Ion Măndoiu

SC1: A Tool for Interactive Web-Based Single Cell RNA-Seq Data Analysis

SC1 is a web-based tool for scRNA-Seq analysis that offers interactive workflows, gene selection via TF-IDF, clustering, differential expression, and visualization.

Computational cell cycle analysis of single cell RNA-Seq data

This paper introduces SC1CC, a tool for clustering and ordering single cell RNA-Seq data by cell cycle phase using a new metric called Gene Smoothness Score.

TreeFix-TP: Phylogenetic Error-Correction for Infectious Disease Transmission Network Inference

TreeFix-TP improves transmission phylogeny inference by correcting phylogenetic errors using intra-host diversity and host information, enhancing accuracy in outbreak analysis.

SMART: Statistical Mitogenome Assembly with Repeats

SMART improves mitochondrial genome assembly from WGS data by addressing coverage differences and repeats, achieving higher success rates than existing tools.

Locality Sensitive Imputation for Single-Cell RNA-Seq Data

The paper evaluates existing scRNA-Seq imputation methods and introduces a novel iterative approach based on similar cells, assessing performance on real datasets with varying sequencing depth.

CircMarker: A Fast and Accurate Algorithm for Circular RNA Detection

CircMarker detects circular RNA using k-mers instead of read mapping, achieving higher accuracy and efficiency than existing tools.