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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

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Circulating Tumor DNA Linked to Post-Treatment Relapse in Breast Cancer

Post-treatment detection of circulating tumor DNA may identify breast cancer patients who are more likely to relapse, a new JCO Precision Oncology study finds.

Genetics Influence Level of Depression Tied to Trauma Exposure, Study Finds

Researchers examine the interplay of trauma, genetics, and major depressive disorder in JAMA Psychiatry.

UCLA Team Reports Cost-Effective Liquid Biopsy Approach for Cancer Detection

The researchers report in Nature Communications that their liquid biopsy approach has high specificity in detecting all- and early-stage cancers.