Mangul Lab to present at Workshop on Computational Biology in ICML 2020

Serghei will present a highlight talk titled, “Profiling immunoglobulin repertoires across multiple human tissues using RNA Sequencing,” at the ICML 2020 Workshop on Computational Biology. The talk will highlight a paper recently published in Nature Communications. ICML 2020 received 68 submissions for highlight talks, and only six highlighted talks were [...]

By |2020-07-17T15:31:46+00:00July 17th, 2020|Categories: Lab News|Tags: , |

Mangul Lab publishes fifth paper presenting a novel method for profiling immunoglobulin (Ig) receptor repertoires from RNA-Seq

Mangul Lab at USC published a paper presenting ImReP – a novel computational tool that uses RNA-Seq data for rapid and accurate profiling of the immunoglobulin (Ig) repertoire. RNA-Seq data presents a unique opportunity to examine the adaptive immune system by profiling the both light and heavy chains that [...]

Mangul Lab releases fourth paper that recommends ways to enhance rigor and reproducibility in biomedical research

Mangul Lab at USC has published our fourth paper in GigaScience, which presents our group’s review of efforts to improve scientific rigor and reproducibility via open-source data and academic software. Recommendations to enhance rigor and reproducibility in biomedical research Computational methods have reshaped the landscape of modern [...]

By |2020-06-01T21:09:33+00:00June 1st, 2020|Categories: Commentary, Publications|Tags: , , |

Mangul Lab submits preprint of a WGS-based structural variant callers benchmarking study

Mangul Lab at USC shared a new preprint which presents a benchmarking study of structural variant (SV) callers – computational tools for identifying genomic regions that have altered DNA and may be implicated in various diseases and disorders. Varuni Sarwal, alumnus of Serghei’s group at UCLA, is the first [...]

Mangul Lab pens commentary piece on conference travel for junior scientists in the wake of climate change

Mangul Lab at USC shared a new preprint of 2020 which presents a conversational editorial on the difficult choices that junior scholars face when choosing to travel via airplane to scientific conferences. With the ever-increasing carbon footprint associated with conferences, scientists can learn to refine their conference experiences when [...]

By |2020-04-21T17:41:39+00:00April 13th, 2020|Categories: Commentary, Preprints|Tags: , , |

Mangul Lab publishes third paper – an analysis of microbial reference databases

Today we celebrate the publication of our third peer-reviewed paper since Mangul Lab launched at USC! Consensus of fungal and bacterial genome representation across multiple reference databases. Cailtin Loeffler and Aaron Karlsberg, both alumnus of Serghei’s group at UCLA and currently scientific research staff with Mangul Lab [...]

Interview in Nature Methods: Bench pressing with genomics benchmarkers

A journalist with Nature Methods recently interviewed Serghei on the increasingly important role that benchmarking studies play in biomedical and life science research. Benchmarking studies, which rank bioinformatics software according to variables such as speed, accuracy, and precision, help researchers select the best tool for a given dataset and research [...]

By |2020-04-16T21:59:07+00:00April 6th, 2020|Categories: Lab News|Tags: , |

Mangul Lab submits preprint presenting recommendations to enhance rigor and reproducibility in biomedical research

Mangul Lab at USC has shared a new preprint, which presents our group’s review of efforts to improve scientific rigor and reproducibility via open-source data and academic software. Computational methods have reshaped the landscape of modern biology. While the biomedical community is increasingly dependent on computational tools, the mechanisms [...]

By |2020-04-21T17:41:12+00:00March 30th, 2020|Categories: Commentary, Preprints|Tags: , , |

Mangul Lab submits preprint presenting Metalign, software that boosts accuracy of existing metagenomic profiling methods

Mangul Lab at USC shared a new preprint which presents Metalign - a tool developed by our group that significantly improves the taxonomic profiling accuracy of a metagenomic sample. Overview of Metalign Microorganisms play a critical role in almost every natural setting, including soil, ocean water, and [...]

Mangul Lab publishes second paper – a benchmarking study of error correction methods

Today we celebrate the publication of our second peer-reviewed paper since Mangul Lab launched at USC Keith Mitchell, alumnus of Serghei’s group at UCLA, is the first author of  “Benchmarking of computational error-correction methods for next-generation sequencing data,” which is now available online. Jaque (our postdoc), Lana (our project [...]