相关论文: Phase transition in the computational complexity o…

De novo genome assembly focuses on finding connections between a vast amount of short sequences in order to reconstruct the original genome. The central problem of genome assembly could be described as finding a Hamiltonian path through a…

We introduce a prime number generator in the form of a stochastic algorithm. The character of such algorithm gives rise to a continuous phase transition which distinguishes a phase where the algorithm is able to reduce the whole system of…

The problem of distributing the workload on a parallel computer to minimize the overall runtime is known as Multiprocessor Scheduling Problem. It is NP-hard, but like many other NP-hard problems, the average hardness of random instances…

Number partitioning is one of the classical NP-hard problems of combinatorial optimization. It has applications in areas like public key encryption and task scheduling. The random version of number partitioning has an "easy-hard" phase…

De novo assembly is the process of reconstructing the genome sequence of an organism from sequencing reads. Genome sequences are essential to biology, and assembly has been a central problem in bioinformatics for four decades. Until…

Genome assembly using high throughput data with short reads, arguably, remains an unresolvable task in repetitive genomes, since when the length of a repeat exceeds the read length, it becomes difficult to unambiguously connect the flanking…

Phase transitions in combinatorial problems have recently been shown to be useful in locating "hard" instances of combinatorial problems. The connection between computational complexity and the existence of phase transitions has been…

Number partitioning is an NP-complete problem of combinatorial optimization. A statistical mechanics analysis reveals the existence of a phase transition that separates the easy from the hard to solve instances and that reflects the…

Technical signs of progress during the last decades has led to a situation in which the accumulation of genome sequence data is increasingly fast and cheap. The huge amount of molecular data available nowadays can help addressing new and…

Genome assembly asks to reconstruct an unknown string from many shorter substrings of it. Even though it is one of the key problems in Bioinformatics, it is generally lacking major theoretical advances. Its hardness stems both from…

De novo genome assembly is challenging in highly repetitive regions; however, reference-guided assemblers often suffer from bias. We propose a framework for pangenome-guided sequence assembly, which can resolve short-read data in complex…

As computer scientists working in bioinformatics/computational biology, we often face the challenge of coming up with an algorithm to answer a biological question. This occurs in many areas, such as variant calling, alignment, and assembly.…

Over the past two decades, a series of works have aimed at studying the problem of genome assembly: the process of reconstructing a genome from sequence reads. An early formulation of the genome assembly problem showed that genome…

Genome sequencing is essential to decode genetic information, identify organisms, understand diseases and advance personalized medicine. A critical step in any genome sequencing technique is genome assembly. However, de novo genome…

Co-clustering, that is, partitioning a numerical matrix into homogeneous submatrices, has many applications ranging from bioinformatics to election analysis. Many interesting variants of co-clustering are NP-hard. We focus on the basic…

A major challenge in next-generation genome sequencing (NGS) is to assemble massive overlapping short reads that are randomly sampled from DNA fragments. To complete assembling, one needs to finish a fundamental task in many leading…

Genome rearrangements are events in which large blocks of DNA exchange pieces during evolution. The analysis of such events is a tool for understanding evolutionary genomics, based on finding the minimum number of rearrangements to…

(An updated version of this manuscript has been accepted to Scientific Reports in 2016, please refer to http://www.nature.com/articles/srep31900) The highly anticipated transition from next generation sequencing (NGS) to third generation…

We study the computational complexity of a very basic problem, namely that of finding solutions to a very large set of random linear equations in a finite Galois Field modulo q. Using tools from statistical mechanics we are able to identify…

The assembly index of assembly theory quantifies the minimal number of composition steps required to construct an object from elementary components. The study proves that the decision version of the assembly index problem is NP-complete,…