Massachusetts Institute of Technology

Rutgers, the State University of New Jersey

Boston University

Desmond S Lun

Muriel Medard

Ralf Koetter

Tracey Ho

Xiaomeng Shi

Nuala Koetter, Legal Representative

Catherine M Grgicak

Niranjan Ratnakar

Harish Swaminathan

Computerized analysis methods and systems to implement the computerized analysis methods are disclosed herein. Specifically, the present disclosure relates to systems and methods for determining an unknown characteristic of a sample.

Systems and methods for determining an unknown characteristic of a sample

In some aspects, a method of automated base-calling using at least one image obtained from a chemical sequencing process performed simultaneously on a plurality of DNA strands, the at least one image including intensity information corresponding to locations of at least one base in the plurality of DNA strands is provided. The method comprises processing the at least image to obtain a function corresponding to the intensity information in the at least one image for the at least one base, the function incorporating intensity information corresponding to each of the plurality of DNA strands, identifying a plurality of peaks in the function, the plurality of peaks indicating possible locations for the at least one base in the plurality of DNA strands, assigning membership to each of the plurality of peaks by determining whether each of the plurality of peaks is believed to have resulted from none, one or multiple of the plurality of DNA strands, and computing a sequence for the at least one base for each of the plurality of DNA strands based, at least in part, on the membership assignment.

Methods and apparatus for automated base-calling on multiple DNA strands

A method and computer program product for performing minimum cost routing with network coding is presented. The method and system model a network as a directed graph. A cost per unit flow is associated with each link of the directed graph. A link capacity is associated with each link of the directed graph. A network code is then computed that sets up a routing connection that achieves an optimal cost using the cost per unit flow for each link of the directed graph and using the link capacity for each link of the directed graph.

Minimum-cost routing with network coding

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Philadelphia, PA, United States of America

Desmond S Lun