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In Print: Last Week's Sequencing-Related Papers of Note: Feb 26, 2013


The de novo assembly of mitochondrial genomes of the extinct passenger pigeon (Ectopistes migratorius) with next generation sequencing.
Hung CM, Lin RC, Chu JH, Yeh CF, et al.
PLoS One. 2013;8(2):e56301.

Predicting the molecular complexity of sequencing libraries.
Daley T, Smith AD.
Nat Methods. 2013 Feb 24. [Epub ahead of print]

The draft genome of the fast-growing non-timber forest species moso bamboo (Phyllostachys heterocycla).
Peng Z, Lu Y, Li L, Zhao Q, et al.
Nat Genet. 2013 Feb 24. [Epub ahead of print]

Sequencing of the sea lamprey (Petromyzon marinus) genome provides insights into vertebrate evolution.
Smith JJ, Kuraku S, Holt C, Sauka-Spengler T, et al.
Nat Genet. 2013 Feb 24. [Epub ahead of print]

MeRIP-PF: An easy-to-use pipeline for high-resolution peak-finding in MeRIP-seq data.
Li Y, Song S, Li C, Yu J.
Genomics Proteomics Bioinformatics. 2013 Jan 20. pii: S1672-0229(13)00006-5.

Orthology guided assembly in highly heterozygous crops: creating a reference transcriptome to uncover genetic diversity in Lolium perenne.
Ruttink T, Sterck L, Rohde A, Bendixen C, et al.
Plant Biotechnol J. 2013 Feb 21. [Epub ahead of print]

Reference-free SNP discovery for the Eurasian beaver from restriction site-associated DNA paired-end data.
Senn H, Ogden R, Cezard T, Gharbi K, et al.
Mol Ecol. 2013 Feb 21. [Epub ahead of print]

Assessing DNA barcoding as a tool for species identification and data quality control.
Shen YY, Chen X, Murphy RW.
PLoS One. 2013;8(2):e57125.

Precise maps of RNA polymerase reveal how promoters direct initiation and pausing.
Kwak H, Fuda NJ, Core LJ, Lis JT.
Science. 2013 Feb 22;339(6122):950-3.

High-throughput chromatin immunoprecipitation for genome-wide mapping of in vivo protein-DNA interactions and epigenomic states.
Blecher-Gonen R, Barnett-Itzhaki Z, Jaitin D, Amann-Zalcenstein D, et al.
Nat Protoc. 2013 Feb 21;8(3):539-54.

Quantifying copy number variations using a hidden Markov model with inhomogeneous emission distributions.
McCallum KJ, Wang JP.
Biostatistics. 2013 Feb 20. [Epub ahead of print]

DeconRNASeq: a statistical framework for deconvolution of heterogeneous tissue samples based on mRNA-seq data.
Gong T, Szustakowski JD.
Bioinformatics. 2013 Feb 21. [Epub ahead of print]

EBSeq: An empirical Bayes hierarchical model for inference in RNA-seq experiments.
Leng N, Dawson JA, Thomson JA, Ruotti V, et al.
Bioinformatics. 2013 Feb 21. [Epub ahead of print]

Poisson factor models with applications to non-normalized microRNA profiling.
Lee S, Chugh PE, Shen H, Eberle RW, Dittmer DP.
Bioinformatics. 2013 Feb 21. [Epub ahead of print]

From binding motifs in ChIP-seq data to improved models of transcription factor binding sites.
Kulakovskiy I, Levitsky V, Oshchepkov D, Bryzgalov L, et al.
J Bioinform Comput Biol. 2013 Feb;11(1):1340004.

RNA-seq analysis of transcriptomes in thrombin-treated and control human pulmonary microvascular endothelial cells.
Cheranova D, Gibson M, Chaudhary S, Zhang LQ, et al.
J Vis Exp. 2013 Feb 13;(72). pii: 4393.

A de novo assembly of the newt transcriptome combined with proteomic validation identifies new protein families expressed during tissue regeneration.
Looso M, Preussner J, Sousounis K, Bruckskotten M, et al.
Genome Biol. 2013 Feb 20;14(2):R16.

A computational method for detecting copy number variations using scale-space filtering.
Lee J, Lee U, Kim B, Yoon J.
BMC Bioinformatics. 2013 Feb 18;14(1):57.

The Scan

Positive Framing of Genetic Studies Can Spark Mistrust Among Underrepresented Groups

Researchers in Human Genetics and Genomics Advances report that how researchers describe genomic studies may alienate potential participants.

Small Study of Gene Editing to Treat Sickle Cell Disease

In a Novartis-sponsored study in the New England Journal of Medicine, researchers found that a CRISPR-Cas9-based treatment targeting promoters of genes encoding fetal hemoglobin could reduce disease symptoms.

Gut Microbiome Changes Appear in Infants Before They Develop Eczema, Study Finds

Researchers report in mSystems that infants experienced an enrichment in Clostridium sensu stricto 1 and Finegoldia and a depletion of Bacteroides before developing eczema.

Acute Myeloid Leukemia Treatment Specificity Enhanced With Stem Cell Editing

A study in Nature suggests epitope editing in donor stem cells prior to bone marrow transplants can stave off toxicity when targeting acute myeloid leukemia with immunotherapy.