Team – Peng Lab: Systems Analysis of Host-Microbiome-Pathogen Interactions

Xinxia Peng, PhD

I am a tenured Associate Professor of Infectious diseases in the Department of Molecular Biomedical Sciences, and a member of NC State Bioinformatics Research Center. I received my PhD in Computational Biology and Bioinformatics from the University of Tennessee – Oak Ridge National Laboratory Graduate School of Genome Science and Technology, under Computer Science Professor Dr. Michael Langston. I started as a Bioinformatics Manager at Seattle BioMed (now Center for Global Infectious Disease Research) after graduation. In 2008 I joined the University of Washington Department of Microbiology as a Computational Research Scientist, and was promoted to a Research Assistant Professor in 2012. I moved here at NC State in July 2016 as one of the Dean’s Faculty Excellence cluster hires, in the field of “Translational Genomics of Infectious Diseases,” and to be part of the Bioinformatics Research Center.

Visiting Researcher

Wei Wang, PhD

I am currently a Research Scientist in Meta BCR Ads Ranking CoreML Team and a Visiting Researcher in Peng Lab. My research interests include machine learning and its application in ads personalization experience, computational methodologies for efficient, accurate, and highly scalable genomic analysis. Also please visit my personal page.

Research Staff

Tammy Tollison, MS, Lab Manager and CBS PhD student

I received a MS in Microbiology and Molecular Genetics (2011) from Emory University and a BS in Genetics (2007) from Clemson University. Prior to joining the Peng Lab, I worked as an educator for 8 years with most of this time spent as a member of the Natural Sciences department at Wake Tech Community College. I joined the Peng Lab near the end of 2019.

I have been developing single-cell-based species-specific immune repertoire profiling assays. I also analyze both human clinical specimens and samples from animal studies provided by our collaborators using both long and short read high-throughput sequencing analysis.

Becca Yeamans, MS, Research Associate

I received an MS in Environmental Sciences from the University of Virginia (2011) and a BS in Biology from Saint Michael’s College (2004). I have had a quite eclectic collection of jobs, from a research technician in an immunology lab in Boston to freelance writing about wine science, and everywhere in between!

For the better part of a decade, I have been a stay-at-home mom, moonlighting as a wine writer. Desperately missing adult conversations and intellectual pursuits, I re-entered the workforce in early 2024 by joining the Peng Lab, where I assist with lab management duties, as well as providing assistance wherever I can in various projects in the lab. Currently, I am spearheading the development of Nanopore sequencing in the Peng Lab, and doing my part to help keep the Peng Lab on the forefront of molecular and microbial biological processes.

Postdoctoral Researcher

Jessica (Chao Ye), PhD, Postdoctoral Researcher

I received my PhD in Bioinformatics from the University of New South Wales in July 2024, where I focused on using machine learning to predict antibody-antigen interactions. Prior to my PhD, I gained years of experience in IT and web-software development, which now enhances my bioinformatics work with a strong technical foundation. In November 2024, I joined the Peng Lab at North Carolina State University as a postdoctoral researcher.

My current research focuses on single-cell RNA sequencing to profile immune repertoires, with plans to expand into broader RNA analysis for deeper transcriptomic insights. I also analyze clinical and animal samples to advance understanding of microbiome interactions and immune responses. I’m excited to develop these methods to open new perspectives in immune profiling and disease treatment.

Outside of research, I practice meditation and yoga to maintain focus and balance, and I enjoy listening to classical music, which complements my reflective approach to scientific exploration.

Graduate Student

Kayleigh Diveley, Genetics

I received a MS in Microbiology (2016) and a BS in Zoology (2014) from Western Illinois University with minors in Mathematics and Chemistry. At North Carolina State University I entered as part of the PhD Genetics program with interests in Genetics and Immunology.

Working with Dr. Li at the University of Pittsburgh, I have set up high-throughput techniques developed by Dr. Li SNP-seq and Reel-seq in the lab to screen for functional genetic variations in human complex immune loci such as Fc receptors. Now I am using long read sequencing, CRISPR/Cas9 based genome editing, and other molecular techniques to investigate the functional mechanisms of human genetic variants identified by the high-throughput screens.

Kristen John, Genetics

I graduated with a B.S. in Cell & Molecular Biology from Liberty University in 2019. I am pursuing a PhD in Genetics and Genomics.

My general research interests are in understanding the biological mechanisms behind human disease. I work with our Bioinformatics graduate students to prioritize human long noncoding RNAs (lncRNAs) involved in viral infection and innate immunity that are identified by the analysis of large-scale bulk and single cell RNA-seq data. I am currently studying the functional mechanisms of selected human lncRNAs using various molecular techniques in human cells, with the helps from the Carpenter Lab at UC Santa Cruz.

Nicole Adams, Bioinformatics

I received a B.S. in Biological Sciences at the University of Tennessee, Knoxville in 2020, and I am pursuing a PhD in Bioinformatics.

My research interests lie in identifying and understanding genetic predispositions that cause human diseases. Currently I am developing computational pipeline and methods for long read sequencing data to extend our single cell sequencing based studies.

Sangmi Jeong, Bioinformatics

I received a MA in Statistics in 2021 from Yonsei University in Seoul, South Korea, and I am pursuing a PhD in Bioinformatics at North Carolina State University.

I am interested in microbiome research in general. Through the analysis of microbiome deep sequencing data, I aim to identify microbial features that are predictive of disease progression and risk of infection in humans and rhesus macaques.

Ethan Smith, Bioinformatics

I received my B.S. in Genetics with a minor in Computer Science from the University of Georgia in 2022. Currently, I am pursuing a PhD in Bioinformatics at North Carolina State University.

My research interests include the characterization of non-coding RNA regulatory networks and the use of machine learning to identify conserved non-coding RNA elements across multiple species.

Rotation student

Jonathan Caradonna, Bioinformatics

I am currently a Bioinformatics PhD student rotating in this lab and I received my BS in Biochemistry from Stony Brook University with a minor in Computer Science earlier this year (2024).

I am interested in delving into the topics of single-cell RNA seq and transcriptomics and how they can be used to better infer disease progression, immunology and changes in cell state in tissues through the use of various programming and statistical analysis, differential gene expression analysis, and other computational approaches.

Kate Everly, Bioinformatics

I received my B.S. in Biology at Georgia Tech in 2021 and I am in my first year at NC State pursuing a PhD in Bioinformatics. Overall, my research interests lie in understanding genetic and epigenetic causes and regulation of human diseases. I am currently rotating in the Peng Lab and my rotation project will focus on analyzing Nanopore data, specifically for phasing. I will be looking at methylation patterns in Nanopore data to further improve phasing capabilities.

Noor Zamamiri, Genetics & Genomics

I received my B.S. in Biology and Neuroscience at Syracuse University in 2024, and am currently in my first year of pursuing a PhD in Genetics & Genomics at NC State University. My research interests broadly include the genetic basis of disease and immunity, and its applications to the discovery of therapeutic targets. My rotation project uses qPCR to examine Fc gamma receptor polymorphisms.

Undergraduate

Alexandra (Lexi) Istishin, Microbiology and Biomanufacturing

I am currently pursuing a B.S. in Microbiology with a minor in Biomanufacturing. I joined the Peng lab in Fall 2023 as an undergraduate research assistant.

I’m excited to have the opportunity to discover and pursue a multitude of research interests within genetics, immunology, and infectious disease. Under the mentorship of Kristen, my current lab responsibilities include supportive projects relating to human cell culture and the creation and maintenance of long noncoding RNA CRISPR knockdown/overexpression human cell lines.

Lab Alumni

Name, Position / First position

Ian Huntress, PhD in Bioinformatics (2023) In Memoriam
Silvia Shui, Undergraduate (Cellular, Molecular, and Developmental Biology), 2021-2022 / Cold Spring Harbor Laboratory
Evan Walsh, PhD in Bioinformatics (2022) / Capsida Biotherapeutics
Christal Dita, Undergraduate (Zoology), 2022 Summer
Hsuan (Tina) Chou, Research Associate, 2019-2021 / Owlstone Medical
Hayden Brochu, PhD in Bioinformatics (2021) / Labcorp
Aiden Jones, MR in Genetics (2021) / Cell Microsystems
Anna Chernikov, Undergraduate (Computer Science & Biology), 2019-2020 / PhD student in Computer Science, University of Arizona
Anne Crews, Laboratory Supervisor (part-time), 2019-2020 / Retired
Amy Nipper, Research Assistant, 2018-2019
Ashley Kilgore, Visiting student (Biotechnology, Johns Hopkins University), 2019 Spring
Ryan Li, Undergraduate (Mathematics), 2016-2018 / PhD student in Statistics, NC State
Alexis Johnson, Undergraduate (Microbiology), 2018
Manfred Meng, Research Scientist, 2018 / Duke University
Connor Campbell, Graduate Intern (Analytics), 2017-2018 / Fidelity Investments
Fang Yang, Research Associate, 2017-2018 / Texas A&M University
Erin Harrell, Research Associate, 2016-2018 / NC State
David Lemler, Postdoctoral Fellow, 2016-2017 / Medical Writer

	Xinxia Peng, PhD I am a tenured Associate Professor of Infectious diseases in the Department of Molecular Biomedical Sciences, and a member of NC State Bioinformatics Research Center. I received my PhD in Computational Biology and Bioinformatics from the University of Tennessee – Oak Ridge National Laboratory Graduate School of Genome Science and Technology, under Computer Science Professor Dr. Michael Langston. I started as a Bioinformatics Manager at Seattle BioMed (now Center for Global Infectious Disease Research) after graduation. In 2008 I joined the University of Washington Department of Microbiology as a Computational Research Scientist, and was promoted to a Research Assistant Professor in 2012. I moved here at NC State in July 2016 as one of the Dean’s Faculty Excellence cluster hires, in the field of “Translational Genomics of Infectious Diseases,” and to be part of the Bioinformatics Research Center.
Visiting Researcher
	Wei Wang, PhD I am currently a Research Scientist in Meta BCR Ads Ranking CoreML Team and a Visiting Researcher in Peng Lab. My research interests include machine learning and its application in ads personalization experience, computational methodologies for efficient, accurate, and highly scalable genomic analysis. Also please visit my personal page.
Research Staff
	Tammy Tollison, MS, Lab Manager and CBS PhD student I received a MS in Microbiology and Molecular Genetics (2011) from Emory University and a BS in Genetics (2007) from Clemson University. Prior to joining the Peng Lab, I worked as an educator for 8 years with most of this time spent as a member of the Natural Sciences department at Wake Tech Community College. I joined the Peng Lab near the end of 2019. I have been developing single-cell-based species-specific immune repertoire profiling assays. I also analyze both human clinical specimens and samples from animal studies provided by our collaborators using both long and short read high-throughput sequencing analysis.
	Becca Yeamans, MS, Research Associate I received an MS in Environmental Sciences from the University of Virginia (2011) and a BS in Biology from Saint Michael’s College (2004). I have had a quite eclectic collection of jobs, from a research technician in an immunology lab in Boston to freelance writing about wine science, and everywhere in between! For the better part of a decade, I have been a stay-at-home mom, moonlighting as a wine writer. Desperately missing adult conversations and intellectual pursuits, I re-entered the workforce in early 2024 by joining the Peng Lab, where I assist with lab management duties, as well as providing assistance wherever I can in various projects in the lab. Currently, I am spearheading the development of Nanopore sequencing in the Peng Lab, and doing my part to help keep the Peng Lab on the forefront of molecular and microbial biological processes.
Postdoctoral Researcher
	Jessica (Chao Ye), PhD, Postdoctoral Researcher I received my PhD in Bioinformatics from the University of New South Wales in July 2024, where I focused on using machine learning to predict antibody-antigen interactions. Prior to my PhD, I gained years of experience in IT and web-software development, which now enhances my bioinformatics work with a strong technical foundation. In November 2024, I joined the Peng Lab at North Carolina State University as a postdoctoral researcher. My current research focuses on single-cell RNA sequencing to profile immune repertoires, with plans to expand into broader RNA analysis for deeper transcriptomic insights. I also analyze clinical and animal samples to advance understanding of microbiome interactions and immune responses. I’m excited to develop these methods to open new perspectives in immune profiling and disease treatment. Outside of research, I practice meditation and yoga to maintain focus and balance, and I enjoy listening to classical music, which complements my reflective approach to scientific exploration.
Graduate Student
	Kayleigh Diveley, Genetics I received a MS in Microbiology (2016) and a BS in Zoology (2014) from Western Illinois University with minors in Mathematics and Chemistry. At North Carolina State University I entered as part of the PhD Genetics program with interests in Genetics and Immunology. Working with Dr. Li at the University of Pittsburgh, I have set up high-throughput techniques developed by Dr. Li SNP-seq and Reel-seq in the lab to screen for functional genetic variations in human complex immune loci such as Fc receptors. Now I am using long read sequencing, CRISPR/Cas9 based genome editing, and other molecular techniques to investigate the functional mechanisms of human genetic variants identified by the high-throughput screens.
	Kristen John, Genetics I graduated with a B.S. in Cell & Molecular Biology from Liberty University in 2019. I am pursuing a PhD in Genetics and Genomics. My general research interests are in understanding the biological mechanisms behind human disease. I work with our Bioinformatics graduate students to prioritize human long noncoding RNAs (lncRNAs) involved in viral infection and innate immunity that are identified by the analysis of large-scale bulk and single cell RNA-seq data. I am currently studying the functional mechanisms of selected human lncRNAs using various molecular techniques in human cells, with the helps from the Carpenter Lab at UC Santa Cruz.
	Nicole Adams, Bioinformatics I received a B.S. in Biological Sciences at the University of Tennessee, Knoxville in 2020, and I am pursuing a PhD in Bioinformatics. My research interests lie in identifying and understanding genetic predispositions that cause human diseases. Currently I am developing computational pipeline and methods for long read sequencing data to extend our single cell sequencing based studies.
	Sangmi Jeong, Bioinformatics I received a MA in Statistics in 2021 from Yonsei University in Seoul, South Korea, and I am pursuing a PhD in Bioinformatics at North Carolina State University. I am interested in microbiome research in general. Through the analysis of microbiome deep sequencing data, I aim to identify microbial features that are predictive of disease progression and risk of infection in humans and rhesus macaques.
	Ethan Smith, Bioinformatics I received my B.S. in Genetics with a minor in Computer Science from the University of Georgia in 2022. Currently, I am pursuing a PhD in Bioinformatics at North Carolina State University. My research interests include the characterization of non-coding RNA regulatory networks and the use of machine learning to identify conserved non-coding RNA elements across multiple species.
Rotation student
	Jonathan Caradonna, Bioinformatics I am currently a Bioinformatics PhD student rotating in this lab and I received my BS in Biochemistry from Stony Brook University with a minor in Computer Science earlier this year (2024). I am interested in delving into the topics of single-cell RNA seq and transcriptomics and how they can be used to better infer disease progression, immunology and changes in cell state in tissues through the use of various programming and statistical analysis, differential gene expression analysis, and other computational approaches.
	Kate Everly, Bioinformatics I received my B.S. in Biology at Georgia Tech in 2021 and I am in my first year at NC State pursuing a PhD in Bioinformatics. Overall, my research interests lie in understanding genetic and epigenetic causes and regulation of human diseases. I am currently rotating in the Peng Lab and my rotation project will focus on analyzing Nanopore data, specifically for phasing. I will be looking at methylation patterns in Nanopore data to further improve phasing capabilities.
	Noor Zamamiri, Genetics & Genomics I received my B.S. in Biology and Neuroscience at Syracuse University in 2024, and am currently in my first year of pursuing a PhD in Genetics & Genomics at NC State University. My research interests broadly include the genetic basis of disease and immunity, and its applications to the discovery of therapeutic targets. My rotation project uses qPCR to examine Fc gamma receptor polymorphisms.
Undergraduate
	Alexandra (Lexi) Istishin, Microbiology and Biomanufacturing I am currently pursuing a B.S. in Microbiology with a minor in Biomanufacturing. I joined the Peng lab in Fall 2023 as an undergraduate research assistant. I’m excited to have the opportunity to discover and pursue a multitude of research interests within genetics, immunology, and infectious disease. Under the mentorship of Kristen, my current lab responsibilities include supportive projects relating to human cell culture and the creation and maintenance of long noncoding RNA CRISPR knockdown/overexpression human cell lines.
Lab Alumni	Name, Position / First position
	Ian Huntress, PhD in Bioinformatics (2023) In Memoriam Silvia Shui, Undergraduate (Cellular, Molecular, and Developmental Biology), 2021-2022 / Cold Spring Harbor Laboratory Evan Walsh, PhD in Bioinformatics (2022) / Capsida Biotherapeutics Christal Dita, Undergraduate (Zoology), 2022 Summer Hsuan (Tina) Chou, Research Associate, 2019-2021 / Owlstone Medical Hayden Brochu, PhD in Bioinformatics (2021) / Labcorp Aiden Jones, MR in Genetics (2021) / Cell Microsystems Anna Chernikov, Undergraduate (Computer Science & Biology), 2019-2020 / PhD student in Computer Science, University of Arizona Anne Crews, Laboratory Supervisor (part-time), 2019-2020 / Retired Amy Nipper, Research Assistant, 2018-2019 Ashley Kilgore, Visiting student (Biotechnology, Johns Hopkins University), 2019 Spring Ryan Li, Undergraduate (Mathematics), 2016-2018 / PhD student in Statistics, NC State Alexis Johnson, Undergraduate (Microbiology), 2018 Manfred Meng, Research Scientist, 2018 / Duke University Connor Campbell, Graduate Intern (Analytics), 2017-2018 / Fidelity Investments Fang Yang, Research Associate, 2017-2018 / Texas A&M University Erin Harrell, Research Associate, 2016-2018 / NC State David Lemler, Postdoctoral Fellow, 2016-2017 / Medical Writer