Shengdong Ke from Ellsworth, ME, age 41

Quantitative Total Definition Of Biologically Active Sequence Elements And Positions
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US Patent:

20130225419, Aug 29, 2013
Filed:

Feb 25, 2013
Appl. No.:

13/776696
Inventors:

The Trustees of Columbia University in the City of New York - , US
Shengdong Ke - New York NY, US
Assignee:

The Trustees of Columbia University in the City of New York - New York NY
International Classification:

C12Q 1/68
US Classification:

506 2, 506 26, 506 16
Abstract:

A library includes H unique nucleotide sequences involving every position along I continuous positions in a molecule. A method to prepare the library includes obtaining a microarray with a bound probe of up to J nucleotides, J=I+L, for H different probes. The first L nucleotides are reverse complementary to a constant portion in the library at a 5′ end. The remaining nucleotides of different probes are reverse complementary to corresponding different library members. A primer equal to the constant portion in the library is introduced. The primer is extended along the probe as a library strand using DNA polymerase. A first strand of a double stranded linker is ligated with a phosphate group to the library strand. The first strand has a sequence that matches a constant portion in the library at a 3′ end. The library strand is stripped from the probe and from a different second strand of the linker.

Quantitative Total Definition Of Biologically Active Sequence Elements
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US Patent:

20130217585, Aug 22, 2013
Filed:

Aug 25, 2011
Appl. No.:

13/818777
Inventors:

Lawrence A. Chasin - Leonia NJ, US
Shengdong Ke - New York NY, US
Assignee:

THE TRUSTEES OF THE UNIVERSITY OF COLUMBIA IN THE CITY OF NEW YORK - New York NY
International Classification:

C12Q 1/68
US Classification:

506 2
Abstract:

A method and apparatus include preparing a library of molecules that can be sequenced. The library includes multiple instances of each possible member of a k-mer. The library is sequenced to determine the relative frequency of each member of the k-mer in the library. The library is contacted with a biochemical system. A population of output molecules is sequenced to determine the relative frequency of each member of the k-mer in the population of output molecules. Each output molecule is related to a product of a process of the biochemical system and carries a k-mer related to a corresponding k-mer of a library molecule involved in the process. Effectiveness of each member of the k-mer is determined based on the relative frequency of each member of the k-mer in the population of output molecules and the relative frequency of the corresponding k-mer in the library.

Shengdong Ke