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Papers of Note: Dec 7, 2010


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]

The Scan

Octopus Brain Complexity Linked to MicroRNA Expansions

Investigators saw microRNA gene expansions coinciding with complex brains when they analyzed certain cephalopod transcriptomes, as they report in Science Advances.

Study Tracks Outcomes in Children Born to Zika Virus-Infected Mothers

By following pregnancy outcomes for women with RT-PCR-confirmed Zika virus infections, researchers saw in Lancet Regional Health congenital abnormalities in roughly one-third of live-born children.

Team Presents Benchmark Study of RNA Classification Tools

With more than 135 transcriptomic datasets, researchers tested two dozen coding and non-coding RNA classification tools, establishing a set of potentially misclassified transcripts, as they report in Nucleic Acids Research.

Breast Cancer Risk Related to Pathogenic BRCA1 Mutation May Be Modified by Repeats

Several variable number tandem repeats appear to impact breast cancer risk and age at diagnosis in almost 350 individuals carrying a risky Ashkenazi Jewish BRCA1 founder mutation.