Biology subjects

Wafula, E.

Publications and source records attributed to Wafula, E..

3 recordsLinked to original sources

bioRxiv2025

SWANS: A highly configurable analysis pipeline for single-cell and single-nuclei RNA-sequencing data

BackgroundSingle-cell RNA sequencing (scRNA-seq) is a powerful technique that enables the analysis of gene expression at the individual cell level. Bioinformatic tools for scRNA-seq data analysis have many different options throughout the typical scRNA-seq workflow (normalization, integration, annotation, clustering, and visualization), and the choice of method(s) and parameter(s) at each stage can impact results. ResultsHere, we introduce SWANS (v2.0), a configurable analysis pipeline that, in a single run, can employ multiple analysis methods, resolutions, and modifiable parameters. The resulting clustering arrangements, differential gene expression results, and other quantitative measurements can be dynamically visualized and compared in a Shiny interactive report to assist in choosing a single analysis schema for annotation and downstream analysis. Once a final approach is chosen, SWANS will perform differential gene expression (DGE) analysis based on experimental conditions and gene set enrichment analysis (GSEA) in addition to creating reports that display figures and interactive tables, quality control metrics, and benchmarking information. SWANS uses Snakemake as a workflow manager, Cell Ranger for alignment and gene expression quantification, Seurat for single cell data analysis, and additional single cell R packages for quality control and downstream single cell analysis. ConclusionSWANS is a tailorable pipeline that provides options for quality control, dimensionality reduction, clustering, differential gene expression analysis, gene set enrichment analysis, and trajectory analysis. Additionally, SWANS generates a series of reports that facilitate sharing large volumes of complex data in a clear and concise manner with other investigators.

bioinformatics↗

bioRxiv2024

The Open Pediatric Cancer Project

BackgroundIn 2019, the Open Pediatric Brain Tumor Atlas (OpenPBTA) was created as a global, collaborative open-science initiative to genomically characterize 1,074 pediatric brain tumors and 22 patient-derived cell lines. Here, we present an extension of the OpenPBTA called the Open Pediatric Cancer (OpenPedCan) Project, a harmonized open-source multi-omic dataset from 6,112 pediatric cancer patients with 7,096 tumor events across more than 100 histologies. Combined with RNA-Seq from the Genotype-Tissue Expression (GTEx) and The Cancer Genome Atlas (TCGA), OpenPedCan contains nearly 48,000 total biospecimens (24,002 tumor and 23,893 normal specimens). FindingsWe utilized Gabriella Miller Kids First (GMKF) workflows to harmonize WGS, WXS, RNA-seq, and Targeted Sequencing datasets to include somatic SNVs, InDels, CNVs, SVs, RNA expression, fusions, and splice variants. We integrated summarized CPTAC whole cell proteomics and phospho-proteomics data, miRNA-Seq data, and have developed a methylation array harmonization workflow to include m-values, beta-vales, and copy number calls. OpenPedCan contains reproducible, dockerized workflows in GitHub, CAVATICA, and Amazon Web Services (AWS) to deliver harmonized and processed data from over 60 scalable modules which can be leveraged both locally and on AWS. The processed data are released in a versioned manner and accessible through CAVATICA or AWS S3 download (from GitHub), and queryable through PedcBioPortal and the NCIs pediatric Molecular Targets Platform. Notably, we have expanded PBTA molecular subtyping to include methylation information to align with the WHO 2021 Central Nervous System Tumor classifications, allowing us to create research-grade integrated diagnoses for these tumors. ConclusionsOpenPedCan data and its reproducible analysis module framework are openly available and can be utilized and/or adapted by researchers to accelerate discovery, validation, and clinical translation.

genomics↗

bioRxiv2017

MicroRNAs from the parasitic plant Cuscuta campestris target host messenger RNAs

First paragraphDodders (Cuscuta spp.) are obligate parasitic plants that obtain water and nutrients from the stems of host plants via specialized feeding structures called haustoria. Dodder haustoria facilitate bi-directional movement of viruses, proteins, and mRNAs between host and parasite1, but the functional effects of these movements are not clear. Here we show that C. campestris haustoria accumulate high levels of many novel microRNAs (miRNAs) while parasitizing Arabidopsis thaliana hosts. Many of these miRNAs are 22 nts long, a usually rare size of plant miRNA associated with amplification of target silencing through secondary small interfering RNA (siRNA) production2. Several A. thaliana mRNAs are targeted by C. campestris 22 nt miRNAs during parasitism, resulting in mRNA cleavage, secondary siRNA production, and decreased mRNA accumulation levels. Hosts with mutations in two of the targets supported significantly higher growth of C. campestris. Homologs of target mRNAs from diverse plants also have predicted target sites to induced C. campestris miRNAs, and the same miRNAs are expressed and active against host targets when C. campestris parasitizes a different host, Nicotiana benthamiana. These data show that C. campestris miRNAs act as trans-species regulators of host gene expression, and suggest that they may act as virulence factors during parasitism.

plant biology↗