269 citations · 344 across the 9 of their papers we have counts for
11 papers
Probabilistic Models of k-mer Frequencies (Extended Abstract)
Askar Gafurov, Tomáš Vinař, Broňa Brejová
In this article, we review existing probabilistic models for modeling abundance of fixed-length strings (k-mers) in DNA sequencing data. These models capture dependence of the abun…
Dynamic Pooling Improves Nanopore Base Calling Accuracy
Vladimír Boža, Peter Perešíni, Broňa Brejová +1
In nanopore sequencing, electrical signal is measured as DNA molecules pass through the sequencing pores. Translating these signals into DNA bases (base calling) is a highly non-tr…
B.1.258, a SARS-CoV-2 variant with H69/V70 in the Spike protein circulating in the Czech Republic and Slovakia
Broňa Brejová, Viktória Hodorová, Kristína Boršová +7
SARS-CoV-2 mutants carrying the H69/V70 deletion in the amino terminal domain of the Spike protein emerged independently in at least six lineages of the virus (namely, B.1.1.…
Nanopore Base Calling on the Edge
Peter Perešíni, Vladimír Boža, Broňa Brejová +1
We developed a new base caller DeepNano-coral for nanopore sequencing, which is optimized to run on the Coral Edge Tensor Processing Unit, a small USB-attached hardware accelerator…
Using Sequence Ensembles for Seeding Alignments of MinION Sequencing Data
Rastislav Rabatin, Broňa Brejová, Tomáš Vinař
Oxford Nanopore MinION sequencer is currently the smallest sequencing device available. While being able to produce very long reads (reads of up to 100~kbp were reported), it is pr…
DeepNano: Deep Recurrent Neural Networks for Base Calling in MinION Nanopore Reads
Vladimír Boža, Broňa Brejová, Tomáš Vinař
Motivation: The MinION device by Oxford Nanopore is the first portable sequencing device. MinION is able to produce very long reads (reads over 100~kBp were reported), however it s…
Probabilistic Approaches to Alignment with Tandem Repeats
Michal Nánási, Tomáš Vinař, Broňa Brejová
We propose a simple tractable pair hidden Markov model for pairwise sequence alignment that accounts for the presence of short tandem repeats. Using the framework of gain functions…
Sequence Annotation with HMMs: New Problems and Their Complexity
Michal Nánási, Tomáš Vinař, Broňa Brejová
Hidden Markov models (HMMs) and their variants were successfully used for several sequence annotation tasks. Traditionally, inference with HMMs is done using the Viterbi and poster…
The Highest Expected Reward Decoding for HMMs with Application to Recombination Detection
Michal Nánási, Tomáš Vinař, Broňa Brejová
Hidden Markov models are traditionally decoded by the Viterbi algorithm which finds the highest probability state path in the model. In recent years, several limitations of the Vit…
Bayesian History Reconstruction of Complex Human Gene Clusters on a Phylogeny
Tomáš Vinař, Broňa Brejová, Giltae Song +1
Clusters of genes that have evolved by repeated segmental duplication present difficult challenges throughout genomic analysis, from sequence assembly to functional analysis. Impro…
On-line Viterbi Algorithm and Its Relationship to Random Walks
Rastislav Šrámek, Broňa Brejová, Tomáš Vinař
In this paper, we introduce the on-line Viterbi algorithm for decoding hidden Markov models (HMMs) in much smaller than linear space. Our analysis on two-state HMMs suggests that t…