Concept

Sequence analysis

Related publications (30)

Towards automating de novo protein design for novel functionalities: controlling protein folds and protein-protein interactions

The sheer size of the protein sequence space is massive: a protein of 100 residues can have 20^100 possible sequence combinations; and knowing that this exceeds the number of atoms in the universe, the chance of randomly discovering a stable new sequence w ...

EPFL2022

KRAB zinc-finger proteins and their transposable element targets: between antagonism and cooperation

Jonas Caspar De Tribolet-Hardy

There are 377 Krüppel-associated box (KRAB) domain-containing zinc finger proteins (KZFPs) in the human genome, making them the largest family of transcription factors. KZFPs are defined by a N-terminal KRAB domain and several zinc-finger domains arranged ...

EPFL2022

Plasma confinement mode classification using a sequence-to-sequence neural network with attention

Alessandro Pau, Gino Marceca

In a typical fusion experiment, the plasma can have several possible confinement modes. At the tokamak a configuration variable, aside from the low (L) and high (H) confinement modes, an additional mode, dithering (D), is frequently observed. Developing me ...

IOP Publishing Ltd2021

Ultrafast homomorphic encryption models enable secure outsourcing of genotype imputation

Jean-Pierre Hubaux, Juan Ramón Troncoso-Pastoriza, David Jules Froelicher, Jean-Philippe Léonard Bossuat

Genotype imputation is a fundamental step in genomic data analysis, where missing variant genotypes are predicted using the existing genotypes of nearby "tag"variants. Although researchers can outsource genotype imputation, privacy concerns may prohibit ge ...

CELL PRESS2021

A Rosetta-based protein design protocol converging to natural sequences

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

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

Crypt4GH: a file format standard enabling native access to encrypted data

Juan Ramón Troncoso-Pastoriza

Motivation: The majority of genome analysis tools and pipelines require data to be decrypted for access. This potentially leaves sensitive genetic data exposed, either because the unencrypted data is not removed after analysis, or because the data leaves t ...

Oxford University Press2021

m6A methylation potentiates cytosolic dsDNA recognition in a sequence-specific manner

Andrea Ablasser, Muhammet Fatih Gülen

Nucleic acid sensing through pattern recognition receptors is critical for immune recognition of microbial infections. Microbial DNA is frequently methylated at the N-6 position of adenines (m6A), a modification that is rare in mammalian host DNA. We show ...

ROYAL SOC2021

Optimal Adversarial Policies in the Multiplicative Learning System With a Malicious Expert

Negar Kiyavash, Seyed Jalal Etesami

We consider a learning system based on the conventional multiplicative weight ( MW) rule that combines experts' advice to predict a sequence of true outcomes. It is assumed that one of the experts is malicious and aims to impose the maximum loss on the sys ...

IEEE-INST ELECTRICAL ELECTRONICS ENGINEERS INC2021

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

John Maddocks, Daiva Petkeviciute, Rahul Sharma, Marco Pasi

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

Structural design methodology in Integrally-Attached Timber Plate structures

Aryan Rezaei Rad, Petras Vestartas

The immediate application of research discoveries requires a global and exact understanding of the structure under consideration. To gain insight into the complex behavior of structures, numerical simulations are carried out in parallel to physical experim ...

Routledge, Taylor & Francis Group2021