13 papers · ranked by Valyu relevance
Shiyi Du, Gün Kaynar, Jiayi Li, Zhaoyi You + 2 more
Optimizing synonymous codon sequences to improve translation efficiency, RNA stability, and compositional properties is challenging because the search space grows exponentially with protein length and objectives interact through long range RNA structure. Dynamic programming-based methods can provide strong solutions…
Ramy Khabbaz, Jérémy Mateos, Marc Antonini, Serge Kas Hanna
The biochemical processes underlying DNA data storage, including synthesis, amplification, and sequencing, are inherently noisy. Consequently, base-level insertion, deletion, and substitution (IDS) errors, as well as sequence-level dropouts, occur and pose major challenges for reliable data retrieval. Here we introduce…
Zhimeng Zhou, Yang Nan, Minjie Mou, Yuntao Qian + 16 more
Artificial intelligence (AI) is increasingly permeating the drug development pipeline. Numerous algorithms for accelerating this multi-stage and multi-task process have been constructed, which depends heavily on expert design and labor-intensive task-specific optimization. Given that AI-driven acceleration of drug…
Weize Xu, Erwin Poussi, Quan Zhong, Zehua Zeng + 29 more
The convergence of large language model-powered autonomous agent systems and single-cell biology promises a paradigm shift in biomedical discovery. However, existing biological agent systems, building upon single-agent architectures, are narrowly specialized or overly general, limiting applications to routine analyses.…
Max Ward, Mary Richardson, Haining Lin, Michael Stamm + 7 more
mRNA medicines hold great promise, but designing sequences with high translation efficiency, robust in-solution stability, and manufacturability remains a major challenge due to the vast combinatorial space of synonymous coding sequences. Computational approaches such as mRNA folding algorithms have emerged as powerful…
Aditi T. Merchant, Daniel Guo, Ben Viggiano, Lucas Brennan-Almaraz + 6 more
Programmable composition of complex systems is a longstanding goal of biological research. Generative modeling has improved the reliability of computational design, but existing methods are highly specialized and are difficult to extend or compose. Here, we introduce Proto, a high-level programming language for…
Matthew Aquilina, Florian Katzmeier, Minke A.D. Nijenhuis, Siyuan Stella Wang + 8 more
Crisscross polymerization enables the assembly of hundreds of unique DNA origami ‘slats’ into micron-sized structures with nanoscale precision. To design these megastructures, thousands of handle sequences from a fixed library must be assigned to individual slats to encode the desired binding architecture. This…
Thomas A. Hopf, Artem Gazizov, Sergio Garcia Busto, Ethan Eschbach + 9 more
Machine learning methods for protein engineering are rarely interoperable, require bespoke workflows, and remain inaccessible to non-experts. Yet the design problems that matter most – conditional design subject to real-world constraints, multi-objective optimization, and iterative lab-in-the-loop workflows where…
Anh Phong Tran, Dhruv D. Jatkar, M. Ali Al-Radhawi, Elizabeth A. Ernst + 1 more
Minimal synthesis of Boolean functions is an NP-hard problem, and heuristic approaches typically give suboptimal circuits. However, in the emergent field of synthetic biology, genetic logic designs that use even a single additional Boolean gate can render a circuit unimplementable in a cell. This has led to a renewed…
Geraldene Munsamy, Gavin Ayres, Carla Greco, Keith Kam + 52 more
The ability to interpret, modify, and design DNA has driven many of the most significant advances in modern medicine, from diagnostics, biologics, and vaccines to cell and gene therapies. However, the inherent complexity of biological systems means that most modern medicines are still engineered using bespoke…
Chaitanya K. Joshi, Edoardo Gianni, Samantha L. Y. Kwok, Simon V. Mathis + 2 more
The design of RNA molecules with bespoke three-dimensional structures and functions is a central goal in synthetic biology and biotechnology. However, progress has been limited by the challenges of designing complex tertiary interactions such as pseudoknots, as well as engineering novel catalytic functions—problems…
Jeonghyeon Kim, Philip Romero
Large language models (LLMs) are increasingly deployed as agents for scientific discovery, but standardized frameworks for evaluating their performance and behavior in scientific workflows are lacking. Protein design provides a demanding test case because modern workflows combine stochastic generative models, structure…
Akashaditya Das, Janessa Grech, Selina Hung, Jiali Wu + 9 more
Precision proteome engineering requires tools that leverage CRISPR technologies, yet most current design platforms remain gene-centric. To bridge this gap, we introduce CORe Designer. Featuring an intuitive graphical user interface, CORe Designer enables researchers to design guide RNAs and homology-directed repair…