http://lin-group.cn/server/iRNAD/

Address of the bookmark: http://lin-group.cn/server/iRNAD/

Biocon, India's largest publicly-held biotechnology firm, launched its second novel 'lab-to-market' molecule, Alzumab, to treat chronic plaque psoriasis at a cost 50 per cent lower than the existing one.

Biocon is bringing Alzumab (a biologic) in the form of a vial after working on it for nearly a decade. The work had initially started in a joint effort with the Center of Molecular Immunology, Havana, but Biocon took control of the programme soon after and also bought out its partner a few years ago. Biocon tell to the media that genotypic played a critical role in functional studies and clinical trial Genomics.

The Biocon drug, at around ₹ 7,500 a vial, will cost half as much as the currently available drugs - from Pfizer and J&J - to treat psoriasis, a skin disease that causes rough red areas where the skin comes off in small pieces. A patient is usually prescribed to consume more than 40 vials in a 24-week course.

Address of the bookmark: http://www.gigasciencejournal.com/content/2/1/15?utm_content=buffer25ee0&utm_medium=social&utm_source=twitter.com&utm_campaign=buffer

More @ http://www.ncbs.res.in/sowdhamini/groups_sowdhamini.htm

De Bruijn Graphs for NGS Assembly
Algorithms for PacBio Reads
Software and Hardware Concepts for Bioinformatics
Finding us in Homolog.us (Search Algorithms)
NGS Genome and RNAseq Assembly - a Hands on Primer
Introduction to PERL, Python, R and C/C++ for Bioinformatics

Address of the bookmark: http://www.homolog.us/Tutorials/

Reference

Cuccuru G1, Orsini M, Pinna A, Sbardellati A, Soranzo N, Travaglione A, Uva P, Zanetti G, Fotia G. (2014) Orione, a web-based framework for NGS analysis in microbiology. Bioinformatics [Epub ahead of print]. [article]

Address of the bookmark: http://orione.crs4.it/

Stay at home if you have coronavirus symptoms

Stay at home if you have either:

• a high temperature – you feel hot to touch on your chest or back
• a new, continuous cough – this means you've started coughing repeatedly

DO NOT TAKE

Ibrufen

https://amp.theguardian.com/world/2020/mar/14/anti-inflammatory-drugs-may-aggravate-coronavirus-infection

How to avoid catching and spreading coronavirus (social distancing)

Everyone should do what they can to stop coronavirus spreading.

It is particularly important for people who:

• are 70 or over
• have a long-term condition
• are pregnant
• have a weakened immune system

Below are the 52 Coronavirus COVID-19 Testing sites/locations in India.

State: Andhra Pradesh       

1. Sri Venkateswara Institute of Medical Sciences, Tirupati
2. Andhra Medical College, Visakhapatnam, Andhra Pradesh
3. GMC, Anantapur, AP

State: Andaman & Nicobar islands

1. Regional Medical Research Centre, Port Blair, Andaman, and Nicobar

State: Assam

1. Gauhati Medical College, Guwahati
2.  Regional Medical Research Center, Dibrugarh

State: Bihar

1. Rajendra Memorial Research Institute of Medical Sciences, Patna

State: Chandigarh

1. Post Graduate Institute of Medical Education & Research, Chandigarh

State: Chhattisgarh

1. All India Institute Medical Sciences, Raipur

Union Territory: Delhi-NCT 

1. All India Institute Medical Sciences, Delhi
2. National Centre for Disease Control, Delhi

State: Gujarat

1. BJ Medical College, Ahmedabad
2. M.P.Shah Government Medical College, Jamnagar

State: Haryana

1. Pt. B.D. Sharma Post Graduate Inst. of Med. Sciences, Rohtak, Haryana
2. BPS Govt Medical College, Sonipat

State: Himachal Pradesh

1. Indira Gandhi Medical College, Shimla, Himachal Pradesh
2. Dr.Rajendra Prasad Govt. Med. College, Kangra, Tanda, HP

Union Territory: Jammu and Kashmir

1. Sher‐e‐ Kashmir Institute of Medical Sciences, Srinagar
2. Government Medical College, Jammu

State: Jharkhand

1. MGM Medical College, Jamshedpur

State: Karnataka

1. Bangalore Medical College & Research Institute, Bangalore
2. National Institute of Virology Field Unit Bangalore
3. Mysore Medical College & Research Institute, Mysore
4. Hassan Inst. of Med. Sciences, Hassan, Karnataka
5. Shimoga Inst. of Med. Sciences, Shivamogga, Karnataka

State: Kerala

1. National Institute of Virology Field Unit, Kerala
2. Govt. Medical College, Thiruvananthapuram, Kerala
3. Govt. Medical College, Kozhikode, Kerala

State: Madhya Pradesh

1. All India Institute Medical Sciences, Bhopal
2. National Institute of Research in Tribal Health (NIRTH), Jabalpur

State: Meghalaya

1. NEIGRI of Health and Medical Sciences, Shillong, Meghalaya

State: Maharashtra

1. Indira Gandhi Government Medical College, Nagpur
2. Kasturba Hospital for Infectious Diseases, Mumbai

State: Manipur

1. J N Inst. of Med. Sciences Hospital, Imphal‐East, Manipur

State: Odisha

1. Regional Medical Research Center, Bhubaneswar

Union Territory: Puducherry

1. Jawaharlal Institute of Postgraduate Medical Education & Research, Puducherry

State: Punjab

1. Government Medical College, Patiala, Punjab
2. Government Medical College, Amritsar

State: Rajasthan

1. Sawai Man Singh, Jaipur
2. Dr. S.N Medical College, Jodhpur
3. Jhalawar Medical College, Jhalawar, Rajasthan
4. SP Med. College, Bikaner, Rajasthan

State: Tamil Nadu

1. King’s Institute of Preventive Medicine & Research, Chennai
2. Government Medical College, Theni

State: Tripura

1. Government Medical College, Agartala

State: Telangana

1. Gandhi Medical College, Secunderabad

State: Uttar Pradesh

1. King’s George Medical University, Lucknow
2. Institute of Medical Sciences, Banaras, Hindu University, Varanasi
3. Jawaharlal Nehru Medical College, Aligarh

State: Uttarakhand

1. Government Medical College, Haldwani

State: West Bengal

1. National Institute of Cholera and Enteric Diseases, Kolkata
2. IPGMER, Kolkata

Most people who have a balanced translocation have the right amount of chromosome material but it has been rearranged in some way. This may happen if two chromosomes swap pieces (a reciprocal translocation). In other cases two whole chromosomes may become stuck together (a Robertsonian translocation). This page describes what happens when someone has a reciprocal translocation.

Reciprocal chromosomal translocations occur following double-strand breaks (DSBs) in DNA when a section of one chromosome is exchanged with that of another, non-homologous chromosome. These exchanges may produce a dysfunctional fusion gene that disrupts cell growth and survival pathways, such as the translocations seen in leukemia and childhood sarcomas.

Chromosomal translocations have been well studied in cancer cell lines which are associated with two types of cancer, acute myeloid leukemia and Ewing's sarcoma, but determining how they contribute to cancer development is complicated by additional mutations and altered gene expression profiles in these cultured cells. Now, Juan Carlos Ramirez, head of the Viral Vector Facility at the Fundacion Centro Nacional de Investigaciones Cardiovasculares (CNIC) and his colleagues Raul Torres at CNIC and Sandra Rodriguez-Peralez at the Spanish National Cancer Center (CNIO) in Madrid, Spain have used a new genome editing tool, CRISPR-Cas9, to induce chromosomal translocations for the first time in a human cell line and in primary cells. The study's authors conclude by stating that the use of this technology will allow for the clarification of how and why chromosomal translocation occurs, which without doubt will allow new anti-cancer therapeutic strategies to be tackled.

Using RNA-Guided Endonuclease (RGEN) technology or CRISPR/Cas9 genome engineering technology, CNIO and CNIC researchers have shown that it is possible to obtain such chromosomal translocations. The CRISPR-Cas9 system is extremely simple to introduce a cut at the desired locus, easier to design, and cheaper than many other systems. Using the CRISPR-Cas9 system, Ramirez and his colleagues reproduced the translocations observed in Ewing’s Sarcoma (ES) and Acute Myeloid Leukemia (AML) patient cell lines in HEK293 cells and also generated the ES translocation in human mesenchymal stem cells and the AML translocation in umbilical cord blood cells.

By focusing on chromosomal translocation without the confounding characteristics of established cell lines, these new cells lines should help answer the fundamental question of what causes a cell to become cancerous. Ramirez and his team now look forward to modeling other chromosome translocations in a variety of cell types.

Reference:

http://en.wikipedia.org/wiki/Chromosomal_translocation

http://www.nature.com/ncomms/2014/140603/ncomms4964/abs/ncomms4964.html

Following are the list of journals publishing pint-sized articles go by various names, such as genome reports, genome announcements, genome notes or genome letters, but will be referred to here broadly as genome reports.

1. Genome Announcements, American Society for Microbiology, Genome announcement, Impact factor 1.3,  A 500-word report stating that the genome of a particular organism (prokaryote, eukaryote or virus) has been sequenced and providing a citable record of the corresponding GenBank submission. Must include abstract but no text headings can be used except for ‘Acknowledgments’ and ‘References’. Cannot include figures, tables or supplemental material to present data or analysis.

Link: https://mra.asm.org/

2. Genome Biology and Evolution, Oxford University Press, Genome report, Impact factor 4.2, Focused 1500-word papers (up to six tables or figures) that publish the main evolutionary message of new genome sequences as they become submitted to GenBank. May also contain specifically focused comparative analyses of previously published genomes that contain a substantial and novel insight of broadest evolutionary significance.

Link: https://academic.oup.com/gbe

3. Journal of Biotechnology, Elsevier, Genome announcement, Impact factor 2.9, A 500-word report announcing the availability of the completely annotated genome sequence of a biotechnologically relevant organism in the corresponding database (for eukaryotes, advanced draft genomes will also be considered). Articles can contain an Abstract, a brief report on the organism and its biotechnological relevance, a table summarizing the genome features, References and an Acknowledgement. Figures are generally not allowed.

Link: https://www.journals.elsevier.com/journal-of-biotechnology

4. Journal of Genomics, Ivyspring, Genome note, Impact factor N/A, A 1000-word report (10 reference limit; conclusions not permitted) describing novel data sets from high-throughput analysis of genotypes, phenotypes, gene expression, metabolomes, proteomes or genome assemblies.Standard metrics for data quality and the experimental design must be clearly reported.

Link: http://www.jgenomics.com/

5. Memórias do Instituto, Oswaldo Cruz Oswaldo Cruz Foundation, Genome announcement and highlight, Impact factor 1.6, Dedicated to publishing new genome information from eukaryote parasites, virus, bacteria and their respective vectors, as well as re-sequencing or comparative genome analyses. Should occupy no more than three printed pages including figures and/or tables.

Link: http://memorias.ioc.fiocruz.br/

6. Molecular Ecology Resources, Wiley, Genomic resources note,  Impact factor 3.7, Short notes on newly assembled and annotated transcriptomes, genome fractions or whole genomes, and/or a library of SNP/SSR markers.Authors submit a short manuscript describing how the resource was developed and where the data can be accessed. Do not appear in journal as individual papers but are instead published as part of a summary article.

Link: https://onlinelibrary.wiley.com/journal/17550998

7. Standards in Genomic Science, BioMed Central (Springer), Short genome report, Impact factor 3.2, Short (∼500-word) article on newly sequenced genome. Article format must follow guidelines and template (available from journal Web site) put forward by the SGS. Any manuscripts not using template or that are missing key figures, tables and/or references (as per the guidelines) will be returned to authors. Rationale of the content model is to provide information that is consistently and uniformly presented for rapid and easy consumption by both human and machine readers. 

Link: https://standardsingenomics.biomedcentral.com/

8. 3biotech, Springer, Short genome report, Impact factor 1.3, Short (∼500-word) article on newly sequenced genome. Article format must follow guidelines (available from journal Web site).  Genome of a particular organism (prokaryote, eukaryote or virus) has been sequenced and providing a citable record of the corresponding GenBank submission.

Link: https://link.springer.com/journal/13205

Following are the comprehensive list of visualization tools for biological pathways:

BiNA

Drawings of metabolic networks supporting hiding of cofactors and drawing of chemical structures

http://bina.unipax.info/

BioTapestry

Interactive tool for building, visualizing and sharing gene regulatory network models over the web

http://www.biotapestry.org/

Caleydo

Visual analysis framework targeted at biomolecular data. Visualization of interdependencies between multiple datasets

http://www.caleydo.org/

CellDesigner

A modeling tool for biochemical networks

http://www.celldesigner.org/

Edinburgh Pathway Editor

Edit and draw pathway diagrams

http://epe.sourceforge.net/SourceForge/EPE.html

GenMAPP

Visualization of gene expression and other genomic data on maps representing biological pathways and groupings of genes

http://www.genmapp.org/

Ingenuity IPA

Data integration platform and manually annotated pathways

http://tinyurl.com/IngenuityPath

JDesigner

Graphical modeling environment for biochemical reaction networks

http://jdesigner.sourceforge.net/Site/JDesigner.html

KaPPA View

Plant pathways

http://kpv.kazusa.or.jp/

KEGG Atlas

Interactive Kyoto Encyclopedia of Genes and Genomes pathways

http://www.genome.jp/kegg/

Omix 

Visualizing multi-omics data in metabolic networks

https://www.omix-visualization.com

PathVisio 

Biological pathway analysis software that allows drawing, editing and analysis of biological pathways

http://www.pathvisio.org/

VitaPad 

Application to visualize biological pathways and map experimental data to them

http://tinyurl.com/vitapad/

Web tools for pathways

ArrayXPath 

Mapping and visualizing microarray gene-expression data and integrated biological pathway resources using SVG

http://tinyurl.com/ArrayXPath/

GEPAT 

Integrated analysis of transcriptome data in genomic, proteomic and metabolic contexts

http://gepat.sourceforge.net/

iPath 

Web-based tool for the visualization, analysis and customization of pathway maps

http://pathways.embl.de/

Kegg-Based Viewer 

KEGG-based pathway visualization tool for complex high-throughput data

http://www.g-language.org/data/marray/

MapMan 

User-driven tool that displays large datasets onto diagrams of metabolic pathways or other processes

http://mapman.gabipd.org/web/guest/mapman

MetPA 

Analysis and visualization of metabolomic data within the biological context of metabolic pathways

http://metpa.metabolomics.ca

Omics Viewer 

Data mapping on BioCyc pathways (collection of 5500 pathway/genome databases)

http://www.biocyc.org/

Pathway Explorer

Interactive Java drawing tool for the construction of biological pathway diagrams in a visual way and the annotation of the components and interactions between them

http://genome.tugraz.at/pathwayexplorer/pathwayexplorer_description.shtml

Pathway projector 

Zoomable pathway browser using KEGG atlas and Google Maps API

http://www.g-language.org/PathwayProjector/

PATIKA 

Integrated environment composed of a central database and a visual editor, built around an extensive ontology and an integration framework

http://www.cs.bilkent.edu.tr/~patikaweb/

Reactome SkyPainter 

Visualization of over-represented pathways and reactions from gene lists

http://www.reactome.org/skypainter-2

WikiPathways

Wiki-based, open, public platform dedicated to the curation of biological pathways by and for the scientific community

http://www.wikipathways.org/