A complete guide for graduate students and early-career researchers on how to prepare, submit, and publish scientific papers
· 5 min read
This guide explains the entire process of publishing a scientific paper, from manuscript preparation to final publication, suitable for graduate students and researchers.
1. Overview of the Publication Process
Scientific publishing generally includes seven stages:
- Research preparation and identifying innovation
- Manuscript writing and formatting
- Journal selection and submission
- Peer review and revision
- Acceptance
- Proof and In Press (online-first publication)
- Final publication and post-release maintenance
2. Editorial Workflow Stages
| Status | Editorial Stage (CN) | Available Online | DOI Assigned | Volume/Issue Assigned | Citable |
|---|---|---|---|---|---|
| Submitted | 投稿 | No | No | No | No |
| Under Review | 审稿中 | No | No | No | No |
| Accepted | 录用 | No | No | No | Yes (mark as “accepted”) |
| In Press | 排版中 | No | Yes | No | Yes |
| Online / Early Access | 在线发表 | Yes | Yes | No | Yes |
| Published | 出版 | Yes | Yes | Yes | Yes (final version) |
Explanation:
- "Accepted" means approved after peer review.
- "In Press" means accepted and assigned a DOI but not yet in a journal issue.
- "Online/Early Access" means available on the journal website ahead of print.
- "Published" indicates final pagination and indexing.
3. Research Preparation
3.1 Define the Core Contribution
- Identify one clear innovation: a method, instrument, or biological insight.
- Choose paper type:
- Research Article: new findings
- Method Paper: new algorithms or tools
- Review: literature summary
3.2 Select a Suitable Journal
| Field | Example Journals |
|---|---|
| Crop phenotyping and photosynthesis | Plant Phenomics, Plant Methods |
| Remote sensing and modeling | Remote Sensing of Environment, Agricultural and Forest Meteorology |
| Agronomy and breeding | Field Crops Research, European Journal of Agronomy |
Selection criteria:
- Impact Factor
- Review time and acceptance rate
- Open Access policy
- Scope and audience fit
4. Manuscript Writing
4.1 IMRaD Structure
| Section | Content |
|---|---|
| Introduction | Background, question, innovation |
| Materials and Methods | Experiments, data, algorithms |
| Results | Findings and figures |
| Discussion | Interpretation and implications |
| Conclusion | Summary and perspectives |
4.2 Writing Tips
- Follow journal guidelines precisely.
- Use English language tools such as Grammarly or Writefull.
- Manage references with Zotero or EndNote.
- Prefer vector graphics (SVG, EPS) or 300 dpi images.
5. Submission Process
5.1 Common Submission Systems
- Elsevier: Editorial Manager or EVISE
- Springer/Nature: Manuscript Tracking System
- Wiley, MDPI, Frontiers: proprietary platforms
5.2 Files to Prepare
| File | Description |
|---|---|
| Main Manuscript | Full text with references |
| Figures/Tables | Uploaded separately if required |
| Cover Letter | Briefly describe novelty and importance |
| Supplementary Material | Additional data or methods |
5.3 Workflow
- Log in to the submission portal
- Fill in author and affiliation details
- Upload all required files
- Select section or topic
- Submit and obtain a Manuscript ID
6. Peer Review
6.1 Status Flow
| Status | Meaning |
|---|---|
| Submitted | Awaiting editor decision |
| With Editor | Under editorial check |
| Under Review | Sent to reviewers |
| Reviews Completed | Reviews returned |
| Decision in Process | Editorial decision pending |
| Major/Minor Revision | Revisions requested |
| Accepted | Approved for publication |
6.2 Responding to Reviewers
- Prepare a document titled "Response to Reviewers."
- Reply point-by-point to each comment.
- Highlight or track all changes.
- Example: We thank the reviewers for their constructive suggestions. All modifications are highlighted in red in the revised manuscript.
7. Acceptance and Publication
7.1 Acceptance
- Once accepted, the paper can be cited as “Accepted” or “in press” in CVs and proposals.
- A formal acceptance letter is issued.
7.2 Proof and In Press
- After acceptance, the paper is typeset and assigned a DOI.
- It is citable even before it appears in a journal issue.
7.3 Online / Early Access
- The paper appears on the journal website before pagination.
- It has a DOI and is considered officially published.
7.4 Final Publication
- The paper receives volume, issue, and page numbers.
- It is indexed in major databases (Web of Science, Scopus).
8. Citation Examples (APA 7th Edition)
| Stage | Example |
|---|---|
| Accepted (no DOI) | Deng, L., … (in press).Leaf Optical Properties Predicted… Plant Phenomics. |
| In Press (with DOI) | Deng, L., … (2025, in press).Leaf Optical Properties Predicted… Plant Phenomics. https://doi.org/10.1016/j.plaphe.2025.100135 |
| Published (final) | Deng, L., Yu, L. X., Mao, L., Wang, Y., Guo, X., Wang, M., Zhang, Y., Song, Q., & Zhu, X.-G. (2025).Leaf Optical Properties Predicted with BRDF and Phenotypic Traits in Four Species: Development of Novel Analysis Tools. Plant Phenomics, 7(3), 100135. https://doi.org/10.1016/j.plaphe.2025.100135 |
9. Post-Publication Maintenance
9.1 Update Academic Profiles
- Google Scholar: usually automatic
- ORCID, ResearchGate, Publons: update manually
- Personal website: update with latest APA citations
9.2 Data and Code Sharing
- Upload data to Zenodo, Figshare, or Dryad
- Assign a DOI for data citation
9.3 Promote Your Work
- Share via LinkedIn, ResearchGate, or institutional news
- Monitor citations and Altmetric statistics
10. Summary
Publishing a scientific paper is a systematic and transparent process of communicating new research findings. Success depends on rigorous methodology, precise writing, and consistent improvement.
Define innovation → Write carefully → Submit strategically → Revise seriously → Cite correctly.
Here I'm sharing the journal analysis I've compiled, hoping it can be helpful to everyone. CSV
Citation of this Guide Deng, L. (2025). Academic Paper Publication Workflow. Digital Crop Photosynthesis Phenotyping Platform Documentation.