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Article
Open AccessRevisiting the complexity of and algorithms for the graph traversal edit distance and its variants
The graph traversal edit distance (GTED), introduced by Ebrahimpour Boroojeny et al. (2018), is an elegant distance measure defined as the minimum edit distance between strings reconstructed from Eulerian trai...
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Chapter and Conference Paper
Graph-Based Genome Inference from Hi-C Data
Three-dimensional chromosome structure plays an important role in fundamental genomic functions. Hi-C, a high-throughput, sequencing-based technique, has drastically expanded our comprehension of 3D chromosome...
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Chapter and Conference Paper
A Scalable Optimization Algorithm for Solving the Beltway and Turnpike Problems with Uncertain Measurements
The Beltway and Turnpike problems entail the reconstruction of circular and linear one-dimensional point sets from unordered pairwise distances. These problems arise in computational biology when the measurements...
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Chapter and Conference Paper
DeepMinimizer: A Differentiable Framework for Optimizing Sequence-Specific Minimizer Schemes
Minimizers are k-mer sampling schemes designed to generate sketches for large sequences that preserve sufficiently long matches between sequences. Despite their widespread application, learning an effective mi...
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Article
Open AccessVariantStore: an index for large-scale genomic variant search
Efficiently scaling genomic variant search indexes to thousands of samples is computationally challenging due to the presence of multiple coordinate systems to avoid reference biases. We present VariantStore, ...
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Article
Open AccessExact transcript quantification over splice graphs
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...
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Article
Open AccessHarvestman: a framework for hierarchical feature learning and selection from whole genome sequencing data
Supervised learning from high-throughput sequencing data presents many challenges. For one, the curse of dimensionality often leads to overfitting as well as issues with scalability. This can bring about inacc...
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Article
Open AccessAlignment and map** methodology influence transcript abundance estimation
The accuracy of transcript quantification using RNA-seq data depends on many factors, such as the choice of alignment or map** method and the quantification model being adopted. While the choice of quantific...
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Article
Open AccessContext-aware seeds for read map**
Most modern seed-and-extend NGS read mappers employ a seeding scheme that requires extracting t non-overlap** seeds in each read in order to find all valid map**s under an edit distance threshold of t. As t g...
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Article
Open AccessDetecting transcriptomic structural variants in heterogeneous contexts via the Multiple Compatible Arrangements Problem
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...
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Chapter and Conference Paper
Lower Density Selection Schemes via Small Universal Hitting Sets with Short Remaining Path Length
Universal hitting sets are sets of words that are unavoidable: every long enough sequence is hit by the set (i.e., it contains a word from the set). There is a tight relationship between universal hitting sets...
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Article
Open AccessQuantifying the benefit offered by transcript assembly with Scallop-LR on single-molecule long reads
Single-molecule long-read sequencing has been used to improve mRNA isoform identification. However, not all single-molecule long reads represent full transcripts due to incomplete cDNA synthesis and sequencing...
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Article
Open AccessSemi-nonparametric modeling of topological domain formation from epigenetic data
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...
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Article
Open AccessSQUID: transcriptomic structural variation detection from RNA-seq
Transcripts are frequently modified by structural variations, which lead to fused transcripts of either multiple genes, known as a fusion gene, or a gene and a previously non-transcribed sequence. Detecting th...
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Article
Open AccessKourami: graph-guided assembly for novel human leukocyte antigen allele discovery
Accurate ty** of human leukocyte antigen (HLA) is important because HLA genes play important roles in immune responses and disease genesis. Previously available computational methods are database-matching ap...
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Protocol
Accurate Assembly and Ty** of HLA using a Graph-Guided Assembler Kourami
Accurate ty** of human leukocyte antigen (HLA) is essential for successful organ transplantation and HLA genes are heavily associated with various diseases. Widely used ty** assays often involve a set of s...
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Article
Accurate assembly of transcripts through phase-preserving graph decomposition
Scallop improves identification of multi-exon and transcripts expressed at low levels by retaining phasing information during assembly.
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Article
Salmon provides fast and bias-aware quantification of transcript expression
Salmon is a computational tool that uses sample-specific models and a dual-phase inference procedure to correct biases in RNA-seq data and rapidly quantify transcript abundances.
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Chapter and Conference Paper
Improved Search of Large Transcriptomic Sequencing Databases Using Split Sequence Bloom Trees
Enormous databases of short-read RNA-seq sequencing experiments such as the NIH Sequencing Read Archive (SRA) are now available. These databases could answer many questions about the condition-specific express...
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Article
Open AccessA pathway-centric view of spatial proximity in the 3D nucleome across cell lines
In various contexts, spatially proximal genes have been shown to be functionally related. However, the extent to which spatial proximity of genes in a pathway contributes to the pathway’s context-specific acti...
