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The probability of sequencing a set of RNA-seq reads can be directly modeled using the abundances of splice junctions in splice graphs instead of the abundances of a list of transcripts. We call this model gra...
Citation: Algorithms for Molecular Biology 2021 16:5
A classical problem in comparative genomics is to compute the rearrangement distance, that is the minimum number of large-scale rearrangements required to transform a given genome into another given genome. Th...
Citation: Algorithms for Molecular Biology 2021 16:4
Metagenomic sequencing allows us to study the structure, diversity and ecology in microbial communities without the necessity of obtaining pure cultures. In many metagenomics studies, the reads obtained from m...
Citation: Algorithms for Molecular Biology 2021 16:3
With an increasing number of patient-derived xenograft (PDX) models being created and subsequently sequenced to study tumor heterogeneity and to guide therapy decisions, there is a similarly increasing need fo...
Citation: Algorithms for Molecular Biology 2021 16:2
In computational structural biology, structure comparison is fundamental for our understanding of proteins. Structure comparison is, e.g., algorithmically the starting point for computational studies of struct...
Citation: Algorithms for Molecular Biology 2021 16:1
Simultaneous alignment and folding (SA&F) of RNAs is the indispensable gold standard for inferring the structure of non-coding RNAs and their general analysis. The original algorithm, proposed by Sankoff, solv...
Citation: Algorithms for Molecular Biology 2020 15:19
The construction of a suffix array for a collection of strings is a fundamental task in Bioinformatics and in many other applications that process strings. Related data structures, as the Longest Common Prefix...
Citation: Algorithms for Molecular Biology 2020 15:18
Data about herpesvirus microRNA motifs on human circular RNAs suggested the following statistical question. Consider independent random counts, not necessarily identically distributed. Conditioned on the sum, ...
Citation: Algorithms for Molecular Biology 2020 15:17
The history of gene families—which are equivalent to event-labeled gene trees—can to some extent be reconstructed from empirically estimated evolutionary event-relations containing pairs of orthologous, paralo...
Citation: Algorithms for Molecular Biology 2020 15:16
Identifying the secondary structure of an RNA is crucial for understanding its diverse regulatory functions. This paper focuses on how to enhance target identification in a Boltzmann ensemble of structures via...
Citation: Algorithms for Molecular Biology 2020 15:15
Cytoplasmic incompatibility (CI) relates to the manipulation by the parasite Wolbachia of its host reproduction. Despite its widespread occurrence, the molecular basis of CI remains unclear and theoretical models...
Citation: Algorithms for Molecular Biology 2020 15:14
Association studies have been widely used to search for associations between common genetic variants observations and a given phenotype. However, it is now generally accepted that genes and environment must be...
Citation: Algorithms for Molecular Biology 2020 15:13
The classical gene and species tree reconciliation, used to infer the history of gene gain and loss explaining the evolution of gene families, assumes an independent evolution for each family. While this assum...
Citation: Algorithms for Molecular Biology 2020 15:12
Geometric comparisons of binding sites and their electrostatic properties can identify subtle variations that select different binding partners and subtle similarities that accommodate similar partners. Becaus...
Citation: Algorithms for Molecular Biology 2020 15:11
Most modern seed-and-extend NGS read mappers employ a seeding scheme that requires extracting t non-overlapping seeds in each read in order to find all valid mappings under an edit distance threshold of t. As t g...
Citation: Algorithms for Molecular Biology 2020 15:10
Transcriptomic structural variants (TSVs)—large-scale transcriptome sequence change due to structural variation - are common in cancer. TSV detection from high-throughput sequencing data is a computationally c...
Citation: Algorithms for Molecular Biology 2020 15:9
In the field of genome rearrangement algorithms, models accounting for gene duplication lead often to hard problems. For example, while computing the pairwise distance is tractable in most duplication-free mod...
Citation: Algorithms for Molecular Biology 2020 15:8
Non-parametric and semi-parametric resampling procedures are widely used to perform support estimation in computational biology and bioinformatics. Among the most widely used methods in this class is the stand...
Citation: Algorithms for Molecular Biology 2020 15:7
We consider two fundamental computational problems that arise when comparing phylogenetic trees, rooted or unrooted, with non-identical leaf sets. The first problem arises when comparing two trees where the le...
Citation: Algorithms for Molecular Biology 2020 15:6
Many of the commonly used methods for orthology detection start from mutually most similar pairs of genes (reciprocal best hits) as an approximation for evolutionary most closely related pairs of genes (recipr...
Citation: Algorithms for Molecular Biology 2020 15:5
The increasing amount of available genome sequence data enables large-scale comparative studies. A common task is the inference of phylogenies—a challenging task if close reference sequences are not available,...
Citation: Algorithms for Molecular Biology 2020 15:4
Advances in molecular biology have resulted in big and complicated data sets, therefore a clustering approach that able to capture the actual structure and the hidden patterns of the data is required. Moreover...
Citation: Algorithms for Molecular Biology 2020 15:3
Recent large-scale community sequencing efforts allow at an unprecedented level of detail the identification of genomic regions that show signatures of natural selection. Traditional methods for identifying su...
Citation: Algorithms for Molecular Biology 2020 15:2
Estimated gene trees are often inaccurate, due to insufficient phylogenetic signal in the single gene alignment, among other causes. Gene tree correction aims to improve the accuracy of an estimated gene tree ...
Citation: Algorithms for Molecular Biology 2020 15:1
Genome-wide optical maps are ordered high-resolution restriction maps that give the position of occurrence of restriction cut sites corresponding to one or more restriction enzymes. These genome-wide optical m...
Citation: Algorithms for Molecular Biology 2019 14:25
Species networks generalize the notion of species trees to allow for hybridization or other lateral gene transfer. Under the network multispecies coalescent model, individual gene trees arising from a network ...
Citation: Algorithms for Molecular Biology 2019 14:24
As the number of sequenced genomes grows, researchers have access to an increasingly rich source for discovering detailed evolutionary information. However, the computational technologies for inferring biologi...
Citation: Algorithms for Molecular Biology 2019 14:23
Genomic data analyses such as Genome-Wide Association Studies (GWAS) or Hi-C studies are often faced with the problem of partitioning chromosomes into successive regions based on a similarity matrix of high-re...
Citation: Algorithms for Molecular Biology 2019 14:22
The evolutionary distance between two genomes can be estimated by computing a minimum length sequence of operations, called genome rearrangements, that transform one genome into another. Usually, a genome is mode...
Citation: Algorithms for Molecular Biology 2019 14:21
Full Bayesian inference for detecting copy number variants (CNV) from whole-genome sequencing (WGS) data is still largely infeasible due to computational demands. A recently introduced approach to perform Forw...
Citation: Algorithms for Molecular Biology 2019 14:20
Tumors exhibit extensive intra-tumor heterogeneity, the presence of groups of cellular populations with distinct sets of somatic mutations. This heterogeneity is the result of an evolutionary process, describe...
Citation: Algorithms for Molecular Biology 2019 14:19
The statistical distribution of the similarity or difference between pairs of paralogous genes, created by whole genome doubling, or between pairs of orthologous genes in two related species is an important so...
Citation: Algorithms for Molecular Biology 2019 14:18
We introduce a new dissimilarity measure between a pair of “clonal trees”, each representing the progression and mutational heterogeneity of a tumor sample, constructed by the use of single cell or bulk high t...
Citation: Algorithms for Molecular Biology 2019 14:17
The area of genome rearrangements has given rise to a number of interesting biological, mathematical and algorithmic problems. Among these, one of the most intractable ones has been that of finding the median ...
Citation: Algorithms for Molecular Biology 2019 14:16
This paper generalizes previous studies on genome rearrangement under biological constraints, using double cut and join (DCJ). We propose a model for weighted DCJ, along with a family of optimization problems ...
Citation: Algorithms for Molecular Biology 2019 14:15
Divide-and-conquer methods, which divide the species set into overlapping subsets, construct a tree on each subset, and then combine the subset trees using a supertree method, provide a key algorithmic framewo...
Citation: Algorithms for Molecular Biology 2019 14:14
High-throughput sequencing technologies have led to explosive growth of genomic databases; one of which will soon reach hundreds of terabytes. For many applications we want to build and store indexes of these ...
Citation: Algorithms for Molecular Biology 2019 14:13
We study a preprocessing routine relevant in pan-genomic analyses: consider a set of aligned haplotype sequences of complete human chromosomes. Due to the enormous size of such data, one would like to represe...
Citation: Algorithms for Molecular Biology 2019 14:12
Hidden Markov models of haplotype inheritance such as the Li and Stephens model allow for computationally tractable probability calculations using the forward algorithm as long as the representative reference ...
Citation: Algorithms for Molecular Biology 2019 14:11
We study the problem of identifying differentially mutated subnetworks of a large gene–gene interaction network, that is, subnetworks that display a significant difference in mutation frequency in two sets of ...
Citation: Algorithms for Molecular Biology 2019 14:10
Boolean models of biological signalling-regulatory networks are increasingly used to formally describe and understand complex biological processes. These models may become inconsistent as new data become avail...
Citation: Algorithms for Molecular Biology 2019 14:9
With long reads getting even longer and cheaper, large scale sequencing projects can be accomplished without short reads at an affordable cost. Due to the high error rates and less mature tools, de novo assemb...
Citation: Algorithms for Molecular Biology 2019 14:8
Reconciling gene trees with a species tree is a fundamental problem to understand the evolution of gene families. Many existing approaches reconcile each gene tree independently. However, it is well-known that...
Citation: Algorithms for Molecular Biology 2019 14:7
Sequencing technologies produce larger and larger collections of biosequences that have to be stored in compressed indices supporting fast search operations. Many compressed indices are based on the Burrows–Wh...
Citation: Algorithms for Molecular Biology 2019 14:6
Network connectivity problems are abundant in computational biology research, where graphs are used to represent a range of phenomena: from physical interactions between molecules to more abstract relationship...
Citation: Algorithms for Molecular Biology 2019 14:5
Hi-C experiments capturing the 3D genome architecture have led to the discovery of topologically-associated domains (TADs) that form an important part of the 3D genome organization and appear to play a role in...
Citation: Algorithms for Molecular Biology 2019 14:4
Sequencing technologies keep on turning cheaper and faster, thus putting a growing pressure for data structures designed to efficiently store raw data, and possibly perform analysis therein. In this view, ther...
Citation: Algorithms for Molecular Biology 2019 14:3
Absolute fast converging (AFC) phylogeny estimation methods are ones that have been proven to recover the true tree with high probability given sequences whose lengths are polynomial in the number of number of...
Citation: Algorithms for Molecular Biology 2019 14:2
A key factor in computational drug design is the consistency and reliability with which intermolecular interactions between a wide variety of molecules can be described. Here we present a procedure to efficien...
Citation: Algorithms for Molecular Biology 2019 14:1
Motif analysis methods have long been central for studying biological function of nucleotide sequences. Functional genomics experiments extend their potential. They typically generate sequence lists ranked by ...
Citation: Algorithms for Molecular Biology 2018 13:17
Algorithms for Molecular Biology