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In Print: Last Week's Sequencing-Related Papers of Note: Apr 2, 2013


SeqEntropy: genome-wide assessment of repeats for short read sequencing.
Chu HT, Hsiao WW, Tsao TT, Hsu DF, et al.
PLoS One. 2013;8(3):e59484.

High-throughput sequencing of small RNA transcriptome reveals salt stress regulated microRNAs in sugarcane.
Carnavale Bottino M, Rosario S, Grativol C, Thiebaut F, et al.
PLoS One. 2013;8(3):e59423.

Enabling interspecies epigenomic comparison with CEpBrowser.
Cao X, Zhong S.
Bioinformatics. 2013 Mar 29. [Epub ahead of print]

The genome of the platyfish, Xiphophorus maculates, provides insights into evolutionary adaptation and several complex traits.
Schartl M, Walter RB, Shen Y, Garcia T, et al.
Nat Genet. 2013 Mar 31. [Epub ahead of print]

RF: A method for filtering short reads with tandem repeats for genome mapping.
Misawa K.
Genomics. 2013 Mar 28. [Epub ahead of print]

Sequencing of the Dutch elm disease fungus genome using the Roche/454 GS-FLX Titanium system in a comparison of multiple genomics core facilities.
Forgetta V, Leveque G, Dias J, Grove D, et al.
J Biomol Tech. 2013 Apr;24(1):39-49.

The first symbiont-free genome sequence of marine red alga, susabi-nori (Pyropia yezoensis).
Nakamura Y, Sasaki N, Kobayashi M, Ojima N, et al.
PLoS One. 2013;8(3):e57122.

Aegilops tauschii draft genome sequence reveals a gene repertoire for wheat adaptation.
Jia J, Zhao S, Kong X, Li Y, et al.
Nature. 2013 Mar 24. [Epub ahead of print]

Enriching pathogen transcripts from infected samples: A capture based approach to enhanced host-pathogen RNA-seq.
Bent ZW, Tran-Gyamfi MB, Langevin SA, Brazel DM, et al.
Anal Biochem. 2013 Mar 24. [Epub ahead of print]

FishingCNV: a graphical software package for detecting rare copy number variations in exome sequencing data.
Shi Y, Majewski J.
Bioinformatics. 2013 Mar 28. [Epub ahead of print]

Microbial community analysis of swine wastewater anaerobic lagoons by next generation DNA sequencing.
Ducey TF, Hunt PG.
Anaerobe. 2013 Mar 25. [Epub ahead of print]

Low concordance of multiple variant-calling pipelines: practical implications for exome and genome sequencing.
O'Rawe J, Guangqing S, Wang W, Hu J, et al.
Genome Med. 2013 Mar 27;5(3):28.

CRAC: an integrated approach to the analysis of RNA-seq reads.
Philippe N, Salson M, Commes T, Rivals E.
Genome Biol. 2013 Mar 28;14(3):R30.

The genome sequence of the ground tit Pseudopodoces humilis provides insights into its adaptation to high altitude.
Cai Q, Qian X, Lang Y, Luo Y, et al.
Genome Biol. 2013 Mar 28;14(3):R29.

Compression of FASTQ and SAM format sequencing data.
Bonfield JK, Mahoney MV.
PLoS One. 2013;8(3):e59190.

Patchwork: allele-specific copy number analysis of whole genome sequenced tumor tissue.
Mayrhofer M, Dilorenzo S, Isaksson A.
Genome Biol. 2013 Mar 25;14(3):R24.

Differential expression analysis for paired RNA-seq data.
Chung LM, Ferguson JP, Zheng W, Qian F, et al.
BMC Bioinformatics. 2013 Mar 27;14(1):110.

The human placenta methylome.
Schroeder DI, Blair JD, Lott P, Yu HO, et al.
Proc Natl Acad Sci U S A. 2013 Mar 25. [Epub ahead of print]

Adjusted sequence kernel association test for rare variants controlling for cryptic and family relatedness.
Oualkacha K, Dastani Z, Li R, Cingolani PE, et al.
Genet Epidemiol. 2013 Mar 25. [Epub ahead of print]

The Scan

Cell Atlas of Human Lung Development Gives View of Developing Airway

Researchers have generated a cell atlas of human lung development, which they report in Cell.

Study Finds Costs of Genome Sequencing May Limit Utility in Routine Care

Researchers report in the European Journal of Human Genetics that genome sequencing for rare disease diagnoses currently has similar benefits as less expensive exome analysis.

Study Suggests Nursing Mother's Diet Can Impact Offspring's Gut Microbiome

A new Cell Host and Microbe paper finds that mice whose mothers were fed a low-fiber diet during nursing experience lasting microbiota dysbiosis and increased obesity.

Study Links Genetic Risk for ADHD With Alzheimer's Disease

A higher polygenic risk score for attention-deficit/hyperactivity disorder is also linked to cognitive decline and Alzheimer's disease, a new study in Molecular Psychiatry finds.