Author

Josh Loecker

University of Nebraska–LincolnORCID 0000-0002-6388-2958Unclaimed ORCID profile · follow to get notified of new preprints

Biology Disciplines

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Bioinformatics· 1 Systems Biology· 1

Signature Assays, Organisms & Methods

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Research Focus:benchmarking· 2 Approach:statistical model· 2 Approach:benchmark study· 1 Assay:bulk RNA-seq· 1 Approach:deep learning· 1 Research Focus:differential expression· 1 Research Focus:drug response / drug discovery· 1 Research Focus:gene regulatory network inference· 1

Frequent Co-Authors

Bhanwar Lal PuniyaiD· 2 shared Tomáš HelikariD· 2 shared Ahmed Abdeen HamediD· 1 shared Brandt BesselliD· 1 shared Narayana Pujara· 1 shared Prakash PackrisamyiD· 1 shared William Bryant· 1 shared

Activity by Year

2026-2026 · peak 2/yr

Co-Author Collaboration Network

7 top collaborators · 17 mutual co-author links

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2 shared papersSystems Biology

Bhanwar Lal PuniyaORCID

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2 papers

Recent·Most cited

Systems BiologybioRxivPreprintJul 22, 2026

MechAInistic: An LLM-guided Multi-Agent System for Reasoning over Genome-Scale Constraint-Based Metabolic Models

Josh Loecker, Narayana Pujara, William Bryant…·Tomáš Helikar

MechAInistic uses a multi-agent system guided by LLMs to generate auditable hypotheses from genome-scale metabolic models, identifying potential drug targets and metabolic rewiring in disease states.

DOI 10.64898/2026.05.11.723319

metabolomicsdeep learning

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BioinformaticsbioRxivPreprintApr 23, 2026

AutoRNAseq: Automated Bulk RNA-seq Analysis Pipeline

Josh Loecker, Brandt Bessell, Bhanwar Lal Puniya, Tomáš Helikar

AutoRNAseq provides an automated bulk RNA-seq analysis pipeline to ensure consistent and reproducible processing across experiments.

1 citation

bulk RNA-seqstatistical model

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