Sang Hoon Lim

US Patent:

8140269, Mar 20, 2012

Filed:

Mar 12, 2008

Appl. No.:

12/046988

Inventors:

Bhubaneswar Mishra - Great Neck NY, US
Thomas Anantharaman - DeForest WI, US
Sang Lim - Tarrytown NY, US

Assignee:

New York University - New York NY

International Classification:

G01N 33/48
C12Q 1/68
G06G 7/58

US Classification:

702 19, 435 6, 702 20, 703 11

Abstract:

Methods, computer-accessible medium, and systems for generating a genome wide probe map and/or a genome wide haplotype sequence are provided. In particular, a genome wide probe map can be generated by obtaining a plurality of detectable oligonucleotide probes hybridized to at least one double stranded nucleic acid molecule cleaved with at least one restriction enzyme, and detecting the location of the detectable oligonucleotide probes. For example, genome wide haplotype sequence can be generated by analyzing at least one genome wide restriction map in conjunction with at least one genome wide probe map to determine distances between restriction sites of the at least one genome wide restriction map and locations of detectable oligonucleotide probes of the at least one genome wide probe map and defining a consensus map indicating restriction sites based on each of the at least one genome wide restriction map and locations of detectable oligonucleotide probes based on each of the at least one genome wide probe map.

US Patent:

20030087280, May 8, 2003

Filed:

Aug 21, 2002

Appl. No.:

10/224881

Inventors:

David Schwartz - Madison WI, US
Eileen Dimalanta - Madison WI, US
Sang Lim - Madison WI, US
Galex Yen - Gurnee IL, US
Konstantinos Potamousis - Madison WI, US
Thomas Anantharaman - De Forest WI, US

International Classification:

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

US Classification:

435/006000, 702/020000

Abstract:

Disclosed are consensus optical contig maps of an entire genome of an organism and methods of using the maps to verify, validate, refute and/or access the accuracy of a known nucleic acid sequence or full genomic sequence. The maps are constructed using optical methods wherein DNA is elongated and fixed along their length onto a solid planar surface so that the DNA molecules are individually analyzable and accessible for enzymatic reactions. The DNA molecules are then reacted with a restriction enzyme to yield cleaved fragments of discernable length fixed to the surface. The lengths of the fragments are then determined, using optical methods. From the lengths determined, an optical contig map is assembled and can be compared to a corresponding known sequence, for example, a genomic sequence.

US Patent:

20130045879, Feb 21, 2013

Filed:

Mar 16, 2012

Appl. No.:

13/422703

Inventors:

Bhubaneswar Mishra - New York NY, US
Thomas Anantharaman - San Diego CA, US
Sang Lim - Millburn NJ, US
Pierre Franquin - Westborough MA, US

Assignee:

New York University - New York NY

International Classification:

C40B 30/04
G01N 33/48
G06F 19/00
C40B 60/12

US Classification:

506 9, 506 39, 702 20, 702 19

Abstract:

Methods, computer-accessible medium, and systems for generating a genome wide probe map and/or a genome wide haplotype sequence are provided. In particular, a genome wide probe map can be generated by obtaining a plurality of detectable oligonucleotide probes hybridized to at least one double stranded nucleic acid molecule cleaved with at least one restriction enzyme, and detecting the location of the detectable oligonucleotide probes. For example, genome wide haplotype sequence can be generated by analyzing at least one genome wide restriction map in conjunction with at least one genome wide probe map to determine distances between restriction sites of the genome wide restriction map(s) and locations of detectable oligonucleotide probes of the genome wide probe map(s) and defining a consensus map indicating restriction sites based on the genome wide restriction map(s) and/or locations of detectable oligonucleotide probes based on each of the genome wide probe map(s).

US Patent:

20150120209, Apr 30, 2015

Filed:

May 5, 2014

Appl. No.:

14/269670

Inventors:

Bhubaneswar Mishra - New York NY, US
Thomas Anantharaman - Poughquag NY, US
Sang Lim - Tarrytown NY, US

Assignee:

New York University - New York NY

International Classification:

G06F 19/18
G06F 19/22

US Classification:

702 20

Abstract:

Methods, computer-accessible medium, and systems for generating a genome wide probe map and/or a genome wide haplotype sequence are provided. In particular, a genome wide probe map can be generated by obtaining a plurality of detectable oligonucleotide probes hybridized to at least one double stranded nucleic acid molecule cleaved with at least one restriction enzyme, and detecting the location of the detectable oligonucleotide probes. For example, genome wide haplotype sequence can be generated by analyzing at least one genome wide restriction map in conjunction with at least one genome wide probe map to determine distances between restriction sites of the genome wide restriction map(s) and locations of detectable oligonucleotide probes of the genome wide probe map(s) and defining a consensus map indicating restriction sites based on the genome wide restriction map(s) and/or locations of detectable oligonucleotide probes based on each of the genome wide probe map(s).