Raga Krishnakumar

Benchmarking Large Language Models for Transcriptomic Data Analysis and Visualization: Multi-Model Workflow Evaluation

This study benchmarks large language models for automated transcriptomic data analysis and visualization workflows, finding that prompt specificity improves code quality but performance varies with preprocessing and environment.

Hybrid CNN and Multi-Head Attention Model for Analyzing Epigenetic Mechanisms and Gene Expression Across Fungal Phylogenetic Distances

This paper introduces a deep learning model, MAPLE, to predict gene expression from epigenetic data across fungal species, achieving strong cross-species performance.

Intracellular screening of nanobodies reveals an intrabody that inhibits ITCH E3 ubiquitin ligase

The paper screens nanobodies to find an intrabody that inhibits ITCH E3 ubiquitin ligase activity in human cells using in vitro and intracellular assays.

Integrative multi-omic and phenotypic analysis of open raceway pond production of Monoraphidium minutum 26B-AM reveals distinct stress signatures for scale-up and infection

The paper integrates multi-omic and phenotypic data from algal cultures in open raceway ponds to identify molecular signatures associated with scale-up and infection stressors.

Poplar: A Phylogenetics Pipeline

Poplar is a computational pipeline that streamlines phylogenetic tree construction by integrating state-of-the-art software, offering simplicity and speed compared to manual methods.

OperonSEQer: A set of machine-learning algorithms with threshold voting for detection of operon pairs using short-read RNA-sequencing data

OperonSEQer detects operon pairs using short-read RNA-seq data with machine learning and threshold voting, improving accuracy and flexibility over existing methods.

Augmentation of Antibacterial Activity in Mesenchymal Stromal Cells Through Systems-Level Analysis and CRISPR-mediated Activation of CD14

This study identifies CD14 as a key target to enhance antibacterial activity in mesenchymal stromal cells through systems-level analysis and CRISPR activation.

New candidates for regulated gene integrity revealed through precise mapping of integrative genetic elements

The paper introduces TIGER, a software tool that precisely maps integrative genetic elements, revealing 19 new cases of gene integrity regulation by IGEs.

Real-Time Selective Sequencing with RUBRIC: Read Until with Basecall and Reference-Informed Criteria

The paper introduces RUBRIC, a real-time selective sequencing method for nanopore sequencing that uses on-line basecalling to align against references and make sequence/reject decisions, showing improved performance on mixed samples.