12 papers · ranked by Valyu relevance
Toshitake Asabuki, Claudia Clopath
Recurrent neural circuits often face inherent complexities in learning and generating their desired outputs, especially when they initially exhibit chaotic spontaneous activity. While the celebrated FORCE learning rule can train chaotic recurrent networks to produce coherent patterns by suppressing chaos, it requires…
Morten Nielsen, Claus Lundegaard, Ole Lund
Background Antigen presenting cells (APCs) sample the extra cellular space and present peptides from here to T helper cells, which can be activated if the peptides are of foreign origin. The peptides are presented on the surface of the cells in complex with major histocompatibility class II (MHC II) molecules.…
Shahroudi, Novin, Komisarenko, Viacheslav + 2 more
Every prediction is ultimately used in a downstream task. Consequently, evaluating prediction quality is more meaningful when considered in the context of its downstream use. Metrics based solely on predictive performance often diverge from measures of real-world downstream impact. Existing approaches incorporate the…
Byung-Jun Yoon
Background Sequence alignment has become an indispensable tool in modern molecular biology research, and probabilistic sequence alignment models have been shown to provide an effective framework for building accurate sequence alignment tools. One such example is the pair hidden Markov model (pair-HMM), which has been…
Zhen Tan, Yinghan Fu, Gaurav Sharma, David H. Mathews
This paper presents TurboFold II, an extension of the TurboFold algorithm for predicting secondary structures for multiple RNA homologs. TurboFold II augments the structure prediction capabilities of TurboFold by additionally providing multiple sequence alignments. Probabilities for alignment of nucleotide positions…
Tao Fang, Damian Szklarczyk, Radja Hachilif, Christian von Mering
Protein-protein interactions (PPIs) play essential roles in most biological processes. The binding interfaces between interacting proteins impose evolutionary constraints that have successfully been employed to predict PPIs from multiple sequence alignments (MSAs). To construct MSAs, critical choices have to be made…
Evan Hubinger, Adam S. Jermyn, Johannes Treutlein, Rubi Hudson + 1 more
'Kate Woolverton'] Unfortunately, such approaches also raise a variety of potentially fatal safety problems, particularly surrounding situations where predictive models predict the output of other AI systems, potentially unbeknownst to us. There are numerous potential solutions to such problems, however, primarily via…
Maryam Gillani, Gianluca Pollastri
Alignments in bioinformatics refer to the arrangement of sequences to identify regions of similarity that can indicate functional, structural, or evolutionary relationships. They are crucial for bioinformaticians as they enable accurate predictions and analyses in various applications, including protein subcellular…
Maurits Dijkstra, Punto Bawono, Sanne Abeln, K. Anton Feenstra + 3 more
'Wan Fokkink' 'Jaap Heringa' 'Ilya Ioshikhes'] Protein or DNA motifs are sequence regions which possess biological importance. These regions are often highly conserved among homologous sequences. The generation of multiple sequence alignments (MSAs) with a correct alignment of the conserved sequence motifs is still…
Maurits J J Dijkstra, Atze J van der Ploeg, K Anton Feenstra, Wan J Fokkink + 3 more
Multiple sequence alignment (MSA) is one of the fundamental tasks in bioinformatics, essential to a wide variety of workflows, including fold prediction, phylogenetic analysis and mutation impact prediction. The exact solution with dynamic programming is not feasible for more than a handful of sequences. For protein…
David Medina-Ortiz, Sebastián Contreras, Juan Amado-Hinojosa, Jorge Torres-Almonacid + 3 more
'Jorge Torres-Almonacid' 'Juan A. Asenjo' 'Marcelo A. Navarrete' 'Álvaro Olivera‐Nappa'] Predicting the effect of mutations in proteins is one of the most critical challenges in protein engineering; by knowing the effect a substitution of one (or several) residues in the protein's sequence has on its overall…
Z. Shreif, Deborah A. Striegel, Vipul Periwal
A nucleotide sequence 35 base pairs long can take 1,180,591,620,717,411,303,424 possible values. An example of systems biology datasets, protein binding microarrays, contain activity data from about 40000 such sequences. The discrepancy between the number of possible configurations and the available activities is…