Resources
This page includes our open-sourced softwares, some information we find useful, our lab videos and the news in which Mangul Lab was present.
We develop omics software!
a comprehensive jupyter notebook based platform for T-Cell receptor (TCR) data analysis to facilitate reproducibility and rigor of immunogenomics research.
an open-source web application that tracks the progress of jobs submitted to remote servers using Sun Grid Engine (SGE) on-demand scheduling system
a software platform to mine discarded tumor sequences from clinical sequencing
a computational method for rapid and accurate profiling of the adaptive immune repertoire from bulk RNA-Seq data
a computational protocol to discover the source of all reads, which originate from complex RNA molecules, recombined B and T cell receptors and microbial communities
a method for comprehensive virome, mycobiome, and eukaryome profiling on the strain level. Needle combines alignment and assembly strategies
a method for detecting low abundance viral and fungal organisms in metagenomic sample
a method to visualize the metagenomics data in the form of interactive coverage plots. It allows to detect false positives based on the coverage corresponding microbial genomes
a computational method to reconstruct the haploid transcriptome of a diploid organism from long single molecule reads
a computational protocol allowing to differentiate PCR duplicates from biological duplicates using UMIs; designed in collaboration with Prof. Kelsey Martin
a computational method for rapid and accurate profiling of the adaptive immune repertoire from bulk RNA-Seq data
Information we find useful!
A collection of pure bash alternatives to external processes.
Video recordings and live streamings of workshops for coding and NGS data analysis.
Tutorials for learning basic through advanced concepts in biology, genomics, and computational biosciences.
A guide for editing scientific figures in Adobe Illustrator, prepared by the Arun Raj Lab for Systems Biology at UPenn.
Watch our lab videos!
Talk presented by Mangul Lab undergraduate researcher Varuni Sarwal at the BCC2020 Virtual Conference on July 20, 2020:
Talk presented by Mangul Lab undergraduate researcher Niko Darci-Maher at the BCC2020 Virtual Conference on July 19, 2020:
Talk presented by Mangul Lab postdoctoral scholar Dr. Jaque Brito at the BCC2020 Virtual Conference on July 19, 2020:
Talk presented by Mangul Lab collaborator Nathan LaPierre at the RECOMB-Seq 2020 Virtual Conference on June 26, 2020
Seminar presented by Mangul Lab postdoctoral scholar Dr. Jaque Brito at the USC Preventive Medicine Biostatistics Seminar Series Preventive Medicine on February 27, 2020
Intro to Unix Workshop taught by Serghei Mangul at UCLA’s Collaboratory; parts 1
Intro to Unix Workshop taught by Serghei Mangul at UCLA’s Collaboratory; parts 2
Intro to Unix Workshop taught by Serghei Mangul at UCLA’s Collaboratory; parts 3
We’re in the news!
Our paper ‘Virtual meetings promise to eliminate geographical and administrative barriers and increase accessibility, diversity and inclusivity’ was highlighted in the USC Pharmacy news.
Congratulations to Dottie Yu for winning the Summer 2022 Provost Undergraduate Research Fellowship award. She is awarded for continuing work on project titled ‘Rigorous Benchmarking of HLA callers for RNA sequencing data.’ Dottie is an junior undergraduate student in the Quantitative and Computational Biology department at USC and has been working on the HLA project for the past year.
In their comment,’Another recent study affirms that online meetings can promote participant diversity by minimizing barriers to attendance. The authors analyzed the demographics of attendees at scientific conferences before and after the adoption of a virtual format. They observed a significant increase in attendees from underrepresented groups at the virtual events and suggest online platforms may be more inclusive by offering increased accessibility and programming flexibility compared to in-person convenings.’
In their comment, Serghei Mangul and colleagues discuss how genomics and metagenomics methods have become essential public health tools. Once the virus was detected, scientists immediately set about identifying and characterizing the pathogen, enabled by access to reliable and accurate sequencing methods. Similarly, computational tools allowed phylogenetic analyses of the genetic fingerprint of the virus that traced its origin and evolution; by these methods, SARS-CoV-2 was found to have close ancestral ties with bat coronavirus species. Genomic and bioinformatic methods continue to be used across the globe to monitor the emergence of new SARS-CoV-2 variants and track transmission routes.
Dottie Yu is a third year undergraduate in the QCB department and has been working on this project since June 2021. This project evaluates and benchmarks the performance of the 12 existing RNA-seq based HLA callers for their performance in allele typing of the HLA genes, an essential immune-related locus of the human genome. Systematic and comprehensive benchmarking is crucial to helping researchers and clinicians make informed decisions on which HLA caller tool is best for their purposes.
State University of Medicine and Pharmacy (Moldova) Newsroom: Bioinformatics - A new trends in mdeical research
Bench pressing with genomics benchmarkers: Some -omics tools can be accurate, sensitive or efficient than others. Yet benchmarking is no tell-all
Tech Xplore reports on Telescope: a tool to manage bioinformatics analyses on mobile devices
UCLA Newsroom: Team proposes plan to use bioinformatics, open data to boost science in developing countries
George Washington School of Medicine and Health Sciences: Researchers Propose Using Bioinformatics, Open Data to Boost Basic Science Globally
AAAS EurekAlert! Schizophrenics’ blood has more genetic material from microbes
USC School of Pharmacy scientists united researchers worldwide to promote inclusivity in immunology studies