DAVID J SCHWARTZ
Pilots at Middleton Bch Rd, Madison, WI

2012025, Oct 4, 2012

Feb 2, 2010

12/698224

David Charles Schwartz - Madison WI, US
Jessica Severin - Cambridge, GB

G06F 3/048, G06F 17/00, G06F 17/30

715230, 707705, 715800, 715780, 715733, 707E17005

There is provided a computer system for visualizing and editing single molecule fragments and one or more previously-produced single molecule assemblies or “contigs.” The present visualization and editing system allows a user to visualize large data sets resulting from single molecule map assembly operations, and to rapidly discern important features while errors and other discrepancies are conveniently resolved. The system includes one or more connectors connecting each to one or more databases capable of storing a diverse array of biomedical information, in addition to the single molecule data against which a user may validate the prior alignment and assembly. Embodiments described herein are thus useful in studies of macromolecules such as DNA, RNA, peptides and proteins. The visualization and editing system may be implemented and deployed over a computer network, and may be ergonomically optimized to facilitate user interaction.

6713263, Mar 30, 2004

Sep 9, 2002

10/238407

David C Schwartz - Madison WI

Wisconsin Alumni Research Foundation - Madison WI

C12Q 168

435 6, 436 94

A method for observing and determining the size of individual molecules and for determining the weight distribution of a sample containing molecules of varying size, which involves placing a deformable or nondeformable molecule in a medium, subjecting the molecule to an external force, thereby causing conformational and/or positional changes, and then measuring these changes. Preferred ways to measure conformational and positional changes include: (1) determining the rate at which a deformable molecule returns to a relaxed state after termination of the external force, (2) determining the rate at which a molecule becomes oriented in a new direction when the direction of the perturbing force is changed, (3) determining the rate at which a molecule rotates, (4) measuring the length of a molecule, particularly when it is at least partially stretched, or (5) measuring at least one diameter of a spherical or ellipsoidal molecule. Measurements of relaxation, reorientation, and rotation rates, as well as length and diameter can be made using a light microscope connected to an image processor. Molecule relaxation, reorientation and rotation also can be determined using a microscope combined with a spectroscopic device.

6610256, Aug 26, 2003

Sep 24, 2001

09/962802

David C. Schwartz - Madison WI

Wisconsin Alumni Research Foundation - Madison WI

B01J 1908

422186, 422 55, 422 58, 422 99, 422129, 435 6, 536 231

A method for observing and determining the size of individual molecules and for determining the weight distribution of a sample containing molecules of varying size, which involves placing a deformable or nondeformable molecule in a medium, subjecting the molecule to an external force, thereby causing conformational and/or positional changes, and then measuring these changes. Preferred ways to measure conformational and positional changes include: (1) determining the rate at which a deformable molecule returns to a relaxed state after termination of the external force, (2) determining the rate at which a molecule becomes oriented in a new direction when the direction of the perturbing force is changed, (3) determining the rate at which a molecule rotates, (4) measuring the length of a molecule, particularly when it is at least partially stretched, or (5) measuring at least one diameter of a spherical or ellipsoidal molecule. Measurements of relaxation, reorientation, and rotation rates, as well as length and diameter can be made using a light microscope connected to an image processor. Molecule relaxation, reorientation and rotation also can be determined using a microscope combined with a spectroscopic device.

2012024, Oct 4, 2012

Jul 12, 2004

10/888517

David Charles Schwartz - Madison WI, US
Jessica Severin - Cambridge, GB

G09G 5/00

345629

There are provided computer systems for visualizing and annotating single molecule images. Annotation systems in accordance with this disclosure allow a user to mark and annotate single molecules of interest and their restriction enzyme cut sites thereby determining the restriction fragments of single nucleic acid molecules. The markings and annotations may be automatically generated by the system in certain embodiments and they may be overlaid translucently onto the single molecule images. An image caching system may be implemented in the computer annotation systems to reduce image processing time. The annotation systems include one or more connectors connecting to one or more databases capable of storing single molecule data as well as other biomedical data. Such diverse array of data can be retrieved and used to validate the markings and annotations. The annotation systems may be implemented and deployed over a computer network. They may be ergonomically optimized to facilitate user interactions.

7960105, Jun 14, 2011

Nov 29, 2006

11/633232

David C. Schwartz - Madison WI, US
Kyubong Jo - Champaign IL, US
Dalia M. Dhingra - Arlington Heights IL, US

National Institutes of Health - Bethesda MD
The United States of America as represented by the Department of Health and Human Services - Washington DC
U.S. Government NIH Division of Extramural Inventions and Technology Resources - Washington DC

C12Q 1/68, C12M 1/34, C07H 21/04, G01N 33/53

435 6, 4352872, 536 231, 436800

Methods are provided for tagging, characterizing and sorting double-stranded biomolecules while maintaining the integrity of the biomolecules.

8034550, Oct 11, 2011

May 29, 2008

12/128928

David C. Schwartz - Madison WI, US

Wisconsin Alumni Research Foundation - Madison WI

C12Q 1/00

435 4

Arrays of distinct chemically reactive materials used for assaying or screening are assembled by arranging premanufactured strips, each having a linear array of chemically reactive materials on its surface, into a frame to be exposed to a substance to be analyzed. The strips provide great flexibility in generating different types of arrays while still permitting efficiencies to be gained by batch processing of each strip type. The arrays further provide for novel read-out and reaction promotion techniques making use of the ability of the strips to direct and received energy to and from particular sites.

7775368, Aug 17, 2010

Oct 17, 2003

10/688416

David Charles Schwartz - Madison WI, US
Eileen T. Dimalanta - Madison WI, US
Juan J. de Pablo - Madison WI, US

Wisconsin Alumni Research Foundation - Madison WI

B03B 13/00, C12Q 1/68

209 1, 435 6

Laminar flow of a carrier liquid and polymeric molecules through micro-channels is used to straighten, align, separate, and/or sort the polymeric molecules. The polymeric molecules may be analyzed and/or manipulated in the carrier liquid or attached to a wall of the micro-channel for subsequent treatment and analysis. Micro-channels can be manufactured using an elastic molding material. One micro-channel embodiment provides fluid flow using a standard laboratory centrifuge.

8221973, Jul 17, 2012

Oct 17, 2008

12/253625

David C. Schwartz - Madison WI, US
Konstantinos D. Potamousis - Madison WI, US
Shiguo Zhou - Madison WI, US
Steven J. Goldstein - Madison WI, US
Michael A. Newton - Madison WI, US
Rodney A. Runnheim - Madison WI, US
Daniel K. Forrest - Fitchburg WI, US
Christopher P. Churas - La Jolla CA, US

Wisconsin Alumni Research Foundation - Madison WI

C12Q 1/68

435 61

Methods are provided for ascertaining the sequence of a genomic DNA sample by nicking the DNA sample with a restriction nicking enzyme, followed by nick translation with labeled nucleotides, such that the labeled nucleotides can be quantified and compared to a known, reference genome.