Optimized application of penalized regression methods to diverse genomic data. - Levi Waldron; Melania Pintilie; Ming-Sound Tsao; Frances A. Shepherd; Curtis Huttenhower; Igor Jurisica (Bioinform., 2011)

curatedOvarianData: clinically annotated data for the ovarian cancer transcriptome. - Benjamin Frederick Ganzfried; Markus Riester; Benjamin Haibe-Kains; Thomas Risch; Svitlana Tyekucheva; Ina Jazic; Xin Victoria Wang; Mahnaz Ahmadifar; Michael J. Birrer; Giovanni Parmigiani; Curtis Huttenhower; Levi Waldron (Database J. Biol. Databases Curation, 2013)

A Guide to Enterotypes across the Human Body: Meta-Analysis of Microbial Community Structures in Human Microbiome Datasets. - Omry Koren; Dan Knight; Antonio González; Levi Waldron; Nicola Segata; Rob Knight 001; Curtis Huttenhower; Ruth E. Ley (PLoS Comput. Biol., 2013)

Cross-study validation for the assessment of prediction algorithms. - Christoph Bernau; Markus Riester; Anne-Laure Boulesteix; Giovanni Parmigiani; Curtis Huttenhower; Levi Waldron; Lorenzo Trippa (Bioinform., 2014)

Más-o-menos: a simple sign averaging method for discrimination in genomic data analysis. - Sihai Dave Zhao; Giovanni Parmigiani; Curtis Huttenhower; Levi Waldron (Bioinform., 2014)

Meta-Analysis in Gene Expression Studies. - Levi Waldron; Markus Riester (Statistical Genomics, 2016)

Public data and open source tools for multi-assay genomic investigation of disease. - Lavanya Kannan; Marcel Ramos; Angela Re; Nehme Hachem; Zhaleh Safikhani; Deena M. A. Gendoo; Sean Davis 001; David Gomez-Cabrero; Robert Castelo; Kasper D. Hansen; Vincent J. Carey; Martin Morgan; et al. (Briefings Bioinform., 2016)

Machine Learning Meta-analysis of Large Metagenomic Datasets: Tools and Biological Insights. - Edoardo Pasolli; Duy Tin Truong; Faizan Malik; Levi Waldron; Nicola Segata (PLoS Comput. Biol., 2016)

Control of Gene Expression by RNA Binding Protein Action on Alternative Translation Initiation Sites. - Angela Re; Levi Waldron; Alessandro Quattrone (PLoS Comput. Biol., 2016)

bioBakery: a meta'omic analysis environment. - Lauren J. McIver; Galeb Abu-Ali; Eric A. Franzosa; Randall Schwager; Xochitl C. Morgan; Levi Waldron; Nicola Segata; Curtis Huttenhower (Bioinform., 2018)

Orchestrating a community-developed computational workshop and accompanying training materials. - Sean Davis 001; Marcel Ramos; Lori A. Shepherd; Nitesh Turaga; Ludwig Geistlinger; Martin T. Morgan; Benjamin Haibe-Kains; Levi Waldron (F1000Research, 2018)

restfulSE: A semantically rich interface for cloud-scale genomics with Bioconductor. - Shweta Gopaulakrishnan; Samuela Pollack; BJ Stubbs; Hervé Pagès; John Readey; Sean Davis 001; Levi Waldron; Martin Morgan; Vincent J. Carey (F1000Research, 2019)

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

Toward a gold standard for benchmarking gene set enrichment analysis. - Ludwig Geistlinger; Gergely Csaba; Mara Santarelli; Marcel Ramos; Lucas Schiffer; Nitesh Turaga; Charity W. Law; Sean Davis 001; Vincent J. Carey; Martin Morgan; Ralf Zimmer; Levi Waldron (Briefings Bioinform., 2021)

SIMON: Open-Source Knowledge Discovery Platform. - Adriana Tomic; Ivan Tomic; Levi Waldron; Ludwig Geistlinger; Max Kuhn; Rachel L. Spreng; Lindsay C. Dahora; Kelly E. Seaton; Georgia D. Tomaras; Jennifer Hill; Niharika A. Duggal; Ross D. Pollock; et al. (Patterns, 2021)

Multivariable association discovery in population-scale meta-omics studies. - Himel Mallick; Ali Rahnavard; Lauren J. McIver; Siyuan Ma; Yancong Zhang; Long H. Nguyen; Timothy L. Tickle; George Weingart; Boyu Ren; Emma H. Schwager; Suvo Chatterjee; Kelsey N. Thompson; et al. (PLoS Comput. Biol., 2021)

High-sensitivity pattern discovery in large, paired multiomic datasets. - Andrew R. Ghazi; Kathleen Sucipto; Ali Rahnavard; Eric A. Franzosa; Lauren J. McIver; Jason Lloyd-Price; Emma H. Schwager; George Weingart; Yo Sup Moon; Xochitl C. Morgan; Levi Waldron; Curtis Huttenhower (Bioinform., 2022)

Evaluation of software impact designed for biomedical research: Are we measuring what's meaningful? - Awan Afiaz; Andrey Ivanov; John Chamberlin; David Hanauer; Candace Savonen; Mary J. Goldman; Martin Morgan; Michael Reich; Alexander Getka; Aaron Holmes; Sarthak Pati; Dan Knight; et al. (CoRR, 2023)

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