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Search: authors:"Juntao Liu"

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TransComb: genome-guided transcriptome assembly via combing junctions in splicing graphs

Transcriptome assemblers aim to reconstruct full-length transcripts from RNA-seq data. We present TransComb, a genome-guided assembler developed based on a junction graph, weighted by a bin-packing strategy and paired-end information. A newly designed extension method based on weighted junction graphs can accurately extract paths representing expressed transcripts, whether they...

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 challenging task to assemble vast amounts of short RNA-seq reads into transcriptomes with alternative splicing isoforms. In this study, we present a novel de novo assembler, BinPacker, by modeling the...

MicroRNAs Are Involved in the Regulation of Ovary Development in the Pathogenic Blood Fluke Schistosoma japonicum

Schistosomes, blood flukes, are an important global public health concern. Paired adult female schistosomes produce large numbers of eggs that are primarily responsible for the disease pathology and critical for dissemination. Consequently, understanding schistosome sexual maturation and egg production may open novel perspectives for intervening with these processes to prevent...

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 assemblers. When tested on dog, human, and mouse RNA-seq data, Bridger assembled more full-length reference transcripts while reporting considerably fewer candidate transcripts, hence greatly reducing false positive...

Rapid detection of Cyfra 21-1 by optical-biosensing based on chemiluminescence immunoassay using bio-functionlized magnetic nanocomposites

This letter reports a chemiluminescene immunoassay method combined with immunomagnetic separation to rapidly detect Cyfra 21-1, in which bio-functionlized magnetic nanocomposites were used as mobile substrate for capturing and isolating the cyfra 21-1 proteins. After the captured Cyfra 21-1 further reacted with horseradish peroxidase-conjugated anti-Cyfra 21-1 antibody to form a...

Bi-Factor Analysis Based on Noise-Reduction (BIFANR): A New Algorithm for Detecting Coevolving Amino Acid Sites in Proteins

Previous statistical analyses have shown that amino acid sites in a protein evolve in a correlated way instead of independently. Even though located distantly in the linear sequence, the coevolved amino acids could be spatially adjacent in the tertiary structure, and constitute specific protein sectors. Moreover, these protein sectors are independent of one another in structure...

Association of Six Single Nucleotide Polymorphisms with Gestational Diabetes Mellitus in a Chinese Population

Background To investigate whether the candidate genes that confer susceptibility to type 2 diabetes mellitus are also correlated with gestational diabetes mellitus (GDM) in pregnant Chinese women. Methodology/Principal Findings In this study, 1764 unrelated pregnant women were recruited, of which 725 women had GDM and 1039 served as controls. Six single nucleotide polymorphisms...

Array-based comparative genomic hybridization is more informative than conventional karyotyping and fluorescence in situ hybridization in the analysis of first-trimester spontaneous abortion

Background Array-based comparative genomic hybridization (aCGH) is a new technique for detecting submicroscopic deletions and duplications, and can overcome many of the limitations associated with classic cytogenetic analysis. However, its clinical use in spontaneous abortion needs comprehensive evaluation. We used aCGH to investigate chromosomal imbalances in 100 spontaneous...