no code implementations • 23 Sep 2023 • Viorel Munteanu, Michael Saldana, Dumitru Ciorba, Viorel Bostan, Justin Maine Su, Nadiia Kasianchuk, Nitesh Kumar Sharma, Sergey Knyazev, Victor Gordeev, Eva Aßmann, Andrei Lobiuc, Mihai Covasa, Keith A. Crandall, Wenhao O. Ouyang, Nicholas C. Wu, Christopher Mason, Braden T Tierney, Alexander G Lucaci, Alex Zelikovsky, Fatemeh Mohebbi, Pavel Skums, Cynthia Gibas, Jessica Schlueter, Piotr Rzymski, Helena Solo-Gabriele, Martin Hölzer, Adam Smith, Serghei Mangul
The existing bioinformatics tools used to analyze wastewater sequencing data are often based on previously developed methods for quantifying the expression of transcripts or viral diversity.
no code implementations • 28 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.
1 code implementation • 1 Feb 2021 • Halie M. Rando, Adam L. MacLean, Alexandra J. Lee, Ronan Lordan, Sandipan Ray, Vikas Bansal, Ashwin N. Skelly, Elizabeth Sell, John J. Dziak, Lamonica Shinholster, Lucy D'Agostino McGowan, Marouen Ben Guebila, Nils Wellhausen, Sergey Knyazev, Simina M. Boca, Stephen Capone, Yanjun Qi, YoSon Park, Yuchen Sun, David Mai, Joel D. Boerckel, Christian Brueffer, James Brian Byrd, Jeremy P. Kamil, Jinhui Wang, Ryan Velazquez, Gregory L Szeto, John P. Barton, Rishi Raj Goel, Serghei Mangul, Tiago Lubiana, COVID-19 Review Consortium, Anthony Gitter, Casey S. Greene
While this viral species was unknown prior to January 2020, its similarity to other coronaviruses that infect humans has allowed for rapid insight into the mechanisms that it uses to infect human hosts, as well as the ways in which the human immune system can respond.
2 code implementations • 28 Feb 2020 • Mohammed Alser, Jeremy Rotman, Kodi Taraszka, Huwenbo Shi, Pelin Icer Baykal, Harry Taegyun Yang, Victor Xue, Sergey Knyazev, Benjamin D. Singer, Brunilda Balliu, David Koslicki, Pavel Skums, Alex Zelikovsky, Can Alkan, Onur Mutlu, Serghei Mangul
We separately discuss how longer read lengths produce unique advantages and limitations to read alignment techniques.