Ling X Shen

US Patent:

7115372, Oct 3, 2006

Filed:

Sep 26, 2002

Appl. No.:

10/256987

Inventors:

Ling X. Shen - Marlboro MA, US
Gregory L. Verdine - Lexington MA, US
James P. Basilion - Brookline MA, US

Assignee:

Variagenics, Inc. - Cambridge MA

International Classification:

C12Q 1/68
G01N 33/53
C12P 19/00
C07G 3/00
A61K 31/70

US Classification:

435 6, 435 78, 435 72, 536 41, 514 25

Abstract:

Described are methods for identifying targets in RNA molecules based on differences in RNA secondary structure related to sequence variances between different allelic forms. Also described are methods for identifying or developing small molecules which can be used to modulate a target RNA by creation of protein-small-molecule-RNA complexes, as well as compositions which include such small molecules and methods of using those small molecules and compositions.

US Patent:

8389484, Mar 5, 2013

Filed:

Nov 29, 2004

Appl. No.:

10/999171

Inventors:

Ling X. Shen - Marlboro MA, US
Gregory L. Verdine - Lexington MA, US
James P. Basilion - Brookline MA, US

International Classification:

C12N 15/11
C12N 15/113
C12N 15/115
C12Q 1/68

US Classification:

514 44A, 514 1, 514 2, 435455, 435 61, 435 78

Abstract:

Described are methods for identifying targets in RNA molecules based on differences in RNA secondary structure related to sequence variances between different allelic forms. Also described are methods for identifying or developing small molecules which can be used to modulate a target RNA by creation of protein-small-molecule-RNA complexes, as well as compositions which include such small molecules and methods of using those small molecules and compositions.

US Patent:

6686148, Feb 3, 2004

Filed:

Feb 29, 2000

Appl. No.:

09/515721

Inventors:

Ling X. Shen - Marlboro MA
Gregory L. Verdine - Lexington MA
James P. Basilion - Brookline MA

Assignee:

Nuvelo, Inc. - Sunnyvale CA

International Classification:

C12Q 168

US Classification:

435 6, 536 231, 536 243, 536 2431, 536 2432

Abstract:

Methods are described for identifying an RNA target for an allele-specific RNA inhibitor by identifying a sequence variance in an RNA encoded by a gene of interest, and determining whether the secondary structure of the RNA comprising the variance differs from that of an otherwise identical RNA not comprising the variance.

US Patent:

20190316209, Oct 17, 2019

Filed:

Apr 15, 2019

Appl. No.:

16/384784

Inventors:

- Menlo Park CA, US
Samuel S. Gross - Sunnyvale CA, US
Darya Filippova - Sunnyvale CA, US
Ling Shen - Redwood City CA, US
Oliver Claude Venn - San Francisco CA, US
Alexander Weaver Blocker - Mountain View CA, US
Nan Zhang - Fremont CA, US
Tara Maddala - Sunnyvale CA, US
Alex Aravanis - San Mateo CA, US
Qinwen Liu - Fremont CA, US
Anton Valouev - Palo Alto CA, US
Virgil Nicula - Cupertino CA, US

International Classification:

C12Q 1/6886
G16H 50/30
G16H 50/20
C12Q 1/6806
C40B 40/06
C12Q 1/6869

Abstract:

A predictive cancer model generates a cancer prediction for an individual of interest by analyzing values of one or more types of features that are derived from cfDNA obtained from the individual. Specifically, cfDNA from the individual is sequenced to generate sequence reads using one or more physical assays, examples of which include a small variant sequencing assay, whole genome sequencing assay, and methylation sequencing assay. The sequence reads of the physical assays are processed through corresponding computational analyses to generate each of small variant features, whole genome features, and methylation features. The values of features can be provided to a predictive cancer model that generates a cancer prediction. In some embodiments, the values of different types of features can be separately provided into different predictive models. Each separate predictive model can output a score that can serve as input into an overall model that outputs the cancer prediction.

US Patent:

20150056612, Feb 26, 2015

Filed:

Mar 4, 2013

Appl. No.:

13/784345

Inventors:

LING X. SHEN - MARLBORO MA, US
GREGORY L. VERDINE - LEXINGTON MA, US
JAMES P. BASILION - ARLINGTON MA, US

International Classification:

G01N 33/50

US Classification:

435 61

Abstract:

Described are methods for identifying targets in RNA molecules based on differences in RNA secondary structure related to sequence variances between different allelic forms. Also described are methods for identifying or developing small molecules which can be used to modulate a target RNA by creation of protein-small-molecule-RNA complexes, as well as compositions which include such small molecules and methods of using those small molecules and compositions.