Search Results for author: Rob Knight

Found 4 papers, 1 papers with code

Enabling microbiome research on personal devices

no code implementations8 Jul 2021 Igor Sfiligoi, Daniel McDonald, Rob Knight

Microbiome studies have recently transitioned from experimental designs with a few hundred samples to designs spanning tens of thousands of samples.

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.

Utilizing stability criteria in choosing feature selection methods yields reproducible results in microbiome data

no code implementations30 Nov 2020 Lingjing Jiang, Niina Haiminen, Anna-Paola Carrieri, Shi Huang, Yoshiki Vazquez-Baeza, Laxmi Parida, Ho-Cheol Kim, Austin D. Swafford, Rob Knight, Loki Natarajan

In our paper, we compare the performance of popular model prediction metric MSE and proposed reproducibility criterion Stability in evaluating four widely used feature selection methods in both simulations and experimental microbiome applications.

feature selection

Ten Simple Rules for Reproducible Research in Jupyter Notebooks

2 code implementations13 Oct 2018 Adam Rule, Amanda Birmingham, Cristal Zuniga, Ilkay Altintas, Shih-Cheng Huang, Rob Knight, Niema Moshiri, Mai H. Nguyen, Sara Brin Rosenthal, Fernando Pérez, Peter W. Rose

For example, what are the technical and non-technical barriers to reproducible computational studies?

Other Computer Science Computers and Society

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