BOL: Related items

Mpox Public Health Emergency of International Concern

BioStar — Thu, 15 Aug 2024 07:28:39 -0500

The World Health Organization Health Organization has also declared Mpox Public Health Emergency of International Concern barely 24 hours after Africa CDC declaration
The World Health Organization Health Organization (WHO) declared the mpox outbreak a Public Health Emergency of International Concern
(PHEIC) just 24 hours after the Africa CDC declared a public health emergency of continental security.
This rapid escalation underscores the severe threat the outbreak poses and the urgency of a coordinated global response.
What does PHEIC mean
1 Global Recognition of the Threat
→ The WHO's PHEIC declaration is a global call to action, prompting nations worldwide to prepare for potential mpox spread beyond Africa.
→ This designation unlocks international resources, including vaccines and treatments, crucial for controlling the outbreak.
2 Vaccine Availability
→ The WHO has invited vaccine manufacturers to apply for emergency use listing.
→ This is essential for distributing vaccines in low-income countries.
→ It is estimated that 10 million doses of Mpox vaccine will be needed to control the outbreak.
3 International Support and Action
→ The WHO's PHEIC declaration is intended to catalyze international cooperation, ensuring that vaccines, treatments, and other resources are swiftly distributed to the most affected areas.
→ A rapid global response is essential to prevent further spread and protect vulnerable populations, including children and those with weakened immune systems.
4. The Need for Swift Action
→ With the potential for global spread, this outbreak requires immediate and comprehensive action from African nations and the international community.
→ The coordinated efforts of the African CDC and WHO are critical to halting transmission and preventing further devastation.
These declarations highlight the critical nature of the current mpox outbreak and the need for urgent, concerted efforts to safeguard global public health

When Chromosomes Shift: Understanding Chromosome Rearrangement and Human Disease

BioStar — Fri, 11 Apr 2025 01:07:17 -0500

In the vast and complex world of genetics, our chromosomes are like carefully arranged bookshelves — each holding critical information that defines who we are. But what happens when those books are shuffled, inverted, or swapped? The answer lies in a phenomenon known as chromosome rearrangement, a powerful force behind many human diseases, from developmental disorders to cancer.

What Are Chromosome Rearrangements?

Chromosome rearrangements are structural changes that alter the normal configuration of chromosomes. These changes can involve large segments of DNA — from thousands to millions of base pairs — and can occur spontaneously, be inherited, or result from exposure to mutagens (like radiation or chemicals).

Common Types of Rearrangements:

Deletions – Loss of a chromosome segment
Duplications – Repetition of a segment
Inversions – A segment breaks off, flips, and reattaches
Translocations – Segments exchange places between non-homologous chromosomes
Insertions – A segment is inserted into another part of the genome

These changes can disrupt genes directly or affect gene regulation, leading to disease.

How Do Chromosome Rearrangements Cause Disease?

The impact of a rearrangement depends on which genes are involved, how much DNA is affected, and when the rearrangement occurs (in development vs. adulthood). Here are some key mechanisms:

Gene disruption: Breaking a gene can lead to loss of function or the creation of a non-functional protein.
Gene fusion: Joining parts of two genes may form a novel hybrid gene with new functions (common in cancer).
Dosage effects: Extra or missing gene copies can disturb the balance of gene expression.
Position effects: Moving a gene to a new regulatory environment may silence or over-activate it.

Chromosome Rearrangements in Human Disease

1. Developmental Disorders

Cri-du-chat syndrome: Caused by a deletion on chromosome 5p. Affected infants often have a high-pitched cry and intellectual disability.
Williams syndrome: Results from a microdeletion on chromosome 7q, affecting genes related to cardiovascular and cognitive function.

2. Cancer

Cancer is perhaps the most striking example of disease caused by chromosome rearrangements.

Chronic Myeloid Leukemia (CML): Caused by a translocation between chromosomes 9 and 22, forming the Philadelphia chromosome. This creates the BCR-ABL fusion gene, which drives uncontrolled cell growth.
Burkitt lymphoma: Involves translocation of the MYC gene, leading to excessive cell division.
Ewing sarcoma: A fusion of EWSR1 and FLI1 genes through translocation promotes tumor development.

3. Infertility and Miscarriages

Balanced rearrangements (like inversions or translocations) in carriers may not cause disease directly but can result in:

Recurrent miscarriages
Infertility
Birth defects in offspring

Detecting Rearrangements

Thanks to modern genomics, chromosome rearrangements can now be detected with high precision using:

Karyotyping – Classic method for detecting large rearrangements
FISH (Fluorescence In Situ Hybridization) – Uses fluorescent probes to target specific DNA sequences
Array CGH (Comparative Genomic Hybridization) – Detects copy number changes across the genome
Whole Genome Sequencing (WGS) – Identifies even small or complex rearrangements at base-pair resolution

Looking Forward: The Future of Chromosome Medicine

Understanding chromosome rearrangements is now central to:

Personalized medicine
Genetic counseling
Targeted therapies, especially in cancer (e.g., tyrosine kinase inhibitors for BCR-ABL fusion)

With the rise of long-read sequencing and single-cell genomics, even previously “invisible” rearrangements are being uncovered, offering new insights into both rare diseases and common conditions.

Final Thoughts

Chromosome rearrangements remind us that genetics isn't just about which genes we have — but where they are, how they're arranged, and when they're active. As our tools grow sharper, so does our ability to diagnose, understand, and treat diseases rooted in genomic architecture.

In a way, the genome is like a book not just defined by its words, but also by how the chapters are ordered. Rearranging them can create a new story — sometimes harmful, sometimes insightful — and understanding these changes is key to writing a healthier future.

Enrichr: a comprehensive gene set enrichment analysis

Jit — Thu, 27 Apr 2017 05:42:09 -0500

Enrichment analysis is a popular method for analyzing gene sets generated by genome-wide experiments. Here we present a significant update to one of the tools in this domain called Enrichr. Enrichr currently contains a large collection of diverse gene set libraries available for analysis and download. In total, Enrichr currently contains 180 184 annotated gene sets from 102 gene set libraries. New features have been added to Enrichr including the ability to submit fuzzy sets, upload BED files, improved application programming interface and visualization of the results as clustergrams. Overall, Enrichr is a comprehensive resource for curated gene sets and a search engine that accumulates biological knowledge for further biological discoveries. Enrichr is freely available at: http://amp.pharm.mssm.edu/Enrichr.

https://academic.oup.com/nar/article-lookup/doi/10.1093/nar/gkw377

Address of the bookmark: http://amp.pharm.mssm.edu/Enrichr/

The Centre for Bioinformatics (MCB) Lab

Sun, 14 Jul 2013 12:41:20 -0500

The Centre for Bioinformatics (MCB) is a diverse collection of professors, postdoctoral fellows, and students, who share a common interest in Bioinformatics.

Research Area

We are interested in the development of the statistics and computational methods for the analysis of this data in breast cancer.
We have worked on probabilistic models for subcellular localization, protein-protein interactions, and problems related to chemical genomics.
We are interested in the development of bioinformatics/biostatistical methodology in the analysis of epigenetic/epigenomic data.
We are interested in integrative bioinformatics approaches to learn the gene, gene products, interactions, and regulatory mechanisms involved in mental retardation.

Link @ http://www.mcgill.ca/mcb/

Jayaram Lab

Sun, 14 Jul 2013 14:04:37 -0500

Responsible (a) for developing Chemgenome, Bhageerath & Sanjeevini methods & softwares for genome annotation, protein tertiary structure prediction & computer aided drug design respectively, (b) for setting up a multi-teraflop supercomputing facility for Bioinformatics & Computational Biology at IIT Delhi, and (c) for making the hardware and software freely accessible at (www.scfbio-iitd.res.in) to the global scientific user community.

Faculty facilitator/Founder Director for two start-up companies (Leadinvent incubated at IIT, Delhi from 2006-2009 & Novoinformatics, under incubation at IIT Delhi since 2011).

Research Interest
Genome Analysis, Protein Structure Prediction and Drug Design.

Link @ http://www.scfbio-iitd.res.in/

Genomics for Bioinformatician

Jitendra Narayan — Sat, 20 Jul 2013 07:03:00 -0500

Genomics is the study of the genomes of organisms. The field includes intensive efforts to determine the entire DNA sequence of organisms and fine-scale genetic mapping efforts. The field also includes studies of intragenomic phenomena such as heterosis, epistasis, pleiotropy and other interactions between loci and alleles within the genome. In contrast, the investigation of the roles and functions of single genes is a primary focus of molecular biology or genetics and is a common topic of modern medical and biological research. Research of single genes does not fall into the definition of genomics unless the aim of this genetic, pathway, and functional information analysis is to elucidate its effect on, place in, and response to the entire genome's networks.

Genomics was established by Fred Sanger when he first sequenced the complete genomes of a virus and a mitochondrion. His group established techniques of sequencing, genome mapping, data storage, and bioinformatic analyses in the 1970-1980s. A major branch of genomics is still concerned with sequencing the genomes of various organisms, but the knowledge of full genomes has created the possibility for the field of functional genomics, mainly concerned with patterns of gene expression during various conditions. The most important tools here are microarrays and bioinformatics. Study of the full set of proteins in a cell type or tissue, and the changes during various conditions, is called proteomics. A related concept is materiomics, which is defined as the study of the material properties of biological materials (e.g. hierarchical protein structures and materials, mineralized biological tissues, etc.) and their effect on the macroscopic function and failure in their biological context, linking processes, structure and properties at multiple scales through a materials science approach. The actual term 'genomics' is thought to have been coined by Dr. Tom Roderick, a geneticist at the Jackson Laboratory (Bar Harbor, ME) over beer at a meeting held in Maryland on the mapping of the human genome in 1986.

The outcome of almost two years of intense discussions with literally hundreds of scientists and members of the public, has three major areas of focus: Genomics to Biology, Genomics to Health, and Genomics to Society.

Genomics to Biology:
The human genome sequence provides foundational information that now will allow development of a comprehensive catalog of all of the genome's components, determination of the function of all human genes, and deciphering of how genes and proteins work together in pathways and networks.

Genomics to Health:
Completion of the human genome sequence offers a unique opportunity to understand the role of genetic factors in health and disease, and to apply that understanding rapidly to prevention, diagnosis, and treatment. This opportunity will be realized through such genomics-based approaches as identification of genes and pathways and determining how they interact with environmental factors in health and disease, more precise prediction of disease susceptibility and drug response, early detection of illness, and development of entirely new therapeutic approaches.

Genomics to Society:
Just as the HGP has spawned new areas of research in basic biology and in health, it has created new opportunities in exploring the ethical, legal, and social implications (ELSI) of such work. These include defining policy options regarding the use of genomic information in both medical and non-medical settings and analysis of the impact of genomics on such concepts as race, ethnicity, kinship, individual and group identity, health, disease, and "normality" for traits and behaviors.

This vision for the future of genomics is not just about the NHGRI. It encompasses the whole field of genomics, including the work of all the other Institutes and Centers at the NIH and of a number of other federal agencies. All of the NIH Institutes are already taking full advantage of the sequence and will apply its data to the better understanding of both rare and common diseases, almost all of which have a genetic component. A recent example of the way that the HGP and the knowledge and new technologies it has spawned are already facilitating science is the extremely rapid sequencing by groups in Canada and at the Centers for Disease Control and Prevention (CDC) in Atlanta of the genome of the virus that causes Severe Acute Respiratory Syndrome (SARS). The sequencing of the SARS virus genome provides insight into this new and deadly disease at a speed never before possible in science. In turn, this should lead to the rapid development of diagnostic tests and, in time, vaccines and effective treatments.

Links for the addition material available on Net

Genomes and genomics:

Bioinformatics and Genomics:

Structural genomics tutorial:

Comparative Genomics Tutorial:

GENOME TUTORIAL:

Tools and resources for identifying protein families, domains and motifs

Bioinformatics Tools
Tips, Tutorials, and Terminology for Using Selected Resources in Genome Database Guide:

A Web-Based Comparative Genomics Tutorial for Investigating Microbial Genomes:

Free Online Tutorials Teach Anyone How to Use Genome Databases:

Circos to create concise, explanatory, unique and print-ready visualizations of your data:

Genomics and Comparative Genomics Learning Module:

Computational Challenges in Comparative Genomics

A Tutorial:

A Comparative Genomics Resource for Grains:

PLAZA: A Comparative Genomics Resource to Study Gene and Genome Evolution in Plants:

VISTA :

Software for Genomics

Artemis Artemis is a free genome viewer and annotation tool that allows visualization of sequence features and the results of analyses within the context of the sequence, and its six-frame translation.
Chromas It will display and prints chromatogram files from ABI automated DNA sequencers, and Staden SCF files which the analysis programs for ALF, Li-Cor and Visible Genetics OpenGene sequencers can create.
Glimmer A system for finding genes in microbial DNA, especially the genomes of bacteria and archaea.Glimmer (Gene Locator and Interpolated Markov Modeler) uses interpolated Markov models (IMMs) to identify the coding regions and distinguish them from noncoding DN
Glimmer HMM A fast and accurate gene finder based on a GHMM architecture, developed specifically for eukaryotes. It incorporates splice site models adapted from the GeneSplicer program and uses interpolated Markov models for evaluating the coding regions.
Glimmer M A gene finder derived from Glimmer, but developed specifically for eukaryotes. It is based on a dynamic programming algorithm that considers all combinations of possible exons for inclusion in a gene model and chooses the best of these combinations. The d
MUMmer MUMmer is a system for rapidly aligning entire genomes, whether in complete or draft form.
pDRAW pDRAW32 is being developed as a free time hobby project. It is far from finished, but as it has reached a point where it could be helpful for many labs, it is now available to the scientific community.
Sequin Sequin is a stand-alone software tool developed by the NCBI for submitting and updating entries to the GenBank, EMBL, or DDBJ sequence databases. It is capable of handling simple submissions that contain a single short mRNA sequence, and complex submissio
Staden The Staden Package consists of a series of tools for DNA sequence preparation (pregap4), assembly (gap4), editing (gap4) and DNA/protein sequence analysis (spin).

For more software @ http://bioinformaticsonline.com/bookmarks/view/926/list-of-popular-bioinformatics-softwaretools

Personalised Medicine - Animation

Tue, 27 Aug 2013 10:07:24 -0500

Two animated case scenarios set now and in the future. These highlight potential differences in the way patients are treated now, and how they might be treated as healthcare becomes more tailored.

List of pharmacogenomics companies in India

Jitendra Narayan — Fri, 09 Aug 2013 13:26:56 -0500

pharmacogenomics companies in India are making their good impacts. Here is the list of few pharmacogenomics companies. Please add more if not mentioned here.

Genomics in India
www.ganitlabs.in
www.sandor.co.in
www.igib.res.in
www.genotypic.co.in
www.ocimumbio.com
www.abcgenomics.com
www.xcelrisgenomics.com
www.ayugen.com
www.geneombiotech.com

IBL laboratory

Mon, 12 Aug 2013 02:02:29 -0500

The IBL laboratory focuses on the multi-disciplinary analyses of the global responses of model microorganisms, cyanobacteria (mainly Synechocystis PCC6803) and yeasts (mainly Saccharomyces cerevisae) to environmental stresses triggered by oxidative agents, heavy metals, or drastic changes in nutrients availability. The genome-wide responses studied with the "omics" techniques (transcriptomics, proteomics, metabolomics and genetics) generate a wealth of experimental data, which are processed, archived, integrated and represented as working models through bioinformatics and mathematics.

Link : http://www-dsv.cea.fr/en/instituts/institut-de-biologie-et-de-technologies-de-saclay-ibitec-s/unites-de-recherche/service-de-biologie-integrative-et-genetique-moleculaire-sbigem/laboratoire-de-biologie-integrative-lbi/presentation__1

Cancer's origins revealed

Jitendra Narayan — Thu, 15 Aug 2013 13:06:56 -0500

Researchers have provided the first comprehensive compendium of mutational processes that drive tumour development. Together, these mutational processes explain most mutations found in 30 of the most common cancer types. This new understanding of cancer development could help to treat and prevent a wide-range of cancers.

More at >> http://www.sanger.ac.uk/about/press/2013/130814.html