Author

José Ignacio Martín-Subero

Institució Catalana de Recerca i Estudis AvançatsORCID 0000-0001-8809-5195Unclaimed ORCID profile · follow to get notified of new preprints

Biology Disciplines

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Genomics· 5 Cancer Biology· 2 Immunology· 1

Signature Assays, Organisms & Methods

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Organism:human· 7 Approach:statistical model· 6 Research Focus:differential expression· 4 Research Focus:cell type annotation· 3 Assay:ChIP-seq· 3 Research Focus:gene regulatory network inference· 3 Assay:DNA methylation· 2 Assay:Hi-C· 2

Frequent Co-Authors

Elı́as CampoiD· 4 shared Marta KulisiD· 4 shared Alfonso ValenciaiD· 2 shared Daniel RicoiD· 2 shared Dolors ColomeriD· 2 shared Felipe PrósperiD· 2 shared Holger HeyniD· 2 shared Xabier AgirreiD· 2 shared

Activity by Year

2017-2026 · peak 2/yr

Co-Author Collaboration Network

10 top collaborators · 23 mutual co-author links

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4 shared papersGenomics

Elı́as CampoORCID

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Author profile →

8 papers

Recent·Most cited

Hierarchical classification of hematologic malignancies using epigenetic and genetic information

Maximilian Schönung, Melissa Türe, Panna Lajer, Simon Renders, Tobias Rausch, Til L. Steinicke, Anna Dolnik, Eric Sträng, Meghana S. Oak, Jessica Heilmann, K Roth, Lena Katzenstein, Christian Rohde, Etienne Sollier, Peter Horak, , Daniel B. Lipka

The paper develops a hierarchical classification framework combining epigenetic and genetic data with machine learning to improve diagnosis and risk stratification in hematologic malignancies.

bioRxiv · Jul 3, 2026 · PreprintCancer Biology

A transcriptional map of human tonsil architecture:beyond the sum of (single cell) parts

Helena Lucia Crowell, Laura Llaó Cid, Gerard Frigola, Samuel Gunz, Irene Ruano, Patricia Lorden, Max Ruiz, Marta Kulis, José Ignacio Martín-Subero, Holger Heyn, Elı́as Campo, Anna Pascual‐Reguant

The paper uses spatial molecular imaging data to map human tonsil architecture and provides an analytical framework for Spatial Immunology.

European Journal of Immunology · Jan 1, 2026Peer-reviewedImmunology

Three-Dimensional Epigenome Roadmap of Human B-cell Differentiation Uncovers Mechanisms of Humoral Immunity and Oncogenesis

Raul de Haro-Blazquez, Laureano Tomás-Daza, Lucía Fanlo, Paula López-Martí, Nicolas Byrne-Alvarez, Llorenç Rovirosa, Blanca Valero, Juan Ochoteco Asensio, Maria Rigau, Galina Medvedeva, Lucía Álvarez-González, Blanca Urmeneta, Ainoa Planas‐Riverola, J. Carbonell, Teresa Robert-Finestra, , Biola M. Javierre

This paper creates a 3D epigenomic roadmap of human B-cell differentiation, revealing regulatory mechanisms in immunity and cancer.

bioRxiv · Dec 24, 2025 · PreprintGenomics

Mapping Disease Transitions from Premalignant, Asymptomatic to Advanced Myeloma through Integrative Epigenomic and Transcriptional Analyses

Aleksandra K. Kurowska, Azari Bantan, Raghad Shuwaikan, Nahia Gómez-Echarte, Itziar Cenzano, Paula Aguirre‐Ruiz, Estíbaliz Miranda, Leire Gárate, Amaia Vilas‐Zornoza, Patxi San-Martin, Marta Larráyoz, Beñat Ariceta, Ane Amundarain, Daniel Soto Ortiz, Markos Tsitsianopoulos, , David Gómez-Cabrero

This study maps epigenetic and transcriptional changes in myeloma progression from precursor to advanced stages, identifying key transcription factors involved in disease development.

Blood · Nov 5, 2024Peer-reviewedCancer Biology

Dynamics of genome architecture and chromatin function during human B cell differentiation and neoplastic transformation

Roser Vilarrasa‐Blasi, Paula Soler-Vila, Núria Verdaguer-Dot, Núria Russiñol, Marco Di Stefano, Vicente Chapaprieta, Guillem Clot, Irene Farabella, Pol Cuscó, Marta Kulis, Xabier Agirre, Felipe Prósper, Renée Beekman, Sı́lvia Beà, Dolors Colomer, , José Ignacio Martín-Subero

This study examines 3D genome architecture changes during B cell differentiation and in B cell neoplasias using Hi-C and multi-omic data, revealing dynamic compartment shifts and tumor-specific chromatin reorganization.

Nature Communications · Jan 28, 2021Peer-reviewedGenomics

Sampling artifacts in single-cell genomics cohort studies

Ramon Massoni-Badosa, Giovanni Lo Iacono, Cátia Moutinho, Marta Kulis, Núria Palau, Doménica Marchese, Javier Rodríguez‐Ubreva, Esteban Ballestar, Gustavo Rodríguez-Esteban, Sara Marsal, Marta Aymerich, Dolors Colomer, Elı́as Campo, Antonio Julià, José Ignacio Martín-Subero, Holger Heyn

The paper identifies sampling artifacts in single-cell genomics and proposes solutions to mitigate them in cohort studies.

bioRxiv · Jan 15, 2020 · PreprintGenomics

Differential genomic and transcriptomic events associated with high-grade transformation of Chronic Lymphocytic Leukemia

Jenny Klintman, Basile Stamatopoulos, Kate E. Ridout, Toby Andrew Eyre, L. Lopez Pascua, Niamh Appleby, Samantha J.L. Knight, Helene Marie-Pierre Dreau, Mats Ehinger, José Ignacio Martín-Subero, Elı́as Campo, Robert Månsson, Davide Rossi, Jenny C. Taylor, Dimitris V. Vavoulis, Anna Schuh

The paper identifies genomic and transcriptomic changes in CLL transforming to RS, finding pathway mutations and non-coding mutations in PAX5 enhancers associated with transformation.

HemaSphere · Jun 1, 2019Peer-reviewedGenomics

Automatic identification of informative regions with epigenomic changes associated to hematopoiesis

Enrique Carrillo de Santa Pau, David Juan, Véra Pancaldi, Felipe Were, José Ignacio Martín-Subero, Daniel Rico, Alfonso Valencia

The paper develops a bioinformatic workflow to classify blood epigenomes by cell type and identifies chromatin determinant regions linked to cell identity and disease.

Nucleic Acids Research · Jul 6, 2017Peer-reviewedGenomics