Publications related to Chemical approach for the study of the 'kissing complex' of Moloney murine leukaemia Virus

Related publications (32)

Ancestral genome reconstruction enhances transposable element annotation by identifying degenerate integrants

Wayo Matsushima, Didier Trono, Evaristo Jose Planet Letschert

Growing evidence indicates that transposable elements (TEs) play important roles in evolution by providing genomes with coding and non-coding sequences. Identification of TE-derived functional elements, however, has relied on TE annotations in individual s ...

2024

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

Zhidian Zhang

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

DNA methylation sites in early adulthood characterised by pubertal timing and development: a twin study

Markus Kirolos Youssef

Background Puberty is a highly heritable and variable trait, with environmental factors having a role in its eventual timing and development. Early and late pubertal onset are both associated with various diseases developing later in life, and epigenetic c ...

BMC2023

Recycling of Polymerase Chain Reaction (PCR) Kits

Francesco Stellacci, Yong Zhu, Weina Liu

Polymerase chain reaction (PCR) kits have been used as common diagnosing tools during the outbreak of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic, with daily worldwide usage in the millions. It is well known that at the beginn ...

AMER CHEMICAL SOC2023

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

Characterizing Conical Intersections in DNA/RNA Nucleobases with Multiconfigurational Wave Functions of Varying Active Space Size

Francesco Aquilante

We characterize the photochemically relevant conical intersections between the lowest-lying accessible electronic excited states of the different DNA/RNA nucleobases using Cholesky decomposition-based complete active space self-consistent field (CASSCF) al ...

Amer Chemical Soc2023

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

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

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

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

Fast Transformers with Clustered Attention

François Fleuret, Apoorv Vyas, Angelos Katharopoulos

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

Statistical physics of interacting proteins: Impact of dataset size and quality assessed in synthetic sequences

Pierre Mergny, Anne-Florence Raphaëlle Bitbol

Identifying protein-protein interactions is crucial for a systems-level understanding of the cell. Recently, algorithms based on inverse statistical physics, e.g., direct coupling analysis (DCA), have allowed to use evolutionarily related sequences to addr ...

2020

Protein language models trained on multiple sequence alignments learn phylogenetic relationships

Anne-Florence Raphaëlle Bitbol, Damiano Sgarbossa, Umberto Lupo

Self-supervised neural language models with attention have recently been applied to biological sequence data, advancing structure, function and mutational effect prediction. Some protein language models, including MSA Transformer and AlphaFold's EvoFormer, ...

Nature Portfolio2022

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

Genome Sequence Alignment - Design Space Exploration for Optimal Performance and Energy Architectures

David Atienza Alonso, Marina Zapater Sancho, Yasir Mahmood Qureshi

Next generation workloads, such as genome sequencing, have an astounding impact in the healthcare sector. Sequence alignment, the first step in genome sequencing, has experienced recent breakthroughs, which resulted in next generation sequencing (NGS). As ...

2020

Electronic Relaxation Dynamics of UV-Photoexcited 2-Aminopurine-Thymine Base Pairs in Watson-Crick and Hoogsteen Conformations

Rebecca Ann Ingle, Hugo Jean Baptiste Marroux

The fluorescent analogue 2-aminopurine (2AP) of the canonical nucleobase adenine (6-aminopurine) base-pairs with thymine (T) without disrupting the helical structure of DNA. It therefore finds frequent use in molecular biology for probing DNA and RNA struc ...

AMER CHEMICAL SOC2019

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

Toward a Dynamic Threshold for Quality-Score Distortion in Reference-Based Alignment

Marco Mattavelli, Claudio Paolo Alberti, Ana Angelica Hernandez Lopez

The intrinsic high entropy metadata, known as quality scores, are largely the cause of the substantial size of sequence data files. Yet, there is no consensus on a viable reduction of the resolution of the quality score scale, arguably because of collatera ...

2019

Circadian dynamics of RNA localisation in the mammalian liver

Clémence Yumie Syloun Hurni

Gene expression in eukaryotes is a complex multi-step process. It starts in the nucleus with transcription, the synthesis of a mRNA copy from a DNA template. While in the nucleus, the RNA transcript is subject to multiple co- and post-transcriptional modif ...

EPFL2021

On the relevance of quality score metadata in genomic sequence data for omics applications

Ana Angelica Hernandez Lopez

High-throughput sequencing of DNA molecules has revolutionized biomedical research by enabling the quantitative analysis of the genome to study its function, structure and dynamics. It is driving sequencing-based experiments in life sciences as evidenced b ...

EPFL2019