Joel S. Bader, Ph.D., is Professor of Biomedical Engineering at Johns Hopkins University and Interim Director of the High-Throughput Biology Center at the Johns Hopkins School of Medicine, with secondary appointments in Computer Science and Human Genetics. Prior to joining Johns Hopkins, Dr. Bader was employed by CuraGen Corporation (1995-2003) and is co-inventor of the Roche/454 Genome Sequencer. Dr. Bader has a Ph.D. in Theoretical Chemistry from U.C. Berkeley (1991), where he was an NSF Predoctoral Fellow, and performed post-doctoral research at Columbia University (1992-1995). Dr. Bader has a B.S. in Biochemistry from Lehigh University (1986, Phi Beta Kappa, Tau Beta Pi).
Research in the Bader lab aims to understand the connection between genotype and phenotype. General research areas are as follows.
(1) Human genetics: identifying genes and variants that control specific phenotypes, particularly those that cause disease or increase disease risk. We develop Bayesian methods to improve genome-wide association studies through gene-based and pathway-based analysis.
(2) Systems biology: mapping how upstream perturbations result in downstream biological responses. We introduce new algorithms to integrate high-throughput data sets to infer biological networks and pathways and prioritize candidate genes for validation.
(3) Synthetic biology: designing, building, and testing DNA at the chromosome scale. We are founding members of the Sc2.0 project, which aims to build a yeast cell with an entirely synthetic genome, and we are now focusing on design of neochromosomes, synthetic eukaryotic chromosomes that encode modular pathways.
Disease areas of particular focus are cancer, tuberculosis, and complex genetic disorders.
Current and previous funding sources include US NIH, NSF, DOE, DARPA, the Jayne Koskinas Ted Giovanis Foundation for Health and Policy, Microsoft External Research, and the Kleberg Foundation. Dr. Bader is co-founder of Neochromosome, Inc., a synthetic biology company, and is on the Scientific Advisory Board of LAM Therapeutics, Inc., which develops drugs for cancer and rare diseases associated with lymphangioleiomyomatosis.
The overwhelming majority of deaths from cancer are attributable to metastasis, rather than growth of the primary tumor. In breast cancer, metastatic recurrence can occur years to decades after apparently successful surgery. Current methods do not allow individualized assessment of metastatic recurrence risk nor do they offer effective therapies for metastatic breast cancer patients. We are developing and applying methods to identify the basic mechanisms of metastasis. We will describe work with experimental partners using organoids, clusters of 300-500 primary mammary cells, to interrogate metastasis-related phenotypes. We will describe genes and pathways whose activation changes cellular behavior to create an invasive phenotype. We will also present results using spectral methods to convert images of organoid invasion into quantitative phenotypes representing the invasive boundary between the organoid and the surrounding matrix. We plan to use these methods in population studies to understand the genetic basis of metastasis and in well-defined model systems to validate candidate genes.