Related papers: A stitch in time: Efficient computation of genomic…
We propose an efficient algorithm for density fitting of Bloch waves for Hamiltonian operators with periodic potential. The algorithm is based on column selection and random Fourier projection of the orbital functions. The computational…
Large pools of synthetic DNA molecules have been recently used to reliably store significant volumes of digital data. While DNA as a storage medium has enormous potential because of its high storage density, its practical use is currently…
In this work we seek clusters of genomic words in human DNA by studying their inter-word lag distributions. Due to the particularly spiked nature of these histograms, a clustering procedure is proposed that first decomposes each…
Current high-resolution imaging techniques require an intact sample that preserves spatial relationships. We here present a novel approach, "puzzle imaging," that allows imaging a spatially scrambled sample. This technique takes many…
Protein motifs are conserved fragments occurred frequently in protein sequences. They have significant functions, such as active site of an enzyme. Search and clustering protein sequence motifs are computational intensive. Most existing…
The Beeping Network (BN) model captures important properties of biological processes. Paradoxically, the extremely limited communication capabilities of such nodes has helped BN become one of the fundamental models for networks. Since in…
Superbubbles are acyclic induced subgraphs of a digraph with single entrance and exit that naturally arise in the context of genome assembly and the analysis of genome alignments in computational biology. These structures can be computed in…
Many signal processing problems can be solved by maximizing the fitness of a segmented model over all possible partitions of the data interval. This letter describes a simple but powerful algorithm that searches the exponentially large…
We study the theoretical and practical runtime limits of k-means and k-median clustering on large datasets. Since effectively all clustering methods are slower than the time it takes to read the dataset, the fastest approach is to quickly…
Motivation: Predicting the secondary structure of an RNA sequence is useful in many applications. Existing algorithms (based on dynamic programming) suffer from a major limitation: their runtimes scale cubically with the RNA length, and…
The problem of fast items retrieval from a fixed collection is often encountered in most computer science areas, from operating system components to databases and user interfaces. We present an approach based on hash tables that focuses on…
The emergence and development of cancer is a consequence of the accumulation over time of genomic mutations involving a specific set of genes, which provides the cancer clones with a functional selective advantage. In this work, we model…
We present a new algorithm for the widely used density-based clustering method DBscan. Our algorithm computes the DBscan-clustering in $O(n\log n)$ time in $\mathbb{R}^2$, irrespective of the scale parameter $\varepsilon$ (and assuming the…
We present Brownian dynamics simulations of the facilitated diffusion of a protein, modelled as a sphere with a binding site on its surface, along DNA, modelled as a semi-flexible polymer. We consider both the effect of DNA organisation in…
We present a calculation technique for modeling inhomogeneous DNA replication kinetics, where replication factors such as initiation rates or fork speeds can change with both position and time. We can use our model to simulate data sets…
Sequencing by synthesis is used in many next-generation DNA sequencing technologies. Some of the technologies, especially those exploring the principle of single-molecule sequencing, allow incomplete nucleotide incorporation in each cycle.…
For decades, researchers have been applying computer simulation to address problems in biology. However, many of these "grand challenges" in computational biology, such as simulating how proteins fold, remained unsolved due to their great…
At the core of high throughput DNA sequencing platforms lies a bio-physical surface process that results in a random geometry of clusters of homogenous short DNA fragments typically hundreds of base pairs long - bridge amplification. The…
Most density based stream clustering algorithms separate the clustering process into an online and offline component. Exact summarized statistics are being employed for defining micro-clusters or grid cells during the online stage followed…
The optimal runtime of a quantum computer searching a database is typically cited as the square root of the number of items in the database, which is famously achieved by Grover's algorithm. With parallel oracles, however, it is possible to…