Related papers: Reconstructing Isoform Graphs from RNA-Seq data
The main challenge in de novo assembly of NGS data is certainly to deal with repeats that are longer than the reads. This is particularly true for RNA- seq data, since coverage information cannot be used to flag repeated sequences, of which…
The development of novel high-throughput sequencing (HTS) methods for RNA (RNA-Seq) has provided a very powerful mean to study splicing under multiple conditions at unprecedented depth. However, the complexity of the information to be…
In this thesis, we address the problem of identifying and quantifying variants (alternative splicing and genomic polymorphism) in RNA-seq data when no reference genome is available, without assembling the full transcripts. Based on the…
The high-throughput short-reads RNA-seq protocols often produce paired-end reads, with the middle portion of the fragments being unsequenced. We explore if the full-length fragments can be computationally reconstructed from the sequenced…
Repetitive DNA (repeats) poses significant challenges for accurate and efficient genome assembly and sequence alignment. This is particularly true for metagenomic data, where genome dynamics such as horizontal gene transfer, gene…
RNA-Seq technology allows for studying the transcriptional state of the cell at an unprecedented level of detail. Beyond quantification of whole-gene expression, it is now possible to disentangle the abundance of individual alternatively…
As opposed to natural languages, source code understanding is influenced by grammatical relationships between tokens regardless of their identifier name. Graph representations of source code such as Abstract Syntax Tree (AST) can capture…
Next-generation sequencing technologies provide a revolutionary tool for generating gene expression data. Starting with a fixed RNA sample, they construct a library of millions of differentially abundant short sequence tags or "reads",…
Recently, ultra high-throughput sequencing of RNA (RNA-Seq) has been developed as an approach for analysis of gene expression. By obtaining tens or even hundreds of millions of reads of transcribed sequences, an RNA-Seq experiment can offer…
Isoforms are mRNAs produced from the same gene site in the phenomenon called Alternative Splicing. Studies have shown that more than 95% of human multi-exon genes have undergone alternative splicing. Although there are few changes in mRNA…
Ising models are a simple generative approach to describing interacting binary variables. They have proven useful in a number of biological settings because they enable one to represent observed many-body correlations as the separable…
Reconstructing components of a genomic mixture from data obtained by means of DNA sequencing is a challenging problem encountered in a variety of applications including single individual haplotyping and studies of viral communities.…
The advent of DNA and RNA sequencing has revolutionized the study of genomics and molecular biology. Next generation sequencing (NGS) technologies like Illumina, Ion Torrent, SOLiD sequencing etc. have brought about a quick and cheap way to…
With the increasing demands of training graph neural networks (GNNs) on large-scale graphs, graph data condensation has emerged as a critical technique to relieve the storage and time costs during the training phase. It aims to condense the…
There is little debate about the importance of the ancestral recombination graph in population genetics. An important theoretical tool, the main obstacle to its widespread usage is the computational cost required to match the…
Graphs are a powerful tool for analyzing large data sets, but many real-world phenomena involve interactions that go beyond the simple pairwise relationships captured by a graph. In this paper we introduce and study a simple combinatorial…
Cell formation is a critical step in the design of cellular manufacturing systems. Recently, it was tackled using a cut-based-graph-partitioning model. This model meets real-life production systems requirements as it uses the actual amount…
Subgraph isomorphism counting is an important problem on graphs, as many graph-based tasks exploit recurring subgraph patterns. Classical methods usually boil down to a backtracking framework that needs to navigate a huge search space with…
Representative Selection (RS) is the problem of finding a small subset of exemplars from a dataset that is representative of the dataset. In this paper, we study RS for attributed graphs, and focus on finding representative nodes that…
Integrating data from heterogeneous sources is often modeled as merging graphs. Given two or more 'compatible', but not-isomorphic graphs, the first step is to identify a graph alignment, where a potentially partial mapping of vertices…