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Papers of Note: Jun 28, 2011


Direct measurement of DNA affinity landscapes on a high-throughput sequencing instrument.
Nutiu R, Friedman RC, Luo S, et al.
Nat Biotechnol. 2011 Jun 26. [Epub ahead of print]

Multiple platform assessment of the EGF dependent transcriptome by microarray and deep tag sequencing analysis.
Llorens F, Hummel M, Pastor X, Ferrer A, et al.
BMC Genomics. 2011 Jun 23;12(1):326.

Statistical quantification of methylation levels by next-generation sequencing.
Wu G, Yi N, Absher D, Zhi D.
PLoS One. 2011;6(6):e21034.

A Monte Carlo method for assessing the quality of duplication-aware alignment algorithms.
Freschi V, Bogliolo A.
Evol Bioinform Online. 2011;7:31-40.

In-depth annotation of SNPs arising from resequencing projects using NGS-SNP.
Grant JR, Arantes AS, Liao X, Stothard P.
Bioinformatics. 2011 Jun 22. [Epub ahead of print]

Identification of novel transcripts in annotated genomes using RNA-seq.
Roberts A, Pimentel H, Trapnell C, Pachter L.
Bioinformatics. 2011 Jun 21. [Epub ahead of print]

Finished genome of the fungal wheat pathogen Mycosphaerella graminicola reveals dispensome structure, chromosome plasticity, and stealth pathogenesis.
Goodwin SB, Ben M'barek S, Dhillon B, Wittenberg AH, et al.
PLoS Genet. 2011 Jun;7(6):e1002070.

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Characterization of the diversity and temporal stability of bacterial communities in human milk.
Hunt KM, Foster JA, Forney LJ, Schütte UM, et al.
PLoS One. 2011;6(6):e21313.

Directed sequencing and annotation of three Dicentrarchus labrax L. chromosomes by applying Sanger- and pyrosequencing technologies on pooled DNA of comparatively mapped BAC clones.
Kuhl H, Tine M, Beck A, Timmermann B, et al.
Genomics. 2011 Jun 14. [Epub ahead of print]:

CONTIGuator: a bacterial genomes finishing tool for structural insights on draft genomes.
Galardini M, Biondi EG, Bazzicalupo M, Mengoni A.
Source Code Biol Med. 2011 Jun 21;6(1):11.

CASSys: an integrated software-system for the interactive analysis of ChIP-seq data.
Alawi M, Kurtz S, Beckstette M.
J Integr Bioinform. 2011 Jun 21;8(2):155. doi: 10.2390/biecoll-jib-2011-155.

The MspJI family of modification-dependent restriction endonucleases for epigenetic studies.
Cohen-Karni D, Xu D, Apone L, Fomenkov A, et al.
Proc Natl Acad Sci U S A. 2011 Jun 20. [Epub ahead of print]

Integrative analysis of environmental sequences using MEGAN4.
Huson DH, Mitra S, Ruscheweyh HJ, Weber N, et al.
Genome Res. 2011 Jun 20. [Epub ahead of print]

False positive peaks in ChIP-seq and other sequencing-based functional assays caused by unannotated high copy number regions.
Pickrell JK, Gaffney DJ, Gilad Y, Pritchard JK.
Bioinformatics. 2011 Jun 19. [Epub ahead of print]

Long dwell-time passage of DNA through nanometer-scale pores: kinetics and sequence dependence of motion.
Jetha NN, Feehan C, Wiggin M, Tabard-Cossa V, et al.
Biophys J. 2011 Jun 22;100(12):2974-80.

Sniper: Improved SNP discovery by multiply mapping deep sequenced reads.
Simola DF, Kim J.
Genome Biol. 2011 Jun 20;12(6):R55.

The Scan

Study Links Genetic Risk for ADHD With Alzheimer's Disease

A higher polygenic risk score for attention-deficit/hyperactivity disorder is also linked to cognitive decline and Alzheimer's disease, a new study in Molecular Psychiatry finds.

Study Offers Insights Into Role of Structural Variants in Cancer

A new study in Nature using cell lines shows that structural variants can enable oncogene activation.

Computer Model Uses Genetics, Health Data to Predict Mental Disorders

A new model in JAMA Psychiatry finds combining genetic and health record data can predict a mental disorder diagnosis before one is made clinically.

Study Tracks Off-Target Gene Edits Linked to Epigenetic Features

Using machine learning, researchers characterize in BMC Genomics the potential off-target effects of 19 computed or experimentally determined epigenetic features during CRISPR-Cas9 editing.