RNA Design Reviews, Workshops, and Advisory Support

I work with research groups and biotech teams on RNA questions where the bottleneck is no longer computation itself, but deciding what the current structural evidence really supports.

Sometimes that means deciding whether a construct is mature enough to justify synthesis. Sometimes it means working out whether SHAPE or DMS data really changes the interpretation, or whether a local structural alternative is the more serious risk.

The work is usually less about producing one more prediction than about deciding whether a structural claim is strong enough to act on. I offer that support in three formats: independent design reviews, hands-on workshops, and selected longer-running advisory support.

When This Kind of Support Is Useful

  • You have an RNA construct or design concept and want an independent expert view before committing to synthesis or experiments.
  • Your team needs practical training in ViennaRNA, RNA structure prediction, chemical probing analysis, or structure-aware RNA design.
  • You have RNA structure data from SHAPE, SHAPE-MaP, DMS-MaPseq, or related probing workflows and need mechanistic interpretation to move forward with confidence.
  • You are preparing a grant, a go/no-go decision, or an internal review and need focused, credible scientific input.

RNA Design Review

An RNA design review is an independent written assessment of your construct, design strategy, probing-informed interpretation, or computational approach. You send the relevant materials such as sequences, SHAPE or DMS reactivity profiles, design notes, slides, or a manuscript section. I then prepare a structured technical review that looks at the design logic, the assumptions that carry the argument, the points where the inference is still underdetermined, and the places where kinetics, accessibility, or local alternatives are likely to matter. A follow-up call can be added if discussion would help.

This format is often useful when a team wants a credible external view before committing time, synthesis, or experimental effort.

What You Receive

Depending on the material you provide and the scope we agree on, a design review typically includes:

  • a short written memo or annotated slide deck
  • a clear statement of the main technical risks, uncertainties, and assumptions
  • practical recommendations for the next computational or experimental step, including when probing data materially changes the interpretation
  • an optional follow-up discussion to clarify tradeoffs and priorities

Who This Is Best Suited For

This kind of support is usually most useful for:

  • research groups planning a new RNA construct or assay series
  • biotech teams making a go or no-go decision on a candidate design
  • projects where computational results or SHAPE / DMS probing data need interpretation before further experiments are commissioned
  • teams that want an external expert view without building a full in-house RNA informatics function

Example Review Question

A typical request sounds like this:

"We have three candidate switch designs that all satisfy the same equilibrium constraints, but they differ in local alternatives around the aptamer and expression platform. We also have SHAPE-MaP data that does not fully agree with the predicted fold. Which construct is least likely to fail once folding kinetics, accessibility, and the assay conditions are taken into account?"

Questions like that are usually really about whether the current evidence is strong enough to justify synthesis.

Computational RNA Workshops

I also offer hands-on training in RNA structure prediction, ViennaRNA, SHAPE- and DMS-guided interpretation, and structure-aware RNA design for research teams, academic groups, and doctoral programmes. Workshops are available in short, half-day, and full-day formats, either remotely or onsite, and are scoped in advance to fit the background of the group.

These sessions build on formats already used in university courses at the University of Vienna, the University of Freiburg, and FH Campus Wien, as well as invited workshops and small-group training settings.

See the workshops page for full details on available formats and how sessions are organised.

Advisory Support

For teams that need ongoing input rather than a single review or workshop, I offer selected advisory arrangements. These usually combine regular calls with asynchronous review of materials and short written notes. The focus stays close to the decisions the team is actively working through, whether that means weighing a probing result against a folding model, deciding which construct variant deserves follow-up, or working out where additional computation is still informative and where it is not.

Get in Touch

If you are unsure which format fits your situation, write a few lines about the system, the current bottleneck, and the decision you are trying to make.