Biology subjects

Sheldon, K.

Publications and source records attributed to Sheldon, K..

5 recordsLinked to original sources

bioRxiv2026

GROQ-seq Datasets Across Transcription Factors (LacI, RamR, VanR), T7 RNA Polymerase and TEV Protease

Predicting any proteins function from its sequence alone would be a significant breakthrough in molecular biology. Although machine learning approaches have sought to tackle this, their limited generalizability reflects the absence of sufficiently large, open, diverse, and unified datasets. To address this data gap, we developed a high-throughput experimental platform called GROQ-seq (Growth-based Quantitative Sequencing). In GROQ-seq, a proteins function can be linked to a sequencing-based readout that enables scalable characterization of large variant libraries in Escherichia coli. Here, we present pilot datasets demonstrating its performance across three distinct protein function classes: transcription factors, polymerases, and proteases. The objective of this report is to present the datasets and to provide users with a clear and transparent characterization of their properties, including both the strengths and limitations.

bioengineering↗

bioRxiv2026

GROQ-seq Enables Cross-site Reproducibility for High-Throughput Measurement of Protein Function

High-throughput functional assays are increasingly used to generate large-scale protein function datasets for protein engineering and machine learning applications. However, the utility of such datasets depends on the reproducibility of the underlying measurements. Here we report reproducible, quantitative measurements of protein sequence-to-function data at scale across two facilities. We analyze GROQ-seq (Growth-based Quantitative Sequencing) measurements of three bacterial transcription factors. Independent barcode measurements of the same sequence produce highly consistent functional estimates, demonstrating strong biological reproducibility (across all transcription factors the mean Root Mean Square Deviation [RMSD] {approx} 0.53 and mean Spearman {approx} 0.63). We also compared experiments performed at two facilities using a shared protocol, but with differing levels of automation and system integration. We observe strong agreement between measurements taken at the two sites (mean RMSD {approx} 0.41 and mean Spearman {approx} 0.730). Orthogonal tests further support this agreement: a classifier trained to distinguish data by site performs near random (AUC = 0.559), and top-ranking variants show strong statistical overlap between experiments. Together, these results demonstrate that GROQ-seq enables reproducible, scalable measurement of protein function suitable for large aggregated datasets.

bioengineering↗

bioRxiv2024

Genome Instability Precedes Viral Integration in Human Papilloma Virus Transformed Tonsillar Keratinocytes

Approximately 70% of oropharyngeal squamous carcinomas (OPSCC) are associated with human papillomavirus (HPV). While HPV-positive (HPV+) OPSCC responds better to standard therapies and patients with HPV+ tumor generally have better outcomes than those with HPV-negative (HPV-) tumors, a subset of HPV+ patients do have poor outcomes. Our previous work suggested that tumors with integrated virus exhibit significantly greater genome wide genomic instability than those with only episomal viral genomes and patients with HPV+ OPSCC with episomal viral genomes had better outcomes. To explore the causal relation between viral integration and genomic instability, we have examined the time course of viral integration and genetic instability in tonsillar keratinocytes transformed with HPV16. HPV-infected human tonsil keratinocyte cell lines were continuously passaged and every fifth passage some cells were retained for genomic analysis. Whole genome sequencing and optical genomic mapping confirmed that virus integrated in five of six cell lines while remaining episomal in the sixth. In all lines genome instability occurred during early passages, but essentially ceased following viral integration but continued to occur later passages in the episomal line. To test tumorigenicity of the cell lines, cells were injected subcutaneously into the flanks of nude mice. A cell line with the integrated virus induced tumors following injection in the nude mouse while that with the episomal virus did not. We conclude that genomic instability is not the result of viral integration but likely promotes integration. Moreover, those transformants with episomal virus appear to be less tumorigenic than those with integrated virus.

cancer biology↗

bioRxiv2020

Vaginal Microbiome Topic Modelling of Laboring Ugandan Women With and Without Fever

The composition of the maternal vaginal microbiome may influence the duration of pregnancy, onset of labor and even neonatal outcomes. Maternal microbiome research in sub Saharan-Africa has focused on non-pregnant and postpartum composition of the vaginal microbiome. We examined the vaginal microbiome composition of 99 laboring Ugandan women using routine microbiology and 16S ribosomal DNA sequencing from two hypervariable regions (V1-V2 and V3-V4), using standard hierarchical methods. We then introduce Grades of Membership (GoM) modeling for the vaginal microbiome, a method often used in the text mining machine learning literature. Leveraging GoM models, we create a basis composed of a small number of microbial topics whose linear combination optimally represents each patient yielding more accurate associations. We identified relationships between defined communities and the presentation or absence of intrapartum fever. Using a random forest model we showed that by including novel microbial topic models we improved upon clinical variables to predict maternal fever. We also show by integrating clinical variables with a microbial topic model into this model found young maternal age, fever report earlier in the current pregnancy, and longer labors, as well as a more diverse, less Lactobacillus dominated microbiome were features of labor associated with intrapartum fever. These results better define relationships between presentation or absence of intrapartum fever, demographics, peripartum course, and vaginal microbial communities, and improve our understanding of the impact of the microbiome on maternal and neonatal infection risk.

genomics↗

bioRxiv2019

An Integrated Framework for Genome Analysis Reveals Numerous Previously Unrecognizable Structural Variants in Leukemia Patients' Samples

While genomic analysis of tumors has stimulated major advances in cancer diagnosis, prognosis and treatment, current methods fail to identify a large fraction of somatic structural variants in tumors. We have applied a combination of whole genome sequencing and optical genome mapping to a number of adult and pediatric leukemia samples, which revealed in each of these samples a large number of structural variants not recognizable by current tools of genomic analyses. We developed computational methods to determine which of those variants likely arose as somatic mutations. The method identified 97% of the structural variants previously reported by karyotype analysis of these samples and revealed an additional fivefold more such somatic rearrangements. The method identified on average tens of previously unrecognizable inversions and duplications and hundreds of previously unrecognizable insertions and deletions. These structural variants recurrently affected a number of leukemia associated genes as well as cancer driver genes not previously associated with leukemia and genes not previously associated with cancer. A number of variants only affected intergenic regions but caused cis-acting alterations in expression of neighboring genes. Analysis of TCGA data indicates that the status of several of the recurrently mutated genes identified in this study significantly affect survival of AML patients. Our results suggest that current genomic analysis methods fail to identify a majority of structural variants in leukemia samples and this lacunae may hamper diagnostic and prognostic efforts.

genomics↗