Search · four archives
Search · four archives
10 papers · ranked by Valyu relevance
Eliezer Masliah
How transient neural representations become integrated and stable enough to function as internal neural models remains incompletely understood. Grounded in efficient coding, Bayesian and predictive frameworks, recurrent and attractor dynamics, neural state-space models, and systems neuroscience, the Principle of…
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…
Christoph Li, Josh Lawrimore, Dustin Moraczewski, Adam G. Thomas
labapi is a Python library that enables computational workflows to connect to LabArchives’ electronic lab notebook (ELN). Without an Application Programming Interface (API) connection, researchers must manually add workflow outputs through the LabArchives web interface, navigating to the appropriate page and uploading…
Fabio Cumbo, Kabir Dhillon, M. Hassan Najafi, Sercan Aygun + 1 more
The exponential growth of genomic databases necessitates alignment-free methods for comparing genomes. While MinHash-based tools have revolutionized this field by efficiently estimating the Average Nucleotide Identity based on k-mer sets, they inherently discard structural genomic information. We introduce HyperSketch…
Hayden Johnson, Boris A. Vinatzer, Reza Mazloom, Kassaye Belay + 2 more
Rapid and accurate microbial identification is critical for interpreting biological data in basic research and when making applied decisions on how to effectively treat patients and control human, animal, and plant diseases. Advancements in high-throughput sequencing have the potential to expedite fungal species…
Mame Seynabou Diop, Florian Bénitière, Kuldeep Kumar, Benjamin Clark + 5 more
Copy-number variants (CNVs) contribute to human disease and population trait variation. CNV detection from large whole-genome sequencing cohorts remains computationally demanding, as most methods require BAM or CRAM files. Genomic VCF (gVCF) files are smaller, routinely generated by standard variant-calling workflows…
Priyanka Bhutada, Nitin Goyal, Tatsam K. Lakhankiya, Sai D. Narahari + 8 more
Artificial Intelligence (AI) frameworks for automating scientific research have shown strong performance on benchmarks, but their utility for real-world industrial research remains insufficiently characterized. Extending the analysis presented in the first paper of this series, we evaluated the same five advanced AI…
Filippo Groppi, Jessica Ferrari
Spontaneous population bursts repeatedly expose synapses to correlated spike activity, but it is unclear whether such events reinforce pre-existing synaptic weight differences when precise firing order carries little information. We asked this in a conductance-based model of a bursting neuronal culture: 48 excitatory…
Namasi G Sankar, Georgios Miliotis, Simon Caton
Genome assembly is important in infectious disease surveillance, antimicrobial resistance monitoring, and cancer genomics. The task of reconstructing full genomic sequences from fragmented reads, can be framed as a large scale combinatorial optimisation problem. Recent advances in quantum computing have introduced new…
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…