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Last Week's Sequencing-Related Papers of Note: May 13, 2014


SAMBLASTER: fast duplicate marking and structural variant read extraction.
Faust GG, Hall IM.
Bioinformatics. 2014 May 7. [Epub ahead of print]

Probabilistic partitioning methods to find significant patterns in ChIP-seq data.
Nair NU, Kumar S, Moret BM, Bucher P.
Bioinformatics. 2014 May 7. [Epub ahead of print]

RNASeqGUI: a GUI for analysing RNA-seq data.
Russo F, Angelini C.
Bioinformatics. 2014 May 7. [Epub ahead of print]

Single-cell genomics for dissection of complex malaria infections.
Nair S, Nkhoma SC, Serre D, Zimmerman PA, et al.
Genome Res. 2014 May 8. [Epub ahead of print]

Theoretical and experimental assessment of degenerate primer tagging in ultra-deep applications of next-generation sequencing.
Liang RH, Mo T, Dong W, Lee GQ, et al.
Nucleic Acids Res. 2014 May 7. [Epub ahead of print]

mrsFAST-Ultra: a compact, SNP-aware mapper for high performance sequencing applications.
Hach F, Sarrafi I, Hormozdiari F, Alkan C, et al.
Nucleic Acids Res. 2014 May 8. [Epub ahead of print]

A comparison of peak callers used for DNase-seq data.
Koohy H, Down TA, Spivakov M, Hubbard T.
PLoS One. 2014 May 8;9(5):e96303.

Comprehensive evaluation and optimization of amplicon library preparation methods for high-throughput antibody sequencing.
Menzel U, Greiff V, Khan TA, Haessler U, et al.
PLoS One. 2014 May 8;9(5):e96727.

Comprehensive analysis of RNA-protein interactions by high-throughput sequencing-RNA affinity profiling.
Tome JM, Ozer A, Pagano JM, Gheba D, et al.
Nat Methods. 2014 May 8. [Epub ahead of print]

Population genomic analysis of ancient and modern genomes yields new insights into the genetic ancestry of the Tyrolean iceman and the genetic structure of Europe.
Sikora M, Carpenter ML, Moreno-Estrada A, Henn BM, et al.
PLoS Genet. 2014 May 8;10(5):e1004353.

The tobacco genome sequence and its comparison with those of tomato and potato.
Sierro N, Battey JN, Ouadi S, Bakaher N, et al.
Nat Commun. 2014 May 8;5:3833.

SimRAD: a R package for simulation-based prediction of the number of loci expected in RADseq and similar genotyping by sequencing approaches.
Lepais O, Weir JT.
Mol Ecol Resour. 2014 May 7. [Epub ahead of print]

Comparative next-generation sequencing of adeno-associated virus inverted terminal repeats.
Petri K, Fronza R, Gabriel R, Käppel C, et al.
Biotechniques. 2014 May 1;56(5):269-73.

DNA translocation through short nanofluidic channels under asymmetric pulsed electric field.
Gupta C, Liao WC, Gallego-Perez D, Castro CE, Lee LJ.
Biomicrofluidics. 2014 Apr 16;8(2):024114.

Influence of artifact removal on rare species recovery in natural complex communities using high-throughput sequencing.
Zhan A, Xiong W, He S, Macisaac HJ.
PLoS One. 2014 May 6;9(5):e96928.

deepTools: a flexible platform for exploring deep-sequencing data.
Ramírez F, Dündar F, Diehl S, Grüning BA, Manke T.
Nucleic Acids Res. 2014 May 5. [Epub ahead of print]

Nano-dissection and sequencing of DNA at single sub-nuclear structures.
Chen BK, Anchel D, Gong Z, Cotton R, et al.
Small. 2014 May 3. [Epub ahead of print]

Evaluation and comparison of multiple aligners for next-generation sequencing data analysis.
Shang J, Zhu F, Vongsangnak W, Tang Y, et al.
Biomed Res Int. 2014;2014:309650.

Influence of DNA extraction on oral microbial profiles obtained via 16S rRNA gene sequencing.
Abusleme L, Hong BY, Dupuy AK, Strausbaugh LD, Diaz PI.
J Oral Microbiol. 2014 Apr 23;6.

Control of the conductance of engineered protein nanopores through concerted loop motions.
Zhuang T, Tamm LK.
Angew Chem Int Ed Engl. 2014 Apr 28. [Epub ahead of print]

Using next-generation sequencing to detect mutations endowing resistance to pesticides: application to acetolactate-synthase (ALS) based resistance in barnyard-grass, a polyploid grass weed.
Délye C, Causse R, Gautier V, Poncet C, Michel S.
Pest Manag Sci. 2014 Apr 28. [Epub ahead of print]

Deep transcriptome profiling of mammalian stem cells supports a regulatory role for retrotransposons in pluripotency maintenance.
Fort A, Hashimoto K, Yamada D, Salimullah M, et al.
Nat Genet. 2014 Apr 28. [Epub ahead of print]

PlasmidFinder and pMLST: in silico detection and typing of plasmids.
Carattoli A, Zankari E, Garcìa-Fernandez A, Volby Larsen M, et al.
Antimicrob Agents Chemother. 2014 Apr 28. [Epub ahead of print]

Protocols for metagenomic DNA extraction and Illumina amplicon library preparation for fecal and swab samples.
Vo AE, Jedlicka JA.
Mol Ecol Resour. 2014 Apr 29. [Epub ahead of print]

Single-molecule positioning in zeromode waveguides by DNA origami nano-adapters.
Pibiri E, Holzmeister P, Lalkens B, Acuna GP, Tinnefeld P.
Nano Lett. 2014 Apr 29. [Epub ahead of print]

Methylated DNA immunoprecipitation and high-throughput sequencing (MeDIP-seq) using low amounts of genomic DNA.
Zhao MT, Whyte JJ, Hopkins GM, Kirk MD, Prather RS.
Cell Reprogram. 2014 Apr 28. [Epub ahead of print]

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.