Agentic biology, checked at the bench

Activity updated 3 November 2026

• How do you check an agent's analysis without redoing it by hand?

  BioinformaticsWet lab

  An agent can hand back a full analysis quickly, and the Cell Genomics review argues that checking it is now the hard part. Redoing it by hand defeats the point. Reading only the summary can miss quiet errors, such as the wrong reference or a filter that was dropped. I want to know which checks catch the most for the least effort. Help would look like a checklist you use, an example of an agent mistake you caught and how you caught it, or a paper that measures this.

• What actually predicts prime-editing efficiency at a new site?

  Wet labML

  Tools such as PRIDICT 2.0 predict prime-editing efficiency. I want to understand how well any efficiency predictor transfers to a new site, a new cell type or a different edit. Local chromatin, cell type and the edit itself could each matter, and I do not know which do. Finding out would take predictions set against measurements across sites and cell types. Papers that make that comparison would help, as would your own experience of which features held up and which did not.

• Which proteins tolerate a C-terminal tag, and how would you know in advance?

  Wet lab

  A C-terminal tag works for many proteins, but it can break function when the end of the protein carries something important, such as a localisation signal or an interaction motif. Finding out usually means making the edit and testing, which costs weeks. I would like a way to flag the risky ones before starting. Rules of thumb, sequence or structure based predictors, and published datasets that compare tagged and untagged protein function would all help.

• What would a benchmark for agentic genomics have to measure?

  MLBioinformatics

  Papers on agentic systems report wins on benchmark datasets. A benchmark that scores only the final answer says little about whether the analysis was right for the right reasons. A better one might also score the plan, the code, the intermediate outputs and whether the agent flagged its own uncertainty. Help would look like your view on what belongs in such a benchmark, and pointers to existing ones that already do some of this.

mrinal.joshi@imperial.ac.uk

• paperAgentic genomics: from pipeline automation to autonomous validationA good first read on what agentic genomics means. Its argument is that the bottleneck has moved from building pipelines to validating what agents produce. It is a review, so it will not tell you how any one system performs on your data.No background neededBioinformaticsMLAdded 21 October 2026
• toolAgentomicsThe claim to check is that it beat human expert solutions on a number of benchmark datasets. Performance on benchmarks does not always carry over to messier data, so I would want to see how it does on a new dataset before relying on it. Most interesting to people who build models from biomedical data and want an automated baseline.MLBioinformaticsAdded 21 October 2026
• agentAutoBAMinimal user input is the appeal and also the risk. Someone still has to check the plan and the output, and that checking is the validation problem the Cell Genomics review puts at the centre.BioinformaticsAdded 21 October 2026
• agentBio-CopilotThe interesting part is that human-agent interaction is built into the design. A person sits inside the analysis loop. Worth a look if you want an agent to help with large omics analyses without handing over the whole thing.BioinformaticsAdded 21 October 2026
• agentCellAtriaAn agentic framework from AstraZeneca that ingests and standardises single-cell RNA-seq data, with a chat interface in front of a pipeline called CellExpress. Worth a look if you work with single-cell data and want to see how an agent can handle the ingestion and standardisation step.BioinformaticsWet labAdded 21 October 2026
• agentClawBio skill libraryI contribute to this project, so weigh my view accordingly. It gives agents bioinformatics-specific skills to work from. The local-first design is the thing to check if your data is sensitive.BioinformaticsAdded 21 October 2026