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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
Superbubbles are distinctive subgraphs in direct graphs that play an important role in assembly algorithms for high-throughput sequencing (HTS) data. Their practical importance derives from the fact they are c...
Citation: Algorithms for Molecular Biology 2018 13:16
Genome sequences and genome annotation data have become available at ever increasing rates in response to the rapid progress in sequencing technologies. As a consequence the demand for methods supporting compa...
Citation: Algorithms for Molecular Biology 2018 13:15
Liquid chromatography combined with tandem mass spectrometry is an important tool in proteomics for peptide identification. Liquid chromatography temporally separates the peptides in a sample. The peptides tha...
Citation: Algorithms for Molecular Biology 2018 13:14
One way to estimate the evolutionary distance between two given genomes is to determine the minimum number of large-scale mutations, or genome rearrangements, that are necessary to transform one into the other. I...
Citation: Algorithms for Molecular Biology 2018 13:13
Most phylogenetic studies using molecular data treat gaps in multiple sequence alignments as missing data or even completely exclude alignment columns that contain gaps.
Citation: Algorithms for Molecular Biology 2018 13:12
Horizontal gene transfer (HGT), a process of acquisition and fixation of foreign genetic material, is an important biological phenomenon. Several approaches to HGT inference have been proposed. However, most o...
Citation: Algorithms for Molecular Biology 2018 13:11
Haplotype assembly, reconstructing haplotypes from sequence data, is one of the major computational problems in bioinformatics. Most of the current methodologies for haplotype assembly are designed for diploid...
Citation: Algorithms for Molecular Biology 2018 13:10
The double cut and join (DCJ) model of genome rearrangement is well studied due to its mathematical simplicity and power to account for the many events that transform gene order. These studies have mostly been...
Citation: Algorithms for Molecular Biology 2018 13:9
Patterns with wildcards in specified positions, namely spaced seeds, are increasingly used instead of k-mers in many bioinformatics applications that require indexing, querying and rapid similarity search, as the...
Citation: Algorithms for Molecular Biology 2018 13:8
An important task in a metagenomic analysis is the assignment of taxonomic labels to sequences in a sample. Most widely used methods for taxonomy assignment compare a sequence in the sample to a database of kn...
Citation: Algorithms for Molecular Biology 2018 13:7
For a combination of reasons (including data generation protocols, approaches to taxon and gene sampling, and gene birth and loss), estimated gene trees are often incomplete, meaning that they do not contain a...
Citation: Algorithms for Molecular Biology 2018 13:6
A profile-comparison method with position-specific scoring matrix (PSSM) is among the most accurate alignment methods. Currently, cosine similarity and correlation coefficients are used as scoring functions of...
Citation: Algorithms for Molecular Biology 2018 13:5
Microbial typing methods are commonly used to study the relatedness of bacterial strains. Sequence-based typing methods are a gold standard for epidemiological surveillance due to the inherent portability of s...
Citation: Algorithms for Molecular Biology 2018 13:4
Reconstructing the genome of a species from short fragments is one of the oldest bioinformatics problems. Metagenomic assembly is a variant of the problem asking to reconstruct the circular genomes of all bact...
Citation: Algorithms for Molecular Biology 2018 13:3
In the absence of horizontal gene transfer it is possible to reconstruct the history of gene families from empirically determined orthology relations, which are equivalent to event-labeled gene trees. Knowledge o...
Citation: Algorithms for Molecular Biology 2018 13:2
Species tree estimation from gene trees can be complicated by gene duplication and loss, and “gene tree parsimony” (GTP) is one approach for estimating species trees from multiple gene trees. In its standard ...
Citation: Algorithms for Molecular Biology 2018 13:1
Various approaches to alignment-free sequence comparison are based on the length of exact or inexact word matches between pairs of input sequences. Haubold et al. (J Comput Biol 16:1487–1500, 2009) showed how the...
Citation: Algorithms for Molecular Biology 2017 12:27
Suffix arrays, augmented by additional data structures, allow solving efficiently many string processing problems. The external memory construction of the generalized suffix array for a string collection is a ...
Citation: Algorithms for Molecular Biology 2017 12:26
Multiple sequence alignment (MSA) plays a key role in biological sequence analyses, especially in phylogenetic tree construction. Extreme increase in next-generation sequencing results in shortage of efficient...
Citation: Algorithms for Molecular Biology 2017 12:25
In order to find correlated pairs of positions between proteins, which are useful in predicting interactions, it is necessary to concatenate two large multiple sequence alignments such that the sequences that ...
Citation: Algorithms for Molecular Biology 2017 12:24
The history of gene families—which are equivalent to event-labeled gene trees—can be reconstructed from empirically estimated evolutionary event-relations containing pairs of orthologous, paralogous or xenologous...
Citation: Algorithms for Molecular Biology 2017 12:23
Genomic DNA frequently undergoes rearrangement of the gene order that can be localized by comparing the two DNA sequences. In mitochondrial genomes different mechanisms are likely at work, at least some of whi...
Citation: Algorithms for Molecular Biology 2017 12:22
Mixtures of beta distributions are a flexible tool for modeling data with values on the unit interval, such as methylation levels. However, maximum likelihood parameter estimation with beta distributions suffe...
Citation: Algorithms for Molecular Biology 2017 12:21
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Algorithms for Molecular Biology
