David A Stenger

US Patent:

7623997, Nov 24, 2009

Filed:

Jun 6, 2006

Appl. No.:

11/422431

Inventors:

Anthony P. Malanoski - Greenbelt MD, US
Baochuan Lin - Bethesda MD, US
Joel M Schnur - Burke VA, US
David A Stenger - Herndon VA, US

Assignee:

The United States of America as represented by the Secretary of the Navy - Washington DC

International Classification:

G06F 17/10

US Classification:

703 2, 702 20, 702179, 702193, 703 11, 707 6

Abstract:

A method of: submitting reference sequences to a taxonomic database to produce taxonomic results; and reporting a taxonomic identification based on the taxonomic results. The reference sequences are the output of genetic database queries that return a score for each reference sequence. A method for processing a biological sequence obtained from an assay by: converting base calls located in a predetermined list of positions within the biological sequence to N; and determining the ratio of single nucleotide polymorphisms in the biological sequence relative to a reference sequence. Each entry in the predetermined list of positions represents the capability of a substance hybridizing to a microarray used to generate the biological sequence. The substance is not the nucleic acid of a target pathogen.

US Patent:

7668664, Feb 23, 2010

Filed:

Aug 22, 2007

Appl. No.:

11/843126

Inventors:

Anthony P. Malanoski - Greenbelt MD, US
Zheng Wang - Burke VA, US
Baochuan Lin - Bethesda MD, US
David A Stenger - Herndon VA, US
Joel M Schnur - Burke VA, US

Assignee:

The United States of America as represented by the Secretary of the Navy - Washington DC

International Classification:

G01N 33/48

US Classification:

702 20, 702 33, 702179, 703 2, 703 11, 706 13, 706 48, 707 3, 707 6, 435 6, 4352872, 4352884

Abstract:

A computer-implemented method as follows. Providing a list of target sequences associated with one or more organisms. Providing a list of candidate prototype sequences suspected of hybridizing to one or more of the target sequences. Generating a collection of probes corresponding to each candidate prototype sequence, each collection of probes having a set of probes for every subsequence. The sets consist of the corresponding subsequence and every variation of the corresponding subsequence formed by varying a center nucleotide of the corresponding subsequence. Generating a set of fragments corresponding to each target sequence. Calculating the binding free energy of each fragment with a perfect complimentary sequence of the fragment. Determining which extended fragments are perfect matches to any of the probes. Assembling a base call sequence corresponding to each candidate prototype sequence.

US Patent:

7695941, Apr 13, 2010

Filed:

Jun 6, 2006

Appl. No.:

11/422425

Inventors:

Baochuan Lin - Bethesda MD, US
Kate M. Blaney - Alexandria VA, US
Anthony P. Malanoski - Greenbelt MD, US
Joel M Schnur - Burke VA, US
David A Stenger - Herndon VA, US

Assignee:

The United States of America as represented by the Secretary of the Navy - Washington DC

International Classification:

C12Q 1/68
C12P 19/34

US Classification:

435 912, 435 6, 435 911

Abstract:

A PCR method involving: providing a biological sample suspected of containing one or more pathogen nucleic acids; adding a plurality of PCR primers corresponding to genes found in the pathogens; and performing a polymerase chain reaction on the sample to amplify a subset of the nucleic acids that correspond to the genes. The primers include at least one primer pair for each pathogen, and the primers contain a tail sequence that is not homologous any pathogen DNA or to any background DNA in the sample. The concentration of at least one primer in the polymerase chain reaction is no more than about 100 nM.

US Patent:

7785769, Aug 31, 2010

Filed:

Jul 25, 2003

Appl. No.:

10/627143

Inventors:

Mark S. Spector - Springfield VA, US
David A. Stenger - Herndon VA, US
Brett D. Martin - Washington DC, US
Paul T. Charles - Bowie MD, US

Assignee:

The United States of America as reprsented by the Secretary of the Navy - Washington DC

International Classification:

C12Q 1/00

US Classification:

435 4, 435 6, 4352872, 435 14, 526 72, 526 89, 530300, 530350

Abstract:

The use of sugar-containing hydrogels as very highly porous, aqueous support material for the immobilization of oligonucleotides, peptides, proteins, antigens, antibodies, polysaccharides, and other biomolecules for sensor applications. Unusually large sizes of interconnected pores allow large target molecules to pass rapidly into and through the gel and bind to immobilized biomolecules. Sugar-containing hydrogels have extremely low non-specific absorption of labeled target molecules, providing low background levels. Some hydrogel materials do not have this type of homogeneous interconnected macroporosity, thus large target molecules cannot readily diffuse through them. Additionally, they nearly always experience non-specific absorption of labeled target molecules, limiting their usefulness in sensor applications. A method is provided for preparing sugar polyacrylate hydrogels with functional chemical groups which covalently bond oligonucleotides and peptides. A method for copolymerizing acrylate-terminated oligonucleotides with sugar acrylate monomers and diacrylate cross-linking agents is also provided.

US Patent:

7785770, Aug 31, 2010

Filed:

May 19, 2006

Appl. No.:

11/444819

Inventors:

Mark S. Spector - Springfield VA, US
David A. Stenger - Herndon VA, US
Brett D. Martin - Washington DC, US
Paul T. Charles - Bowie MD, US

Assignee:

The United States of America as represented by the Secretary of the Navy - Washington DC

International Classification:

C12Q 1/00

US Classification:

435 4, 435 6, 4352872, 435 14, 526 72, 526 89, 530300, 530350

Abstract:

The use of sugar-containing hydrogels as very highly porous, aqueous support material for the immobilization of oligonucleotides, peptides, proteins, antigens, antibodies, polysaccharides, and other biomolecules for sensor applications. Unusually large sizes of interconnected pores allow large target molecules to pass rapidly into and through the gel and bind to immobilized biomolecules. Sugar-containing hydrogels have extremely low non-specific absorption of labeled target molecules, providing low background levels. Some hydrogel materials do not have this type of homogeneous interconnected macroporosity, thus large target molecules cannot readily diffuse through them. Additionally, they nearly always experience non-specific absorption of labeled target molecules, limiting their usefulness in sensor applications. A method is provided for preparing sugar polyacrylate hydrogels with functional chemical groups which covalently bond oligonucleotides and peptides. A method for copolymerizing acrylate-terminated oligonucleotides with sugar acrylate monomers and diacrylate cross-linking agents is also provided.

US Patent:

7979446, Jul 12, 2011

Filed:

Nov 12, 2009

Appl. No.:

12/617025

Inventors:

Anthony P. Malanoski - Washington DC, US
Baochuan Lin - Bethesda MD, US
Joel M Schnur - Burke VA, US
David A Stenger - Herndon VA, US

Assignee:

The United States of America as represented by the Secretary of the Navy - Washington DC

International Classification:

G06F 7/00
G06F 17/30

US Classification:

707749, 702 20, 703 2, 703 11, 706 48, 707706, 707723, 707776

Abstract:

A method of: submitting reference sequences to a taxonomic database to produce taxonomic results; and reporting a taxonomic identification based on the taxonomic results. The reference sequences are the output of genetic database queries that return a score for each reference sequence. A method for processing a biological sequence obtained from an assay by: converting base calls located in a predetermined list of positions within the biological sequence to N; and determining the ratio of single nucleotide polymorphisms in the biological sequence relative to a reference sequence. Each entry in the predetermined list of positions represents the capability of a substance hybridizing to a microarray used to generate the biological sequence. The substance is not the nucleic acid of a target pathogen.

US Patent:

8032310, Oct 4, 2011

Filed:

Jul 2, 2005

Appl. No.:

11/177647

Inventors:

David A Stenger - Herndon VA, US
Jennifer Thornton - Alexandria VA, US

Assignee:

The United States of America as represented by the Secretary of the Navy - Washington DC

International Classification:

G01N 33/48

US Classification:

702 20, 703 2, 703 11, 211 4112

Abstract:

A computer-implemented biological sequence identifier (CIBSI) system and method for selecting a subsequence from biological sequence data according to at least one selection parameter. The at least one selection parameter corresponds to a likelihood of returning a meaningful result from a similarity search.

US Patent:

20030054333, Mar 20, 2003

Filed:

Jun 12, 2001

Appl. No.:

09/880138

Inventors:

James Hickman - Pendleton SC, US
Douglas Kirkpatrick - Great Falls VA, US
David Stenger - Springfield VA, US

International Classification:

C12Q001/00
C12M001/34
C12N005/08

US Classification:

435/004000, 435/287100, 435/368000

Abstract:

A biosensor for detecting a bioeffecting substance in a test sample includes a cell network of at least one electrically excitable cell provided on a substrate in a predetermined geometry with a predefined axonal/dendritic polarity. The at least one cell is capable of producing a signal in response to the presence of the bioeffecting substance. At least one signal transducer is provided with the substrate in a predetermined geometry and is capable of detecting the signal produced by the cell. A culture medium capable of supporting metabolism of the cell is also provided.