Yi-Hui Zhou selected as a Provost’s Faculty Fellow and Ben Callahan selected as a Faculty Scholar

2023-24 Provost’s Faculty Fellows Announced

The Office of the Executive Vice Chancellor and Provost and the Office for Faculty Excellence have announced the 2023-24 class of Provost’s Faculty Fellows.

The Provost’s Faculty Fellows Program supports talented faculty in the exploration of academic leadership roles at the university’s highest levels. Current NC State faculty interested in learning more about academic affairs administration can hone their skills as faculty leaders through working closely with Provost’s Office staff on projects that are meaningful to them and the university.

The home departments of the faculty members selected as Faculty Fellows will be provided with 25 percent salary release funds to cover the time commitment required for participation. Fellowships are for a full academic year.

The 2023-24 Faculty Fellows program will be split into two tracks this year, with the Provost’s Office working in conjunction with the Office for Faculty Excellence, the Office of Global Engagement and the Shelton Leadership Center. Fellows will work in teams of three (University Leadership Track) or with the Office of Global Engagement staff and representatives of partner institutions (Global Leadership Track) to address an assigned theme or issue relating to higher education leadership. All fellows will participate in a cohort-based, academic-year-long training program structured around strategy, leadership and cultural competence.

This year’s class of fellows includes:

  • Yi-Hui Zhou
    • Associate Professor, Department of Biological Sciences; ​​Associate Director of Outreach, Bioinformatics Research Center
    • University Leadership Track


2022-23 University Faculty Scholars Named

NC State’s 2022-23 class of University Faculty Scholars was announced today. These 22 early- and mid-career faculty receive this designation in recognition of their outstanding academic achievements and contributions to NC State through their teaching, scholarship and service to the university and beyond.

Since the program’s inception in 2012, 236 faculty have been named University Faculty Scholars. These faculty members carry the title for the duration of their faculty appointment at NC State and receive an increase to their base salary.

Each college may submit nominations for assistant professors appointed for a second term, associate professors and professors within the first three years of their appointment. Senior faculty then review nominations, evaluating them on research and scholarship productivity, excellence in teaching and mentoring, and leadership in extension, professional societies and public service initiatives.

This year’s class of University Faculty Scholars includes:

Ben Callahan


Maddy Bursell publishes “Whole genome analysis of clouded leopard species reveals an ancient divergence and distinct demographic histories”


“Similar to other apex predator species, populations of mainland (Neofelis nebulosa) and Sunda (Neofelis diardi) clouded leopards are declining. Understanding their patterns of genetic variation can provide critical insights on past genetic erosion and a baseline for understanding their long-term conservation needs. As a step toward this goal, we present draft genome assemblies for the two clouded leopard species to quantify their phylogenetic divergence, genome-wide diversity, and historical population trends. We estimate that the two species diverged 5.1 Mya, much earlier than previous estimates of 1.41 Mya and 2.86 Mya, suggesting they separated when Sundaland was becoming increasingly isolated from mainland Southeast Asia. The Sunda clouded leopard displays a distinct and reduced effective population size trajectory, consistent with a lower genome-wide heterozygosity and SNP density, relative to the mainland clouded leopard. Our results provide new insights into the evolutionary history and genetic health of this unique lineage of felids” (Bursell et al., 2022).

Additional details about the genome analysis of the clouded leopard species and Maddy Bursell’s research are described.

Here: https://www.cell.com/iscience/fulltext/S2589-0042(22)01919-8


Professor Benjamin Callahan to receive the ASM’s Microbiome Data Prize for 2023

Benjamin Callahan, BRC member and Associate Professor of Department of Population Health and Pathobiology, has been selected to receive the 2023 Microbiome Data Prize by the American Society for Microbiology. Dr. Callahan is widely known for the development of the DADA2 package for sample inference from amplicon data, which has received over 12.000 citations. More generally, he has been instrumental in developing standard and reproducible workflows for handling metagenomic data.

Callahan joined the faculty of North Carolina State University in Jan. 2017 as a Chancellor’s Faculty Excellence Program cluster hire in microbiomes and complex microbial communities. Callahan’s research program at N.C. State focuses on microbomes and the high-throughput methods used to characterize them, in particular marker-gene and metagenomic sequencing. He develops new statistical and bioinformatic methods to better characterize microbial communities from high-throughput biological data. Callahan uses those methods to study important problems, such as the relationship between the maternal microbiome and preterm birth and the barriers to reproducibility and interoperability between microbiome measurements made in different laboratories. Callahan and his group also develop and support software used by the wider microbiome research community in a wide variety of applications.

Additional details about DADA2 and Dr. Callahan’s research are described here: https://asm.org/Articles/2022/October/Advancing-Microbiome-Data-Analysis-with-Benjamin-C

David Reif named to the U.S. Environmental Protection Agency (EPA) Science Advisory Committee on Chemicals (SACC)

David Reif was named to the U.S. Environmental Protection Agency (EPA) Science Advisory Committee on Chemicals (SACC) for a four-year term by Administrator Michael Regan. The Science Advisory Committee on Chemicals provides independent scientific advice, information and recommendations to the EPA Office of Pollution Prevention and Toxics on the scientific basis for risk assessments, methodologies and pollution prevention measures or approaches. Its major objectives are to provide expert advice and recommendations to the EPA on risk assessments, models, tools, guidance documents, chemical category documents and other chemical assessment and pollution prevention products as deemed appropriate.

The COVID-19 Pandemic Vulnerability Index (PVI)

The COVID-19 Pandemic Vulnerability Index (PVI)

Dr. David Reif has led teams at North Carolina State University, NIEHS, and Texas A&M University in developing the Pandemic Vulnerability Index (PVI) dashboard, which offers a view and real-time analysis of county-level U.S. data on the coronavirus pandemic. “The dashboard helps officials allocate resources and update responses, as well as providing both county-level and a nationwide overview of various statistics” explained Dr. Reif.  The team developed risk profiles, called PVI scorecards, are available for every county in the United States. The resource has now been added to the COVID Data Tracker resources curated on the U.S. Centers for Disease Control and Prevention website

https://covid.cdc.gov/covid-data-tracker/#pandemic-vulnerability-index), and was featured in the Environmental Factor (https://factor.niehs.nih.gov/2021/2/feature/1-feature-pandemic/index.htm)

The original publication appeared  in Environmental Health Perspectives (https://ehp.niehs.nih.gov/doi/10.1289/EHP8690).

Additional NC State co-authors include Dr. Yi-Hui Zhou, Dr. Fred A. Wright, and Kuncheng Song.

Collaboration points to potential dangers of energy drinks

Collaboration points to potential dangers of energy drinks

Dr. Yi-Hui Zhou and colleagues reported on the potential dangers of popular energy drinks in the March 2021 issue of Food and Chemical Toxicology. The study, led by Dr. Ivan Rusyn, a professor in the Veterinary Integrative Biosciences at Texas A&M University, showed that cardiomyocytes – human heart cells grown in a laboratory – exposed to some energy drinks showed an increased beat rate and other factors affecting cardiac function. Dr. Zhou used complex patterns from mass spectrometry to show that certain chemical profiles from the energy drink constituents were associated with aspects such as QT prolongation,  which is associated with serious human heart conditions. “This was a great collaboration showing the power of machine learning methods to learn features of the data that have direct relevance to human health,” explained Dr. Zhou. The project has gained considerable media attention, due to the popularity of energy drinks, which has a $61 billion worldwide market. “Many consumers don’t realize that energy drinks are marketed as regular beverages or dietary supplements, and as such don’t really undergo extensive safety testing” said Dr. Zhou.  “Some ingredients may be available from natural sources but still have worrisome effects on heart function.  Further research should be performed, as some people, even children, consume these drinks every day.”

Link to the article : https://www.sciencedirect.com/science/article/abs/pii/S0278691521000132

Other NC State authors include Fred A. Wright and Erin Baker.

4D- quantitative structure–activity relationship modeling: making a comeback

Predictive Quantitative Structure–Activity Relationship (QSAR) modeling has become an essential methodology for rapidly assessing various properties of chemicals. The vast majority of these QSAR models utilize numerical descriptors derived from the two- and/or three-dimensional structures of molecules. However, the conformation-dependent characteristics of flexible molecules and their dynamic interactions with biological target(s) is/are not encoded by these descriptors, leading to limited prediction performances and reduced interpretability. 2D/3D QSAR models are successful for virtual screening, but typically suffer at lead optimization stages. That is why conformation-dependent 4D-QSAR modeling methods were developed two decades ago. However, these methods have always suffered from the associated computational cost. Recently, 4D-QSAR has been experiencing a significant come-back due to rapid advances in GPU-accelerated molecular dynamic simulations and modern machine learning techniques.

To continue reading this paper click here

Adipocytes as Anticancer Drug Delivery Depot

Tumor-associated adipocytes promote tumor growth by providing energy and causing chronic inflammation. Here, we have exploited the lipid metabolism to engineer adipocytes that serve as a depot to deliver cancer therapeutics at the tumor site. Rumenic acid (RA), as an anticancer fatty acid, and a doxorubicin prodrug (pDox) with a reactive oxygen species (ROS)-cleavable linker, are encapsulated in adipocytes to deliver therapeutics in a tumor-specific bioresponsive manner. After intratumoral or postsurgical administration, lipolysis releases the RA and pDox that is activated by intracellular ROS-responsive conversion, subsequently promoting antitumor efficacy. Furthermore, downregulation of PD-L1 expression is observed in tumor cells, favoring the emergence of CD4+ and CD8+ T cell-mediated immune responses.

To read the rest of this paper, please click here

USDA/NIFA grants awarded to faculty members Drs. David Rasmussen & Benjamin Callahan

Two faculty members, Dr. David Rasmussen and Dr. Benjamin Callahan, were awarded USDA NIFA grants through a new program called FACT: Food and Agricultural Cyberinformatics and Tools Initiative.

Dr. Rasmussen’s project is called, “Next Generation Spatial Epidemiology for Tracking the Spread of Plant Pathogens”.  The main goal is: “To develop the next generation of phylogenetic tools for tracking the spread of plant pathogens ranging from viruses to fungi through complex agricultural landscapes. Since many of these pathogens undergo occasional recombination, another goal is to use information about recombination events across pathogen genomes to identify the spatial location of historical recombination events and the geographic source of particular genes involved in pathogenesis.”

Dr. Callahan’s project is called, “Rapid Detection and Tracking of Foodborne Pathogens with Long-read Amplicon Sequencing”. Food-borne pathogens enact substantial harms on the American people in the form of illness, lost productivity, and expenses related to mitigation and regulatory compliance. Surveillance and tracing of foodborne pathogens is a key control strategy, but its efficacy is reduced by the long-times associated with current culture and whole-genome-sequencing approaches. Rapid, accurate and comprehensive pathogen detection would improve the safety and lower the costs of our food supply.

We aim to develop a targeted metagenomics methodology that can rapidly (<24 hrs) and precisely identify a broad range of foodborne pathogens from heterogeneous environmental samples. In order to achieve this, we propose to combine the GenomeTrakr and NCBI RefSeq databases with cutting-edge bioinformatics tools developed by the PD that achieve single-nucleotide resolution from amplicon sequencing data of full-length genes to identify E. coli and Salmonella strains to the serovar level (e.g. E. coli O157:H7 or S. enterica Heidelberg). We will validate the resolution and accuracy of this new methodology in silico, on isolates of various pathogenic serovars, and in environmental samples of various types for which pathogen presence and identity were previously established by standard culture-based methods. Our methodology will be distributed to the broader food safety community as open-source and actively-supported software, alongside extensive documentation of its efficacy and best-practices guidance. Successful completion of this project will yield a powerful, usable, and broad-spectrum pathogen surveillance technique that will improve food safety by detecting foodborne pathogens before they reach consumers, and by rapidly tracing outbreaks to their source.”

“A Class Approach to Hazard Assessment of Organohalogen Flame Retardants”

A new report from the National Academies of Sciences, Engineering, and Medicine offers guidance to the Consumer Product Safety Commission (CPSC) on how to conduct a hazard assessment of nonpolymeric, additive organohalogen flame retardants (OFRs), which are used in some consumer products.

OFRs cannot be treated as a single class for hazard assessment, the report says, but they can be divided into subclasses based on chemical structure, physical and chemical properties, and predicted biologic activity. The report identifies 14 subclasses that CPSC can use to conduct a class-based hazard assessment of OFRs. Such an approach is likely to be more efficient and less costly than the traditional approach of evaluating each chemical individually, the report notes.

There is mounting evidence that many flame retardants are associated with adverse human health effects, and some flame retardants have been banned, restricted, or voluntarily phased out of use. A coalition of organizations and individuals petitioned CPSC to initiate regulatory action to ban use of OFRs in four product categories: infant, toddler, or children’s products; upholstered furniture; mattresses; and plastic electronic casings. The petitioners argued that the entire chemical class is toxic and poses a risk to consumers.

CPSC voted to grant the petition, but in order to decide whether a ban should be enacted, the agency must first conduct a hazard assessment to determine whether a chemical is toxic. CPSC asked the National Academies for guidance on how to conduct the hazard assessment for OFRs as a chemical class.

The National Academies study committee first conducted an analysis to determine whether OFRs can be treated as a single class. This involved identifying known OFRs and other structurally related organohalogen compounds. The committee found that OFRs cannot be distinguished as a single class from these other chemically similar analogues. In addition, OFRs do not have a common chemical structure or predicted biologic activity and therefore cannot be treated as a single class.

However, an approach that uses subclasses to assess the chemicals is scientifically justifiable, the committee determined.  The report outlines a process for assessing the toxicity of the 14 identified subclasses and identifies four scenarios that might occur, depending on how much data is available for the chemicals in a subclass. The report also uses two subclasses to illustrate how the proposed approach to the hazard assessment would work.

A multidisciplinary group will be needed to execute the hazard assessment, the report says. Needed expertise includes cheminformatics, computational chemistry, computational toxicology, traditional and modern toxicology, epidemiology, and risk assessment. Furthermore, integrating the evidence at various steps will require expert judgment, and policy decisions involving value judgments – for example, about what health endpoints to investigate and how much uncertainty is acceptable – will be needed to complete the assessment.

The study — undertaken by the Committee to Develop a Scoping Plan to Assess the Hazards of Organohalogen Flame Retardants — was sponsored by the Consumer Product Safety Commission. The National Academies are private, nonprofit institutions that provide independent, objective analysis and advice to the nation to solve complex problems and inform public policy decisions related to science, technology, and medicine. They operate under an 1863 congressional charter to the National Academy of Sciences, signed by President Lincoln. For more information, visit nationalacademies.org.

Visit the original press release here