Congratulations to Jaque Brito, Mangul Lab postdoctoral scholar, Niko Darci-Maher, Mangul Lab undergraduate researcher, and Varuni Sarwal, Mangul Lab alumni, on the acceptance of their papers to the Bioinformatics Community Conference (BCC) 2020 virtual meeting.

Niko will be presenting his short talk, “Secondary analysis of publicly available omics data across almost 3 million publications,” in the Bioinformatics Open Source Conference (BOSC) track of BCC2020. Along with co-authors Kerui Peng (Mangul Lab PhD student), Dat Duong, Richard J. Abdill, Eleazar Eskin (Professor of Computational Medicine, Computer Science, and Human Genetics at UCLA), and Serghei Mangul, Niko’s presentation presents a quantitative analysis of the reusability of omics datasets in two online repositories, the Sequence Read Archive (SRA) and the Gene Expression Omnibus (GEO).

→ Read our post on Kerui’s presentation of this project at ICCABS 2019: http://www.sergheimangul.com/2019/11/06/kerui-iccabs-2019/.

 

Jaque will be presenting her short talk, “Enhancing rigor and reproducibility in biomedical research,” in the BOSC track of BCC2020. Jaque and her co-authors, Jun Li, Jason H. Moore, Casey S. Greene, Nicole A. Nogoy, Lana X. Garmire, and Serghei Mangul present  recommendations for improving software availability, usability, and archival stability aim to foster a sustainable data science ecosystem in life science research.

→ Read the full article: https://doi.org/10.1093/gigascience/giaa056.
→ Read our blog post reporting on the preprint: http://www.sergheimangul.com/2020/03/30/mangul-lab-preprint-rigor-and-reproducibility/.
→ Read our blog post presenting the paper: http://www.sergheimangul.com/2020/06/01/mangul-lab-releases-fourth-paper-that-recommends-ways-to-enhance-rigor-and-reproducibility-in-biomedical-research/.

 

Varuni, past undergraduate researcher and future PhD student in Mangul Lab, will present her short talk, “A comprehensive benchmarking of WGS-based structural variant callers,” in the BOSC track of BCC2020. Varuni and her co-authors, Sebastian Niehus, Ram Ayyala (undergraduate researcher in Mangul Lab), and Serghei Mangul evaluated the performance of 15 SV-detection tools based on their ability to detect deletions from aligned WGS reads using a comprehensive PCR-confirmed gold standard set of SVs to find methods with a good balance between sensitivity and precision.

→ Read the full article: https://www.biorxiv.org/content/10.1101/2020.04.16.045120v2.
→ Read our blog post reporting on the preprint: http://www.sergheimangul.com/2020/04/29/mangul-lab-preprint-sv-callers/.

BCC2020 brings together the Galaxy Community Conference and Bioinformatics Open Source Conference to meet jointly online. BCC2020 takes place remotely from July 19 to 21, 2020. For more information on registration: https://bcc2020.github.io/Registration/.

Reference:

Jaqueline J Brito, Jun Li, Jason H Moore, Casey S Greene, Nicole A Nogoy, Lana X Garmire, Serghei Mangul: Recommendations to enhance rigor and reproducibility in biomedical research. In: GigaScience, 9 (6), pp. giaa056, 2020.

Varuni Sarwal, Sebastian Niehus, Ram Ayyala, Sei Chang, Angela Lu, Nicholas Darci-Maher, Russell Jared Littman, Emily Wesel, Jacqueline Castellanos, Rahul Chikka, Margaret G Distler, Eleazar Eskin, Jonathan Flint, Serghei Mangul: A comprehensive benchmarking of WGS-based structural variant callers. In: bioRxiv, 2020.