seren_

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seren_ · HSC Gene Correction · AAV6 vs lentiviral

seren_

Here is how I would frame that:

Research question

"Does AAV6 produce more durable HSC engraftment than lentiviral delivery under matched transduction conditions?"

Comparison AAV6 vs lentiviral vector
Outcome Engraftment durability · 6m
Context BM-derived HSCs · ex vivo
Scope Clinical · Phase 1 design

Preliminary signal: 12 papers found

7 support AAV6 advantage · 1 gap

the workspace

Everything a researcher needs.
From hypothesis to final draft.

One workspace. Every stage of the research lifecycle. Nothing separate, nothing disconnected.

Hypothesis Tree4 nodes

● HSC AAV6 vs lentiviral · root

9 papers · evidence amber

● CD34+ tropism limits dose

6 papers · evidence green

○ Ex vivo → in vivo translation

2 papers · evidence grey

seren_ > gap = BM-HSC matched conditions

Evidence Foundation47 papers · ranked
Dever et al., 201696

Nature Methods · directly addresses

Romero et al., 201988

Blood · matched transduction protocol

Naldini et al., 202171

Cell · contradicts dose assumption

Sort: Relevance ↓ · Re-rank
Analysis Library · 9 methodsRun all

Theory Mapper

Map frameworks across all papers

Method Auditor

Compare methodology + blind spots

Evolution Timeline

How the field's thinking changed

Quote Miner

10 most citable sentences

Weakness Scanner

5 weakest arguments in the field

Bridge Builder

Adjacent fields your field ignores

Replication Audit

What has and hasn't replicated

Future Agenda

What the field needs to ask next

Jargon Translator

Plain English from all your papers

Mechanisms4 confirmed
Capsid entrygreen Strong · Naldini 2022Integrationgreen Strong · Aiuti 2022Innate sensingamber Building · 2 papersDose curvegrey Unknown · no pub data

seren_ > linking [Naldini 2022] to capsid pathway

Research Terminallive

you_ > /find papers on CD34 engraftment post-myeloablation

→ 8 papers found · 3 relevant · added to review queue

you_ > /add mechanism capsid tropism limits CD34 dose

→ mechanism logged · linked to root hypothesis

you_ > /decision proceed AAV6 phase-1 ex vivo

→ decision recorded · confidence: high · Mar 8

Research Proposalin progress
Specific Aims✓ complete
Background & Significance✓ complete
Innovation◐ draft
Approach — Aim 1◐ outline
Approach — Aim 2○ not started

seren_ > Aim 1 references 6 papers from your foundation

Data Artifacts3 files · parsed
csv

flow_cyto_run3.csv

2.1 MB · 847 events · 3 populations · QC flag on col 7

xlsx

engraftment_week6.xlsx

n=24 · primary endpoint · 3 arms

seren_ > The QC flag in run3 affects 12% of events — do you want to exclude col 7 before running the engraftment comparison?

Uncertainty Map3 unknowns

KNOWN

● AAV6 efficiency above 800bp payload

CONTESTED

⚡ Dose translation ex vivo → in vivo

Naldini 2021 vs Aiuti 2022

UNKNOWN

○ BM-HSC matched conditions · no pub data

Writing Review2 flags

§2.1 — unsupported claim

"...well-established safety profile..." — no citation. Naldini 2021 should support this.

§3.2 — contradicts decision log

Claims BM-HSC data exists. Your uncertainty map flags this as unknown.

Monitoring2 new papers

Scanning PubMed every 6h against your hypothesis

Mimitou et al., 2025 — new

Addresses your BM-HSC gap directly · review

Schiroli et al., 2025 — new

Contradicts Naldini 2021 on dose curve · review

1 paper in your foundation retracted — flag

Decision Log2 decisions

Mar 8 · High confidence

Proceed with AAV6 ex vivo protocol

Based on: Dever 2016 · Romero 2019

Uncertainty accepted: no BM-HSC data

Feb 22 · Medium confidence

Exclude mobilised HSCs from Phase 1 arm

Based on: Aiuti 2022 · Naldini 2021

what makes seren different

Zotero / Mendeley

Stores your papers. Organises your library. Tells you nothing about what the collection means for your question.

Seren connects every paper to your hypothesis. You see what supports it, what contradicts it, and what the literature has not answered yet.

Elicit / Consensus

Summarises papers. Finds relevant results. Produces outputs with no memory of your specific question or what you decided.

Seren tracks what you decided based on the evidence — and builds a permanent record of why, so you can always prove you thought carefully.

ChatGPT / Claude

Answers questions. Starts fresh every session. Has no knowledge of your specific study, your hypothesis tree, or your prior decisions.

Seren is a persistent workspace. It remembers every hypothesis, every evidence card, every uncertainty you accepted — and searches the literature in that context.

A research question structured.

Evidence mapped against a hypothesis.

Decisions logged with the reasoning behind them.

A workspace that remembers what you built.

Finally a tool that treats my research question as the starting point, not an afterthought.

— Postdoctoral researcher, biomedical sciences

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Free for individual researchers.

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