Citations

Transcription-associated mutation promotes RNA complexity in highly expressed genes — a major new source of selectable variation

February 2018

Authors:
Shengkai Pan, Michael Bruford, Yusong Wang, Zhenzhen Lin, et al.

Info:

In this project, researchers studied transcriptomes in falcons, mice, and chickens and found that highly expressed genes are more likely to alternatively spliced. They also studied methylation patterns and its effect on alternative splicing. For this work, the team used SageELF to size and separate fractions for Iso-Seq analysis on the PacBio RS II system.

Citation:

Molecular Biology and Evolution
doi: 10.1093/molbev/msy017

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Assembly and RNA‐free annotation of highly heterozygous genomes: The case of the thick‐billed murre (Uria lomvia)

January 2018

Authors:
Anna Tigano, Timothy Sackton, and Vicki Friesen

Info:
Researchers at Queen’s University and Harvard teamed up for an effort to assemble the highly heterozygous genome of an arctic colonial seabird. The found that the platanus assembler outperformed other methods, producing an assembly with an impressive 15.8 Mb N50. DNA integrity was evaluated using the Pippin Pulse.

Citation:
Molecular Ecology Resources
doi.org: 10.1111/1755-0998.12712

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Genomics of Corynebacterium striatum, an emerging multidrug-resistant pathogen of immunocompromised patients

January 2018

Authors:
K. Nudel, X. Zhao, S. Basu, X. Dong, et al.

Info:
Scientists from Harvard Medical School and other institutions used whole genome sequencing and MALDI/TOF to analyze seven C. striatum infections, all resistant to multiple drugs. They found that three of the pathogens were related, and that complex resistance profiles could be spread by a single recombination event. BluePippin was used for size-selecting libraries prior to PacBio sequencing.

Citation:
Clinical Microbiology and Infection

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Isoform Sequencing and State-of-Art Applications for Unravelling Complexity of Plant Transcriptomes

January 2018

Authors:
Dong An, Hieu X. Cao, Changsheng Li, Klaus Humbeck and Wenqin Wang

Info:
In this paper, researchers offer best practices for using the Iso-Seq method with PacBio sequencing to analyze plant transcriptomes. They recommend BluePippin for size partitioning, noting that it allows for more even representation of cDNAs even when their lengths vary.

Citation:
Genes 2018, 9(1), 43
doi:10.3390/genes9010043

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Finding Nemo: Hybrid assembly with Oxford Nanopore and Illumina reads greatly improves the Clownfish (Amphiprion ocellaris) genome assembly

January 2018

Authors:
Mun Hua Tan, Christopher Austin, Michael Hammer, Yin Peng Lee, Laurence Croft, Han Ming Gan

Info:
This paper presents the first hybrid genome assembly of Amphiprion ocellaris, the clown anemonefish. The team combined data from Illumina and Oxford Nanopore sequencing, reducing the number of scaffolds compared to a short-read-only assembly by 94%. BluePippin was used to select large DNA fragments for nanopore sequencing.

Citation:
GigaScience
doi: 10.1093/gigascience/gix137

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