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In Print: Last Week's Sequencing-Related Papers of Note: May 15, 2012


Using a priori knowledge to align sequencing reads to their exact genomic position.
Böttcher R, Amberg R, Ruzius FP, Guryev V, et al.
Nucleic Acids Res. 2012 May 11. [Epub ahead of print]

Fast and sensitive mapping of bisulfite-treated sequencing data.
Otto C, Stadler PF, Hoffmann S.
Bioinformatics. 2012 May 10. [Epub ahead of print]

De novo transcriptome sequencing of Momordica cochinchinensis to identify genes involved in the carotenoid biosynthesis.
Hyun TK, Rim Y, Jang HJ, Kim CH, et al.
Plant Mol Biol. 2012 May 12. [Epub ahead of print]

Reference genome sequence of the model plant Setaria.
Bennetzen JL, Schmutz J, Wang H, Percifield R, et al.
Nat Biotechnol. 2012 May 13. [Epub ahead of print]

The local transcriptome in the synaptic neuropil revealed by deep sequencing and high-resolution imaging.
Cajigas IJ, Tushev G, Will TJ, Tom Dieck S, et al.
Neuron. 2012 May 10;74(3):453-66.

Unsupervised two-way clustering of metagenomic sequences.
Prabhakara S, Acharya R.
J Biomed Biotechnol. 2012;2012:153647. Epub 2012 Apr 5.

CPSS: A computational platform for the analysis of small RNA deep sequencing data.
Zhang Y, Xu B, Yang Y, Cooke HJ, et al.
Bioinformatics. 2012 May 9. [Epub ahead of print]

CUSHAW: a CUDA compatible short read aligner to large genomes based on the Burrows-Wheeler transform.
Liu Y, Schmidt B, Maskell DL.
Bioinformatics. 2012 May 9. [Epub ahead of print]

Topology of the human and mouse m6A RNA methylomes revealed by m6A-seq.
Dominissini D, Moshitch-Moshkovitz S, Schwartz S, Salmon-Divon M, et al.
K, Jacob-Hirsch J, Amariglio N, Kupiec M, Sorek R, Rechavi G.
Nature. 2012 Apr 29;485(7397):201-6.

Improving ancient DNA read mapping against modern reference genomes.
Schubert M, Ginolhac A, Lindgreen S, Thompson JF, et al.
BMC Genomics. 2012 May 10;13(1):178.

Improving the performance of True Single Molecule Sequencing for ancient DNA.
Ginolhac A, Vilstrup J, Stenderup J, Rasmussen M, et al.
BMC Genomics. 2012 May 10;13(1):177.

Digital gene expression profiling by 5'-end sequencing of cDNAs during reprogramming in the moss Physcomitrella patens.
Nishiyama T, Miyawaki K, Ohshima M, Thompson K, et al.
PLoS One. 2012;7(5):e36471.

RNA-seq identifies SNP markers for growth traits in rainbow trout.
Salem M, Vallejo RL, Leeds TD, Palti Y, et al.
PLoS One. 2012;7(5):e36264.

Sequencing by hybridization of long targets.
Qin Y, Schneider TM, Brenner MP.
PLoS One. 2012;7(5):e35819.

High-throughput sequencing to reveal genes involved in reproduction and development in Bactrocera dorsalis (Diptera: Tephritidae) .
Zheng W, Peng T, He W, Zhang H.
PLoS One. 2012;7(5):e36463.

Using whole-genome sequence data to predict quantitative trait phenotypes in Drosophila melanogaster.
Ober U, Ayroles JF, Stone EA, Richards S, et al.
PLoS Genet. 2012 May;8(5):e1002685.

Rapid incorporation kinetics and improved fidelity of a novel class of 3'-OH unblocked reversible terminators.
Gardner AF, Wang J, Wu W, Karouby J, et al.
Nucleic Acids Res. 2012 May 8. [Epub ahead of print]

FusionAnalyser: a new graphical, event-driven tool for fusion rearrangements discovery.
Piazza R, Pirola A, Spinelli R, Valletta S, et al.
Nucleic Acids Res. 2012 May 8. [Epub ahead of print]

Association testing for next-generation sequencing data using score statistics.
Skotte L, Korneliussen TS, Albrechtsen A.
Genet Epidemiol. 2012 May 8. [Epub ahead of print]

Exploring single-sample SNP and INDEL calling with whole-genome de novo assembly.
Li H.
Bioinformatics. 2012 May 7. [Epub ahead of print]

OnlineCall: fast online parameter estimation and base calling for Illumina's next-generation sequencing.
Das S, Vikalo H.
Bioinformatics. 2012 May 7. [Epub ahead of print]

The genome of Ganderma lucidum provides insights into triterpense biosynthesis and wood degradation.
Liu D, Gong J, Dai W, Kang X, et al.
PLoS One. 2012;7(5):e36146.

A novel partial sequence alignment tool for finding large deletions.
Aruk T, Ustek D, Kursun O.
ScientificWorldJournal. 2012;2012:694813.

Chromatin interaction analysis with paired-end tag sequencing (ChIA-PET) for mapping chromatin interactions and understanding transcription regulation.
Goh Y, Fullwood MJ, Poh HM, Peh SQ, et al.
J Vis Exp. 2012 Apr 30;(62). pii: 3770.

Next-generation sequencing reveals significant bacterial diversity of botrytized wine.
Bokulich NA, Joseph CM, Allen G, Benson AK, Mills DA.
PLoS One. 2012;7(5):e36357.

BreakFusion: targeted assembly-based identification of gene fusions in whole transcriptome paired-end sequencing data.
Chen K, Wallis JW, Kandoth C, Kalicki-Veizer JM, et al.
Bioinformatics. 2012 May 4. [Epub ahead of print]

Identifying differentially expressed transcripts from RNA-seq data with biological variation.
Glaus P, Honkela A, Rattray M.
Bioinformatics. 2012 May 3. [Epub ahead of print]

Low sequencing efforts bias analyses of shared taxa in microbial communities.
Lemos LN, Fulthorpe RR, Roesch LF.
Folia Microbiol (Praha) . 2012 May 5. [Epub ahead of print]

Standardized collection of MNase-seq experiments enables unbiased dataset comparisons.
Rizzo JM, Bard JE, Buck MJ.
BMC Mol Biol. 2012 May 6;13(1):15.

PhenoLink — a web-tool for linking phenotype to ~omics data for bacteria: application to gene-trait matching for Lactobacillus plantarum strains.
Bayjanov JR, Molenaar D, Tzeneva V, Siezen RJ, van Hijum SA.
BMC Genomics. 2012 May 4;13(1):170.

GeSICA: Genome segmentation from intrachromosomal associations.
Liu L, Zhang Y, Feng J, Zheng N, et al.
BMC Genomics. 2012 May 4;13(1):164.

Readjoiner: a fast and memory efficient string graph-based sequence assembler.
Gonnella G, Kurtz S.
BMC Bioinformatics. 2012 May 6;13(1):82.

Bioinformatic clonality analysis of next-generation sequencing-derived viral vector integration sites.
Arens A, Appelt JU, Bartholomae CC, Gabriel R, et al.
Hum Gene Ther Methods. 2012 May 4. [Epub ahead of print]

Solution-based targeted genomic enrichment for precious DNA samples.
Shearer AE, Hildebrand MS, Smith RJ.
BMC Biotechnol. 2012 May 4;12(1):20.

The Scan

Shape of Them All

According to BBC News, researchers have developed a protein structure database that includes much of the human proteome.

For Flu and More

The Wall Street Journal reports that several vaccine developers are working on mRNA-based vaccines for influenza.

To Boost Women

China's Ministry of Science and Technology aims to boost the number of female researchers through a new policy, reports the South China Morning Post.

Science Papers Describe Approach to Predict Chemotherapeutic Response, Role of Transcriptional Noise

In Science this week: neural network to predict chemotherapeutic response in cancer patients, and more.