Hui Chang Huang

US Patent:

7644409, Jan 5, 2010

Filed:

Jun 4, 2004

Appl. No.:

10/861795

Inventors:

David Dice - Foxborough MA, US
Hui Huang - Sunnyvale CA, US
Mingyao Yang - Santa Clara CA, US

Assignee:

Sun Microsystems, Inc. - Santa Clara CA

International Classification:

G06F 9/46
G06F 12/00
G06F 9/44
G06F 9/45

US Classification:

718104, 718100, 718101, 718108, 711100, 711130, 711147, 711155, 711163, 711154, 719312, 717106, 717159

Abstract:

A technique for accessing a shared resource of a computerized system involves running a first portion of a first thread within the computerized system, the first portion (i) requesting a lock on the shared resource and (ii) directing the computerized system to make operations of a second thread visible in a correct order. The technique further involves making operations of the second thread visible in the correct order in response to the first portion of the first thread running within the computerized system, and running a second portion of the first thread within the computerized system to determine whether the first thread has obtained the lock on the shared resource. Such a technique alleviates the need for using a MEMBAR instruction in the second thread.

US Patent:

20030200033, Oct 23, 2003

Filed:

Apr 12, 2002

Appl. No.:

10/123085

Inventors:

Jonathan Segal - Newtonville MA, US
Hui Huang - Newton MA, US

International Classification:

G06F019/00
G01N033/48
G01N033/50

US Classification:

702/020000

Abstract:

The invention provides an automated method of simultaneously identifying sequence information extending a plurality of seed sequences. The method consists of: (a) searching a plurality of target sequences with a multiplex query comprising a plurality of seed sequences; (b) identifying a plurality of target sequences substantially aligning with a plurality of seed sequences; (c) selecting a plurality of substantially aligned target sequences containing sequence extending information for a plurality of seed sequences, and (d) repeating steps (a) through (c) using the selected plurality of substantially aligned target sequences as a plurality of seed sequences. Also provided is an automated method of simultaneous identifying a plurality of gene sequences within a plurality of genomic region sequences. The method consists of: (a) pruning nucleic acid sequence elements from a plurality of genomic region sequences to produce a plurality of genomic seed sequences; (b) searching a plurality of target gene sequences with a multiplex query comprising a plurality of genomic seed sequences; (c) identifying a plurality of target gene sequences substantially aligning with a plurality of genomic seed sequences, and (d) locating regions of substantial alignment of the identified plurality of target gene sequences within the plurality of genomic region sequences, the regions of substantial alignment identifying a plurality of gene sequences.

US Patent:

20030211504, Nov 13, 2003

Filed:

Oct 9, 2002

Appl. No.:

10/268058

Inventors:

Kim Fechtel - Arlington MA, US
Shashi Prabhakar - Burlington MA, US
Hui Huang - Newton MA, US
Michael FitzGerald - Waltham MA, US
Joann Prescott-Roy - Concord MA, US
Michelle Runge - Bedford NH, US
Huajun Wang - Newton MA, US
Rene Gibson - Bedford MA, US

International Classification:

C12Q001/68
G06F019/00
G01N033/48
G01N033/50

US Classification:

435/006000, 702/020000

Abstract:

The invention provides an automated method of identifying a plurality of different polymorphisms within two or more related nucleic acid sequences. The method consists of: (a) obtaining a data set comprising a nucleic acid sequence assembly and a plurality of sequence characteristic parameters associated with said assembly; (b) indexing said nucleic acid assembly and said plurality of sequence characteristic parameters in a database; (c) selecting a region of said nucleic acid assembly having sequence characteristic parameters indicative of a polymorphic sequence, and (d) displaying two or more nucleic acid sequences of said region, said two or more sequences identifying different polymorphisms within said nucleic acid assembly. Also provided is a method of identifying a nucleic acid containing an indel region within a set of related nucleic acid sequences. The method consists of comprising: (a) dentifying a nucleic acid within two or more related nucleic acid sequences suspected of containing an indel region, said nucleic acid containing one or more regions having a plurality of polymorphisms, and (b) determining the occurrence of two or more criteria indicating the presence of an indel region associated with said one or more regions having a plurality of polymorphisms, said occurrence characterizing said nucleic acid as containing an indel region. Further provides is a method of determining the sequence of an allele containing an indel region within a set of related nucleic acid sequences. The method consists of comprising: (a) identifying a nucleic acid containing an indel region within two or more related nucleic acid sequences; (b) generating a consensus sequence within said indel region for said two or more related nucleic acid sequences; (c) identifying a matching string to said consensus sequence within at least one of said two or more related nucleic acid sequences, and (d) subtracting said consensus sequence from said two or more related nucleic acid sequences, the presence or absence of a unique sequence in one of said related nucleic acid sequences indicating the presence of an actual indel region. The invention additionally provides an automated system for identifying a plurality of different polymorphisms within two or more related nucleic acid sequences. The system consists of: (a) a sample submission module capable of transmitting data; (b) a core statistics loading and post processing module containing sequence characteristic parameters; (c) an assembly module capable constructing sequence assemblies from sequence database extracted data; (d) a SNP prospector module capable of identifying polymorphisms; (e) a polymorphism loader submodule capable of parsing polymorphic region sequence and sequence characteristic parameters from sequence assemblies; (f) a SNP database structured to contain the information produced in steps (a) through (e), and (g) an output module for display or further manipulation of specified data in step (f).

US Patent:

20070292866, Dec 20, 2007

Filed:

Dec 6, 2006

Appl. No.:

11/634755

Inventors:

Huajan Wang - Newton MA, US
Anthony Anisowicz - West Newton MA, US
Richard Del Mastro - Norfolk MA, US
Hui Huang - Lexington MA, US
Sergey Mamaev - West Roxbury MA, US

International Classification:

C12Q 1/68

US Classification:

435006000

Abstract:

This invention relates to methodologies that detect global changes in the methylation of human genomic DNA as well as changes in methylation in specific regions of the human genome. The methodologies have utility in the diagnosis, prognosis and monitoring of therapeutic treatment for any human disease. Further, the invention relates to methodologies that can detect global changes in the methylation of human genomic DNA that is a consequence of diet and/or dietary supplements. The invention also relates to identifying novel DNA methylation biomarkers that are associated with human disease.