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This Month in Bioinformatics- Research Updates of October 2021

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Monthly Bioinformatics Research Updates

In this article, we summarize the latest interesting findings made this month in bioinformatics.

1. Mechanistic understanding of the cryptic transmission of SARS-CoV-2 in Europe & USA.

A new study has been published stating the cryptic transmission of SARS-CoV-2 during the first wave in Europe and USA [1]. The authors have implemented a global metapopulation epidemic model to provide the mechanistic understanding behind the spread of SARS-CoV-2 in the two countries. The study has revealed that the SARS-CoV-2 was transmitted in Europe and USA in January 2020 and by early March only 1-3 in 100 infections were detected. This approach complements phylogenetic analyses and other methods to provide insights into the spread of the infection [1].

For more information, read here.

2. New method to predict variant pathogenicity using deep generative models of evolutionary data.

A new method has been developed based on deep generative models of evolutionary data to predict the variant pathogenicity [2]. This method does not rely on labels that are based on machine learning models to avoid biases and insufficient reliability. It performs better than the other state-of-the-art methods and also provides better predictions from high-throughput experiments. The model is freely accessible and available on GitHub.

For more information, read here.

3. New open-source toolkit for genomic data visualization.

A new toolkit called CoolBox is developed for the visual analysis of genomic data [3]. It makes it easy to visualize patterns in a large-scale genomic dataset. CoolBox is an open-source toolkit that is highly compatible with the Python ecosystem. Its plotting system is based on the matplotlib package. CoolBox is implemented in Python and is available for Linux, Windows, and macOS operating systems. CoolBox can be downloaded from GitHub.

For more information, read here.

4. A new software for the discovery of circular RNAs from paired-end RNA sequencing data.

New software is developed for the discovery of circular RNAs from paired-end RNA sequencing data. This tool is called Circall [4]. Circall is highly efficient as it uses a quasi-mapping algorithm for fast and accurate RNA read alignment. It controls false positives by applying a robust multidimensional local false discovery rate method. Circall is written in C++ and R. It is freely available to use at https://www.meb.ki.se/sites/biostatwiki/circall and can be easily downloaded from GitHub.

For more information, read here.

5. New method for compound activity prediction based on binding pocket information.

A new end-to-end learning method is proposed for compound activity based on binding pocket information [5]. This method uses structure information of a binding pocket present in a target protein. It implements end-to-end learning by using a graph neural network to learn the important features for both the compound and the binding pocket structure. The new method showed equivalent accuracy to docking simulation using AutoDock Vina with a much shorter computing time.

For more information, read here.

6. New tool for progressive MSA with Poison indel process.

A new tool called ProPIP [6] is developed that uses the Poison indel process (PIP) to describe insertions and deletions. The tool is developing in a frequentist framework. It is available for Linux, macOS, and Microsoft Windows platforms. The source code is freely available on GitHub.

For more information, read here.


References

  1. Davis, J.T., Chinazzi, M., Perra, N. et al. (2021). Cryptic transmission of SARS-CoV-2 and the first COVID-19 wave. Nature.
  2. Frazer, J., Notin, P., Dias, M. et al. (2021). Disease variant prediction with deep generative models of evolutionary data. Nature.
  3. Xu, W., Zhong, Q., Lin, D. et al. (2021). CoolBox: a flexible toolkit for visual analysis of genomics data. BMC Bioinformatics 22, 489.
  4. Nguyen, D.T., Trac, Q.T., Nguyen, TH. et al. (2021). Circall: fast and accurate methodology for discovery of circular RNAs from paired-end RNA-sequencing data. BMC Bioinformatics 22, 495.
  5. Tanebe, T., Ishida, T. (2021). End-to-end learning for compound activity prediction based on binding pocket information. BMC Bioinformatics 22, 529.
  6. Maiolo, M., Gatti, L., Frei, D. et al. (2021). ProPIP: a tool for progressive multiple sequence alignment with Poisson Indel Process. BMC Bioinformatics 22, 518.

Bioinformatics News

Proteins shape analyses reveal novel forms and connections.

Dr. Muniba Faiza

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Protein shape analyses reveal novel forms and connections.

A new study has revealed new forms of proteins that have never been seen before along with unexpected connections. Last year, Google DeepMind predicted the structure of all known proteins from organisms using AlphaFold [1].

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What is MANE project?

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What is mane project?

MANE is a collaborative project between NCBI and EMBL-EBI. It stands for Matched Annotation from NCBI and EMBL-EBI [1]. The datasets provided by NCBI and EMBL-EBI on the human genome are not identical across every gene.

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This Month in Bioinformatics- Research Updates of March 2022

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This Month in Bioinformatics- Research Updates of March 2022

Here are the latest research developments in the field of bioinformatics made in the month of March 2022. (more…)

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This month in Bioinformatics- Research Updates of November 2021

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This month in Bioinformatics- Research Updates of November 2021

We summarize the latest research published this month in the field of bioinformatics. (more…)

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BLAST+ 2.12.0- A more efficient version of BLAST is available

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BLAST+ 2.12.0- New version

A new more efficient version of BLAST+ 2.12.o is available now [1]. This version provides more efficient multithreaded searches. (more…)

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This Month in Bioinformatics- Research Updates of June 2021

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This Month in Bioinformatics- Research Updates of June 2021

In this article, we summarize the latest interesting findings made this month of June in bioinformatics. (more…)

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This Month in Bioinformatics- Research Updates of May 2021

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This Month in Bioinformatics- Research Updates of May 2021

In this article, we summarize the latest interesting findings made this month in bioinformatics. (more…)

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This Month in Bioinformatics- Research Updates of April 2021

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This Month in Bioinformatics- Research Updates of April 2021

In this article, we summarize the latest interesting findings made this month in bioinformatics. (more…)

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This Month in Bioinformatics- Research Updates of March 2021

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Bioinformatics Monthly Research Updates- March 2021

Here, we summarize the latest interesting findings made this month in bioinformatics. (more…)

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This Month in Bioinformatics- Research Updates of February 2021

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Monthly Research Updates- February 2021

We summarize the research done in bioinformatics in the month of February. (more…)

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This Month in Bioinformatics- Research Updates of January 2021

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This month in Bioinformatics- January 2021

In this article, we summarize the main findings made in bioinformatics this month. (more…)

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This Month in Bioinformatics- Research Updates of December 2020

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This Month in Bioinformatics- Research Updates of December 2020

In this article, we summarize the latest research in bioinformatics published this month. (more…)

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Join Bioinformatics Review Research Group

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We are going to lead a few bioinformatics research projects. For that, we are creating a new research group of Bioinformatics Review. (more…)

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This Month in Bioinformatics- Research Updates of November 2020

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Research updates of bioinformatics- November 2020

In this article, we summarize the latest research in bioinformatics published this month. (more…)

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This Month in Bioinformatics- Research Updates of October 2020

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Some of the important findings made this month in bioinformatics are mentioned in this article. (more…)

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This Month in Bioinformatics: Research Updates of September 2020

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Bioinformatics Monthly updates- September 2020

Some of the important findings made this month in bioinformatics are mentioned in this article. (more…)

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This Month in Bioinformatics: Research Updates of August 2020

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Bioinformatics Research Updates- August 2020

Some of the important findings made this month in bioinformatics are mentioned in this article. (more…)

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This month in Bioinformatics: Research Updates of July 2020

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This month in Bioinformatics

Some of the important findings made this month in bioinformatics are mentioned in this article. (more…)

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Inviting Nominations for ‘Top 5 Bioinformaticians in India 2020’

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Bioinformaticians Awards

Bioinformatics Review compiles a list of top bioinformaticians every two years. We are inviting nominations for the second edition of this award after the 2018 List. We invite you to contribute to this endeavor by nominating your colleague or friends if you think they can make it to our list.

Nominations start from 20th June 2020 till 15th August 2020. All the nominees will be informed via email on 5th September 2020. We use a well-established ranking method called ScipRank. Our data collection is open-source. ScipRank methodology is publicly available for scrutiny.

Also, we are completing 5th year of success in Bioinformatics Review this year. On this occasion, we are organizing an International Conference on Advanced Research in Bioinformatics 2020. The award will be declared at the conclusion of ConARB 2020 –  3 & 4th Oct 2020).

We invite you to contribute to this endeavor by nominating your colleague or friends. You can also submit your papers, which if accepted, can be presented at the conference.

We have set up a dedicated portal for ConARB 2020 accessible here https://conarb.bioinformaticsreview.com.
To attend or to submit your abstract or to nominate someone, kindly visit this website. Accepted papers will be published in a special issue of Bioinformatics Review.

We are looking forward to your continued support, contributions, nominations, and suggestions for the conference as well as your active participation.

 

 

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A workshop on Genome Editing Tools and Techniques

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Department of Biotechnology (DBT), India is organizing a 5-day workshop on CRISPR/Cas mediated genome editing in plants: Applications, tools, and experimental design” to address the strategies and methods involved in genome modification utilized as essential tools in research and development. (more…)

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