Incyte Genomics, Inc.

Affymetrix, Inc.

Genomic Health, Inc.

Incyte Pharmaceuticals, Inc.

Incyte Corporation

Octave Bioscience, Inc.

Michael Graham Walker

Robert J Lipshutz

Joffre B Baker

Michael C Kiefer

Maureen T Cronin

Steve Shak

Tod M Klingler

Wayne D Volkmuth

Laura L Stuve

Richard D Goold

Harold H Hibbert

Tod M Klinger

Randi E Krasnow

Michael P Wood

Robert E Lagace

Anne L Curtis

Philippe E Rigault

David A Hadley

Henry Yue

Yalda Azimzai

Eldar Y Giladi

Robert Schmidt

Melinda Thomas

James Z Wang

William A Hagstrom

Karen A Jones

Markers useful for determining multiple sclerosis activity in a human subject are provided, along with kits for measuring quantitative expression values of the markers. Also provided are computer systems and software embodiments of predictive models for scoring and determining multiple sclerosis activity in human subjects based on the quantitative expression values of the markers.

Methods for assessment of multiple sclerosis activity

The invention concerns sensitive methods to measure mRNA levels in biopsied tumor tissues, including archived paraffin-embedded biopsy material. The invention also concerns breast cancer gene sets important in the diagnosis and treatment of breast cancer, and methods for assigning the most optimal treatment options to breast cancer patient based upon knowledge derived from gene expression studies.

Gene expression profiling in biopsied tumor tissues

The invention concerns sensitive methods to measure mRNA levels in biopsied tumor tissues, including archived paraffin-embedded biopsy material. Th invention also concerns breast cancer gene sets important in the diagnosis and treatment of breast cancer, and methods for assigning the most optimal treatment options to breast cancer patient based upon knowledge derived from gene expression studies.

A computer system for analyzing nucleic acid sequences is provided. The computer system is used to calculate probabilities for determining unknown bases by analyzing the fluorescence intensities of hybridized nucleic acid probes on biological chips. Additionally, information from multiple experiments is utilized to improve the accuracy of calling unknown bases.

Computer-aided probability base calling for arrays of nucleic acid probes on chips

A method and system for generating and searching a tree-structured index of window vectors that represent database sequences comprise a window vector generation module, a tree-structured index generation module, a query sequence partitioning module, and a retrieval component. The window vector generation module partitions a database sequence into a plurality of overlapping windows. Each window has a fixed length W comprising a fixed number of nucleotides, and the offset among windows is determined by a parameter &Dgr;. The window vector generation module then maps each database sequence window into a window vector. The database sequence window vector indicates the frequency of appearance of each k-tuple in the corresponding database sequence window. The tree-structured index generation module then generates a tree-structured index using the database sequence window vectors. The query sequence partitioning module partitions a query sequence into a plurality of windows and maps each query sequence window into a query sequence window vector. Each query sequence window vector is then compared against the tree-structured index to locate the database sequences that are similar to the query sequence. The list of database sequences that are similar to the query sequence is then returned as the result of the search.

Sequence database search with sequence search trees

The invention provides compositions and novel polynucleotides and proteins that co-express with known marker genes for inflammatory disorders. The invention also provides expression vectors, host cells, proteins encoded by the polynucleotides and antibodies which specifically bind the proteins. The invention also provides methods for the diagnosis, prognosis, evaluation of therapies and treatment of inflammatory disorders.

Inflammation-associated polynucleotides

The invention provides a mammalian cDNA which encodes a mammalian AQP8V. It also provides for the use of the cDNA, fragments, complements, and variants thereof and of the encoded protein, portions thereof and antibodies thereto for diagnosis and treatment of pancreatic disorders, particularly type I diabetes. The invention additionally provides expression vectors and host cells for the production of the protein and a transgenic model system.

Aquaporin-8 variant

The invention provides mammalian cDNAs which encode mammalian SPARC-related proteins. It also provides for the use of the cDNA, fragments, complements, and variants thereof and of the encoded protein, portions thereof and antibodies thereto for diagnosis and treatment of atherosclerosis and cell proliferative disorders. The invention additionally provides expression vectors and host cells for the production of the proteins and transgenic model systems.

DNA encoding sparc-related proteins

The invention provides a mammalian cDNA which encodes a mammalian Ras association domain containing protein. It also provides for the use of the cDNA, fragments, complements, and variants thereof and of the encoded protein, portions thereof and antibodies thereto for diagnosis and treatment of cell proliferative and inflammatory disorders, particularly thymus hyperplasia, allergies, asthma, and hypereosinophilia. The invention additionally provides expression vectors and host cells for the production of the protein and a transgenic model system.

Ras association domain containing protein

The invention provides polynucleotides and polypeptides that are co-expressed with genes known to be involved in bone remodeling and osteoporosis. The invention also provides expression vectors, host cells, and methods for making a polypeptide, for screening or purifying ligands, and for diagnosing disorders associated with bone remodeling or osteoporosis.

Bone remodeling genes

A computer system stores biomolecular data in a database in a memory. The biomolecular database has a set of entities. Each entity stores attributes for a plurality of entries. At least one attribute is stored in an array. Data associated with an entry is stored at a location in the array. An entity offset designates the location of the data in the array. The same entity offset value is used to access data associated with a particular entry for all attributes within the entity.

Growing community of inventors

Sunnyvale, CA, United States of America

Michael Graham Walker