Publications related to Statistical Analysis of Protein Sequences: A Coevolutionary Study of Molecular Chaperones

Related publications (36)

Multimodal Prediction Framework for Total Shoulder Arthroplasty Outcomes: Integrating Morphological, Musculoskeletal, Finite Element, and Bayesian Causal Models

This thesis aimed to estimate the effect of demographic and biomechanical preoperative variables on total shoulder arthroplasty (TSA) outcomes. To achieve this, various biomechanical variables were calculated using a clinical database comprising normal and ...

EPFL2025

Observation of the ${{{\varLambda } ^0_{b}} \!\rightarrow {{J \hspace{-1.66656pt}/\hspace{-1.111pt}\psi }} {{\varXi } ^-} {{K} ^+} }$ and ${{{{\varXi } ^0_{b}} \!\rightarrow {{J \hspace{-1.66656pt}/\hspace{-1.111pt}\psi }} {{\varXi } ^-} {{\pi } ^+} }}$ decays

Olivier Schneider, Aurelio Bay, Tatsuya Nakada, Frédéric Blanc, Lesya Shchutska, Elena Graverini, Marie Theres Christin Bachmayer, Ettore Zaffaroni, Aravindhan Venkateswaran, Luis Miguel Garcia Martin, Yunxuan Song, Vitalii Lisovskyi, Federico Ronchetti, Radoslav Marchevski, Anni Matilda Kauniskangas, Dimitrios Kaminaris, Raphaël van Laak, Pierre Paul Louis Mayencourt, Brianna Leililani Thielen, Arnaud Merlin Gauthey, Gianluca Zunica, Abdul-Kerim Guseinov, Roberto Ribatti, Louis André Marie Jean Henry, Spencer Edward Collaviti, Julius Christian Daniel Schulte

The first observation of the

{{{{\varXi } ^0_{b}} \!\rightarrow {{J \hspace{-1.66656pt}/\hspace{-1.111pt}\psi }} {{\varXi } ^-} {{\pi } ^+} }}

decay and the most precise measurement of the branching fraction of the ${{{\varLambda } ^0_{b}} !\rightarrow ...

Springer Science and Business Media LLC2025

Plane Reciprocal Diagrams

Corentin Jean Dominique Fivet

James Clerk Maxwell is one of the giants of scientific thought, and whilst his groundbreaking contributions to electromagnetism and statistical physics are well known, his profound insights into the theory of structures are appreciated less widely. Maxwell ...

Cambridge University Press2025

Search for Ηc (2s) →ωω and Ωφ and Measurements of Χcj → Ωω and Ωφ in Ψ(2s) Radiative Processes

Yunxuan Song

Using (2712 +/- 14) x 10(6) psi(2S) events collected with the BESIII detector at the BEPCII collider, we search for the decays eta(c) (2S) -> omega omega and eta(c) (2S) -> omega phi via the process psi(2S) -> gamma eta(c)(2S). No statistically significant ...

AMER PHYSICAL SOC2025

Automated plasmid design for marker-free genome editing in budding yeast

Lazar Stojkovic, Mahsa Geramimanesh, Sahand Jamal Rahi, Vojislav Gligorovski, Marco Labagnara

Scarless genome editing in budding yeast with elimination of the selection marker has many advantages. Some markers such as URA3 and TRP1 can be recycled through counterselection. This permits seamless genome modification with pop-in/pop-out, in which a DN ...

OXFORD UNIV PRESS INC2025

Functional dynamics of G protein-coupled receptors reveal new routes for drug discovery

Patrick Daniel Barth

G protein-coupled receptors (GPCRs) are the largest human membrane protein family that transduce extracellular signals into cellular responses. They are major pharmacological targets, with approximately 26% of marketed drugs targeting GPCRs, primarily at t ...

2025

Microsecond time-resolved cryo-electron microscopy

Ulrich Lorenz

Microsecond time-resolved cryo-electron microscopy has emerged as a novel approach for directly observing protein dynamics. By providing microsecond temporal and near-atomic spatial resolution, it has the potential to elucidate a wide range of dynamics tha ...

2024

Ion Spectroscopy Reveals Structural Difference for Proteins Microhydrated by Retention and Condensation of Water

Oleg Boyarkine, Andrei Zviagin

Protein ubiquitin in its +7 charge state microhydrated by 5 and 10 water molecules has been interrogated in the gas phase by cold ion UV/IR spectroscopy. The complexes were formed either by condensing water onto the unfolded bare proteins in a temperature- ...

Amer Chemical Soc2024

Development of tools and methods for protein identification: From single molecules to in vivo applications

Salome Riccarda Püntener

As the fundamental machinery orchestrating cellular functions, proteins influence the state of every cell profoundly. As cells exhibit significant variations from one to another, analyzing the proteome on a single-cell level is imperative to unravel their ...

EPFL2024

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

Engineering novel protein interactions with therapeutic potential using deep learning-guided surface design

Anthony Marchand

Proteins are foundational biomolecules of life playing a crucial role in a myriad of biological processes. Their function often requires interplay with other biomolecules, including proteins themselves. Protein-protein interactions (PPIs) are essential for ...

EPFL2024

Toward universal cell embeddings: integrating single-cell RNA-seq datasets across species with SATURN

Maria Brbic

Analysis of single-cell datasets generated from diverse organisms offers unprecedented opportunities to unravel fundamental evolutionary processes of conservation and diversification of cell types. However, interspecies genomic differences limit the joint ...

Nature Publishing Group2024

Recording physiological history of cells with chemical labeling

Kai Johnsson, Julien Hiblot

Recordings of the physiological history of cells provide insights into biological processes, yet obtaining such recordings is a challenge. To address this, we introduce a method to record transient cellular events for later analysis. We designed proteins t ...

American Association for the Advancement of Science2024

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

From Sequence to Dynamics to Function: Computational Design of Allostery and Ligand Selectivity in G-Protein Coupled Receptors

Mahdi Hijazi

The phenomenon of allostery, a general property in proteins that has been heralded as "the second secret of life" remains elusive to our understanding and even more challenging to incorporate into protein design. One example of allosteric proteins with gre ...

EPFL2024

Prolamins' 3D structure: A new insight into protein modeling using the language of numbers and shapes

Niloufar Sharif

This study combined protein modeling methods to generate the prolamins' fractions as precise as possible. Hence, gliadins, zeins, kafirins, hordeins, secalins, avenins and oryzins were generated based on their characteristics and disulfide mapping. Finding ...

Elsevier Sci Ltd2024

Structure-function analysis of the cyclic β-1,2-glucan synthase from Agrobacterium tumefaciens

Henning Paul-Julius Stahlberg, Dongchun Ni

The synthesis of complex sugars is a key aspect of microbial biology. Cyclic beta-1,2-glucan (C beta G) is a circular polysaccharide critical for host interactions of many bacteria, including major pathogens of humans (Brucella) and plants (Agrobacterium). ...

Nature Portfolio2024

Predicting protein interactions using geometric deep learning on protein surfaces

Freyr Sverrisson

In the domain of computational structural biology, predicting protein interactions based on molecular structure remains a pivotal challenge. This thesis delves into this challenge through a series of interconnected studies. The first chapter introduces th ...

EPFL2024

Structure and dynamics of liquid water from ab initio simulations: adding Minnesota density functionals to Jacob's ladder

Ursula Röthlisberger, Martin Peter Bircher, Justin Villard

The accurate representation of the structural and dynamical properties of water is essential for simulating the unique behavior of this ubiquitous solvent. Here we assess the current status of describing liquid water using ab initio molecular dynamics, wit ...

Royal Soc Chemistry2024