Characterization of vaginal microbiomes in clinician-collected bacterial vaginosis diagnosed samples

Authors: Hayden N. Brochu, Qimin Zhang, Kuncheng Song, Ling Wang, Emily A. Deare, Jonathan D. Williams, Crystal R. Icenhour, Lakshmanan K. Iyer

Source: Microbiology Spectrum, Vol 13, Iss 4 (2025)

Subject Terms: bacterial vaginosis, vaginal microbiome, 16S rRNA, Microbiology, QR1-502

File Description: electronic resource

Relation: https://doaj.org/toc/2165-0497

Access URL: https://doaj.org/article/955912da29334e16a7dbf6af846f72c1

A program for real-time surveillance of SARS-CoV-2 genetics

Authors: Hayden N. Brochu, Kuncheng Song, Qimin Zhang, Qiandong Zeng, Adib Shafi, Matthew Robinson, Jake Humphrey, Bobbi Croy, Lydia Peavy, Minoli Perera, Scott Parker, John Pruitt, Jason Munroe, Rama Ghatti, Thomas J. Urban, Ayla B. Harris, David Alfego, Brian Norvell, Michael Levandoski, Brian Krueger, Jonathan D. Williams, Deborah Boles, Melinda B. Nye, Suzanne E. Dale, Michael Sapeta, Christos J. Petropoulos, Jonathan Meltzer, Marcia Eisenberg, Oren Cohen, Stanley Letovsky, Lakshmanan K. Iyer

Source: Scientific Reports, Vol 14, Iss 1, Pp 1-15 (2024)

Subject Terms: Medicine, Science

File Description: electronic resource

Relation: https://doaj.org/toc/2045-2322

Access URL: https://doaj.org/article/9fe54c9c14ac49e5854ada0811ba5483

Functional annotation of proteins for signaling network inference in non-model species

Authors: Lisa Van den Broeck, Dinesh Kiran Bhosale, Kuncheng Song, Cássio Flavio Fonseca de Lima, Michael Ashley, Tingting Zhu, Shanshuo Zhu, Brigitte Van De Cotte, Pia Neyt, Anna C. Ortiz, Tiffany R. Sikes, Jonas Aper, Peter Lootens, Anna M. Locke, Ive De Smet, Rosangela Sozzani

Source: Nature Communications, Vol 14, Iss 1, Pp 1-14 (2023)

Subject Terms: Science

File Description: electronic resource

Relation: https://doaj.org/toc/2041-1723

Access URL: https://doaj.org/article/d4b2817c52f34a10ac17fd0675610d4d

C3NA: correlation and consensus-based cross-taxonomy network analysis for compositional microbial data

Authors: Kuncheng Song, Yi-Hui Zhou

Source: BMC Bioinformatics, Vol 23, Iss 1, Pp 1-16 (2022)

Subject Terms: Co-occurrence network analysis, Microbiome, R package, Consensus clustering, Module preservation analysis, Computer applications to medicine. Medical informatics, R858-859.7, Biology (General), QH301-705.5

File Description: electronic resource

Relation: https://doaj.org/toc/1471-2105

Access URL: https://doaj.org/article/b7a68942605745c086ca7b5c0d69a035

An In Silico Analysis of PCR-Based Monkeypox Virus Detection Assays: A Case Study for Ongoing Clinical Surveillance

Authors: Kuncheng Song, Hayden N. Brochu, Qimin Zhang, Jonathan D. Williams, Lakshmanan K. Iyer

Source: Viruses, Vol 15, Iss 12, p 2327 (2023)

Subject Terms: monkeypox virus, monkeypox, poxvirus, quantitative polymerase chain reaction, in silico analysis, Microbiology, QR1-502

File Description: electronic resource

Relation: https://www.mdpi.com/1999-4915/15/12/2327; https://doaj.org/toc/1999-4915

Access URL: https://doaj.org/article/5d63cab16c87444d9be57737aefac52a

Leveraging Scheme for Cross-Study Microbiome Machine Learning Prediction and Feature Evaluations

Authors: Kuncheng Song, Yi-Hui Zhou

Source: Bioengineering, Vol 10, Iss 2, p 231 (2023)

Subject Terms: feature selection, machine learning, microbiome, random forest, support vector machine, logistic regression, Technology, Biology (General), QH301-705.5

File Description: electronic resource

Relation: https://www.mdpi.com/2306-5354/10/2/231; https://doaj.org/toc/2306-5354

Access URL: https://doaj.org/article/38412581d1254a1ab1879c11d5caaa69

Systematic Comparisons for Composition Profiles, Taxonomic Levels, and Machine Learning Methods for Microbiome-Based Disease Prediction

Authors: Kuncheng Song, Fred A. Wright, Yi-Hui Zhou

Source: Frontiers in Molecular Biosciences, Vol 7 (2020)

Subject Terms: phenotype prediction, machine learning method, k-mers, operational taxonomic unit (OTU), amplicon sequence variant (ASV), phylogenetic analysis, Biology (General), QH301-705.5

File Description: electronic resource

Relation: https://www.frontiersin.org/articles/10.3389/fmolb.2020.610845/full; https://doaj.org/toc/2296-889X

Access URL: https://doaj.org/article/ecfa8f06a7794a2b8128ef06cab5a628