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In Print: Last Week's Sequencing-Related Papers of Note: Jan 10, 2012


Genome-wide occupancy links Hoxa2 to Wnt-β-catenin signaling in mouse embryonic development.
Donaldson IJ, Amin S, Hensman JJ, Kutejova E, et al.
Nucleic Acids Res. 2012 Jan 5. [Epub ahead of print]

ABrowse — a customizable next-generation genome browser framework.
Kong L, Wang J, Zhao S, Gu X, et al.
BMC Bioinformatics. 2012 Jan 5;13(1):2.

Genome-wide DNA polymorphisms in elite indica rice inbreds discovered by whole-genome sequencing.
Subbaiyan GK, Waters DL, Katiyar SK, Sadananda AR, et al.
Plant Biotechnol J. 2012 Jan 6. [Epub ahead of print]

Minimal absent words in four human genome assemblies.
Garcia SP, Pinho AJ.
PLoS One. 2011;6(12):e29344.

PASSion: a Pattern growth algorithm based pipeline for splice junction detection in paired-end RNA-seq data.
Zhang Y, Lameijer EW, 't Hoen PA, Ning Z, et al.
Bioinformatics. 2012 Jan 4. [Epub ahead of print]

Probing access resistance of solid-state nanopores with a scanning-probe microscope tip.
Hyun C, Rollings R, Li J.
Small. 2011 Dec 28. [Epub ahead of print]

Sequencing and de novo analysis of the Chinese Sika deer antler-tip transcriptome during the ossification stage using Illumina RNA-seq technology.
Yao B, Zhao Y, Zhang H, Zhang M, et al.
Biotechnol Lett. 2012 Jan 3. [Epub ahead of print]

Diffusional motion of a particle translocating through a nanopore.
Lan WJ, White HS.
ACS Nano. 2012 Jan 2. [Epub ahead of print]

RAD tag sequencing as a source of SNP markers in Cynara cardunculus L.
Scaglione D, Acquadro A, Portis E, Tirone M, et al.
BMC Genomics. 2012 Jan 3;13(1):3.

Optimizing Illumina next-generation sequencing library preparation for extremely AT-biased genomes.
Oyola SO, Otto TD, Gu Y, Maslen G, et al.
BMC Genomics. 2012 Jan 3;13(1):1.

The Scan

Expanded Genetic Testing Uncovers Hereditary Cancer Risk in Significant Subset of Cancer Patients

In Genome Medicine, researchers found pathogenic or likely pathogenic hereditary cancer risk variants in close to 17 percent of the 17,523 patients profiled with expanded germline genetic testing.

Mitochondrial Replacement Therapy Embryos Appear Largely Normal in Single-Cell 'Omics Analyses

Embryos produced with spindle transfer-based mitochondrial replacement had delayed demethylation, but typical aneuploidy and transcriptome features in a PLOS Biology study.

Cancer Patients Report Quality of Life Benefits for Immune Checkpoint Inhibitors

Immune checkpoint inhibitor immunotherapy was linked in JAMA Network Open to enhanced quality of life compared to other treatment types in cancer patients.

Researchers Compare WGS, Exome Sequencing-Based Mendelian Disease Diagnosis

Investigators find a diagnostic edge for whole-genome sequencing, while highlighting the cost advantages and improving diagnostic rate of exome sequencing in EJHG.