Cover Letter & Response Letter

大家好，又见面了，我是你们的朋友全栈君。

1. Cover Letter

Cover Letter是写给期刊编辑、用于描述投稿论文的创新与工作内容，明确地告知编辑稿件的研究内容与期刊刊物领域契合度，并作一些额外的陈述和声明（比如，不存在一稿多投的声明，投稿的期刊存在预印本的声明，推荐的审稿人等）。大部分期刊投稿的时候都会要求独立提交一份Cover Letter，或者是在投稿流程中有一个写给编辑的文本框，把Cover Letter的内容直接粘进去。

Cover Letter的内容在于浓缩手稿的摘要、研究方法、研究结果和结论，需要简明扼要的表达出论文的创新点。

下面以我投稿期刊Neurocomputong （中科院2区，JCR Q1）时附上的Cover Letter进行解释（隐去了某些信息，保留论文中方法的名字），解释内容我以/**/的形式写在下方，需要的崽崽照着这个模板进行修改即可。

Dec 6, 2019

Dear Editors,

/*客套话，注意修改一下期刊的名字*/

We would like to submit the manuscript entitled “@Title”, which we wish to be considered for publication in
Neurocomputing.

/*简要阐述研究的目的和创新内容，建议时态都使用现在时*/

In this study, we propose the differential network flow (DNF) method based on network flow and information theory to identify key regulators of progression in development or disease, e.g. driver genes in neural stem cell differentiation. DNF characterizes biological networks by optimal flow, which has not been widely explored by other methods. This flow of information, inherent in biological networks, takes into account the nonlinear contribution of all nodes. Thus, key genes that are not necessarily identifiable as single-scale features or linear combinations of other features can be detected by DNF. The proposed method provides a quantitative approach to gain insight into prioritizing the essentiality of genes across different networks.

/*简要阐述一下论文的研究工作和成果*/

To assess the performance of DNF against other methods in prioritizing key regulators between different networks, DNF is compared with four state-of-the-art methods, including one local method (DCloc), one global method (DEC), one hybrid method (DiffRank), and one perturbation-based method (DiffNet).

DNF is applied first to simulated datasets and second to clinical and experimental datasets (four TCGA bulk RNA-seq datasets, three single-cell RNA-seq datasets of cell differentiation). For the clinical data, DNF detected more known cancer genes and survival-related genes, demonstrating superior prediction of cancer biomarkers and prognosis genes. Additionally, we identify a novel link between neural stem cell differentiation and neurodegenerative disease via gene set enrichment of DNF-identified markers.

/*客套话，大概就是说我这研究内容和你期刊太配了*/

In summary, we believe that our study will be of interest to the readership of
Neurocomputing as it is broadly applicable to systematic and practical analysis of temporal RNA-seq data and produces actionable information for studying related biological questions such as cell differentiation and cancer-driver discovery.

/*非必须，某些期刊可能会要求由作者提供4-6名审稿人*/

For reviewers, our suggestion of experts related to this topic in the field of
systems biology are as follows:

(1) NAME, INSTITUTION, EMAIL

(2) NAME, INSTITUTION, EMAIL

/*必要的声明，修改一下期刊名字，其他照抄即可*/

We have prepared our manuscript according to the “Guide for authors” document from
Neurocomputing. This paper has not been published or accepted for publication. It is not under consideration by any other journals.

Thank you very much for your attention and consideration.

/*落款*/

With kind regards,

XX XX

XXXXX

Shanghai , China

2. Response Letter

如果你需要写Response Letter的时候，首先祝贺你，论文只要认真修改就离Accept不远了。

Response Letter是编辑和审稿人返回修改意见（Major revision、Minor revision）的时候，需要根据编辑和审稿人的意见，逐点修改后将修改内容写到Response Letter，并提交给期刊编辑。Response Letter非常重要，一般审稿人只会看Response Letter，所以在针对每一条修改意见写Response Letter的时候，必须将其中的前因后果阐述清楚，某些缩写也需要重新写一遍全称。因此Response Letter写的比正文还长一点都不奇怪。

模板可以参考以下内容。

Response to reviewers #1

/*客套话*/

Thank you for the many insightful comments and suggestions. We have made revisions to address all the comments. A list of our responses to each of the specific comments is listed below.

/*对于审稿人的每一条列出的审稿意见（Comment），都应该像下面这种形式回复（Response），必要的时候加上参考文献*/

Comment:

/*这里是审稿人的意见，直接粘贴进来，弄成斜体*/

1. The proposed method characterizes a node based on the flow reaching out to common destination nodes, which makes sense in networks with large overlapping or sequential networks. But this design decision could ignore the impact to non-overlapping destination nodes, which seems to limit its usage. It would be nice to see statement about how to handle cases where the overlapping nodes are limited.

Response:

/*这边就是根据不同的审稿意见，进行阐述观点，补充实验，增加文献。注意审稿人的措辞，这里用了nice to see statement，所以不需要补充实验，只需要简单描述几句可行的方案。*/

That is a very good point. To compare networks of limited overlapping nodes, one can potentially first use a network alignment method (e.g. HGA method [1]) to construct the most similar mapping between the two networks, and then directly apply DNF based on this mapping.

/*最后一定要指明在正文哪里作了修改*/

We have added this point and the new reference in Discussion.

/*添加必要的参考文献*/

[1] J. Xie, C. Xiang, J. Ma, J. Tan, T. Wen, J. Lei, Q. Nie, An Adaptive Hybrid Algorithm for Global Network Alignment, IEEE/ACM Trans Comput Biol Bioinform, 13 (2016) 483-493