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A Fast and Exact Algorithm for the Exemplar Breakpoint Distance

Related publications (40)

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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 p ...

EPFL2023

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

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Ru/CNF catalysts of different Ru nanoparticle (NP) sizes (0.9-2.7 nm) were assessed for their performance in continuous supercritical water gasification (SCWG) of glycerol. A structure sensitivity of Ru was demonstrated, with high initial turnover frequenc ...

2022

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

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

Genome-wide variation in nucleotides and retrotransposons in alpine populations of Arabis alpina (Brassicaceae)

Stéphane Joost, Aude Rogivue

Advances in high‐throughput sequencing have promoted the collection of reference genomes and genome‐wide diversity. However, the assessment of genomic variation among populations has hitherto mainly been surveyed through single‐nucleotide polymorphisms (SN ...

2019

New Algorithmic Paradigms for Discrete Problems using Dynamical Systems and Polynomials

Damian Mateusz Straszak

Optimization is a fundamental tool in modern science. Numerous important tasks in biology, economy, physics and computer science can be cast as optimization problems. Consider the example of machine learning: recent advances have shown that even the most s ...

EPFL2018

Many modern services need to routinely perform tasks on a large scale. This prompts us to consider the following question: How can we design efficient algorithms for large-scale computation? In this thesis, we focus on devising a general strategy to addr ...

EPFL2018

Block Oriented Programming: Automating Data-Only Attacks

Mathias Josef Payer

With the widespread deployment of Control-Flow Integrity (CFI), control-flow hijacking attacks, and consequently code reuse attacks, are significantly more difficult. CFI limits control flow to well-known locations, severely restricting arbitrary code exec ...

ASSOC COMPUTING MACHINERY2018

A fundamental problem in comparative genomics is to compute the distance between two genomes in terms of its higher level organization (given by genes or syntenic blocks). For two genomes without duplicate genes, we can easily define (and almost always eff ...

Mary Ann Liebert, Inc2017

Many important questions in molecular biology, evolution, and biomedicine can be addressed by comparative genomic approaches. One of the basic tasks when comparing genomes is the definition of measures of similarity (or dissimilarity) between two genomes, ...

Mary Ann Liebert2017