Jorge Duitama

Breast Cancer Clustering Integrating Complete Gene Expression Profiles and Genetic Ancestry

This study integrates genetic ancestry and bulk RNA-seq data to subtype breast cancer, identifying three clusters with distinct biological and therapeutic characteristics.

Genic Position and Methylation Context Shape DNA Methylation-Expression Relationships in Rice Internode Development

The paper investigates DNA methylation-expression relationships in rice internode development using RNA-seq and bisulfite sequencing, finding specific methylation contexts correlate with gene expression patterns.

Single Cell Transcriptomics of Refractory Epilepsy patients in Colombia

This study analyzes single-cell transcriptomics data from five pediatric refractory epilepsy patients in Colombia, identifying glia-driven dysregulation and neuroinflammatory processes.

New algorithms for unsupervised cell clusteringfrom scRNA-seq data

This paper introduces new algorithms for clustering scRNA-seq data, showing competitive accuracy and highlighting factors affecting performance.

QTL Mapping for Pod Quality and Yield Traits in Snap Bean (Phaseolus vulgaris L.)

This study identifies QTL for pod quality and yield traits in snap bean using a RIL population, finding 44 QTL across chromosomes with some novel and overlapping with previous studies.

A graph clustering algorithm for detection and genotyping of structural variants from long reads

This paper introduces a graph clustering algorithm for detecting and genotyping structural variants from long-read sequencing data, achieving high accuracy in benchmark tests.

A nearly complete and phased genome assembly of a Colombian Trypanosoma cruzi TcI strain and the evolution of gene families

The paper presents a chromosome-level phased genome assembly of a T. cruzi strain and analyzes gene family evolution and genomic variation.

New algorithms for accurate and efficient de-novo genome assembly from long DNA sequencing reads

This paper introduces new algorithms for de-novo genome assembly from long DNA reads, showing competitive efficiency and accuracy across multiple species.

NGSEP 4: Efficient and Accurate Identification of Orthogroups and Whole Genome Alignment

NGSEP 4 improves orthogroup identification and whole genome alignment with better efficiency and visualization tools.

Robust and efficient software for reference-free genomic diversity analysis of GBS data on diploid and polyploid species

The paper introduces a reference-free variant detection and genotyping method for GBS data in diploid and polyploid species, showing comparable accuracy and better efficiency than existing tools.