Introduction & Research Interests
I am currently working as a pathology resident at Johns Hopkins. I have a background in genetics, genomics, and programming. I am interested in harnessing the rapidly increasing quantity of genomic data to solve problems facing the medical and scientific community.
Professional Positions
| Start Date | End Date | Title | Employer |
|---|---|---|---|
| 2006 | 2008 | Software Developer | LexisNexis, Risk Solutions |
| 2013 | 2015 | Postdoctoral Fellow National Library of Medicine | University of Colorado |
Education
| Start Date | End Date | Degree |
|---|---|---|
| 2002 | 2006 | B.S. |
| 2008 | 2013 | Ph.D. |
| 2015 | 2019 | M.D. |
| 2019 | present | Clinical Pathology |
Honors
| Year | Honor | Institution |
|---|---|---|
| 2002 | Gemstone Honors Program | University of Maryland |
| 2006 | Gemstone Outstanding Thesis | University of Maryland |
| 2016 | Research Track | University of Colorado |
| 2019 | Informatics Track | Johns Hopkins University |
| 2021 | SanFilippo Fellow | Johns Hopkins University |
Presentations
1. Halper-Stromberg, E. Visualization of Low Confidence Sequencing Variants. National Institute of Standards and Technology, Genome in a Bottle Consortium.Gaithersburg, MD 2012.
2. Halper-Stromberg, E. Assessing Next Generation Sequencing Alignments: a reView. 6th Annual Young Investigator’s Symposium on Genomics and Bioinformatics. Baltimore, MD 2012.
3. Halper-Stromberg, E. Detecting Structural Variants and Copy Number Changes in the Human Genome: Where are we still making mistakes? Johns Hopkins School of Medicine Genomics Seminar Series. Baltimore, MD 2013
4. Halper-Stromberg, E. Creating Tools to Detect Genomic Structural Variants: Moving From Reasonable Ad-hoc Approaches to Even Better Systematic Ones. University of Colorado Postdoctoral Seminar Series. Aurora, CO 2013.
5. Halper-Stromberg, E. Genetic Association Testing in COPD Using Visual Assessment of Chest CT Images. National Library of Medicine, Informatics Training Conference. Bethesda, MD 2015.
6. Halper-Stromberg, E. Circulating Lymphocyte Sub-Populations Define Molecular Subtypes of COPD. Center for Genes, Environment, and Health. Denver, CO 2017.
7. Manning, Aaron, Halper-Stromberg, E, Cunningham, Maureen. Reversible pulmonary hypertension: A surprising case of scurvy and its complications. American College of Physicians Colorado Chapter Meeting. Colorado Springs, CO 2018.
8. Halper-Stromberg, E. Technology in Pathology: Frontiers in Image Analysis. Pathology Dept, University of Colorado. Aurora, CO, 2018.
9. Halper-Stromberg, E. Sub-I Quality Improvement Project: Putting Labs on Signout At the Denver VA. VA Hospital Noon Conference. Denver, CO, 2018.
10. Halper-Stromberg, E. Pathology Grand Rounds Short Topics: Single Drop of Blood Diagnostics. Johns Hopkins Hospital, Baltimore, MD, 2020
11. Halper-Stromberg, E. Xian, R. Haley, L, Lin, M. Glantz, M, Vogt, S, Ambinder, R, Gocke, C,Eshleman, J. McCall, C, Bettegowda, C, Epeldegui, M, Holdhoff, M. CloneRetriever: An Automated Algorithm to Identify Clonal Immunoglobulin Gene Rearrangements by Next-Generation Sequencing. Association for Molecular Pathology (15 Minute Talk and Poster). Virtual Conference, 2020
12. Halper-Stromberg, E. Pathology Grand Rounds Short Topics: RoopKund Lake. Johns Hopkins Hospital, Baltimore, MD, 2021
13. Halper-Stromberg, E. Pathology Grand Rounds Short Topics: Identifying Subclones using Next-generation-sequencing. Johns Hopkins Hospital, Baltimore, MD, 2021
14. Halper-Stromberg, E. Haley, L. He, K. Mbonu, P. Xian, R. CloneSeer: Sequence Alignment-Based Detection and Quantification of Lymphoma Sub-Clones. Association For Molecular Pathology (15 Minute Talk and Poster). Virtual Conference, 2021
2. Halper-Stromberg, E. Assessing Next Generation Sequencing Alignments: a reView. 6th Annual Young Investigator’s Symposium on Genomics and Bioinformatics. Baltimore, MD 2012.
3. Halper-Stromberg, E. Detecting Structural Variants and Copy Number Changes in the Human Genome: Where are we still making mistakes? Johns Hopkins School of Medicine Genomics Seminar Series. Baltimore, MD 2013
4. Halper-Stromberg, E. Creating Tools to Detect Genomic Structural Variants: Moving From Reasonable Ad-hoc Approaches to Even Better Systematic Ones. University of Colorado Postdoctoral Seminar Series. Aurora, CO 2013.
5. Halper-Stromberg, E. Genetic Association Testing in COPD Using Visual Assessment of Chest CT Images. National Library of Medicine, Informatics Training Conference. Bethesda, MD 2015.
6. Halper-Stromberg, E. Circulating Lymphocyte Sub-Populations Define Molecular Subtypes of COPD. Center for Genes, Environment, and Health. Denver, CO 2017.
7. Manning, Aaron, Halper-Stromberg, E, Cunningham, Maureen. Reversible pulmonary hypertension: A surprising case of scurvy and its complications. American College of Physicians Colorado Chapter Meeting. Colorado Springs, CO 2018.
8. Halper-Stromberg, E. Technology in Pathology: Frontiers in Image Analysis. Pathology Dept, University of Colorado. Aurora, CO, 2018.
9. Halper-Stromberg, E. Sub-I Quality Improvement Project: Putting Labs on Signout At the Denver VA. VA Hospital Noon Conference. Denver, CO, 2018.
10. Halper-Stromberg, E. Pathology Grand Rounds Short Topics: Single Drop of Blood Diagnostics. Johns Hopkins Hospital, Baltimore, MD, 2020
11. Halper-Stromberg, E. Xian, R. Haley, L, Lin, M. Glantz, M, Vogt, S, Ambinder, R, Gocke, C,Eshleman, J. McCall, C, Bettegowda, C, Epeldegui, M, Holdhoff, M. CloneRetriever: An Automated Algorithm to Identify Clonal Immunoglobulin Gene Rearrangements by Next-Generation Sequencing. Association for Molecular Pathology (15 Minute Talk and Poster). Virtual Conference, 2020
12. Halper-Stromberg, E. Pathology Grand Rounds Short Topics: RoopKund Lake. Johns Hopkins Hospital, Baltimore, MD, 2021
13. Halper-Stromberg, E. Pathology Grand Rounds Short Topics: Identifying Subclones using Next-generation-sequencing. Johns Hopkins Hospital, Baltimore, MD, 2021
14. Halper-Stromberg, E. Haley, L. He, K. Mbonu, P. Xian, R. CloneSeer: Sequence Alignment-Based Detection and Quantification of Lymphoma Sub-Clones. Association For Molecular Pathology (15 Minute Talk and Poster). Virtual Conference, 2021
Software
| Title | URL | Description |
|---|---|---|
| ArrayTV | https://bioconductor.org/packages/release/bioc/html/ArrayTV.html | GC correction in microarrays |
| SeqView | https://github.com/Eitan177/targetSeqView | Realigning and visualizing next generation sequencing short reads |
Grants
1. Butcher Seed Grant to fund collaborative and potentially transformative bioscience research. Characterizing Structural Variants in a Mouse Model of Alcohol Dependence. March 2014, Lead Investigator. $2,000.
2. Fred and Janet SanFilippo Fellowship Research Grant. Minimal Residual Disease Detection of Clonal Immunoglobulin Sequences in Lymphoid Malignancies. March, 2021. Lead Investigator. $3,500.
2. Fred and Janet SanFilippo Fellowship Research Grant. Minimal Residual Disease Detection of Clonal Immunoglobulin Sequences in Lymphoid Malignancies. March, 2021. Lead Investigator. $3,500.
Invited Peer Review
| Year | Publication |
|---|---|
| 2014 | Nucleic Acids Research Web Server Issue |
| 2014 | Bioinformatics |
| 2015 | BMC Bioinformatics |
Professional and Student Organization Membership
| Dates | Organization |
|---|---|
| 2014 - present | COPDGene Consortium Investigator |
| 2014 - 2016 | American Thoracic Society |
| 2017 - 2018 | American College of Physicians |
| 2018 - 2019 | Pathology Student Interest Group Treasurer |
| 2019 - Present | SPIROMICS Consortium Trainee Investigator |
| 2020 - Present | Association for Molecular Pathologists Member |
| 2021 - Present | Association for Molecular Pathologists Membership Affairs Committee |
| 2021 - Present | Digital Pathology Association Member |
Websites
| Description | URL |
|---|---|
| Formatting daily Labs in CPRS | https://eitanhs.shinyapps.io/shin/ |
| Repairing EPIC text for GI pathology | https://eitanhs.shinyapps.io/Allparts/ |
| Suspect Results Patterns in Chemistry | https://ehalperstromberg.shinyapps.io/SuspectChemMapper/ |
| Clone Calling with NGS | https://clone-retriever.herokuapp.com/ |
Publications
1. Halper-Stromberg E, Frelin L, Ruczinski I, Scharpf R, Jie C, Carvalho B, Hao H, Hetrick K, Jedlicka A, Dziedzic A, Doheny K, Scott AF, Baylin S, Pevsner J, Spencer F, Irizarry RA: Performance assessment of copy number microarray platforms using a spike-in experiment. Bioinformatics 2011, 27:1052–1060.
2. Halper-Stromberg E, Steranka J, Giraldo-Castillo N, Fuller T, Desiderio S, Burns KH: Fine mapping of V(D)J recombinase mediated rearrangements in human lymphoid malignancies. BMC Genomics 2013, 14:565.
3. Wang R, Halper-Stromberg E, Szymanski-Pierce M, Bassett SS, Avramopoulos D: Genetic determi- nants of neuroglobin transcription. Neurogenetics 2014, 15:65–75.
4. Halper-Stromberg E, Steranka J, Burns KH, Sabunciyan S, Irizarry RA: Visualization and probability- based scoring of structural variants within repetitive sequences. Bioinformatics 2014, 30:1514–1521.
5. Scharpf RB, Mireles L, Yang Q, Köttgen A, Ruczinski I, Susztak K, Halper-Stromberg E, Tin A, Cristiano S, Chakravarti A, Boerwinkle E, Fox11 CS, Coresh J, Linda Kao WH: Copy number poly- morphisms near SLC2A9 are associated with serum uric acid concentrations. BMC Genet 2014, 15:81.
6. Castaldi P, Obeidat M, Halper-Stromberg E, Lamb A, Chase R, Parker M, Carey V, Tal-Singer R, Silverman E, Pare P, Sin D, Hersh C: Buffet-Style Expression Factor-Adjusted Discovery Increases the Yield of Robust Expression Quantitative Trait Loci. bioRxiv 2015.
7. Dowell R, Odell A, Richmond P, Malmer D, Halper-Stromberg E, Bennett B, Larson C, Leach S, Radcliffe RA: Genome characterization of the selected long- and short-sleep mouse lines. Mamm Genome 2016, 27:574–586.
8. Boueiz A, Lutz SM, Cho MH, Hersh CP, Bowler RP, Washko GR, Halper-Stromberg E, Bakke P, Gulsvik A, Laird NM, Beaty TH, Coxson HO, Crapo JD, Silverman EK, Castaldi PJ, DeMeo DL, COPDGene and ECLIPSE Investigators: Genome-Wide Association Study of the Genetic Determinants of Emphysema Distribution. Am J Respir Crit Care Med 2017, 195:757–771.
9. Halper-Stromberg E, Cho MH, Wilson C, Nevrekar D, Crapo JD, Washko G, San José Estépar R, Lynch DA, Silverman EK, Leach S, Castaldi PJ: Visual Assessment of Chest CT Images is Independently Useful for Genetic Association Analysis in Studies of Chronic Obstructive Pulmonary Disease. Ann Am Thorac Soc 2016:AnnalsATS.201606-427OC.
10. Pollack RA, Jones RB, Pertea M, Bruner KM, Martin AR, Thomas AS, Capoferri AA, Beg SA, Huang S-H, Karandish S, Hao H, Halper-Stromberg E, Yong PC, Kovacs C, Benko E, Siliciano RF, Ho Y-C: Defective HIV-1 Proviruses Are Expressed and Can Be Recognized by Cytotoxic T Lymphocytes, which Shape the Proviral Landscape. Cell Host Microbe 2017, 21:494–506.e4.
11. Halper-Stromberg E, Yun JH, Parker MM, Tal Singer R, Gaggar A, Silverman EK, Leach S, Bowler RP, Castaldi PJ. Systemic Markers of Adaptive and Innate Immunity are Associated with COPD Severity and Spirometric Disease Progression. Am J Respir Cell Mol Biol 2017.rcmb:2017-0373OC.
12. Dietert, k, Tak, T, R, Knipe, Halper-Stromberg, E. April Highlights/Papers by Junior Investigators/NIH News. Am J of Respir Cell Mol Bio: 2018,58(4), p. iv
13. Halper-Stromberg E, Gillenwater L, Cruickshank-Quinn C, O’Neal W.K, Reisdorph N, Petrache I, Zhuang Y, Labaki W.W, Curtis J.L, Wells J, Rennard S, Pratte K.A, Woodruff P, Stringer K.A, Kechris K, Bowler R.P, Bronchoalveolar Lavage Fluid from COPD Patients Reveals More Compounds Associated with Disease than Matched Plasma. Metabolites 2019, 9, 157.
14. Halper-Stromberg E, Gallo T, Champakanath A, Taki I, Rewers M, Snell-Bergeon J, Frohnert B, Shah VN, Bone Mineral Density across the Lifespan in Patients with Type 1 Diabetes, The Journal of Clinical Endocrinology & Metabolism, Volume 105, Issue 3, March 2020, dgz153
15. Lucas A. Gillenwater, Katherine A. Pratte, Brian D. Hobbs, Michael H. Cho, Yonghua Zhuang, Eitan Halper-Stromberg, Charmion Cruickshank-Quinn, Nichole Reisdorph, Irina Petrache, Wassim W. Labaki, Wanda K. O'Neal, Victor E. Ortega, Dean P. Jones, Karan Uppal, Sean Jacobson, Gregory Michelotti, Christine H. Wendt, Katerina J. Kechris, and Russell P. Bowler. Plasma Metabolomic Signatures of Chronic Obstructive Pulmonary Disease and the Impact of Genetic Variants on Phenotype-Driven Modules. Network and Systems Medicine. Dec 2020.159-181
16. Halper-Stromberg E, McCall C, Haley L, Lin M, Vogt S, Gocke C, Eshleman J, Stevens W, Martinson N, Epeldegui M, Holdhof M, Bettegowda C, Glantz M, Ambinder R, Xian R, CloneRetriever: An Automated Algorithm to Identify Clonal B and T Cell Gene Rearrangements by Next-Generation Sequencing for the Diagnosis of Lymphoid Malignancies, Clinical Chemistry, Volume 67, Issue 11, November 2021, Pages 1524–1533, https://doi.org/10.1093/clinchem/hvab141
2. Halper-Stromberg E, Steranka J, Giraldo-Castillo N, Fuller T, Desiderio S, Burns KH: Fine mapping of V(D)J recombinase mediated rearrangements in human lymphoid malignancies. BMC Genomics 2013, 14:565.
3. Wang R, Halper-Stromberg E, Szymanski-Pierce M, Bassett SS, Avramopoulos D: Genetic determi- nants of neuroglobin transcription. Neurogenetics 2014, 15:65–75.
4. Halper-Stromberg E, Steranka J, Burns KH, Sabunciyan S, Irizarry RA: Visualization and probability- based scoring of structural variants within repetitive sequences. Bioinformatics 2014, 30:1514–1521.
5. Scharpf RB, Mireles L, Yang Q, Köttgen A, Ruczinski I, Susztak K, Halper-Stromberg E, Tin A, Cristiano S, Chakravarti A, Boerwinkle E, Fox11 CS, Coresh J, Linda Kao WH: Copy number poly- morphisms near SLC2A9 are associated with serum uric acid concentrations. BMC Genet 2014, 15:81.
6. Castaldi P, Obeidat M, Halper-Stromberg E, Lamb A, Chase R, Parker M, Carey V, Tal-Singer R, Silverman E, Pare P, Sin D, Hersh C: Buffet-Style Expression Factor-Adjusted Discovery Increases the Yield of Robust Expression Quantitative Trait Loci. bioRxiv 2015.
7. Dowell R, Odell A, Richmond P, Malmer D, Halper-Stromberg E, Bennett B, Larson C, Leach S, Radcliffe RA: Genome characterization of the selected long- and short-sleep mouse lines. Mamm Genome 2016, 27:574–586.
8. Boueiz A, Lutz SM, Cho MH, Hersh CP, Bowler RP, Washko GR, Halper-Stromberg E, Bakke P, Gulsvik A, Laird NM, Beaty TH, Coxson HO, Crapo JD, Silverman EK, Castaldi PJ, DeMeo DL, COPDGene and ECLIPSE Investigators: Genome-Wide Association Study of the Genetic Determinants of Emphysema Distribution. Am J Respir Crit Care Med 2017, 195:757–771.
9. Halper-Stromberg E, Cho MH, Wilson C, Nevrekar D, Crapo JD, Washko G, San José Estépar R, Lynch DA, Silverman EK, Leach S, Castaldi PJ: Visual Assessment of Chest CT Images is Independently Useful for Genetic Association Analysis in Studies of Chronic Obstructive Pulmonary Disease. Ann Am Thorac Soc 2016:AnnalsATS.201606-427OC.
10. Pollack RA, Jones RB, Pertea M, Bruner KM, Martin AR, Thomas AS, Capoferri AA, Beg SA, Huang S-H, Karandish S, Hao H, Halper-Stromberg E, Yong PC, Kovacs C, Benko E, Siliciano RF, Ho Y-C: Defective HIV-1 Proviruses Are Expressed and Can Be Recognized by Cytotoxic T Lymphocytes, which Shape the Proviral Landscape. Cell Host Microbe 2017, 21:494–506.e4.
11. Halper-Stromberg E, Yun JH, Parker MM, Tal Singer R, Gaggar A, Silverman EK, Leach S, Bowler RP, Castaldi PJ. Systemic Markers of Adaptive and Innate Immunity are Associated with COPD Severity and Spirometric Disease Progression. Am J Respir Cell Mol Biol 2017.rcmb:2017-0373OC.
12. Dietert, k, Tak, T, R, Knipe, Halper-Stromberg, E. April Highlights/Papers by Junior Investigators/NIH News. Am J of Respir Cell Mol Bio: 2018,58(4), p. iv
13. Halper-Stromberg E, Gillenwater L, Cruickshank-Quinn C, O’Neal W.K, Reisdorph N, Petrache I, Zhuang Y, Labaki W.W, Curtis J.L, Wells J, Rennard S, Pratte K.A, Woodruff P, Stringer K.A, Kechris K, Bowler R.P, Bronchoalveolar Lavage Fluid from COPD Patients Reveals More Compounds Associated with Disease than Matched Plasma. Metabolites 2019, 9, 157.
14. Halper-Stromberg E, Gallo T, Champakanath A, Taki I, Rewers M, Snell-Bergeon J, Frohnert B, Shah VN, Bone Mineral Density across the Lifespan in Patients with Type 1 Diabetes, The Journal of Clinical Endocrinology & Metabolism, Volume 105, Issue 3, March 2020, dgz153
15. Lucas A. Gillenwater, Katherine A. Pratte, Brian D. Hobbs, Michael H. Cho, Yonghua Zhuang, Eitan Halper-Stromberg, Charmion Cruickshank-Quinn, Nichole Reisdorph, Irina Petrache, Wassim W. Labaki, Wanda K. O'Neal, Victor E. Ortega, Dean P. Jones, Karan Uppal, Sean Jacobson, Gregory Michelotti, Christine H. Wendt, Katerina J. Kechris, and Russell P. Bowler. Plasma Metabolomic Signatures of Chronic Obstructive Pulmonary Disease and the Impact of Genetic Variants on Phenotype-Driven Modules. Network and Systems Medicine. Dec 2020.159-181
16. Halper-Stromberg E, McCall C, Haley L, Lin M, Vogt S, Gocke C, Eshleman J, Stevens W, Martinson N, Epeldegui M, Holdhof M, Bettegowda C, Glantz M, Ambinder R, Xian R, CloneRetriever: An Automated Algorithm to Identify Clonal B and T Cell Gene Rearrangements by Next-Generation Sequencing for the Diagnosis of Lymphoid Malignancies, Clinical Chemistry, Volume 67, Issue 11, November 2021, Pages 1524–1533, https://doi.org/10.1093/clinchem/hvab141
