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Papers of Note: Oct 5, 2010


The complete sequence of a UK strain of black raspberry necrosis virus.
McGavin WJ, McMenemy LS, Macfarlane SA.
Arch Virol. 2010 Sep 28. [Epub ahead of print]

Reference-free validation of short read data.
Schröder J, Bailey J, Conway T, Zobel J.
PLoS One. 2010 Sep 22;5(9). pii: e12681.

Establishment and characterization of a new breast cancer xenograft obtained from a woman carrying a germline BRCA2 mutation.
de Plater L, Laugé A, Guyader C, Poupon MF, Assayag F, de Cremoux P, et. al.
Br J Cancer. 2010 Sep 28. [Epub ahead of print]

Complete characterization of the microRNAome in a patient with acute myeloid leukemia.
Ramsingh G, Koboldt DC, Trissal M, Chiappinelli KB, Wylie T, Koul S, Chang LW, Nagarajan R, Fehniger TA, Goodfellow P, Magrini V, Wilson RK, Ding L, Ley TJ, Mardis ER, Link DC.
Blood. 2010 Sep 28. [Epub ahead of print]

Complexity of the microRNA repertoire revealed by next generation sequencing.
Lee LW, Zhang S, Etheridge A, Ma L, Martin D, Galas D, Wang K.
RNA. 2010 Sep 28. [Epub ahead of print]

Fine-scale population structure and the era of next-generation sequencing.
Henn BM, Gravel S, Moreno-Estrada A, Acevedo S, Bustamante CD.
Hum Mol Genet. 2010 Sep 28. [Epub ahead of print]

SLOPE: A quick and accurate method for locating non-SNP structural variation from targeted next-generation sequence data.
Abel HJ, Duncavage EJ, Becker N, Armstrong JR, Magrini VJ, Pfeifer JD.
Bioinformatics. 2010 Sep 27. [Epub ahead of print]

Whole-exome sequencing-based discovery of STIM1 deficiency in a child with fatal classic Kaposi sarcoma.
Byun M, Abhyankar A, Lelarge V, Plancoulaine S, Palanduz A, Telhan L, Boisson B, Picard C, Dewell S, Zhao C, Jouanguy E, Feske S, Abel L, Casanova JL.
J Exp Med. 2010 Sep 27. [Epub ahead of print]

The complete mitochondrial genome of Radix balthica (Pulmonata, Basommatophora), obtained by low coverage shotgun next generation sequencing.
Feldmeyer B, Hoffmeier K, Pfenninger M.
Mol Phylogenet Evol. 2010 Sep 25. [Epub ahead of print]

Deep sequencing analysis of viral short RNAs from an infected Pinot Noir grapevine.
Pantaleo V, Saldarelli P, Miozzi L, Giampetruzzi A, Gisel A, Moxon S, Dalmay T, Bisztray G, Burgyan J.
Virology. 2010 Sep 25. [Epub ahead of print]

Emergence of Oseltamivir-Resistant Pandemic (H1N1) 2009 Virus within 48 Hours.
Inoue M, Barkham T, Leo YS, Chan KP, Chow A, Wong CW, Tze Chuen Lee R, Maurer-Stroh S, Lin R, Lin C.
Emerg Infect Dis. 2010 Oct;16(10):1633-6.

SolexaQA: At-a-glance quality assessment of Illumina second-generation sequencing data.
Cox MP, Peterson DA, Biggs PJ.
BMC Bioinformatics. 2010 Sep 27;11(1):485. [Epub ahead of print]

Pathogenicity of two Egyptian H5N1 highly pathogenic avian influenza viruses in domestic ducks.
Wasilenko JL, Arafa AM, Selim AA, Hassan MK, Aly MM, Ali A, Nassif S, Elebiary E, Balish A, Klimov A, Suarez DL, Swayne DE, Pantin-Jackwood MJ.
Arch Virol. 2010 Sep 30. [Epub ahead of print]

Comparison of two next-generation sequencing technologies for resolving highly complex microbiota composition using tandem variable 16S rRNA gene regions.
Claesson MJ, Wang Q, O'Sullivan O, Greene-Diniz R, Cole JR, Ross RP, O'Toole PW.
Nucleic Acids Res. 2010 Sep 29. [Epub ahead of print]

ASXL1 mutation is associated with poor prognosis and acute transformation in chronic myelomonocytic leukemia.
Gelsi-Boyer V, Trouplin V, Roquain J, Adélaïde J, Carbuccia N, Esterni B, Finetti P, Murati A, Arnoulet C, Zerazhi H, Fezoui H, Tadrist Z, Nezri M, Chaffanet M, Mozziconacci MJ, Vey N, Birnbaum D.
Br J Haematol. 2010 Sep 29. [Epub ahead of print]

Resequencing of 200 human exomes identifies an excess of low-frequency non-synonymous coding variants.
Li Y, Vinckenbosch N, Tian G, Huerta-Sanchez E, Jiang T, Jiang H, Albrechtsen A, Andersen G, Cao H, Korneliussen T, Grarup N, Guo Y, Hellman I, Jin X, Li Q, Liu J, Liu X, Sparsø T, Tang M, Wu H, Wu R, Yu C, Zheng H, Astrup A, Bolund L, Holmkvist J, Jørgensen T, Kristiansen K, Schmitz O, Schwartz TW, Zhang X, Li R, Yang H, Wang J, Hansen T, Pedersen O, Nielsen R, Wang J.
Nat Genet. 2010 Oct 3. [Epub ahead of print]

Level of HOXA5 Hypermethylation in Acute Myeloid Leukemia is Associated with Short-term Outcome.
Kim SY, Hwang SH, Song EJ, Shin HJ, Jung JS, Lee EY.
Korean J Lab Med. 2010 Oct;30(5):469-73.

Draft Genome Sequence of Streptomyces clavuligerus NRRL 3585, Producer of Diverse Secondary Metabolites.
J Bacteriol. 2010 Oct 1. [Epub ahead of print]

Detection of cytosine methylation in RNA using bisulfite sequencing.
Pollex T, Hanna K, Schaefer M.
Cold Spring Harb Protoc. 2010 Oct 1;2010:pdb.prot5505.

Metagenomics of the intestinal microbiota: potential applications.
Dusko Ehrlich S; MetaHIT consortium.
Gastroenterol Clin Biol. 2010 Sep;34S1:S23-S28.

Sequencing the genome of the Atlantic salmon (Salmo salar).
Davidson WS, Koop BF, Jones SJ, Iturra P, Vidal R, Maass A, Jonassen I, Lien S, Omholt SW.
Genome Biol. 2010 Sep 30;11(9):403.

Clinical and Immunological Characteristics of Patients with 2009 Pandemic Influenza A (H1N1) Virus Infection after Vaccination.
Liu W, de X00a0 Vlas SX, Tang F, Ma MX, Wei MX, Liu LX, Li ZX, Zhang L, Xin ZX, Tong YX, Jiang T, Zhang XX, He C, Li C, Xu XX, Yang H, Richardus JX, Cao WX
Clin Infect Dis. 2010 Oct 1. [Epub ahead of print]

An insect herbivore microbiome with high plant biomass-degrading capacity.
Suen G, Scott JJ, Aylward FO, Adams SM, Tringe SG, Pinto-Tomás AA, Foster CE, Pauly M, Weimer PJ, Barry KW, Goodwin LA, Bouffard P, Li L, Osterberger J, Harkins TT, Slater SC, Donohue TJ, Currie CR.
PLoS Genet. 2010 Sep 23;6(9). pii: e1001129.

Medical genetics: An Indian family with Sjögren-Larsson syndrome caused by a novel ALDH3A2 mutation.
Sakai K, Akiyama M, Yanagi T, Nampoothiri S, Mampilly T, Sunitha V, Shimizu H.
Int J Dermatol. 2010 Sep;49(9):1031-3.

The Scan

Mosquitos Genetically Modified to Prevent Malaria Spread

A gene drive approach could be used to render mosquitos unable to spread malaria, researchers report in Science Advances.

Gut Microbiomes Allow Bears to Grow to Similar Sizes Despite Differing Diets

Researchers in Scientific Reports find that the makeup of brown bears' gut microbiomes allows them to reach similar sizes even when feasting on different foods.

Finding Safe Harbor in the Human Genome

In Genome Biology, researchers present a new approach to identify genomic safe harbors where transgenes can be expressed without affecting host cell function.

New Data Point to Nuanced Relationship Between Major Depression, Bipolar Disorder

Lund University researchers in JAMA Psychiatry uncover overlapping genetic liabilities for major depression and bipolar disorder.