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Analysis

1.20200372973AUTOMATED DETECTION OF BOUNDARIES IN MASS SPECTROMETRY DATA
US 26.11.2020
Int.Class G16B 40/00
GPHYSICS
16INFORMATION AND COMMUNICATION TECHNOLOGY SPECIALLY ADAPTED FOR SPECIFIC APPLICATION FIELDS
BBIOINFORMATICS, i.e. INFORMATION AND COMMUNICATION TECHNOLOGY SPECIALLY ADAPTED FOR GENETIC OR PROTEIN-RELATED DATA PROCESSING IN COMPUTATIONAL MOLECULAR BIOLOGY
40ICT specially adapted for biostatistics; ICT specially adapted for bioinformatics-related machine learning or data mining, e.g. knowledge discovery or pattern finding
Appl.No 16833324 Applicant Venn Biosciences Corporation Inventor Daniel SERIE

A system and method for automated detection of the presence or absence of a quantity based on intensities expressed in terms of, or derived from frequency or time dependent data. According to one example intensities from mass spectrometry are identified using a non-linear mathematical model, such as an artificial neural network trained to find start and stop peaks of an intensity, from which an abundance may be determined.

2.WO/2020/234497CHITIN DEACETYLASE INHIBITORS AND USE THEREOF AS AGRICULTURAL FUNGICIDES, ARTHOPOCIDES AND NEMATICIDES
WO 26.11.2020
Int.Class G16B 15/30
GPHYSICS
16INFORMATION AND COMMUNICATION TECHNOLOGY SPECIALLY ADAPTED FOR SPECIFIC APPLICATION FIELDS
BBIOINFORMATICS, i.e. INFORMATION AND COMMUNICATION TECHNOLOGY SPECIALLY ADAPTED FOR GENETIC OR PROTEIN-RELATED DATA PROCESSING IN COMPUTATIONAL MOLECULAR BIOLOGY
15ICT specially adapted for analysing two-dimensional or three-dimensional molecular structures, e.g. structural or functional relations or structure alignment
30Drug targeting using structural data; Docking or binding prediction
Appl.No PCT/ES2020/070314 Applicant UNIVERSIDAD DE MÁLAGA Inventor PÉREZ GARCÍA, Alejandro
The invention relates to a method for identifying a compound with potential pesticide activity against an organism containing chitin, the compound being an inhibitor of chitin deacetylase (CDA). The method comprises cheminformatics and experimental approximations that include molecular topology equations to examine the experimental chemical and analysis databases of the identified compounds to test their activities as pesticides. More specifically, the invention relates to the experimental analysis of a set of 20 compounds and their use as fungicides, arthopocides and/or nematicides. In addition, the specificity of these compounds as CDA inhibitors was confirmed using enzyme inhibition testing and docking. The method of the invention is useful for identifying CDA inhibitors useful as agricultural fungicides or for controlling other pests such as insects or nematodes that are harmful for crops and/or mammals.
3.WO/2020/237237METHODS FOR DETECTING A LEVEL OF H. PYLORI IN A FECAL SAMPLE
WO 26.11.2020
Int.Class G16B 30/00
GPHYSICS
16INFORMATION AND COMMUNICATION TECHNOLOGY SPECIALLY ADAPTED FOR SPECIFIC APPLICATION FIELDS
BBIOINFORMATICS, i.e. INFORMATION AND COMMUNICATION TECHNOLOGY SPECIALLY ADAPTED FOR GENETIC OR PROTEIN-RELATED DATA PROCESSING IN COMPUTATIONAL MOLECULAR BIOLOGY
30ICT specially adapted for sequence analysis involving nucleotides or amino acids
Appl.No PCT/US2020/034508 Applicant AMERICAN MOLECULAR LABORATORIES, INC. Inventor ZHOU, Yi
The present disclosure provides methods and materials for detecting a level of H. pylori in a sample.
4.20200370111MOLECULAR TAGGING SYSTEM WITH NANOPORE-ORTHOGONAL DNA BARCODES
US 26.11.2020
Int.Class C12Q 1/6869
CCHEMISTRY; METALLURGY
12BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
QMEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS; COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES
1Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions
68involving nucleic acids
6869Methods for sequencing
Appl.No 16879214 Applicant University of Washington Inventor Luis H. Ceze

In some embodiments, a molecular tagging system that uses synthetic DNA-based tags is provided. In some embodiments, a kit for tagging objects with molecular tags is provided that comprises a plurality of molbit reservoirs. Each molbit reservoir is associated with a molbit and includes nucleic acid molecules that represent the molbit. In some embodiments, a method is provided wherein a digital tag value is determined, the digital tag value is converted to a molbit tag value, nucleic acid molecules associated with each molbit value indicated as present in the molbit tag value are combined, and the combined nucleic acid molecules are applied to an object to tag the object. In some embodiments, a system is provided that includes a computing system configured to receive raw nanopore signals from a sequencing device, to identify molbits based on the signals, and to determine a digital tag based on the identified molbits.

5.20200370121SYSTEM FOR DETERMINING A HEALTH STATUS OF A TISSUE OF INTEREST
US 26.11.2020
Int.Class C12Q 1/6883
CCHEMISTRY; METALLURGY
12BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
QMEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS; COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES
1Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions
68involving nucleic acids
6876Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes
6883for diseases caused by alterations of genetic material
Appl.No 16986057 Applicant The Board of Trustees of the Leland Stanford Junior University Inventor Lian Chye Winston Koh

The invention generally relates to methods for assessing the health of a tissue by characterizing circulating nucleic acids in a biological sample. According to certain embodiments, methods for assessing the health of a tissue include the steps of detecting a sample level of RNA in a biological sample, comparing the sample level of RNA to a reference level of RNA specific to the tissue, determining whether a difference exists between the sample level and the reference level, and characterizing the tissue as abnormal if a difference is detected.

6.20200371111SYSTEM AND METHOD FOR DISCOVERY OF GENE-ENVIRONMENT INTERACTIONS
US 26.11.2020
Int.Class G01N 33/68
GPHYSICS
01MEASURING; TESTING
NINVESTIGATING OR ANALYSING MATERIALS BY DETERMINING THEIR CHEMICAL OR PHYSICAL PROPERTIES
33Investigating or analysing materials by specific methods not covered by groups G01N1/-G01N31/131
48Biological material, e.g. blood, urine; Haemocytometers
50Chemical analysis of biological material, e.g. blood, urine; Testing involving biospecific ligand binding methods; Immunological testing
68involving proteins, peptides or amino acids
Appl.No 15888005 Applicant Genteract Corporation Inventor Brody Holohan

A system and method for detecting gene-environment interactions, a method of making predictions about individual response to a specific environmental factor with respect to a single phenotype and a simulation method determining the optimal parameters for use of the gene-environment interaction detection method. Gene-environment interaction detection and the discovery of previously unknown interactions are facilitated.

7.20200372031Flexible Seed Extension for Hash Table Genomic Mapping
US 26.11.2020
Int.Class G06F 16/2455
GPHYSICS
06COMPUTING; CALCULATING OR COUNTING
FELECTRIC DIGITAL DATA PROCESSING
16Information retrieval; Database structures therefor; File system structures therefor
20of structured data, e.g. relational data
24Querying
245Query processing
2455Query execution
Appl.No 16882158 Applicant Illumina, Inc. Inventor Michael Ruehle

Methods, systems, and apparatuses, including computer programs for generating and using a hash table configured to improve mapping of reads are disclosed that include obtaining a first seed of K nucleotides from a reference sequence, generating a seed extension tree having a nodes, wherein each node of the nodes corresponds to (i) an extended seed that is an extension of the first seed and has a nucleotide length of K* and (ii) one or more locations, in a seed extension table, that include data describing reference sequence locations that match the extended seed, and for each node: storing interval information at a location of the hash table that corresponds to an index key for the extended seed, wherein the interval information references one or more locations in the seed extension table that include reference sequence locations that match the extended seed associated with the node.

8.20200372972SAMPLE DATA ANALYSIS METHOD BASED ON GENOMIC MODULE NETWORK
US 26.11.2020
Int.Class G16B 40/00
GPHYSICS
16INFORMATION AND COMMUNICATION TECHNOLOGY SPECIALLY ADAPTED FOR SPECIFIC APPLICATION FIELDS
BBIOINFORMATICS, i.e. INFORMATION AND COMMUNICATION TECHNOLOGY SPECIALLY ADAPTED FOR GENETIC OR PROTEIN-RELATED DATA PROCESSING IN COMPUTATIONAL MOLECULAR BIOLOGY
40ICT specially adapted for biostatistics; ICT specially adapted for bioinformatics-related machine learning or data mining, e.g. knowledge discovery or pattern finding
Appl.No 16635433 Applicant Industry-University Cooperation Foundation Hanyang University Inventor Jin Hyuk KIM

Provided is a method of analyzing sample data based on a genomic module network by means of a computer apparatus. The method includes filtering first gene expression data for a normal or tumor tissue, which is the same tissue as a specific tissue, and second gene expression data for a target tissue to be analyzed, which is the same tissue as the specific tissue, on the basis of a specific module among a plurality of genomic modules; and classifying genes into a plurality of new genomic modules on the basis of an entropy determined using the filtered first gene expression data and determining, for genes belonging to at least one of the plurality of new genomic modules, a first degree of variation of the target tissue relative to the normal or tumor tissue in the at least one genomic module using the filtered first gene expression data and the filtered second gene expression data.

9.WO/2020/234666DEEP LEARNING BASED SYSTEM AND METHOD FOR PREDICTION OF ALTERNATIVE POLYADENYLATION SITE
WO 26.11.2020
Int.Class G16B 20/30
GPHYSICS
16INFORMATION AND COMMUNICATION TECHNOLOGY SPECIALLY ADAPTED FOR SPECIFIC APPLICATION FIELDS
BBIOINFORMATICS, i.e. INFORMATION AND COMMUNICATION TECHNOLOGY SPECIALLY ADAPTED FOR GENETIC OR PROTEIN-RELATED DATA PROCESSING IN COMPUTATIONAL MOLECULAR BIOLOGY
20ICT specially adapted for functional genomics or proteomics, e.g. genotype-phenotype associations
30Detection of binding sites or motifs
Appl.No PCT/IB2020/053867 Applicant KING ABDULLAH UNIVERSITY OF SCIENCE AND TECHNOLOGY Inventor GAO, Xin
A method for calculating usage of all alternative polyadenylation sites (PAS) in a genomic sequence includes receiving (1800) plural genomic sub-sequences (204I) centered on corresponding PAS; processing (1802) each genomic sub-sequence (204I) of the plural genomic sequences, with a corresponding neural network (210I) of plural neural networks (210I); supplying (1804) plural outputs (206I) of the plural neural networks (210I) to an interaction layer (220) that includes plural forward Bidirectional Long Short Term Memory Network (Bi-LSTM) cells (612I) and plural backward Bi-LSTM cells (614I), wherein each pair of a forward Bi-LSTM cell (612I) and a backward Bi-LSTM cell (614I) uniquely receives a corresponding output (206I), of the plural outputs (206I), from a corresponding neural network (210I); and generating (1806) a scalar value for each PAS, based on an output from a corresponding pair of the forward Bi-LSTM cell (612) and the backward Bi-LSTM cell (614).
10.20200372971METHODS FOR DETECTING NUCLEIC ACID VARIANTS
US 26.11.2020
Int.Class G16B 20/20
GPHYSICS
16INFORMATION AND COMMUNICATION TECHNOLOGY SPECIALLY ADAPTED FOR SPECIFIC APPLICATION FIELDS
BBIOINFORMATICS, i.e. INFORMATION AND COMMUNICATION TECHNOLOGY SPECIALLY ADAPTED FOR GENETIC OR PROTEIN-RELATED DATA PROCESSING IN COMPUTATIONAL MOLECULAR BIOLOGY
20ICT specially adapted for functional genomics or proteomics, e.g. genotype-phenotype associations
20Allele or variant detection, e.g. single nucleotide polymorphism detection
Appl.No 16864981 Applicant Ultima Genomics, Inc. Inventor Yoav ETZIONI

Methods for detecting a short genetic variant in a test sample are described herein. In some exemplary methods, the short genetic variant is called using one or match scores, which are determined using one or more sequencing data sets obtained from a test nucleic acid molecule, wherein the test sequencing data sets are determined by sequencing the test nucleic acid molecule using non-terminating nucleotides provided in separate nucleotide flows according to a flow-cycle order. Also described herein are methods of sequencing a test nucleic acid molecule using two or more different flow-cycle orders and/or extended flow cycle orders having five or more nucleotide flows per flow cycle.