Search Results for author: Serghei Mangul

Found 13 papers, 5 papers with code

A rigorous benchmarking of methods for SARS-CoV-2 lineage abundance estimation in wastewater

no code implementations29 Sep 2023 Viorel Munteanu, Victor Gordeev, Justin Maine Su, Khooshbu Kantibhai Patel, Nicolae Drabcinski, Abdullah Al Nahid, Oksana Zlenko, Maryna Kit, Yidian Xu, Pooja Jaiswal, Alex Zelikovsky, Serghei Mangul

However, the inherent physical and chemical heterogeneity of wastewater samples, the low viral load, viral RNA degradation, background genetic material, and PCR inhibitors, can significantly affect the quality of the sequencing data, negatively impacting the performance of the bioinformatics algorithms employed for wastewater sequencing data analysis.


Genomic reproducibility in the bioinformatics era

no code implementations18 Aug 2023 Pelin Icer Baykal, Paweł P. Łabaj, Florian Markowetz, Lynn M. Schriml, Daniel J. Stekhoven, Serghei Mangul, Niko Beerenwinkel

In biomedical research, validation of a new scientific discovery is tied to the reproducibility of its experimental results.

Unlocking capacities of viral genomics for the COVID-19 pandemic response

no code implementations28 Apr 2021 Sergey Knyazev, Karishma Chhugani, Varuni Sarwal, Ram Ayyala, Harman Singh, Smruthi Karthikeyan, Dhrithi Deshpande, Zoia Comarova, Angela Lu, Yuri Porozov, Aiping Wu, Malak Abedalthagafi, Shivashankar Nagaraj, Adam Smith, Pavel Skums, Jason Ladner, Tommy Tsan-Yuk Lam, Nicholas Wu, Alex Zelikovsky, Rob Knight, Keith Crandall, Serghei Mangul

More than any other infectious disease epidemic, the COVID-19 pandemic has been characterized by the generation of large volumes of viral genomic data at an incredible pace due to recent advances in high-throughput sequencing technologies, the rapid global spread of SARS-CoV-2, and its persistent threat to public health.

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