About me

Dileep Kishore

Hi, I'm Dileep Kishore!

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  • Postdoctoral Research Associate, Oak Ridge National Laboratory
  • Agentic workflows & AI co-scientists for research
  • Microbial systems biology & plant microbiome
  • Machine learning, data infrastructure & open-source
  • Open-source software & reproducible workflows
Education
  • Mar 2023–Present
    Oak Ridge National Laboratory, USA. Postdoctoral Research Associate.
  • Jan 2023–Mar 2023
    Boston University, USA. Postdoctoral Fellow (Bridge Appointment).
  • Jun 2016–Dec 2022
    Boston University, USA. Ph.D. in Bioinformatics, GPA 4.00/4.00. Advisor: Dr. Daniel Segrè.
  • Sep 2011–May 2016
    Indian Institute of Technology Madras, India. B.Tech (Honors) & M.Tech (Dual Degree) in Biotechnology, GPA 9.23/10.00. Advisor: Dr. Karthik Raman.

I am a Postdoctoral Research Associate in the Computational and Predictive Biology group at Oak Ridge National Laboratory. Recently I have been focused on developing agentic workflows and building AI co-scientists for various projects—agentic systems that enable natural language querying of scientific databases, multi-agent orchestration (LangChain, LangGraph), MCP integrations with data lakehouses, and RAG for domain literature and datasets. I also work on understanding and predicting microbial interactions in the plant microbiome, end-to-end ML pipelines for phenotypes such as carbon utilization, FastAPI-based interfaces for genomic and microbial data, and reproducible workflows with Nextflow and Snakemake. I collaborate closely with experimental biologists and domain scientists at Oak Ridge National Laboratory and Lawrence Berkeley National Laboratory.

Publications

Peer-reviewed

  • Kishore, Dileep; Birzu, Gabriel; Hu, Zhenjun; DeLisi, Charles; Korolev, Kirill S; Segrè, Daniel; . Inferring microbial co-occurrence networks from amplicon data: a systematic evaluation. mSystems. 2023.
  • Pacheco, Alan R; Pauvert, Charlie; Kishore, Dileep; Segrè, Daniel; . Toward FAIR Representations of Microbial Interactions. mSystems. 2022.
  • Federico, Anthony; Karagiannis, Tanya; Karri, Kritika; Kishore, Dileep; Koga, Yusuke; Campbell, Joshua D; Monti, Stefano; . Pipeliner: A Nextflow-Based Framework for the Definition of Sequencing Data Processing Pipelines. Frontiers in Genetics. 2019.

Preprints

  • Hu, Zhenjun; Kishore, Dileep; Wang, Yan; Birzu, Gabriel; DeLisi, Charles; Korolev, Kirill S; Segrè, Daniel; . A resource for the comparison and integration of heterogeneous microbiome networks. BioRxiv. 2022 (2022.08.07.503059).
  • Kishore, Dileep; Chandrasekaran, Srikiran; . Introducing and benchmarking the accuracy of cayenne: A Python package for stochastic simulations. BioRxiv. 2020 (2020.10.10.334623).