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Last Week's Sequencing-Related Papers of Note: Oct 18, 2011

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The complete genome sequence of Thermoproteus tenax: a physiologically versatile member of the crenarchaeota.
Siebers B, Zaparty M, Raddatz G, Tjaden B, et al.
PLoS One. 2011;6(10):e24222.


Normalization, testing, and false discovery rate estimation for RNA-sequencing data.
Li J, Witten DM, Johnstone IM, Tibshirani R.

Biostatistics. 2011 Oct 14. [Epub ahead of print]


Targeted amplicon sequencing (TAS): A scalable next-gen approach to multi-locus, multi-taxa phylogenetics.
Bybee SM, Bracken-Grissom H, Haynes BD, Hermansen RA, et al.
Genome Biol Evol. 2011 Oct 13. [Epub ahead of print]


Genome sequencing and comparison of two nonhuman primate animal models, the cynomolgus and Chinese rhesus macaques.
Yan G, Zhang G, Fang X, Zhang Y, et al.
Nat Biotechnol. 2011 Oct 16. [Epub ahead of print]


Sequencing wheat chromosome arm 7BS delimits the 7BS/4AL translocation and reveals homoeologous gene conservation.
Berkman PJ, Skarshewski A, Manoli S, Lorenc MT, et al.
Theor Appl Genet. 2011 Oct 15. [Epub ahead of print]


Sequencing of BAC pools by different next generation sequencing platforms and strategies.
Taudien S, Steuernagel B, Ariyadasa R, Schulte D, et al.
BMC Res Notes. 2011 Oct 14;4(1):411.


Paired de Bruijn graphs: a novel approach for incorporating mate pair information into genome assemblers.
Medvedev P, Pham S, Chaisson M, Tesler G, Pevzner P.
J Comput Biol. 2011 Oct 14. [Epub ahead of print]


S-MART, a software toolbox to aid RNA-seq data analysis.
Zytnicki M, Quesneville H.
PLoS One. 2011;6(10):e25988.


DNA-based fecal dietary analysis: a comparison of qPCR and high throughput sequencing approaches.
Murray DC, Bunce M, Cannell BL, Oliver R, et al.
PLoS One. 2011;6(10):e25776.


GENE-Counter: a computational pipeline for the analysis of RNA-seq data for gene expression differences.
Cumbie JS, Kimbrel JA, Di Y, Schafer DW, et al.
PLoS One. 2011;6(10):e25279.


Translocation of single-stranded DNA through the α-hemolysin protein nanopore in acidic solutions.
de Zoysa RS, Krishantha DM, Zhao Q, Gupta J, Guan X.
Electrophoresis. 2011 Oct 14. [Epub ahead of print]


De novo sequence assembly of Albugo candida reveals a small genome relative to other biotrophic oomycetes.
Links MG, Holub E, Jiang RH, Sharpe AG, et al.
BMC Genomics. 2011 Oct 13;12(1):503.


Visualization and quality assessment of de novo genome assemblies.
Riba-Grognuz O, Keller L, Falquet L, Xenarios I, Wurm Y.
Bioinformatics. 2011 Oct 12. [Epub ahead of print]


Pyicos: A versatile toolkit for the analysis of high-throughput sequencing data.
Althammer S, González-Vallinas J, Ballaré C, Beato M, Eyras E.
Bioinformatics. 2011 Oct 12. [Epub ahead of print]


SVseq: an approach for detecting exact breakpoints of deletions with low-coverage sequence data.
Zhang J, Wu Y.
Bioinformatics. 2011 Oct 12. [Epub ahead of print]


A draft genome of Yersinia pestis from victims of the Black Death.
Bos KI, Schuenemann VJ, Golding GB, Burbano HA, et al.
Nature. 2011 Oct 12. [Epub ahead of print]


Genome sequencing reveals insights into physiology and longevity of the naked mole rat.
Kim EB, Fang X, Fushan AA, Huang Z, et al.
Nature. 2011 Oct 12. [Epub ahead of print]


A high-resolution map of human evolutionary constraint using 29 mammals.
Lindblad-Toh K, Garber M, Zuk O, Lin MF, et al.
Nature. 2011 Oct 12. [Epub ahead of print]


454 antibody sequencing — error characterization and correction.
Prabakaran P, Streaker E, Chen W, Dimitrov DS.
BMC Res Notes. 2011 Oct 12;4(1):404.


Nucleotide discrimination with DNA immobilized in the MspA nanopore.
Manrao EA, Derrington IM, Pavlenok M, Niederweis M, Gundlach JH.
PLoS One. 2011;6(10):e25723.


ReCoil — an algorithm for compression of extremely large datasets of DNA data.
Yanovsky V.
Algorithms Mol Biol. 2011 Oct 11;6(1):23.


Platinum plasmonic nanostructure arrays for massively parallel single-molecule detection based on enhanced fluorescence measurements.
Saito T, Takahashi S, Obara T, Itabashi N, Imai K.
Nanotechnology. 2011 Oct 11;22(44):445708.


Blocking human contaminant DNA during PCR allows amplification of rare mammal species from sedimentary ancient DNA.
Boessenkool S, Epp LS, Haile J, Bellemain E, et al.
Mol Ecol. 2011 Oct 12. [Epub ahead of print]


Ten new complete mitochondrial genomes of pulmonates (Mollusca: Gastropoda) and their impact on phylogenetic relationships.
White TR, Conrad MM, Tseng R, Balayan S, et al.
BMC Evol Biol. 2011 Oct 10;11(1):295

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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.