laboratoire de Physique Théorique in Toulouse (CNRS/Univ.). I am a theoretical physicist working on living matter-related issues, notably nucleic acids, in collaboration with experimentalists. | Biological physics;Polymer modeling;Numerical simulations;Molecular Dynamics;Kinetic Monte-Carlo | Maybe | 0000-0003-3867-5102 |
Manoel Manghi | France | Statistical physics in biological polymers: DNA denaturation, electrostatic interactions in DNA, plectonemes, statistical analysis of tethered particle motion experiments | Biological physics;Polymer modeling;Numerical simulations;Kinetic Monte-Carlo | No | 0000-0002-0146-3950 |
Fabian Erdel | France | We want to understand how patterns of histone marks along the genome are established and maintained and how this is linked to the formation of chromatin subcompartments. | Immunofluorescence, Genome engineering, Biochemistry, Single-cell technologies, Biological physics;Bioinformatics;NGS data analysis;Image analysis;Software/pipeline development | Maybe | |
Nelle Varoquaux | France | I develop statistical learning tool for analysing and integrating -omics data. My group is interested in understanding the mechanisms underling the evolution and adaptation of micro-organisms. | Biostatistics;Bioinformatics;Machine learning & AI;Software/pipeline development;Algorithmics;Visualization/graphics | No | |
Sandrine Le Noir | France | By using mouse models, I am studying (i) how the IgH enhancers orchestrate B cell nuclear organization (nuclear and supranucleosomal scales) and (ii) how this organization is mandatory to maintain genome stability. | Hi-C & similar 'C' techniques; DNA/RNA FISH; ATAC-Seq; Immunofluorescence; Transcriptomics, Bioinformatics;NGS data analysis;Image analysis;Software/pipeline development | Maybe | 0000-0002-2297-4186 |
Kerstin Bystricky | France | Hi-D, ANCHOR, image analysis | Yes | 0000-0001-6717-3721 |
|
Yegor Vassetzky | France | My laboratory works on the role of nuclear organization in cancer and genetic diseases | Hi-C & similar 'C' techniques; DNA/RNA FISH; Chip-Seq;ATAC-Seq; Immunofluorescence; Genome engineering; Transcriptomics; Single-cell technologies; Biostatistics;Bioinformatics; Image analysis; Visualization/graphics | Yes | 0000-0003-3101-7043 |
| 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 | ||
| Michael Hausmann | Germany | Experimental and Radiation Biophysics; DNA labelling by computer designed nano-probes; chromatin architecture on the micro- and nano-scale; sequence patterning for chromatin organization; nano-scale protein arrangements in membranes. | DNA/RNA FISH, ATAC-Seq, Superresolution Microscopy, Immunofluorescence, Single-cell technologies, Biological physics, Biomathematics, Biostatistics, Image analysis, Software/pipeline development, Visualization/graphics, Biological physics;Biomathematics;Biostatistics;Image analysis;Software/pipeline development;Visualization/graphics | Maybe | 0000-0002-0177-2884 |
| Marieke Oudelaar | Germany | We study how regulatory elements interact within 3D chromatin structures, when and how such structures are formed during development, and how disruptions of these structures cause mis-regulation of gene expression and contribute to disease. | Hi-C & similar 'C' techniques;Chip-Seq;ATAC-Seq;Genome engineering;Transcriptomics;Biochemistry, Bioinformatics, NGS data analysis, Software/pipeline development | Maybe | 0000-0002-4016-6158 |
| Sonja Prohaska | Germany | Computational analysis of the phylogenetic distribution of histone modifying enzymes. Rule-based simmulation of histone modification dynamics. Theoretical consideration of the role of histone modification in development and evolution. | Bioinformatics, NGS data analysis, Software/pipeline development, Dynamical systems, Algorithmics | Maybe | |
Gero Wedemann | Germany | Our focus is the application of computer models for the simulation of biological systems, in particular the spatial structure of chromatin. | Biological physics; Bioinformatics; Polymer modeling; Numerical simulations; Software/pipeline development; Visualization/graphics | Yes | 0000-0001-7869-774X |
| 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 |
| Andrea Maria Chiariello | Italy | Biological physics, Bioinformatics, Polymer modeling, Numerical simulations, Molecular Dynamics, Visualization/graphics | Maybe | 0000-0002-6112-0167 | |
| 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 |
Michele Caselle | Italy | Our main research interests are in gene regulation. We combine different computational approaches, ranging from network theory to machine learning methods, to infer regulatory interactions from various types of 'omics data. | Biological physics;Biomathematics;Bioinformatics;Machine learning & AI;Numerical simulations | Maybe | 0000-0001-5488-142X |
Cristian Micheletti | Italy | Development and use of statistical mechanical models and methods to study entanglement in biopolymers and its effect on static, kinetics and functional properties. | Biological physics;Bioinformatics;Polymer modeling;Numerical simulations;Molecular Dynamics;Software/pipeline development | Yes | 0000-0002-1022-1638 |
Angelo Rosa | Italy | We develop first-principles polymer models and state-of-the-art computer simulations for understanding the role of chromosome structure and dynamics in nuclear organization. | Biological physics;Polymer modeling;Integrative/restraint-based modeling;Numerical simulations;Molecular Dynamics;Kinetic Monte-Carlo | Yes | 0000-0002-9627-2486 |
| 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 |
Elzo de Wit | Netherlands | Hi-C & similar 'C' techniques, Micro-C, DNA/RNA FISH, Chip-Seq, ATAC-Seq, BisulfiteSeq, Immunofluorescence, Genome engineering, Transcriptomics, Single-cell technologies, Biostatistics;Bioinformatics;NGS data analysis | Maybe | 0000-0003-2883-1415 |
|
Tineke Lenstra | Netherlands | The goal of our lab is to understand the mechanisms of transcription variation and dynamics in single cells. We use and develop single-molecule imaging techniques to visualize individual protein and RNA molecules in living cells. | DNA/RNA FISH; Single-cell technologies; Nanopore sequencing, Numerical simulations;Kinetic Monte-Carlo;Image analysis;Software/pipeline development | Maybe | 0000-0002-4440-9962 |
| 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 |
Nikolina Sekulic | Norway | Our research focuses on centromeres. We want to understand: 1) What are the structural determinants of centromere formation and maintenance? 2) How does the centromere recruit major effector proteins in mitosis? | Structural Biology; Biochemistry; Biological physics; Visualization/graphics | Yes | 0000-0002-8027-9114 |
Eskeland Ragnhild | Norway | Hi-C & similar 'C' techniques ;DamID; DNA/RNA FISH; Chip-Seq; ATAC-Seq; CUT&RUN; Immunofluorescence; Genome engineering; Transcriptomics; Proteomics; Biochemistry; Single-cell technologies; Nanopore sequencin; Bioinformatics; Image analysis; Software/pipeline development Stralsund | Yes | 0000-0003-2789-3171 |
|
| 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 |
Aleksandra Pekowska | Poland | Hi-C & similar 'C' techniques; Chip-Seq; ATAC-Seq; CUT&RUN; Immunofluorescence; Genome engineering; Transcriptomics; Proteomics; Single-cell technologies, Biostatistics;Bioinformatics;NGS data analysis;Image analysis | Maybe | 0000-0002-0425-4388 |
|
| 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 |
Igor Kireev | Russia | We use multimodal and correlative microscopy appreaches for studies of higher order chromatin structure and dynamics during the cell cycle (replication, mitotic compaction) and upon transcription activation. | Superresolution Microscopy, Electron microscopy, Immunofluorescence, Machine learning & AI;Image analysis | Maybe | 0000-0001-9252-6808 |
| 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 |
Biola M. Javierre | Spain | We aim to understand the specific 3D chromatin organization of haematopoietic cells and its alteration in blood cancers. | Hi-C & similar 'C' techniques, DNA/RNA FISH, Chip-Seq, ATAC-Seq, CUT&RUN, Immunofluorescence, Genome engineering, Transcriptomics, Proteomics, Single-cell technologies, Biostatistics;Bioinformatics;Polymer modeling;NGS data analysis;Image analysis;Visualization/graphics | Maybe | 0000-0002-8682-6748 |
Alvaro Rada-Iglesias | Spain | The major interest of our laboratory is to uncover the main genetic and epigenetic factors that allow enhancers to control the deployment of specific gene expression profiles as vertebrate developmental programs unroll. | Hi-C & similar 'C' techniques, HiChip, DNA/RNA FISH, Chip-Seq, ATAC-Seq, Immunofluorescence, Genome engineering, Transcriptomics, Biochemistry, Single-cell technologies, Bioinformatics; NGS data analysis | Yes | 0000-0001-7137-1341 |
Miguel A. Peinado | Spain | We aim to dissect the functional anatomy of cancer cell’s genome to understand the mechanisms underlying tumor progression. Applications include detection and clinical validation of early biomarkers in many cancer types. | DNA/RNA FISH, Chip-Seq, BisulfiteSeq, Genome engineering, Transcriptomics, Biostatistics;Bioinformatics;NGS data analysis;Software/pipeline development;Algorithmics | Maybe | 0000-0002-4090-793X |
Francesc Posas | Spain | Hi-C & similar 'C' techniques, DNA/RNA FISH, Chip-Seq, ATAC-Seq, CUT&RUN, Immunofluorescence, Genome engineering, Transcriptomics, Proteomics, Biochemistry, Single-cell technologies, Drop-Seq, Biostatistics; Bioinformatics | Yes | 0000-0002-4164-7076 |
|
Maria Pia Cosma | Spain | We use super resolution microscopy and modeling approaches to study 3D genome organization and chromatin looping in somatic and stem cells. | Chip-Seq, Superresolution Microscopy, Transcriptomics, Bioinformatics;Machine learning & AI;Deep learning/neural networks;Kinetic Monte-Carlo;Image analysis | Maybe | |
Eulàlia de Nadal | Spain | Hi-C & similar 'C' techniques, DNA/RNA FISH, Chip-Seq, ATAC-Seq, CUT&RUN, Immunofluorescence, Genome engineering, Transcriptomics, Proteomics, Biochemistry, Single-cell technologies, Drop-Seq, Biostatistics;Bioinformatics | Yes | 0000-0003-0039-5607 |
|
Pedro Lazo | Spain | Hi-C & similar 'C' techniques, Chip-Seq, Biochemistry, NGS data analysis;Image analysis | Maybe | 0000-0001-8997-3025 |
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Miguel Manzanares | Spain | We aim to understand how genome activity is regulated during early stages of mammalian development and how regulatory and genome structure variations can contributes to human disease. | Hi-C & similar 'C' techniques; CUT&RUN; Superresolution Microscopy; Genome engineering;Transcriptomics; Proteomics; Bioinformatics ;Image analysis | Yes | 0000-0003-4849-2836 |
Magda Bienko | Sweden | Hi-C & similar 'C' techniques, DNA/RNA FISH, Immunofluorescence, Transcriptomics, Biochemistry, Single-cell technologies, Molecular Dynamics;NGS data analysis;Image analysis;Software/pipeline development | Yes | 0000-0002-6499-9082 |
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| 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 |
Aykut Erbas | Turkey | Biological physics; Polymer modeling; Molecular Dynamics | Yes | 0000-0003-2192-8804 |
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| 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 |
Christopher Toseland | UK | We are interested in nuclear organisation with respect to transcription and DNA repair. In particular, we focus on a group of molecular motors called myosin. | DNA/RNA FISH, Superresolution Microscopy, Immunofluorescence, Transcriptomics, Proteomics, Structural Biology, Biochemistry, Image analysis | Yes | 0000-0002-1641-7535 |
Chris Brackley | UK | We do computational research, mainly using polymer physics simulations of chromosome organization. Our work spans length scales from chromosome compartments and topological domains, to DNA models at bp resolution. | Biological physics;Biomathematics;Bioinformatics;Polymer modeling;Numerical simulations;Molecular Dynamics;Kinetic Monte-Carlo;NGS data analysis;Software/pipeline development | Maybe | 0000-0002-5973-8179 |
Ilya Flyamer | UK | 3D genome organization, mostly using Hi-C and similar techniques, and computation analysis | Hi-C & similar 'C' techniques, DNA/RNA FISH, Bioinformatics;NGS data analysis;Software/pipeline development;Visualization/graphics | Maybe | 0000-0002-4892-4208 |
Mikhail Spivakov | UK | The logic of gene control by enhancers | Hi-C & similar 'C' techniques, Chip-Seq, ATAC-Seq, CUT&RUN, Single-cell technologies, Bioinformatics;Machine learning & AI;NGS data analysis;Software/pipeline development;Algorithmics;Visualization/graphics | Maybe | 0000-0002-0383-3943 |
Frederic Leymarie | UK | Interactive scientific visualisation of biomolecules | Machine learning & AI;Deep learning/neural networks;Numerical simulations;Molecular Dynamics;Kinetic Monte-Carlo;Image analysis;Software/pipeline development;Dynamical systems;Algorithmics;Visualization/graphics | Maybe | 0000-0002-3221-8966 |
Stephen Todd | UK | Molecular Dynamics;Dynamical systems;Visualization/graphics | No | ||
Mikhail Dozmorov | USA | Hi-C methods and software development | Biostatistics; Bioinformatics; Machine learning & AI; Deep learning/neural networks; NGS data analysis; Software/pipeline development; Algorithmics; Visualization/graphics | Yes | 0000-0002-0086-8358 |
Hossein Salari | France | Using polymer physics modelling and data analysis, we are investigating 4D genome organisation at varies genome scales, especially during transcription. | Bioinformatics, Polymer modeling, Numerical simulations, Molecular Dynamics, Kinetic Monte-Carlo | Maybe | |
Julien Mozziconacci | France | Hi-C & similar 'C' techniques, DNA/RNA FISH, Chip-Seq, Genome engineering. Biological physics, Biomathematics, Biostatistics, Bioinformatics, Polymer modeling, Integrative/restraint-based modeling, Machine learning & AI, Deep learning/neural networks, Numerical simulations, Molecular Dynamics, Kinetic Monte-Carlo, NGS data analysis, Image analysis, Software/pipeline development, Dynamical systems, Algorithmics, Visualization/graphics. | No | 0000-0001-5652-0302 |
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Maria Barbi | France | Physical mechanisms underlying the functioning of biological systems involving DNA, from the functional dynamics of the nucleosome to the properties of chromosomes on a larger scale, which can be approached using polymer physics. | Biological physics, Polymer modeling, Numerical simulations, Molecular Dynamics | Maybe | 0000-0003-1977-6880 |
Ralf Blossey | France | Proteomics, Structural Biology, Biochemistry. Biological physics, Bioinformatics, Polymer modeling, Machine learning & AI, Deep learning/neural networks, Molecular Dynamics, Kinetic Monte-Carlo, Dynamical systems | Yes | 0000-0002-4823-7037 |
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Raphaël Mourad | France | Biostatistics, Bioinformatics, Machine learning & AI, Deep learning/neural networks, NGS data analysis, Software/pipeline development | Yes | 0000-0001-6700-5728 |
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Marco Cosentino Lagomarsino | Italy | We are a theoretical group with statistical and soft-matter physics expertise, studying stress-propagation in chromosomes and its impact on cellular physiology. | Biological physics, Polymer modeling, Image analysis, Software/pipeline development, Dynamical systems, Visualization/graphics | Yes | 0000-0003-0235-0445 |
Guido Tiana | Italy | Theory and simulation of chromosomal structure and dynamics. | Biological physics, Polymer modeling, Integrative/restraint-based modeling, Machine learning & AI, Deep learning/neural networks, Numerical simulations, Molecular Dynamics, Kinetic Monte-Carlo, Dynamical systems. | Yes | 0000-0001-9868-1809 |
Enzo Orlandini | Italy | Physics and topology of DNA and chromosome organisation using polymer models and simulations. Interplay between epigenetic and chromosome 3D dynamics and the topology of polymer rings in good and concentrated solutions. | Biological physics, Polymer modeling, Machine learning & AI, Deep learning/neural networks, Numerical simulations, Molecular Dynamics, Kinetic Monte-Carlo, Dynamical systems. Optical tweezers. | Yes | 0000-0003-3680-9488 |
Andrea Maria Chiariello | Italy | Biological physics, Bioinformatics, Polymer modeling, Numerical simulations, Molecular Dynamics, Visualization/graphics | Maybe | 0000-0002-6112-0167 |
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Modesto Orozco | Spain | We work on the theoretical study of DNA and chromatin using experimental data as retrains in simulations. | Hi-C & similar 'C' techniques, Micro-C, HiChip, Chip-Seq, ATAC-Seq, BisulfiteSeq, Immunofluorescence, Structural Biology, Biochemistry, Nanopore sequencing. MNAseq. | Yes | 0000-0002-8608-3278 |
Alice Pyne | UK | Structural Biology, Atomic Force Microscopy, Biological physics, Image analysis, Software/pipeline development. | Yes | 0000-0002-2658-8987 |
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Gabor Szabo | Hungary | Chip-Seq, CUT&RUN, Superresolution Microscopy, Immunofluorescence, Biochemistry. Bioinformatics, NGS data analysis, Image analysis. | Maybe | 0000-0002-9163-3465 |
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Erna Magnusdóttir | Iceland | Chip-Seq, ATAC-Seq, CUT&RUN, Immunofluorescence, Genome engineering, Transcriptomics, Biochemistry. Bioinformatics, NGS data analysis. | Yes | 0000-0002-3369-4390 |