<![CDATA[BOL: Related items]]> https://bioinformaticsonline.com/related/39372?offset=140 https://bioinformaticsonline.com/bookmarks/view/41916/truvari-structural-variant-comparison-tool-for-vcfs Tue, 30 Jun 2020 21:30:44 -0500 https://bioinformaticsonline.com/bookmarks/view/41916/truvari-structural-variant-comparison-tool-for-vcfs <![CDATA[truvari: Structural variant comparison tool for VCFs]]> Structural variant comparison tool for VCFs

Given benchmark and comparsion sets of SVs, calculate the recall, precision, and f-measure.

Spiral Genetics

Motivation

Address of the bookmark: https://github.com/spiralgenetics/truvari

]]> Jit https://bioinformaticsonline.com/bookmarks/view/42155/clustergrammer-is-a-web-based-tool-for-visualizing-high-dimensional-data-as-an-interactive-and-shareable-hierarchically-clustered-heatmap Sun, 23 Aug 2020 19:30:17 -0500 https://bioinformaticsonline.com/bookmarks/view/42155/clustergrammer-is-a-web-based-tool-for-visualizing-high-dimensional-data-as-an-interactive-and-shareable-hierarchically-clustered-heatmap <![CDATA[Clustergrammer is a web-based tool for visualizing high-dimensional data as an interactive and shareable hierarchically clustered heatmap]]> Clustergrammer is a web-based tool for visualizing high-dimensional data (e.g. a matrix) as an interactive and shareable hierarchically clustered heatmap. Clustergrammer's front end (Clustergrammer-JS) is built using D3.js and its back-end (Clustergrammer-PY) is built using Python. Clustergrammer produces highly interactive visualizations that enable intuitive exploration of high-dimensional data and has several biology-specific features (e.g. enrichment analysis, see Biology-Specific Features) to facilitate the exploration of gene-level biological data. 

Address of the bookmark: https://github.com/MaayanLab/clustergrammer

]]> BioStar https://bioinformaticsonline.com/bookmarks/view/43791/comparative-genomics-visualisation-tools Thu, 17 Feb 2022 05:37:55 -0600 https://bioinformaticsonline.com/bookmarks/view/43791/comparative-genomics-visualisation-tools <![CDATA[Comparative genomics visualisation tools !]]> Comparative genomics visualisation tools !

Address of the bookmark: https://cmdcolin.github.io/awesome-genome-visualization/?latest=true&selected=%23BRIG&tag=Comparative

]]> Neel https://bioinformaticsonline.com/bookmarks/view/44527/alvis-a-tool-for-contig-and-read-alignment-visualisation-and-chimera-detection Wed, 08 May 2024 07:02:55 -0500 https://bioinformaticsonline.com/bookmarks/view/44527/alvis-a-tool-for-contig-and-read-alignment-visualisation-and-chimera-detection <![CDATA[Alvis: a tool for contig and read ALignment VISualisation and chimera detection]]> Alvis, a simple command line tool that can generate visualisations for a number of common alignment analysis tasks. Alvis is a fast and portable tool that accepts input in a variety of alignment formats and will output production ready vector images. Additionally, Alvis will highlight potentially chimeric reads or contigs, a common source of misassemblies.

More at https://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-021-04056-0

Address of the bookmark: https://github.com/SR-Martin/alvis

]]> LEGE https://bioinformaticsonline.com/bookmarks/view/44655/ngenomesyn-an-easy-to-use-and-flexible-tool-for-publication-ready-visualization-of-syntenic-relationships-across-multiple-genomes Tue, 10 Sep 2024 04:54:55 -0500 https://bioinformaticsonline.com/bookmarks/view/44655/ngenomesyn-an-easy-to-use-and-flexible-tool-for-publication-ready-visualization-of-syntenic-relationships-across-multiple-genomes <![CDATA[NGenomeSyn: an easy-to-use and flexible tool for publication-ready visualization of syntenic relationships across multiple genomes]]> NGenomeSyn: an easy-to-use and flexible tool for publication-ready visualization of syntenic relationships across multiple genomes 

image

NGenomeSyn [multiple (N) Genome Synteny], for publication-ready visualization of syntenic relationships of the whole genome or local region and genomic features (e.g. repeats, structural variations, genes) across multiple genomes with a high customization. NGenomeSyn provides an easy way for its users to visualize a large amount of data with a rich layout by simply adjusting options for moving, scaling, and rotation of target genomes. Moreover, NGenomeSyn could be applied on the visualization of relationships on non-genomic data with similar input formats.

https://academic.oup.com/bioinformatics/article/39/3/btad121/7072460

Address of the bookmark: https://github.com/hewm2008/NGenomeSyn

]]> LEGE https://bioinformaticsonline.com/blog/view/32358/list-of-goi-approved-peer-reviewed-bioinformatics-and-computational-biology-journals Tue, 25 Apr 2017 05:03:27 -0500 https://bioinformaticsonline.com/blog/view/32358/list-of-goi-approved-peer-reviewed-bioinformatics-and-computational-biology-journals <![CDATA[List of GOI approved peer reviewed bioinformatics and computational biology journals]]> 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

]]> Jit https://bioinformaticsonline.com/opportunity/view/41978/senior-scientist-computational-biology-at-nipgr Sun, 19 Jul 2020 23:30:04 -0500 <![CDATA[Senior Scientist Computational Biology at NIPGR]]> Senior Scientist Computational Biology
Level 13

₹ 1,66,378 (Consolidated)

01

(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

]]> https://bioinformaticsonline.com/opportunity/view/40503/3-phd-positions-available-in-the-area-of-bioinformaticscomputational-biology-at-ulsteracuk Thu, 02 Jan 2020 12:41:10 -0600 <![CDATA[3 PhD positions available in the area of Bioinformatics/Computational Biology at ulster.ac.uk]]> 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

]]> https://bioinformaticsonline.com/opportunity/view/35267/a-computational-postdoc-position-and-a-bioinformatician-position Thu, 18 Jan 2018 16:29:42 -0600 <![CDATA[A computational postdoc position and a bioinformatician position]]> 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).

]]> https://bioinformaticsonline.com/researchlabs/view/40881/liu-lab Tue, 04 Feb 2020 06:27:02 -0600 <![CDATA[Liu Lab]]> 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/

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