Related papers: Constrained Consensus Sequence Algorithm for DNA A…
DNA based storage systems received attention by many researchers. This includes archival and re-writable random access DNA based storage systems. In this work, we have developed an efficient technique to encode the data into DNA sequence by…
Aggregating different pieces of similar information is necessary to generate concise and easy to understand reports in technical domains. This paper presents a general algorithm that combines similar messages in order to generate one or…
(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…
As a medium for cold data storage, DNA stands out as it promises significant gains in storage capacity and lifetime. However, it comes with its own data processing challenges to overcome. Constrained codes over the DNA alphabet…
In this paper, we study achievable rates of concatenated coding schemes over a deoxyribonucleic acid (DNA) storage channel. Our channel model incorporates the main features of DNA-based data storage. First, information is stored on many,…
Composite DNA is a recent method to increase the base alphabet size in DNA-based data storage.This paper models synthesizing and sequencing of composite DNA and introduces coding techniques to correct substitutions, losses of entire…
Constraint-based pattern discovery is at the core of numerous data mining tasks. Patterns are extracted with respect to a given set of constraints (frequency, closedness, size, etc). In the context of sequential pattern mining, a large…
DNA, with remarkable properties of high density, durability, and replicability, is one of the most appealing storage media. Emerging DNA storage technologies use composite DNA letters, where information is represented by probability…
Connected acyclic graphs (trees) are data objects that hierarchically organize categories. Collections of trees arise in a diverse variety of fields, including evolutionary biology, public health, machine learning, social sciences and…
This paper describes a linear-time algorithm that finds the longest stretch in a sequence of real numbers (``scores'') in which the sum exceeds an input parameter. The algorithm also solves the problem of finding the longest interval in…
Data mining is the task of discovering interesting patterns from large amounts of data. There are many data mining tasks, such as classification, clustering, association rule mining, and sequential pattern mining. Sequential pattern mining…
We propose an assembly algorithm {\sc Barnacle} for sequences generated by the clone-based approach. We illustrate our approach by assembling the human genome. Our novel method abandons the original physical-mapping-first framework. As we…
Privacy-preserving data aggregation in ad hoc networks is a challenging problem, considering the distributed communication and control requirement, dynamic network topology, unreliable communication links, etc. Different from the widely…
In DNA-based data storage, DNA codes with biochemical constraints and error correction are designed to protect data reliability. Single-stranded DNA sequences with secondary structure avoidance (SSA) help to avoid undesirable secondary…
We propose generative neural network methods to generate DNA sequences and tune them to have desired properties. We present three approaches: creating synthetic DNA sequences using a generative adversarial network; a DNA-based variant of…
In array-based DNA synthesis, multiple strands of DNA are synthesized in parallel to reduce the time cost from the sum of their lengths to the length their shortest common supersequences. To maximize the amount of information that can be…
Next-generation sequencing technologies generate millions of short sequence reads, which are usually aligned to a reference genome. In many applications, the key information required for downstream analysis is the number of reads mapping to…
Previous divide-and-conquer segmentation analyses of DNA sequences do not provide a satisfactory stopping criterion for the recursion. This paper proposes that segmentation be considered as a model selection process. Using the tools in…
In this paper, we present a study of a kernel-based consensual aggregation on randomly projected high-dimensional features of predictions for regression. The aggregation scheme is composed of two steps: the high-dimensional features of…
Motivation: Despite significant advances in Third-Generation Sequencing (TGS) technologies, Next-Generation Sequencing (NGS) technologies remain dominant in the current sequencing market. This is due to the lower error rates and richer…