Publications by authors named "Marcel Ramos"

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Meta-analysis of 22,710 human microbiome metagenomes defines an oral-to-gut microbial enrichment score and associations with host health and disease.
Paolo Manghi, Giacomo Antonello, Lucas Schiffer, Davide Golzato, Andres Wokaty, Marcel Ramos

Nat Commun· December 2025

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Squat lobster latitudinal life habitat shifts and metabolic response to combined temperature and oxygen conditions in the Humboldt Current System.
María de Los Ángeles Gallardo, Kurt Paschke, Katherina Brokordt, Marcel Ramos, Martin Thiel

Sci Rep· November 2025

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Influence of rainfall and winds on the arrival of marine litter on two beaches in northern-central Chile.
Josefa Araya-Campano, Diamela De Veer, Mauricio Ergas, David Jofré-Madariaga, Ninoshka López-Xalín, Marcel Ramos

Mar Pollut Bull· November 2025

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Orchestrating Spatial Transcriptomics Analysis with Bioconductor.
Helena L Crowell, Yixing Dong, Ilaria Billato, Peiying Cai, Martin Emons, Marcel Ramos

bioRxiv· November 2025

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Bioconductor's Computational Ecosystem for Genomic Data Science in Cancer.
Marcel Ramos, Lori Shepherd, Nathan C Sheffield, Alexandru Mahmoud, Hervé Pagès

Methods Mol Biol· August 2025

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Learning and teaching biological data science in the Bioconductor community.
Jenny Drnevich, Frederick J Tan, Fabricio Almeida-Silva, Robert Castelo, Aedin C Culhane, Marcel Ramos

PLoS Comput Biol· April 2025

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: a Bioconductor package for rapid, cross-cohort variant and allelic bias analysis.
Yizhou Peter Huang, Lauren Harmon, Eve Deering-Gardner, Xiaotu Ma, Josiah Harsh, Marcel Ramos

Bioinform Adv· April 2025

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Eleven quick tips for writing a Bioconductor package.
Charlotte Soneson, Lori Shepherd, Marcel Ramos, Kevin Rue-Albrecht, Johannes Rainer

PLoS Comput Biol· March 2025

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Learning and teaching biological data science in the Bioconductor community.
Jenny Drnevich, Frederick J Tan, Fabricio Almeida-Silva, Robert Castelo, Aedin C Culhane, Marcel Ramos

ArXiv· March 2025

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AnVILWorkflow: A runnable workflow package for Cloud-implemented bioinformatics analysis pipelines.
Sehyun Oh, Kai Gravel-Pucillo, Marcel Ramos, Michael C Schatz, Sean Davis

F1000Res· December 2024

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: a Bioconductor package for rapid, cross-cohort variant and allelic bias analysis.
Yizhou Peter Huang, Lauren Harmon, Eve Deering-Gardner, Xiaotu Ma, Josiah Harsh, Marcel Ramos

bioRxiv· November 2024

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lefser: implementation of metagenomic biomarker discovery tool, LEfSe, in R.
Asya Khleborodova, Samuel D Gamboa-Tuz, Marcel Ramos, Nicola Segata, Levi Waldron

Bioinformatics· November 2024

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AnVILWorkflow: A runnable workflow package for Cloud-implemented bioinformatics analysis pipelines.
Sehyun Oh, Kai Gravel-Pucillo, Marcel Ramos, Sean Davis, Vince Carey

Res Sq· May 2024

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Curated single cell multimodal landmark datasets for R/Bioconductor.
Kelly B Eckenrode, Dario Righelli, Marcel Ramos, Ricard Argelaguet, Christophe Vanderaa

PLoS Comput Biol· August 2023

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RaggedExperiment: the missing link between genomic ranges and matrices in Bioconductor.
Marcel Ramos, Martin Morgan, Ludwig Geistlinger, Vincent J Carey, Levi Waldron

Bioinformatics· June 2023

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GenomicSuperSignature facilitates interpretation of RNA-seq experiments through robust, efficient comparison to public databases.
Sehyun Oh, Ludwig Geistlinger, Marcel Ramos, Daniel Blankenberg, Marius van den Beek

Nat Commun· June 2022

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Toward a gold standard for benchmarking gene set enrichment analysis.
Ludwig Geistlinger, Gergely Csaba, Mara Santarelli, Marcel Ramos, Lucas Schiffer

Brief Bioinform· January 2021

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HGNChelper: identification and correction of invalid gene symbols for human and mouse.
Sehyun Oh, Jasmine Abdelnabi, Ragheed Al-Dulaimi, Ayush Aggarwal, Marcel Ramos

F1000Res· December 2020

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Multiomic Analysis of Subtype Evolution and Heterogeneity in High-Grade Serous Ovarian Carcinoma.
Ludwig Geistlinger, Sehyun Oh, Marcel Ramos, Lucas Schiffer, Rebecca S LaRue

Cancer Res· October 2020

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Multiomic Integration of Public Oncology Databases in Bioconductor.
Marcel Ramos, Ludwig Geistlinger, Sehyun Oh, Lucas Schiffer, Rimsha Azhar

JCO Clin Cancer Inform· October 2020

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Global Alliance for Genomics and Health Meets Bioconductor: Toward Reproducible and Agile Cancer Genomics at Cloud Scale.
Vincent J Carey, Marcel Ramos, Benjamin J Stubbs, Shweta Gopaulakrishnan, Sehyun Oh

JCO Clin Cancer Inform· May 2020

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Reliable Analysis of Clinical Tumor-Only Whole-Exome Sequencing Data.
Sehyun Oh, Ludwig Geistlinger, Marcel Ramos, Martin Morgan, Levi Waldron

JCO Clin Cancer Inform· April 2020

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CNVRanger: association analysis of CNVs with gene expression and quantitative phenotypes.
Vinicius da Silva, Marcel Ramos, Martien Groenen, Richard Crooijmans, Anna Johansson

Bioinformatics· February 2020

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A longitudinal analysis of albendazole treatment effect on neurocysticercosis cyst evolution using multistate models.
Michelle A Montgomery, Marcel Ramos, Elizabeth A Kelvin, Arturo Carpio, Alexander Jaramillo

Trans R Soc Trop Med Hyg· December 2019

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In search for the sources of plastic marine litter that contaminates the Easter Island Ecoregion.
Simon Jan van Gennip, Boris Dewitte, Véronique Garçon, Martin Thiel, Ekaterina Popova, Marcel Ramos

Sci Rep· December 2019

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