Multi Omics Applications in Biological Systems

Round 1

Reviewer 1 Report

Comments and Suggestions for Authors

Dear authors

Thank you for submitting your draft titled "Multi omics applications in biological systems." I appreciate a lot your effort and  I am grateful to submit my comments and suggest changes to improve the paper.

My main concern are the review in self... the review is very general and does not provide more information than other similar papers of the topic in recent literature. I strongly suggest making an effort to work in more detail on the definitions of related technologies, and delve into the details of the platforms, collections and data sites to enrich the information and make it attractive to the reader, and generate differentials with respect to other reviews on the subject.

I consider can be published once this is done and by making some major clarifications in the remarks that I add in the draft in the attached .pdf file.

 

Comments for author File: Comments.pdf

Author Response

Thank you for your valuable comments, see the attached report and the corrected manuscript.

Author Response File: Author Response.pdf

Reviewer 2 Report

Comments and Suggestions for Authors

This review by Reyes et al broadly discusses the various up-to-date omics applications and provides examples of where they have been utilized to address knowledge gaps in important fields. The author’s primary approach is to provide broad coverage of these technologies but does not go into significant detail on each one including their strengths, weaknesses, and where they would be most beneficially applied. The authors also provide many citations of studies in which integration of multi-omic approaches was key to advancing their fields of research. The authors do a decent job of covering all the technologies available with a few exceptions (see major comments below). There is limited to no discussion of statistical approaches for integrating multiple omic technologies which is a key component to their valid application

Major comments:

1) In the genomics section, the authors exclude reviewing any new omics-associated technology with spatial gene expression. These technologies incorporate some of the same strengths of single cell RNA seq but overlayed with tissue sections or clarified tissue. Further, while not necessarily genomic based, technologies that incorporate multiple antibody panels for spatialomic analysis of proteins is also a cutting-edge technology. An example of this is the MACSima system from Miltenyi Biotec. The authors would benefit from including a short discussion on spatial omics techniques. 

2) The authors list 10x genomic sequencing but some newer technologies are available with strengths that 10x does not have such as the BD Rhapsody. Mentioning this technology would strengthen the genomics section.

3) Citation is missing for lines 157 -159

4) In the metabolomics section a significant amount of focus is spent on single cell approaches, ignoring advances in targeted, semi-targeted, or untargeted approaches as well as heavy isotope tracing techniques and MALDI for spatial correlates. I think these should be mentioned with supportive citations.

5) While multi-omics approaches are listed and examples of manuscripts that used them listed, there is no review of the statistical approaches used to integrate these technologies. A discussion of methods and approaches to statistical handling of data produced by these different technologies and how they can be compared to each other would significantly strengthen the review.

 

Minor comments:

-          Line 75 Inside eukaryotic nucleus… a comma needs to be inserted to separate ideas. It’s a little confusing and run-on sentence without it.

-          Lines 219 -221 are a confusing. I think there is a missing word.

Author Response

Thank you for your valuable comments, see the attached report and the corrected manuscript.

Author Response File: Author Response.pdf

Round 2

Reviewer 1 Report

Comments and Suggestions for Authors

Dear authors

We appreciate your effort to present your titled work "Multi omics applications in biological systems." After analyzing their responses and modifications to the manuscript, I am satisfied with its arguments and content, considering that it can be published in the journal in the format that they have sent us.

Congratulations.

Reviewer 2 Report

Comments and Suggestions for Authors

The authors sufficiently responded to my comments considering the "mini" review format limitations.