| Class / Patent application number | Description | Number of patent applications / Date published |
|---|
| 506024000 | In silico or mathematical conception of a library | 21 |
| 20080248971 | METHOD FOR PROVIDING MICROARRAYS - An interactive method of providing an array of nucleic acid sequences in which a remote user enters a query to generate a listing of desired sequence probes, which are then selected and returned to the host for use in producing a custom microarray designed by a remote user. | 10-09-2008 |
| 20090011956 | Versatile nucleic acid hairpin motif for programming biomolecular self-assembly pathways - The present invention relates generally to programming of biomolecular self-assembly pathways and related methods and constructs. A versatile nucleic acid hairpin motif for programming biomolecular self-assembly pathways for a wide variety of dynamic functions, reaction graphs for specifying pathways, and methods of using the hairpin motif are provided. | 01-08-2009 |
| 20090270277 | METHOD FOR INDEXING NUCLEIC ACID SEQUENCES FOR COMPUTER BASED SEARCHING - The present invention relates to a method for indexing nucleic acid sequences to aid computer based searching of nucleic acid sequences by indexing a nucleotide sequence by the presence of unique Kmers in the sequence. The method of the present invention comprises utilizing an algorithm to automatically index a nucleic acid sequence. | 10-29-2009 |
| 20090318310 | DNA Sequence Assembly Methods of Short Reads - Certain embodiments of the invention provide systems and methods for the automated assembly of DNA sequence data into contiguous DNA segments using a computer a system. DNA sequence data is entered into the system. The system indexes and groups a plurality of DNA fragment reads utilizing an anchor sequence and consolidates the fragments into larger sequences by merging the fragment reads within a group. | 12-24-2009 |
| 20090318311 | COMMON PROTEIN SURFACE SHAPES AND USES THEREFOR - A method of determining common three-dimensional structural features of protein surfaces is provided, as is use of representations of these common structures in molecular database searching and in designing focused molecular libraries. The method is particularly concerned with the analysis and representation of protein surfaces such as b-turns, loops and contact surfaces. In one form, the method identifies common locations and orientations of amino acid side-chains, simplified as Cα-Cβ vectors. In another form, the method identifies common regions of surface charge represented by grid points in three-dimensional space. Further provided are common three dimensional structural features of proteins that can be used to search molecular databases for the purposes of identifying molecules that match these common three dimensional structural features. The common three dimensional structural features can also be used to focus de novo molecular generation to produce libraries containing molecules that have these common three dimensional structural features. Libraries of these structurally-related molecules may then be produced for the purposes of drug discovery. | 12-24-2009 |
| 20100144554 | METHODS FOR ASSEMBLING PANELS OF CANCER CELL LINES FOR USE IN TESTING THE EFFICACY OF ONE OR MORE PHARMACEUTICAL COMPOSITIONS - The present invention relates to algorithms for use in defining genomic subgroups of tumors and cancer cell lines. The present invention also relates to methods for assembling panels of tumors and cancer cell lines according to genomic subgroups for use in testing the efficacy of one or more pharmaceutical compounds in the treatment of subjects suffering from at least one cancer. | 06-10-2010 |
| 20100144555 | QUALITATIVE DIFFERENTIAL SCREENING - The invention concerns a method for identifying and/or cloning nucleic acid regions representing qualitative differences associated with alternative splicing events and/or with insertions, deletions located in RNA transcribed genome regions, between two physiological situations, comprising either hybridization of RNA derived from the test situation with cDNA's derived from the reference situation and/or reciprocally, or double-strand hybridization of cDNA derived from the test situation with cDNA's derived from the reference situation; and identifying and/or cloning nucleic acids representing qualitative differences. The invention also concerns compositions or banks of nucleic acids representing qualitative differences between two physiological situations, obtainable by the above method, and their use as probe, for identifying genes or molecules of interest, or still for example in methods of pharmacogenomics, and profiling of molecules relative to their therapeutic and/or toxic effects. The invention further concerns the use of dysregulation of splicing RNA as markers for predicting molecule toxicity and/or efficacy, and as markers in pharmacogenomics. | 06-10-2010 |
| 20100267588 | SYSTEMS AND METHODS FOR PRODUCING CHEMICAL ARRAY LAYOUTS - Systems and methods for using the same to obtain a chemical array layout are provided. Also provided are computer program products for executing the subject methods. | 10-21-2010 |
| 20110039735 | PROBE DESIGN FOR OLIGONUCLEOTIDE FLUORESCENCE IN SITU HYBRIDIZATION (FISH) - A method and a system for selecting a set of FISH probe oligonucleotide sequences from a plurality of overlapping tiled candidate FISH probe oligonucleotide sequences are provided. A composition that includes FISH probes with sequences from the set of FISH probe oligonucleotide sequences is also provided. | 02-17-2011 |
| 20110124528 | Generation and affinity maturation of antibody library in silico - The present invention provides a methodology for efficiently generating and screening protein libraries for optimized proteins with desirable biological functions, such as improved binding affinity towards biologically and/or therapeutically important target molecules. The process is carried out computationally in a high throughput manner by mining the ever-expanding databases of protein sequences of all organisms, especially human. In one embodiment, a method for constructing a library of designed proteins, comprising the steps of: providing an amino acid sequence derived from a lead protein, the amino acid sequence being designated as a lead sequence; comparing the lead sequence with a plurality of tester protein sequences; and selecting from the plurality of tester protein sequences at least two peptide segments that have at least 15% sequence identity with the lead sequence, the selected peptide segments forming a hit library; and forming a library of designed proteins by substituting the lead sequence with the hit library. The library of designed proteins can be expressed in vitro or in vivo to produce a library of recombinant proteins that can be screened for novel or improved function(s) over the lead protein, such as an antibody against therapeutically important target. | 05-26-2011 |
| 20110224103 | METHOD FOR DESIGN OF AN OLIGINUCLEOTIDE ARRAY - A method is provided allowing for automatic selection of enzymes to be used in protocols such as methylation profiling, chip-on-chip, and comparative genomic hybridization experiments. The method may also maximize the space on a micro array for a given experiment. This means that the results from the micro array are improved. The method also improves zero-in and focus of significant patterns on a micro array. This enhances the ability to distinguish two separate classes of samples, e.g. tumour vs. normal, aggressive vs. non-aggressive, male vs. female, etc. Furthermore, a computer readable medium and a device are also provided. | 09-15-2011 |
| 20110257044 | Structure-based construction of human antibody library - Methods and systems are provided for constructing recombinant antibody libraries based on three-dimensional structures of antibodies from various species including human. In one aspect, a library of antibodies with diverse sequences is efficiently constructed in silico to represent the structural repertoire of the vertebrate antibodies. Such a functionally representative library provides a structurally diverse and yet functionally more relevant source of antibody candidates which can then be screened for high affinity binding to a wide variety of target molecules, including but not limited to biomacromolecules such as protein, peptide, and nucleic acids, and small molecules. | 10-20-2011 |
| 20110281772 | Methods, systems and computer software for designing and synthesizing sequence arrays - Embodiments of the invention provides methods, computer software products and systems for arranging polymers during combinatorial polymer synthesis so that the border or edge between synthesis site is minimized. In one embodiment, travelling salesman algorithm is used to minimize the edges. In another embodiment, a locally greedy optimization method is provided. In addition, methods and software products are provided for solving the robust arrangement problem for multi-probe gene expression arrays. | 11-17-2011 |
| 20120190585 | CONCURRENT OPTIMIZATION IN SELECTION OF PRIMER AND CAPTURE PROBE SETS FOR NUCLEIC ACID ANALYSIS - Disclosed is a method of iteratively optimizing two (or more) interrelated sets of probes for the multi-step analysis of sets of designated sequences, each such sequence requiring, for conversion, at least one conversion probe (“primer”), and each converted sequence requiring, for detection, at least one capture probe. The iterative method disclosed herein for the concurrent optimization of primer and probe selection invokes fast logical string matching functions to perform a complete cross-correlation of probe sequences and target sequences. The score function assigns to each probe-target alignment a “degree of matching” score on the basis of position-weighted Hamming distance functions introduced herein. Pairs of probes in the final selection may differ in several positions, while other pairs of probes may differ in only a single position. Not all such positions are of equal importance, and a score function is introduced, reflecting the position of the mismatch within the probe sequence. | 07-26-2012 |
| 20120202716 | Construction of diverse synthetic peptide and polypeptide libraries - The present invention concerns the design and construction of diverse peptide and polypeptide libraries. In particular, the invention concerns methods of analytical database design for creating datasets using multiple relevant parameters as filters, and methods for generating sequence diversity by directed multisyntheses oligonucleotide synthesis. The present methods enable the reduction of large complex annotated databases to simpler datasets of related sequences, based upon relevant single or multiple key parameters that can be individually directly defined. The methods further enable the creation of diverse libraries based on this approach, using multisynthetic collections of discrete and degenerate oligonucleotides to capture the diverse collection of sequences, or portions thereof. | 08-09-2012 |
| 20130090265 | SYSTEMS AND METHODS FOR GENERATION OF CONTEXT-SPECIFIC, MOLECULAR FIELD-BASED AMINO ACID SUBSTITUTION MATRICES - Provided are systems and methods for generating context-specific, field based amino acid substitution matrices. In some implementations, the systems and methods utilize a set of characteristics including sequence length, sequence, variable position, backbone conformation, sidechain conformation, and charge and/or ionization state to construct a number of instantiated virtual peptide variants that vary an amino acid at the variable position. Molecular fields are then calculated for each instantiated variant. The fields for each variant are then compared to one another in a pairwise fashion. Values representing the similarity of the fields resulting from the comparison are then assembled into an amino acid substitution matrix. | 04-11-2013 |
| 20130090266 | METHODS AND SYSTEMS FOR OPTIMIZATION OF PEPTIDE SCREENING - The invention provides systems and methods for improved peptide screening library design. In some implementations the systems and methods utilize screening data relating to a plurality of peptides used in a peptide screen against a target molecule to construct a consensus binding sequence alignment using least a subset of the plurality of peptides. For one or more positions of the sequence alignment an observed distance matrix is constructed, the matrix describing a distance between the relative binding activity of pairwise comparisons of each amino acid in a given position. The observed distance matrix is then compared to a plurality of molecular field-based amino acid substitution matrices so as to identify one or more preferred amino acids for use in the design of novel predicted binding peptide sequences for a subsequent peptide screen. | 04-11-2013 |
| 20130345095 | METHOD AND DEVICE FOR ASSEMBLING GENOME SEQUENCE - A method and an apparatus for genome assembly are provided. The method comprises: filtering a short-fragment-sequence output from end sequencing of an large insert-size library to remove unqualified sequence; aligning the filtered short-fragment-sequence onto a reference genome sequence, wherein, the filtered short-fragment-sequences comprise paired short-fragment-sequences; sorting the paired short-fragment-sequence after alignment into soap reads sequence, single reads sequence and unmap reads sequence based on the aligning result, and counting the number of each sort of sequence; calculating a distance between the paired soap reads on a fragment of the reference genome sequence, wherein a pair of the paired soap reads can be aligned onto a same fragment of the reference genome sequence; and counting a distance distribution of each pair of soap reads on the reference genome sequence; and assembling the genome sequence by using the paired single reads upon the distance distribution meeting a requirement of a threshold, wherein a pair of the paired single reads can be aligned onto two different fragments of the reference genome sequence. | 12-26-2013 |
| 20150119289 | METHODS TO DETERMINE CANDIDATE BIOMARKER PANELS FOR A PHENOTYPIC CONDITION OF INTEREST - A panel of lymphoma related biomarkers are provided. The panel allows the identification of a subject at risk for a lymphoma. Further provided are methods of optimizing therapeutic efficacy associated with treatment of a lymphoma related disorder. Methods of identifying biomarkers affiliated with a condition of interest are provided. | 04-30-2015 |
| 20160125124 | Obtaining an Improved Therapeutic Ligand - Methods and associated apparatus involving designing a ligand ab initio that will bind to a binding site of a macromolecular target, or of identifying a modification to a ligand for improving the affinity of the ligand to a binding site of a macromolecular target, comprising using information about non-bonding, intra-molecular or inter-molecular atom to atom contacts extracted from a database of biological macromolecules to identify favoured regions adjacent to the binding site for particular atom types and modifying a candidate ligand to increase the intersection between atoms of the candidate ligand and the favoured regions. One or more steps of the methods may be performed by a computer. | 05-05-2016 |
| 20170235876 | SYSTEMS, METHODS, AND MEDIA FOR DE NOVO ASSEMBLY OF WHOLE GENOME SEQUENCE DATA | 08-17-2017 |
