6 papers · ranked by Valyu relevance
Weimin Zhang, Luciana Lazar-Stefanita, Hitoyoshi Yamashita, Michael J. Shen + 61 more
Whether synthetic genomes can power life has attracted broad interest in the synthetic biology field, especially when the synthetic genomes are extensively modified with thousands of designer features. Here we report de novo synthesis of the largest eukaryotic chromosome thus far, synIV, a 1,454,621-bp Saccharomyces…
Lukas Forer, Sebastian Schönherr
The workflow management system Nextflow builds together with the nf-core community an essential ecosystem in Bioinformatics. However, ensuring the correctness and reliability of large and complex pipelines is challenging, since a unified and automated unit-style testing framework specific to Nextflow is still missing.…
Shreyansh Agrawal, Harsh B. Anadkat, Kiran K. Athimoolam, Harsh Bhardwaj + 8 more
Recent advances in artificial intelligence (AI) have prompted claims about autonomous “AI scientists,” yet systematic evaluations of these capabilities remain scarce. This exploratory study investigates whether current AI frameworks can execute scientific research tasks beyond isolated demonstrations. We tested eight…
Sana Gul, Rizwan Bin Faiz, Mohammad Aljaidi, Ghassan Samara + 2 more
Cross-project defect prediction (CPDP) is a significant way of defect identification in the project. In cross-project defect prediction, we extract knowledge from the source project and apply that learned knowledge to predict labels for the target project. However, the model performance can be affected by features that…
Matthew Shang, Eric Klavins, Gilbert Bernstein
Formalizing protocols used in wetlab biological research as programs improves reproducibility by making protocols replicable and standardized. However, existing protocol languages have limited capacity for codifying error sources and standardizing error handling. When protocols inevitably go wrong, debugging must still…
Hongda Jiang, Jahziel Chase, Lianxiang Fu, Sathvik Shivaram + 1 more
This study presents a case analysis of using AI systems as co-pilots in biological research, focusing on functional protein networks in invasive colorectal cancer. We used public proteomic data alongside ChatGPT, GitHub Copilot, and PaperQA to automate parts of the workflow, including literature review, code…