We further employ heuristics to accelerate read mapping.
Comparing genomic sequences is one of the most fundamental computational steps in most genomic analyses.
no code implementations • 29 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.
no code implementations • 23 Sep 2023 • Viorel Munteanu, Michael Saldana, Nitesh Kumar Sharma, Wenhao O. Ouyang, Eva Aßmann, Victor Gordeev, Nadiia Kasianchuk, Braden T Tierney, Alexander G Lucaci, Sergey Knyazev, Dumitru Ciorba, Viorel Bostan, Christopher Mason, Pavel Skums, Nicholas C. Wu, Piotr Rzymski, Martin Hölzer, Alex Zelikovsky, 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.
In biomedical research, validation of a new scientific discovery is tied to the reproducibility of its experimental results.
no code implementations • 30 Mar 2022 • Mohammed Alser, Sharon Waymost, Ram Ayyala, Brendan Lawlor, Richard J. Abdill, Neha Rajkumar, Nathan LaPierre, Jaqueline Brito, Andre M. Ribeiro-dos-Santos, Can Firtina, Nour Almadhoun, Varuni Sarwal, Eleazar Eskin, Qiyang Hu, Derek Strong, Byoung-Do, Kim, Malak S. Abedalthagafi, Onur Mutlu, Serghei Mangul
Omics software tools have reshaped the landscape of modern biology and become an essential component of biomedical research.
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.
no code implementations • 20 Oct 2020 • Kerui Peng, Yana Safonova, Mikhail Shugay, Alice Popejoy, Oscar Rodriguez, Felix Breden, Petter Brodin, Amanda M. Burkhardt, Carlos Bustamante, Van-Mai Cao-Lormeau, Martin M. Corcoran, Darragh Duffy, Macarena Fuentes Guajardo, Ricardo Fujita, Victor Greiff, Vanessa D. Jonsson, Xiao Liu, Lluis Quintana-Murci, Maura Rossetti, Jianming Xie, Gur Yaari, Wei zhang, Malak S. Abedalthagafi, Khalid O. Adekoya, Rahaman A. Ahmed, Wei-Chiao Chang, Clive Gray, Yusuke Nakamura, William D. Lees, Purvesh Khatri, Houda Alachkar, Cathrine Scheepers, Corey T. Watson, Gunilla B. Karlsson Hedestam, Serghei Mangul
With the advent of high-throughput sequencing technologies, the fields of immunogenomics and adaptive immune receptor repertoire research are facing both opportunities and challenges.
no code implementations • 5 Oct 2020 • Dhrithi Deshpande, Karishma Chhugani, Yutong Chang, Aaron Karlsberg, Caitlin Loeffler, Jinyang Zhang, Agata Muszynska, Jeremy Rotman, Laura Tao, Lana S. Martin, Brunilda Balliu, Elizabeth Tseng, Fangqing Zhao, Pejman Mohammadi, Pawel P Labaj, Serghei Mangul
RNA-seq is a method of analyzing the RNA content of a sample using the modern sequencing platforms.
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.
Computational methods have reshaped the landscape of modern biology.
no code implementations • 26 Nov 2019 • Caitlin Loeffler, Keylie M. Gibson, Lana Martin, Liz Chang, Jeremy Rotman, Ian V. Toma, Christopher E. Mason, Eleazar Eskin, Joseph P. Zackular, Keith A. Crandall, David Koslicki, Serghei Mangul
The human-associated microbiome is closely tied to human health and is of substantial clinical interest.