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Papers of Note: Dec 7, 2010

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Whole-genome sequencing and intensive analysis of the undomesticated soybean.(Glycine soja Sieb. and Zucc.) genome.
Kim MY, Lee S, Van K, Kim TH, et al.
Proc Natl Acad Sci U S A. 2010 Dec 3. [Epub ahead of print]


Alu repeat discovery and characterization within human genomes.
Hormozdiari F, Alkan C, Ventura M, Hajirasouliha I, et al.
Genome Res. 2010 Dec 3. [Epub ahead of print]


EpiChIP: gene-by-gene quantification of epigenetic modification levels.
Hebenstreit D, Gu M, Haider S, Turner DJ, Liò P, Teichmann SA.
Nucleic Acids Res. 2010 Dec 3. [Epub ahead of print]


Chromatin particle spectrum analysis: a method for comparative chromatin structure analysis using paired-end mode next-generation DNA sequencing.
Kent NA, Adams S, Moorhouse A, Paszkiewicz K.
Nucleic Acids Res. 2010 Dec 3. [Epub ahead of print]


Labeled nucleoside triphosphates with reversibly terminating aminoalkoxyl groups.
Hutter D, Kim MJ, Karalkar N, Leal NA, et al.
Nucleosides Nucleotides Nucleic Acids. 2010 Nov;29(11):879-95.


Structural basis for the synthesis of nucleobase modified DNA by Thermus aquaticus DNA polymerase.
Obeid S, Baccaro A, Welte W, Diederichs K, Marx A.
Proc Natl Acad Sci U S A. 2010 Dec 1. [Epub ahead of print]


maxAlike: Maximum-likelihood based sequence reconstruction with application to improved primer design for unknown sequences.
Menzel P, Stadler PF, Gorodkin J.
Bioinformatics. 2010 Dec 1. [Epub ahead of print]


De novo assembled expressed gene catalog of a fast-growing Eucalyptus tree produced by Illumina mRNA-seq.
Mizrachi E, Hefer CA, Ranik M, Joubert F, Myburg AA.
BMC Genomics. 2010 Dec 1;11(1):681.


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Processive replication of single DNA molecules in a nanopore catalyzed by phi29 DNA polymerase.
Lieberman KR, Cherf GM, Doody MJ, Olasagasti F, et al.
J Am Chem Soc. 2010 Dec 1. [Epub ahead of print]


Haplotype inference from short sequence reads using a population genealogical history model.
Zhang J, Wu Y.
Pac Symp Biocomput. 2011:288-99.


Matching cancer genomes to established cell lines for personalized oncology.
Dudley JT, Chen R, Butte AJ.
Pac Symp Biocomput. 2011:243-52.


The reference human genome demonstrates high risk of type 1 diabetes and other disorders.
Chen R, Butte AJ.
Pac Symp Biocomput. 2011:231-42.


Penalized regression for genome-wide association screening of sequence data.
Zhou H, Alexander DH, Sehl ME, Sinsheimer JS, et al.
Pac Symp Biocomput. 2011:106-17.


Statistical inference of allelic imbalance from transcriptome data.
Nothnagel M, Wolf A, Herrmann A, Szafranski K, et al.
Hum Mutat. 2010 Nov 30. [Epub ahead of print]


DNA strands attached inside single conical nanopores: ionic pore characteristics and insight into DNA biophysics.
Nguyen G, Howorka S, Siwy ZS.
J Membr Biol. 2010 Dec 1. [Epub ahead of print]


Deep resequencing reveals excess rare recent variants consistent with explosive population growth.
Coventry A, Bull-Otterson LM, Liu X, Clark AG, et al.
Nat Commun. 2010 Nov;1(8):131.


HiTEC: accurate error correction in high-throughput sequencing data.
Ilie L, Fazayeli F, Ilie S.
Bioinformatics. 2010 Nov 26. [Epub ahead of print]


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Quake: quality-aware detection and correction of sequencing errors.
Kelley DR, Schatz MC, Salzberg SL.
Genome Biol. 2010 Nov 29;11(11):R116. [Epub ahead of print]


STITCH: Algorithm to Splice, Trim, Identify, Track, and Capture the uniqueness of 16S rRNAs sequence pairs using public or in-house database.
Zhu D, Vaishampayan PA, Venkateswaran K, Fox GE.
Microb Ecol. 2010 Nov 27. [Epub ahead of print]


High-fidelity gene synthesis by retrieval of sequence-verified DNA identified using high-throughput pyrosequencing.
Matzas M, Stähler PF, Kefer N, Siebelt N, et al.
Nat Biotechnol. 2010 Nov 28. [Epub ahead of print]


Deep-sequencing identification of the genomic targets of the cytidine deaminase AID and its cofactor RPA in B lymphocytes.
Yamane A, Resch W, Kuo N, Kuchen S, et al.
Nat Immunol. 2010 Nov 28. [Epub ahead of print]


Hybrid pore formation by directed insertion of α-haemolysin into solid-state nanopores.
Hall AR, Scott A, Rotem D, Mehta KK, et al.
Nat Nanotechnol. 2010 Nov 28. [Epub ahead of print]


A manually curated ChIP-seq benchmark demonstrates room for improvement in current peak-finder programs.
Rye MB, Sætrom P, Drabløs F.
Nucleic Acids Res. 2010 Nov 26. [Epub ahead of print]


A five-microRNA signature identified from genome-wide serum microRNA expression profiling serves as a fingerprint for gastric cancer diagnosis.
Liu R, Zhang C, Hu Z, Li G, et al.
Eur J Cancer. 2010 Nov 26. [Epub ahead of print]


Effect of PCR extension temperature on high-throughput sequencing.
López-Barragán MJ, Quiñones M, Cui K, Lemieux J, et al.
Mol Biochem Parasitol. 2010 Nov 25. [Epub ahead of print]


Distinguishable populations report on the interactions of single DNA molecules with solid-state nanopores.
van den Hout M, Krudde V, Janssen XJ, Dekker NH.
Biophys J. 2010 Dec 1;99(11):3840-8.


A human genome structural variation sequencing resource reveals insights into mutational mechanisms.
Kidd JM, Graves T, Newman TL, Fulton R, et al.
Cell. 2010 Nov 24;143(5):837-47.


In-depth analysis of G-to-A hypermutation rate in HIV-1 env DNA induced by endogen ous APOBEC3 proteins using massively parallel sequencing.
Knoepfel SA, Di Giallonardo F, Däumer M, Thielen A, Metzner KJ.
J Virol Methods. 2010 Nov 23. [Epub ahead of print]

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