JHU Center for Computational Biology

Center for Computational Biology

Center for Computational Biology
Johns Hopkins University
1900 E. Monument St., Room 115
Baltimore, MD 21205

Email: jlu26@jhmi.edu

CV Jennifer Lu

Photo Credit: Jami Cheng

Jennifer Lu

Biomedical Engineering Ph.D. Candidate in Salzberg Lab, Johns Hopkins University

About me:

I am a Biomedical Engineering Ph.D. Candidate in Professor Steven Salzberg's lab at the Center for Computational Biology at Johns Hopkins University. I began my Ph.D. work in August 2015.

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.

Current Projects:

Completed Projects:

  • Development of Bracken (Bayesian Reestimation of Abundance with KraKEN) (with Florian Breitwieser, PhD). Bracken is a highly accurate statistical method that computes the abundance of species in DNA sequences from a metagenomics sample. This program is developed to be used alongside Kraken, a fast, accurate metagenomics classifier.

  • On October 21st, 2017, I discussed my work with Roman Cheplyaka as part of the Bioinformatics Chat Podcast. We discussed the Bracken algorithm, species abundance estimation and the computational tools currently available in the field of metagenomics classification and abundance estimation.

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.
  • Kraken: Metagenomics Classifier [Collaborator]: As of September 2017, I am one of the collaborators to this metagenomics classification software. I focus on maintainence of Kraken v1.0, improving functionality in database-building and downstream analysis.
  • Pavian: Visualization for Metagenomics Classification: Pavian is an visualization software for the analysis of classification information for Kraken and Centrifuge. This program is developed and maintained by Florian Breitwieser, PhD.


  • First-Authored, Peer-Reviewed Publications

  • Co-Authored, Peer-Reviewed Publications
    • Z. Li, F.P. Breitwieser, J. Lu, A.S. Jun, S.L. Salzberg, C.G. Eberhart, (2018). "Identifying corneal infections in formalin fixed specimens using next generation sequencing." Investigative Ophthalmology & Visual Science (IOVS). https://doi.org/10.1167/iovs.17-21617.
    • F. P. Breitwieser, J. Lu, S. L. Salzberg, (2017). "A review of methods and databases for metagenomic classification and assembly." Briefings in Bioinformatics bbx120, https://doi.org/10.1093/bib/bbx120.
    • J. Fern, J. Lu, R. Schulman, (2016). "The Energy Landscape for the Self-Assembly of Two-Dimensional DNA Origami Complex." ACS Nano, 10(2), 1835-1844. htps://doi.org/10.1021/acsnano.5b05309
    • A. Merouane, N. Rey-Villamizar, Y.Lu, I. Liadi, G. Romain, J.S. Lee, J. Lu, A. Rao, N. Varadarajan, B. Roysam. (2015). "Automated Profiling of Individual Cell-Cell Interactions from High-throughput Time-lapse Imaging Microscopy in Nanowell Grids (TIMING)". Journal of Bioinformatics, 31(19), 3189-3197. https://doi.org/10.1093/bioinformatics/btv355
For an updated list of my publications, please visit the following: Google Scholar profile
or download my Curriculum Vitae.