9 papers · ranked by Valyu relevance
Xuebin Feng, Emma R. Master
Sequence similarity networks (SSNs) are graphical representations of sequence relationship frequently used for exploring protein sequence space. Conventional SSN workflows typically use BLAST to calculate sequence similarities and rely on external visualization tools to generate the final networks. Consequently, raw…
Yuqiao Liu, Siyu Yi, Hengchuang Yin, Wei Ju
Single-cell RNA sequencing profiles cellular heterogeneity at atlas scale, making automated annotation essential. However, target datasets often contain novel cell types missing from incomplete references. We present scOLAR, an ontology-guided open-set framework that learns prototypes over the Cell Ontology and uses…
Julius F. Witte, Artur Lissin, Isabel Schober, Christian Ebeling + 16 more
The vast amount of existing data on microbial strains holds immense potential to revolutionize bioindustry through the application of Artificial Intelligence (AI). However, the training of robust predictive AI models requires large-scale, unified, and non-redundant microbial datasets, which is currently severely…
Seonghwan Seo, Hyeongwoo Kim, Seokhyun Moon, Woo Youn Kim
Protein language models (PLMs) trained on evolutionary sequences learn representations that encode protein structure, enabling direct structure prediction without multiple-sequence alignments (MSAs). Here we present the Atlas model family, an open and trainable system spanning protein language modeling, monomer…
Lianne Gahan, Adélaïde Raguin, Partho Sakha De
Lignin’s complex and highly branched architecture plays a critical role in biomass utilisation. Yet, unravelling the intricate relation between lignin’s measurable structural features and the underlying biosynthesis dynamics remains a major challenge. This difficulty stems from the variability in monolignol and bond…
Yuichi Kodama, Colman O’Cathail, Linda Yankie, {'email': '', 'name': '', 'type': 'author'}
Members of the International Nucleotide Sequence Database Collaboration (INSDC; [https://www.insdc.org/]()) collect, exchange, and preserve comprehensive open nucleotide sequence information and provide tools for its access. The INSDC has stated its commitment to welcoming new members into the collaboration to be more…
Noémie Aubert Bonn, Andrew J. Stewart, Lukas Hughes-Noehrer
Open research practices are increasingly promoted to improve research transparency, reproducibility, accessibility, and societal impact. Despite growing support from research funders, institutions, and policy initiatives, adoption remains uneven across disciplines and research communities. This study examined perceived…
Lou Thomas, Gaia Scerif, Hodo Yusuf, Mackenzie Laird + 3 more
Diffusion decision models (DDMs) offer the potential to go beyond standard accuracy and response-time indices to better understand perceptual decision-making in autism. One unanswered question is whether autistic participants can flexibly adjust the speed and accuracy of their decision-making according to task demands.…
Amélie Barozet, Vincent Cabeli, Jean Ogier du Terrail, Alexey Rukhovich + 6 more
The development of climate-resilient crops would be greatly accelerated by models able to reason directly over plant genomic sequences and to pinpoint trait-associated regions or loci. Anticipating the impact of DNA base changes (variants) remains challenging, and understanding regulatory mechanisms is still an active…