Radoje T. Drmanac - Palo Alto CA 94303 Snezana Drmanac - Palo Alto CA 94303
International Classification:
C12Q 168
US Classification:
435 6, 536 231, 536 243, 4352872
Abstract:
The present invention provides a method for detecting a target nucleic acid species including the steps of providing an array of probes affixed to a substrate and a plurality of labeled probes wherein each labeled probe is selected to have a first nucleic acid sequence which is complementary to a first portion of a target nucleic acid and wherein the nucleic acid sequence of at least one probe affixed to the substrate is complementary to a second portion of the nucleic acid sequence of the target, the second portion being adjacent to the first portion; applying a target nucleic acid to the array under suitable conditions for hybridization of probe sequences to complementary sequences; introducing a labeled probe to the array; hybridizing a probe affixed to the substrate to the target nucleic acid; hybridizing the labeled probe to the target nucleic acid; affixing the labeled probe to an adjacently hybridized probe in the array; and detecting the labeled probe affixed to the probe in the array.
Enhanced Sequencing By Hybridization Using Pools Of Probes
Radoje Drmanac - Palo Alto CA, US Snezana Drmanac - Palo Alto CA, US David Kita - Foster City CA, US Cory Cooke - Newark CA, US Chongjun Xu - San Jose CA, US
The invention provides methods for sequencing by hybridization (SBH) using pools of probes that allow greater efficiency in conducting SBH by reducing the number of separate measurements of hybridization signals required to identify each particular nucleotide in a target nucleic acid sequence. The invention also provides pools and sets of pools of probes, as well as methods of generating pools of probes.
Lewis T. Williams - Tiburon CA, US Jaime Escobedo - Alamo CA, US Michael A. Innis - Moraga CA, US Pablo Dominguez Garcia - San Francisco CA, US Julie Sudduth-Klinger - Kensington CA, US Christoph Reinhard - Alameda CA, US Klaus Giese - Berlin, DE Filippo Randazzo - San Francisco CA, US Giulia C. Kennedy - San Francisco CA, US David Pot - San Francisco CA, US Altaf Kassam - Oakland CA, US George Lamson - Moraga CA, US Radoje Drmanac - Palo Alto CA, US Radomir Crkvenjakov - Sunnyvale CA, US Mark Dickson - Hollister CA, US Snezana Drmanac - Palo Alto CA, US Ivan Labat - San Francisco CA, US Dena Leshkowitz - Sunnyvale CA, US David Kita - Foster City CA, US Veronica Garcia - Sunnyvale CA, US Lee William Jones - San Jose CA, US
Assignee:
Nuvelo, Inc. - Sunnyvale CA
International Classification:
C12N005/10 C12N015/63 C12N001/21 C12N015/12
US Classification:
435325, 4353201, 4352523, 536 235
Abstract:
This invention relates to novel human polynucleotides and variants thereof, their encoded polypeptides and variants thereof, to genes corresponding to these polynucleotides and to proteins expressed by the genes. The invention also relates to diagnostic and therapeutic agents employing such novel human polynucleotides, their corresponding genes or gene products, e. g. , these genes and proteins, including probes, antisense constructs, and antibodies.
Lewis T. Williams - Tiburon CA, US Jaime Escobedo - Alamo CA, US Michael A. Innis - Moraga CA, US Pablo Dominguez Garcia - San Francisco CA, US Julie Sudduth-Klinger - Kensington CA, US Christoph Reinhard - Alameda CA, US Klaus Giese - Berlin, DE Filippo Randazzo - San Francisco CA, US Giulia C. Kennedy - San Francisco CA, US David Pot - San Francisco CA, US Altaf Kassam - Oakland CA, US George Lamson - Moraga CA, US Radoje Drmanac - Palo Alto CA, US Radomir Crkvenjakov - Sunnyvale CA, US Mark Dickson - Hollister CA, US Snezana Drmanac - Palo Alto CA, US Ivan Labat - Sunnyvale CA, US Dena Leshkowitz - Sunnyvale CA, US David Kita - Foster City CA, US Veronica Garcia - Sunnyvale CA, US Lee William Jones - Sunnyvale CA, US
Assignee:
Nuvelo, Inc. - Sunnyvale CA
International Classification:
C12N 5/10 C12N 15/63 C12N 15/11
US Classification:
435325, 4353201, 536 235
Abstract:
This invention relates to novel human polynucleotides and variants thereof, their encoded polypeptides and variants thereof, to genes corresponding to these polynucleotides and to proteins expressed by the genes. The invention also relates to diagnostic and therapeutic agents employing such novel human polynucleotides, their corresponding genes or gene products, e. g. , these genes and proteins, including probes, antisense constructs, and antibodies.
Enhanced Sequencing By Hybridization Using Pools Of Probes
Radoje Drmanac - Palo Alto CA, US Snezana Drmanac - Palo Alto CA, US David Kita - Foster City CA, US Cory Cooke - San Mateo CA, US Chongjun Xu - San Jose CA, US
The invention provides methods for sequencing by hybridization (SBH) using pools of probes that allow greater efficiency in conducting SBH by reducing the number of separate measurements of hybridization signals required to identify each particular nucleotide in a target nucleic acid sequence. The invention also provides pools and sets of pools of probes, as well as methods of generating pools of probes.
Enhanced Sequencing By Hybridization Using Pools Of Probes
Radoje T. Drmanac - Palo Alto CA, US Snezana Drmanac - Palo Alto CA, US David Kita - San Mateo CA, US Cory Cooke - San Mateo CA, US Chongjun Xu - San Jose CA, US
Assignee:
Callida Genomics, Inc. - Sunnyvale CA
International Classification:
C12Q 1/68
US Classification:
435 611, 435 61
Abstract:
The invention provides methods for sequencing by hybridization (SBH) using pools of probes that allow greater efficiency in conducting SBH by reducing the number of separate measurements of hybridization signals required to identify each particular nucleotide in a target nucleic acid sequence. The invention also provides pools and sets of pools of probes, as well as methods of generating pools of probes.
Radoje Drmanac - Los Altos Hills CA, US Matthew J. Callow - Redwood City CA, US Snezana Drmanac - Los Altos Hills CA, US Brian K. Hauser - Campbell CA, US George Yeung - Mountain View CA, US
Random arrays of single molecules are provided for carrying out large scale analyses, particularly of biomolecules, such as genomic DNA, cDNAs, proteins, and the like. In one aspect, arrays of the invention comprise concatemers of DNA fragments that are randomly disposed on a regular array of discrete spaced apart regions, such that substantially all such regions contain no more than a single concatemer. Preferably, such regions have areas substantially less than 1 μmand have nearest neighbor distances that permit optical resolution of on the order of 10single molecules per cm. Many analytical chemistries can be applied to random arrays of the invention, including sequencing by hybridization chemistries, sequencing by synthesis chemistries, SNP detection chemistries, and the like, to greatly expand the scale and potential applications of such techniques.
Radoje Drmanac - Los Altos Hills CA, US Matthew J. Callow - Redwood City CA, US Snezana Drmanac - Los Altos Hills CA, US
Assignee:
Callida Genomics, Inc. - Sunnyvale CA
International Classification:
C12Q 1/68 C12P 19/34 C12M 1/36
US Classification:
435 61, 435 911, 435 912, 4352872, 536 231
Abstract:
The present invention is directed to methods and compositions for acquiring nucleotide sequence information of target sequences using adaptors interspersed in target polynucleotides. The sequence information can be new, e. g. sequencing unknown nucleic acids, re-sequencing, or genotyping. The invention preferably includes methods for inserting a plurality of adaptors at spaced locations within a target polynucleotide or a fragment of a polynucleotide. Such adaptors may serve as platforms for interrogating adjacent sequences using various sequencing chemistries, such as those that identify nucleotides by primer extension, probe ligation, and the like. Encompassed in the invention are methods and compositions for the insertion of known adaptor sequences into target sequences, such that there is an interruption of contiguous target sequence with the adaptors. By sequencing both “upstream” and “downstream” of the adaptors, identification of entire target sequences may be accomplished.
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