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 densities, ...

PMLR2024

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

Jaspreet Singh Saini

Understanding the ecological impacts of viruses on natural and engineered ecosystems relies on the accurate identification of viral sequences from community sequencing data. To maximize viral recovery from metagenomes, researchers frequently combine viral ...

Amer Soc Microbiology2024

Opportunities and challenges in design and optimization of protein function

Bruno Emanuel Ferreira De Sousa Correia, Casper Alexander Goverde

The field of protein design has made remarkable progress over the past decade. Historically, the low reliability of purely structure-based design methods limited their application, but recent strategies that combine structure-based and sequence-based calcu ...

Nature Portfolio2024

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

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

Anne-Florence Raphaëlle Bitbol, Umberto Lupo, Damiano Sgarbossa

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, Umberto Lupo, Nicola Dietler

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, Lloyd Haydn Hughes, Javiera Francisca Castillo Navarro

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

A generic diffusion-based approach for 3D human pose prediction in the wild

Alexandre Massoud Alahi, Saeed Saadatnejad, Taylor Ferdinand Mordan

Predicting 3D human poses in real-world scenarios, also known as human pose forecasting, is inevitably subject to noisy inputs arising from inaccurate 3D pose estimations and occlusions. To address these challenges, we propose a diffusion-based approach th ...

IEEE2023

Combining phylogeny and coevolution improves the inference of interaction partners among paralogous proteins

Anne-Florence Raphaëlle Bitbol

Author summaryWhen two protein families interact, their sequences feature statistical dependencies. First, interacting proteins tend to share a common evolutionary history. Second, maintaining structure and interactions through the course of evolution yiel ...

PUBLIC LIBRARY SCIENCE2023

A Geometric Transformer for Structural Biology: Development and Applications of the Protein Structure Transformer

Lucien Fabrice Krapp

Proteins, the central building blocks of life, play pivotal roles in nearly every biological function. To do so, these macromolecular structures interact with their surrounding environment in complex ways, leading to diverse functional behaviors. The predi ...

EPFL2023

Smart filter aided domain adversarial neural network for fault diagnosis in noisy industrial scenarios

Olga Fink, Gaëtan Michel Frusque, Tianfu Li, Qi Li, Baorui Dai

The application of unsupervised domain adaptation (UDA)-based fault diagnosis methods has shown significant efficacy in industrial settings, facilitating the transfer of operational experience and fault signatures between different operating conditions, di ...

2023

Robust Outlier Rejection for 3D Registration with Variational Bayes

Mathieu Salzmann, Zheng Dang, Jiancheng Yang, Zhen Wei, Haobo Jiang

Learning-based outlier (mismatched correspondence) rejection for robust 3D registration generally formulates the outlier removal as an inlier/outlier classification problem. The core for this to be successful is to learn the discriminative inlier/outlier f ...

Ieee Computer Soc2023

De novo designed proteins: a study in engineering novel folds and functions

Alexandra Krina Van Hall-Beauvais

Proteins control nearly every facet of life on a molecular level. Proteins are formed from linear strings of amino acids, which fold into three-dimensional structures that can enact functions. Evolution has created highly efficient proteins in diverse fold ...

EPFL2023

Effective field theory of the two Higgs doublet model

Timothy Cohen

We revisit the effective field theory of the two Higgs doublet model at tree level. The introduction of a novel basis in the UV theory allows us to derive matching coefficients in the effective description that resum important contributions from the Higgs ...

Springer Nature2023

Alignment & stability challenges for FCC-ee

Léon Van Riesen-Haupt, Frank Zimmermann

In order to achieve its ultra-low vertical emittance (1 pm) and high luminosity (of up to 230 x 10(34) cm(-2) s(-1) per collision point), the e(+)e(-) Future Circular Collider (FCC-ee) requires a well-informed alignment strategy, powerful correction method ...

SPRINGER2023

Improved antibody pharmacokinetics by disruption of contiguous positive surface potential and charge reduction using alternate human framework

Andrea Pfeifer, Florence Gauye, Tariq Afroz, Monisha Ratnam

Optimal pharmacokinetic (PK) properties of therapeutic monoclonal antibodies (mAbs) are essential to achieve the desired pharmacological benefits in patients. To accomplish this, we followed an approach comprising structure-based mAb charge engineering in ...

TAYLOR & FRANCIS INC2023

Learnable Wavelet Transform and Domain Adversarial Learning for Enhanced Bearing Fault Diagnosis

Olga Fink, Gaëtan Michel Frusque, Qi Li, Baorui Dai

The application of unsupervised domain adaptation (UDA)-based fault diagnosis methods has shown significant efficacy in industrial settings, facilitating the transfer of operational experience and fault signatures between different operating conditions, di ...

Research Publishing2023

End-to-end kernel learning via generative random Fourier features

Fanghui Liu, Jie Yang

Random Fourier features (RFFs) provide a promising way for kernel learning in a spectral case. Current RFFs-based kernel learning methods usually work in a two-stage way. In the first-stage process, learn-ing an optimal feature map is often formulated as a ...

ELSEVIER SCI LTD2023