Author

A. Berrio

Listed by name: these papers carry no ORCID for this author, so different people with the same name may be mixed together.

Biology Disciplines

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Evolutionary Biology· 6

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Research Focus:chromatin & epigenetic regulation· 5 Approach:statistical model· 5 Research Focus:cell type annotation· 3 Research Focus:gene regulatory network inference· 3 Organism:human· 3 Organism:chicken / avian· 2 Assay:ChIP-seq· 2 Research Focus:development & morphogenesis· 2

Frequent Co-Authors

G. A. Wray· 5 shared A. J. Massri· 2 shared G. E. Crawford· 2 shared M. Byrne· 2 shared A. Afanassiev· 1 shared A. Edgar· 1 shared A. S. Allen· 1 shared A. Saffi· 1 shared

Activity by Year

2019-2024 · peak 3/yr

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10 top collaborators · 20 mutual co-author links

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5 shared papersEvolutionary Biology

G. A. Wray

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6 papers

Recent·Most cited

Single-cell transcriptomics reveals evolutionary reconfiguration of embryonic cell fate specification in the sea urchin Heliocidaris erythrogramma

A. J. Massri, A. Berrio, A. Afanassiev, L. Greenstreet, K. Pipho, M. Byrne, G. Schiebinger, D. R. McClay, G. A. Wray

The paper uses single-cell RNA sequencing to compare embryonic development in two sea urchin species, identifying evolutionary changes in cell fate specification and signaling.

bioRxiv · Apr 30, 2024 · PreprintEvolutionary Biology

Recent Reconfiguration Of An Ancient Developmental Gene Regulatory Network In Heliocidaris Sea Urchins

P. L. Davidson, H. Guo, J. S. Swart, A. J. Massri, A. Edgar, L. Wang, A. Berrio, H. R. Devens, D. Koop, P. Cisternas, H. Zhang, Y. Zhang, M. Byrne, G. Fan, G. A. Wray

This study shows how natural selection rapidly reshapes developmental gene regulatory networks in sea urchins with divergent life histories, revealing evolutionary changes in gene regulation and chromatin status.

bioRxiv · Mar 3, 2022Evolutionary Biology

Positive selection within the genomes of SARS-CoV-2 and other Coronaviruses independent of impact on protein function

A. Berrio, V. Gartner, G. A. Wray

The paper identifies positive selection in SARS-CoV-2 and other coronaviruses, including non-protein-coding regions, using mutation patterns and RNA structure analysis.

bioRxiv · Sep 16, 2020Evolutionary Biology

Evaluating chromatin accessibility differences across multiple primate species using a joint modelling approach

L. E. Edsall, A. Berrio, W. H. Majoros, D. Swain-Lenz, S. Morrow, Y. Shibata, A. Safi, G. A. Wray, G. E. Crawford, A. S. Allen

The paper develops a joint modeling approach to identify chromatin accessibility differences across primate species and finds distinct classes of DHS sites with varying conservation and regulatory features.

bioRxiv · Aug 24, 2019Evolutionary Biology

Identifying branch-specific positive selection throughout the regulatory genome using an appropriate neutral proxy

A. Berrio, R. Haygood, G. A. Wray

The paper introduces adaptyPhy, a method for detecting branch-specific positive selection in regulatory DNA, validated using simulations and human genomic data.

bioRxiv · Aug 2, 2019Evolutionary Biology

Comparative analyses of chromatin landscape in white adipose tissue suggest humans may have less beigeing potential than other primates

D. S. Swain Lenz, A. Berrio, A. Saffi, G. E. Crawford, G. Wray

The paper compares chromatin accessibility in human, chimpanzee, and macaque adipose tissue to identify regulatory regions under positive selection linked to lipid metabolism and beigeing potential.

bioRxiv · Jan 18, 2019Evolutionary Biology