| Center for Computational Biology |
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Address:
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:
- 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, a former post-doctoral researcher in Salzberg Lab.
- Related Paper: Identifying corneal infections in formalin-fixed specimens using next generation sequencing(IOVS, 2018)
- 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, a former post-doctoral researcher in Salzberg Lab.
- Related Paper: Next-generation sequencing neuropathologic diagnosis of infections of the nervous system (Neurol Neuroimmunol Neuroinflamm 2016)
- Nanopore Sequencing Projects:
- Redwood Sequencing Project: Project Information
- Sequencing of Chardonnay
- Computational Support for Microbiome Analysis of Nanopore Data
- Bracken (Bayesian Reestimation of Abundance with KraKEN):
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 or Kraken 2
- Related Website: https://ccb.jhu.edu/software/bracken/
- Related Github: https://github.com/jenniferlu717/Bracken/
- Related Podcast: On October 21st, 2017, I discussed my work with Roman Cheplyaka as part of the Bioinformatics Chat Podcast.
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.
Publications:
- First-Authored, Peer-Reviewed Publications
- J. Lu, S.L. Salzberg (2020). "SkewIT: The Skew Index Test for large-scale GC Skew analysis of bacterial genomes." PLoS Comput Biol
- J. Lu, S.L. Salzberg (2020). "Ultrafast and accurate 16S rRNA microbial community analysis using Kraken 2" Microbiome
- J. Lu, S.L. Salzberg (2018). "Removing contaminants from databases of draft genomes." . PLoS Comput Biol
- J. Lu, F.P. Breitwieser, P. Thielen, S.L. Salzberg (2017). "Bracken: estimating species abundance in metagenomics data." . PeerJ Computer Science,
- 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).
- F. P. Breitwieser, J. Lu, S. L. Salzberg, (2017). "A review of methods and databases for metagenomic classification and assembly." . Briefings in Bioinformatics
- J. Fern, J. Lu, R. Schulman, (2016). "The Energy Landscape for the Self-Assembly of Two-Dimensional DNA Origami Complex." ACS Nano
- 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