A workflow for phylogenomic analysis based on single-cell RNA sequencing 

Working with ciliate and other microbial eukaryotic genomic and transcriptomic data requires bioinformatic expertise to identify orthologs and paralogs. To overcome this challenge, as a postdoc at Smith College, I developed a workflow that can be adapted for phylogenomic analyses based on single-cell RNA sequencing of uncultivable microbial eukaryotes

https://github.com/shahed30/Phylogenomic-pipeline-for-microbial-eukaryotes 

Shazib, S. U. A., Ahsan, R., Leleu, M., McManus, G. B., Katz, L. A., & Santoferrara, L. F. (2025). Phylogenomic workflow for uncultivable microbial eukaryotes using single-cell RNA sequencing− A case study with planktonic ciliates (Ciliophora, Oligotrichea). Molecular Phylogenetics and Evolution, 108239. (weblink).

A workflow for species delimitation using a multispecies coalescent approach and scRNA-seq data

We also developed workflows

1. To define species boundaries among microbial eukaryotes, specifically focusing on cryptic species at the molecular level using the Morphological Species Concept (MSC) approach and single-cell RNA sequencing (scRNA-seq) data.  (Part A and B)

2. To reconstruct nuclear ribosomal RNA gene sequences from transcriptome data using a read mapping approach. Additionally, we compare various mapping methods to confirm the reconstruction of reliable contigs. (Part C) - SeqToDNA