Felicia New, Ph.D.

Felicia New, Ph.D.

Computational Biology · Genomics · Statistics

Publications

Spatial Transcriptomics Resolve an Emphysema-specific Lymphoid Follicle B Cell Signature in COPD

Published in American Journal of Respiratory and Critical Care Medicine, 2023

Characterization of the transcriptomic signatures from lymphoid follicles (LFs) in ever-smokers without COPD and COPD patients with varying degrees of emphysema using proteomic and transcriptomic profiling.

Recommended citation: Rojas-Quintero J, Ochsner SA, New F, Divakar P, Yang CX, Wu TD, Robinson J, Shimoga Chandrashekar D, Banovich NE, Rosas IO, Sauler M, Kheradmand F, Gaggar A, Margaroli C, San Jose Estepar R, McKenna NJ, Polverino F. Spatial Transcriptomics Resolve an Emphysema-specific Lymphoid Follicle B Cell Signature in COPD. Am J Respir Crit Care Med. 2023 Nov 7. doi 10.1164/rccm.202303-0507LE. Epub ahead of print. PMID 37934672.

Ultra High-plex Spatial Proteogenomic Investigation of Giant Cell Glioblastoma Multiforme Immune Infiltrates Reveals Distinct Protein and RNA Expression Profiles

Published in Cancer Research Communications, 2023

We describe ultra high-plex spatial proteogenomics; profiling whole transcriptome and high-plex proteomics on a single FFPE tissue section with spatial resolution. Investigation of gcGBM versus GBM revealed distinct protein and RNA expression profiles.

Recommended citation: Bonnett SA, Rosenbloom AB, Ong GT, Conner M, Rininger ABE, Newhouse D, New F, Phan CQ, Ilcisin S, Sato H, Lyssand JS, Geiss G, Beechem JM. Ultra High-plex Spatial Proteogenomic Investigation of Giant Cell Glioblastoma Multiforme Immune Infiltrates Reveals Distinct Protein and RNA Expression Profiles. Cancer Res Commun. 2023 May 3;3(5):763-779. doi 10.1158/2767-9764.CRC-22-0396. PMID 37377888; PMCID PMC10155752.

Collective effects of human genomic variation on microbiome function

Published in Scientific Reports, 2022

In this work, we examine the collective impact of human host genetics on gut microbiome composition and functions using a flexible computational and statistical framework for analyzing host-microbiome genetic interactions.

Recommended citation: New, F. N., Baer, B. R., Clark, A. G., Wells, M. T., & Brito, I. L. (2022). Collective effects of human genomic variation on microbiome function. Scientific Reports, 12. https://doi.org/10.1038/s41598-022-07632-3

Linking plasmid-based beta-lactamases to their bacterial hosts using single-cell fusion PCR

Published in eLife, 2021

In this study, we put forth a robust, accessible, and high-throughput platform for sensitively surveying the bacterial hosts of mobile genes in complex microbial communities.

Recommended citation: Diebold, P. J., New, F. N., Hovan, M., Satlin, M. J., & Brito, I. L. (2021). Linking plasmid-based beta-lactamases to their bacterial hosts using single-cell fusion pcr. ELife, 10. https://doi.org/10.7554/elife.66834

What Is Metagenomics Teaching Us, and What Is Missed?

Published in Annual Reviews Microbiology, 2020

Review article focusing on the many benefits of using metagenomics and outlining the breadth of conclusions that can be made using currently available tools, while also highlighting the challenges of metagenomic data analysis.

Recommended citation: New FN, Brito IL. (2020). "What Is Metagenomics Teaching Us, and What Is Missed?" Annual Reviews Microbiology. 74:117-35.

Disease-specific biases in alternative splicing and tissue-specific dysregulation revealed by multitissue profiling of lymphocyte gene expression in type 1 diabetes.

Published in Genome Res., 2017

This paper is about the substantial, and previously underrecognized, role for alternative splicing in the pathogenesis of autoimmune disorders and particularly for Type I Diabetes. Our findings highlight a substantial, and previously underrecognized, role for alternative splicing in the pathogenesis of autoimmune disorders and particularly for Type I Diabetes.

Recommended citation: Newman JRB, Conesa A, Mika M, New FN, Onengut-Gumuscu S, Atkinson MA, Rich SS, McIntyre LM, Concannon P. (2017). "Disease-specific biases in alternative splicing and tissue-specific dysregulation revealed by multitissue profiling of lymphocyte gene expression in type 1 diabetes." Genome Res.. 27(11).

Neurons That Underlie Drosophila melanogaster Reproductive Behaviors: Detection of a Large Male-Bias in Gene Expression in fruitless-Expressing Neurons.

Published in G3, 2016

Male and female reproductive behaviors in Drosophila melanogaster are vastly different, but neurons that express sex-specifically spliced fruitless transcripts (fru P1) underlie these behaviors in both sexes. How this set of neurons can generate such different behaviors between the two sexes is an un- resolved question. These results suggest a possible global mechanism for how distinct behaviors can arise from a shared set of neurons.

Recommended citation: Newell NR*, New FN*, Dalton JE, McIntyre LM, Arbeitman MN. (2016). "Neurons That Underlie Drosophila melanogaster Reproductive Behaviors: Detection of a Large Male-Bias in Gene Expression in fruitless-Expressing Neurons." G3. 6(8).

Sex Differences in Drosophila Somatic Gene Expression: Variation and Regulation by doublesex.

Published in G3, 2016

In this study, we focus on the mechanisms used by doublesex (dsx) to generate sexual dimorphism in gene expression, and address the relationship between dsx regulation and consistent sex-differential gene expression across strains. These results provide insights into a more complete pool of potential DSX targets, as well as revealing the molecular flexibility of DSX regulation.

Recommended citation: Arbeitman MN, New FN, Fear JM, Howard TS, Dalton JE, Graze RM. (2016). "Sex Differences in Drosophila Somatic Gene Expression: Variation and Regulation by doublesex." G3. 6(7).