I am a Biomedical Engineering Post-Doctoral Fellow in Professor Steven Salzberg's lab
at the Center for Computational Biology at Johns Hopkins University.
I completed my Ph.D. in November 2020.
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.
This is a continuously developing project to provide a set of tools to
be used alongside any of the Kraken
set of tools (Kraken 1, Kraken 2, KrakenUniq, and Bracken). The tools
are designed to help with downstream analysis and upstream debugging of
- SkewIT: GC Skew Index Test:
For analysis of the 15,000+ bacterial chromosomes in NCBI Refseq,
I have developed a method for assigning each genome a single
"Skew Index" (SkewI) based on the GC Skew of that genome.
I have found that chromosomes with abnormally low SkewI values
as compared to others within the same genus have a high probability
of being mis-assembled.
- 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
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.
- 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
identify potential pathogens within the brain samples.
- 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.
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.
- 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).
- 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."
- 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
For an updated list of my publications, please visit the following: Google Scholar profile
or download my Curriculum Vitae