Created by: Belinda R. Fouché Published by: The Sciencey Company® Version: 1.0 (January 2026) Copyright © 2026 The Sciencey Company. All rights reserved. The Brain-to-Paper Pipeline

Welcome to The Brain-to-Paper Pipeline

Congratulations! You have just opened the document that will save your future self hours of stress, "blank-page syndrome," and frantic searching.

The Brain-to-Paper Pipeline is not just a document; it is a system. It is designed to be the central repository for every piece of information you read during your research. By the time you sit down to write your thesis or article, the "writing" part will simply be a matter of connecting the dots you’ve already placed here.

The Golden Rules of the Pipeline

To make this system work for you, you must commit to these three core principles:

Never Paste Without a Citation: If it enters this document, it must have a reference attached immediately.

Don't Rephrase (Yet): This is a "dump" for raw data. Keep direct quotes in black so you always know exactly what the original author said.

Own Your Insights: Whenever a thought, a "Why?", or a hypothesis pops into your head, write it down immediately in blue (or any other colour that’s different from your direct quotes). These blue notes are the seeds of your future Discussion section.

How to Build Your Pipeline

Step 1: Structure is key

Organize this file with clear Headings and Subheadings. Use the "Navigation Pane" in your word processor to jump between sections instantly. In MS Word, go to the View tab and check Navigation Pane. This allows you to see your headings as a clickable Table of Contents on the left.

Step 2: Extract & Cite

When you read an interesting paper, copy the relevant paragraph and paste it under the correct heading. Import the article into your reference manager (e.g., EndNote, Mendeley) and immediately add the citation to the paragraph you just pasted.

Step 3: Use Keywords

Bold or highlight the specific words in that paragraph that made it relevant. When you have a 100-page document, these highlights act as "visual anchors" for your eyes.

Step 4: "Blue Text" Annotation

Write notes to your future self. Explain why you saved this quote. These notes will stay with you even if you take a three-month break for lab work or holidays. Always keep your annotations in a separate colour from the direct quotes. This creates a clear visual "firewall" between the authors' words and your own. When you eventually copy these notes into your thesis, you can do so with the confidence that you aren't accidentally plagiarizing.

Step 5: Cross-Reference Power-Move

If a paragraph mentions two different topics (e.g., Mitochondria and Cerebellum), paste it in both sections. It is better to have the same text repeated 10 times than to miss it when you are writing a specific chapter.

Ready to write?

When the time comes to transform your research into a manuscript, your Brain-to-Paper Pipeline becomes your most valuable asset. Follow these steps to begin:

Create a New Draft: When you are ready to draft your article, open a blank document on one side of your screen and this Pipeline on the other.

Scan via Keywords: Select the heading you intend to write about. Instead of re-reading every paragraph, scan for the bolded keywords you created earlier. This will instantly remind you why each excerpt was saved and how it fits into your narrative.

Consult Your "Blue Text": Look at your personal notes. These are your pre-written arguments. Often, you can simply "stitch" these blue-text insights together with the evidence from your black-text quotes to form a paragraph.

Verify with Stored Citations: If a quote feels out of context, use the citation you immediately added during the collection phase to jump back to the original paper and verify the details.

You aren't "writing" in the traditional sense—you are synthesizing. By the time you sit down to work, the blank page is already gone.

The Sciencey Company

The Brain-to-Paper Pipeline

VISUAL KEY

Element	Format	Purpose
Direct Quote	Black Text	Raw evidence. Do not change a single word.
Personal Insight	Blue Text	Your thoughts, hypotheses, and "Why?" notes.
Keywords	Bold/Highlight	Visual anchors to help you scan the file at high speed.
Citations	(Author, Year)	Links the evidence to your Reference Manager.

PERSONAL INSIGHTS AND META-DATA

Questions & Hypothesis

Use this section to dump all your thoughts, questions, hypotheses, and general “rabbit holes”. Revisit this section whenever you feel stuck. This section helps you avoid getting sidetracked while reading a specific article. If a "random" brilliant idea pops up, park it here and get back to your reading. Remember to write these entries in your Personal Insight Color (e.g., Blue) so they never get confused with direct evidence.

For example:

Why are different tissues affected to different extents? Is it resilience or function?

How do VGlut2 neurons fit into our olfactory bulb hypothesis?

Advisor Feedback

When your advisors give you general feedback on a draft, paste those comments there so you can see the "evolution" of their requirements in one place.

For example:

Supervisor 1: Suggested focusing the Literature section on new methods rather than just the disease.

Supervisor 2: Focus on mechanisms of pathology in the Discussion.

THE BRAIN DUMP

This is where your research starts taking shape. Organisation is key for this pipeline to be successful. This document will end up being huge, which is fine if it’s organised (headings and sub-headings, citations, highlighted keywords).

Phase 1: Structure Your Universe

Start by typing out the headings and sub-headings you anticipate using in your thesis. Under each heading, add a short block of text describing what you intend to discuss there. Copy the text to all relevant headings.

Phase 2: The "Citation-within-a-Citation" Hack

If an article references another source, copy that reference into square brackets [ ]. Use the format: [Primary Source] as cited in (Secondary Source). This allows you to go back to the primary source later. You can then double-check if the author you are currently reading interpreted the original data correctly.

For example: To date, NDUFS4 mutations have been described in 22 patients... [Quintana., 2015] (Di Meo et al., 2017).

Phase 3: Synthesize with Tables and Data

Don't just use walls of text. Use tables to compare clinical studies or store your own experimental results.

Patients	Sample size (n)	Citation
Infant 7 months	1	(Leigh, 1951)
Swedish children with LS	25	(Naess et al., 2009)

Integrate your own data. Paste your own results directly into the pipeline. This allows you to compare your findings with the literature in real-time. For example:

Proteins associated with neuroimmune and inflammation, including markers of microglial and astrocyte activation (LEG3, CD180, GFAP and S100A4), complement components (C1QA and C1QB) and the interferon response (IFIT1 and IFIT3)41–43, were significantly upregulated in KO mice compared to WT, and largely suppressed by doxycycline (Perry et al., 2021)

Gene symbol	Gene name	Fold change	Adjusted p-value
Ifit1	Interferon-induced protein	11.17	3.42E-04
Cd180	25	3.42	1.15E-04

Phase 4: Interleaving Insights

Add your personal insights in your specific color between citations.

For example: Normoxia-treated (normal thus no treatment) KO mice exhibited substantial neuronal degeneration. Lesions were accompanied by Iba-1+ microglial proliferation... (Jain et al., 2016). This is a key finding—it suggests that even without external stress, the Ndufs4 deficiency is sufficient for neurodegeneration.

BRAIN DUMP (USING LEIGH SYNDROME AS AN EXAMPLE):

Typical presentation of patients with Leigh syndrome

Human patients with Leigh syndrome

Typical symptoms.

Age of onset of symptoms

patients with mitochondrial disease may be highly sensitive to oxygen toxicity (Jain et al., 2016).

Currently, mutations in 24 CI subunit-encoding genes have been implicated in Leigh syndrome (Table 1) (van de Wal et al., 2022)

NDUFS4 knockout mice as a model to study mitochondrial disease/ pathology.

Ndufs4 knockout mice are used to study mitochondrial disease.

Why are these models so useful? - Focus.

What have we learned about mitochondrial disease by studying these animals?

Limitations of these models

(van de Wal et al., 2022) gives an excellent review of various aspects of the mouse model, including different types of KO, interventions etc.

Tissue specificity

Focus on heart, olfactory bulb, liver and cerebellum

Different brain regions is important.

How are different tissues affected differently

In the KO the respiratory capacity of synaptosomes from the degeneration prone regions olfactory bulb, brainstem and cerebellum was significantly decreased (Kayser et al., 2016).

The basal ganglia, brain stem and cerebellum appear preferentially vulnerable to mitochondrial dysfunction [4, 7] (Kayser et al., 2016; Leigh, 1951).

It seems that brain regions are highly affected by Leigh syndrome. Could this be something to investigate further?

Cerebellum

In the KO the respiratory capacity of synaptosomes from the degeneration prone regions olfactory bulb, brainstem and cerebellum was significantly decreased (Kayser et al., 2016).

The basal ganglia, brain stem and cerebellum appear preferentially vulnerable to mitochondrial dysfunction [4, 7] (Kayser et al., 2016; Leigh, 1951).

Mitochondria

Mitochondria are involved in several metabolic pathways, including carbon metabolism, nitrogen metabolism (van de Wal et al., 2022).

OXPHOS complexes

Metabolic compensation

Reactive oxygen species

References

Jain, I.H., Zazzeron, L., Goli, R., Alexa, K., Schatzman-Bone, S., Dhillon, H., ... Mootha, V.K. 2016. Hypoxia as a therapy for mitochondrial disease. Science, 352(6281):54-61. https://www.ncbi.nlm.nih.gov/pubmed/26917594 10.1126/science.aad9642

Kayser, E.B., Sedensky, M.M. & Morgan, P.G. 2016. Region-Specific Defects of Respiratory Capacities in the Ndufs4(KO) Mouse Brain. PLoS One, 11(1):e0148219. https://www.ncbi.nlm.nih.gov/pubmed/26824698 https://doi.org/10.1371/journal.pone.0148219

Leigh, D. 1951. Subacute necrotizing encephalomyelopathy in an infant. J Neurol Neurosurg Psychiatry, 14(3):216-221. https://www.ncbi.nlm.nih.gov/pubmed/14874135 https://doi.org/10.1136/jnnp.14.3.216

Naess, K., Freyer, C., Bruhn, H., Wibom, R., Malm, G., Nennesmo, I., ... Larsson, N.G. 2009. MtDNA mutations are a common cause of severe disease phenotypes in children with Leigh syndrome. Biochim Biophys Acta, 1787(5):484-490. https://www.ncbi.nlm.nih.gov/pubmed/19103152 10.1016/j.bbabio.2008.11.014

Perry, E.A., Bennett, C.F., Luo, C., Balsa, E., Jedrychowski, M., O’Malley, K.E., ... Puigserver, P. 2021. Tetracyclines promote survival and fitness in mitochondrial disease models. Nature Metabolism, 3(1):33-42. https://www.scopus.com/inward/record.uri?eid=2-s2.0-85099954574&doi=10.1038%2fs42255-020-00334-y&partnerID=40&md5=ef6ee7f4793419be606ef503a8828eb7 https://doi.org/10.1038/s42255-020-00334-y

van de Wal, M.A.E., Adjobo-Hermans, M.J.W., Keijer, J., Schirris, T.J.J., Homberg, J.R., Wieckowski, M.R., ... Koopman, W.J.H. 2022. Ndufs4 knockout mouse models of Leigh syndrome: pathophysiology and intervention. Brain, 145(1):45-63. https://www.ncbi.nlm.nih.gov/pubmed/34849584 https://doi.org/10.1093/brain/awab426

About the author

Belinda R. Fouché is a PhD candidate specializing in transcriptomics and mitochondrial disease. She developed the Brain-to-Paper Pipeline during her postgraduate studies as a strategic solution to the common struggles of synthesizing complex literature and drafting academic text. Belinda is also the founder of The Sciencey Company, where she combines her passion for rigorous scientific research with the creation of functional stationery and tools designed specifically for the modern scholar.