Publications - Molecular HealthMolecular Health




Explore a selection of articles and posters that have been published over the years. 

Consolidated BRCA1/2 Variant Interpretation by MH BRCA Correlates with Predicted PARP Inhibitor Efficacy Association by MH Guide
Yosuke Hirotsu, Udo Schmidt-Edelkraut et al. Int. J. Mol. Sci. 2020, 21(11), 3895; (registering DOI).

Onset of Hippocampal Network Aberration and Memory Deficits in P301S Tau Mice Are Associated With an Early Gene Signature

Przybyla M., von Eersel  J., van Hummel A., van der Hoven J., Sabale M., Harasta A., Müller J., Gajwani M., Prikas E., Mueller T., Stevens C., Power J., Housley G., Karl T., Kassiou M., Ke Y., Ittner A., Ittner L.; Brain 2020 May 6; awaa133. doi: 10.1093/brain/awaa133.

Adverse Event Circumstances and the Case of Drug Interactions.
Soldatos, Jackson. Healthcare (Basel). 2019 Mar 19;7(1). pii: E45. doi: 10.3390/healthcare7010045.

Precision Oncology – The Quest for Evidence

Soldatos TG, Kaduthanam S, Jackson DB. 2019 Sep 5;9(3). pii: E43. doi: 10.3390/jpm9030043.

Target-Adverse Event Profiles to Augment Pharmacovigilance: A Pilot Study With Six New Molecular Entities
Peter Schotland, Rebecca Racz, David Jackson, Robert Levin, David G. Strauss and Keith Burkhart 

Association Between Serotonin Syndrome and Second-Generation Antipsychotics via Pharmacological Target-Adverse Event Analysis 
Racz, Soldatos, Jackson, Burkhart. Clin Transl Sci (2018) 00, 1–8; doi:10.1111/cts.12543 

In Silico Profiling of Clinical Phenotypes for Human Targets Using Adverse Event Data.
Soldatos, Taglang, Jackson. High Throughput. 2018 Nov 23;7(4). pii: E37. doi: 10.3390/ht7040037.

Retrospective Side Effect Profiling of the Metastatic Melanoma Combination Therapy Ipilimumab-Nivolumab Using Adverse Event Data.
Soldatos. Diagnostics (Basel). 2018 Oct 31;8(4). pii: E76. doi: 10.3390/diagnostics8040076.

Reliability of algorithmic somatic copy number alteration detection from targeted capture data 
Rieber, Bohnert, Ziehm, Jansen Bioinformatics. 2017 Sep 15;33(18):2791-2798 

Comprehensive Benchmarking of SNV Callers for Highly Admixed Tumors 
Bohnert R, Vivas S, Jansen G; 2017, PLoS ONE 12(10): e0186175.

Bioinformatory-assisted analysis of next-generation sequencing data for precision medicine in pancreatic cancer
Stecker, Huelsewig, Brock, Jackson. 2017; Mol Oncol. 2017 Oct;11(10):1413-1429.



Improving drug safety with a systems pharmacology approach. 
Bojunga, Zien Eur J Pharm Sci. 2016 Oct 30;94:84-92. doi: 10.1016/j.ejps.2016.06.009 

A multigene mutation classification of 468 colorectal cancers reveals a prognostic role for APC 
Bien-Willner Nat. Commun. 7, 11743. doi:10.1038/ncomms11743 

Data mining FAERS to analyse molecular targets highly associated with Stevens Johnson Syndrome 
Jackson J Med Toxicol. 2015 Jun;11(2):265-73. doi: 10.1007/s13181-015-0472-1. 

Erythropoietin Stimulates Tumor Growth via EphB4 
Jackson, Brock, Stein Cancer Cell. 2015 Nov 9;28(5):610-22. PMID: 26481148 

How to learn about gene function: text-mining or ontologies? 
Soldatos; Perdigão; Brown; Sabir; O’Donoghue Methods. 2015 Mar;74:3-15. PMID:25088781 

Relationships of clinical response to relevant molecular signal during Phase I testing of Aurora Kinase A inhibitor: Retrospective assessment 
Bien-Willner, Jackson Integrative Molecular Medicine: DOI: 10.15761/IMM.1000162 

Visual Analytics of Gene Sets Comparison 
Perdigao; Soldatos; Sabir; O’Donoghue Big Data Visual Analytics (BDVA), 2015 

Drugs Highly Associated with Infusion Reactions Reported Using Two Different Data-mining Methodologies 
Moore, Burkhart, Jackson J Blood Disord Transfus 5:195. doi: 10.4172/2155-9864.1000195 

Biggest challenges in bioinformatics. 
Fuller; Khoueiry; Dinkel; Forslund; Stamatakis; Barry; Budd; Soldatos; Linssen; Rajput; HUB Participants. EMBO Rep. 2013 Apr;14(4):302-4 PMID:23492829

Src activation by b-adrenoreceptors is a key switch for tumour metastasis 
Zien, Soldatos, Jackson Nat Commun. 2013;4:1403. PMID: 23360994 

Systemic microRNA measurement, a useful tool for predicting diagnosis in bladder cancer 
Zien, Jackson Urol Oncol. 2013 Nov;31(8):1701-8 PMID: 22863868  

A Scatter-Based Prototype Framework and Multi-Class Extension of Support Vector Machines 
Jenssen R, Kloft M, Zien A, Sonnenburg S, Müller KR. Plos One 7(10): e42947. PMID: 23118845 

Caipirini: using gene sets to rank literature. 
Soldatos; O’Donoghue; Satagopam; Barbosa-Silva; Pavlopoulos; Wanderley-Nogueira; Soares-Cavalcanti; Schneider BioData Min. 2012 Feb 1;5(1):1 PMID:22297131 

Mining Cell Cycle Literature Using Support Vector Machines 
Soldatos; Pavlopoulos Artificial Intelligence: Theories and Applications, Volume 7297 of the series Lecture Notes in Computer Science pp 278-284 

EMT is the dominant program in human colon cancer.
Jackson BMC Med Genomics. 2011 Jan 20;4:9. PMID: 21251323 

Genetic determinants of anticancer drug activity: towards a global approach to personalized cancer medicine. 
Picker, Jackson Expert Rev Mol Diagn. 2011 Jul;11(6):567-77. PMID: 21745011 

Intelligent Clinical Decision Support Systems for Non-invasive Bladder Cancer Diagnosis 
Zien, Jackson Computational Intelligence Methods for Bioinformatics and Biostatistics Volume 6685 of the series Lecture Notes in Computer Science pp 253-262 

Personalized cancer medicine–advances and socio-economic challenges. 
Jackson, Sood Nat Rev Clin Oncol. 2011 Oct 11;8(12):735-41: PMID: 21989071 

Using graph theory to analyze biological networks 
Pavlopoulos; Secrier; Moschopoulos; Soldatos; Kossida; Aerts; Schneider; Bagos BioData Min. 2011 Apr 28;4:10 PMID:21527005 

Drug profiling: knowing where it hits. 
Jackson Drug Discov Today. 2010 Sep;15(17-18):749-56. 

LAITOR – Literature Assistant for Identification of Terms co-Occurrences and Relationships 
Barbosa-Silva; Soldatos; Magalhães; Pavlopoulos; Fontaine; Andrade-Navarro; Schneider; Ortega. MC Bioinformatics. 2010 Feb 1;11:70. PMID:20122157 

Clinical and economic impact of the nonresponder phenomenon–implications for systems based discovery. 
Jackson Drug Discov Today. 2009 Apr;14(7-8):380-5. PMID: 19200855 

Molecular perspectives on the non-responder phenomenon. 
Jackson Drug Discov Today. 2009 Apr;14(7-8):373-9. PMID: 19200455 

Serum-based microRNAs: are we blinded by potential? 
Jackson Proc Natl Acad Sci U S A. 2009 Jan 6;106(1):E5 PMID: 19106287 


Increased BRCA1/2 classification confidence: comparison of ACMG to public database classification – call for systematic molecular profiling 
Kaduthanam, Schmidt-Edelkraut, Santiago-Mozos, Hartenfeller, Narang, Hermanns, Stein, Jackson, Weber, Hettich, Brock, Soldatos ESHG Mailand 2018 Poster abstract (P16.09A (Section P16 – Omics/Bioinformatics)) 

A machine-learning based functional and clinical impact score for prioritizing variants of unknown significance 
Hayat, Hartenfeller, Soldatos, Jansen, Stein WIN 2016 – Poster abstract (e-Poster Session Bioinformatics P1.1) 


Adverse effects of erythropoietin stimulates tumor growth via EphB4 
Jackson Proceedings of the 106th Annual Meeting of the American Association for Cancer Research; 2015 Apr 18-22; Philadelphia, PA. Philadelphia (PA): AACR; Cancer Res 2015;75(15 Suppl):Abstract nr 1952. 


Identification of ERBB2 gene variants in HER2 positive disease associated with trastuzumab response in an adjuvant trastuzumab chemotherapy trial 
Zien, Gunn, Hartenfeller, Diella, Brock, Stein, Badbanchi,Doerks, Jackson Proceedings of the Thirty-Seventh Annual CTRC-AACR San Antonio Breast Cancer Symposium: 2014 Dec 9-13; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2015;75(9 Suppl):Abstract nr P3-06-22. 


Automated retrieval and assessment of biomarker-related evidence for cancer treatment decision support 
Zien, Hartenfeller, Diella, Doerks, Soldatos, Jackson Proceedings of the AACR Precision Medicine Series: Drug Sensitivity and Resistance: Improving Cancer Therapy; Jun 18-21, 2014; Orlando, FL. Philadelphia (PA): AACR; Clin Cancer Res 2015;21(4 Suppl): Abstract nr A41. 


Pilot study characterizing the combined clinical actionability of multiplexed germline and tumor biomarkers. 
Soldatos; Morandell; Diella; Badbanchi; Doerks; Sulzer; Stecher; Bien-Willner; Jackson; Stein  


Knowledge prioritization of cancer genomes using oncoscores and functional impact scores to support biomarker discovery and clinical decision making 
Soldatos; Badbanchi; Vivas; Zien; Diella; Hartenfeller; Picker; Stein; Jackson Proceedings of the AACR Special Conference on Translation of the Cancer Genome; Feb 7-9, 2015; San Francisco, CA. Philadelphia (PA): AACR; Cancer Res 2015;75(22 Suppl 1):Abstract nr A1-33. 


Prevalence of secondary genetic modifiers on cancer drug biomarkers and implications for the clinical utility of gene-based diagnostics 
Sonia Vivas, Francesca Diella, Alexander Zien 

Bisphosphonates: New strategies for targeting angiogenesis in ovarian cancer 
Zien, Jackson Proceedings of the 105th Annual Meeting of the American Association for Cancer Research; 2014 Apr 5-9; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2014;74(19 Suppl):Abstract nr 2983


Systems-level analysis of drug interactions in cancer patients supports the need for a broader analytical approach to personalized cancer medicine 
Taglang; Soldatos; Sulzer; Jackson 


A knowledge-driven strategy based on cancer-specific disease mechanisms provides a new tool for clinical trial prioritization 
Soldatos; Sulzer; Hartenfeller; Badbanchi; Diella; Stein; Jackson 

Development of a computational framework for disease knowledge modeling and clinical treatment decision support and its application to a rare cancer, malignant peripheral nerve sheath tumor (MPNST) 
Proceedings of the 103rd Annual Meeting of the American Association for Cancer Research; 2012 Mar 31-Apr 4; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2012;72(8 Suppl):Abstract nr 3003 


Molecular dynamics of SrcS17 activation in chronic stress-induced tumor growth 
Zien, Jackson Proceedings of the 102nd Annual Meeting of the American Association for Cancer Research; 2011 Apr 2-6; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2011;71(8 Suppl):Abstract nr 937. 


MASE: A system for the molecular analysis of side effect information and its application to marketed cancer therapeutics 
Soldatos, Diella, Zien, Brock, Taglang, Jackson FDA drug safety workshop


Systemic microRNA measurement, a useful tool for intelligent clinical decision support systems in bladder cancer 


Conquering resistance to targeted therapies through system-based analysis of clinico-molecular information 
Stein, Jackson Mol. Cancer Ther. 8, A34–A34. doi:10.1158/1535-7163.TARG-09-A34