Patents by Inventor Isidore Rigoutsos
Isidore Rigoutsos 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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Publication number: 20080171904Abstract: The relationship between an amino acid sequence of a protein and its three-dimensional structure is at the very core of structural biology and bioinformatics. The occurrence and conservation of non-canonical conformations is a “local” phenomenon, i.e., non-canonical conformations are encoded intra-helically by short peptide sequences (heptapeptides at most). Effective descriptors can be formed for these short sequences employing training sets. Multiple, distinct patterns are created representing these sequences. A composite descriptor is formed by selecting from among the patterns discovered. The composite descriptor has a high level of sensitivity and specificity while, at the same time, a boosted signal-to-noise ratio.Type: ApplicationFiled: September 10, 2007Publication date: July 17, 2008Applicant: International Business Machines CorporationInventors: Isidore Rigoutsos, Peter Riek, Robert M. Graham, Jiri Novotny
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Publication number: 20080133142Abstract: The relationship between an amino acid sequence of a protein and its three-dimensional structure is at the very core of structural biology and bioinformatics. The occurrence and conservation of non-canonical conformations is a “local” phenomenon, i.e., non-canonical conformations are encoded intra-helically by short peptide sequences (heptapeptides at most). Effective descriptors can be formed for these short sequences employing training sets. Multiple, distinct patterns are created representing these sequences. A composite descriptor is formed by selecting from among the patterns discovered. The composite descriptor has a high level of sensitivity and specificity while, at the same time, a boosted signal-to-noise ratio.Type: ApplicationFiled: September 10, 2007Publication date: June 5, 2008Applicant: International Business Machines CorporationInventors: Isidore Rigoutsos, Peter Riek, Robert M. Graham, Jiri Novotny
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Publication number: 20080125583Abstract: Ribonucleic acid interference molecules are provided. For example, in one aspect of the invention, at least one nucleic acid molecule comprising at least one of one or more precursor sequences having SEQ ID NO: 1 through SEQ ID NO: 103,948 and one or more mature sequences having SEQ ID NO: 1 through SEQ ID NO: 126,499 is provided. One or more of the at least one of one or more precursor sequences and one or more mature sequences may be computationally predicted, e.g., from publicly available genomes, using a pattern discovery method. In another aspect of the invention, a method for regulating gene expression comprises the following step. At least one nucleic acid molecule comprising at least one of one or more precursor sequences having SEQ ID NO: 1 through SEQ ID NO: 103,948, each one of the precursor sequences containing one or more mature sequences having SEQ ID NO: 1 through SEQ ID NO: 126,499, is used to regulate the expression of one or more genes, e.g.Type: ApplicationFiled: February 10, 2006Publication date: May 29, 2008Applicant: International Business Machines CorporationInventors: Isidore Rigoutsos, Tien Huynh, Kevin Charles Miranda
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Publication number: 20080052008Abstract: Techniques for linking non-coding and gene coding regions of a genome are provided. In one aspect, a method of determining associations between non-coding sequences and gene coding sequences in a genome of an organism comprises the following steps. At least one conserved region is identified from one or more non-coding sequences. Additional instances of the conserved region are located in the untranslated or amino acid coding regions of one or more genes in the organism under consideration, and the conserved region is associated with the one or more biological processes in which these one or more genes participate.Type: ApplicationFiled: October 30, 2007Publication date: February 28, 2008Applicant: International Business Machines CorporationInventors: Isidore Rigoutsos, Tien Huynh, Aristotelis Tsirigos, Alice McHardy, Kevin Miranda
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Publication number: 20080015789Abstract: Generally, the present invention provides a way of determining in an unsupervised manner additional members for a family that is defined initially through exemplar sequences. The present invention is unsupervised in that it proceeds without any information related to the exemplar sequences defining the family, without aligning the sequences, without prior knowledge of any patterns in the exemplar sequences, and without knowledge of the cardinality or characteristics of any features that may be present in the exemplar sequences. In one aspect of the invention, a method is used to take a set of unaligned sequences and discover several of many patterns common to some or all of the sequences. These patterns can then be used to determine if candidate sequences are members of the family.Type: ApplicationFiled: June 21, 2007Publication date: January 17, 2008Applicant: International Business Machines CorporationInventors: Isidore Rigoutsos, Yuan Gao, Aristidis Floratos
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Patent number: 7248971Abstract: Generally, the present invention provides a way of determining in an unsupervised manner additional members for a family that is defined initially through exemplar sequences. The present invention is unsupervised in that it proceeds without any information related to the exemplar sequences defining the family, without aligning the sequences, without prior knowledge of any patterns in the exemplar sequences, and without knowledge of the cardinality or characteristics of any features that may be present in the exemplar sequences. In one aspect of the invention, a method is used to take a set of unaligned sequences and discover several or many patterns common to some or all of the sequences. These patterns can then be used to determine if candidate sequences are members of the family. In another aspect of the invention, a method is used to take a set of sequences and to determine a set of maximal patterns common to a number of sequences.Type: GrantFiled: November 14, 2000Date of Patent: July 24, 2007Assignee: International Business Machines CorporationInventors: Isidore Rigoutsos, Yuan Gao, Aristidis Floratos
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Publication number: 20070154896Abstract: A method for determining whether a nucleotide sequence contains a microRNA binding site and which microRNA will bind thereto is provided. For example, in one aspect of the invention, a method for determining whether a nucleotide sequence contains a microRNA binding site and which microRNA sequence will bind thereto is comprised of the following steps. One or more patterns are generated by processing a collection of known mature microRNA sequences. The reverse complement of each generated patter is then computed. One or more attributes are then assigned to the reverse complement of the one or more generated patterns. The one or more patterns that correspond to a reverse complement having one or more assigned attributes that satisfy at least one criterion are thereafter subselected. Each subselected pattern is then used to analyze the nucleotide sequence, such that a determination is made whether the nucleotide sequence contains a microRNA binding site and which microRNA sequence will bind thereto.Type: ApplicationFiled: February 10, 2006Publication date: July 5, 2007Applicant: International Business Machines CorporationInventors: Tien Huynh, Kevin Miranda, Isidore Rigoutsos
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Publication number: 20070042397Abstract: Techniques for linking non-coding and gene coding regions of a genome are provided. In one aspect, a method of determining associations between non-coding sequences and gene coding sequences in a genome of an organism comprises the following steps. At least one conserved region is identified from one or more non-coding sequences. Additional instances of the conserved region are located in the untranslated or amino acid coding regions of one or more genes in the organism under consideration, and the conserved region is associated with the one or more biological processes in which these one or more genes participate.Type: ApplicationFiled: March 3, 2006Publication date: February 22, 2007Applicant: International Business Machines CorporationInventors: Isidore Rigoutsos, Tien Huynh, Aristotelis Tsirigos, Alice McHardy, Kevin Miranda
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Publication number: 20060263798Abstract: A method for determining microRNA precursors and their corresponding mature microRNAs from genomic sequences is provided. For example, in one aspect of the invention, a method for determining whether a nucleotide sequence contains a microRNA precursor comprises the following steps. Patterns are generated by processing a collection of already known microRNA precursor sequences. One or more attributes are assigned to the generated patterns. Only the patterns whose attributes satisfy certain criteria are subselected, and then the subselected patterns are used to analyze the nucleotide sequence. In another aspect of the invention, a method for identifying a mature microRNA sequence in a microRNA precursor sequence comprises the following steps. One or more patterns are generated by processing a collection of known mature microRNA sequences. The one or more patterns are filtered, and then used to locate instances of the one or more filtered patterns in one or more candidate precursor sequences.Type: ApplicationFiled: February 10, 2006Publication date: November 23, 2006Applicant: International Business Machines CorporationInventors: Tien Huynh, Kevin Miranda, Isidore Rigoutsos
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Publication number: 20050267692Abstract: A method and system for determining whether a sequence fragment g is atypical with respect to a reference sequence G using compositional methods and including constructing a template from G and g respectively containing a sequence of characters for a comparison with one another, wherein a number of characters contained in the template exceeds two. For the case where the sequences at hand are genetic, the atypicality detection can be used to determine whether a given sequence fragment g is the result of a horizontal transfer event.Type: ApplicationFiled: May 28, 2004Publication date: December 1, 2005Applicant: International Business Machines CorporationInventors: Aristotelis Tsirigos, Isidore Rigoutsos
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Publication number: 20050120019Abstract: Techniques for annotating email messages. In one aspect of the invention, a method is provided for annotating a query email message. According to the method, patterns associated with a database, comprising annotated email messages, which may typically be known unwelcome email messages (“SPAM), are accessed, as by use of a pattern discovery algorithm (e.g. the Teiresias pattern algorithm). Attributes are assigned to the patterns based on the annotated SPAM email messages. The patterns with assigned attributes are used to analyze the query email message.Type: ApplicationFiled: November 29, 2003Publication date: June 2, 2005Applicant: International Business Machines CorporationInventors: Isidore Rigoutsos, Tien Huynh
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Patent number: 6785672Abstract: In a sequence homology detection aspect of the invention, a computer-based method of detecting homologies between a plurality of sequences in a database and a query sequence comprises the following steps. First, the method includes accessing patterns associated with the database, each pattern representing at least a portion of one or more sequences in the database. Next, the query sequence is compared to the patterns to detect whether one or more portions of the query sequence are homologous to portions of the sequences of the database represented by the patterns. Then, a score is generated for each sequence detected to be homologous to the query sequence, wherein the sequence score is based on individual scores generated in accordance with each homologous portion of the sequence detected, and the sequence score represents a degree of homology between the query sequence and the detected sequence.Type: GrantFiled: June 21, 2000Date of Patent: August 31, 2004Assignee: International Business Machines CorporationInventors: Aris Floratos, Isidore Rigoutsos
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Publication number: 20040101903Abstract: Techniques for annotating sequences. In one aspect of the invention, a method is provided for annotating a query sequence. The method comprises the following steps. Patterns associated with a database, comprising annotated sequences, are accessed. Attributes are assigned to the patterns based on the annotated sequences. The patterns with assigned attributes are used to analyze the query sequence.Type: ApplicationFiled: November 27, 2002Publication date: May 27, 2004Applicant: International Business Machines CorporationInventor: Isidore Rigoutsos
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Publication number: 20030157524Abstract: The relationship between an amino acid sequence of a protein and its three-dimensional structure is at the very core of structural biology and bioinformatics. The occurrence and conservation of non-canonical conformations is a “local” phenomenon, i.e., non-canonical conformations are encoded intra-helically by short peptide sequences (heptapeptides at most). Effective descriptors can be formed for these short sequences employing training sets. Multiple, distinct patterns are created representing these sequences. A composite descriptor is formed by selecting from among the patterns discovered. The composite descriptor has a high level of sensitivity and specificity while, at the same time, a boosted signal-to-noise ratio.Type: ApplicationFiled: November 27, 2002Publication date: August 21, 2003Applicant: International Business Machines CorporationInventors: Isidore Rigoutsos, Peter Riek, Robert M. Graham, Jiri Novotny
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Patent number: 6571199Abstract: In a dictionary formation aspect of the invention, a computer-based method of processing a plurality of sequences in a database comprises the following steps. First, the method includes evaluating each of the plurality of sequences including characters which form each sequence. Then, at least one pattern of characters is generated representing at least a subset of the sequences in the database. The pattern has a statistical significance associated therewith, the statistical significance of the pattern being determined by a value representing a minimum number of sequences that the pattern supports in the database.Type: GrantFiled: June 21, 2000Date of Patent: May 27, 2003Assignee: International Business Machines CorporationInventors: Aris Floratos, Isidore Rigoutsos
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Publication number: 20020173978Abstract: A method and apparatus for generating an itinerary. User values assigned to a set of factors relating to travel from a first location to a second location are identified. These user values are compared to travel data for a route of travel from the first location to the second location to form a score.Type: ApplicationFiled: May 17, 2001Publication date: November 21, 2002Applicant: International Business Machines CorporationInventors: Stephen J. Boies, Samuel H. Dinkin, David Perry Greene, William Grey, Paul Andrew Moskowitz, Isidore Rigoutsos, Philip Shi-lung Yu
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Publication number: 20020173918Abstract: A system and method for identifying genes that employs a pattern database, an input device for inputting a DNA sequence, and a processor for processing the DNA sequence and patterns to identify a putative gene. The processor may determine open reading frames (ORFs) in the DNA sequence, generate an amino acid translation for each ORF, and identify a match of a pattern in the amino acid translation.Type: ApplicationFiled: January 31, 2002Publication date: November 21, 2002Applicant: International Business Machines CorporationInventors: Tetsuo Shibuya, Isidore Rigoutsos
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Patent number: 6446011Abstract: An algorithm which detects tandem repeats (TR) is provided. In an illustrative embodiment, a set of repeating units contained in an input sequence is identified, wherein each given repeating unit satisfies at least the following conditions: (a) a first measure of similarity between adjacent repeating units in the set is greater than a first user defined threshold, and (b) the given repeating unit includes at least one unit having a second measure of similarity with any other unit in the set that is a greater than a second user defined threshold. The method then provides for reporting positions in the input sequence that are covered by the set of repeating units.Type: GrantFiled: March 20, 2000Date of Patent: September 3, 2002Assignee: International Business Machines CorporationInventors: Aris Floratos, Isidore Rigoutsos, Gustavo A. Stolovitzky
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Patent number: 6373971Abstract: The method of the present invention discovers patterns in a protein sequences in two phases. In a sampling phase, preferably proper templates corresponding to a group of protein sequences are generated. Patterns corresponding to the templates are then generated and stored in memory. In a convolution phase, the patterns stored in memory are combined to identify a set of maximal patterns.Type: GrantFiled: February 13, 1998Date of Patent: April 16, 2002Assignee: International Business Machines CorporationInventors: Aristidis Floratos, Isidore Rigoutsos
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Patent number: 6341284Abstract: The present invention utilizes a set of D descriptors for each of N items. A value K′ representing a number of descriptors, and a value K for a number of items that should support an hypothesis are generated, preferably via user input. Collections involving K or more items for which there is an association involving a selection of values across at least K′ of the D descriptors are identified, and preferably reported to the user.Type: GrantFiled: December 28, 1999Date of Patent: January 22, 2002Assignee: International Business Machines CorporationInventors: Aris Floratos, Isidore Rigoutsos, B. David Silverman