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I appreciate the authors addressing the reviewer comments. I have reviewed the article myself. I am happy with this version and believe the manuscript is now ready for publication.
[# PeerJ Staff Note - this decision was reviewed and approved by Paula Soares, a PeerJ Section Editor covering this Section #]
No comment. The authors have improved their paper accordingly.
No comment.
No comment.
My former comments have been addressed.
no comment
no comment
no comment
The authors have adequately addressed the reviewers’ comments, and I believe the manuscript now meets the requirements for publication.
Both reviewers provided brief, but helpful comments. Please address these comments in your next round of revisions. I would focus on clarifying some of the key points and highlighting the biological implications.
**PeerJ Staff Note:** Please ensure that all review, editorial, and staff comments are addressed in a response letter and that any edits or clarifications mentioned in the letter are also inserted into the revised manuscript where appropriate.
In this paper, the authors introduced a Bayesian network–based pipeline called BCTI that simultaneously reconstructs dynamic gene-regulatory networks and pinpoints critical transition states in time-course or stage-course transcriptomic data.
Validated on simulated and real datasets (TCGA tumors and human embryonic-lung scRNA-seq), BCTI achieves superior or comparable GRN accuracy and signals tipping points ahead of clinical metastasis or developmental switches.
The comparison studies need to be implemented. The authors need to demonstrate the superiority of the proposed method over existing approaches.
The authors need to discuss how the findings were validated and the potential limitations or future directions.
The authors need to provide interpretations of the biological significance of the identified biomarkers.
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1. In equation (7), when estimating the mutual information between X_i and X_j, when p(x) or p(y) approaches zero, the logarithmic function will collapse. We need more details on how to avoid this problem when doing the experiment
2. In the same step, the authors have mentioned that the threshold is chosen as 0.1; to make it convincing, they would need literature to support the choice
In step 5, the critical point is defined by comparing the current state and the previous one. How to make sure the chosen time point is a change point instead of an anomaly point?
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