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About
Associate Professor
UAMS College of Medicine
Biomedical Informatics
UAMS, Little Rock
Publications
- Johann, D, "The Design of the MATE Test Executive", IEEE Symposium on Automatic Test Equipment, November, 1987.
- Johann, D, "A General Purpose Expert System", MUG Quarterly, June, 1991.
- Margolin D, Johann D, Fallon W, Malangoni M, "Response after Out-of-Hospital Cardiac Arrest in the Trauma Patient Should Determine Aeromedical Transport to a Trauma Center", The Journal of Trauma, Injury, Infection, and Critical Care, 1996 41(4) 721-725.
- Hingorani S, Petricoin E, Maitra A, Rajapakse V, King C, Conrads T, Veenstra T, Hitt B, Kawaguchi Y, Johann D, Liotta L, Crawford H, Putt M, Jacks T, Wright C, Hruban R, Lowy A, Tuveson D, “Preinvasive and Invasive Ductal Pancreatic Cancer and its Early Detection in the Mouse”, Cancer Cell, 2003: 4(6): 437-450.
- Johann D, McGuigan M, Tomov S, Fusaro V, Ross S, Conrads T, Veenstra T, Fishman D, Whiteley G, Petricoin, E, Liotta L. “Novel Approaches to Visualization and Data Mining Reveals Enrichment of Diagnostic Information in the Low Amplitude Region of Serum Mass Spectra from Ovarian Cancer Patients”, Disease Markers. 2003- 2004; 19(4-5): 197-207.
- Conrads, T. P., Fusaro, V. A., Ross, S., Johann, D., Rajapakse V., Hitt, B. A., Steinberg, S. M., Kohn, E. C., David A. Fishman, Whiteley, G., Barrett, J. C., Liotta, L. A., Petricoin, E. F., and Veenstra, T. D. High-resolution serum proteomic features for ovarian cancer detection. Endocrine Related Cancer . 2004 (11) 163-178.
- Petricoin E, Rajapaske V, Herman E, Arekani A, Ross S, Johann D, Knapton A, Zhang J, Hitt B, Conrads T, Veenstra T, Liotta L, Sistare F. “Toxicoproteomics: Serum Proteomic Pattern Diagnostics for Early Detection of Drug Induced Cardiac Toxicities and Cardioprotection”, Toxicologic Pathology, 2004 32(Suppl. 1): 122-130.
- Johann D, Liotta L, Petricoin E. “Some Statistical Issues and Utility of Surrogate Biomarker Endpoints”, International Chinese Statistical Association. 2004: p. 37-40.
- Johann D, McGuigan M, Tomov S, Petricoin E, Liotta L. “Towards a Systems Biology Toolkit”, Proceedings of the 17th IEEE Symposium on Computer-Based Medical Systems (CBMS ’04)”, 2004, 500-505.
- Johann D, McGuigan M, Patel A, Tomov S, Ross S, Conrads T, Veenstra T, Fishman D, Whiteley G, Petricoin E, Liotta L. “Clinical Proteomics and Biomarker Discovery”, Annals of the New York Academy of Sciences, 2004: (1022) 295-305.
- Brouwers F, Petricoin E, Ksinantova L, Breza J, Rajapakse V, Ross S, Johann D, Mannelli M, Shulkin B, Kvetnansky R, Eisenhofer G, McClellan W, Hitt B, Conrads T, Veenstra T, Mannion D, Wall M, Wolfe G, Fusaro V, Liotta L, Pacak K. “Low Molecular Weight Proteomic Information Distinguishes Metastatic from Benign Pheochromocytoma”, Endrocine-Related Cancer, 2005, 12, 263-272.
- Menard C, Johann D, Lowenthal M, Muanza T, Sproull M, Ross S, Gulley J, Liotta L, Coleman N, Petricoin E, Camphausen K. “Discovering Clinical Biomarkers of Ionizing Radiation Exposure with Serum Proteomic Analysis”, Cancer Research, 2006; 66: (3) 1844 – 1850.
- Geho D, Cheng MC, Killian K, Lowenthal M, Ross S, Frogale K, Nijdam J, Lahar N, Johann D, Herrmann P, Whiteley G, Ferrari M, Petricoin E, Liotta L “Fractionation of Serum Components Using Nanoporous Substrates”, Bioconjugate Chem. 2006, 17, 654-661.
- Petricoin E, Espina V, Araujo R, Midura B, Yeung C, Wan X, Eichler G, Johann D, Meyer W, Qualman S, Anderson J, Steinberg S, Tsokos M, Kartik K, Helman L, Liotta L. “Phosphoprotein pathway mapping: AKT/mammalian target of rapamycin activation is negatively associated with childhood Rhabdomyosarcoma Survival”, Cancer Research. 2007 Apr 1;67(7):3431-40
- Johann DJ Jr, Veenstra TD. “Multiple Biomarkers in Molecular Oncology”, Expert Reviews in Molecular Diagnostics. 2007. May; 7(3):223-5.
- Johann DJ, Blonder J. “Fluids vs. Tissues vs. Both”, Expert Reviews in Molecular Diagnostics. 2007. Sept; 7(5):473-5.
- Blonder J, Johann DJ, Veenstra TD, Xiao Z, Emmert-Buck MR, Ziegler RG, Rodriguez-Canales J, Hanson JA, Xu X. Quantitation of steroid hormones in thin fresh frozen tissue sections. Analytical Chem. 2008 Nov 15;80(22):8845-52.
- Mbeunkui F, Johann DJ Jr. Cancer and the tumor microenvironment: a review of an essential relationship. Cancer Chemother Pharmacol. 2009 Mar;63(4):571-82.
- Johann DJ, Rodriguez-Canales J, Mukherjee S, Prieto DA, Hanson JC, Emmert-Buck M, Blonder J. Approaching solid tumor heterogeneity on a cellular basis by tissue proteomics using laser capture microdissection and biological mass spectrometry. J Proteome Res. 2009 May; 8(5):2310-8.
- Ye X, Johann DJ Jr, Hakami RM, Xiao Z, Meng Z, Ulrich RG, Issaq HJ, Veenstra TD, Blonder J. Optimization of protein solubilization for the analysis of the CD14 human monocyte membrane proteome using LC-MS/MS. J Proteomics. 2009 Nov 2;73(1): 112-22.
- Johann DJ, Bih-Rong W, Prieto DA, Chan KC, Ye X, Rudnick PA, Xiao Z, Stein SE, Issaq HJ, Veenstra TD, Blonder J. Combined Blood/Tissue Analysis for Cancer Biomarker Discovery: Application to Renal Cell Carcinoma. Analytical Chemistry. 2010 March 1;82(5): 1584-8.
- Ye X, Luke BT, Johann DJ, Ono A, Prieto DR, Chan KC, Issaq HJ, Veenstra TD, Blonder J. Optimized method for computing 18O/16O ratios of differentially stable-isotope labeled peptides in the context of post digestion 18O exchange/labeling. Analytical Chemistry. 2010 July 82(13): 5878-86.
- Johann DJ, Mukherjee S, Prieto DA, Veenstra TD, Blonder J. Profiling solid tumor heterogeneity by LCM and biological MS of fresh frozen tissue sections. Methods in Molecular Biology. 2011; 755: 95-106.
- Wei BH, Simpson RM, Johann DJ, Dwyer J, Prieto DA, Ye X, Luke B, Shive HR, Webster JD, Hoover SB, Veenstra TD, Blonder J. Proteomic profiling of H-Ras-G12V induced hypertrophic cardiomyopathy in transgenic mice using comparative LC-MS analysis of thin fresh-frozen tissue sections. J of Proteome Res. 2012 Mar 2;11(3) 1561-70.
- Ye X, Luke BT, Johann DJ, Chan CC, Prieto DA, Ono A, Veentra TD, Blonder J. Post-digestion 18O exchange/labeling for quantitative shotgun proteomics of membrane proteins. Methods in Molecular Biology. 2012 893: 223-40.
- Usmani SZ, Sawyer J, Rosenthal A, Cottler-Fox M, Epstein J, Yaccoby S, Sexton R, Hoering A, Singh Z, Heuck CJ, Waheed S, Chauhan N, Johann D, Abdallah AO, Muzaffar J, Petty N, Baily C, Crowley J, van Rhee F, Barlogie B. Risk factors for MDS and acute leukemia following total therapy 2 and 3 for multiple myeloma. Blood, April 19, 4753-7.
- Mukherjee S, Rodriquez-Canales J, Hanson J, Emmert-Buck MR, Tangrea MA, Prieto DA, Blonder J, Johann D. Proteomic Analysis of Frozen Tissue Samples Using Laser Capture Microdissection. Methods in Molecular Biology. 2013 1002: 71-83.
- Ye X, Chan KC, Prieto DA, Luke BT, Johann DJ Jr, Stockwin LH, Newton DL, Blonder J. Trypsin-mediated 18O/16O labeling for biomarker discovery. 2013 Methods in Molecular Biology. 2013 1002:133-49
- Papanikolaou X, Szymonifka J, Rosenthal A, Heuck CJ, Mitchell A, Johann D, Keller J, Waheed S, Usmani SZ, van Rhee F, Bailey, C, Petty N, Hoering A, Crowley J, Barlogie B. Metronomic therapy is an effective salvage treatment for heavily pretreated relapsed/refractory multiple myeloma. Haematologica. 2013, May 28. 1147-53.
- Chavan SS, Bauer MA, Peterson EA, Heuck CJ, Johann DJ. Towards the integration, annotation and association of historical microarray experiments with RNA-seq. 2013 BMC Bioinformatics Suppl 14:S4.
- Abdallah AO, Atrash S, Shahid Z, Jameel M, Grazziutti M, Apewokin S, Kumar NS, Restrepo A, Waheed S, Van Rhee F, Heuck CJ,Johann D Jr, Barlogie B, Usmani SZ. Patterns of Central Nervous System Involvement in Relapsed and Refractory Multiple Myeloma. 2013 Clin Lymphoma Myeloma Leuk. 211-4
- Sawyer JR, Tian E, Heuck CJ, Epstein J, Johann DJ, Swanson CM, Lukacs JL, Johnson M, Binz R, Boast A, Sammartino G, Usmani S, Zangari M, Waheed S, van Rhee F, Barlogie B. Jumping translocations of 1q12 in multiple myeloma: a novel mechanism for deletion of 17p in cytogenetically defined high-risk disease. 2014 April 14. 2504-12.
- Prieto DA, Johann DJ, Wei B, Ye X, Chan KC, Nissley DV, Simpson RM, ACitrin DE, Mackall CL, Blonder J. Clinical proteomics in cancer biomarker research: A case for immunodepletion of abundant blood-derived proteins from tissue homogenates. 2014 Future Medicine, 269-86.
- Bauer MA, Peterson EA, Chavan SS, Heuck CJ, Johann DJ. Leveraging the new with the old: providing a framework for the integration of historic microarray studies with next generation sequencing. 2014 BMC Bioinformatics, Oct 21, Suppl 11:S3.
- Peterson EA, Chavan SS, Bauer MA, Heuck CJ, Johann DJ. Revealing the inherent heterogeneity of human malignancies by variant consensus strategies coupled with cancer clonal analysis. 2014 BMC Bioinformatics Oct 21, Suppl 11:S9.
- Sawyer, Jeffrey R; Erming Tian; Christoph J. Heuck; Donald J. Johann; Epstein, Joshua; Swanson, Charles M; Janet L. Lukacs; Binz, Regina K; Marian Johnson; Gael Sammartino; Zangari, Maurizio; Faith E. Davies; Frits van Rhee; Gareth J. Morgan; Barlogie, Bart. Evidence of an Epigenetic Origin for High-Risk 1q21 Copy Number Aberrations in Multiple Myeloma. 2015 Blood June 11. 3756-9.
- Peterson EA, Bauer MA, Chavan SS, Ashby C, Weinhold N, Heuck CJ, Morgan GJ, Johann DJ. Enhancing Cancer Clonality Analyses with Integrative Genomics. 2015 BMC Bioinformatics, Sep 25;16 Suppl 13:S1 PMID: 26424691
- Wren JD, Thakkar S, Homayouni R, Johann DJ, Dozmorov MG. Proceeding of the 2015 MidSouth Computational Biology and Bioinformatics Society (MCBIOS) Conference – Editorial. 2015 BMC Bioinformatics, Suppl 1:S14.
- Prieto DA, Chan KC, Johann DJ, Ye X, Whitely G, Blonder J. Preparation and Immunoaffinity Depletion of Fresh Frozen Tissue Homogenates for Mass Spectrometry-Based Proteomics in the Context of Drug Target/Biomarker Discovery. 2017 Methods in Molecular Biology. 1647: 71-90.
- Prieto DA, Whiteley G, Blonder, J, Johann DJ. Protocol for the Analysis of Laser Capture Microdissected Fresh-Frozen Tissue Homogenates by Silver-Stained 1D SDS-PAGE. Methods in Molecular Biology, 2018, 1723: 95-110.
- Johann DJ, Steliga M, Shin IJ, Yoon D, Jeffers S, Arnaoutakis K, Hutchins L, Liu M, Liem J, Walker K, Pereira A, Yang M, Peterson E, Xu J. Liquid Biopsy and its Role in an Advanced Clinical Trial for Lung Cancer, 2018 Experimental Biology and Medicine, 262-71.
- Ye X, Luke BT, Wei BR, Kaczmarczyk JA, Loncarek J, Dwyer JE, Johann DJ, Saul RG, Nissley DV, McCormick F, Whiteley GR, Blonder J. Direct Molecular Dissection of Tumor Parenchyma from Tumor Stroma in Tumor Xenografts Using Mass Spectrometry Based Glyco-Proteomics. 2018 Oncotarget, 26431-26452.
- Hipp JD, Johann DJ, Chen Y, Madabhushi A, Monaco J, Chemg J, Rodriguez-Canales J, Stumpe MC, Riedlinger G, Rosenberg AZ, Hanson JC, Kunju LP, Emmert-Buck MR, Balis UJ, Tangrea MA. Computer Aided Laser Dissection: A Microdissection Workflow Leveraging Image Analysis Tools. 2018 Journal of Pathology Informatics, 9:45, 1-9.
- Ashby C, Peterson EA, Bauer M, Johann DJ. A Scalable and Adaptive Approach for NGS Analyses Leveraging High-Performance Computing. Pathological Specimens and Genomic Medicine: Emerging Issues, p.248
- Vara N, Yuqing L, Yan Y, Lensing SY, Colorado N, Robinson D, Zhang X, Peterson, EA, Baltz NJ, Zhou D, Johann DJ, Emanuel PD, Liu YL. Sustained fetal hematopoiesis causes juvenile death from leukemia: evidence from a dual-age-specific mouse model. 2020 Blood Advances – accepted for publication 6/20
- Johann DJ and Authors – Blood Profiling Atlas in Cancer (BloodPAC) Consortium. Minimal Technical Data Elements for Liquid Biopsy Data Submitted to Public Databases. 2020, Clinical Pharmacology & Therapeutics PMID: 32017048
- Johann DJ and Authors – Blood Profiling Atlas in Cancer (BloodPAC) Consortium. Generic Protocols for the Analytical Validation of Next-Generation Sequencing-Based ctDNA Assays: A Joint Consensus Recommendation of the BloodPAC’s Analytical Variables Working Group. 2020, Clinical Chemistry, 1156-1166.
- Johann DJ, Stephens O, Roberge A, Emmert-Buck M, Laun S, Tangrea M. Microdissection methods utilizing single cell subtype analysis and the impact on precision medicine. 2021 (Accepted for publication, Methods in Molecular Biology)
- Johann DJ and Authors – SEQC2 Deep Sequencing Group. Evaluating the analytical validity of circulating tumor DNA sequencing for precision oncology. 2021. (Accepted for publication, Nature Biotechnology). *Corresponding author
- Johann DJ and Authors – Blood Profiling Atlas in Cancer (BloodPAC) Consortium. The BloodPAC Data Commons for Liquid Biopsy Data. 2021, (Manuscript in review, JCO Clinical Cancer Informatics [ASCO Journal])
- Johann DJ and Authors – SEQC2 Deep Sequencing Group. A validated genomic reference material for assessing performance of cancer panels detecting small variants of low allele frequency. 2021. (Manuscript in review, Genome Biology).
- Johann DJ and Authors – SEQC2 Deep Sequencing Group. Cross-oncopanel study reveals high sensitivity and accuracy with overall analytical performance depending on genomic regions. 2021. (Accepted for publication, Genome Biology).
- Johann DJ and Authors – SEQC2 Deep Sequencing Group. Assessing synthetic reference sequence internal standards as quality-control for NGS measurement of actionable mutations in circulating tumor DNA. 2021. (Manuscript in review, Cell Genomics).
- Johann DJ and Authors – SEQC2 Deep Sequencing Group. Deep oncopanel sequencing reveals fixation time and within block position-dependent quality degradation in FFPE processed samples. 2021. (Manuscript in review, Cell Genomics).
- Johann DJ and Authors muliti-institutional. Targeting Ras-driven cancers via downstream effectors. 2021. Manuscript in review, Cancer Cell).
- Johann DJ, Liu M, Roberge A, Emmert-Buck M, Tangrea M. Enhancing the specificity of precision medicine assays via optimized immuno-microdissection. 2021 (manuscript in progress)
- Johann DJ, Mukherjee S, Prieto DA, Wei BH, Blonder J. Towards a cancer proteome atlas: lessons learned from proteomic profiling of renal cell carcinoma. 2021 (manuscript in progress)
- Johann DJ, Mukherjee S, Prieto DA, Blonder J. Towards the use of clinical tissue proteomics for differential molecular profiling of breast tumor subtypes for individualized therapy. 2021 (manuscript in progress)