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Author Details

Marc A Marti-Renom
Universitat Pompeu Fabra (UPF)
1998
121
49
Andrej Sali (CM4AI)
PMIDPaper TitleJournal TitlePublished Year
36996041The anti-immune dengue subgenomic flaviviral RNA is present in vesicles in mosquito saliva and is associated with increased infectivity.PLoS Pathog2023
37989525Enhancer-driven 3D chromatin domain folding modulates transcription in human mammary tumor cells.Life Sci Alliance2023
34455421Insights into the mechanisms underlying aberrant SOX11 oncogene expression in mantle cell lymphoma.Leukemia2022
35380694Coordinated changes in gene expression, H1 variant distribution and genome 3D conformation in response to H1 depletion.Nucleic Acids Res2022
35450883In vivo temporal resolution of acute promyelocytic leukemia progression reveals a role of <i>Klf4</i> in suppressing early leukemic transformation.Genes Dev2022
36543130Principles of 3D chromosome folding and evolutionary genome reshuffling in mammals.Cell Rep2022
35274099Identification of chromatin loops from Hi-C interaction matrices by CTCF-CTCF topology classification.NAR Genom Bioinform2022
32896099TADs enriched in histone H1.2 strongly overlap with the B compartment, inaccessible chromatin, and AT-rich Giemsa bands.FEBS J2021
33731935Publisher Correction: LifeTime and improving European healthcare through cell-based interceptive medicine.Nature2021
33510161Dynamics of genome architecture and chromatin function during human B cell differentiation and neoplastic transformation.Nat Commun2021
337784923D reconstruction of genomic regions from sparse interaction data.NAR Genom Bioinform2021
34648034STAG2 loss-of-function affects short-range genomic contacts and modulates the basal-luminal transcriptional program of bladder cancer cells.Nucleic Acids Res2021
34759378Three-dimensional genome organization via triplex-forming RNAs.Nat Struct Mol Biol2021
34016985The impact of chromosomal fusions on 3D genome folding and recombination in the germ line.Nat Commun2021
33963351Benchmarking experiments with polymer modeling.Nat Methods2021
332539964D nucleome modeling.Curr Opin Genet Dev2021
33444439Polymer modelling unveils the roles of heterochromatin and nucleolar organizing regions in shaping 3D genome organization in Arabidopsis thaliana.Nucleic Acids Res2021
32820398Analysis, Modeling, and Visualization of Chromosome Conformation Capture Experiments.Methods Mol Biol2021
322203034D Genome Rewiring during Oncogene-Induced and Replicative Senescence.Mol Cell2020
31907200Impact of Chromosome Fusions on 3D Genome Organization and Gene Expression in Budding Yeast.Genetics2020
32083658Hierarchical chromatin organization detected by TADpole.Nucleic Acids Res2020
33277476Muscle progenitor specification and myogenic differentiation are associated with changes in chromatin topology.Nat Commun2020
33077914CHESS enables quantitative comparison of chromatin contact data and automatic feature extraction.Nat Genet2020
32747821TADs without borders.Nat Genet2020
327195313D mapping and accelerated super-resolution imaging of the human genome using in situ sequencing.Nat Methods2020
32894860LifeTime and improving European healthcare through cell-based interceptive medicine.Nature2020
32444798Transcriptional activation during cell reprogramming correlates with the formation of 3D open chromatin hubs.Nat Commun2020
32514124CTCF is dispensable for immune cell transdifferentiation but facilitates an acute inflammatory response.Nat Genet2020
30419242Communicating Genome Architecture: Biovisualization of the Genome, from Data Analysis and Hypothesis Generation to Communication and Learning.J Mol Biol2019
31216471Specific Contributions of Cohesin-SA1 and Cohesin-SA2 to TADs and Polycomb Domains in Embryonic Stem Cells.Cell Rep2019
31267103RNA proximity sequencing reveals the spatial organization of the transcriptome in the nucleus.Nat Biotechnol2019
31291573Three-Dimensional Genomic Structure and Cohesin Occupancy Correlate with Transcriptional Activity during Spermatogenesis.Cell Rep2019
31253982Human pancreatic islet three-dimensional chromatin architecture provides insights into the genetics of type 2 diabetes.Nat Genet2019
31028255Binless normalization of Hi-C data provides significant interaction and difference detection independent of resolution.Nat Commun2019
29335546Transcription factors orchestrate dynamic interplay between genome topology and gene regulation during cell reprogramming.Nat Genet2018
29867216Distinct roles of cohesin-SA1 and cohesin-SA2 in 3D chromosome organization.Nat Struct Mol Biol2018
30143639Lamin B1 mapping reveals the existence of dynamic and functional euchromatin lamin B1 domains.Nat Commun2018
30224650Promoter bivalency favors an open chromatin architecture in embryonic stem cells.Nat Genet2018
30262815Challenges and guidelines toward 4D nucleome data and model standards.Nat Genet2018
30586358Walking along chromosomes with super-resolution imaging, contact maps, and integrative modeling.PLoS Genet2018
29394371OneD: increasing reproducibility of Hi-C samples with abnormal karyotypes.Nucleic Acids Res2018
29785028The reference epigenome and regulatory chromatin landscape of chronic lymphocytic leukemia.Nat Med2018
28771695Challenges for visualizing three-dimensional data in genomic browsers.FEBS Lett2017
28436422Rational design of non-resistant targeted cancer therapies.Sci Rep2017
28272414Defined chromosome structure in the genome-reduced bacterium Mycoplasma pneumoniae.Nat Commun2017
29170434Single-cell absolute contact probability detection reveals chromosomes are organized by multiple low-frequency yet specific interactions.Nat Commun2017
29048533Parallel sequencing lives, or what makes large sequencing projects successful.Gigascience2017
28723903Automatic analysis and 3D-modelling of Hi-C data using TADbit reveals structural features of the fly chromatin colors.PLoS Comput Biol2017
26987712Biological insertion of computationally designed short transmembrane segments.Sci Rep2016
27635856Should network biology be used for drug discovery?Expert Opin Drug Discov2016
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Collaborators

Andrej Sali (CM4AI)
University of California San Francisco
Co-authored papers 33
Narayanan Eswar
University of California at San Francisco
Co-authored papers 15
Mallur S Madhusudhan
Indian Institute of Science Education and Research Pune
Co-authored papers 13
Ursula Pieper
University of California san francisco
Co-authored papers 13
Enrique Querol
Institut de Biotecnologia i Biomedicina, Universitat Autonoma de Barcelona
Co-authored papers 9
Baldo Oliva
Universitat Pompeu Fabra
Co-authored papers 8
Francesc X Avil??s
Clinical Institute of Hematology and Oncology, Hospital Clinic Barcelona
Co-authored papers 8
Francisco Melo
Pontificia Universidad Catolica de Chile
Co-authored papers 7
Job Dekker
University of Massachusetts Chan Medical School
Co-authored papers 6
Francisco Mart??nez-Jim??nez
Center for Molecular Medicine and Oncode Institute, University Medical Center Utrecht
Co-authored papers 6
Benjamin Webb
University of California san francisco
Co-authored papers 6
Andras Fiser
Albert Einstein College of Medicine
Co-authored papers 5
Fred P Davis
Howard Hughes Medical Institute
Co-authored papers 5
David Eramian
University of California at San Francisco
Co-authored papers 5
Alfonso Valencia
Josep Carreras Leukaemia Research Institute (IJC)
Co-authored papers 5
Guillaume J Filion
University of Toronto Scarborough
Co-authored papers 5
Andrea Rossi
Pfizer Inc.
Co-authored papers 5
Min-Yi Shen
National Chung Hsing University
Co-authored papers 4
Yannick G Spill
CNRS, University of Strasbourg
Co-authored papers 4
Ashley C Stuart
Columbia University
Co-authored papers 4
Nebojsa Mirkovic
Weill Medical College of Cornell University
Co-authored papers 4
Burkhard Rost
Technical University of Munich (TUM)
Co-authored papers 3
Jordi Espadaler
Autonomous University of Barcelona
Co-authored papers 3
Susan M Gasser
L'Institut Suisse de Recherche Experimentale sur le Cancer (ISREC) Foundation
Co-authored papers 3
Patrick Aloy
Institucio Catalana de Recerca i Estudis Avancats (ICREA)
Co-authored papers 3
Valentin A Ilyin
Carnegie Mellon University Qatar
Co-authored papers 3
Ram??n Arag????s
Universitat Pompeu Fabra-IMIM
Co-authored papers 3
Elias Campo
Institute for Biomedical Research August Pi I Sunyer
Co-authored papers 3
Ana Pombo
Polytechnic Institute of Leiria
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Release 1.2