Publications related to Searching the coding region for microRNA targets

Reach For the Arcs: Reconstructing Surfaces from SDFs via Tangent Points

We introduce an algorithm to reconstruct a mesh from discrete samples of a shape's Signed Distance Function (SDF). A simple geometric reinterpretation of the SDF lets us formulate the problem through a point cloud, from which a surface can be extracted wit ...

Association for Computing Machinery2024

A ride time-oriented scheduling algorithm for dial-a-ride problems

Nikolaos Geroliminis, Claudia Bongiovanni, Mor Kaspi

This paper offers a new algorithm to efficiently optimize scheduling decisions for dial-a-ride problems (DARPs), including problem variants considering electric and autonomous vehicles (e-ADARPs). The scheduling heuristic, based on linear programming theor ...

Pergamon-Elsevier Science Ltd2024

Towards improving full-length ribosome density prediction by bridging sequence and graph-based representations

Felix Naef, Pierre Vandergheynst, Cédric Gobet, Mohan Vamsi Nallapareddy, Francesco Craighero

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

Adaptive projected variational quantum dynamics

Giuseppe Carleo, Stefano Barison, David Linteau

We propose an adaptive quantum algorithm to prepare accurate variational time evolved wave functions. The method is based on the projected variational quantum dynamics (pVQD) algorithm, that performs a global optimization with linear scaling in the number ...

Amer Physical Soc2024

Gibbs sampling the posterior of neural networks

Giovanni Piccioli, Lenka Zdeborová, Emanuele Troiani

In this paper, we study sampling from a posterior derived from a neural network. We propose a new probabilistic model consisting of adding noise at every pre- and post-activation in the network, arguing that the resulting posterior can be sampled using an ...

Iop Publishing Ltd2024

Variants of the gain domain of adhesion g protein-coupled receptors

Louis Georges Baptiste Dumas, Matthieu François Marfoglia, Patrick Daniel Barth

The present invention relates to variants of the GAIN domain (G-protein-coupled receptor autoproteolysis-inducing domain) of an adhesion G protein-coupled receptor (ADGRG), such as a GAIN domain variant comprising or consisting of the amino acid sequence o ...

2023

Single-Molecule Peptide Identification Using Fluorescence Blinking Fingerprints

Pablo Rivera Fuentes, Salome Riccarda Püntener

The ability to identify peptides with single-molecule sensitivity would lead to next-generation proteomics methods for basic research and clinical applications. Existing single-molecule peptide sequencing methods can read some amino acid sequences, but the ...

AMER CHEMICAL SOC2023

Landscapes of DNA Mechanics and Genomes

Thomas Antonin Zwahlen

The local physical properties - such as shape and flexibility - of the DNA double-helix is today widely believed to be influenced by nucleic acid sequence in a non-trivial way. Furthermore, there is strong evidence that these properties play a role in many ...

EPFL2023

Bayesian reconstruction of memories stored in neural networks from their connectivity

Florent Gérard Krzakala, Lenka Zdeborová

The advent of comprehensive synaptic wiring diagrams of large neural circuits has created the field of connectomics and given rise to a number of open research questions. One such question is whether it is possible to reconstruct the information stored in ...

2023

Results on Sparse Integer Programming and Geometric Independent Sets

Jana Tabea Cslovjecsek

An integer linear program is a problem of the form max{c^T x : Ax=b, x >= 0, x integer}, where A is in Z^(n x m), b in Z^m, and c in Z^n. Solving an integer linear program is NP-hard in general, but there are several assumptions for which it becomes fixed ...

EPFL2023

cgNA+: A sequence-dependent coarse-grain model of double-stranded nucleic acids

Rahul Sharma

DNA mechanics plays a crucial role in many biological processes, including nucleosome positioning and protein-DNA interactions. It is believed that nature employs epigenetic modifications in DNA to further regulate gene expression. Moreover, double-strande ...

EPFL2023

Diverse cell-specific patterns of alternative polyadenylation in Drosophila

Bart Deplancke, Sandy Lee

Most genes in higher eukaryotes express isoforms with distinct 3' untranslated regions (3' UTRs), generated by alternative polyadenylation (APA). Since 3' UTRs are predominant locations of post-transcriptional regulation, APA can render such programs condi ...

Nature Portfolio2022

Approximate CVPp in time 2(0.802n)

Friedrich Eisenbrand, Moritz Andreas Venzin

We show that a constant factor approximation of the shortest and closest lattice vector problem in any l(p)-norm can be computed in time 2((0.802 + epsilon)n). This matches the currently fastest constant factor approximation algorithm for the shortest vect ...

ACADEMIC PRESS INC ELSEVIER SCIENCE2022

Hybrid Flock - Formation Control Algorithms

Alcherio Martinoli, Cyrill Silvan Baumann, Jonas Perolini, Emna Tourki

Two prominent categories for achieving coordinated multirobot displacement are flocking and navigation in formation. Both categories have their own body of literature and characteristics, including their respective advantages and disadvantages. While typic ...

Springer Nature Switzerland2022

A mitochondria-specific mutational signature of aging: increased rate of A > G substitutions on the heavy strand

Jacques Fellay, Stepan Denisov, Konstantin Popadin, Dmitrii Iliushchenko

The mutational spectrum of the mitochondrial DNA (mtDNA) does not resemble any of the known mutational signatures of the nuclear genome and variation in mtDNA mutational spectra between different organisms is still incomprehensible. Since mitochondria are ...

OXFORD UNIV PRESS2022

Tight Vector Bin Packing with Few Small Items via Fast Exact Matching in Multigraphs

Adam Teodor Polak, Alexandra Anna Lassota

We solve the Bin Packing problem in O^*(2^k) time, where k is the number of items less or equal to one third of the bin capacity. This parameter measures the distance from the polynomially solvable case of only large (i.e., greater than one third) items. O ...

Schloss Dagstuhl – Leibniz-Zentrum fur Informatik2022

Ribo-DT: An automated pipeline for inferring codon dwell times from ribosome profiling data

Felix Naef, Cédric Gobet

Protein synthesis is an energy consuming process characterised as a pivotal and highly regulated step in gene expression. The net protein output is dictated by a combination of translation initiation, elongation and termination rates that have remained dif ...

ACADEMIC PRESS INC ELSEVIER SCIENCE2022

Equivalence Checking for Orthocomplemented Bisemilattices in Log-Linear Time

Viktor Kuncak, Simon Guilloud

We present a quasilinear time algorithm to decide the word problem on a natural algebraic structures we call orthocomplemented bisemilattices, a subtheory of boolean algebra. We use as a base a variation of Hopcroft, Ullman and Aho algorithm for tree isomo ...

Springer2022

Geometrical Treatise on the Modelling of 3D Particulate Inclusion-Matrix Microstructures with an Application to Historical Stone Masonry Walls

Mahmoud S. M. Shaqfa

As historical stone masonry structures are vulnerable and prone to damage in earthquakes, investigating their structural integrity is important to reduce injuries and casualties while preserving their historical value. Stone masonry is a composite material ...

EPFL2022

Learning-Augmented Dynamic Power Management with Multiple States via New Ski Rental Bounds

Adam Teodor Polak, Marek Elias

We study the online problem of minimizing power consumption in systems with multiple power-saving states. During idle periods of unknown lengths, an algorithm has to choose between power-saving states of different energy consumption and wake-up costs. We d ...

2021