12 papers · ranked by Valyu relevance
Odin Zhang, Jiaqi Wang, Tuscan Rock Thompson, Ziyi You + 3 more
Biomolecular interactions, including protein–protein interactions, protein–nucleic acid recognition, and protein–small molecule binding, underlie a wide range of biological processes and therapeutic mechanisms. Although recent de novo design methods can generate candidate binders for diverse molecular targets…
Ivan Specht, Soyoon Park, Seyone Chithrananda, Claudia L. Driscoll + 3 more
Viral mutation forecasting plays a key role in pandemic preparedness by enabling researchers to anticipate novel variants and design proactive interventions. Evolutionary histories, represented as phylogenetic trees, offer key insights into the emergence of past and present strains, yet their role in predicting future…
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…
Haziq Moinudeen, Alp Duygu
Functional protein sequence space is often described either by the sparsity of functional sequences or by the connectivity of neutral networks. These quantities characterize different properties: density measures the fraction of all sequences that are functional, whereas connectivity describes relationships among…
John McEnany, Benjamin H. Good
In fluctuating environments, the fates of new mutations depend on the fitness tradeoffs they experience across multiple environmental conditions. Selection on these tradeoffs is well-understood when mutations compete in isolation, but much less is known in the empirically relevant case where multiple mutations compete…
Hossameldin Loay, Gertjan Bisschop, Derek Setter, Abdelmajid Omarjee + 2 more
Sequentially Markovian Coalescent (SMC) models are a central element of contemporary population genetics, underlying many inferential methods. While the SMC has been shown to closely approximate the canonical Coalescent with Recombination (CwR) in terms of lowdimensional, two-locus summaries, its effects on the deeper…
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…
Kasper P. Hendriks, Ihsan A. Al-Shehbaz, Dmitry A. German, Marcus A. Koch + 49 more
Derived woodiness—the evolution of woody growth from herbaceous ancestors—has arisen hundreds of times across flowering plants, yet the environmental conditions associated with its repeated evolution remain poorly understood. Here, we analyse woodiness evolution in the mustard family (Brassicaceae; ∼4,150 species)…
Jordan Eizenga, Mira Mastoras, Julian K. Lucas, Julian Menendez + 14 more
Centromeres play essential roles in chromosome segregation and genome stability, yet they remain among the least characterized regions of the human genome. Despite advances in long-read sequencing and complete genome assembly, the extreme repetitiveness and structural complexity of these regions still challenge…
Henrique Reis Aguiar, Matthias H. Hennig
Predictive coding is a powerful normative framework for understanding cortical computation, but it is still an open question how biologically plausible networks with local plasticity support predictive inference and representation learning. In this work we show that a recurrent excitatory-inhibitory circuit with purely…
Fabio Barteri, Arcadi Navarro, Omar E. Cornejo
Continuous traits evolve unevenly across phylogenies, producing patterns of phenotypic differentiation shaped by both shared ancestry and lineage-specific change. Identifying exceptionally differentiated species pairs may therefore improve genome–phenome comparisons, but existing approaches rarely rank such contrasts…
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…