University of Washington

Phase Genomics Inc.

Ivan Liachko

Maitreya J Dunham

Jay Ashok Shendure

Jacob Otto Kitzman

Andrew Colin Adey

Shawn Thomas Sullivan

Joshua Burton

Stephen M Eacker

Kyle Langford

Maitreye J Dunham

Maitreya Dunham

Methods and compositions are provided for performing an in vivo proximity-ligation in combination with DNA capture technology to cross-link physically adjacent DNA sequences within a mixed population of cells and isolate cross-linked DNA junctions where at least one DNA sequence of interest is present.

Method for the clustering of DNA sequences

Computational methods used for large scale scaffolding of a genome assembly are provided. Such methods may include a step of applying a location clustering model to a test set of contigs to form two or more location cluster groups, each location cluster group comprising one or more location-clustered contigs; a step of applying an ordering model to each of the two or more location cluster groups to form an ordered set of one or more location-clustered contigs within each cluster group; and a step of applying an orienting model to each ordered set of one or more location-clustered contigs to assign a relative orientation to each of the location-clustered contigs within each location cluster group. In some aspects, the test set of contigs are generated from aligning a set of reads generated by a chromosome conformation analysis technique (e.g., Hi-C) with a draft assembly, a reference assembly, or both.

Method for large scale scaffolding of genome assemblies

A DNA sequence that functions as an origin in many different yeast species. From 1 to 17 mutations can be introduced into this sequence to improve its function across multiple yeasts. The resulting synthetic DNA sequence confers stable plasmid replication function in all yeast species tested, including but not limited to, and. Also provided are sequences that function as an optimal origin in the industrially useful

Pan-yeast autonomously replicating sequence

Growing community of inventors

Seattle, WA, United States of America

Ivan Liachko