BOL: Related items

List of GOI approved peer reviewed bioinformatics and computational biology journals

Jit — Tue, 25 Apr 2017 05:03:27 -0500

Unfortunately, we now live in a world where the integrity of peer-reviewed journals is being threatened by the rise of the academic version of fake news – something many call “predatory publishing". Mostly in academic publishing world, "predatory open access publishing" is an exploitative open-access publishing business model that involves charging publication fees to authors without providing the editorial and publishing services associated with legitimate journals (open access or not).

Nearly 20% of the such journals have a flashy impact factor and quick publication time, which are quick give-aways. Interestingly, under contact address, some journal websites do not even provide any address to contact. All of this has led to the emergence of a new and dark market of deceptive publishers that exploit the concept of open access and provide channels for “scientific journal” publication with little or no peer review. For a fee, they will publish almost anything – even if the study was fatally flawed. And these journals provide a forum that can be used as a channel to publish fraudulent “advocacy research.” You can find list of certain such publishers at "Beall's List" http://beallslist.weebly.com/

Keeping all these in mind, Government of India (GOI) decided to approved certain bioinformatics and computational biology journals for your research publication.

Following are the list of GOI validated and peer reviewed bioinformatics and computational biology journals:

NOTE:Each journal details are in following order Tittle\nSource\nSubject.
Point to remember: The list of journals are NOT sorted in any ascending or descending order.

If I missed any other GOI validated bioinformatics journal, then please report me in comment section.

Open Bioinformatics Journal
Scopus
Computer Science; Engineering; Medicine

PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS
WoS
BIOLOGY & BIOCHEMISTRY

Advances and Applications in Bioinformatics and Chemistry
Scopus
Biochemistry, Genetics and Molecular Biology Chemistry; Computer Science

Advances in Bioinformatics
Scopus
Biochemistry, Genetics and Molecular Biology; Computer Science; Engineering

Applied Bioinformatics
Scopus
Agricultural and Biological Sciences; Computer Science

BIOINFORMATICS
WoS & Scopus
COMPUTER SCIENCE

Bioinformatics and Biology Insights
Scopus
Biochemistry, Genetics and Molecular Biology; Computer Science; Mathematics

BMC BIOINFORMATICS
WoS & Scopus
COMPUTER SCIENCE

BRIEFINGS IN BIOINFORMATICS
WoS & Scopus
COMPUTER SCIENCE

Computational systems bioinformatics / Life Sciences Society. Computational Systems Bioinformatics Conference
Scopus
Medicine

Current Bioinformatics
WoS & Scopus
COMPUTER SCIENCE

Current Protocols in Bioinformatics
Scopus
Biochemistry, Genetics and Molecular Biology

JOURNAL OF COMPUTATIONAL INTELLIGENCE IN BIOINFORMATICS
ICI
BIOLOGICAL SCIENCE

Journal of integrative bioinformatics
Scopus
Medicine

Journal of Proteomics and Bioinformatics
Scopus
Biochemistry, Genetics and Molecular Biology; Computer Science

Mathematical Biology and Bioinformatics
Scopus
Engineering; Mathematics

Trends in Bioinfprmatics
Scopus
Computer Science

Eurasip Journal on Bioinformatics and Systems Biology
Scopus
General; Computer Science; Mathematics; Medicine

Evolutionary Bioinformatics
WoS & Scopus
COMPUTER SCIENCE

Genomics, Proteomics and Bioinformatics
Scopus
Biochemistry, Genetics and Molecular Biology;Mathematics

IEEE/ACM Transactions on Computational Biology and Bioinformatics
Scopus
Biochemistry, Genetics and Molecular Biology;Mathematics

IEEE-ACM Transactions on Computational Biology and Bioinformatics
WoS
COMPUTER SCIENCE

International Journal of Bioinformatics Research and Application
Scopus
Biochemistry, Genetics and Molecular Biology; Medicine, Health

International Journal o f Data M ining and Bioinformatics
WoS & Scopus
COMPUTER SCIENCE

IPSJ Transactions on Bioinformatics
Scopus
Biochemistry, Genetics and Molecular Biology;Computer Science

Journal of Bioinformatics and Computational Biology
WoS & Scopus
COMPUTER SCIENCE

Journal of Clinical Bioinformatics
Scopus
Medicine

PLoS Computational Biology
WoS & Scopus
BIOLOGY & BIOCHEMISTRY

Reviews in Computational Chemistry
WoS & Scopus
CHEMISTRY

RSC Theoretical and Computational Chemistry Series
Scopus
Chemistry; Computer Science

Annual Reports in Computational Chemistry
Scopus
Chemistry; Mathematics

Computational and Structural Biotechnology Journal
Scopus
Biochemistry, Genetics and Molecular Biology; Computer Science

Computational and Theoretical Chemistry
WoS & Scopus
CHEMISTRY

COMPUTATIONAL BIOLOGY AND CHEMISTRY
WoS & Scopus
COMPUTER SCIENCE

COMPUTATIONAL CHEMISTRY
WoS
CHEMISTRY

Journal of Theoretical and Computational Chemistry
Scopus
Chemistry; Computer Science

Theoretical and Computational Chemistry
Scopus
Chemistry

Wiley Interdisciplinary Reviews: Computational Molecular Science
Scopus
Biochemistry, Genetics and Molecular Biology;Chemistry; Computer Science; Materials Science; Mathematics

Wiley Interdisciplinary Reviews- Computational Molecular Science
WoS
CHEMISTRY

Interdisciplinary sciences, computational life sciences
Scopus
Medicine

Interdisciplinary Sciences-Computational Life Science
WoS
Biology and Biochemistry

International Journal of Computational Biology and Drug Design
Scopus
Computer Science; Pharmacology, Toxicology and Pharmaceutics

Senior Scientist Computational Biology at NIPGR

Sun, 19 Jul 2020 23:30:04 -0500

Senior Scientist Computational Biology
Level 13

₹ 1,66,378 (Consolidated)

(UR)

Ph.D. in the area of Computational Biology/Bioinformatics/Biotechnology/Life Sciences with at least 6 years of relevant experience.
OR
M. Tech with 8 years of relevant experience.

The relevant experience shall be in the area of sequencing/genome assembly and annotation and high throughput genotyping for facilitating Genomic assisted Breeding
Age: Not exceeding 50 years

• The incumbent will assist the Programme Director of the Facility to discharge various activities of the NGGF

• Co-ordination with the service provider, DBT/academic institutions/anchoring institute (NIPGR) for execution of activities of the Facility.

• The incumbent will be expected to identify the requirements of Private Sector and Government laboratories in the area of Marker assisted selection and develop linkages to facilitate the same.

• Interact with multiple stake holders including Government and Private Sector in the area of agriculture Biotechnology.

• Oversee the establishment of relevant Standard Operational Procedures (SOP), Quality Accreditation of Genomics and Genotyping facility.

More at http://www.nipgr.ac.in/careers/vacancies_latest.php#vacancy2

3 PhD positions available in the area of Bioinformatics/Computational Biology at ulster.ac.uk

Thu, 02 Jan 2020 12:41:10 -0600

3 PhD positions available in the area of Bioinformatics/Computational Biology, Machine Learning (ML)/Artificial Intelligence (AI), Biomarker Discovery, Stratified/Personalized Medicine in Mental Health, Diabetes and Multimorbidity. Please see details (weblinks) below:

1. https://www.ulster.ac.uk/doctoralcollege/find-a-phd/510894
2. https://www.ulster.ac.uk/doctoralcollege/find-a-phd/511458
3. https://www.ulster.ac.uk/doctoralcollege/find-a-phd/512618

Looking for students with good computational/programming skills (preferable in Linux/Shell, Python and/or R) and knowledge in computational biology and statistics. However, students from more biology oriented background but strong interest to learn bioinformatics and programming are also encouraged to apply.

Informal inquiries are welcomed at: p.shukla@ulster.ac.uk

Dr Priyank Shukla PhD FHEA FCHERP
Lecturer (Asst Prof) in Stratified Medicine (Bioinformatics)

Northern Ireland Centre for Stratified Medicine
Biomedical Sciences Research Institute
University of Ulster (Magee Campus)
C-TRIC Building, Altnagelvin Area Hospital
Glenshane Road, Derry/Londonderry
BT47 6SB, Northern Ireland, United Kingdom

T: +44 28 7167 5690
E: p.shukla@ulster.ac.uk
W: https://www.ulster.ac.uk/staff/p-shukla

A computational postdoc position and a bioinformatician position

Thu, 18 Jan 2018 16:29:42 -0600

A computational postdoc position and a bioinformatician position are available in Alessandro Romanel's Lab recently established at the Centre for Integrative Biology (CIBIO) in Trento, Italy. The positions are in the context of an AIRC grant and are immediately available.

Successful candidates will be involved in the design and implementation of strategies to study the role of inherited polymorphisms in combination with timedependent variables and somatic events on cancer genesis, progression and resistance.
The ideal postdoc candidate will have a PhD in Computer Science, Bioinformatics, Computational Biology or equivalent, experience in the analysis of next generation sequencing and high-density array data from human cells, strong analytical and quantitative background and programming skills. Background in cancer genomics is recommended.
The ideal bioinformatician candidate will have a four or five years degree in Computer Science, Bioinformatics or equivalent, experience in the management of large datasets, implementation of processing pipelines and strong programming skills. Background in biology/genomics is a plus.
Highly motivated individuals are invited to send a detailed CV, a cover letter describing research interests and experience, and contact information for two references to Alessandro Romanel (alessandro.romanel@unitn.it).

Liu Lab

Tue, 04 Feb 2020 06:27:02 -0600

Shirley is a computational biologist with expertise in cancer epigenetics. Her research focuses on algorithm development and integrative mining from big data generated on microarrays, massively parallel sequencing, and other high throughput techniques to model the specificity and function of transcription factors, chromatin regulators and lncRNAs in tumor development, progression, drug response and resistance.

https://liulab-dfci.github.io/software/

NgAgo challenge CRISPR !!

Abhimanyu Singh — Tue, 17 May 2016 03:31:32 -0500

A recent Nature Biotechnology paper from Chunyu Han’s lab, DNA-guided genome editing using the Natronobacterium gregoryi Argonaute, is a must-read for genome editing folks who want to learn about NgAgo. Their team sums up NgAgo’s potential pluses this way (emphasis mine):

“The useful features of NgAgo for genome editing include the following.First, it has a low tolerance to guide–target mismatch. A single nucleotide mismatch at each position of the gDNA impaired the cleavage efficiency of NgAgo, and mismatches at three positions completely blocked cleavage in our experiments. Second, 5′ phosphorylated short ssDNAs are rare in mammalian cells, which minimizes the possibility of cellular oligonucleotides misguiding NgAgo.Third, NgAgo follows a ‘one-guide-faithful’ rule, that is, a guide can only be loaded when NgAgo protein is in the process of expression, and, once loaded, NgAgo cannot swap its gDNA with other free ssDNA at 37 °C. All of these features could minimize off-target effects. Finally, it is easy to design and synthesize ssDNAs and to adjust their concentration, which is difficult with the Cas9-sgRNA system, if the sgRNA is expressed from a plasmid and the normal dosage of an ssDNA guide is only ~1/10 of that of a sgRNA expression plasmid.

NgAgo might be a more orderly way and perhaps even simpler way to go about genome editing than CRISPR, but the jury is still out on that until there are more papers and data. The NgAgo edit efficiency at this preliminary stage of technology development seems very strong. See the pics below

Reference: http://www.nature.com/nbt/journal/vaop/ncurrent/full/nbt.3547.html

320000 viruses in mammals yet to sequenced in future!!!

Rahul Agarwal — Tue, 03 Sep 2013 08:35:30 -0500

With current biological technique improvements, finally it is now possible to look at millions of unknown viruses at genomic level and understand the mechanism. According to available data, close to 70 per cent of emerging viral diseases such as HIV/AIDS, West Nile, Ebola, SARS, and influenza, are zoonoses - infections of animals that cross into humans.

To address the challenges of describing and estimating virodiversity, a team of investigators from Center for Infection and Immunity (CII) and EcoHealth Alliance began in jungles of Bangladesh - home to the flying fox.

Reference:

http://economictimes.indiatimes.com/news/news-by-industry/et-cetera/mammals-harbour-at-least-320000-new-viruses/articleshow/22253268.cms

http://www.bbc.co.uk/news/science-environment-23932400

The Graveley Lab

Tue, 19 Nov 2013 18:02:48 -0600

Research in the Graveley lab is primarily focused on the regulation of alternative splicing and small RNA mediated gene regulation. These are fascinating and extraordinarily important mechanisms by which genes can be regulated. Our long-term goals are to understand how these processes are regulated at a mechanistic level and to understand the logic of these processes in significant biological settings. To achieve these goals, we strive to think outside the box to creatively attack the problems being addressed using a wide variety of approaches that include biochemistry, genetics, imaging, deep sequencing, large-scale RNAi screening and bioinformatics.

Lab page @ http://graveleylab.cam.uchc.edu/Graveley/index.html

Genetic code - Amino Acid

Poonam Mahapatra — Sun, 26 Oct 2014 07:45:58 -0500

The genetic code consists of 64 triplets of nucleotides. These triplets are called codons.With three exceptions, each codon encodes for one of the 20 amino acids used in the synthesis of proteins. That produces some redundancy in the code: most of the amino acids being encoded by more than one codon.

The image summarise all in one.

More at http://users.rcn.com/jkimball.ma.ultranet/BiologyPages/C/Codons.html

R-chie

Jit — Thu, 01 Sep 2016 11:47:24 -0500

R-chie allows you to make arc diagrams of RNA secondary structures, allowing for easy comparison and overlap of two structures, rank and display basepairs in colour and to also visualize corresponding multiple sequence alignments and co-variation information.
R4RNA is the R package powering R-chie, available for download and local use for more customized figures and scripting.

http://www.e-rna.org/r-chie/plot.cgi?eg=single

Address of the bookmark: http://www.e-rna.org/r-chie/plot.cgi?eg=single