JHU Center for Computational Biology

Center for Computational Biology

Address:
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:

  • Removal of Low-Complexity and/or Contaminated DNA Sequences: I am working on several mechanisms for detecting and removing low-complexity and/or contaminated DNA sequences in microbial genomes, focused specifically on draft genomes of pathogenic organisms. In particular, I am analyzing eukaryotic pathogen genomes.

  • Sequencing and DNA Analysis in Detecting Pathogenic Infections in the Cornea: Using the DNA classification tools of Kraken and Centrifuge, we are investigating the ability of NGS sequencing to identify the pathogens in corneal infections. For this particular project, we are focusing on eukaryotic pathogen-based infections, including Acanthamoeba Keratitis and Herpetic Keratitis.
    (This project is in collaboration with Charles Eberhart, MD PhD, Director of Neuropathology and Ophthalmic Pathology, and Florian Breitwieser, PhD, Postdoctoral researcher in Salzberg Lab).

  • Sequencing and DNA Analysis in Detecting Pathogenic Infections in the Brain: Following the sequencing of cerospinal fluid and brain biopsy samples from patients with neuroimmune disorders, we use the DNA classification tools of Kraken and Centrifuge to identify potential pathogens within the brain samples.
    (This project is in collaboration with Carlos Pardo-Villamizar, MD, Director of the Johns Hopkins Transverse Myelitis Center, and Florian Breitwieser, PhD, Postdoctoral researcher in Salzberg Lab).
    Related Paper: Next-generation sequencing neuropathologic diagnosis of infections of the nervous system Neurol Neuroimmunol Neuroinflamm (2016)

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:


Publications:

  • Submitted
    • Z. Li, F.P. Breitwieser, J. Lu, A.S. Jun, S.L. Salzberg, C.G. Eberhart, (awaiting review). "Identifying corneal infections in formalin fixed specimens using next generation sequencing." Investigative Ophthalmology & Visual Science (IOVS).

  • First-Authored, Peer-Reviewed Publications
    • J. Lu, F.P. Breitwieser, P. Thielen, S.L. Salzberg (2017). "Bracken: estimating species abundance in metagenomics data." PeerJ Computer Science, 3:e104 https://doi.org/10.7717/peerj-cs.104.

  • Co-Authored, Peer-Reviewed Publications
    • 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.
    • 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.
For an updated list of my publications, please visit the following: Google Scholar profile
or download my Curriculum Vitae.