Author

José Alejandro Romero Herrera

University of CopenhagenORCID 0000-0002-4765-2087Unclaimed ORCID profile · follow to get notified of new preprints

Biology Disciplines

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Developmental Biology· 2 Bioinformatics· 1

Signature Assays, Organisms & Methods

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Approach:experimental assay· 3 Research Focus:cell type annotation· 2 Research Focus:differential expression· 2 Research Focus:benchmarking· 1 Assay:bulk RNA-seq· 1 Assay:ChIP-seq· 1 Research Focus:gene regulatory network inference· 1 Organism:human· 1

Frequent Co-Authors

Joshua M. BrickmaniD· 2 shared Martin ProksiD· 2 shared Abigail Laura JacksoniD· 1 shared Christine EbeidiD· 1 shared Henrik SembiD· 1 shared Jakub SedzinskiiD· 1 shared Jelena Miskovic KrivokapiciD· 1 shared Michaela RothováiD· 1 shared

Activity by Year

2022-2023 · peak 2/yr

Co-Author Collaboration Network

10 top collaborators · 18 mutual co-author links

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2 shared papersBioinformatics

Joshua M. BrickmanORCID

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3 papers

Recent·Most cited

Real time quantification reveals novel dynamic processes in pancreatic lumenal network establishment and remodeling

Abigail Laura Jackson, Silja Heilmann, Christine Ebeid, Jelena Miskovic Krivokapic, José Alejandro Romero Herrera, Henrik Semb, Pia Nyeng

The paper uses real-time imaging to reveal dynamic processes in pancreatic lumen formation and remodeling, challenging existing models of polarity acquisition and network development.

bioRxiv · Aug 18, 2023 · PreprintDevelopmental Biology

nf-core/marsseq: systematic pre-processing pipeline for MARS-seq experiments

Martin Proks, José Alejandro Romero Herrera, Jakub Sedzinski, Joshua M. Brickman

The paper presents a standardized pre-processing pipeline for MARS-seq data using the nf-core framework, improving transparency, scalability, and RNA velocity estimation.

bioRxiv · Jun 28, 2023 · PreprintBioinformatics

Expansion of Ventral Foregut Primes the Enhancer Landscape for Organ Specific Differentiation

Yan Fung Wong, Yatendra Kumar, Martin Proks, José Alejandro Romero Herrera, Michaela Rothová, Rita S. Monteiro, Sara Pozzi, Rachel E. Jennings, Neil A. Hanley, Wendy A. Bickmore, Joshua M. Brickman

The paper shows that cell proliferation in human embryonic stem cell-derived endodermal progenitors primes enhancer landscapes for organ-specific differentiation by modulating chromatin accessibility and enhancer decommissioning.

bioRxiv · Apr 11, 2022 · PreprintDevelopmental Biology