Leland Stanford Junior University

Other

Sri International

Deutsches Krebsforschungszentrum

Conrad, Carol

Tirouvanziam, Rabindra

Herzenberg, Leonore A.

Leonore A Herzenberg

David R Parks

Wayne A Moore

Leonard A Herzenberg

Stephen W Meehan

Guenther Walther

Mario Roederer

Darya Y Orlova

Kari C Nadeau

Denong Wang

Vernon T Oi

Rabindra M Tirouvanziam

Ronald L Rabin

Noah Zimmerman

Stephen C De Rosa

James Andrus

Jinhui Pan

Ilana Belitskaya-Levy

Yael Gernez

Lawrence Steinman

David Miklos

Martin Bigos

Mark Musen

Andrei Vitalievich Chernyshev

William E Benitz

Bita Sahaf

Yvonne Maldonado

Stephen C DeRosa

Connor Meehan

Subramanian Sriram

Matthew K Waldor

Wulf Dr Oge

Antonio Y Hardan

Lawrenes Steinman

Connor G W Meehan

Donna M Peehl

Alexander E Moskalensky

James Tung

Stephan M Weissman

Adam S Treister

Erica E Weirich

Carol Conrad

Rabindra Tirouvanziam

Some embodiments provide methods, systems and computer-readable media that employ adaptive binning and dissimilarity scores based on a quadratic form distance for multidimensional data for matching clusters in data corresponding to different sample. Some embodiments provide methods, systems and computer-readable media for rendering a first interactive display including a two-dimensional plot of at least a portion of a multidimensional data set and a corresponding second interactive display including a plurality of single parameter charts or histograms, each displaying information corresponding to one-dimensional measurements of a different parameter in the multidimensional data set.

Systems and methods for cluster matching across samples and guided visualization of multidimensional cytometry data

The described invention provides a method and/or system for analyzing data using population clustering through density based merging, and a method for guiding clustering strategy through entropy-based ranking score.

Cluster processing and ranking methods including methods applicable to clusters developed through density based merging

A method and apparatus for quantitatively measuring differences between portions of a multivariate, multi-dimensional sample distribution, may comprise summarizing the data by dividing the data into clusters each having a signature representative of a position of the cluster and a fraction of the entire distribution within the cluster; matching a plurality of first supplier signatures to a respective one of a plurality of second receiver signatures using a cost factor indicative of the separation between first signature elements and second signature elements; and determining a measurement of the work required to transform the first signature to the second signature. The step of determining a measurement of the work may comprise applying the earth mover distance ('EMD') algorithm between the first signature or elements of the first signature and the respective second signatures or elements of the respective second signature.

Quantitative comparison of sample populations using earth mover's distance

The described invention provides a method for quantifying cellular antigens that is independent of specially prepared calibration beads and antibody reagents. The described method can be applied to both low and high affinity antibodies, under both saturating and non-saturating binding conditions.

Quantification of antigen molecules using dynamic flow cytometry

The invention describes a system and method for searching, organizing and displaying information in a user-specified flexible context that enables users to create customized hierarchical views and groupings. The formats for acquiring search results may be stored so that they may be re-applied to the same data or any similarly structured data in subsequent sessions.

System and method for organizing data in a dynamic user-customizable interface for search and display

Methods for detecting nonactivated basophils in a whole blood sample obtained from a normal healthy subject, methods for determining a subject's susceptibility to an allergic reaction to an allergen, where the subject has no known allergy to the allergen, methods for measuring a response to challenge with a potential allergen in a whole blood sample obtained from a subject with known allergic reactivity to allergens other than the potential allergen; and an in vitro system for reliable detection or quantification of a specific white blood cell population in a whole blood sample are described.

Methods and assays for detecting and quantifying pure subpopulations of white blood cells in immune system disorders

Methods are provided for determining a subject's susceptibility to an allergic reaction upon exposure to an offending allergen. Methods are also provided for determining and monitoring a subject's responsiveness to ongoing allergy treatment

Granulocyte-based methods for detecting and monitoring immune system disorders

The described invention comprises a method for detecting the onset or monitoring the recurrence of chronic graft versus host disease (cGVHD) in a transplantation patient. The method comprises isolating peripheral blood mononuclear cells (PBMCs) from the transplantation patient and analyzing the isolated PBMCs to detect a biomarker specific for a donor cell. The detection of the biomarker is indicative of the onset or recurrence of cGVHD in the transplantation patient.

Method to detect the onset and to monitor the recurrence of chronic graft versus host disease in transplantation patients

A method and/or system for analyzing data using population clustering through density based merging.

Method for identifying clusters of fluorescence-activated cell sorting data points

This invention provides novel liposome-based articles of manufacture and microarrays and methods of making and using them (1) to detect the presence of one or more agents in a sample, (2) to determine the amount of one or more agents in a sample, and (3) to determine whether a subject is afflicted with a disorder. This invention also provides kits which comprise the instant microarrays.

Liposome-based microarray and methods of use thereof

The invention provides a system and method for selecting an optimal multimarker reagent combination for the identification and/or quantification of molecules in or on cells with or without reference to fluorescence or other properties of at least one fluorescent dye or other instrument-measurable atom or molecule associated directly or indirectly with the reagent combination. The method includes specifying, using a computer, a plurality of markers to be detected by a plurality of reagents, generating, using a computer, a plurality of reagent combinations comprising the plurality of reagents to detect the plurality of markers, wherein the reagent combinations are ranked according to at least one user-defined or system-defined criterion, and selecting the optimal reagent combination or providing a rank-ordered list of combinations.

System and method for selecting a multiparameter reagent combination and for automated fluorescence compensation

Disclosed is a method and system for archiving data. A server computer (or any computing device) receives data transmitted over a network from a client computer, wherein at least some of the data was previously collected by a scientific instrument during an experiment. After receiving the data, the server computer updates (e.g., creates) an index for the received data, archives the received data, and automatically transmits a notification to the client computer that the received data has been archived.

Method and system for data archiving

Method for clustering data items through distance-merging and density-merging techniques

Disclosed are methods for probing the immunogenic sugar moieties of prostate cancer cells. The methods detect a number of glyco-epitopes that are highly and differentially expressed among prostate cancers of various Gleason grades. The glyco-epitopes exist on the surfaces of prostate cells. The methods also comprise the detection of autoantibodies in prostate cancer subjects. The antibodies bound to a glyco-motif of N-glycans that is normally 'cryptic.' This target is highly expressed in prostate cancers. Lectins and antibodies that detect these glyco-epitopes that expressed in prostate cancer tissues includelectin (EEL);Lectin-I (PTL-I);Lectin-I-A4 (GSL-I-A4);Lectin-I-B4 (GSL-I-B4);I agglutinin (SNA-I;-L (PHA-L;agglutinin (GNA);agglutinin (NPA);agglutinin (Jacalin); and mAb TM10 (IgM).

Prostate cancer glycan markers and autoantibody signatures

The present invention provides computer program products, systems, and related methods of coordinating a knowledge base.

Methods, software, and systems for knowledge base coordination

Growing community of inventors

Stanford, CA, United States of America

Leonore A Herzenberg