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
Ghanem P, Fatteh M, Kamson DO, Balan A, Chang M, Tao J, Blakeley J; Johns Hopkins Molecular Tumor Board Investigators; Canzoniero J, Grossman SA, Marrone K, Schreck KC, Anagnostou V.: Druggable genomic landscapes of high-grade gliomas Front Med (Lausanne) 10 : 1254955,2023.
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 : 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 : 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 : 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 : L32-L37,2023.
Ghosh AJ, Hobbs BD, Yun JH, Saferali A, Moll M, Xu Z, Chase RP, Morrow J, Ziniti J, Sciurba F, Barwick L, Limper AH, Flaherty K, Criner G, Brown KK, Wise R, Martinez FJ, McGoldrick D, Cho MH, DeMeo DL, Silverman EK, Castaldi PJ; NHLBI Trans-Omics for Precision Medicine (TOPMed) Consortium; Hersh CP.: Lung tissue shows divergent gene expression between chronic obstructive pulmonary disease and idiopathic pulmonary fibrosis Respir Res 23 : 97,2022.
Moll M, Boueiz A, Ghosh AJ, Saferali A, Lee S, Xu Z, Yun JH, Hobbs BD, Hersh CP, Sin DD, Tal-Singer R, Silverman EK, Cho MH, Castaldi PJ; HAPIN Investigators.: Development of a Blood-based Transcriptional Risk Score for Chronic Obstructive Pulmonary Disease Am J Respir Crit Care Med 205 : 161-170,2022.
Iyer AS, Parekh TM, O'Toole J, Bhatt SP, Eakin MN, Krishnan JA, Yohannes AM, Woodruff PG, Cooper CB, Kanner RE, Hanania NA, Dransfield MT, Regan EA, Hoth KF, Kim V; COPDGene and SPIROMICS Investigators.: Clinically Significant and Comorbid Anxiety and Depression Symptoms Predict Severe Respiratory Exacerbations in Smokers: A Post Hoc Analysis of the COPDGene and SPIROMICS Cohorts Ann Am Thorac Soc : 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 : 1524-1533,2021.
Kim V, Dolliver WR, Nath HP, Grumley SA, Terry N, Ahmed A, Yen A, Jacobs K, Kligerman S, Diaz AA; COPDGene Investigators.: Mucus plugging on computed tomography and chronic bronchitis in chronic obstructive pulmonary disease Respir Res 22 : 110,2021.
Academic Contact Information
3020 Market Street
Suite 220
Philadelphia,
PA
19104