1-channel: sample RNA is labeled by single dye, 2-channel: sample and reference RNA are labeled by differentdyes and competitively hybridized.GEO: National Center for Biotechnology Information's Gene Expression Omnibus (www.ncbi.nlm.nih.gov/geo/),GPL and GSE are accession number for miceroarray platform and gene set, respectively, depositted in th GEO.(a) http://www.broad.mit.edu/cgi-bin/cancer/datasets.cgix(b) http://llmpp.nih.gov/DLBCL/(c) http://www.rii.com/publications/default.htmMicroarrays manufactured by *Affymetrix (Santa Clara, CA) or ** Agilent Technologies (Palo Alto, CA)

The Forensic Genetics Bioinformatics Market report segments the industry into By Application (Criminal Investigation, Paternity Testing, Disaster Victim Identification, Others), By Technology (DNA Sequencing, Data Analysis Software, Bioinformatics Tools), By End User (Forensic Laboratories, Law Enforcement Agencies, Research Institutes), and Geography (North America, Europe, Asia-Pacific, Middle East and Africa, South America).

The global Genetic Data Analysis Software market is experiencing robust growth, projected to reach a market size of $348.5 million in 2025. While the provided CAGR (Compound Annual Growth Rate) is missing, considering the rapid advancements in genomics and the increasing adoption of precision medicine, a conservative estimate of the CAGR for the forecast period (2025-2033) would be around 15%. This growth is fueled by several key drivers. The rising prevalence of genetic disorders necessitates sophisticated software for analysis and interpretation. Furthermore, the decreasing cost of genomic sequencing is making large-scale genetic studies more feasible, leading to a greater demand for robust and efficient analysis tools. The market is segmented by deployment (web-based and cloud-based) and application (hospitals and health systems, research organizations, and others). Cloud-based solutions are gaining traction due to their scalability and accessibility, while hospitals and health systems represent a significant portion of the market share due to their increasing focus on personalized medicine. Major players like Agilent Technologies, Illumina, and QIAGEN Digital Insights are driving innovation through continuous product development and strategic partnerships. Technological advancements such as artificial intelligence and machine learning are enhancing the capabilities of these software solutions, leading to improved accuracy and faster analysis times. The integration of these advanced analytics with electronic health records (EHRs) is another significant trend further propelling market expansion. The market's growth trajectory is influenced by several factors. The increasing availability of high-throughput sequencing technologies continues to generate massive amounts of genomic data, further stimulating demand for advanced analytics. However, the complexity of genomic data analysis and the need for skilled professionals can act as a restraint, alongside data privacy and security concerns. Despite these challenges, the long-term outlook for the Genetic Data Analysis Software market remains highly positive, driven by the continuous advancements in genomics research, the expanding applications of genomic information in healthcare, and the increasing investments in precision medicine initiatives globally. The market is expected to witness considerable expansion across all geographical regions, with North America and Europe maintaining a significant market share due to their well-established healthcare infrastructure and advanced research capabilities.

Introductory curriculum for high school students (grades 9-12) that explores genetic research and bioinformatics. Posted on-line October 2012. Funded by NSF grant DRL-0833779

T, training data set; V, validation data set.BC, breast cancer; OC, ovarian cancer; DLBCL, diffuse large-B-cell lymphoma; PC, prostate cancer.RD, residual disease; CR, complete response.

Typical example of the gene expression data obtained from microarray experiments. Each number represents the change (increase or decrease) of the gene expression level of the corresponding gene in Condition i (Condi), relative to its level of expression in a given reference condition. This change is measure as a log ratio in base 2. Thus, a positive number corresponds to an increase in the level of expression, whereas a negative number represents a decrease.

Code, logs, data, and summaries for detection and genotyping of genomic structural variants in the D.melanogaster Sussex LHM hemiclones (and one in-house reference line individual), using Genomestrip/2.0

The unfiltered CNV pipleline results are lhm_gs.cnvs.raw.vcf.gz

Filtered CNV results (including removal of bad samples) are filtered.goodS.lhm_gs.cnvs.raw.vcf.gz

The file uploaded to NCBI dbVAR (which comprises of the filtered CNVs and indels >50bp from the HaplotypeCaller method) is lhm_sx16.dbVAR.vcf.gz

The NCBI dbVAR accession number is nstd134. Code, logs and summary data are in the zipped archives, named accordingly. The archive reference_data.zip contains additional input files required for Genomestrip, including a shell script for making some of them. The file gstrip_lhm_RG_bams.list is also an input for Genomestrip, indicating bam file names and paths.

The pre-print manuscript for this data is available on biorxiv: "Whole genome resequencing of a laboratory-adapted Drosophila melanogaster population sample" http://biorxiv.org/content/early/2016/10/17/081554 doi: http://dx.doi.org/10.1101/081554

This data collection contains all currently published nucleotide (DNA/RNA) and protein sequences from Australian Amphibolis antarctica, commonly known as Sea Nymph. Other information about this group:

The nucleotide (DNA/RNA) and protein sequences have been sourced through the European Nucleotide Archive (ENA) and Universal Protein Resource (UniProt), databases that contains comprehensive sets of nucleotide (DNA/RNA) and protein sequences from all organisms that have been published by the International Research Community.

The identification of species in Amphibolis antarctica as Australian dwelling organisms has been achieved by accessing the Australian Plant Census (APC) or Australian Faunal Directory (AFD) through the Atlas of Living Australia.

BOCK is a knowledge graph integrating oligogenic disease information (originally from the Oligogenic Disease Database (Natchtegael et al. 2022)) together with multiple biological networks and ontologies.

Compared to more generic knowledge graphs, we selected specifically networks relevant to understand the molecular mechanisms of epistasis, placing genes as the central entities, and focused on trusted resources describing a large set of human genes and their interactions.

All entities in the KG are linked to their source database entry via an URI (Uniform Resource Identifier) to facilitate integrations within larger bioinformatics linked data repositories.

BOCK 2.0 integrates recent versions of the used ontologies and databases, as well as additional pathway-specific (The Reactome Pathway Knowledgebase 2024, Milacic et al.) and tissue-specific information (COXPRESdb v8, Obayashi et al.). Additionally the database used for the coexpression relation between genes, has been replaced by COXPRESdb v8.

We provide BOCK 2.0 in three formats:

1. GraphML (Graph Markup Language): a network format enabling the fast import of the KG by multiple libraries (e.g networkx) and tools (e.g Cytoscape).
2. XML (Extensible Markup Language): a text-encoding system that is human-readable and compatible with many systems.
3. Neo4J import files: tab-separated files that can be easily imported into Neo4J using the neo4j-admin utils.

This data collection contains all currently published nucleotide (DNA/RNA) and protein sequences from the Australian dwelling organism Pityrodia uncinata.

The nucleotide (DNA/RNA) and protein sequences have been sourced through the European Nucleotide Archive (ENA) and Universal Protein Resource (UniProt), databases that contains comprehensive sets of nucleotide (DNA/RNA) and protein sequences from all organisms that have been published by the International Research Community.

The identification of the species Pityrodia uncinata as an Australian dwelling organism has been achieved by accessing the Australian Plant Census (APC) or Australian Faunal Directory (AFD) through the Atlas of Living Australia.

This data collection contains all currently published nucleotide (DNA/RNA) and protein sequences from the Australian dwelling organism Banksia hiemalis.

The nucleotide (DNA/RNA) and protein sequences have been sourced through the European Nucleotide Archive (ENA) and Universal Protein Resource (UniProt), databases that contains comprehensive sets of nucleotide (DNA/RNA) and protein sequences from all organisms that have been published by the International Research Community.

The identification of the species Banksia hiemalis as an Australian dwelling organism has been achieved by accessing the Australian Plant Census (APC) or Australian Faunal Directory (AFD) through the Atlas of Living Australia.

This data collection contains all currently published nucleotide (DNA/RNA) and protein sequences from the Australian research institution University of Notre Dame.The nucleotide (DNA/RNA) and protein sequences have been sourced through the European Nucleotide Archive (ENA) and Universal Protein Resource (UniProt), databases that contains comprehensive sets of nucleotide (DNA/RNA) and protein sequences from all organisms that have been published by the International Research Community.

This data collection contains all currently published nucleotide (DNA/RNA) and protein sequences from the Australian research institution Brain Research Institute.The nucleotide (DNA/RNA) and protein sequences have been sourced through the European Nucleotide Archive (ENA) and Universal Protein Resource (UniProt), databases that contains comprehensive sets of nucleotide (DNA/RNA) and protein sequences from all organisms that have been published by the International Research Community.

This data collection contains all currently published nucleotide (DNA/RNA) and protein sequences from the Australian dwelling organism Planorbis corneus.

The nucleotide (DNA/RNA) and protein sequences have been sourced through the European Nucleotide Archive (ENA) and Universal Protein Resource (UniProt), databases that contains comprehensive sets of nucleotide (DNA/RNA) and protein sequences from all organisms that have been published by the International Research Community.

The identification of the species Planorbis corneus as an Australian dwelling organism has been achieved by accessing the Australian Plant Census (APC) or Australian Faunal Directory (AFD) through the Atlas of Living Australia.

Influenza A viruses (IAVs) pose a persistent global health threat, necessitating a comprehensive understanding of their dynamics, diversity, evolution, and transmission to inform pandemic preparedness. This thesis provides a multi-scale investigation into the IAVs, establishing Hong Kong as an important place for zoonotic risk and global viral spread.Firstly, surveillance in Hong Kong's animal populations (wild birds, swine, and poultry) identified significant threats. Highly pathogenic avian influenza viruses of clade 2.3.4.4b H5 were detected in wild birds, with viruses from two spoonbills from late 2022 being genetically related to a virus from a human in China. In swine, an Eurasian avian-like H1N1 swine influenza virus with PB1 and M segments derived from the H9N2 subtype, suggesting that H9N2 viruses are infecting pigs and reassorting with swine influenza viruses in China. Novel H3N8 viruses were identified in chicken in live poultry markets and chicken farms in Hong Kong, that are genetically similar to the zoonotic H3N8 viruses reported in mainland China. These findings highlight the region as a dangerous place for the emergence of high-risk strains.Secondly, a decade-long phylogeographic analysis of low pathogenetic avian influenza viruses in wild birds conclusively demonstrated Hong Kong's important role in global AIV dissemination. Significant viral migrations were observed from Hong Kong to adjacent regions (Japan/Korea, East China, Bangladesh) and to geographically distant continents (Australia, Europe, North America). The study identified Hong Kong as a source for the PA gene segment during an early stage (2010-2015) and documented extended circulation (longer persistence) of polymerase genes (PA, PB2, PB1). Furthermore, H6 viruses were pinpointed as "genetic hubs" due to their consistent role as donors for PB2 and PA segments, while H3 viruses served as primary sources for NP and M segments, underscoring subtype-specific contributions to reassortment.Thirdly, investigating genetic drift at a finer scale, intra-host analysis in human patients revealed significantly greater genetic diversity in H3N2 viruses compared to H1N1 within infected individuals. Evidence of anatomical compartmentalisation was found, with the throat hosting more diverse H3N2 viral populations than the nose, particularly in PA, PB2, and neuraminidase genes. Furthermore, a codon-deoptimized '8-mut' influenza virus, engineered with 373 silent mutations to mimic avian codon usage, demonstrated accelerated genetic diversification (predominantly synonymous mutations) over 11 passages in human A549 cells, compared to the wild-type strain. Critically, secondary often non-synonymous mutations consistently emerged directly adjacent to engineered silent mutations, especially when short dinucleotide repeats were introduced, suggesting genome destabilisation and potential compensatory adaptation mechanisms. These findings provide crucial lessons for the rational design of influenza vaccines with enhanced safety and efficacy profiles.Collectively, this thesis highlights the dynamic and complex evolutionary landscape of IAVs, affirming the continuous pandemic threat and the indispensable role of integrated surveillance and genetic characterisation in Hong Kong.

This data collection contains all currently published nucleotide (DNA/RNA) and protein sequences from the Australian dwelling organism Eodelena spenceri.

The nucleotide (DNA/RNA) and protein sequences have been sourced through the European Nucleotide Archive (ENA) and Universal Protein Resource (UniProt), databases that contains comprehensive sets of nucleotide (DNA/RNA) and protein sequences from all organisms that have been published by the International Research Community.

The identification of the species Eodelena spenceri as an Australian dwelling organism has been achieved by accessing the Australian Plant Census (APC) or Australian Faunal Directory (AFD) through the Atlas of Living Australia.

This data collection contains all currently published nucleotide (DNA/RNA) and protein sequences from the Australian dwelling organism Tubbia tasmanica, commonly known as Mauve Ruffe.

The nucleotide (DNA/RNA) and protein sequences have been sourced through the European Nucleotide Archive (ENA) and Universal Protein Resource (UniProt), databases that contains comprehensive sets of nucleotide (DNA/RNA) and protein sequences from all organisms that have been published by the International Research Community.

The identification of the species Tubbia tasmanica as an Australian dwelling organism has been achieved by accessing the Australian Plant Census (APC) or Australian Faunal Directory (AFD) through the Atlas of Living Australia.

This data collection contains all currently published nucleotide (DNA/RNA) and protein sequences from the Australian dwelling organism Duchesnea indica, commonly known as Potentilla Indica.

The nucleotide (DNA/RNA) and protein sequences have been sourced through the European Nucleotide Archive (ENA) and Universal Protein Resource (UniProt), databases that contains comprehensive sets of nucleotide (DNA/RNA) and protein sequences from all organisms that have been published by the International Research Community.

The identification of the species Duchesnea indica as an Australian dwelling organism has been achieved by accessing the Australian Plant Census (APC) or Australian Faunal Directory (AFD) through the Atlas of Living Australia.

This data collection contains all currently published nucleotide (DNA/RNA) and protein sequences from the Australian dwelling organism Apogon endekataenia, commonly known as Candystripe Cardinalfish.

The nucleotide (DNA/RNA) and protein sequences have been sourced through the European Nucleotide Archive (ENA) and Universal Protein Resource (UniProt), databases that contains comprehensive sets of nucleotide (DNA/RNA) and protein sequences from all organisms that have been published by the International Research Community.

The identification of the species Apogon endekataenia as an Australian dwelling organism has been achieved by accessing the Australian Plant Census (APC) or Australian Faunal Directory (AFD) through the Atlas of Living Australia.

This data collection contains all currently published nucleotide (DNA/RNA) and protein sequences from Australian Dinebra, commonly known as Dinebra Jacq.. Other information about this group:

The nucleotide (DNA/RNA) and protein sequences have been sourced through the European Nucleotide Archive (ENA) and Universal Protein Resource (UniProt), databases that contains comprehensive sets of nucleotide (DNA/RNA) and protein sequences from all organisms that have been published by the International Research Community.

The identification of species in Dinebra as Australian dwelling organisms has been achieved by accessing the Australian Plant Census (APC) or Australian Faunal Directory (AFD) through the Atlas of Living Australia.