Bioinformatics and Genomics

16 April 2021

NGScloud2: optimized bioinformatic analysis using Amazon Web Services

Fernando Mora-Márquez, José Luis Vázquez-Poletti, Unai López de Heredia

Yuriy Orlov –– Novel update for NGS cloud computing would be widely used for RNA-sequencing data analysis in model organisms.

15 April 2021

Bioinformatics analysis for the identification of differentially expressed genes and related signaling pathways in H. pylori-CagA transfected gastric cancer cells

Dingyu Chen, Chao Li, Yan Zhao, Jianjiang Zhou, Qinrong Wang, Yuan Xie

Alexander Bolshoy –– H. pylori is a very important interesting organism and all new knowledge is valuable.

13 April 2021

ZebraShare: a new venue for rapid dissemination of zebrafish mutant data

April DeLaurier, Douglas G. Howe, Leyla Ruzicka, Adam N. Carte, Lacie Mishoe Hernandez, Kali J Wiggins, Mika M. Gallati, Kayce Vanpelt, Frances Loyo Rosado, Katlin G. Pugh, Chasey J. Shabdue, Khadijah Jihad, Summer B. Thyme, Jared C. Talbot

Mason Posner –– Zebrashare will be a valuable resource for the large and growing zebrafish research community to share gene edited mutants and collaborate on follow up studies. This crowdsourcing of mutants, built right into ZFIN, will help prevent redundant work and facilitate sharing of data.

5 April 2021

Multi-schema computational prediction of the comprehensive SARS-CoV-2 vs. human interactome

Kevin Dick, Anand Chopra, Kyle K. Biggar, James R. Green

Shawn Gomez –– This manuscript describes the identification of a set of predicted protein-protein interactions between SARS-CoV-2 and its human host. This work is relevant on its own, as well as being highly complementary to other efforts focused on accelerating our understanding of this virus and potential mechanisms of pathogenesis.

16 March 2021

Reproducible, portable, and efficient ancient genome reconstruction with nf-core/eager

James A. Fellows Yates, Thiseas C. Lamnidis, Maxime Borry, Aida Andrades Valtueña, Zandra Fagernäs, Stephen Clayton, Maxime U. Garcia, Judith Neukamm, Alexander Peltzer

Alexander Schliep –– A great community-wide framework to reproducibly, efficiently and robustly analyze ancient DNA.

2 March 2021

The methylation level of TFAP2A is a potential diagnostic biomarker for retinoblastoma: an analytical validation study

Qi Zeng, Sha Wang, Jia Tan, Lu Chen, Jinwei Wang

Jesus Vera –– This may help to the diagnosis of retinoblastoma and others eye conditions.

23 February 2021

Characterization of the GRAS gene family reveals their contribution to the high adaptability of wheat

Yanfeng Liu, Wei Wang

Alexander Bolshoy –– GRAS gene family is very important in plants. This study promotes research in the field.

5 February 2021

Syncmers are more sensitive than minimizers for selecting conserved k‑mers in biological sequences

Robert Edgar

Joseph Gillespie –– In this novel work, Dr. Edgar makes a significant advance on using k-mer selection for sequence analysis: selected k-mers act as seeds for sequence matching, with generated "syncmers" having attractive properties of minimizers without having to depend on neighboring sequence.

3 February 2021

Development and clinical validation of a 3-miRNA signature to predict prognosis of gastric cancer

Wenqian Qi, Qian Zhang

Cheng Zhan –– This manuscript constructed a 3-miRNA signature to predict prognosis of gastric cancer.

3 February 2021

Assessing the effects of time-dependent restrictions and control actions to flatten the curve of COVID-19 in Kazakhstan

Ton Duc Do, Meei Mei Gui, Kok Yew Ng

Antonio Palazón-Bru –– The authors assessed the spread of COVID-19 in central Asia, giving us relevant information about this new disease.