See also my Google Scholar profile.
- Oligonucleotides for modulating RTEL1 expression. (2020)
- Pyrrolo[2,3-b]pyrazine compounds as cccDNA inhibitors for the treatment of Hepatitis B Virus (HBV) infection. (2018)
- Edited by Adetayo Kasim, S. H., Ziv Shkedy, Sebastian Kaiser & Talloen, W. Applied Biclustering Methods for Big and High-Dimensional Data Using R (Chapman & Hall/CRC Biostatistics Series). Chapman and Hall/CRC (2016). (Publisher’s Link, Amazon).
- Fang, T., Davydov, I., Marbach, D. & Zhang, J. D. Gene-set enrichment with regularized regression (2019).
- Zhang, Y. et al. A Novel, Anatomy-Similar in Vitro Model of 3D Airway Epithelial for Anti-Coronavirus Drug Discovery (2021)
- Geser, P. and Zhang, J. D. Gene symbol recognition with GeneOCR (2022)
- Michoel, T. and Zhang, J. D. Causal inference in drug discovery and development (2022)
Conference posters and papers
- Klughammer, B et al. P805 Selnoflast, a potent NLRP3 inhibitor - results from a phase 1b experimental medicine study in patients with Ulcerative Colitis. Journal of Crohn’s and Colitis (2023)
- Wang, L. et al. Discovery of a first-in-class orally available HBV cccDNA inhibitor, Journal of Hepatology (2022)
- Chen, D. et al. Discovery of Novel cccDNA Reducers toward the Cure of Hepatitis B Virus Infection, Journal of Medicinal Chemistry (2022)
- Gatti, L. et al. Cross-reactive immunity potentially drives global oscillation and opposed alternation patterns of seasonal influenza A viruses, Scientific Reports (2022)
- Jaklin, M. et al. Optimization of the TeraTox assay for preclinical teratogenicity assessment, Toxicological Sciences (2022)
- Mädler, S. et al. Besca, a single-cell transcriptomics analysis toolkit to accelerate translational research, NAR Genomics and Bioinformatics (2021)
- Sturm, G. et al. Tissue heterogeneity is prevalent in gene expression studies, NAR Genomics and Bioinformatics (2021)
- Zhang, J. D. Ten Simple Rules for Doing A Postdoc In Pharma, PLOS Computational Biology (2021)
- Reich, et al. Alzheimer’s Risk Gene TREM2 Determines Functional Properties of New Type of Human iPSC-Derived Microglia, Frontiers in Immunology (2021)
- Jaklin, et al. Focus on germ-layer markers: A human stem cell-based model for in vitro teratogenicity testing. Reproductive Toxicology (2020)
- Roudnicky, F. et al. Inducers of the endothelial cell barrier identified through chemogenomic screening in genome-edited hPSC-endothelial cells. Proceedings of the National Academy of Sciences (2020)
- Gutbier, S. et al. Large-Scale Production of Human iPSC-Derived Macrophages for Drug Screening. International Journal of Molecular Sciences (2020)
- Zaidan, M. et al. Signaling pathways predisposing to chronic kidney disease progression. JCI Insight (2020)
- Badillo, S. et al. An Introduction to Machine Learning. Clinical Pharmacology & Therapeutics (2020).
- Zhang, J. D., Sach-Peltason, L., Kramer, C., Wang, K. & Ebeling, M. Multiscale modelling of drug mechanism and safety. Drug Discovery Today (2019).
- Sturm, G. et al. Comprehensive evaluation of transcriptome-based cell-type quantification methods for immuno-oncology. Bioinformatics 35, i436–i445 (2019).
- Roudnicky, F. et al. Modeling the Effects of Severe Metabolic Disease by Genome Editing of hPSC-Derived Endothelial Cells Reveals an Inflammatory Phenotype. International Journal of Molecular Sciences 20, 6201 (2019).
- Choobdar, S. et al. Assessment of network module identification across complex diseases. Nature Methods 16, 843–852 (2019).
- Mueller, H. et al. A novel orally available small molecule that inhibits hepatitis B virus expression. Journal of Hepatology 68, 412–420 (2018).
- Zhang, J. D. et al. Detect tissue heterogeneity in gene expression data with BioQC. BMC Genomics 18, 277 (2017).
- Moisan, A. et al. Inhibition of EGF Uptake by Nephrotoxic Antisense Drugs In Vitro and Implications for Preclinical Safety Profiling. Molecular Therapy-Nucleic Acids 6, 89–105 (2017).
- Drawnel, F. M. et al. Molecular Phenotyping Combines Molecular Information, Biological Relevance, and Patient Data to Improve Productivity of Early Drug Discovery. Cell Chemical Biology 24, 624–634 (2017).
- Boess, F. et al. Use of early phenotypic in vivo markers to assess human relevance of an unusual rodent non-genotoxic carcinogen in vitro. Toxicology 379, 48–61 (2017).
- Raza, U. et al. The miR-644a/CTBP1/p53 axis suppresses drug resistance by simultaneous inhibition of cell survival and epithelial-mesenchymal transition in breast cancer. Oncotarget (2016).
- Grabole, N. et al. Genomic analysis of the molecular neuropathology of tuberous sclerosis using a human stem cell model. Genome Medicine 8, 94 (2016).
- Zhang, J. D., Küng, E., Boess, F., Certa, U. & Ebeling, M. Pathway reporter genes define molecular phenotypes of human cells. BMC Genomics 16, 342 (2015).
- Xu, J. et al. 14-3-3$\zeta$ turns TGF-$\beta$’s function from tumor suppressor to metastasis promoter in breast cancer by contextual changes of Smad partners from p53 to Gli2. Cancer Cell 27, 177–192 (2015).
- van der Vries, E. et al. Outcomes and susceptibility to neuraminidase inhibitors in individuals infected with different influenza B lineages: the influenza resistance information study. The Journal of Infectious Diseases 213, 183–190 (2015).
- Moisan, A. et al. White-to-brown metabolic conversion of human adipocytes by JAK inhibition. Nature Cell Biology 17, 57–67 (2015).
- Lenz, N. et al. Antiviral Innate Immune Activation in HIV-Infected Adults Negatively Affects H1/IC31-Induced Vaccine-Specific Memory CD4+ T Cells. Clinical and Vaccine Immunology 22, 688–696 (2015).
- Haller, F. et al. Combined DNA methylation and gene expression profiling in gastrointestinal stromal tumors reveals hypomethylation of SPP1 as an independent prognostic factor. International Journal of Cancer 136, 1013–1023 (2015).
- Zhang, J. D., Schindler, T., Küng, E., Ebeling, M. & Certa, U. Highly sensitive amplicon-based transcript quantification by semiconductor sequencing. BMC Genomics 15, 565 (2014).
- Zhang, J., Berntenis, N., Roth, A. & Ebeling, M. Data mining reveals a network of early-response genes as a consensus signature of drug-induced in vitro and in vivo toxicity. The Pharmacogenomics Journal 14, 208–216 (2014).
- Yuk, I. H. et al. Effects of copper on CHO cells: insights from gene expression analyses. Biotechnology Progress 30, 429–442 (2014).
- Rehman, S. K. et al. 14-3-3$\zeta$ Orchestrates Mammary Tumor Onset and Progression via miR-221–Mediated Cell Proliferation. Cancer Research 74, 363–373 (2014).
- Raza, U., Zhang, J. D. & Sahin, Ö. MicroRNAs: master regulators of drug resistance, stemness, and metastasis. Journal of Molecular Medicine 92, 321–336 (2014).
- Aigner, S., Heckel, T., Zhang, J. D., Andreae, L. C. & Jagasia, R. Human pluripotent stem cell models of autism spectrum disorder: emerging frontiers, opportunities, and challenges towards neuronal networks in a dish. Psychopharmacology 231, 1089–1104 (2014).
- Ward, A. et al. Re-expression of microRNA-375 reverses both tamoxifen resistance and accompanying EMT-like properties in breast cancer. Oncogene 32, 1173–1182 (2013).
- Horvát, E.-Á., Zhang, J. D., Uhlmann, S., Sahin, Ö. & Zweig, K. A. A network-based method to assess the statistical significance of mild co-regulation effects. PLOS One 8, e73413 (2013).
- Adam, L. et al. Plasma microRNA profiles for bladder cancer detection. Urologic Oncology: Seminars and Original Investigations vol. 31 1701–1708 (Elsevier, 2013).
- Ward, A. et al. Abstract A14: Re-expression of microRNA-375 reverses both tamoxifen resistance and accompanying EMT-like properties in breast cancer. Clinical Cancer Research 18, A14–A14 (2012).
- Uhlmann, S. et al. Global miRNA regulation of a local protein network: Case study with the EGFR-driven cell cycle network in breast cancer. Molecular Systems Biology 8, 570 (2012).
- Keklikoglou, I. et al. MicroRNA-520/373 family functions as a tumor suppressor in estrogen receptor negative breast cancer by targeting NF-kappaB and TGF-ß signaling pathways. Oncogene 31, 4150 (2012).
- Jurmeister, S. et al. MicroRNA-200c represses migration and invasion of breast cancer cells by targeting actin-regulatory proteins FHOD1 and PPM1F. Molecular and Cellular Biology 32, 633–651 (2012).
- Zhang, J. D. et al. Time-resolved human kinome RNAi screen identifies a network regulating mitotic-events as early regulators of cell proliferation. PLOS One 6, e22176 (2011).
- Uhlmann, S. et al. miR-200bc/429 cluster targets PLC$\gamma$1 and differentially regulates proliferation and EGF-driven invasion than miR-200a/141 in breast cancer. Oncogene 29, 4297–4306 (2010).
- Haller, F. et al. Localization-and mutation-dependent microRNA (miRNA) expression signatures in gastrointestinal stromal tumours (GISTs), with a cluster of co-expressed miRNAs located at 14q32. 31. The Journal of Pathology 220, 71-86 (2010).
- Zhang, J. D. & Wiemann, S. KEGGgraph: a graph approach to KEGG PATHWAY in R and Rioconductor. Bioinformatics 25, 1470-1471 (2009).