Application and challenge of 3rd generation sequencing for clinical bacterial studies
Over the past 25 years, the powerful combination of genome sequencing and bioinformatics
analysis has played a crucial role in interpreting information encoded in bacterial genomes …
analysis has played a crucial role in interpreting information encoded in bacterial genomes …
Transcriptome assembly from long-read RNA-seq alignments with StringTie2
RNA sequencing using the latest single-molecule sequencing instruments produces reads
that are thousands of nucleotides long. The ability to assemble these long reads can greatly …
that are thousands of nucleotides long. The ability to assemble these long reads can greatly …
Intron retention and its impact on gene expression and protein diversity: A review and a practical guide
DF Grabski, L Broseus, B Kumari… - Wiley …, 2021 - Wiley Online Library
Intron retention (IR) occurs when a complete and unspliced intron remains in mature mRNA.
An increasing body of literature has demonstrated a major role for IR in numerous biological …
An increasing body of literature has demonstrated a major role for IR in numerous biological …
Flow decomposition with subpath constraints
Flow network decomposition is a natural model for problems where we are given a flow
network arising from superimposing a set of weighted paths and would like to recover the …
network arising from superimposing a set of weighted paths and would like to recover the …
Using metatranscriptomics to estimate the diversity and composition of zooplankton communities
DNA metabarcoding is a rapid, high‐resolution tool used for biomonitoring complex
zooplankton communities. However, diversity estimates derived with this approach can be …
zooplankton communities. However, diversity estimates derived with this approach can be …
Safety in multi-assembly via paths appearing in all path covers of a DAG
A multi-assembly problem asks to reconstruct multiple genomic sequences from mixed
reads sequenced from all of them. Standard formulations of such problems model a solution …
reads sequenced from all of them. Standard formulations of such problems model a solution …
Using minimum path cover to boost dynamic programming on DAGs: co-linear chaining extended
Aligning sequencing reads on graph representations of genomes is an important ingredient
of pan-genomics. Such approaches typically find a set of local anchors that indicate …
of pan-genomics. Such approaches typically find a set of local anchors that indicate …
TALC: transcript-level aware long-read correction
Motivation Long-read sequencing technologies are invaluable for determining complex RNA
transcript architectures but are error-prone. Numerous 'hybrid correction'algorithms have …
transcript architectures but are error-prone. Numerous 'hybrid correction'algorithms have …
CStone: A de novo transcriptome assembler for short-read data that identifies non-chimeric contigs based on underlying graph structure
With the exponential growth of sequence information stored over the last decade, including
that of de novo assembled contigs from RNA-Seq experiments, quantification of chimeric …
that of de novo assembled contigs from RNA-Seq experiments, quantification of chimeric …
A novel model based on immune-related genes for differentiating biliary atresia from other cholestatic diseases
T Li, Q Zheng, R Zhang, S Liu, Y Lin, J Zhan - Pediatric Surgery …, 2022 - Springer
Purpose Based on a public gene expression database, this study established the immune-
related genetic model that distinguished BA from other cholestasis diseases (DC) for the first …
related genetic model that distinguished BA from other cholestasis diseases (DC) for the first …