Patents by Inventor Michael A. Siani
Michael A. Siani has filed for patents to protect the following inventions. This listing includes patent applications that are pending as well as patents that have already been granted by the United States Patent and Trademark Office (USPTO).
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Patent number: 7680601Abstract: Methods for the computational analysis of polyketides and the computer-assisted design of PKS genes are facilitated by representing the structure of a polyketide and/or a PKS gene that encodes the PKS that produces the polyketide by alphanumeric symbols that facilitates computer assisted analysis. A database of polyketides and corresponding PKS genes that can be rapidly searched and information extracted for a variety of applications, including the design and specification of PKS genes via the recombining of modules or portions of modules or sets of modules from already known and available PKS genes.Type: GrantFiled: May 29, 2001Date of Patent: March 16, 2010Assignee: Kosan BiosciencesInventors: Chaitan Khosla, Ralph C. Reid, Daniel V. Santi, Michael A. Siani
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Patent number: 7133780Abstract: Methods, software products and systems are provided for automated high throughout gene characterization. In one exemplary embodiment, HMM models are used to characterize genes. Biological sequences are classified according to their hit with different HMM models using a curve analysis.Type: GrantFiled: December 5, 2001Date of Patent: November 7, 2006Assignee: Affymetrix, Inc.Inventors: Michael A Siani-Rose, Ron Shigeta
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Patent number: 6844161Abstract: Novel proteins and protein libraries are disclosed. The proteins possess one or more functional protein modules from different parent protein molecules. The proteins and protein libraries are exemplified by the preparation of cross-over chemokines that contain various combinations of peptide segments derived from RANTES, SDS-1 and vMIP-I and to vMIP-II. The proteins and libraries are extremely pure and can be provided in non-limiting high yields suitable for diagnostic and high-throughput screening assays.Type: GrantFiled: August 31, 1998Date of Patent: January 18, 2005Assignee: Gryphon Therapeutics, Inc.Inventors: Michael A. Siani, Jill Wilken, Reyna Simon, Stephen B. H. Kent
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Publication number: 20040229252Abstract: Immune response to pathogens and tumors includes the activation of T cell receptors. Methods for detecting set of polymorphisms in the TCR gene(s) can be very useful for monitoring disease and disease susceptibility. High density nucleic acid arrays may be used to identify single nucleotide polymorphisms in the T cell receptor and the precise T cell receptor species responsible for immunity or self-immune reactions.Type: ApplicationFiled: February 19, 2004Publication date: November 18, 2004Applicant: Affmetrix, INC.Inventor: Michael A. Siani-Rose
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Publication number: 20040126840Abstract: A genomic web portal provides an ontological map having nodes and edges. The computer-implemented portal system makes use of information correlating one or more probe-set identifiers with a plurality of ontological categories or terms, thereby generating probe-set identifier association data. The probe-set identifiers are associated with one or more probe sets of one or more probe arrays that may be involved in microarray experiments. The system correlates the probe-set identifier association data with graph traversal data and displays an ontological map based on this correlation.Type: ApplicationFiled: December 23, 2002Publication date: July 1, 2004Applicants: Affymetrix, Inc., a Corporation Organized under the laws of DelawareInventors: Jill Cheng, Michael A. Siani-Rose, Shaw Sun
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Publication number: 20040049354Abstract: A system for analyzing alternative splice variant sequences is described, comprising an input manager for receiving alternative splice variant sequences that are identified by one or more probe sets, a correlator that correlates functional domains with each of the alternative splice variant sequences and an associater that associates putative functions with the alternative splice variant sequences based upon a combination of the functional domains. A method for analyzing alternative splice variant sequences is also described, comprising the acts of receiving alternative splice variant sequences that are identified by one or more probe sets, correlating functional domains with the alternative splice variant sequences and associating putative functions with the alternative splice variant sequences based upon a combination of the functional domains.Type: ApplicationFiled: April 25, 2003Publication date: March 11, 2004Applicants: Affymetrix, Inc., a Corporation Organized under the laws of DelawareInventors: Ann Loraine, Melissa Cline, Gregg A. Helt, Michael A. Siani-Rose, David C. Kulp, Ron T. Shigeta
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Publication number: 20030120432Abstract: A genomic portal system is described that receives user-selected identifiers of potential probes. The system determines verified probes corresponding to the identifiers and generates a custom probe array design. The system then displays the custom probe array design to the user via a graphical user interface and receives a user selection specifying acceptance, modification, or rejection of the design. The system provides the user with the accepted or modified custom probe array. The system may also enable a number of users to share space on a custom probe array. Another optional feature is to enable a number of users to share in ordering portions of a lot of catalog probe arrays to take advantage of economies of scale from lot-size purchases.Type: ApplicationFiled: November 26, 2002Publication date: June 26, 2003Applicant: Affymetrix, Inc.Inventors: Xue Mei Zhou , David P. Smith , Elizabeth M. Kerr , Lianne McLean , Shaw Sun , Michael A. Siani-Rose , Michael A. Mittman , Shawn H. Becker , Lee A. Jacobek
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Publication number: 20030100995Abstract: A genomic web portal is described that receives from a user over the Internet a selection of identifiers of probes for detecting biological molecules. The portal may also receive hybridization intensity values produced from biological probe array experiments. The portal determines alternative splice variants based on factors that may include the hybridization intensity values. The portal correlates alternative splice variants with annotation data and provides for the user a graphical representation of the alternative splice variants and the correlated annotation data. The selection of annotation data to be displayed may be based on a user selection of a genomic, primary-transcript, mRNA, or protein display type.Type: ApplicationFiled: November 26, 2002Publication date: May 29, 2003Applicant: Affymetrix, Inc.Inventors: Ann E. Loraine , Gregg A. Helt , Michael A. Siani-Rose , David C. Kulp
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Publication number: 20030023384Abstract: Methods, software products and systems are provided for automated high throughout gene characterization. In one exemplary embodiment, HMM models are used to characterize genes. Biological sequences are classified according to their hit with different HMM models using a curve analysis.Type: ApplicationFiled: December 5, 2001Publication date: January 30, 2003Inventors: Michael A. Siani-Rose, Ron Shigeta
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Publication number: 20020183936Abstract: A genomic portal system receives from a user a selection of one or more probe-set identifiers associated with one or more probe sets. The probe-set identifiers may be submitted in a batch file and may include one or more annotation terms. The system also correlates the user-selected probe-set identifiers with one or more biological sequences, and correlates the one or more biological sequences with a first set of probe sets. A network server identifies the first set of probe sets to the user. The genomic portal system may also receive from a user a selection of one or more probe-set identifiers associated with one or more probe sets, wherein the probe-set identifiers include one or more biological sequences. The system periodically update one or more local genomic databases, clusters the one or more biological sequences based on the local genomic databases, and provide the clustered data to a user.Type: ApplicationFiled: May 2, 2002Publication date: December 5, 2002Applicant: Affymetrix, Inc.Inventors: David C. Kulp, Michael A. Siani-Rose, Shaw Sun, Ron T. Shigeta, Guoying Liu, Stephen Chervitz Trutane
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Publication number: 20020164709Abstract: The present invention provides a novel growth factor polynucleotide, growth factor polypeptide, gene delivery vehicles comprising and/or expressing the growth factor polynucleotide, antibodies and fragments capable of specifically binding to the growth factor polypeptide, receptors of the growth factor polypeptide, modulators of the growth factor activity, and modulators of growth factor expression. Also provided by the invention are host cells and transgenic organisms comprising the gene delivery vehicle of the present invention. Also provided by the invention are computer readable media containing the polynucleotide or polypeptide sequences of the present invention. Further provided are methods of using these compositions for diagnosis and treatment of growth factor associated diseases.Type: ApplicationFiled: February 26, 2002Publication date: November 7, 2002Applicant: Affymetrix, INC. A corporation organized under the laws of DelawareInventors: Ron T. Shigeta, Michael A. Siani-Rose
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Publication number: 20020123083Abstract: The present invention provides a novel growth factor polynucleotide, growth factor polypeptide, gene delivery vehicles comprising and/or expressing the growth factor polynucleotide, antibodies and fragments capable of specifically binding to the growth factor polypeptide, receptors of the growth factor polypeptide, modulators of the growth factor activity, and modulators of growth factor expression. Also provided by the invention are host cells and transgenic organisms comprising the gene delivery vehicle of the present invention. Also provided by the invention are computer readable media containing the polynucleotide or polypeptide sequences of the present invention. Further provided are methods of using these compositions for diagnosis and treatment of growth factor associated diseases.Type: ApplicationFiled: February 26, 2002Publication date: September 5, 2002Applicant: Affymetrix, INC.Inventors: Ron T. Shigeta, Michael A. Siani-Rose
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Publication number: 20020051996Abstract: Novel proteins and libraries comprising them are disclosed. The proteins comprise one or more functional protein modules from different parent protein molecules. The proteins and libraries are exemplified by the preparation of cross-over chemokines comprising various combinations of peptide segments derived from RANTES, SDF-1 and vMIP-I and vMIP-II. The proteins and libraries are extremely pure and can be provided in non-limiting high yields suitable for diagnostic and high-throughput screening assays.Type: ApplicationFiled: August 31, 1998Publication date: May 2, 2002Inventors: MICHAEL A. SIANI, JILL WILKEN, REYNA SIMON, STEPHEN B.H. KENT
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Patent number: 5840841Abstract: Method and apparatus for synthesizing biopolymers, such as polypeptides and polynucleotides. The apparatus includes plural reaction vessels in which subunit coupling to biopolymers in a particle suspension is carried out. The vessels are connected to common valving structure for use in mixing the suspension and removing suspension liquid. In one embodiment, a robotic arm in the apparatus is operable to transfer reaction solution to the reaction vessels, and to transfer particle suspensions from the reaction vessels to a mixing vessel and back to the reaction vessels. The method can be used to produce preferably equi-molar amounts of different-sequence biopolymers, such as polypeptides and polynucleotides.Type: GrantFiled: May 8, 1997Date of Patent: November 24, 1998Assignee: Chiron CorporationInventors: Ronald N. Zuckermann, Verena D. Heubner, Daniel V. Santi, Michael A. Siani
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Patent number: 5705610Abstract: Method and apparatus for synthesizing biopolymers, such as polypeptides and polynucleotides. The apparatus includes plural reaction vessels in which subunit coupling to biopolymers in a particle suspension is carried out. The vessels are connected to common valving structure for use in mixing the suspension and removing suspension liquid. In one embodiment, a robotic arm in the apparatus is operable to transfer reaction solution to the reaction vessels, and to transfer particle suspensions from the reaction vessels to a mixing vessel and back to the reaction vessels. The method can be used to produce preferably equi-molar amounts of different-sequence biopolymers, such as polypeptides and polynucleotides.Type: GrantFiled: October 1, 1993Date of Patent: January 6, 1998Assignee: Chiron CorporationInventors: Ronald N. Zuckermann, Verena D. Heubner, Daniel V. Santi, Michael A. Siani
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Patent number: 5680331Abstract: A method for generating multiple mimics of an active site of a molecule, such as a protein, using computer modeling of the active site. A putative active site is identified, and the amino acids, or residues, purportedly responsible for the biological activity in question are located. These are represented as virtual residues in a model of the active site. The method generates many different possible representations of the active site of the selected protein, presenting the user with a choice of premodeled molecules for synthesis and testing as a substitute for the protein.Type: GrantFiled: August 15, 1994Date of Patent: October 21, 1997Assignee: Chiron CorporationInventors: Jeffrey M. Blaney, Michael A. Siani
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Patent number: 5252296Abstract: Method and apparatus for synthesizing biopolymers, such as polypeptides and polynucleotides. The apparatus includes plural reaction vessels in which subunit coupling to biopolymers in a particle suspension is carried out. The vessels are connected to common valving structure for use in mixing the suspension and removing suspension liquid. In one embodiment, a robotic arm in the apparatus is operable to transfer reaction solution to the reaction vessels, and to transfer particle suspensions from the reaction vessels to a mixing vessel and back to the reaction vessels. The method can be used to produce preferably equi-molar amounts of different-sequence biopolymers, such as polypeptides and polynucleotides.Type: GrantFiled: February 6, 1991Date of Patent: October 12, 1993Assignee: Chiron CorporationInventors: Ronald N. Zuckermann, Verena D. Heubner, Daniel V. Santi, Michael A. Siani
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Patent number: H2136Abstract: The present invention provides novel GPCR polynucleotides, GPCR polypeptides, gene delivery vehicles comprising and/or expressing the GPCR polynucleotides, antibodies and fragments capable of specifically binding to the GPCR polypeptides, and modulators of the GPCR. Also provided by the invention are host cells, transgenic organisms comprising the gene delivery vehicle of the present invention. Further provided are methods of using these compositions for diagnosis and treatment of GPCR associated diseases.Type: GrantFiled: October 24, 2001Date of Patent: December 6, 2005Assignee: Affymetrix, Inc.Inventors: David C. Kulp, Michael A. Siani-Rose, Alan J. Williams, Cyrus L. Harmon
