Publications

Paolo Manghi, Giacomo Antonello, Lucas Schiffer, Davide Golzato, Andres Wokaty, Francesco Beghini, Chloe Mirzayi, Kaelyn Long, Kai Gravel-Pucillo, Gianmarco Piccinno, Samuel David Gamboa-Tuz, Arianna Bonetti, Giacomo D'Amato, Rimsha Azhar, Kelly Eckenrode, Fatima Zohra, Valentina Giunchiglia, Marisa Keller, Anna Pedrotti, Ilya Likhotkin, Shaimaa Elsafoury, Ludwig Geistlinger, Aitor Blanco-Miguez, Andrew Maltez Thomas, Moreno Zolfo, Marcel Ramos, Mireia Valles-Colomer, Sabrina Tamburini, Francesco Asnicar, Heidi E Jones, Curtis Huttenhower, Vincent Carey, Sean Davis, Edoardo Pasolli, Sehyun Oh, Nicola Segata, Levi Waldron (2025). Meta-analysis of 22,710 human microbiome metagenomes defines an oral-to-gut microbial enrichment score and associations with host health and disease. Nat. Commun..

Jenny Drnevich, Frederick J Tan, Fabricio Almeida-Silva, Robert Castelo, Aedin C Culhane, Sean Davis, Maria A Doyle, Ludwig Geistlinger, Andrew R Ghazi, Susan Holmes, Leo Lahti, Alexandru Mahmoud, Kozo Nishida, Marcel Ramos, Kevin Rue-Albrecht, David J H Shih, Laurent Gatto, Charlotte Soneson (2025). Learning and teaching biological data science in the Bioconductor community. PLoS Comput. Biol..

Yizhou Peter Huang, Lauren Harmon, Eve Deering-Gardner, Xiaotu Ma, Josiah Harsh, Zhaoyu Xue, Hong Wen, Marcel Ramos, Sean Davis, Jr, Timothy J Triche (2025). bamSliceR: a Bioconductor package for rapid, cross-cohort variant and allelic bias analysis. Bioinform. Adv..

Charlotte Soneson, Lori Shepherd, Marcel Ramos, Kevin Rue-Albrecht, Johannes Rainer, Hervé Pagès, Vincent J Carey (2025). Eleven quick tips for writing a Bioconductor package. PLoS Comput. Biol..

Charlotte Soneson, Lori Shepherd, Marcel Ramos, Kevin Rue-Albrecht, Johannes Rainer, Hervé Pagès, Vincent J Carey (2025). Eleven quick tips for writing a Bioconductor package. PLoS Comput. Biol..

Samuel D Gamboa-Tuz, Marcel Ramos, Eric Franzosa, Curtis Huttenhower, Nicola Segata, Sehyun Oh, Levi Waldron (2025). Commonly used compositional data analysis implementations are not advantageous in microbial differential abundance analyses benchmarked against biological ground truth. bioRxiv.

Marcel Ramos, Lori Shepherd, Nathan C Sheffield, Alexandru Mahmoud, Hervé Pagès, Andres Wokaty, Dario Righelli, Davide Risso, Sean Davis, Sehyun Oh, Levi Waldron, Martin Morgan, Vincent Carey (2025). Bioconductor's computational ecosystem for genomic data science in cancer. Methods Mol. Biol..

Asya Khleborodova, Samuel D Gamboa-Tuz, Marcel Ramos, Nicola Segata, Levi Waldron, Sehyun Oh (2024). lefser: implementation of metagenomic biomarker discovery tool, LEfSe, in R. Bioinformatics.

Jenny Drnevich, Frederick J Tan, Fabricio Almeida-Silva, Robert Castelo, Aedin C Culhane, Sean Davis, Maria A Doyle, Ludwig Geistlinger, Andrew R Ghazi, Susan Holmes, Leo Lahti, Alexandru Mahmoud, Kozo Nishida, Marcel Ramos, Kevin Rue-Albrecht, David J H Shih, Laurent Gatto, Charlotte Soneson (2024). Learning and teaching biological data science in the Bioconductor community. arXiv [cs.CY].

Sehyun Oh, Kai Gravel-Pucillo, Marcel Ramos, Michael C Schatz, Sean Davis, Vincent Carey, Martin Morgan, Levi Waldron (2024). AnVILWorkflow: A runnable workflow package for Cloud-implemented bioinformatics analysis pipelines. F1000Res..

Kelly B Eckenrode, Dario Righelli, Marcel Ramos, Ricard Argelaguet, Christophe Vanderaa, Ludwig Geistlinger, Aedin C Culhane, Laurent Gatto, Vincent Carey, Martin Morgan, Davide Risso, Levi Waldron (2023). Curated single cell multimodal landmark datasets for R/Bioconductor. PLoS Comput. Biol..

Marcel Ramos, Martin Morgan, Ludwig Geistlinger, Vincent J Carey, Levi Waldron (2023). RaggedExperiment: the missing link between genomic ranges and matrices in Bioconductor. Bioinformatics.

Sehyun Oh, Ludwig Geistlinger, Marcel Ramos, Daniel Blankenberg, Marius van den Beek, Jaclyn N Taroni, Vincent J Carey, Casey S Greene, Levi Waldron, Sean Davis (2022). GenomicSuperSignature facilitates interpretation of RNA-seq experiments through robust, efficient comparison to public databases. Nat. Commun..

Michael C Schatz, Anthony A Philippakis, Enis Afgan, Eric Banks, Vincent J Carey, Robert J Carroll, Alessandro Culotti, Kyle Ellrott, Jeremy Goecks, Robert L Grossman, Ira M Hall, Kasper D Hansen, Jonathan Lawson, Jeffrey T Leek, Anne O'donnell Luria, Stephen Mosher, Martin Morgan, Anton Nekrutenko, Brian D O'Connor, Kevin Osborn, Benedict Paten, Candace Patterson, Frederick J Tan, Casey Overby Taylor, Jennifer Vessio, Levi Waldron, Ting Wang, Kristin Wuichet (2022). Inverting the model of genomics data sharing with the NHGRI Genomic Data Science Analysis, Visualization, and Informatics Lab-space. Cell Genom.

Ludwig Geistlinger, Gergely Csaba, Mara Santarelli, Marcel Ramos, Lucas Schiffer, Nitesh Turaga, Charity Law, Sean Davis, Vincent Carey, Martin Morgan, Ralf Zimmer, Levi Waldron (2021). Toward a gold standard for benchmarking gene set enrichment analysis. Brief. Bioinform..

Sehyun Oh, Jasmine Abdelnabi, Ragheed Al-Dulaimi, Ayush Aggarwal, Marcel Ramos, Sean Davis, Markus Riester, Levi Waldron (2020). HGNChelper: identification and correction of invalid gene symbols for human and mouse. F1000Res..

Marcel Ramos, Ludwig Geistlinger, Sehyun Oh, Lucas Schiffer, Rimsha Azhar, Hanish Kodali, Ino de Bruijn, Jianjiong Gao, Vincent J Carey, Martin Morgan, Levi Waldron (2020). Multiomic Integration of Public Oncology Databases in Bioconductor. JCO Clin Cancer Inform.

Ludwig Geistlinger, Sehyun Oh, Marcel Ramos, Lucas Schiffer, Rebecca S LaRue, Christine M Henzler, Sarah A Munro, Claire Daughters, Andrew C Nelson, Boris J Winterhoff, Zenas Chang, Shobhana Talukdar, Mihir Shetty, Sally A Mullany, Martin Morgan, Giovanni Parmigiani, Michael J Birrer, Li-Xuan Qin, Markus Riester, Timothy K Starr, Levi Waldron (2020). Multiomic Analysis of Subtype Evolution and Heterogeneity in High-Grade Serous Ovarian Carcinoma. Cancer Res..

Vincent J Carey, Marcel Ramos, Benjamin J Stubbs, Shweta Gopaulakrishnan, Sehyun Oh, Nitesh Turaga, Levi Waldron, Martin Morgan (2020). Global Alliance for Genomics and Health Meets Bioconductor: Toward Reproducible and Agile Cancer Genomics at Cloud Scale. JCO Clin Cancer Inform.

Sehyun Oh, Ludwig Geistlinger, Marcel Ramos, Martin Morgan, Levi Waldron, Markus Riester (2020). Reliable Analysis of Clinical Tumor-Only Whole-Exome Sequencing Data. JCO Clin Cancer Inform.

Vinicius da Silva, Marcel Ramos, Martien Groenen, Richard Crooijmans, Anna Johansson, Luciana Regitano, Luiz Coutinho, Ralf Zimmer, Levi Waldron, Ludwig Geistlinger (2020). CNVRanger: association analysis of CNVs with gene expression and quantitative phenotypes. Bioinformatics.

L Geistlinger, S Oh, M Ramos, L Schiffer, R S LaRue, others (2020). Multiomic Analysis of Subtype Evolution and Heterogeneity in High-Grade Serous Ovarian CarcinomaMultiomic Analysis of Subtype Evolution in Ovarian Cancer. Cancer Res..

Michelle A Montgomery, Marcel Ramos, Elizabeth A Kelvin, Arturo Carpio, Alexander Jaramillo, W Allen Hauser, Hongbin Zhang (2019). A longitudinal analysis of albendazole treatment effect on neurocysticercosis cyst evolution using multistate models. Trans. R. Soc. Trop. Med. Hyg..

Lucas Schiffer, Rimsha Azhar, Lori Shepherd, Marcel Ramos, Ludwig Geistlinger, Curtis Huttenhower, Jennifer B Dowd, Nicola Segata, Levi Waldron (2019). HMP16SData: Efficient Access to the Human Microbiome Project Through Bioconductor. Am. J. Epidemiol..

Levi Waldron, Lucas Schiffer, Rimsha Azhar, Marcel Ramos, Ludwig Geistlinger, Nicola Segata (2019). Improving Accessibility of the Human Microbiome Project Data Through Integration With R/Bioconductor. Am. J. Epidemiol..

Sean Davis, Marcel Ramos, Lori Shepherd, Nitesh Turaga, Ludwig Geistlinger, Martin T Morgan, Benjamin Haibe-Kains, Levi Waldron (2018). Orchestrating a community-developed computational workshop and accompanying training materials. F1000Res..

Marcel Ramos, Lucas Schiffer, Angela Re, Rimsha Azhar, Azfar Basunia, Carmen Rodriguez, Tiffany Chan, Phil Chapman, Sean R Davis, David Gomez-Cabrero, Aedin C Culhane, Benjamin Haibe-Kains, Kasper D Hansen, Hanish Kodali, Marie S Louis, Arvind S Mer, Markus Riester, Martin Morgan, Vince Carey, Levi Waldron (2017). Software for the Integration of Multiomics Experiments in Bioconductor. Cancer Res..

Edoardo Pasolli, Lucas Schiffer, Paolo Manghi, Audrey Renson, Valerie Obenchain, Duy Tin Truong, Francesco Beghini, Faizan Malik, Marcel Ramos, Jennifer B Dowd, Curtis Huttenhower, Martin Morgan, Nicola Segata, Levi Waldron (2017). Accessible, curated metagenomic data through ExperimentHub. Nat. Methods.

Benjamin J Stubbs, Keith Frankston, Marcel Ramos, Nancy Laranjo, Frank M Sacks, Vincent J Carey (2017). ogttMetrics: Data structures and algorithms for oral glucose tolerance tests. F1000Res..

Kezhen Fei, Jesica S Rodriguez-Lopez, Marcel Ramos, Nadia Islam, Chau Trinh-Shevrin, Stella S Yi, Claudia Chernov, Sharon E Perlman, Lorna E Thorpe (2017). Racial and Ethnic Subgroup Disparities in Hypertension Prevalence, New York City Health and Nutrition Examination Survey, 2013-2014. Prev. Chronic Dis..

K Fei (2017). Racial and ethnic subgroup disparities in hypertension prevalence, New York City Health and Nutrition Examination Survey, 2013–2014. Prev. Chronic Dis..

Levi Waldron, Markus Riester, Marcel Ramos, Giovanni Parmigiani, Michael Birrer (2016). The Doppelgänger Effect: Hidden Duplicates in Databases of Transcriptome Profiles. J. Natl. Cancer Inst..

Marcel Ramos, Misato Gbedemah, Heidi Jones, Levi Waldron (2016). Engagement of introductory biostatistics students in a novel hybrid course format. F1000Res..

Lavanya Kannan, Marcel Ramos, Angela Re, Nehme El-Hachem, Zhaleh Safikhani, Deena M A Gendoo, Sean Davis, David Gomez-Cabrero, Robert Castelo, Kasper D Hansen, Vincent J Carey, Martin Morgan, Aedin C Culhane, Benjamin Haibe-Kains, Levi Waldron (2016). Public data and open source tools for multi-assay genomic investigation of disease. Brief. Bioinform..

Jennifer L Hay, Marcel Ramos, Yuelin Li, Susan Holland, Debra Brennessel, M Margaret Kemeny (2016). Deliberative and intuitive risk perceptions as predictors of colorectal cancer screening over time. J. Behav. Med..

S M Torres, M Ramos, R Leverence, others (2014). Pilot Study of Skin Cancer Risk Reduction Behaviors, Cancer Communication, and Skin Cancer Beliefs in Hispanics. Journal of Health ….

Marcel Ramos Pérez, Robert Ford (2013). An example conference paper. In ICW.

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