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

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.

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.

Selina Shiqing K Teh, Eitan Halper-Stromberg, Laura Morsberger, Kirsten Bowland, Alexis Bennett, Robert B Scharpf, Ying S Zou, James R Eshleman: Genomic instability delays cell death in PDAC after simultaneous double strand breaks Cancer Research 83 (7_Supplement): 6103-6103,2023.

Teh SSK, Halper-Stromberg E, Morsberger L, Bennett A, Bowland K, Skaist A, Cai F, Liang H, Hruban RH, Roberts NJ, Scharpf RB, Zou YS, Eshleman JR.: Mechanism of delayed cell death following simultaneous CRISPR-Cas9 targeting in pancreatic cancers bioRxiv no volue (no issue): no page number,2023.

Esther CR Jr, O'Neal WK, Alexis NE, Koch AL, Cooper CB, Barjaktarevic I, Raffield LM, Bowler RP, Comellas AP, Peters SP, Hastie AT, Curtis JL, Ronish B, Ortega VE, Wells JM, Halper-Stromberg E, Rennard SI, Boucher RC; SPIROMICS.: Prolonged, physiologically relevant nicotine concentrations in the airways of smokers Am J Physiol Lung Cell Mol Physiol 324 (1): L32-L37,2023.

Eitan Halper-Stromberg: How to Diagnose Blood Cancer with Streamlit Advocate Posts no volume (no issue): no pages,2022.

Halper-Stromberg E, McCall CM, Haley LM, Lin MT, Vogt S, Gocke CD, Eshleman JR, Stevens W, Martinson NA, Epeldegui M, Holdhoff M, Bettegowda C, Glantz MJ, Ambinder RF, Xian RR.: CloneRetriever: An Automated Algorithm to Identify Clonal B and T Cell Gene Rearrangements by Next-Generation Sequencing for the Diagnosis of Lymphoid Malignancies Clin Chem 67 (11): 1524-1533,2021.

Academic Contact Information

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