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In Print: Last Week's Sequencing-Related Papers of Note: Apr 24, 2012


Performance comparison of benchtop high-throughput sequencing platforms.
Loman NJ, Misra RV, Dallman TJ, Constantinidou C, et al.
Nat Biotechnol. 2012 Apr 22. [Epub ahead of print]
(See our coverage of this paper here.)

Systematic evaluation of factors influencing ChIP-seq fidelity.
Chen Y, Negre N, Li Q, Mieczkowska JO, et al.
Nat Methods. 2012 Apr 22. [Epub ahead of print]
(See our coverage of this paper here.)

lobSTR: A short tandem repeat profiler for personal genomes.
Gymrek M, Golan D, Rosset S, Erlich Y.
Genome Res. 2012 Apr 20. [Epub ahead of print]

Bio-CAP: a versatile and highly sensitive technique to purify and characterize regions of non-methylated DNA.
Blackledge NP, Long HK, Zhou JC, Kriaucionis S, et al.
Nucleic Acids Res. 2012 Feb;40(4):e32.

Genomic landscape of human allele-specific DNA methylation.
Fang F, Hodges E, Molaro A, Dean M, et al.
Proc Natl Acad Sci U S A. 2012 Apr 20. [Epub ahead of print]

Microbial composition of the Korean traditional food "kochujang" analyzed by a massive sequencing technique.
Nam YD, Park SL, Lim SI.
J Food Sci. 2012 Apr;77(4):M250-6.

Deep sequencing of plant and animal DNA contained within traditional Chinese medicines reveals legality issues and health safety concerns.
Coghlan ML, Haile J, Houston J, Murray DC, et al.
PLoS Genet. 2012 Apr;8(4):e1002657.
(See our coverage of this paper in last week's issue here.)

Characterization of squamate olfactory receptor genes and their transcripts by the high-throughput sequencing approach.
Dehara Y, Hashiguchi Y, Matsubara K, Yanai T, et al.
Genome Biol Evol. 2012 Apr 17. [Epub ahead of print]

Transcriptomes of mouse olfactory epithelium reveal sexual differences in odorant detection.
Shiao MS, Ying-Fei Chang A, Liao BY, Ching YH, et al.
Genome Biol Evol. 2012 Apr 17. [Epub ahead of print]

Sequence and expression analysis of gaps in human chromosome 20.
Minocherhomji S, Seemann S, Mang Y, El-Schich Z, et al.
Nucleic Acids Res. 2012 Apr 17. [Epub ahead of print]

Mitogenome sequencing reveals shallow evolutionary histories and recent divergence time between morphologically and ecologically distinct European whitefish (Coregonus spp.).
Jacobsen MW, Hansen MM, Orlando L, Bekkevold D, et al.
Mol Ecol. 2012 Apr 17. [Epub ahead of print]

Characterization of common carp transcriptome: sequencing, de novo assembly, annotation and comparative genomics.
Ji P, Liu G, Xu J, Wang X, et al.
PLoS One. 2012;7(4):e35152.

Simultaneous identification of DNA and RNA viruses present in pig faeces using process-controlled deep sequencing.
Sachsenröder J, Twardziok S, Hammerl JA, Janczyk P, et al.
PLoS One. 2012;7(4):e34631.

Comparison of DNA extraction methods for microbial community profiling with an application to pediatric bronchoalveolar lavage samples.
Willner D, Daly J, Whiley D, Grimwood K, et al.
PLoS One. 2012;7(4):e34605.

TSSi - An R package for transcription start site identification from 5' mRNA tag data.
Kreutz C, Gehring JS, Lang D, Reski R, et al.
Bioinformatics. 2012 Apr 17. [Epub ahead of print]

A transcriptome map of perennial ryegrass (Lolium perenne L.) .
Studer B, Byrne S, Nielsen RO, Panitz F, et al.
BMC Genomics. 2012 Apr 18;13(1):140.

Finding a needle in the virus metagenome haystack — micro-metagenome analysis captures a snapshot of the diversity of a bacteriophage armoire.
Ray J, Dondrup M, Modha S, Steen IH, et al.
PLoS One. 2012;7(4):e34238.

A genome resource to address mechanisms of developmental programming; determination of the fetal sheep heart transcriptome.
Cox LA, Glenn JP, Spradling KD, Nijland MJ, et al.
J Physiol. 2012 Apr 16. [Epub ahead of print]

pIRS: Profile based Illumina pair-end Reads Simulator.
Hu X, Yuan J, Shi Y, Lu J, et al.
Bioinformatics. 2012 Apr 15. [Epub ahead of print]

Standardization and quality controls for the methylated DNA immunoprecipitation technique.
Lisanti S, von Zglinicki T, Mathers J.
Epigenetics. 2012 Jun 1;7(6).

DNA from soil mirrors plant taxonomic and growth form diversity.
Yoccoz NG, Bråthen KA, Gielly L, Haile J, et al.
Mol Ecol. 2012 Apr 16. [Epub ahead of print]

A comparative study of cell-free apoptotic and genomic DNA using FISH and massive parallel sequencing.
Morozkin ES, Loseva EM, Morozov IV, Kurilshikov AM, et al.
Expert Opin Biol Ther. 2012 Apr 16. [Epub ahead of print]

SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing.
Bankevich A, Nurk S, Antipov D, Gurevich AA, et al.
J Comput Biol. 2012 Apr 16. [Epub ahead of print]

The Scan

Researchers Develop Polygenic Risk Scores for Dozens of Disease-Related Exposures

With genetic data from two large population cohorts and summary statistics from prior genome-wide association studies, researchers came up with 27 exposure polygenic risk scores in the American Journal of Human Genetics.

US Survey Data Suggests Ancestry Testing Leads Way in Awareness, Use of Genetic Testing Awareness

Although roughly three-quarters of surveyed individuals in a Genetics in Medicine study reported awareness of genetic testing, use of such tests was lower and varied with income, ancestry, and disease history.

Coral Genome Leads to Alternative Amino Acid Pathway Found in Other Non-Model Animals

An alternative cysteine biosynthesis pathway unearthed in the Acropora loripes genome subsequently turned up in sequences from non-mammalian, -nematode, or -arthropod animals, researchers report in Science Advances.

Mosquitos Genetically Modified to Prevent Malaria Spread

A gene drive approach could be used to render mosquitos unable to spread malaria, researchers report in Science Advances.