Bioinformatics

Robust expansion of phylogeny for fast-growing genome sequence data

1. Yongtao Ye
2. Marcus H. Shum
3. Joseph L. Tsui
4. Guangchuang Yu
5. David K. Smith
6. Huachen Zhu
7. Joseph T. Wu
8. Yi Guan
9. Tommy Tsan-Yuk Lam

Reviewed by ScreenIT

The LOTUS initiative for open knowledge management in natural products research

1. Adriano Rutz
2. Maria Sorokina
3. Jakub Galgonek
4. Daniel Mietchen
5. Egon Willighagen
6. Arnaud Gaudry
7. James G Graham
8. Ralf Stephan
9. Roderic Page
10. Jiří Vondrášek
11. Christoph Steinbeck
12. Guido F Pauli
13. Jean-Luc Wolfender
14. Jonathan Bisson
15. Pierre-Marie Allard

• Curated by eLife

  Evaluation Summary:

  Rutz et al. outline LOTUS, a new open-source database that links natural product structures with the organisms they are present in. It contains over 700,000 referenced structure-organism pairs and search tools that make mining the database intuitive and efficient. The LOTUS Initiative comprises an important data harmonization/integration effort over previous databases. The results are distributed to the public through Wikidata, which additionally supports future curation. This new resource is likely to be of great interest to natural product researchers as well as across fields of biology including ecology, evolution, and biochemistry.

  (This preprint has been reviewed by eLife. We include the public reviews from the reviewers here; the authors also receive private feedback with suggested changes to the manuscript. Reviewer #1 agreed to share their name with the authors.)

Reviewed by eLife

Unsupervised genome-wide cluster analysis: nucleotide sequences of the omicron variant of SARS-CoV-2 are similar to sequences from early 2020

1. Georg Hahn
2. Sanghun Lee
3. Dmitry Prokopenko
4. Tanya Novak
5. Julian Hecker
6. Surender Khurana
7. Lindsey R. Baden
8. Adrienne G. Randolph
9. Scott T. Weiss
10. Christoph Lange

Reviewed by ScreenIT

Early computational detection of potential high-risk SARS-CoV-2 variants

1. Karim Beguir
2. Marcin J. Skwark
3. Yunguan Fu
4. Thomas Pierrot
5. Nicolas Lopez Carranza
6. Alexandre Laterre
7. Ibtissem Kadri
8. Abir Korched
9. Anna U. Lowegard
10. Bonny Gaby Lui
11. Bianca Sänger
12. Yunpeng Liu
13. Asaf Poran
14. Alexander Muik
15. Uğur Şahin

Reviewed by ScreenIT

Comparative analysis of single cell lung atlas of bat, cat, tiger, and pangolin

1. Xiran Wang
2. Peiwen Ding
3. Chengcheng Sun
4. Daxi Wang
5. Jiacheng Zhu
6. Wendi Wu
7. Yanan Wei
8. Rong Xiang
9. Xiangning Ding
10. Lihua Luo
11. Meiling Li
12. Wensheng Zhang
13. Xin Jin
14. Jian Sun
15. Huan Liu
16. Dongsheng Chen

Reviewed by ScreenIT

Peptide-based epitope design on non-structural proteins of SARS-CoV-2

1. R S Swathika
2. S Vimal
3. E Bhagyashree
4. Elakkiya Elumalai
5. Krishna Kant Gupta

Reviewed by ScreenIT

Analyzing the interaction of human ACE2 and RBD of spike protein of SARS-CoV-2 in perspective of Omicron variant

1. Arijit Samanta
2. Syed Sahajada Mahafujul Alam
3. Safdar Ali
4. Mehboob Hoque

Reviewed by ScreenIT

Designing multi-epitope based peptide vaccine targeting spike protein SARS-CoV-2 B1.1.529 (Omicron) variant using computational approaches

1. Meet Parmar
2. Ritik Thumar
3. Jigar Sheth
4. Dhaval Patel

Reviewed by ScreenIT

Computational Mapping of the Human-SARS-CoV-2 Protein-RNA Interactome

1. Marc Horlacher
2. Svitlana Oleshko
3. Yue Hu
4. Mahsa Ghanbari
5. Giulia Cantini
6. Patrick Schinke
7. Ernesto Elorduy Vergara
8. Florian Bittner
9. Nikola S. Mueller
10. Uwe Ohler
11. Lambert Moyon
12. Annalisa Marsico

Reviewed by ScreenIT

Analysis of SARS-CoV-2 synonymous codon usage evolution throughout the COVID-19 pandemic

1. Ezequiel G. Mogro
2. Daniela Bottero
3. Mauricio J. Lozano

Reviewed by ScreenIT