Venkat S. Malladi

The GA4GH Workflow Execution Service: A Standard API for Workflow Execution and Management in Genomics

The paper introduces the GA4GH Workflow Execution Service API, which standardizes workflow execution across different compute environments and demonstrates its cross-site functionality.

X-Linked Cancer-Associated Polypeptide (XCP) from lncRNA1456 Cooperates with PHF8 to Regulate Gene Expression and Cellular Pathways in Breast Cancer

This study identifies XCP, a protein from the lncRNA1456, which interacts with PHF8 to regulate gene expression and cancer pathways in breast cancer.

sciLaMA: A Single-Cell Representation Learning Framework to Leverage Prior Knowledge from Large Language Models

sciLaMA integrates gene embeddings from large language models with scRNA-seq data using a paired-VAE architecture, improving downstream tasks like batch correction and clustering while maintaining computational efficiency.

Optimizing genomics pipeline execution with integer linear programming

This paper uses integer linear programming to optimize genomics pipeline execution by balancing cost and time constraints on cloud platforms.

The ENCODE Uniform Analysis Pipelines

ENCODE's containerised Workflow Description Language pipelines for ChIP-seq, ATAC-seq, DNase-seq, RNA-seq variants, Hi-C and bisulfite sequencing run on cloud or local clusters, with documented compute costs and provenance.

Enhancer and super-enhancer landscape in polycystic kidney disease

This study identifies enhancer and super-enhancer changes in PKD, showing their role in gene dysregulation and potential as therapeutic targets.

TReNCo: Topologically associating domain (TAD) aware regulatory network construction

TReNCo constructs context-specific transcription factor-gene regulatory networks using TAD boundaries, epigenetic marks, and gene expression data to model cardiac development in mice.

SeqWho: Reliable, rapid determination of sequence file identity using k-mer frequencies

SeqWho uses k-mer frequencies and a Random Forest classifier to accurately classify sequencing files by organism and protocol type.

An integrated genomics approach towards deciphering human genome codes shaping HIV-1 proviral transcription and fate

The paper uses integrated genomics data to identify chromatin states and nuclear compartments influencing HIV-1 proviral transcription and fate.