相关论文: Suffix Arrays for Spaced-SNP Databases

The problem of string reconstruction from substring information has found many applications due to its relevance in DNA- and polymer-based data storage. One practically important and challenging paradigm requires reconstructing mixtures of…

The homomorphism problem for relational structures is an abstract way of formulating constraint satisfaction problems (CSP) and various problems in database theory. The decision version of the homomorphism problem received a lot of…

This study presents the first global, 1 Mbp level analysis of patterns of nucleotide substitutions along the human lineage. The study is based on the analysis of a large amount of repetitive elements deposited into the human genome since…

When long-lived, balancing selection can lead to trans-species polymorphisms that are shared by two or more species identical by descent. In this case, the gene genealogies at the selected sites cluster by allele instead of by species and,…

Advances in DNA sequencing mean databases of thousands of human genomes will soon be commonplace. In this paper we introduce a simple technique for reducing the size of conventional indexes on such highly repetitive texts. Given upper…

Diagnosis and risk stratification of cancer and many other diseases require the detection of genomic breakpoints as a prerequisite of calling copy number alterations (CNA). This, however, is still challenging and requires time-consuming…

DNA-based storage offers unprecedented density and durability, but its scalability is fundamentally limited by the efficiency of parallel strand synthesis. Existing methods either allow unconstrained nucleotide additions to individual…

We prove several combinatorial properties of suffix arrays, including a characterization of suffix arrays through a bijection with a certain well-defined class of permutations. Our approach is based on the characterization of…

Polygenic risk scores and other genomic analyses require large individual-level genotype datasets, yet strict data access restrictions impede sharing. Synthetic genotype generation offers a privacy-preserving alternative, but most existing…

While we once thought of cancer as single monolithic diseases affecting a specific organ site, we now understand that there are many subtypes of cancer defined by unique patterns of gene mutations. These gene mutational data, which can be…

A recent paradigm shift in bioinformatics from a single reference genome to a pangenome brought with it several graph structures. These graph structures must implement operations, such as efficient construction from multiple genomes and…

The suffix array $SA[1..n]$ of a text $T$ of length $n$ is a permutation of $\{1,\ldots,n\}$ describing the lexicographical ordering of suffixes of $T$, and it is considered to be among of the most important data structures in string…

We prove that longest common prefix (LCP) information can be stored in much less space than previously known. More precisely, we show that in the presence of the text and the suffix array, o(n) additional bits are sufficient to answer…

This paper introduces a new family of reconstruction codes which is motivated by applications in DNA data storage and sequencing. In such applications, DNA strands are sequenced by reading some subset of their substrings. While previous…

Pedigree data contain family history information that is used to analyze hereditary diseases. These clinical data sets may contain duplicate records due to the same family visiting a clinic multiple times or a clinician entering multiple…

The simplest possible informational heteropolymer requires only a two-letter alphabet to be able to store information. The evolutionary choice of four monomers in the informational biomolecules RNA/DNA or their progenitors is intriguing,…

When building Burrows-Wheeler Transforms (BWTs) of truly huge datasets, prefix-free parsing (PFP) can use an unreasonable amount of memory. In this paper we show how if a dataset can be broken down into small datasets that are not very…

An approach for approximately calculating the number of genes in a genome is presented, which takes into account the average protein length expected for the species. A number of virus, bacterial and eukaryotic genomes are scrutinized.…

Learning algorithms are being increasingly adopted in various applications. However, further expansion will require methods that work more automatically. To enable this level of automation, a more powerful solution representation is needed.…

A graph database is a digraph whose arcs are labeled with symbols from a fixed alphabet. A regular graph pattern (RGP) is a digraph whose edges are labeled with regular expressions over the alphabet. RGPs model navigational queries for…