Description of Research Expertise

My research interests are in the areas of bioinformatics, molecular pathology, next-generation sequencing, AI, software development, digital pathology, and big data.

Before medical training, I worked as a software engineer, then went on to receive a Ph.D. in Human Genetics at Johns Hopkins and completed a computational biology post-doctoral fellowship. During my molecular pathology fellowship at Johns Hopkins, I performed research on Ig and TCR clone detection using NGS and digital WSI analysis using different types of neural networks.

In my observation, there is progress to be made regarding integration of AI and machine learning tools into the clinical workflow and in the research effort. This integration needs vision and hands-on work in the short, medium, and long term. In the short term, existing solutions to molecularly focused problems could be implemented into the routine workflow of the lab. These include classification schemes aimed at describing mechanisms of tumorigenesis and automated identification of case-specific trials exploring genomic targeted therapies. The medium term offers opportunities to develop algorithms for new testing modalities, such as ctDNA and minimal residual disease detection, that will grow in importance in the next few years and that require different bioinformatic paradigms than existing assays. Integration of AI, including large language models and other generative forms, will be necessary in the long-term, especially as the move to cloud-computing makes these functions more accessible for routine tasks. I explore how these tools may be developed and utilized to suite the molecular niche

Selected Publications

R Ramesh, R Colbourn, V Van Deerlin, E Halper-Stromberg: Measuring T Cell Diversity Alongside Clonality May Prove Clinically Useful for Patients Undergoing NGS-Based T Cell Receptor Gamma Gene (TRG) Rearrangement Testing Journal of Molecular Diagnostics 26 (11): S37-S37,2024.

R Colbourn, R Ramesh, V Van Deerlin, E Halper-Stromberg: A Statistical Method for Analysis of T Cell Clonality by Next Generation Sequencing of the T Cell Receptor Gamma Gene Journal of Molecular Diagnostics 26 (11): S76-S76,2024.

Kalghatgi, T., Von Reusner, J. Halper-Stromberg, E: Evaluating Performance of LLMs for Generating Information That Would Appear on a Molecular Pathology Report and Genetic Variant Classification in Molecular Pathology Journal of Molecular Diagnostics 26 (11): S73-S74,2024.

Halper-Stromberg E, Stinnett V, Morsberger L, Pallavajjala A, Levis MJ, DeZern AE, Lei M, Phan B, Xian RR, Gocke CD, Tang G, Zou YS.: 1q jumping translocation as a biomarker in myeloid malignancy: frequently mutated genes associated with bad prognosis and low survival Exp Hematol Oncol 13 : 73,2024.

Selina Shiqing K Teh, Akhil Kotwal, Eitan Halper-Stromberg, Laura Morsberger, Kirsten Bowland, Alexis Bennett, Michael Goldstein, Ying S Zou, James R Eshleman: Simultaneous CRISPR-Cas9 induced double strand breaks causes chromosomal catastrophe in pancreatic cancers: A parallel comparison with ionizing radiation Cancer Research 84 (7 Supplement): LB397-LB397,2024.

Rimal, A., Halper-Stromberg, E: Making Semi-structured Molecular Pathology Information More Accessible and Searchable Using Vector Store Indices Journal of Molecular Diagnostics 26 (11): S86-S87,2024.

Teh, Selina Shiqing K; Bowland, Kirsten; Bennett, Alexis; Halper-Stromberg, Eitan; Skaist, Alyza; Pallavajjala, Aparna; Tang, Jacqueline; Cai, Fidel; Liang, Hong; Wheelan, Sarah; Scharpf, Robert B; Roberts, Nicholas J; Eshleman, James R: Novel PAMs from Somatic Mutations Produce Numerous Pancreatic Cancer-Specific CRISPR-Cas9 Targets for Selective Cell Elimination: A Novel Gene Therapy Approach for Cancer Molecular cancer therapeutics 22 (12_Supplement): LB_B02-LB_B02,2023.

E Halper-Stromberg, Y Zou, V Stinnett, A Pallavajjala, L Morsberger, M Klausner, C Gocke, R Xian, M Lin, J Dudley: 1q Jumping Translocation in Myeloid Malignancies: Frequently Mutated Genes Are Often Associated with Worse Prognosis Journal of Molecular Diagnostics 25 (11): S28-S29,2023.

Li H, Argani P, Halper-Stromberg E, Lotan TL, Merino MJ, Reuter VE, Matoso A.: Positive GPNMB Immunostaining Differentiates Renal Cell Carcinoma With Fibromyomatous Stroma Associated With TSC1/2/MTOR Alterations From Others Am J Surg Pathol 47 (11): 1267-1273,2023.

Teh SSK, Bowland K, Bennett A, Halper-Stromberg E, Skaist A, Tang J, Cai F, Macoretta A, Liang H, Kamiyama H, Wheelan S, Lin MT, Hruban RH, Scharpf RB, Roberts NJ, Eshleman JR.: CRISPR-Cas9 for selective targeting of somatic mutations in pancreatic cancers bioRxiv no volue (no issue): no page number,2023.

Academic Contact Information

Division of Precision and Computational Diagnostics
3020 Market Street
Suite 220
Philadelphia, PA 19104