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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

More Boosters for US

Following US Food and Drug Administration authorization, the Centers for Disease Control and Prevention has endorsed booster doses of the Moderna and Johnson & Johnson SARS-CoV-2 vaccines, the Washington Post writes.

From a Pig

A genetically modified pig kidney was transplanted into a human without triggering an immune response, Reuters reports.

For Privacy's Sake

Wired reports that more US states are passing genetic privacy laws.

Science Paper on How Poaching Drove Evolution in African Elephants

In Science this week: poaching has led to the rapid evolution of tuskless African elephants.