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In Print: Last Week's Sequencing-Related Papers of Note: Jun 4, 2013

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The eukaryotic genome, its reads, and the unfinished assembly.
Muñoz JF, Gallo JE, Misas E, McEwen JG, Clay OK.
FEBS Lett. 2013 May 30. [Epub ahead of print]


Microarray and deep sequencing cross-platform analysis of the mirRNome and isomiR variation in response to epidermal growth factor.
Llorens F, Hummel M, Pantano L, Pastor X, et al.
BMC Genomics. 2013 Jun 1;14(1):371.


A new genomic tool, ultra-frequently cleaving TaqII/sinefungin endonuclease with a combined 2.9-bp recognition site, applied to the construction of horse DNA libraries.
Zylicz-Stachula A, Zolnierkiewicz O, Jasiecki J, Skowron PM.
BMC Genomics. 2013 Jun 1;14(1):370.


Distributions of positive signals in pyrosequencing.
Kong Y.
J Math Biol. 2013 May 31. [Epub ahead of print]


Solid-phase proximity ligation assays for individual or parallel protein analyses with readout via real-time PCR or sequencing.
Nong RY, Wu D, Yan J, Hammond M, et al.
Nat Protoc. 2013 May 30;8(6):1234-48.


The genome sequencing of an albino Western lowland gorilla reveals inbreeding in the wild.
Prado-Martinez J, Hernando-Herraez I, Lorente-Galdos B, Dabad M, et al.
BMC Genomics. 2013 May 31;14(1):363.


Accounting for immunoprecipitation efficiencies in the statistical analysis of ChIP-seq data.
Bao Y, Vinciotti V, Wit E, 't Hoen PA.
BMC Bioinformatics. 2013 May 30;14(1):169.


High-throughput sequencing reveals principles of Adeno-Associated Virus Serotype 2 integration.
Janovitz T, Klein IA, Oliveira T, Mukherjee P, et al.
J Virol. 2013 May 29. [Epub ahead of print]


Nanopore single-molecule detection of circulating microRNAs.
Gu LQ, Wang Y.
Methods Mol Biol. 2013;1024:255-268.


Electron beam-assisted healing of nanopores in magnesium alloys.
Zheng H, Liu Y, Cao F, Wu S, et al.
Sci Rep. 2013 May 30;3:1920.


Gut metagenome in European women with normal, impaired and diabetic glucose control.
Karlsson FH, Tremaroli V, Nookaew I, Bergström G, et al.
Nature. 2013 May 29. [Epub ahead of print]


Heterogeneity of young and aged murine hematopoietic stem cells revealed by quantitative clonal analysis using cellular barcoding.
Verovskaya E, Broekhuis MJ, Zwart E, Ritsema M, et al.
Blood. 2013 May 29. [Epub ahead of print]


Multiplex target capture with double-stranded DNA probes.
Shen P, Wang W, Chi AK, Fan Y, et al.
Genome Med. 2013 May 29;5(5):50.


Targeted next-generation sequencing of head and neck squamous cell carcinoma identifies novel genetic alterations in HPV+ and HPV- tumors.
Lechner M, Frampton G, Fenton T, Feber A, et al.
Genome Med. 2013 May 29;5(5):49.


Characterizing and measuring bias in sequence data.
Ross MG, Russ C, Costello M, Hollinger A, et al.
Genome Biol. 2013 May 29;14(5):R51.


Mutant-Bin: unsupervised haplotype estimation of viral population diversity without reference genome.
Prabhakara S, Malhotra R, Acharya R, Poss M.
J Comput Biol. 2013 Jun;20(6):453-463.


The population structure and recent colonization history of Oregon threespine stickleback determined using restriction-site associated DNA-sequencing.
Catchen J, Bassham S, Wilson T, Currey M, et al.
Mol Ecol. 2013 Jun;22(11):2864-2883.


IMSA: Integrated Metagenomic Sequence Analysis for identification of exogenous reads in a host genomic background.
Dimon MT, Wood HM, Rabbitts PH, Arron ST.
PLoS One. 2013 May 23;8(5):e64546.


VirusFinder: software for efficient and accurate detection of viruses and their integration sites in host genomes through next generation sequencing data.
Wang Q, Jia P, Zhao Z.
PLoS One. 2013 May 24;8(5):e64465.


Home life: factors structuring the bacterial diversity found within and between homes.
Dunn RR, Fierer N, Henley JB, Leff JW, Menninger HL.
PLoS One. 2013 May 22;8(5):e64133.


Computational analysis of bacterial RNA-seq data.
McClure R, Balasubramanian D, Sun Y, Bobrovskyy M, et al.
Nucleic Acids Res. 2013 May 28. [Epub ahead of print]


The genome of the Netherlands: design, and project goals.
Boomsma DI, Wijmenga C, Slagboom EP, Swertz MA, et al.
Eur J Hum Genet. 2013 May 29. [Epub ahead of print]


Phase-defined complete sequencing of the HLA genes by next-generation sequencing.
Hosomichi K, Jinam TA, Mitsunaga S, Nakaoka H, Inoue I.
BMC Genomics. 2013 May 28;14(1):355.


Ethical and legal implications of whole genome and whole exome sequencing in African populations.
Wright GE, Koornhof PG, Adeyemo AA, Tiffin N.
BMC Med Ethics. 2013 May 28;14(1):21.


Efficient high-throughput sequencing of a laser microdissected chromosome arm.
Seifertova E, Zimmerman LB, Gilchrist MJ, Macha J, et al.
BMC Genomics. 2013 May 28;14(1):357.


Detection of long and short DNA using nanopores with graphitic polyhedral edges.
Freedman KJ, Ahn CW, Kim MJ.
ACS Nano. 2013 May 28. [Epub ahead of print]


Stability of airborne microbes in the Louvre Museum over time.
Gaüzère C, Moletta-Denat M, Blanquart H, Ferreira S, et al.
Indoor Air. 2013 May 27. [Epub ahead of print]

The Scan

New Study Investigates Genomics of Fanconi Anemia Repair Pathway in Cancer

A Rockefeller University team reports in Nature that FA repair deficiency leads to structural variants that can contribute to genomic instability.

Study Reveals Potential Sex-Specific Role for Noncoding RNA in Depression

A long, noncoding RNA called FEDORA appears to be a sex-specific regulator of major depressive disorder, affecting more women, researchers report in Science Advances.

New mRNA Vaccines Offer Hope for Fighting Malaria

A George Washington University-led team has developed mRNA vaccines for malaria that appear to provide protection in mice, as they report in NPJ Vaccines.

Unique Germline Variants Found Among Black Prostate Cancer Patients

Through an exome sequencing study appearing in JCO Precision Oncology, researchers have found unique pathogenic or likely pathogenic variants within a cohort of Black prostate cancer patients.