Miguel A. Garcia-Campos, PhD

Miguel A. Garcia-Campos, PhD

A biologist working on RNA modifications.

Posts by Collection

publications

Pathway Analysis: State of the Art

Published in Frontiers in Physiology, 2015

This review’s aim is to give an overview of what pathway analysis is and how different methods have developed encompassing the same idea of trying to identify biologically meaningful categories that are relevant for the results obtained from Omics experimental data.


Recommended citation: García-Campos, M.A., Espinal-Enríquez, J. and Hernández-Lemus, E., 2015. Pathway analysis: state of the art. Frontiers in physiology, 6, p.383.
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Deciphering the m6A code via quantitative profiling of m6A at single-nucleotide resolution

Published in bioRxiv, 2019

In this preprint we present a method to quantify m6a using a m6a sensitive endonuclease, and uncover the mechanistic behaviour of methylation trough a simple and conserved code in cis.


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Recommended citation: Garcia-Campos, M.A., Edelheit, S., Toth, U., Shachar, R., Nir, R., Lasman, L., Brandis, A., Hanna, J.H., Rossmanith, W. and Schwartz, S., 2019. Deciphering the "m6A code" via quantitative profiling of m6A at single-nucleotide resolution. BioRxiv, p.571679.
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Deciphering the “m6A Code” via Antibody-Independent Quantitative Profiling

Published in Cell, 2019

In this paper we present a method to quantify m6a using an m6a sensitive endonuclease, and uncover the mechanistic behaviour of methylation trough a simple and conserved code in cis.


Recommended citation: Garcia-Campos, M. A. et al. (2019) ‘Deciphering the “m6A Code” via Antibody-Independent Quantitative Profiling’, Cell. Elsevier, 0(0). doi: 10.1016/j.cell.2019.06.013.
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Tolerance to Oxidative Stress in Budding Yeast by Heterologous Expression of Catalases A and T from Debaryomyces hansenii

Published in Current Microbiology, 2020

In this study we show the recovery and enhancement of the budding yeast’s resistance to oxidative stress by expressing ortholog catalase genes from D. hansenii, a sea yeast.


Recommended citation: González, J., Castillo, R., García-Campos, M. A., Noriega-Samaniego, D., Escobar-Sánchez, V., Romero-Aguilar, L., ... & Segal-Kischinevzky, C. (2020). Tolerance to Oxidative Stress in Budding Yeast by Heterologous Expression of Catalases A and T from Debaryomyces hansenii. Current Microbiology, 77(12), 4000-4015.
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Multiplexed profiling facilitates robust m6A quantification at site, gene and sample resolution

Published in Nature Methods, 2021

Here we develop m6A-seq2, a multiplexed immunoprecipitation-RNA-seq coupled method that measures m6A across the epitranscriptome reducing technical variability, cost, and labor. Allowing for sample-level m6A relative quantitations, orthogonal to mass-spectrometry methods, as well as gene-level quantitations. We found that m6A-seq2 m6A gene-level measurements explains roughly 30% of the variability in the RNA half life on mouse embryonic stem cells.


Recommended citation: Dierks, D., Garcia-Campos, M.A., Uzonyi, A., Safra, M., Edelheit, S., Rossi, A., Sideri, T., Varier, R.A., Brandis, A., Stelzer, Y. and van Werven, F., 2021. Multiplexed profiling facilitates robust m6A quantification at site, gene and sample resolution. Nature Methods, pp.1-8.
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txtools: an R package facilitating analysis of RNA modifications, structures, and interactions

Published in bioRxiv, 2023

In this preprint we present txtools, an R package that enables the processing, analysis, and visualization of RNA-seq data at the nucleotide-level resolution, seamlessly integrating alignments to the genome with a transcriptomic representation.


Recommended citation: Garcia-Campos, M. A., & Schwartz, S. (2023). txtools: an R package facilitating analysis of RNA modifications, structures, and interactions. bioRxiv, 2023-08.
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Dissecting the sequence and structural determinants guiding m6A deposition and evolution via inter- and intra-species hybrids

Published in BMC - Genome Biology, 2024

In this paper we dissect the determinants governing RNA methylation via interspecies and intraspecies hybrids in yeast and mammalian systems, coupled with massively parallel reporter assays and m6A-QTL reanalysis.


Recommended citation: Shachar, R., Dierks, D., Garcia-Campos, M. A., Uzonyi, A., Toth, U., Rossmanith, W., & Schwartz, S. (2024). Dissecting the sequence and structural determinants guiding m6A deposition and evolution via inter-and intra-species hybrids. Genome Biology, 25(1), 1-29.
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txtools: an R package facilitating analysis of RNA modifications, structures, and interactions

Published in Nucleic Acids Research, 2024

We present txtools, an R package that enables the processing, analysis, and visualization of RNA-seq data at the nucleotide-level resolution, seamlessly integrating alignments to the genome with transcriptomic representation. .


Recommended citation: Miguel Angel Garcia-Campos, Schraga Schwartz, txtools: an R package facilitating analysis of RNA modifications, structures, and interactions, Nucleic Acids Research, 2024;, gkae203, https://doi.org/10.1093/nar/gkae203.
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Passive shaping of intra-and intercellular m6A dynamics via mRNA metabolism

Published in eLife, 2025

eLife assessment: This study presents a fundamental finding on how levels of m6A levels are controlled, invoking a consolidated model where degradation of modified RNAs in the cytoplasm plays a primary role in shaping m6A patterns and dynamics, rather than needing active regulation by m6A erasers and other related processes. The evidence is compelling through its use of transcriptome-wide data and mechanistic modeling. Relevant for any reader with an interest in RNA metabolism, this new framework consolidates previous observations and highlights the importance of careful experimentation for evaluation m6A levels. .


Recommended citation: Dierks, D., Shachar, R., Nir, R., Garcia-Campos, M. A., Uzonyi, A., Wiener, D., ... & Schwartz, S. (2025). Passive shaping of intra-and intercellular m6A dynamics via mRNA metabolism. Elife, 13, RP100448.
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Pan-modification profiling facilitates a cross-evolutionary dissection of the thermoregulated ribosomal epitranscriptome

Published in Cell, 2025

Pan-Mod-seq enables high-throughput profiling of 16 rRNA modifications across diverse species, revealing that while these chemical markers are largely static in mesophiles, they are highly dynamic in hyperthermophiles. Specifically, a conserved m5C-ac4C module is co-induced by heat and serves a critical role in stabilizing ribosome structure at extreme temperatures. Cryo-EM and biophysical analyses confirm that this modification module provides essential thermostability required for hyperthermophilic growth.


Recommended citation: Garcia-Campos, M. A., Georgeson, J., Nir, R., Reichelt, R., Fluke, K. A., Matzov, D., ... & Schwartz, S. (2025). Pan-modification profiling facilitates a cross-evolutionary dissection of the thermoregulated ribosomal epitranscriptome. Cell, 188(24), 6825-6844.
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software

MAZTER-MINE

MAZTER-mine is a computational pipeline to analize MAZTER-seq derived data, a methodology that profiles m6A quantitatively across transcriptomes in a single-base manner.

txtools

An R package that processes GenomicAlignments into their transcriptomic versions.

talks

teaching