New Faculty

Dr. Alex Wagner joins the Department of Medicine

Dr. Alex Wagner joined the Department of Medicine in the Division of Oncology as an Instructor on June 1, 2019.

Dr. Wagner is interested in the development and application of open bioinformatics resources that enable precision medicine. His career interests are to run an academic laboratory overseeing the development of these tools and the analyses they enable, and mentor other scholars to further advance the field.

In support of his interests, Dr. Wagner has co-developed several precision medicine webtools, including the popular CIViC and DGIdb resources. These open-data, open-source tools assist in the interpretation of genomic variants observed in patient tumor genomes, enabling hypotheses for research and informing clinical decision making. Dr. Wagner also leads the Variant Interpretation for Cancer Consortium meta-knowledgebase project, an international collaboration to build interoperability standards between cancer variant interpretation knowledgebases. As a product of this research, he has developed a harmonized somatic interpretation knowledgebase and corresponding analysis that has highlighted the disparity of interpretation from analyzing cancer genomes through isolated resources. These results are under peer review at Nature and have been recognized by the Global Alliance for Genomics and Health, for whom he presented his findings at an invited plenary talk at their annual conference in Basel, Switzerland.

Dr. Wagner has extensive expertise in the analysis of cancer genomics data. He led the combined genomic and transcriptomic analysis of a relapsed small cell lung cancer cohort, which resulted in the discovery of WNT signaling as a characteristic component of acquired chemoresistance in this class of disease, a finding he recently published in Nature Communication. This work also led to his co-authorship on several important works in the field of variant calling by manual sequence review. He has an ongoing interest in the development of integrative analysis pipelines for discovering the molecular mechanisms of cancers.

Dr. Wagner has an interest in mentoring students to code and perform genome sequencing analysis. As an advocate for open science, he has co-developed a freely available, online resource for the analysis of RNA-sequencing data ( He instructs courses covering this workshop annually at the Advanced Sequencing Technologies and Applications course at Cold Spring Harbor Laboratory. He also organizes and instructs the Coding in Python and Ruby workshop at McDonnell Genome Institute.