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In Print: Last Week's Sequencing Papers of Note, Dec. 18, 2012


Whole-genome sequencing of giant pandas provides insights into demographic history and local adaptation.
Zhao S, Zheng P, Dong S, Zhan X, et al.
Nat Genet. 2012 Dec 16. [Epub ahead of print]

Analysis of alternative cleavage and polyadenylation by 3' region extraction and deep sequencing.
Hoque M, Ji Z, Zheng D, Luo W, et al.
Nat Methods. 2012 Dec 16. [Epub ahead of print]

High-throughput sequence analysis reveals structural diversity and improved potency among RNA inhibitors of HIV reverse transcriptase.
Ditzler MA, Lange MJ, Bose D, Bottoms CA, et al.
Nucleic Acids Res. 2012 Dec 14. [Epub ahead of print]

Prediction of novel long non-coding RNAs based on RNA-seq data of mouse Klf1 knockout study.
Sun L, Zhang Z, Bailey TL, Perkins AC, et al.
BMC Bioinformatics. 2012 Dec 13;13(1):331.

Evaluating de Bruijn graph assemblers on 454 transcriptomic data.
Ren X, Liu T, Dong J, Sun L, et al.
PLoS One. 2012;7(12):e51188.

Cross-biome metagenomic analyses of soil microbial communities and their functional attributes.
Fierer N, Leff JW, Adams BJ, Nielsen UN, et al.
Proc Natl Acad Sci U S A. 2012 Dec 10. [Epub ahead of print]

Mapping the ion current distribution in nanopore/electrode devices.
Rutkowska A, Edel JB, Albrecht T.
ACS Nano. 2012 Dec 12. [Epub ahead of print]

A core human microbiome as viewed through 16S rRNA sequence clusters.
Huse SM, Ye Y, Zhou Y, Fodor AA.
PLoS One. 2012;7(6):e34242.

RetroSeq: Transposable element discovery from Illumina paired-end sequencing data.
Keane TM, Wong K, Adams DJ.
Bioinformatics. 2012 Dec 10. [Epub ahead of print]

Direct sequencing of haplotypes from diploid individuals through a modified emulsion PCR-based single-molecule sequencing approach.
Metzger BP, Gelembiuk GW, Lee CE.
Mol Ecol Resour. 2013 Jan;13(1):135-43.

The effects of diffusion on an exonuclease∕nanopore-based DNA sequencing engine.
Reiner JE, Balijepalli A, Robertson JW, Drown BS, et al.
J Chem Phys. 2012 Dec 7;137(21):214903.

Identifying differentially spliced genes from two groups of RNA-seq samples.
Wang W, Qin Z, Feng Z, Wang X, Zhang X.
Gene. 2012 Dec 7. [Epub ahead of print]

Quality control in multi-tag pyrosequencing of microbial communities.
Sikaroodi M, Gillevet PM.
Biotechniques. 2012 Dec;53(6):381-3.

cDNA normalization by hydroxyapatite chromatography to enrich transcriptome diversity in RNA-seq applications.
Vandernoot VA, Langevin SA, Solberg OD, Lane PD, et al.
Biotechniques. 2012 Dec;53(6):373-80.

Direct sequencing of small genomes on the Pacific Biosciences RS without library preparation.
Coupland P, Chandra T, Quail M, Reik W, Swerdlow H .
Biotechniques. 2012 Dec;53(6):365-72.
(See In Sequence's coverage of this paper here.)

RNA deep sequencing as a tool for selection of cell lines for systematic subcellular localization of all human proteins.
Danielsson F, Wiking M, Mahdessian D, Skogs M, et al.
J Proteome Res. 2012 Dec 10. [Epub ahead of print]

The repertoire and features of human platelet microRNAs.
Plé H, Landry P, Benham A, Coarfa C, et al.
PLoS One. 2012;7(12):e50746.

Accurate diagnostics for bovine tuberculosis based on high-throughput sequencing.
Churbanov A, Milligan B.
PLoS One. 2012;7(11):e50147.

Onset of immune senescence defined by unbiased pyrosequencing of human immunoglobulin mRNA repertoires.
Rubelt F, Sievert V, Knaust F, Diener C, et al.
PLoS One. 2012;7(11):e49774.

Differential analysis of gene regulation at transcript resolution with RNA-seq.
Trapnell C, Hendrickson DG, Sauvageau M, Goff L, et al.
Nat Biotechnol. 2012 Dec 9. [Epub ahead of print]

Genomic variation landscape of the human gut microbiome.
Schloissnig S, Arumugam M, Sunagawa S, Mitreva M, et al.
Nature. 2012 Dec 5. [Epub ahead of print]

miRDeep*: an integrated application tool for miRNA identification from RNA sequencing data.
An J, Lai J, Lehman ML, Nelson CC.
Nucleic Acids Res. 2012 Dec 4. [Epub ahead of print]

KungFQ: A simple and powerful approach to compress fastq files.
Grassi E, Gregorio FD, Molineris I.
IEEE/ACM Trans Comput Biol Bioinform. 2012 Nov;9(6):1837-42.

Transcriptome walking: a laboratory-oriented GUI-based approach to mRNA identification from deep-sequenced data.
French AS.
BMC Res Notes. 2012 Dec 5;5(1):673.

Population-based rare variant detection via pooled exome or custom hybridization capture with or without individual indexing.
Ramos E, Levinson BT, Chasnoff S, Hughes A, et al.
BMC Genomics. 2012 Dec 6;13(1):683.

MALINA: a web service for visual analytics of human gut microbiota whole-genome metagenomic reads.
Tyakht AV, Popenko AS, Belenikin MS, Altukhov IA, et al.
Source Code Biol Med. 2012 Dec 7;7(1):13.

Lipid nanobilayers to host biological nanopores for DNA translocations.
Göpfrich K, Kulkarni CV, Pambos OJ, Keyser UF.
Langmuir. 2012 Dec 7. [Epub ahead of print]

The Scan

Germline-Targeting HIV Vaccine Shows Promise in Phase I Trial

A National Institutes of Health-led team reports in Science that a broadly neutralizing antibody HIV vaccine induced bnAb precursors in 97 percent of those given the vaccine.

Study Uncovers Genetic Mutation in Childhood Glaucoma

A study in the Journal of Clinical Investigation ties a heterozygous missense variant in thrombospondin 1 to childhood glaucoma.

Gene Co-Expression Database for Humans, Model Organisms Gets Update

GeneFriends has been updated to include gene and transcript co-expression networks based on RNA-seq data from 46,475 human and 34,322 mouse samples, a new paper in Nucleic Acids Research says.

New Study Investigates Genomics of Fanconi Anemia Repair Pathway in Cancer

A Rockefeller University team reports in Nature that FA repair deficiency leads to structural variants that can contribute to genomic instability.