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In Print: Last Week's Sequencing-Related Papers of Note: Jan 29, 2013


Draft genome sequence of chickpea (Cicer arietinum) provides a resource for trait improvement.
Varshney RK, Song C, Saxena RK, Azam S, et al.
Nat Biotechnol. 2013 Jan 27. [Epub ahead of print]

Single-base resolution methylomes of tomato fruit development reveal epigenome modifications associated with ripening.
Zhong S, Fei Z, Chen YR, Zheng Y, et al.
Nat Biotechnol. 2013 Jan 27. [Epub ahead of print]

Towards practical, high-capacity, low-maintenance information storage in synthesized DNA.
Goldman N, Bertone P, Chen S, Dessimoz C, et al.
Nature. 2013 Jan 23. [Epub ahead of print]
(See our coverage of this paper in this issue here.)

High-resolution enzymatic mapping of genomic 5-hydroxymethylcytosine in mouse embryonic stem cells.
Sun Z, Jolyon T, Borgaro JG, Liu Y, et al.
Cell Rep. 2013 Jan 22. [Epub ahead of print]

Primer effect in the detection of mitochondrial DNA point heteroplasmy by automated sequencing.
Calatayud M, Ramos A, Santos C, Aluja MP.
Mitochondrial DNA. 2013 Jan 25. [Epub ahead of print]

HeurAA: accurate and fast detection of genetic variations with a novel heuristic amplicon aligner program for next generation sequencing.
Pongor LS, Pintér F, Peták I.
PLoS One. 2013;8(1):e54294.

Efficient and comprehensive representation of uniqueness for next-generation sequencing by minimum unique length analyses.
Storvall H, Ramsköld D, Sandberg R.
PLoS One. 2013;8(1):e53822.

Identification of medium-sized genomic deletions with low coverage, mate-paired restricted tags.
Gong Q, Tao Y, Yang JR, Cai J, et al.
BMC Genomics. 2013 Jan 24;14(1):51.

Integration of solid-state nanopores in microfluidic networks via transfer printing of suspended membranes.
Jain T, Aguilar CA, Karnik R.
Anal Chem. 2013 Jan 24. [Epub ahead of print]

The history of Slavs inferred from complete mitochondrial genome sequences.
Mielnik-Sikorska M, Daca P, Malyarchuk B, Derenko M, et al.
PLoS One. 2013;8(1):e54360.

Identification and characterization of microRNAs in channel catfish (Ictalurus punctatus) by using Solexa sequencing technology.
Xu Z, Chen J, Li X, Ge J, et al.
PLoS One. 2013;8(1):e54174.

Incomplete lineage sorting is common in extant gibbon genera.
Wall JD, Kim SK, Luca F, Carbone L, et al.
PLoS One. 2013;8(1):e53682.

A survey of tools for variant analysis of next-generation genome sequencing data.
Pabinger S, Dander A, Fischer M, Snajder R, et al.
Brief Bioinform. 2013 Jan 21. [Epub ahead of print]

Widespread splicing changes in human brain development and aging.
Mazin P, Xiong J, Liu X, Yan Z, et al.
Mol Syst Biol. 2013 Jan 22;9:633.

Single-molecule DNA detection using a novel SP1 protein nanopore.
Wang HY, Li Y, Qin LX, Heyman A, et al.
Chem Commun. (Camb). 2013 Jan 23. [Epub ahead of print]

Empirical assessment of sequencing errors for high throughput pyrosequencing data.
da Fonseca PG, Paiva JA, Almeida LG, Vasconcelos AT, Freitas AT.
BMC Res Notes. 2013 Jan 22;6(1):25.

Enhanced 5-methylcytosine detection in single-molecule, real-time sequencing via Tet1 oxidation.
Clark TA, Lu X, Luong K, Dai Q, et al.
BMC Biol. 2013 Jan 22;11(1):4.

In silico mining of putative microsatellite markers from whole genome sequence of water buffalo (Bubalis bubalis) and development of first BuffSatDB.
Jaiswal S, Arora V, Iquebal MA, Rai A, Kumar D.
BMC Genomics. 2013 Jan 19;14(1):43.

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.