Dr. Kelly Ruggles
Kelly has been a faculty member at NYU SoM since 2015 after completing two postdoctoral positions at NYU with Drs. David Fenyo and Scott Braithwaite in computational proteogenomics and mathematical modeling of HIV, respectively. She received her PhD in Metabolic Biology from Columbia University and a BS in Biological Engineering from Cornell University. Outside of the lab, she enjoys running, karaoke and board games.
Lili is a PhD candidate in the Ruggles lab. She graduated from Cornell University in 2013 with a degree in biology, concentrating in cell and molecular biology. Lili has previously studied the regulation of V(D)J recombination in developing B cells and its connection to genome instability. She also studied the contribution of the non-coding genome to chemotherapeutic resistance in acute lymphoblastic leukemia. Currently, Lili is part of the national Clinical Proteomic Tumor Analysis Consortium (CPTAC); she works on integrating genome-wide data types in an effort to better understand, classify, and treat several cancer types. Lili is passionate about using basic biology and data analysis to improve outcomes for cancer patients.
Emily is a 5th year PhD student from Ames, Iowa who is a member of both the Ruggles and Fenyö labs. She previously attended Carleton College (BA in Computer Science, 2010) and the University of Wisconsin-Madison (MS in Computer Science, 2012). She also worked as a healthcare-focused data scientist with Pivotal Software before coming to NYU. Emily is a leader of the CPTAC project that aims to create a proteogenomic characterization of endometrial cancer and is the designer and maintainer of the current version of QUILTS (http://quilts.fenyolab.org), a tool for creating sample-specific variant protein databases. In her free time Emily enjoys doing crosswords, playing bar trivia, watching “Murder, She Wrote”, and cheering for the Yankees.
Angelina is a PhD Candidate in the Ruggles lab. While working full-time, she earned a degree in Biochemistry with a Bioinformatics concentration with two minors in Computer Science and in Mathematics from Hunter College, CUNY. During this time, Angelina was involved in several different computational biology research projects at MIT and Hunter. Remarkably, during her last year at Hunter, she received the prestigious National Science Foundation Graduate Research Fellowship to fund her graduate education. Currently, she is researching the human gut microbiome in autoimmune diseases using Artificial Intelligence (AI) approaches. She is passionate about adapting AI algorithms to study various biological phenomena. To this end, she is working on applying natural language processing techniques to raw next-generation sequencing data. Angelina has served as a Teacher’s Assistant for three courses at NYU Medical School. She enjoys teaching and leading classes. Outside of lab, you can find Angelina hiking, boxing, or learning about entrepreneurship.
J. Cooper Devlin
Cooper is a graduate student co-mentored by Kelly Ruggles and P’ng Loke. He graduated from the University of Florida in 2016 with a degree in microbiology and a minor in bioinformatics. Cooper has previously studied the human microbiome and developed a metagenomic analysis tool (Wham!) for both data-driven and hypothesis-driven microbiome analysis. More recently, in collaboration with P’ng Loke, Cooper has worked on harnessing multi-omic profiling data to understand complex immune activation in mice and humans. Cooper specializes in the analysis of high-density and highly dimensional datasets to better understand human immunology.
MacIntosh (Tosh) Cornwell
Tosh is a third year MD/PhD student in the first year of his PhD. He graduated from Johns Hopkins University in 2015 with a degree in Biomedical Engineering, and spent two years working at the Dana-Farber Cancer Institute prior to joining NYU School of Medicine. His work includes (1) multi-omic analysis across cancer types as a part of the CPTAC project, with a focus on Glioblastoma, and (2) Big data mining and modeling of ischemic heart disease as a part of the ISCHEMIA project.
Allie is a third year MD/PhD student in the first year of her PhD. She graduated from Duke University in 2017 with a degree in Biology. Allie is co-mentored by Dr. Eva Hernando, and aims to use both wet lab and computational approaches to investigate mechanisms of melanoma metastasis.
Shaleigh is a master’s student in the Biomedical Informatics program. She graduated from the University of Denver in 2017 with a degree in molecular biology and studied cell motility in Porifera as an undergraduate researcher. Currently, Shaleigh is part of the Clinical Proteomic Tumor Analysis Consortium (CPTAC) and is working on the integration and analysis of proteogenomic tumor data to identify therapeutic targets in lung adenocarcinoma.
Lizabeth (Lisa) Katsnelson
Lisa is a masters student in the Biomedical Informatics program and will be staying at NYU for her PhD in Systems and Computational Biomedicine. She graduated from Brandeis University in 2015 with a degree in Biology and Chemical Biology. Before starting her masters in 2018, Lisa worked as a research technician at Weill Cornell Medicine studying the bone marrow microenvironment. Currently, Lisa is finishing her masters thesis on the molecular profiling and drug targeting of copy number high serous endometrial tumors.
Kendall is a master’s student in the Biomedical Informatics program. She graduated from Clemson University in December 2017 with a BS in Genetics. Her current work is focused on utilizing a multi-omics approach to characterize drug resistance during treatment of Acute Myeloid Leukemia.
Dr. Arnon Lieber
Arnon is a Research Instructor with the Department of Medicine at NYU
Dr. Hua Zhou
Hua is a research scientist in the Ruggles lab. He graduated from University of Illinois, Champaign-Urbana in 2013 with a Ph.D in biochemistry/bioinformatics. Hua has been working on both bioinformatics and clinical informatics projects. For bioinformatics, he has been working with RNASeq, WES, proteomics data. For clinical informatics, he’s been working with clinical data related to different cancers, including prostate cancer, lung cancer, and melanoma. He is also part of national Clinical Proteomic Tumor Analysis Consortium (CPTAC). Hua’s expertise is in sequencing data analysis, machine learning and causal network etc.