Microsoft Technology Licensing, LLC

Brown University

Oxford Nanopore Technologies Limited

Ontera Inc.

Nooma Bio, Inc.

Xu Liu

William Dunbar

Yuning Zhang

Steve Chun-Hao Hu

Jose Fernandez

Yingji Ju

Swadhin Ajay Thakkar

Ying Shan

Gunter Leeb

Derek Martin Stein

William Edward Miao

Sravanthi Pereddy

Jordan Robert Fitzgibbon

Raveena Dayani

Abhishank Sahu

Mirna Mihovilovic Skanata

William B Dunbar

The present disclosure provides an automated method of mapping one or more features of a target polynucleotide. Also provided in the present disclosure are automated methods for sequencing a polynucleotide sequence. Also provided in the present disclosure are methods of extended recapture of a polynucleotide in a nanopore device. Also provided in the present disclosure are devices and systems for carrying out the methods of the present disclosure.

Logic driven polynucleotide scanning for mapping features in a nanopore device

Embodiments disclosed herein are related to implementing a near-real-time stream processing system using the same distributed file system as a batch processing system. A data container and partition files are generated according to a partition window that specifies a time range that controls when data is to be included in the partition files. The data container is scanned to determine if the partition files are within a partition lifetime window that specifies a time range that controls how long the partition files are active for processing. For each partition file within the lifetime window, processing tasks are created based on an amount of data included in the partition files. The data in the partition files is accessed and the processing tasks are performed. Information about the partition files is recorded in a configuration data store.

Near-real-time data processing with partition files

A data processing system for providing a distributed timer implements receiving a first timer message associated with a first computing device requesting creation of a first timer having a first duration and a first timer identifier; responsive to the first timer message creating a first timer, and inserting a first timer queue entry into a first timer queue associated with a first timer wait interval; receiving a plurality of second timer messages to reset the first timer; inserting a plurality of second timer queue entries into the first timer queue based on the plurality of second timer messages; and processing timer queue entries in the first timer queue responsive to the first timer wait interval having passed.

Queue-based distributed timer

Described herein are nanopore devices as well as methods for assembling a nanopore device including one or more nanopores that can be used to detect molecules such as nucleic acids, amino acids (proteins), and the like. Specifically, a nanopore device includes an insulating layer that reduces electrical noise and thereby improves the sensing resolution of the one or more nanopores integrated within the nanopore device.

Wafer-scale assembly of insulator-membrane-insulator devices for nanopore sensing

The present invention generally relates to devices and methods for containing molecules. In some embodiments, the device comprises a nanopore, a pore, and a cavity capable of entropically containing (e.g., trapping) a molecule (e.g., a biomolecule), e.g., for minutes, hours, or days. In certain embodiments, the method comprises urging a molecule into a cavity of a device by application of an electric field, and/or by deposition of fluids having different ionic strengths. The molecule may comprise, in some cases, nucleic acids (e.g., DNA). The molecule, when present in the cavity and/or the nanopore, may be capable of being analyzed, determined, or chemically modified. In some instances, a second molecule (e.g., a second molecule which interacts the first molecule) may also be urged into the cavity. In some embodiments, the interaction of the second molecule with the first molecule (e.g., the second molecule binding to or chemically modifying the first molecule) may be determined by, for example, a change in voltage measured across the device.

Devices and methods for containing molecules

Growing community of inventors

Santa Cruz, CA, United States of America

Xu Liu