11 papers · ranked by Valyu relevance
Vincent P. Ferrera, Samuel Lippl, Kenneth Kay, Fabian Munoz + 3 more
Transitive inference (TI) is the ability to reason about transitive relationships in an ordered set of items (e.g., if A>B and B>C, then A>C). TI is widely held to depend on a linear representation of the serial (rank) order of those items. By what computational mechanism is such an ordering constructed during…
Leonard Bohnenkämper, Luca Parmigiani, Cedric Chauve, Jens Stoye
Genomic rearrangements are major drivers of evolution and genetic disease. However, studying rearrangements requires segmenting the genomes of interest into conserved regions, called synteny blocks, that highlight structural differences between genomes. Synteny blocks are typically defined from annotated genes or…
Alexey Markin, Tavis Anderson
Phylogenetic placement is an established approach for rapidly classifying new genetic sequences and updating a phylogeny without fully recomputing it. Popular maximum-likelihood placement methods, such as pplacer and EPA-ng, tend to struggle computationally when the size of the reference tree increases to tens or…
Ahsan Sanaullah, Nathaniel K. Brown, Pramesh Shakya, Arun Deegutla + 4 more
Lossless full text indexes are utilized in a myriad of applications in bioinformatics. The continuously decreasing cost of generating biological data has resulted in the need to build full text indexes on biological datasets of increasing size. Many compressed full text indexes have been developed to address this…
Xinyu Gu, Stefan Ivanovic, Daniel W. Feng, Mohammed El-Kebir
Summarizing a collection P of related RNA secondary structures is a key challenge in applications like evolutionary analysis, alternative fold studies and mRNA vaccine design. This requires both clustering the input structures into similar groups and identifying the core structural motifs on which they agree or differ.…
Ke Chen, Abhishek Talesara, Sanchal Thakkar, Mingfu Shao
The minimum flow decomposition problem abstracts a set of key tasks in bioinformatics, including metagenome and transcriptome assembly. These tasks, collectively known as multi-assembly, aim to reconstruct multiple genomic sequences from reads obtained from mixed samples. The reads are first organized into a directed…
Jacob Gilbert, Chih Hao Wu, Marina Knittel, Alejandro A. Schäffer + 2 more
Understanding and comparing tumor evolutionary histories is fundamental to cancer genomics. Clonal trees, used to model tumor progression, are rooted, unordered trees in which each node represents a subclone labeled by a set of distinct mutations. To compare two clonal trees, we introduce omlta, the optimal multi-label…
Mahmudur Rahman Hera, David Koslicki, Conrado Martínez
With the surge in sequencing data generated from an ever-expanding range of biological studies, designing scalable computational techniques has become essential. One effective strategy to enable large-scale computation is to split long DNA or protein sequences into k-mers, and summarize large k-mer sets into compact…
Richard Durbin
Skiplists (Pugh, 1990) are probabilistic data structures over ordered lists supporting 𝒪 (log N) insertion and search, which share many properties with balanced binary trees. Previously we introduced the graph Burrows-Wheeler transform (GBWT) to support efficient search over pangenome path sets, but current…
Benjamin M. David, Paul A. Jensen
Coordinating multiple liquid handling robots is a complex logistical task when designing biological experiments. Protocol designers must consider the capabilities and constraints of each robot to distribute work optimally across multiple instruments. We developed an optimization framework that finds optimal liquid…
Arseny Shur, Ido Tziony, Yaron Orenstein
Minimizers are sampling schemes which are ubiquitous in almost any high-throughput sequencing analysis. Assuming a fixed alphabet of size σ, a minimizer is defined by two positive integers k, w and a linear order ρ on k-mers. A sequence is processed by a sliding window algorithm that chooses in each window of length w…