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In Print: Last Week's Sequencing-Related Papers of Note: Oct 16, 2012


LoFreq: a sequence-quality aware, ultra-sensitive variant caller for uncovering cell-population heterogeneity from high-throughput sequencing datasets.
Wilm A, Aw PP, Bertrand D, Yeo GH, Ong SH, et al.
Nucleic Acids Res. 2012 Oct 12. [Epub ahead of print]

Predicting the accuracy of multiple sequence alignment algorithms by using computational intelligent techniques.
Ortuño FM, Valenzuela O, Pomares H, Rojas F, et al.
Nucleic Acids Res. 2012 Oct 11. [Epub ahead of print]

NGC: lossless and lossy compression of aligned high-throughput sequencing data.
Popitsch N, von Haeseler A.
Nucleic Acids Res. 2012 Oct 12. [Epub ahead of print]

Sequencing the unsequenceable: Expanded CGG-repeat alleles of the fragile X gene.
Loomis EW, Eid JS, Peluso P, Yin J, et al.
Genome Res. 2012 Oct 11. [Epub ahead of print]

Nurture trumps nature in a longitudinal survey of salivary bacterial communities in twins from early adolescence to early adulthood.
Stahringer SS, Clemente JC, Corley RP, Hewitt J, et al.
Genome Res. 2012 Oct 12. [Epub ahead of print]

SeqFold: Genome-scale reconstruction of RNA secondary structure integrating high-throughput sequencing data.
Ouyang Z, Snyder MP, Chang HY.
Genome Res. 2012 Oct 11. [Epub ahead of print]

Dynamics of DNA translocation in a solid-state nanopore immersed in aqueous glycerol.
Luan B, Wang D, Zhou R, Harrer S, et al.
Nanotechnology. 2012 Oct 12;23(45):455102.

Construction of a rationally designed antibody platform for sequencing-assisted selection.
Larman HB, Jing Xu G, Pavlova NN, Elledge SJ.
Proc Natl Acad Sci U S A. 2012 Oct 11. [Epub ahead of print]

Parallel tagged amplicon sequencing reveals major lineages and phylogenetic structure in the North American tiger salamander (Ambystoma tigrinum) species complex.
O'Neill EM, Schwartz R, Bullock CT, Williams JS, et al.
Mol Ecol. 2012 Oct 12. [Epub ahead of print]

Transcriptome assembly and isoform expression level estimation from biased RNA-seq reads.
Li W, Jiang T.
Bioinformatics. 2012 Oct 11. [Epub ahead of print]

CLEVER: Clique-Enumerating Variant Finder.
Marschall T, Costa I, Canzar S, Bauer M, et al.
Bioinformatics. 2012 Oct 11. [Epub ahead of print]

Tools for mapping high-throughput sequencing data.
Fonseca NA, Rung J, Brazma A, Marioni JC.
Bioinformatics. 2012 Oct 11. [Epub ahead of print]

CD-HIT: accelerated for clustering the next generation sequencing data.
Fu L, Niu B, Zhu Z, Wu S, Li W.
Bioinformatics. 2012 Oct 11. [Epub ahead of print]

Next-generation sequencing coupled with a cell-free display technology for high-throughput production of reliable interactome data.
Fujimori S, Hirai N, Ohashi H, Masuoka K, et al.
Sci Rep. 2012;2:691. Epub 2012 Oct 9.

Read length versus depth of coverage for viral quasispecies reconstruction.
Zagordi O, Däumer M, Beisel C, Beerenwinkel N.
PLoS One. 2012;7(10):e47046.

Transcriptome sequencing and de novo analysis for Ma bamboo (Dendrocalamus latiflorus Munro) using the Illumina platform.
Liu M, Qiao G, Jiang J, Yang H, et al.
PLoS One. 2012;7(10):e46766.

Whole genome sequencing of mutation accumulation lines reveals a low mutation rate in the social amoeba Dictyostelium discoideum.
Saxer G, Havlak P, Fox SA, Quance MA, et al.
PLoS One. 2012;7(10):e46759.

Predicting the functional effect of amino acid substitutions and indels.
Choi Y, Sims GE, Murphy S, Miller JR, Chan AP.
PLoS One. 2012;7(10):e46688.

Improving PacBio long read accuracy by short read alignment.
Au KF, Underwood JG, Lee L, Wong WH.
PLoS One. 2012;7(10):e46679.

Evaluation of different reference based annotation strategies using RNA-seq − a case study in Drososphila pseudoobscura.
Palmieri N, Nolte V, Suvorov A, Kosiol C, Schlötterer C.
PLoS One. 2012;7(10):e46415.

Rapid positional cloning of zebrafish mutations by linkage and homozygosity mapping using whole-genome sequencing.
Obholzer N, Swinburne IA, Schwab E, Nechiporuk AV, et al.
Development. 2012 Oct 10. [Epub ahead of print]

Liver transcriptome profile in pigs with extreme phenotypes of intramuscular fatty acid composition.
Ramayo-Caldas Y, Mach N, Esteve-Codina A, Corominas J, et al.
BMC Genomics. 2012 Oct 11;13(1):547.

CloudMap: a cloud-based pipeline for analysis of mutant genome sequences.
Minevich G, Park DS, Blankenberg D, Poole RJ, Hobert O.
Genetics. 2012 Oct 10. [Epub ahead of print]

miR-BAG: bagging based identification of microRNA precursors.
Jha A, Chauhan R, Mehra M, Singh HR, Shankar R.
PLoS One. 2012;7(9):e45782.

SNP discovery with EST and nextgen sequencing in switchgrass (Panicum virgatum L.).
Ersoz ES, Wright MH, Pangilinan JL, Sheehan MJ, et al.
PLoS One. 2012;7(9):e44112.

A statistical framework for accurate taxonomic assignment of metagenomic sequencing reads.
Jiang H, An L, Lin SM, Feng G, Qiu Y.
PLoS One. 2012;7(10):e46450.

A multi-omic map of the lipid-producing yeast Rhodosporidium toruloides.
Zhu Z, Zhang S, Liu H, Shen H, et al.
Nat Commun. 2012 Oct 9;3:1112.

De novo detection of copy number variation by co-assembly.
Nijkamp JF, van den Broek MA, Geertman JM, Reinders MJ, et al.
Bioinformatics. 2012 Oct 9. [Epub ahead of print]

SCALCE: boosting Sequence Compression Algorithms using Locally Consistent Encoding.
Hach F, Numanagic I, Alkan C, Sahinalp SC.
Bioinformatics. 2012 Oct 9. [Epub ahead of print]

DNA base identification by electron microscopy.
Bell DC, Thomas WK, Murtagh KM, Dionne CA, et al.
Microsc Microanal. 2012 Oct 9:1-5. [Epub ahead of print]
(See our coverage of this paper here.)

Directly observing the motion of DNA molecules near solid-state nanopores.
Ando G, Hyun C, Li J, Mitsui T.
ACS Nano. 2012 Oct 9. [Epub ahead of print]

Genome-wide ribosome profiling reveals complex translational regulation in response to oxidative stress.
Gerashchenko MV, Lobanov AV, Gladyshev VN.
Proc Natl Acad Sci U S A. 2012 Oct 8. [Epub ahead of print]

COPE: An accurate k-mer based pair-end reads connection tool to facilitate genome assembly.
Liu B, Yuan J, Yiu SM, Li Z, et al.
Bioinformatics. 2012 Oct 8. [Epub ahead of print]

MGAviewer: A desktop visualization tool for analysis of metagenomics alignment data.
Zhu Z, Niu B, Chen J, Wu S, et al.
Bioinformatics. 2012 Oct 8. [Epub ahead of print]

ncPRO-seq: a tool for annotation and profiling of ncRNAs in sRNA-seq data.
Chen CJ, Servant N, Toedling J, Sarazin A, et al.
Bioinformatics. 2012 Oct 7. [Epub ahead of print]

Individual RNA base recognition in immobilized oligonucleotides using a protein nanopore.
Ayub M, Bayley H.
Nano Lett. 2012 Oct 8. [Epub ahead of print]

The Scan

Pig Organ Transplants Considered

The Wall Street Journal reports that the US Food and Drug Administration may soon allow clinical trials that involve transplanting pig organs into humans.

'Poo-Bank' Proposal

Harvard Medical School researchers suggest people should bank stool samples when they are young to transplant when they later develop age-related diseases.

Spurred to Develop Again

New Scientist reports that researchers may have uncovered why about 60 percent of in vitro fertilization embryos stop developing.

Science Papers Examine Breast Milk Cell Populations, Cerebral Cortex Cellular Diversity, Micronesia Population History

In Science this week: unique cell populations found within breast milk, 100 transcriptionally distinct cell populations uncovered in the cerebral cortex, and more.