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In Print: Last Week's Sequencing-Related Papers of Note: Apr 3, 2012


High throughput sequence-based analysis of the intestinal microbiota of weanling pigs fed genetically modified Bt MON810 maize for 31 days.
Buzoianu SG, Walsh MC, Rea MC, O'Sullivan O, et al.
Appl Environ Microbiol. 2012 Mar 30. [Epub ahead of print]

Analysis of C. elegans intestinal gene expression and polyadenylation by fluorescence-activated nuclei sorting and 3'-end-seq.
Haenni S, Ji Z, Hoque M, Rust N, et al.
Nucleic Acids Res. 2012 Mar 29. [Epub ahead of print]

PAREsnip: a tool for rapid genome-wide discovery of small RNA/target interactions evidenced through degradome sequencing.
Folkes L, Moxon S, Woolfenden HC, Stocks MB, et al.
Nucleic Acids Res. 2012 Mar 29. [Epub ahead of print]

Ultra-low-input, tagmentation-based whole genome bisulfite sequencing.
Adey A, Shendure J.
Genome Res. 2012 Mar 30. [Epub ahead of print]

Bisulphite-sequencing of chromatin immunoprecipitated DNA (BisChIP-seq) directly informs methylation status of histone-modified DNA.
Statham AL, Robinson MD, Song JZ, Coolen MW, et al.
Genome Res. 2012 Mar 30. [Epub ahead of print]

Sequential ChIP-bisulfite sequencing enables direct genome-scale investigation of chromatin and DNA methylation cross-talk.
Brinkman AB, Gu H, Bartels SJ, Zhang Y, et al.
Genome Res. 2012 Mar 30. [Epub ahead of print]

Using genetic algorithm in reconstructing single individual haplotype with minimum error correction.
Wang TC, Taheri J, Zomaya AY.
J Biomed Inform. 2012 Mar 27. [Epub ahead of print]

Gate effects on DNA translocation through silicon dioxide nanopore.
Yen PC, Wang CH, Hwang GJ, Chou YC.
Rev Sci Instrum. 2012 Mar;83(3):034301.

De novo sequencing and characterization of Picrorhiza kurrooa transcriptome at two temperatures showed major transcriptome adjustments.
Gahlan P, Singh HR, Shankar R, Sharma N, et al.
BMC Genomics. 2012 Mar 31;13(1):126.

A scheduling algorithm for computational grids that minimizes centralized processing in genome assembly of next-generation sequencing data.
Lima J, Cerdeira LT, Bol E, Schneider MP, et al.
Front Genet. 2012;3:38. Epub 2012 Mar 19.

Synthesis, physicochemical properties, and hydrogen bonding of 4(5)-substituted 1-H-imidazole-2-carboxamide, a potential universal reader for DNA sequencing by recognition tunneling.
Liang F, Li S, Lindsay S, Zhang P.
Chemistry. 2012 Mar 29. [Epub ahead of print]

Next-generation small RNA sequencing for microRNAs profiling in Apis mellifera: comparison between nurses and foragers.
Liu F, Peng W, Li Z, Li W, et al.
Insect Mol Biol. 2012 Mar 27. [Epub ahead of print]

Illumina sequencing technology as a method of identifying T-DNA insertion loci in activation-tagged Arabidopsis thaliana plants.
Polko JK, Temanni MR, van Zanten M, van Workum W, et al.
Mol Plant. 2012 Mar 29. [Epub ahead of print]

Widespread site-dependent buffering of human regulatory polymorphism.
Maurano MT, Wang H, Kutyavin T, Stamatoyannopoulos JA.
PLoS Genet. 2012 Mar;8(3):e1002599.

Efficient and robust RNA-seq process for cultured bacteria and complex community transcriptomes.
Giannoukos G, Ciulla DM, Huang K, Haas BJ, et al.
Genome Biol. 2012 Mar 28;13(3):R23.

Annotation of primate miRNAs by high throughput sequencing of small RNA libraries.
Dannemann M, Nickel B, Lizano E, Burbano HA, Kelso J.
BMC Genomics. 2012 Mar 27;13(1):116.

An integrative probabilistic model for identification of structural variation in sequencing data.
Sindi SS, Onal S, Peng L, Wu HT, Raphael BJ.
Genome Biol. 2012 Mar 27;13(3):R22.

Nuclear ribosomal internal transcribed spacer (ITS) region as a universal DNA barcode marker for fungi.
Schoch CL, Seifert KA, Huhndorf S, Robert V, et al.
Natl Acad Sci U S A. 2012 Mar 27. [Epub ahead of print]

A quantitative atlas of polyadenylation in five mammals.
Derti A, Garrett-Engele P, Macisaac KD, Stevens RC, et al.
Genome Res. 2012 Mar 27. [Epub ahead of print]

A new algorithm for quantifying binding site pattern similarity with applications for next generation sequencing.
Bible PW, Loganantharaj R.
Int J Bioinform Res Appl. 2012;8(1):4-17.

De novo sequencing, assembly and analysis of the genome of the laboratory strain Saccharomyces cerevisiae CEN.PK113-7D, a model for modern industrial biotechnology.
Nijkamp JF, van den Broek M, Datema E, de Kok S, et al.
Microb Cell Fact. 2012 Mar 26;11(1):36.

The Scan

UK Pilot Study Suggests Digital Pathway May Expand BRCA Testing in Breast Cancer

A randomized pilot study in the Journal of Medical Genetics points to similar outcomes for breast cancer patients receiving germline BRCA testing through fully digital or partially digital testing pathways.

Survey Sees Genetic Literacy on the Rise, Though Further Education Needed

Survey participants appear to have higher genetic familiarity, knowledge, and skills compared to 2013, though 'room for improvement' remains, an AJHG paper finds.

Study Reveals Molecular, Clinical Features in Colorectal Cancer Cases Involving Multiple Primary Tumors

Researchers compare mismatch repair, microsatellite instability, and tumor mutation burden patterns in synchronous multiple- or single primary colorectal cancers.

FarGen Phase One Sequences Exomes of Nearly 500 From Faroe Islands

The analysis in the European Journal of Human Genetics finds few rare variants and limited geographic structure among Faroese individuals.