Bioinformatics Research Center

Recent Works

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Sorted by most recent date added to the index first, which may not be the same as publication date order.

2025 article

VILMIR is a trans-acting long noncoding RNA that enhances the host interferon response in human epithelial cells

John, K., Smith, E., Istishin, A., Mahmood, N., Diveley, K., Tollison, T. S., … Peng, X. (2025, August 22).

By: K. John, E. Smith, A. Istishin, N. Mahmood, K. Diveley, T. Tollison, S. Carpenter, X. Peng

topics (OpenAlex):
Source: ORCID
Added: August 22, 2025

2025 article

Active regulation of the epidermal growth factor receptor by the membrane bilayer

Srinivasan, S., Lin, X., Chen, X., Regmi, R., Zhang, B., & Schlau-Cohen, G. S. (2025, August 18).

By: S. Srinivasan, X. Lin, X. Chen, R. Regmi, B. Zhang & G. Schlau-Cohen

topics (OpenAlex):
Source: ORCID
Added: August 19, 2025

2025 article

Phased chromosome-level assembly provides insight into the genome architecture of hexaploid sweetpotato

Wu, S., Sun, H., Zhao, X., Hamilton, J. P., Mollinari, M., Gesteira, G. D. S., … Fei, Z. (2025, August 8). NATURE PLANTS.

co-author countries: China 🇨🇳
topics (OpenAlex): Plant Virus Research Studies; Chromosomal and Genetic Variations; Cocoa and Sweet Potato Agronomy
Sources: Web Of Science, NC State University Libraries
Added: August 18, 2025

2025 article

KeySDL: Sparse Dictionary Learning for Keystone Microbe Identification

Gordon, M., Akyol, T. Y., Amos, B., Andersen, S. U., & Williams, C. (2025, August 11).

By: M. Gordon, T. Akyol, B. Amos, S. Andersen & C. Williams

topics (OpenAlex):
Source: ORCID
Added: August 15, 2025

2025 journal article

Cervicovaginal microbial features predict Chlamydia trachomatis spread to the upper genital tract of infected women

Infection and Immunity.

By: S. Jeong, T. Tollison, H. Brochu, H. Chou, I. Huntress, K. Yount, X. Zheng, T. Darville, C. O'Connell, X. Peng

Ed(s): M. Raffatellu

topics (OpenAlex):
Source: ORCID
Added: August 12, 2025

2025 journal article

No more laborious stem counting: AI-powered computer vision enables identification and quantification of solid and hollow alfalfa stems at the pixel level

Smart Agricultural Technology.

By: B. Weihs, Z. Tang, S. Roy, Z. Tian, D. Heuschele, Z. Zhang, C. Williams*, Z. Zhang ...

topics (OpenAlex): Industrial Vision Systems and Defect Detection; Smart Agriculture and AI; Spectroscopy and Chemometric Analyses
Source: ORCID
Added: August 8, 2025

2025 journal article

High-throughput classification and quantification of skinning phenotype in sweet potatoes

PLANT PHENOME JOURNAL, 8(1).

topics (OpenAlex): Postharvest Quality and Shelf Life Management; Plant tissue culture and regeneration; Plant Virus Research Studies
Sources: Web Of Science, ORCID, NC State University Libraries
Added: August 4, 2025

2025 journal article

Experimental Evolution of <i>Phytophthora infestans</i> on Tomato Reveals Rapid Genotypic and Phenotypic Adaptation and Dynamic RXLR Genome Variation

Coomber, A., Rasmussen, D. A., & Ristaino, J. B. (2025, July 31). PHYTOPATHOLOGY, Vol. 7.

By: A. Coomber n, D. Rasmussen n & J. Ristaino n

author keywords: adaptation; experimental evolution; genomics; late blight; <italic>Phytophthora</italic>; RXLR; targeted sequencing; tomato
MeSH headings : Phytophthora infestans / genetics; Phytophthora infestans / physiology; Solanum lycopersicum / microbiology; Plant Diseases / microbiology; Plant Diseases / parasitology; Genotype; Phenotype; Genetic Variation; Adaptation, Physiological
topics (OpenAlex): Plant Pathogens and Resistance; Plant Disease Resistance and Genetics; Plant-Microbe Interactions and Immunity
Sources: ORCID, Web Of Science, NC State University Libraries, Crossref
Added: July 31, 2025

2025 article

Genomic Evaluation of Canine Prostatic Carcinomas as a Model for the Human Disease

Thomas, R., Luff, J. A., Dickey, A. N., Dillon, M. N., Livingston, I. G., Schrag, C. A., … Breen, M. (2025, July 23). VETERINARY AND COMPARATIVE ONCOLOGY, Vol. 7.

By: R. Thomas n, J. Luff n, A. Dickey n, M. Dillon n, I. Livingston n, C. Schrag n, S. Suter n, M. Breen n

author keywords: adenocarcinoma; DNA copy number variations; dogs; mutation; prostatic neoplasms; urologic neoplasms
topics (OpenAlex): Veterinary Oncology Research; Veterinary Medicine and Surgery; Human-Animal Interaction Studies
UN Sustainable Development Goals Color Wheel
UN Sustainable Development Goal Categories
3. Good Health and Well-being (OpenAlex)
Sources: Web Of Science, NC State University Libraries
Added: July 28, 2025

2025 journal article

Spiner, deep learning-based automated detection of spiral ganglion neurons in intact cochleae

ISCIENCE, 28(7).

By: Y. Cai n, G. Leitz-Najarian*, R. Rosen n, K. Hutson*, A. Moatti n, C. Li n, D. Fitzpatrick*, A. Greenbaum n

topics (OpenAlex): Hearing Loss and Rehabilitation; Hearing, Cochlea, Tinnitus, Genetics; Structural Health Monitoring Techniques
Source: Web Of Science
Added: July 28, 2025

2025 journal article

Genetic effects on chromatin accessibility uncover mechanisms of liver gene regulation and quantitative traits

GENOME RESEARCH, 35(7), 1485–1502.

MeSH headings : Humans; Quantitative Trait Loci; Liver / metabolism; Chromatin / genetics; Chromatin / metabolism; Genome-Wide Association Study; Gene Expression Regulation; Transcription Factors / metabolism; Binding Sites; Polymorphism, Single Nucleotide
topics (OpenAlex): Epigenetics and DNA Methylation; Genomics and Chromatin Dynamics; Genetics and Neurodevelopmental Disorders
Source: Web Of Science
Added: July 21, 2025

2025 journal article

Signature gene expression model for quantitative evaluation of MASH-like liver injury in mice☆

TOXICOLOGY AND APPLIED PHARMACOLOGY, 502.

co-author countries: Canada 🇨🇦
author keywords: Mice; MASH; Liver Pathology; Transcriptomics; Machine Leaning Pathologist Assistance
MeSH headings : Animals; Male; Female; Mice; Disease Models, Animal; Diet, High-Fat / adverse effects; Liver / pathology; Liver / metabolism; Transcriptome; Gene Expression Profiling / methods; Collaborative Cross Mice; Fatty Liver / genetics; Fatty Liver / pathology; Fatty Liver / metabolism; Non-alcoholic Fatty Liver Disease / genetics; Non-alcoholic Fatty Liver Disease / pathology
topics (OpenAlex): Liver Disease Diagnosis and Treatment; Endoplasmic Reticulum Stress and Disease; Hepatocellular Carcinoma Treatment and Prognosis
Source: Web Of Science
Added: July 21, 2025

2025 journal article

Spatiotemporal dynamics of NF-κB/Dorsal inhibitor IκBα/Cactus in<i> Drosophila</i> blastoderm embryos

ISCIENCE, 28(7).

By: A. Schloop n, S. Hiremath n, R. Shaikh*, A. Bhakta*, C. Williams n, G. Reeves*, A. Schloop, S. Hiremath ...

topics (OpenAlex): Botanical Research and Applications; Neurobiology and Insect Physiology Research; Bioactive natural compounds
Sources: Web Of Science, NC State University Libraries
Added: July 21, 2025

2025 journal article

Interpretable protein-DNA interactions captured by structure-sequence optimization

ELife.

By: Y. Zhang, I. Silvernail, Z. Lin & X. Lin

topics (OpenAlex):
Source: ORCID
Added: July 17, 2025

2025 journal article

NIAGADS: A data repository for Alzheimer's disease and related dementia genomics

ALZHEIMERS & DEMENTIA, 21(6).

By: A. Kuzma*, O. Valladares*, E. Greenfest-Allen*, H. Nicaretta*, M. Kirsch*, Y. Ren*, Z. Katanic*, H. White* ...

author keywords: Alzheimer's disease; Alzheimer's disease and related dementias; Alzheimer's Disease Sequencing Project; bioinformatics; data repository; dementia; genetics; genomics; National Institute on Aging Genetics of Alzheimer's Disease Data Storage Site; open access; qualified access; sequencing
MeSH headings : Humans; Alzheimer Disease / genetics; Genomics; United States; Databases, Genetic; National Institute on Aging (U.S.); Dementia / genetics; Genome-Wide Association Study; Information Dissemination
topics (OpenAlex): Genomics and Rare Diseases; Bioinformatics and Genomic Networks; Epigenetics and DNA Methylation
Sources: Web Of Science, NC State University Libraries
Added: July 17, 2025

2025 journal article

Structural variation detection and association analysis of whole-genome-sequence data from 16,543 Alzheimer's disease sequencing project subjects

ALZHEIMERS & DEMENTIA, 21(6).

By: H. Wang*, B. Dombroski*, P. Cheng*, A. Tucci n, Y. Si n, J. Farrell*, J. Tzeng n, Y. Leung* ...

author keywords: Alzheimer's disease; copy number variation; NCK2; RNA5SP293; structural variation
MeSH headings : Humans; Alzheimer Disease / genetics; Whole Genome Sequencing; Genetic Predisposition to Disease / genetics; LDL-Receptor Related Proteins / genetics; ATP-Binding Cassette Transporters / genetics; Membrane Transport Proteins / genetics; Male; Polymorphism, Single Nucleotide; Female; Linkage Disequilibrium; Amyloid beta-Protein Precursor / genetics; Genome-Wide Association Study
topics (OpenAlex): Genomics and Rare Diseases; RNA Research and Splicing; Genetic Associations and Epidemiology
Sources: Web Of Science, NC State University Libraries
Added: July 17, 2025

2025 article

A network perspective on the evolution of hybrid incompatibilities

Brud, E., & Guerrero, R. F. (2025, July 15).

By: E. Brud & R. Guerrero

topics (OpenAlex): Complex Network Analysis Techniques; Bioinformatics and Genomic Networks; Peer-to-Peer Network Technologies
Source: ORCID
Added: July 15, 2025

2025 journal article

Yeast Surface Display of Protein Addresses Confers Robust Storage and Access of DNA-Based Data

DNA.

By: M. Lee n, G. Brihadiswaran n, B. Rao n, J. Tuck n & A. Keung n

topics (OpenAlex): DNA and Biological Computing; Genomics and Chromatin Dynamics; Gene expression and cancer classification
Source: ORCID
Added: July 11, 2025

2025 article

Optimizing genomic sampling for demographic and epidemiological inference with Markov decision processes

Rasmussen, D. A., Bursell, M. G., & Burkhart, F. (2025, July 4).

By: D. Rasmussen, M. Bursell & F. Burkhart

topics (OpenAlex): Bayesian Methods and Mixture Models; Statistical Methods and Inference; Artificial Intelligence in Healthcare
Source: ORCID
Added: July 4, 2025

2025 article

Guidelines for preventing and reporting contamination in low-biomass microbiome studies

Fierer, N., Leung, P. M., Lappan, R., Eisenhofer, R., Ricci, F., Holland, S. I., … Greening, C. (2025, June 20). NATURE MICROBIOLOGY, Vol. 6.

co-author countries: Australia 🇦🇺 Canada 🇨🇦 Chile 🇨🇱 China 🇨🇳 Germany 🇩🇪 Denmark 🇩🇰 France 🇫🇷 United Kingdom of Great Britain and Northern Ireland 🇬🇧 Japan 🇯🇵 Singapore 🇸🇬 South Africa 🇿🇦
topics (OpenAlex): Gut microbiota and health; Molecular Biology Techniques and Applications; Microbial Community Ecology and Physiology
UN Sustainable Development Goals Color Wheel
UN Sustainable Development Goal Categories
2. Zero Hunger (OpenAlex)
Sources: Web Of Science, NC State University Libraries
Added: June 30, 2025

2025 article

Knowledge and Opportunities for Managing Plant-Parasitic Nematodes Using Decision Intelligence

Roberts, D. L., Gorny, A., Jones, D. S., Kudenov, M. W., Pratt, L., Malcolm, N., & Williams, C. (2025, June 18). PHYTOFRONTIERS, Vol. 6.

By: D. Roberts n, A. Gorny n, D. Jones n, M. Kudenov n, L. Pratt, N. Malcolm, C. Williams n

author keywords: data science; decision; decision intelligence; modelling; nematodes
topics (OpenAlex): Statistical Methods and Applications; Technology Adoption and User Behaviour
Sources: Web Of Science, ORCID, NC State University Libraries
Added: June 30, 2025

2025 journal article

Optimization of Adventitious Shoot Regeneration Protocols for Six<i> Vaccinium corymbosum </i>Cultivars

HORTSCIENCE, 60(7), 1109–1117.

By: F. Kelso n, K. Da n, R. Dewey n, D. Reiland n, C. Almeyda n, W. Liu n, H. Ashrafi n

author keywords: blueberry; genotype-independent regeneration; tissue culture recalcitrance; 2iP; zeatin
topics (OpenAlex): Plant tissue culture and regeneration; Plant Pathogens and Fungal Diseases; Berry genetics and cultivation research
Sources: Web Of Science, NC State University Libraries
Added: June 30, 2025

2025 article

Minus the Error: Testing for Positive Selection in the Presence of Residual Alignment Errors

Selberg, A., Clark, N. L., Sackton, T. B., Muse, S. V., Lucaci, A. G., Weaver, S., … Pond, S. L. K. (2025, June 26).

By: A. Selberg, N. Clark, T. Sackton, S. Muse, A. Lucaci, S. Weaver, A. Nekrutenko, M. Chikina, S. Pond

topics (OpenAlex): Advanced Statistical Methods and Models
Source: ORCID
Added: June 26, 2025

2025 article

Minus the Error: Testing for Positive Selection in the Presence of Residual Alignment Errors

Selberg, A., Clark, N. L., Sackton, T. B., Muse, S. V., Lucaci, A. G., Weaver, S., … Pond, S. L. K. (2025, June 26).

By: A. Selberg, N. Clark, T. Sackton, S. Muse, A. Lucaci, S. Weaver, A. Nekrutenko, M. Chikina, S. Pond

topics (OpenAlex): Advanced Statistical Methods and Models
Source: ORCID
Added: June 26, 2025

2025 journal article

Characterizing DNA recognition preferences of transcription factors using global couplings and high-throughput sequencing

NUCLEIC ACIDS RESEARCH, 53(12).

By: Q. Zhou, J. Paz, A. Stanowick, X. Lin & F. Morcos

topics (OpenAlex):
Sources: ORCID, Web Of Science, NC State University Libraries
Added: June 15, 2025

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