Publications associées à Sequence motif

Investigating the intra-molecular and inter-molecular effects of post-translational modifications on intrinsically disordered protein regions and structured protein regions

Post-translational modifications (PTMs) play a pivotal role in regulating protein structure, interaction, and function. Aberrant PTM patterns are associated with diseases. Moreover, individual PTMs have a complex interaction with each other, known as PTM c ...

EPFL2024

Computational identification and experimental characterization of preferred downstream positions in human core promoters

Philipp Bucher, René Dreos

Author summary Transcription of genes by the RNA polymerase II enzyme initiates at a genomic region termed the core promoter. The core promoter is a regulatory region that may contain diverse short DNA sequence motifs/elements that confer specific properti ...

2021

Structure-Property Relationships in Complex Materials by Combining Supervised and Unsupervised Machine Learning

Benjamin Aaron Helfrecht

The work presented in this thesis combines supervised and unsupervised machine learning to examine structure-property relationships in databases of materials. While either supervised learning or unsupervised learning alone can be a powerful tool for assess ...

EPFL2021

Sequence-dependent structural properties of B-DNA: what have we learned in 40 years?

John Maddocks, Daiva Petkeviciute, Rahul Sharma, Marco Pasi, Paolo Carloni

The structure of B-DNA, the physiological form of the DNA molecule, has been a central topic in biology, chemistry and physics. Far from uniform and rigid, the double helix was revealed as a flexible and structurally polymorphic molecule. Conformational ch ...

Springernature2021

Bottom-up de novo design of functional proteins with complex structural features

Luciano Andres Abriata, Bruno Emanuel Ferreira De Sousa Correia, Sandrine Madeleine Suzanne Georgeon, Leo Scheller, Jaume Bonet Martinez, Fabian Sesterhenn, Stéphane Rosset, Che Yang, Eva Anna van Aalen

De novo protein design has enabled the creation of new protein structures. However, the design of functional proteins has proved challenging, in part due to the difficulty of transplanting structurally complex functional sites to available protein structur ...

2021

A Rosetta-based protein design protocol converging to natural sequences

Bruno Emanuel Ferreira De Sousa Correia, Stéphane Rosset, Zander Harteveld, Giulia Sormani

Computational protein design has emerged as a powerful tool capable of identifying sequences compatible with pre-defined protein structures. The sequence design protocols, implemented in the Rosetta suite, have become widely used in the protein engineering ...

AMER INST PHYSICS2021

Microfluidic iMITOMI platform to study the architecture of low-affinity transcription factor binding site clusters

Ivan Istomin

Gene regulatory networks (GRNs) determine cellular behaviour, and ultimately the functioning of single- and multicellular organisms. Transcription factors regulate gene expression by binding to DNA or via remodelling chromatin. Recent advances in biotechno ...

EPFL2020

Insights gained from a comprehensive all-against-all transcription factor binding motif benchmarking study

Giovanna Ambrosini, Philipp Bucher, Romain Fernand Pietro Groux

BackgroundPositional weight matrix (PWM) is a de facto standard model to describe transcription factor (TF) DNA binding specificities. PWMs inferred from in vivo or in vitro data are stored in many databases and used in a plethora of biological application ...

2020

Hybrid Transcriptional Regulators for the Screening of Target DNA Motifs in Organohalide-Respiring Bacteria

Christof Holliger, Julien Maillard, Mathilde Stéphanie Willemin, Marie Vingerhoets

The bioremediation of persistent organohalide molecules under anoxic conditions mostly relies on the bacterial process called organohalide respiration (OHR). Organohalide-respiring bacteria (OHRB) are phylogenetically diverse anaerobic bacteria that share ...

Frontiers Media SA2020

Ultraviolet Photodissociation of Peptides: New Insight on the Mobile Proton Model

Oleg Boyarkine, Aleksandr Pereverzev, Elizaveta Solovyeva

In this work, we study the mechanism of peptide photodissociation by ultraviolet irradiation at 193 nm wavelength and discuss the role of ionization proton in this process. We found that substituting the ionization proton for the alkali metal cations (sodi ...

PLEIADES PUBLISHING INC2020

Fast Transformers with Clustered Attention

François Fleuret, Angelos Katharopoulos, Apoorv Vyas

Transformers have been proven a successful model for a variety of tasks in sequence modeling. However, computing the attention matrix, which is their key component, has quadratic complexity with respect to the sequence length, thus making them prohibitivel ...

2020

Atomic Motif Recognition in (Bio)Polymers: Benchmarks From the Protein Data Bank

Michele Ceriotti, Piero Gasparotto, Benjamin Aaron Helfrecht, Federico Giberti

Rationalizing the structure and structure–property relations for complex materials such as polymers or biomolecules relies heavily on the identification of local atomic motifs, e.g., hydrogen bonds and secondary structure patterns, that are seen as buildin ...

2019

An Interactive Gameplay to Crowdsource Multiple Sequence Alignment of Genome Sequences: Genenigma

Kalpani Anuradha Welivita

Comparative genomics is a field of research that compares genomes of different organisms to identify common patterns. It is a powerful method used to identify the genetic diseases that cause mutations. Multiple Sequence Alignment (MSA) is an intermediate s ...

ASSOC COMPUTING MACHINERY2019

Using Regularized Linear-Regression Surrogate Models for Accurate Probabilistic Structural Identification

Ian Smith, Sai Ganesh Sarvotham Pai

Model-based data interpretation has the potential to increase knowledge of structural behavior and support asset management. Models are usually conservative and contain many parameters and sources of systematic uncertainty, which need to be taken into acco ...

AMER SOC CIVIL ENGINEERS2019

The Membrane-Bound C Subunit of Reductive Dehalogenases: Topology Analysis and Reconstitution of the FMN-Binding Domain of PceC

Julien Maillard, Romain Hamelin, Mathilde Stéphanie Willemin, Géraldine Florence Buttet, Aamani Rupakula Boyanapalli

Organohalide respiration (OHR) is the energy metabolism of anaerobic bacteria able to use halogenated organic compounds as terminal electron acceptors. While the terminal enzymes in OHR, so-called reductive dehalogenases, are well-characterized, the identi ...

Frontiers Media SA2018

The membrane-bound C subunit of reductive dehalogenases: topology analysis and reconstitution of the FMN-binding domain of PceC

Julien Maillard, Romain Hamelin, Mathilde Stéphanie Willemin, Géraldine Florence Buttet, Aamani Rupakula Boyanapalli

Organohalide respiration (OHR) is the energy metabolism of anaerobic bacteria able to use halogenated organic compounds as terminal electron acceptors. While the terminal enzymes in OHR, so-called reductive dehalogenases, are well-characterized, the identi ...

Frontiers Media SA2018

The gene family-free median of three

Metin Balaban

Background: The gene family-free framework for comparative genomics aims at providing methods for gene order analysis that do not require prior gene family assignment, but work directly on a sequence similarity graph. We study two problems related to the b ...

2017

A map of human PRDM9 binding provides evidence for novel behaviors of PRDM9 and other zinc-finger proteins in meiosis

Michaël Imbeault

PRDM9 binding localizes almost all meiotic recombination sites in humans and mice. However, most PRDM9-bound loci do not become recombination hotspots. To explore factors that affect binding and subsequent recombination outcomes, we mapped human PRDM9 bind ...

Elife Sciences Publications Ltd2017

Molecular Imaging of Biopolymers Enabled by Electrospray-Ion Beam Deposition

Sabine Abb

Biomolecular functional complexes often serve as inspiration for the development of artificial molecular nanostructures. The functionality of the biomolecular structures is based on complex and adaptable binding motifs that have evolved over billions of ye ...

EPFL2017

SMiLE-seq identifies binding motifs of single and dimeric transcription factors

Didier Trono, Giovanna Ambrosini, Bart Deplancke, Philipp Bucher, Romain Fernand Pietro Groux, Riccardo Dainese, Daniel Alpern, Michaël Imbeault, Alina Isakova, Pernille Yde Rainer

Resolving the DNA-binding specificities of transcription factors (TFs) is of critical value for understanding gene regulation. Here, we present a novel, semiautomated protein-DNA interaction characterization technology, selective microfluidics-based ligand ...

Nature Publishing Group2017