Lijing Bu

Senior Research Scientist - Bioinformatics Specialist
Center for Evolutionary and Theoretical Immunology (CETI)
Department of Biology, University of New Mexico
Castetter Hall MSC03-2020
1 University of New Mexico NE
Albuquerque, New Mexico 87131
USA

Email:
Office: (505) 277 0594

Linux OS is my playground; R is my calculator and sketchpad; public databases are my free resources; Shell and Perl are my data organizer; computer cluster with thousands of nodes and CPUs is my sweet home; PPT/PDF/web page are my showcases. Why Bioinformatics?




Education
Ph.D. in Biology @ University of New Mexico, Albuquerque, NM
Master of Science, Medical Genetics @ Wenzhou Medical University, Zhejiang Province, China
Bachelor of Science, Clinical Medicine @ Taishan Medical University, Shandong Province, China

Here's all the stuff I do.

Bioinformatics, Genome Sequencing, RNASeq

Tools & Databases

Hands on hundreds of Bioinformatics software/web-tools. Familiar with major Bioinformatics databases: NCBI, EBI and KEGG, as well as their FTP sites and API access.

High-Throughput Data Analysis

Drive high performance computer clusters of CARC using the Terascale Open-source Resource and QUEue Manager (TORQUE) version of Portable Batch System (PBS), parallel computing using Message Passing Interface (MPI) and GNU Parallel.
Check out the QuickBytes How Tos.

RNASeq

Differential gene expression, de novo transcriptome assembly and annotation, using TopHat, Cufflinks, cummeRbund, edgeR/DESeq, Blast2GO and Trinity etc.

Genome Sequencing

De novo genome assembly, annotation, genome variation analysis, using ABySS, SOPAPdenovo, Valvet, Blast2GO, Maker, IGV, Samtools, VCFTools and SnpEff etc.

Data Mining

Data processing, statistics and visualization using Unix/Linux shell, R, Perl, HTML, MySQL and Python.

Local Bioinformatics Cloud

Maintain a local instance of the Galaxy platform (developed by Galaxy team of the Penn State University) - a web server capable integrate any Bioinformatics tools developed within an Unix/Linux environment (currently over 700+ tools), and provides friendly web interface to users.
Checkout our Pluto Galaxy

Workshops

I give hands on Galaxy workshops at Center for Advanced Research Computing (CARC) regularly for new users. Here is the PDF of workshop materials.

Here’s some stuff I made recently.

Showcases

Differential Gene Expression

EdgeR Results of pair-wise comparison among 3 samples, each has 4 replicates.




Server Monitor

Summary plots generated by R, monitoring the Galaxy server activity: disk usage by user, tools commonly used, job number and job status. Automatically update every 24 hours and this monitoring website is protected by password.
A joint effort of configuring Apache, PostgreSQL database (used in Galaxy) and R scripts.


Mitochondrial Genome Variation

Comparison of mitochondrial genomes of two snail lines. Synonymous and non-synonymous changes (SNPs) locations are highlighted in lightblue and red colors on the inner-circle.


A New Galaxy Wrapper

The MITOBim uses the NGS reads mapper/assembler MIRA 4.0 to construct mitochondrial genome based on reads baiting and iterative mapping mechanism. It used to have only Unix command line. But now a web interface is available on our local Galaxy server because of this wrapper.


Ideas? Questions?

Please send me a message.