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BioInform s IP Roundup: Recent Patents in Bioinformatics: Apr 4, 2005

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US Patent 6,862,561. Method and apparatus for computer modeling a joint. Inventors: Nadine Defranoux, Todd Dubnicoff, David Klinke, Annette Lewis, Thomas Paterson, Saroja Ramanujan, Lisl Shoda, Karl Petter Soderstrom, Herbert Struemper. Assignee: Entelos.

Protects a mathematical and computer model of a joint. The model includes representation of the biological processes related to the synovial tissue and cartilage. In one embodiment, the model represents a human joint afflicted with rheumatoid arthritis.


US Patent 6,856,914. Method, apparatus, media and signals for identifying associated cell-signaling proteins. Inventor: Steven Pelech. Assignee: The University of British Columbia.

Covers methods, apparatus, media, and signals for identifying associated cell-signaling proteins. The method involves producing and storing a comparison value for each pair of cell-signaling proteins in response to data values representing physical properties of respective cell-signaling proteins. The apparatus includes a receiver that receives the data values representing the physical properties of the respective cell signaling proteins, and a processor circuit in communication with the receiver. The processor circuit is configured to produce and store, in a memory, each of the comparison values, and to identify the cell-signaling protein pairs. The processor circuit may be configured to produce a list of pairs of associated cell-signaling proteins, and/or to produce a list of clusters of associated cell-signaling proteins.


US Patent 6,859,735. Computer systems for identifying pathways of drug action. Inventors: Roland Stoughton, Stephen Friend. Assignee: Rosetta Inpharmatics.

Protects methods and computer systems for identifying and representing the biological pathways of drug action on a cell The invention also provides methods and computer systems for assessing the significance of the identified representation and for verifying that the identified pathways are actual pathway of drug action. The invention also provides methods and computer systems for drug development based on the methods for identifying biological pathways of drug action, and methods and computer systems for representing the biological pathways involved in the effect of an environmental change upon a cell.


US Patent 6,859,736. Method for protein structure alignment. Inventors: Richard Blankenbecler, Mattias Ohlsson, Carsten Peterson, Markus Ringner. Assignee: The Board of Trustees of the Leland Stanford Junior University.

Covers a method for protein structure alignment. The invention involves two key elements: First, an energy or cost function formulation of the problem simultaneously in terms of binary assignment variables and real-valued atomic coordinates; and second, a minimization of the energy or cost function by an iterative method, where in each iteration a mean field method is employed for the assignment variables and exact rotation and/or translation of atomic coordinates is performed, weighted with the corresponding assignment variables.


US Patent 6,865,492. Algorithmic design of peptides for binding and/or modulation of the functions of receptors and/or other proteins. Inventors: Arnold Mandell, Karen Selz, Michael Shlesinger. Assignee: The Cielo Institute.

Protects methods of synthesizing a peptide or peptide-like molecule to a polypeptide or protein target based on mode-matching each member of a set of peptide constituents of the peptide or peptide-like molecule to peptide constituents of the target polypeptide or protein target. Methods are also provided for synthesizing retro-inverso peptides to the mode-matched peptide.


US Patent 6,871,147. Automated method of identifying and archiving nucleic acid sequences. Inventors: John Schlager, Richard Sweeney, Douglas Avery. Assignee: The United States of America as represented by the Secretary of the Army.

Protects a method of identifying and archiving a nucleic acid sequence that includes a) creating a directory of files in a computer, for storing information related to the nucleic acid sequence; b) inputting a raw nucleic acid sequence into the computer; c) trimming the raw nucleic acid sequence to obtain a trimmed nucleic acid sequence; d) submitting the trimmed nucleic acid sequence electronically to a nucleic acid identification database having a search program and receiving search results electronically from the nucleic acid identification database; e) choosing selective information from each search result and inserting the selective information from each search result into a first electronic spreadsheet; and f) selecting at least one of the search results from the first electronic spreadsheet and inserting the at least one search result into a second electronic spreadsheet.


US Patent 6,873,915. Peak selection in multidimensional data. Inventor: Curtis Hastings. Assignee: Surromed.

Protects an automatic peak selection method for multidimensional data that selects peaks from very noisy data, such as two-dimensional liquid chromatography-mass spectrometry data. The method computes local noise thresholds for each one-dimensional component of the data. Each point has a local noise threshold applied to it for each dimension of the data set, and a point is selected as a candidate peak only if its value exceeds all of the applied local noise thresholds. Contiguous candidate peaks are clustered into actual peaks. The method is preferably implemented as part of a high-throughput platform for analyzing complex biological mixtures.


US Patent 6,873,914. Methods and systems for analyzing complex biological systems. Inventors: Stephanie Winfield, Norman Glassbrook, Yasmin Ranasinghe, David Broadwell, Ioana Popa-Burke, Gordon James Nye, Christopher Beecher. Assignee: Icoria.

Protects methods and systems for organizing complex and disparate data into coherent data sets, which serve as models for biological systems. According to the inventors, the disclosed methods are useful for numerous biological applications, including determining gene function, identifying and validating drug and pesticide targets, identifying and validating drug and pesticide candidate compounds, profiling drug and pesticide compounds, producing a compilation of health or wellness profiles, determining compound site(s) of action, identifying unknown samples, and other applications in the agricultural, pharmaceutical, forensic, and biotechnology industries.

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Right Whales' Decline

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Science Papers Tie Rare Mutations to Short Stature, Immunodeficiency; Present Single-Cell Transcriptomics Map

In Science this week: pair of mutations in one gene uncovered in brothers with short stature and immunodeficiency, and more.