Publications related to Sequence alignment

Towards improving full-length ribosome density prediction by bridging sequence and graph-based representations

Pierre Vandergheynst, Felix Naef, Cédric Gobet, Francesco Craighero, Mohan Vamsi Nallapareddy

Translation elongation plays an important role in regulating protein concentrations in the cell, and dysregulation of this process has been linked to several human diseases. In this study, we use data from ribo-seq experiments to model ribosome dwell times ...

2024

Alignment of ND3 molecules in dc-electric fields

Andreas Osterwalder, Viet Le Duc, Junwen Zou

The control of movement and orientation of gas-phase molecules has become the focus of many research areas in molecular physics. Here, ND3 molecules are polarized in a segmented, curved electrostatic guide and adiabatically aligned inside a rotatable mass ...

Aip Publishing2024

The capabilities of deep learning systems have advanced much faster than our ability to understand them. Whilst the gains from deep neural networks (DNNs) are significant, they are accompanied by a growing risk and gravity of a bad outcome. This is tr ...

TTool: A Supervised Artificial Intelligence-Assisted Visual Pose Detector for Tool Heads in Augmented Reality Woodworking

Yves Weinand, Julien Gamerro, Andrea Settimi, Florian Aymanns, Naravich Chutisilp

We present TimberTool (TTool v2.1.1), a software designed for woodworking tasks assisted by augmented reality (AR), emphasizing its essential function of the real-time localization of a tool head’s poses within camera frames. The localization process, a fu ...

2024

Generative power of a protein language model trained on multiple sequence alignments

Anne-Florence Raphaëlle Bitbol, Damiano Sgarbossa, Umberto Lupo

Computational models starting from large ensembles of evolutionarily related protein sequences capture a representation of protein families and learn constraints associated to protein structure and function. They thus open the possibility for generating no ...

eLIFE SCIENCES PUBL LTD2023

Impact of phylogeny on structural contact inference from protein sequence data

Anne-Florence Raphaëlle Bitbol, Nicola Dietler, Umberto Lupo

Local and global inference methods have been developed to infer structural contacts from multiple sequence alignments of homologous proteins. They rely on correlations in amino acid usage at contacting sites. Because homologous proteins share a common ance ...

ROYAL SOC2023

Supplementary dataset for Enzyme promiscuous profiles for protein sequence and reaction annotation

Vassily Hatzimanikatis, Ljubisa Miskovic, Homa Mohammadi Peyhani, Anastasia Sveshnikova

The data and scripts used to produce, analyze, and visualize the results of the manuscript Enzyme promiscuous profiles for protein sequence and reaction annotation by Homa MohammadiPeyhani, Anastasia Sveshnikova, Ljubisa Miskovic, and Vassily Hatzimanikati ...

Zenodo2023

Text as a Richer Source of Supervision in Semantic Segmentation Tasks

Devis Tuia, Valérie Zermatten, Javiera Francisca Castillo Navarro, Lloyd Haydn Hughes

This paper introduces TACOSS a text-image alignment approach that allows explainable land cover semantic segmentation by directly integrating semantic concepts encoded from texts. TACOSS combines convolutional neural networks for visual feature extraction ...

The Institute of Electrical and Electronics Engineers, Inc2023

Species-specific regulation of XIST by the JPX/FTX orthologs

Olga Marie Louise Rosspopoff

X chromosome inactivation (XCI) is an essential process, yet it initiates with remarkable diversity in various mammalian species. XIST, the main trigger of XCI, is controlled in the mouse by an interplay of lncRNA genes (LRGs), some of which evolved concom ...

OXFORD UNIV PRESS2023

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Sequence alignment

Towards improving full-length ribosome density prediction by bridging sequence and graph-based representations

Benchmarking informatics approaches for virus discovery: caution is needed when combining in silico identification methods

Alignment of ND3 molecules in dc-electric fields

Safe Deep Neural Networks

TTool: A Supervised Artificial Intelligence-Assisted Visual Pose Detector for Tool Heads in Augmented Reality Woodworking

Generative power of a protein language model trained on multiple sequence alignments

Impact of phylogeny on structural contact inference from protein sequence data

Supplementary dataset for Enzyme promiscuous profiles for protein sequence and reaction annotation

Text as a Richer Source of Supervision in Semantic Segmentation Tasks

Species-specific regulation of XIST by the JPX/FTX orthologs

Graph Chatbot

Chat with Graph Search

TTool: A Supervised Artificial Intelligence-Assisted Visual Pose Detector for Tool Heads in Augmented Reality Woodworking

Towards improving full-length ribosome density prediction by bridging sequence and graph-based representations

Benchmarking informatics approaches for virus discovery: caution is needed when combining in silico identification methods

Generative power of a protein language model trained on multiple sequence alignments

Species-specific regulation of XIST by the JPX/FTX orthologs

Alignment of ND3 molecules in dc-electric fields

Safe Deep Neural Networks

Impact of phylogeny on structural contact inference from protein sequence data

Supplementary dataset for Enzyme promiscuous profiles for protein sequence and reaction annotation

Text as a Richer Source of Supervision in Semantic Segmentation Tasks