CV

Musaddiq Lodi

Email: musaddiq.k.lodi@gmail.com
Website: lodimk2.github.io

Summary

PhD Candidate with a focus in AI/ML single-cell genomics method development and biological network studies.
Skilled in deep learning and multi-modal data integration approaches to solve biological challenges, as well as open-source software development using Python, R, and Git.

• Proficient in large language models (LLMs), AutoEncoder, and transfer learning implementations
• Experience in Next Generation Sequencing (NGS) analysis and bioinformatics pipelines such as Nextflow RNA-seq, Seurat, and Cellranger
• Team-oriented with excellent communication skills, leadership, and project management experience

Tools and Technologies

Machine Learning, Deep Learning, Large Language Models, Python, R, TensorFlow, PyTorch, Java, SQL, Linux/Bash Scripting, Python Flask, BLAST, Web Server Development, Nextflow, Statistical Analysis

Work Experience

Merck Research Laboratories — Cambridge, MA

AI/ML Co-Op, Methods and Modeling Team (Apr 2025 – Present)

• Developing deep learning models for in silico gene perturbation prediction within the Data, AI, and Genome Sciences (DAGS) department
• Designing multi-modal learning frameworks for gene program discovery
• Building benchmarking pipelines for single-cell RNA-seq method evaluation

Virginia Commonwealth University — Richmond, VA

Graduate Research Assistant (Aug 2023 – Present)

• PhD research in single-cell genomics, biological networks, and AI/ML approaches to precision medicine
• Multiple first-author publications in Q1 journals
• Collaborations with Medical College of Virginia in neurology, psychiatric genetics, and oncology

Intelligent Health Solutions — Richmond, VA

Research Assistant (Sep 2023 – Nov 2023)

• Validated synthetic clinical note generation for diagnostic prediction
• Fine-tuned Clinical BioBERT for NER in radiation oncology, achieving 95% weighted F1 score

Publications

1. Lodi MK, Lodi M, Osei K, Ranganathan V, Hwang P, Ghosh P. CHAI: Consensus Clustering Through Similarity Matrix Integration for Cell-Type Identification. Brief Bioinform. 2024;25(5):bbae411. doi:10.1093/bib/bbae411.
2. Lodi MK, Chernikov A, Ghosh P. COFFEE: Consensus Single Cell-Type Specific Inference for Gene Regulatory Networks. Brief Bioinform. 2024;25(6):bbae457. doi:10.1093/bib/bbae457.
3. Lodi MK, Clark L, Roy S, Ghosh P. CORTADO: Hill Climbing Optimization for Cell-Type Specific Marker Gene Discovery. bioRxiv. 2024 Dec 23. doi:10.1101/2024.12.23.630040.
4. Pateras J, Lodi MK, Rana P, Ghosh P. Heterogeneous Clustering of Multiomics Data for Breast Cancer Subgroup Classification and Detection. Int J Mol Sci. 2025;26(4):1707. doi:10.3390/ijms26041707.
5. Cohen DJ, Van Duyn CM, Deng J, Lodi MK, et al. Bone Marrow Stromal Cells Generate a Pro-Healing Inflammasome…. Biomimetics. 2025;10(1):66. doi:10.3390/biomimetics10010066.

Awards and Recognition

• Early Career Student Researcher Award, VCU Department of Computer Science (May 2025)
• Provost Scholar, VCU (Aug 2019 – Aug 2023)

Projects – In Progress

1. Exosomal MicroRNA Cargo in Alcohol Use Twins
   Mentors: Dr. Preetam Ghosh, Dr. Roxann Roberson-Nay (Nov 2023 – Present)

2. Migration Leading Cells in Breast Cancer
   Mentors: Dr. Preetam Ghosh, Dr. Priscilla Hwang (Nov 2023 – Present)

3. Multimodal Genotype-Phenotype Prediction Methods
   Mentor: Dr. Preetam Ghosh (Aug 2023 – Present)

4. Hippocampal Astrocyte Subclusters in Dystrophinopathy Mouse Model
   Mentors: Dr. Preetam Ghosh, Dr. Mathula Thangarajh (Aug 2023 – Present)

5. Evaluation of FSK Therapeutic in Glioblastoma Mouse Model
   Mentors: Dr. Preetam Ghosh, Dr. Swadesh Das (Mar 2024 – Present)

Talks and Workshops

• Computational Methods for Multimodal Genotype-Phenotype Prediction
  Presented at Virginia Institute for Psychiatric and Behavioral Genetics Seminar (Jun 2024)

• Workshop: Basics of Unsupervised Machine Learning
  Presented at VCU Undergraduate Society of Bioinformatics (Apr 2024)

Education

Virginia Commonwealth University — Richmond, VA

• PhD Student, Integrative Life Sciences (Aug 2023 – Present)
  Biological Networks Lab, Department of Computer Science | PI: Dr. Preetam Ghosh
• MS in Bioinformatics, Accelerated Program (Aug 2023)
• BS in Bioinformatics, Provost Scholar (Aug 2019 – Dec 2022)

Leadership Experience

• Vice President, Bioinformatics Graduate Student Association (2025 – Present)
• Co-Founder, President, Graduate Advisor, Alpha Beta (Diabetes Link Chapter) (2019 – Present)
• Co-Founder, Captain, Vice-President, VCU Cricket Club (2022 – 2023)