John Zinno

As a Genomics Data Scientist, I am very interested in the power of machine learning / deep learning and its applications in genomics and bioinformatics. My recent work particularly emphasizes using Bayesian and generative models to analyze single-cell multiomics data towards understanding somatic mosaicism and characterizing genotype-phenotype relationships.

Publications

Large-scale single-cell phylogenetic mapping of clonal evolution in the human aging esophagus

bioRxiv

Tamara Prieto, Dennis J Yuan, John Zinno, Clayton Hughes, Nicholas Midler, Sheng Kao, Jani Huuhtanen, Ramya Raviram, Fenia Fotopoulou, Neil Ruthen, Srinivas Rajagopalan, Joshua S Schiffman, Andrew R D Avino, Sang-Ho Yoon, Jesus Sotelo, Nathaniel D Omans, Noelle Wheeler, Alejandro Garces, Barun Pradhan, Alexandre Pellan Cheng, Nicolas Robine, Catherine Potenski, Katharine Godfrey, Nobuyuki Kakiuchi, Akira Yokoyama, Seishi Ogawa, Julian Abrams, Ivan Raimondi, Dan A Landau

doi.org/10.1101/2025.10.11.681805

Single-cell mapping of regulatory DNA:Protein interactions

bioRxiv

Wei-Yu Chi, Sang-Ho Yoon, Evrim Goksel, Levan Mekerishvili, Joe Pelt, Yiyun Lin, Tamara Prieto, John Zinno, Saravanan Ganesan, Catherine Potenski, Franco Izzo, Dan A. Landau, Ivan Raimondi

doi.org/10.1101/2024.12.31.630903

Measuring Longitudinal Genome-wide Clonal Evolution of Pediatric Acute Lymphoblastic Leukemia at Single-Cell Resolution

bioRxiv

Yakun Pang, Tamara Prieto, Veronica Gonzalez-Pena, Athena Aragon, Yuntao Xia, Sheng Kao, Sri Rajagopalan, John Zinno, Jean Quentin, Julien Laval, Dennis Yuan, Nathaniel Omans, David Klein, Matthew MacKay, Iwijn De Vlaminck, John Easton, William Evans, Dan A. Landau, Charles Gawad

doi.org/10.1101/2025.03.19.644196

Genotype-to-phenotype mapping of somatic clonal mosaicism via single-cell co-capture of DNA mutations and mRNA transcripts

Cancer Discovery

Dennis J Yuan, John Zinno, Theo Botella, Dalia Dhingra, Shu Wang, Allegra Hawkins, Ariel Swett, Jesus Sotelo, Ramya Raviram, Clayton Hughes, Catherine Potenski, Akira Yokoyama, Nobuyuki Kakiuchi, Seishi Ogawa, Dan A Landau

doi.org/10.1158/2159-8290.CD-24-0853

Omicron Spike protein has a positive electrostatic surface that promotes ACE2 recognition and antibody escape

Frontiers in Virology

Hin Hark Gan, John Zinno, Fabio Piano, Kristin C Gunsalus

doi.org/10.3389/fviro.2022.894531

The Caenorhabditis elegans TDRD5/7-like protein, LOTR-1, interacts with the helicase ZNFX-1 to balance epigenetic signals in the germline

PLoS Genetics

Elisabeth A. Marnik, Miguel V. Almeida, P. Giselle Cipriani, George Chung, Edoardo Caspani, Emil Karaulanov, Falk Butter, Catherine S. Sharp, John Zinno, Hin Hark Gan, Fabio Piano, René F Ketting, Kristin C. Gunsalus, Dustin L. Updike

doi.org/10.1371/journal.pgen.1010245

Novel LOTUS-domain proteins are organizational hubs that recruit C. elegans Vasa to germ granules

eLife

Patricia Giselle Cipriani, Olivia Bay, John Zinno, Michelle Gutwein, Hin Hark Gan, George Chung, Jia-Xuan Chen, Hala Fahs, Yu Guan, Thomas F Duchaine, Matthias Selbach, Fabio Piano, Kristin C Gunsalus

doi.org/10.7554/eLife.60833

Work Experience

(Sr.) Genomics Data Scientist / AI

New York Genome Center & Weill Cornell Medicine

September 2022 - Senior January 2024 - Present

Deep learning models for single-cell multiomics data
Novel phylogenetic methods for single-cell multiomics data
Massive scale data processing pipelines for single-cell multiomics data

Bioinformatics, Data Engineering

NYU Langone Health

December 2021 - January 2023

High-volume genomic data processing pipelines (WGS/ATAC/RNA-seq)
Novel germline genetic markers for improved melanoma prognosis prediction
Integrating various data types to identify complex genetic signatures and markers for immunotherapy response