Genomics

Genomics research and analysis: sequencing studies, variant discovery, gene regulation and the computational methods behind them.

Bioinformatics | Database | Genomics | News | NGS | Sequencing | Trending

The UK Biobank Released the Largest Set of Whole Genome Sequences Together with Population Genetics and Trait Association Studies for 150,119 Individuals
ByTanveen Kaur July 26, 2022November 11, 2022

Scientists discuss the study of 150,119 people’s whole genomes from the UK Biobank, which is a group of high-quality variants that includes 58,707,036 indels and 585,040,410 single-nucleotide polymorphisms, or 7.0 percent of all potential single-nucleotide polymorphisms in humans. A thorough and trustworthy characterization of both sequences and phenotypic variation is necessary to gain a thorough…

Read More The UK Biobank Released the Largest Set of Whole Genome Sequences Together with Population Genetics and Trait Association Studies for 150,119 Individuals
Bioinformatics | Corona Virus | COVID-19 | Covid-19 News | Genomics | News | NGS | Paper Summary | Sequencing | Trending

Scientists Devised a Bioinformatics Method ‘COJAC’ for Early Detection and Surveillance of SARS-CoV-2 Genomic Variants in Wastewater
ByTanveen Kaur July 21, 2022November 11, 2022

Using read pairs with several SARS-CoV-2 variant-specific signature mutations as a reliable signal of low-frequency variants, scientists develop the bioinformatics technique known as COJAC (Co-Occurrence adjusted Analysis and Calling). The genomic sequencing, in conjunction with COJAC, can offer population-level estimates of the prevalence and fitness of emerging variants from wastewater samples earlier and on the basis…

Read More Scientists Devised a Bioinformatics Method ‘COJAC’ for Early Detection and Surveillance of SARS-CoV-2 Genomic Variants in Wastewater
AI | Bioinformatics | Cancer Research | Genomics | News | Paper Summary | Trending

Scientists Used a Netflix-Style Algorithm to Create Blueprint of Cancer Genomes
ByTanveen Kaur June 20, 2022November 9, 2022

The algorithms that track users’ Netflix viewing habits could soon be used to track cancer development in order to direct doctors in managing cancer. An international team of researchers led by Dr. Nischalan Pillay (UCL Cancer Institute) and Dr. Ludmil Alexandrov (University of California, San Diego) used AI to identify 21 frequent faults in the…

Read More Scientists Used a Netflix-Style Algorithm to Create Blueprint of Cancer Genomes
Bioinformatics | Genomics | News | Paper Summary | Tools | Trending

Scientists Develop a New Computational Tool ‘Grit’ to Identify Upstream Transcription Factor Binding Sites More Accurately
ByTanveen Kaur June 16, 2022June 16, 2022

Scientists from Yangtze University, Jingzhou, China developed a computational tool, “Grit,” to identify the upstream transcription factor binding sites in orthologous genes by the utilization of mixed Student’s t-test statistics. The transcription factor (TF) regulates the transcription of DNA to messenger RNA or mRNA by binding to upstream sequence motifs. Distinguishing the locations of known…

Read More Scientists Develop a New Computational Tool ‘Grit’ to Identify Upstream Transcription Factor Binding Sites More Accurately
Bioinformatics | COVID-19 | Drug Discovery | Gene Expression | Genomics | GWAS | Machine Learning | News | OMICS | Paper Summary | Trending

Transcriptome-Wide Association Studies Integrated with 3D Genomic and Epigenomic Data used to Improve Target Gene Discovery and Drug Repurposing
ByTanveen Kaur June 13, 2022October 22, 2026

Scientists from Pennsylvania State University integrated 3D genomic and epigenomic data with transcriptome-wide association studies data to improve gene expression predictions. The researchers propose an integrative method PUMICE that integrates 3D genomic and epigenomic data with expression quantitative trait loci (eQTL) to predict gene expressions more accurately. An extension of the method PUMICE +, also combines transcriptome-wide…

Read More Transcriptome-Wide Association Studies Integrated with 3D Genomic and Epigenomic Data used to Improve Target Gene Discovery and Drug Repurposing
Bioinformatics | Data Science | Featured | Genomics | News | NGS | Sequencing | Tools | Trending

Scientists Use CRISPR Technology and Perturb-seq to Map Every Human Gene to its Function
ByDr. Tamanna Anwar June 11, 2022June 18, 2022

Scientists from Whitehead Institute and collaborators used Perturb-seq, a single-cell sequencing technology, to link every expressed gene in the human genome to its function in the cell, offering a free resource for other researchers that can be accessed via the internet. The Human Genome Project was a huge undertaking that aimed to sequence every single…

Read More Scientists Use CRISPR Technology and Perturb-seq to Map Every Human Gene to its Function
Bioinformatics | Genomics | News | Sequencing | Trending | Virus

First Draft of Monkeypox Virus Genome Sequenced from Current Outbreak Patient
ByDr. Tamanna Anwar May 24, 2022June 18, 2022

In a quest to understand why the monkeypox virus, which is a less lethal relative of smallpox, has infected so many people around the world, the scientists have sequenced its genome. The first draft genome sequence of the monkeypox virus was released recently, derived from a swab of a confirmed case of the current outbreak….

Read More First Draft of Monkeypox Virus Genome Sequenced from Current Outbreak Patient
Algorithm | Bioinformatics | Genomics | Machine Learning | News | NGS | Sequencing | Tools | Trending

‘BWA-MEME’ – Machine Learning-Based Short Read Alignment Algorithm to Speed up DNA Sequencing
ByDr. Tamanna Anwar May 21, 2022June 18, 2022

The algorithm is the first full-fledged machine learning-based short read alignment algorithm to speed up DNA sequencing, that efficiently uses learned indices to solve the exact match search issue for efficient seeding. The human genome is made up of a whole set of DNA that is around 6.4 billion letters long. Reading the entire genome…

Read More ‘BWA-MEME’ – Machine Learning-Based Short Read Alignment Algorithm to Speed up DNA Sequencing
Bioinformatics | Biotech | Data Science | Featured | Genomics | News | NGS | Paper Summary | Precision Medicine | Trending

Scientists Revealed the First Complete, Gapless Human Genome Sequence ‘T2T-CHM13’
ByDr. Tamanna Anwar April 6, 2022June 18, 2022

An international group of scientists has finally published the whole human genome sequence. The new reference genome fills in gaps left by previous versions, allowing researchers to understand better genetic variation and how it can contribute to disease in specific cases. The complete human genome sequence has already provided new perspectives to genome biology and…

Read More Scientists Revealed the First Complete, Gapless Human Genome Sequence ‘T2T-CHM13’
AI | Bioinformatics | Data Science | Deep Learning | Genomics | Machine Learning | Neural Network | News | NGS | Tools | Trending

Scientists from the University of California Developed a Highly Accurate Algorithm ‘La Jolla Assembler (LJA)’ to Scale-up Complete Genome Assembly
ByDr. Tamanna Anwar March 12, 2022June 18, 2022

A team of international researchers led by the University of California San Diego’s Department of Computer Science and Engineering has demonstrated that the La Jolla Assembler (LJA), a new genome assembly algorithm, vastly improves large genome reconstruction, the process of arranging DNA snippets into complete genomes, which is a crucial part of genomic sequencing. Furthermore,…

Read More Scientists from the University of California Developed a Highly Accurate Algorithm ‘La Jolla Assembler (LJA)’ to Scale-up Complete Genome Assembly
Bioinformatics | Drug Discovery | Featured | Genomics | News | NGS | OMICS | Precision Medicine | Tools | Trending

Scientists at Garvan Institute Developed a Single Test for Over 50 Genetic Diseases, Cutting Diagnosis Time from Decades to Days
ByDr. Tamanna Anwar March 11, 2022October 22, 2026

Garvan Institute researchers have demonstrated how new genomic sequencing technologies might help individuals with uncommon neurological and neuromuscular conditions avoid a “diagnostic odyssey.” – A single DNA test capable of screening a patient’s genome for over 50 genetic neurological and neuromuscular diseases (e.g., Huntington’s disease, muscular dystrophies, and fragile X syndrome) has been developed. -…

Read More Scientists at Garvan Institute Developed a Single Test for Over 50 Genetic Diseases, Cutting Diagnosis Time from Decades to Days
AI | Bioinformatics | Genomics | Health | News | NGS | Trending

Fastest DNA Sequencing that Uses AI and Accelerated Computing Sets Guinness World Record For Completing DNA Sequencing in Just Five Hours and Two Minutes
ByDr. Tamanna Anwar February 27, 2022June 18, 2022

Stanford University researchers established the record in collaboration with NVIDIA, Oxford Nanopore Technologies, Google, Baylor College of Medicine, and the University of California, Santa Cruz. This week, Guinness World Records awarded a Stanford University-led research team the first record for quickest DNA sequencing technology — a benchmark established utilizing a workflow enhanced by AI and…

Read More Fastest DNA Sequencing that Uses AI and Accelerated Computing Sets Guinness World Record For Completing DNA Sequencing in Just Five Hours and Two Minutes
Bioinformatics | Genomics | News | NGS | RNA-Seq | Trending

Entire Human Gut Mapped by Scientists at the Single-Cell Resolution
ByDr. Tamanna Anwar February 25, 2022June 18, 2022

Scientists from the University of North Carolina School of Medicine, led by Scott Magness, Ph.D., sequenced the genes expressed in single cells from human digestive tracts to discover new cell-type characteristics and learn more about essential cell functions like nutrient absorption and immune defense. You could feel uneasy in your tummy if you get nervous….

Read More Entire Human Gut Mapped by Scientists at the Single-Cell Resolution
Bioinformatics | Genomics | News | Trending

Reassembling the Chromosomes of Earth’s First Creatures
ByDr. Tamanna Anwar February 6, 2022June 18, 2022

According to the latest research published this week in the journal Science Advances, many modern marine invertebrates, such as sponges and jellyfish, contain chromosomes with the same old structure acquired from their primordial ancestors more than 600 million years ago. The surprising discovery serves as a reminder that evolution is conservative, keeping things that operate…

Read More Reassembling the Chromosomes of Earth’s First Creatures
Bioinformatics | Database | Genomics | Knowledge Graph | News | OMICS | Proteomics

Interpreting Clinical Proteomics Data With A Knowledge Graph
BySwati Yadav February 4, 2022October 22, 2026

Researchers at the University of Copenhagen, Denmark, introduce the Clinical Knowledge Graph (CKG), an open-source platform with about 20 million nodes and 220 million relationships representing relevant experimental data, public databases, and literature. Evidence-based precision medicine has grown to include a more thorough examination of disease characteristics. This necessitates the seamless integration of a wide…

Read More Interpreting Clinical Proteomics Data With A Knowledge Graph
Bioinformatics | Cancer Research | Genomics | Metagenomics | News | OMICS | Sequencing | Trending

A New Sequencing Technique Developed for Low-Biomass, Degraded, or Contaminated Microbiome Samples
ByDr. Tamanna Anwar January 28, 2022September 8, 2022

A low-cost metagenome sequencing technology has been developed by scientists from the Chinese Academy of Sciences’ Qingdao Institute of Bioenergy and Bioprocess Technology (QIBEBT). It allows high-resolution disclosure of a microbiome’s whole ‘landscape’ of species, even from low-biomass, damaged, or polluted samples. The ‘microbiome‘ is referred to a community of microorganisms (bacteria, fungi, protists, and…

Read More A New Sequencing Technique Developed for Low-Biomass, Degraded, or Contaminated Microbiome Samples
Bioinformatics | Biomedical Engineering | Cancer Research | Genomics | News | RNA-Seq | Sequencing | Trending

Safely Inserting Therapeutic Genes into the Human DNA
ByDr. Tamanna Anwar January 27, 2022September 8, 2022

Researchers from Harvard’s Wyss Institute, Harvard Medical School, and the ETH Zurich have predicted and validated genetic safe harbors for therapeutic genes, making gene and cell treatments safer, more efficient, more predictable. According to the researchers, “genomic safe harbors (GSHs)” could enhance the efficacy, persistence, and predictability of future gene and cell therapies that are…

Read More Safely Inserting Therapeutic Genes into the Human DNA
Bioinformatics | Genomics | News | Systems Biology | Trending

iDIRECT – A Framework for Analyzing Network Interactions in Various Complex Biological Systems
ByDr. Tamanna Anwar January 22, 2022June 18, 2022

Scientists from the University of Oklahoma and University of California at Berkeley have developed a framework iDIRECT (Inference of Direct and Indirect Relationships with Effective Copula-based Transitivity) for disentangling direct and indirect relationships in association networks. Despite the importance of networks in understanding the behavior and features of complex systems, recreating networks from large-scale experimental…

Read More iDIRECT – A Framework for Analyzing Network Interactions in Various Complex Biological Systems
Bioinformatics | Biotech | Genomics | News | Sequencing

The Earth BioGenome Project Steadily Started Sequencing Genomes
ByDr. Tamanna Anwar January 19, 2022June 18, 2022

A worldwide endeavor to map the genomes of all life on Earth (plants, animals, fungi, and other microbes) is entering a new phase as it proceeds from pilot studies to full-scale production sequencing. The Earth BioGenome Project (EBP) has entered a new phase, as evidenced by a group of articles published this week in Proceedings…

Read More The Earth BioGenome Project Steadily Started Sequencing Genomes
Bioinformatics | Data Science | Genomics | Health | News | OMICS | Trending

Metagenomics of Human Skin Microbiome Identifies New Bacteria and Viruses
ByDr. Tamanna Anwar January 15, 2022June 18, 2022

Scientists from EMBL-EBI, NIH, NHGRI, and collaborators have discovered new micro-organisms (bacterial, fungal species, and viruses) in the human skin microbiome. The human skin microbiome is essential for skin health and illness, and studying its makeup might help us better understand skin-related diseases. Researchers employed metagenomics to create new human skin microbiome reference genomes. Data…

Read More Metagenomics of Human Skin Microbiome Identifies New Bacteria and Viruses
Bioinformatics | Genomics | News | OMICS | Tools

Multi-omics Data Visualization and Chromosomes Annotation with an R Package “ChromoMap”
ByDr. Tamanna Anwar January 14, 2022June 18, 2022

ChromoMap is a fast and easy-to-use tool for visualizing genomic elements and related data (such as multi-omics data) in relation to their chromosome-by-chromosome occurrence for any genome assembly. ChromoMap provides customizable displays that allow for the comparison of data individually connected with each strand of a specific chromosome, as well as homologous chromosomes of any…

Read More Multi-omics Data Visualization and Chromosomes Annotation with an R Package “ChromoMap”
AI | Bioinformatics | Covid-19 News | Genomics | Machine Learning | News | Precision Medicine | Trending

Transforming DNA-Repair Visualization by Machine Learning Coupled High-Throughput Microscopy
ByDr. Tamanna Anwar January 11, 2022June 18, 2022

Machine learning may aid in repairing genetic damage and avoiding DNA mutations and chronic diseases. Scientists from Massachusetts General Hospital and the National Cancer Research Centre have created novel methods for seeing DNA repair in detail, using machine learning and high-throughput microscopy, and have discovered new repair proteins. The results might open the path for…

Read More Transforming DNA-Repair Visualization by Machine Learning Coupled High-Throughput Microscopy

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Genomics

Interpreting Clinical Proteomics Data With A Knowledge Graph

The Earth BioGenome Project Steadily Started Sequencing Genomes

Multi-omics Data Visualization and Chromosomes Annotation with an R Package “ChromoMap”

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