Author
Memorial Sloan Kettering Cancer CenterORCID 0000-0002-9035-2143Unclaimed ORCID profile · follow to get notified of new preprints
7 papers
Recent·Most cited
Anqi Dai, Annamaria Ballweg, William Jogia, Madhumitha Rangesa, Peter A. Adintori, Mirae Baichoo, Tyler Funnell, Teng Fei, Nicholas R. Waters, Abrielle Swartz, Sukanya Sahu, Brianna Gipson, Sandeep S. Raj, Eiko Hayase, Zoe Pierce, , Jonathan U. Peled
The paper links sugar-rich foods to microbiome disruption during antibiotic treatment in patients and mice.
Nature · Sep 30, 2026Peer-reviewedMicrobiology
Teng Fei, Victoria Donovan, Tyler Funnell, Mirae Baichoo, Nicholas R. Waters, Jenny E. Paredes, Anqi Dai, Francesca Castro, Jennifer Haber, Ana Gradíssimo, Sandeep S. Raj, Alexander M. Lesokhin, Urvi Ashok Shah, Marcel R.M. van den Brink, Jonathan U. Peled
The paper introduces FLORAL, a method for analyzing longitudinal microbiome data to identify biomarkers associated with time-varying outcomes, showing improved sensitivity and FDR control in simulations and real-world applications.
bioRxiv · Feb 17, 2025 · PreprintBioinformatics
Teng Fei, Tyler Funnell, Nicholas R. Waters, Sandeep S. Raj, Mirae Baichoo, Keimya D. Sadeghi, Anqi Dai, Oriana Miltiadous, Roni Shouval, Meng Lv, Jonathan U. Peled, Doris M. Ponce, Miguel‐Angel Perales, Mithat Gönen, Marcel R.M. van den Brink
FLORAL improves microbial feature selection for microbiome data by addressing survival endpoints, longitudinal samples, and sequencing biases, showing better false-positive control and sensitivity in simulations and real data.
Cell Reports Methods · Nov 1, 2024Peer-reviewedBioinformatics
Jinyuan Yan, Chen Liao, Bradford P. Taylor, Emily Fontana, Luigi A. Amoretti, Roberta J. Wright, Anqi Dai, Nicholas R. Waters, Jonathan U. Peled, Ying Taur, Miguel‐Angel Perales, Benjamin A. Siranosian, Ami Siddharth Bhatt, Marcel R.M. van den Brink, Eric G. Pamer, , João B. Xavier
The paper compiles shotgun metagenomic data from stool samples of hospitalized hematopoietic cell transplant patients to enhance microbiome analysis beyond taxonomic composition.
bioRxiv · Aug 23, 2021 · PreprintSystems Biology
Ben Nolan, Florence Abram, Fiona Brennan, Ashleigh Holmes, Vincent O’Flaherty, Leighton Pritchard, Nicholas R. Waters
The paper improves 16S rRNA databases by reassembling whole-genome sequencing data to generate high-quality sequences, enhancing taxonomic classification accuracy.
bioRxiv · Jan 1, 2021 · PreprintBioinformatics
Nicholas R. Waters, Florence Abram, Fiona Brennan, Ashleigh Holmes, Leighton Pritchard
The paper implements an in silico Clermont PCR method for E. coli phylotyping as a web app and command-line tool.
Access Microbiology · Jun 19, 2020Peer-reviewedBioinformatics
Nicholas R. Waters, Florence Abram, Fiona Brennan, Ashleigh Holmes, Leighton Pritchard
riboSeed improves bacterial genome assembly by leveraging conserved ribosomal operon flanking regions to bridge contigs and aid genome closure.
Nucleic Acids Research · Mar 12, 2018Peer-reviewedBioinformatics