14 papers · ranked by Valyu relevance
Aial Sobeh, Simone Shamay-Tsoory, Bruno Kluwe-Schiavon, Giorgio Manenti
Human behavior is shaped by a pervasive motive to align with others, manifesting across a wide range of tendencies-from motor synchrony and emotional contagion to convergence in beliefs and choices. Existing accounts explain how alignment arises through predictive coding and observation-execution mechanisms, but they…
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…
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…
Leela Venkata Soujanya Nallamilli, Faisal Mohiuddin Ansari, Preetham Ravuri, Ajay K. Kubavat + 4 more
Clear aligner therapy is popular, but predicting whether patients will need refinement remains difficult. In this pilot study, 30 adults undergoing aligner therapy were assessed with an AI model trained on 2000 historical cases to forecast outcomes. The model predicted treatment completion without refinement with 70%…
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…
Sung Jong Lee, Keehyoung Joo, Sangjin Sim, Juyong Lee + 3 more
'Jooyoung Lee' 'Michael Assfalg'] Sequence-structure alignment for protein sequences is an important task for the template-based modeling of 3D structures of proteins. Building a reliable sequence-structure alignment is a challenging problem, especially for remote homologue target proteins. We built a method of…
Nimrod Serok, Ksenia Polonsky, Haim Ashkenazy, Itay Mayrose + 3 more
Multiple sequence alignment (MSA) inference is a central task in molecular evolution and comparative genomics, and the reliability of downstream analyses, including phylogenetic inference, depends critically on alignment quality. Despite this importance, most widely used MSA methods optimize the sum-of-pairs (SoP)…
Jiannan Chao, Furong Tang, Lei Xu, Lukasz Kurgan
The continuous development of sequencing technologies has enabled researchers to obtain large amounts of biological sequence data, and this has resulted in increasing demands for software that can perform sequence alignment fast and accurately. A number of algorithms and tools for sequence alignment have been designed…
Megan A. Barela Hudgell, L. Courtney Smith
The SpTransformer (SpTrf) gene family encodes a set of proteins that function in the sea urchin immune system. The gene sequences have a series of internal repeats in a mosaic pattern that is characteristic of this family. This mosaic pattern necessitates the insertion of large gaps, which has made alignments of the…
Daniel Wolf, Gasser Farrag, Tabea Flügge, Lan Huong Timm + 4 more
'Vincenzo Grassia' 'Letizia Perillo' 'Fabrizia d’Apuzzo' 'Juan Martin Palomo'] Background/Objectives: Machine learning (ML) models predicting the risk of refinement (i.e., a subsequent course of treatment being necessary) in clear aligner therapy (CAT) were developed and evaluated. Methods: An anonymized sample of 9942…
Yixiao Zhai, Zitong Zhang, Zhen Li
The reliability of multiple sequence alignment (MSA) results directly determines the credibility of the conclusions drawn from biological research. However, MSA is inherently an NP-hard problem, making it theoretically impossible to guarantee a globally optimal solution. Consequently, in addition to developing more…
Horia Todor, Lili M Kim, Jürgen Jänes, Hannah N Burkhart + 3 more
Accurate prediction of protein complex structures by AlphaFold3 and similar programs has been used to predict the presence of protein-protein interactions (PPIs), but this technique has never been applied to an entire genome due to onerous computational requirements and questionable utility. Here we present pooled-PPI…
Yanying Yu, Sandra Gawlitt, Lisa Barros de Andrade e Sousa, Erinc Merdivan + 3 more
'Erinc Merdivan' 'Marie Piraud' 'Chase L. Beisel' 'Lars Barquist'] CRISPR interference (CRISPRi) is the leading technique to silence gene expression in bacteria; however, design rules remain poorly defined. We develop a best-in-class prediction algorithm for guide silencing efficiency by systematically investigating…
Daria Gutnik, Peter Evseev, Konstantin Miroshnikov, Mikhail Shneider + 1 more
'Quan Zou'] Elucidation of the tertiary structure of proteins is an important task for biological and medical studies. AlphaFold, a modern deep-learning algorithm, enables the prediction of protein structure to a high level of accuracy. It has been applied in numerous studies in various areas of biology and medicine.…