This page includes our open-sourced softwares, some information we find useful, our lab videos and news in which Mangul Lab was featured.

We’re in the news!

Mangul lab publishes study focusing on accessibility, diversity and inclusion at virtual scientific conferences

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 on Provost Undergraduate Research award

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.

Our work about how the virtual meetings promise to eliminate geographical and administrative barriers( was highlighted in NIH guest post by Marie A. Bernard, M.D., NIH Chief Officer for Scientific Workforce Diversity.

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.’

Nature Methods highlighted our work on unlocking the capacities of genomics for the COVID-19 response and future pandemics.

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.

Project "Rigorous benchmarking of HLA Callers for RNA-Sequencing data" featured in the USC QCB department newsletter.

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.

Moldovan University on Serghei's Workshops

State University of Medicine and Pharmacy (Moldova) Newsroom: Bioinformatics - A new trends in mdeical research

Nature Methods interviews Serghei on benchmarking

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

Tech Xplore reports on Telescope: a tool to manage bioinformatics analyses on mobile devices

UCLA Newsroom on Bioinformatics for All

UCLA Newsroom: Team proposes plan to use bioinformatics, open data to boost science in developing countries

GWU School of Medicine on Bioinformatics for All

George Washington School of Medicine and Health Sciences: Researchers Propose Using Bioinformatics, Open Data to Boost Basic Science Globally

AAAS EurekAlert! on Schizophrenia study

AAAS EurekAlert! Schizophrenics’ blood has more genetic material from microbes

USC Investigators Lead International Call for Increased Diversity in Immunogenomics

USC School of Pharmacy scientists united researchers worldwide to promote inclusivity in immunology studies