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In Print: Last Week's Sequencing-Related Papers of Note: Mar 20, 2012


A fine-scale chimpanzee genetic map from population sequencing.
Auton A, Fledel-Alon A, Pfeifer S, Venn O, et al.
Science. 2012 Mar 15. [Epub ahead of print]
(See our coverage in this week's issue here.)

Regulating DNA translocation through functionalized soft nanopores.
Yeh LH, Zhang M, Qian S, Hsu JP.
Nanoscale. 2012 Mar 15. [Epub ahead of print]

Fabrication and characterization of a solid-state nanopore with self-aligned carbon nanoelectrodes for molecular detection.
Spinney PS, Collins SD, Howitt DG, Smith RL.
Nanotechnology. 2012 Apr 6;23(13):135501.

How to infer reliable diploid genotypes from NGS or traditional sequence data: from basic probability to experimental optimization.
Chenuil A.
J Evol Biol. 2012 Mar 16. [Epub ahead of print]

Analysis of microsatellite variation in Drosophila melanogaster with population-scale genome sequencing.
Fondon JW 3rd, Martin A, Richards S, Gibbs RA, Mittelman D.
PLoS One. 2012;7(3):e33036.

Characterization of the active microbiotas associated with honey bees reveals healthier and broader communities when colonies are genetically diverse.
Mattila HR, Rios D, Walker-Sperling VE, Roeselers G, Newton IL.
PLoS One. 2012;7(3):e32962.

Monitoring bacterial community structure and variability in time scale in full-scale anaerobic digesters.
Lee SH, Kang HJ, Lee YH, Lee TJ, et al.
J Environ Monit. 2012 Mar 19. [Epub ahead of print]

Integrated nanopore sensing platform with sub-microsecond temporal resolution.
Rosenstein JK, Wanunu M, Merchant CA, Drndic M, Shepard KL.
Nat Methods. 2012 Mar 18. [Epub ahead of print]

New insights into the Tyrolean Iceman's origin and phenotype as inferred by whole-genome sequencing.
Keller A, Graefen A, Ball M, Matzas M, et al.
Nat Commun. 2012 Feb 28;3:698.

Detection of diverse aquatic microbes in blood and organs of drowning victims: First metagenomic approach using high-throughput 454-pyrosequencing.
Kakizaki E, Ogura Y, Kozawa S, Nishida S, et al.
Forensic Sci Int. 2012 Mar 14. [Epub ahead of print]

Single-nanoparticle detection using a low-aspect-ratio pore.
Tsutsui M, Hongo S, He Y, Taniguchi M, et al.
ACS Nano. 2012 Mar 18. [Epub ahead of print]

MAnorm: a robust model for quantitative comparison of ChIP-seq data sets.
Shao Z, Zhang Y, Yuan GC, Orkin SH, Waxman DJ.
Genome Biol. 2012 Mar 16;13(3):R16.

Fulcrum: condensing redundant reads from high-throughput sequencing studies.
Burriesci MS, Lehnert EM, Pringle JR.
Bioinformatics. 2012 Mar 13. [Epub ahead of print]

SAMSCOPE: An OpenGL based real-time interactive scale-free SAM viewer.
Popendorf K, Sakakibara Y.
Bioinformatics. 2012 Mar 13. [Epub ahead of print]

Aviram-Ratner rectifying mechanism for DNA base-pair sequencing through graphene nanogaps.
Agapito LA, Gayles J, Wolowiec C, Kioussis N.
Nanotechnology. 2012 Mar 14;23(13):135202.

Deep sequencing analyses of low density microbial communities: working at the boundary of accurate microbiota detection.
Biesbroek G, Sanders EA, Roeselers G, Wang X, et al.
PLoS One. 2012;7(3):e32942.

Detecting selective sweeps from pooled next generation sequencing samples.
Boitard S, Schlötterer C, Nolte V, Pandey R, Futschik A.
Mol Biol Evol. 2012 Mar 12. [Epub ahead of print]

Visualizing next-generation sequencing data with JBrowse.
Westesson O, Skinner M, Holmes I.
Brief Bioinform. 2012 Mar 12. [Epub ahead of print]

Synteny-based mapping-by-sequencing enabled by targeted enrichment.
Galvão VC, Nordström KJ, Lanz C, Sulz P, et al.
Plant J. 2012 Mar 12. [Epub ahead of print]

De novo assembly and characterisation of the transcriptome during seed development, and generation of genic-SSR markers in peanut (Arachis hypogaea L.).
Zhang J, Liang S, Duan J, Wang J, et al.
BMC Genomics. 2012 Mar 12;13(1):90.

Single-molecule mechanical identification and sequencing.
Ding F, Manosas M, Spiering MM, Benkovic SJ, et al.
Nat Methods. 2012 Mar 11. [Epub ahead of print]
(See our coverage of this paper in last week's issue here.)

Bayesian estimation of bacterial community composition from 454 sequencing data.
Cheng L, Walker AW, Corander J.
Nucleic Acids Res. 2012 Mar 9. [Epub ahead of print]

Novel insight into the non-coding repertoire through deep sequencing analysis.
Isakov O, Ronen R, Kovarsky J, Gabay A, et al.
Nucleic Acids Res. 2012 Mar 9. [Epub ahead of print]

Profiling bulking and foaming bacteria in activated sludge by high throughput sequencing.
Guo F, Zhang T.
Water Res. 2012 Feb 24. [Epub ahead of print]

The Scan

Study Reveals New Details About Genetics of Major Cause of Female Infertility

Researchers in Nature Medicine conducted a whole-exome sequencing study of mote than a thousand patients with premature ovarian insufficiency.

Circulating Tumor DNA Shows Potential as Biomarker in Rare Childhood Cancer

A study in the Journal of Clinical Oncology has found that circulating tumor DNA levels in rhabdomyosarcoma may serve as a biomarker for prognosis.

Study Recommends Cancer Screening for Dogs Beginning Age Seven, Depending on Breed

PetDx researchers report in PLOS One that annual cancer screening for dogs should begin by age seven.

White-Tailed Deer Harbor SARS-CoV-2 Variants No Longer Infecting Humans, Study Finds

A new study in PNAS has found that white-tailed deer could act as a reservoir of SARS-CoV-2 variants no longer found among humans.