JHU Center for Computational Biology

Center for Computational Biology

Center for Computational Biology
Johns Hopkins University

Email: jennifer.lu717@gmail.com

Jennifer Lu's CV

Jennifer Lu

Biomedical Engineering Staff Scientist in Salzberg and Trish Labs, Johns Hopkins University

About me:

I am a Staff Scientist working with Professor Steven Salzberg in the Johns Hopkins University Center for Computational Biology and working with Dr. Patricia (Trish) Simner in the Johns Hopkins School of Medicine Departments of Pathology and Infectious Diseases.

My research is focused on computational genomics and the usage of next-generation sequencing for diagnosing bacterial, fungal, or viral infections relating to human health and diseases. As part of this research, I develop and use various computational methods for quantifying DNA sequence similarities and complexities.

I also work with analyzing the phylogeny and genomics of microbes isolated in the clinical setting, developing procedures for analyzing sequencing data of microbes and microbiomes.

Current Projects:

Other Miscellaneous/Related Projects:

  • Kraken 2: Metagenomics Classifier [Collaborator]: I work alongisde Derrick Wood in the development and maintenance of Kraken 2, an updated version of the Kraken metagenomics classifier that utilizies minimizers and spaced-seeds to accomodate databases built from a far larger library of sequences. It is now possible to build Kraken 2 databases representing all NCBI refseq libraries, NCBI nt, and NCBI nr. Kraken 2 also supports 16S databases including 16S Greengenes, RDP, and SILVA. Finally, Kraken 2 supports protein databases and will query them by first translating all six reading frames of a nucleotide query sample.


For an updated list of my publications, please visit the following: Google Scholar profile
or download my Curriculum Vitae.