Bridger: a new framework for de novo transcriptome assembly using RNA-seq data
We present a new de novo transcriptome assembler, Bridger, which takes advantage of
techniques employed in Cufflinks to overcome limitations of the existing de novo …
techniques employed in Cufflinks to overcome limitations of the existing de novo …
[图书][B] Genome-scale algorithm design
High-throughput sequencing has revolutionised the field of biological sequence analysis. Its
application has enabled researchers to address important biological questions, often for the …
application has enabled researchers to address important biological questions, often for the …
BinPacker: Packing-Based De Novo Transcriptome Assembly from RNA-seq Data
High-throughput RNA-seq technology has provided an unprecedented opportunity to reveal
the very complex structures of transcriptomes. However, it is an important and highly …
the very complex structures of transcriptomes. However, it is an important and highly …
Identification of long non-coding RNAs in insects genomes
Highlights•Long non-coding RNAs play important roles in the functioning of the cells of
several species.•A few numbers of lncRNAs are experimentally validated in insect genomes …
several species.•A few numbers of lncRNAs are experimentally validated in insect genomes …
Transcriptional profiling in experimental visceral leishmaniasis reveals a broad splenic inflammatory environment that conditions macrophages toward a disease …
F Kong, OA Saldarriaga, H Spratt, EY Osorio… - PLoS …, 2017 - journals.plos.org
Visceral Leishmaniasis (VL), caused by the intracellular protozoan Leishmania donovani, is
characterized by relentlessly increasing visceral parasite replication, cachexia, massive …
characterized by relentlessly increasing visceral parasite replication, cachexia, massive …
The homomorphic self-incompatibility system in Oleaceae is controlled by a hemizygous genomic region expressing a gibberellin pathway gene
In flowering plants, outcrossing is commonly ensured by self-incompatibility (SI) systems.
These can be homomorphic (typically with many different allelic specificities) or can …
These can be homomorphic (typically with many different allelic specificities) or can …
Comparative performance of transcriptome assembly methods for non-model organisms
X Huang, XG Chen, PA Armbruster - BMC genomics, 2016 - Springer
Background The technological revolution in next-generation sequencing has brought
unprecedented opportunities to study any organism of interest at the genomic or …
unprecedented opportunities to study any organism of interest at the genomic or …
Flow decomposition with subpath constraints
L Williams, AI Tomescu… - IEEE/ACM Transactions on …, 2022 - ieeexplore.ieee.org
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 …
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 …
Transcriptome analysis reveals differentially expressed genes associated with germ cell and gonad development in the Southern bluefin tuna (Thunnus maccoyii)
Background Controlling and managing the breeding of bluefin tuna (Thunnus spp.) in
captivity is an imperative step towards obtaining a sustainable supply of these fish in …
captivity is an imperative step towards obtaining a sustainable supply of these fish in …