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!

Telescope

an open-source web application that tracks the progress of jobs submitted to remote servers using Sun Grid Engine (SGE) on-demand scheduling system

SBT

a software platform to mine discarded tumor sequences from clinical sequencing

ImReP

a computational method for rapid and accurate profiling of the adaptive immune repertoire from bulk RNA-Seq data

ROP

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

Needle

a method for comprehensive virome, mycobiome, and eukaryome profiling on the strain level. Needle combines alignment and assembly strategies

MiCoP

a method for detecting low abundance viral and fungal organisms in metagenomic sample

Microbe-scope

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

HapIso

a computational method to reconstruct the haploid transcriptome of a diploid organism from long single molecule reads

UMI-Reducer

a computational protocol allowing to differentiate PCR duplicates from biological duplicates using UMIs; designed in collaboration with Prof. Kelsey Martin

VGA

a computational method for rapid and accurate profiling of the adaptive immune repertoire from bulk RNA-Seq data

Information we find useful!

Dylan Araps' Pure Bash Bible

A collection of pure bash alternatives to external processes.

UCLA Collaboratory Workshops

Video recordings and live streamings of workshops for coding and NGS data analysis.

Big Bio @ UCLA

Tutorials for learning basic through advanced concepts in biology, genomics, and computational biosciences.

Raj Lab Basic Adobe Illustrator (CC) Guide

A guide for editing scientific figures in Adobe Illustrator, prepared by the Arun Raj Lab for Systems Biology at UPenn.

Watch our lab videos!

BCC2020 Virtual Conference on July 20, 2020: Varuni Sarwal

Talk presented by Mangul Lab undergraduate researcher Varuni Sarwal at the BCC2020 Virtual Conference on July 20, 2020:

BCC2020 Virtual Conference on July 19, 2020: Niko Darci-Maher

Talk presented by Mangul Lab undergraduate researcher Niko Darci-Maher at the BCC2020 Virtual Conference on July 19, 2020:

BCC2020 Virtual Conference on July 19, 2020: Dr Jaque Brito

Talk presented by Mangul Lab postdoctoral scholar Dr. Jaque Brito at the BCC2020 Virtual Conference on July 19, 2020:

RECOMB-Seq 2020 Virtual Conference on June 26, 2020 : Nathan LaPierre

Talk presented by Mangul Lab collaborator Nathan LaPierre at the RECOMB-Seq 2020 Virtual Conference on June 26, 2020

USC Preventive Medicine Biostatistics Seminar Series Preventive Medicine on February 27, 2020 : Dr Jaque Brito

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: part 1:

Intro to Unix Workshop taught by Serghei Mangul at UCLA’s Collaboratory; parts 1

Intro to Unix Workshop: part 2: Dr Serghei Mangul

Intro to Unix Workshop taught by Serghei Mangul at UCLA’s Collaboratory; parts 2

Intro to Unix Workshop: part 3: Dr Serghei Mangul

Intro to Unix Workshop taught by Serghei Mangul at UCLA’s Collaboratory; parts 3

We’re in the news!

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

UofL researchers lead call to increase genetic diversity in immunogenomics

Corey T. Watson, Ph.D., assistant professor in the University of Louisville Department of Biochemistry and Molecular Genetics, is leading a call to actively diversify the genetic resources he and fellow immunogenomics researchers use in their work to advance genomic medicine more equitably.

A call to increase genetic diversity in immunogenomics

Corey T. Watson, Ph.D., assistant professor in the University of Louisville Department of Biochemistry and Molecular Genetics, is leading a call to actively diversify the genetic resources he and fellow immunogenomics researchers use in their work to advance genomic medicine more equitably.

Researchers Lead Call to Increase Genetic Diversity in Immunogenomics

Corey T. Watson, Ph.D., assistant professor in the University of Louisville Department of Biochemistry and Molecular Genetics, is leading a call to actively diversify the genetic resources he and fellow immunogenomics researchers use in their work to advance genomic medicine more equitably.