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Papers of Note: May 10, 2011


Genome-wide mapping of 5-hydroxymethylcytosine in embryonic stem cells.
Pastor WA, Pape UJ, Huang Y, Henderson HR, et al.
Nature. 2011 May 8. [Epub ahead of print]

Haplotype-resolved genome sequencing of a Gujarati Indian individual.
Kitzman JO, Mackenzie AP, Adey A, Hiatt JB, et al.
Nat Biotechnol. 2011 May;29(5):459.

Minimum information about a marker gene sequence (MIMARKS) and minimum information about any (x) sequence (MIxS) specifications.
Yilmaz P, Kottmann R, Field D, Knight R, et al.
Nat Biotechnol. 2011 May 6;29(5):415-420.

PathSeq: software to identify or discover microbes by deep sequencing of human tissue.
Kostic AD, Ojesina AI, Pedamallu CS, Jung J, et al.
Nat Biotechnol. 2011 May;29(5):393-6.

BINOCh: Binding Inference from Nucleosome Occupancy Changes.
Meyer CA, He HH, Brown M, Liu XS.
Bioinformatics. 2011 May 5. [Epub ahead of print]

Single-cell genomics reveals organismal interactions in uncultivated marine protists.
Yoon HS, Price DC, Stepanauskas R, Rajah VD, et al.
Science. 2011 May 6;332(6030):714-7.

A comprehensive platform for highly multiplexed mammalian functional genetic screens.
Ketela T, Heisler LE, Brown KR, Ammar R, et al.
BMC Genomics. 2011 May 6;12(1):213.

FusionHunter: identifying fusion transcripts in cancer using paired-end RNA-seq.
Li Y, Chien J, Smith DI, Ma J.
Bioinformatics. 2011 May 5. [Epub ahead of print]

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Boulder ALignment Editor (ALE): a web-based RNA alignment tool.
Stombaugh J, Widmann J, McDonald D, Knight R.
Bioinformatics. 2011 May 5. [Epub ahead of print]

SNiPlay: a web-based tool for detection, management and analysis of SNPs. Application to grapevine diversity projects.
Dereeper A, Nicolas S, Le Cunff L, Bacilieri R, et al.
BMC Bioinformatics. 2011 May 5;12(1):134.

Incorporation of guanosine gels into sieving matrices for length- and sequence-based separation of DNA in capillary electrophoresis.
Dong Y, McGown LB.
Electrophoresis. 2011 May;32(10):1209-16. doi: 10.1002/elps.201000545.

ProViDE: A software tool for accurate estimation of viral diversity in metagenomic samples.
Ghosh TS, Mohammed MH, Komanduri D, Mande SS.
Bioinformation. 2011 Mar 26;6(2):91-4.

Characterization of the single-cell transcriptional landscape by highly multiplex RNA-seq.
Islam S, Kjällquist U, Moliner A, Zajac P, et al.
Genome Res. 2011 May 4. [Epub ahead of print]

DREME: Motif discovery in transcription factor ChIP-seq data.
Bailey TL.
Bioinformatics. 2011 May 4. [Epub ahead of print]

Artificial duplicate reads in sequencing data of 454 Genome Sequencer FLX System.
Dong H, Chen Y, Shen Y, Wang S, et al.
Acta Biochim Biophys Sin. (Shanghai). 2011 May 4. [Epub ahead of print]

Transcript amplification from single bacterium for transcriptome analysis.
Kang Y, Norris MH, Zarzycki-Siek J, Nierman WC, et al.
Genome Res. 2011 May 2. [Epub ahead of print]

De novo assembly and validation of planaria transcriptome by massive parallel sequencing and shotgun proteomics.
Adamidi C, Wang Y, Gruen D, Mastrobuoni G, et al.
Genome Res. 2011 May 2. [Epub ahead of print]

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RNA-sequence analysis of human B-cells.
Toung JM, Morley M, Li M, Cheung VG.
Genome Res. 2011 May 2. [Epub ahead of print]

Sequencing of high G+C microbial genomes using the ultrafast pyrosequencing technology.
Schwientek P, Szczepanowski R, Rückert C, Stoye J, Pühler A.
J Biotechnol. 2011 Apr 23. [Epub ahead of print]

Multiple target loci assembly sequencing (mTAS) .
Han H, Yoon JK, Cho BC, Kim H, Bang D.
Anal Biochem. 2011 Apr 16. [Epub ahead of print]

jMOTU and Taxonerator: Turning DNA barcode sequences into annotated operational taxonomic units.
Jones M, Ghoorah A, Blaxter M.
PLoS One. 2011 Apr 25;6(4):e19259.

Linkage mapping and comparative genomics using next-generation RAD sequencing of a non-model organism.
Baxter SW, Davey JW, Johnston JS, Shelton AM, et al.
PLoS One. 2011 Apr 26;6(4):e19315.

Discovering the unknown: improving detection of novel species and genera from short reads.
Rosen GL, Polikar R, Caseiro DA, Essinger SD, Sokhansanj BA.
J Biomed Biotechnol. 2011;2011:495849. Epub 2011 Mar 23.

Local de novo assembly of RAD paired-end contigs using short sequencing reads.
Etter PD, Preston JL, Bassham S, Cresko WA, Johnson EA.
PLoS One. 2011 Apr 13;6(4):e18561.

Identification of a haemolysin-like peptide with antibacterial activity using the draft genome sequence of S. epidermidis strain A487.
Al-Mahrous MM, Jack RW, Sandiford SK, Tagg JR, et al.
FEMS Immunol Med Microbiol. 2011 May 3. doi: 10.1111/j.1574-695X.2011.00811.x.

The majority of total nuclear-encoded non-ribosomal RNA in a human cell is 'dark matter' un-annotated RNA.
Kapranov P, St Laurent G, Raz T, Ozsolak F, et al.
BMC Biol. 2010 Dec 21;8:149.

The Scan

Study Points to Tuberculosis Protection by Gaucher Disease Mutation

A mutation linked to Gaucher disease in the Ashkenazi Jewish population appears to boost Mycobacterium tuberculosis resistance in a zebrafish model of the lysosomal storage condition, a new PNAS study finds.

SpliceVault Portal Provides Look at RNA Splicing Changes Linked to Genetic Variants

The portal, described in Nature Genetics, houses variant-related messenger RNA splicing insights drawn from RNA sequencing data in nearly 335,700 samples — a set known as the 300K-RNA resource.

Automated Sequencing Pipeline Appears to Allow Rapid SARS-CoV-2 Lineage Detection in Nevada Study

Researchers in the Journal of Molecular Diagnostics describe and assess a Clear Labs Dx automated workflow, sequencing, and bioinformatic analysis method for quickly identifying SARS-CoV-2 lineages.

UK Team Presents Genetic, Epigenetic Sequencing Method

Using enzymatic DNA preparation steps, researchers in Nature Biotechnology develop a strategy for sequencing DNA, along with 5-methylcytosine and 5-hydroxymethylcytosine, on existing sequencers.