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In Print: Sequencing-Related Papers of Note of the Last Two Weeks: Nov 29, 2011


Decoding cell lineage from acquired mutations using arbitrary deep sequencing.
Carlson CA, Kas A, Kirkwood R, Hays LE, et al.
Nat Methods. 2011 Nov 27. [Epub ahead of print]

De novo assembly and characterization of a maternal and developmental transcriptome for the emerging model crustacean Parhyale hawaiensis.
Zeng V, Villanueva KE, Ewen-Campen BS, Alwes F, et al.
BMC Genomics. 2011 Nov 25;12(1):581.

The post-apoptotic fate of RNAs identified through high-throughput sequencing of human hair.
Lefkowitz GK, Mukhopadhyay A, Cowing-Zitron C, Yu BD.
PLoS One. 2011;6(11):e27603.

NovelSNPer: a fast tool for the identification and characterization of novel SNPs and indels.
Aßmus J, Schmitt AO, Bortfeldt RH, Brockmann GA.
Adv Bioinformatics. 2011;2011:657341. Epub 2011 Oct 31.

The genome portal of the Department of Energy Joint Genome Institute.
Grigoriev IV, Nordberg H, Shabalov I, Aerts A, et al.
Nucleic Acids Res. 2011 Nov 22. [Epub ahead of print]

Whole genome sequencing of peach (Prunus persica L.) for SNP identification and selection.
Ahmad R, Parfitt DE, Fass J, Ogundiwin E, et al.
BMC Genomics. 2011 Nov 22;12(1):569.

Comprehensive analysis of the bacterial content of stool from patients with chronic pouchitis, normal pouches, or familial adenomatous polyposis pouches.
Tannock GW, Lawley B, Munro K, Lay C, et al.
Inflamm Bowel Dis. 2011 Nov 23. [Epub ahead of print]

The genome of Tetranychus urticae reveals herbivorous pest adaptations.
Grbić M, Van Leeuwen T, Clark RM, Rombauts S, et al.
Nature. 2011 Nov 23;479(7374):487-92.

GenomicTools: a computational platform for developing high-throughput analytics in genomics.
Tsirigos A, Haiminen N, Bilal E, Utro F.
Bioinformatics. 2011 Nov 22. [Epub ahead of print]

RNA-seq and find: entering the RNA deep field.
Roberts A, Pachter L.
Genome Med. 2011 Nov 22;3(11):74.

Assembler: a package for de novo assembly of Roche-454/Sanger transcriptome sequences.
Zheng Y, Zhao L, Gao J, Fei Z.
BMC Bioinformatics. 2011 Nov 23;12(1):453.

Clustered ChIP-seq-defined transcription factor binding sites and histone modifications map distinct classes of regulatory elements.
Rye MB, Saetrom P, Handstad T, Drablos F.
BMC Biol. 2011 Nov 24;9(1):80.

Non-laser capture microscopy approach for the microdissection of discrete mouse brain regions for total RNA isolation and downstream next-generation sequencing and gene expression profiling.
Atkins N, Miller CM, Owens JR, Turek FW.
J Vis Exp. 2011 Nov 13;(57). pii: 3125.

An RNA-seq strategy to detect the complete coding and non-coding transcriptome including full-length imprinted macro ncRNAs.
Huang R, Jaritz M, Guenzl P, Vlatkovic I, et al.
PLoS One. 2011;6(11):e27288.

The Human OligoGenome Resource: a database of oligonucleotide capture probes for resequencing target regions across the human genome.
Newburger DE, Natsoulis G, Grimes S, Bell JM, et al.
Nucleic Acids Res. 2011 Nov 18. [Epub ahead of print]
[PubMed - as supplied by publisher]

GenomeView: a next-generation genome browser.
Abeel T, Van Parys T, Saeys Y, Galagan J, Van de Peer Y.
Nucleic Acids Res. 2011 Nov 18. [Epub ahead of print]

Fosmid-based whole genome haplotyping of a HapMap trio child: evaluation of single individual haplotyping techniques.
Duitama J, McEwen GK, Huebsch T, Palczewski S, et al.
Nucleic Acids Res. 2011 Nov 18. [Epub ahead of print]

Identification and correction of systematic error in high-throughput sequence data.
Meacham F, Boffelli D, Dhahbi J, Martin DI, et al..
BMC Bioinformatics. 2011 Nov 21;12(1):451.

Sensitive and specific single-molecule sequencing of 5-hydroxymethylcytosine.
Song CX, Clark TA, Lu XY, Kislyuk A, et al.
Nat Methods. 2011 Nov 20. [Epub ahead of print]

Next generation sequencing-based analysis of repetitive DNA in the model dioceous plant Silene latifolia.
Macas J, Kejnovský E, Neumann P, Novák P, et al.
PLoS One. 2011;6(11):e27335.

Automated digital microfluidic sample preparation for next-generation DNA sequencing.
Kim H, Bartsch MS, Renzi RF, He J, et al.
J Lab Autom. 2011 Dec;16(6):405-14.

Preparation of high quality next generation sequencing libraries from picogram quantities of target DNA.
Parkinson NJ, Maslau S, Ferneyhough B, Zhang G, et al.
Genome Res. 2011 Nov 16. [Epub ahead of print]

Nucleobase recognition at alkaline pH and apparent pK(a) of single DNA bases immobilised within a biological nanopore.
Franceschini L, Mikhailova E, Bayley H, Maglia G.
Chem Commun. (Camb). 2011 Nov 17. [Epub ahead of print]

The Medicago genome provides insight into the evolution of rhizobial symbioses.
Young ND, Debellé F, Oldroyd GE, Geurts R, et al.
Nature. 2011 Nov 16. [Epub ahead of print]

QuRe: software for viral quasispecies reconstruction from next-generation sequencing data.
Prosperi MC, Salemi M.
Bioinformatics. 2011 Nov 15. [Epub ahead of print]

AluScan: a method for genome-wide scanning of sequence and structure variations in the human genome.
Mei L, Ding X, Tsang SY, Pun FW, et al.
BMC Genomics. 2011 Nov 17;12(1):564.

ReCount: A multi-experiment resource of analysis-ready RNA-seq gene count datasets.
Frazee AC, Langmead B, Leek JT.
BMC Bioinformatics. 2011 Nov 16;12(1):449.

Next-generation sequencing of apoptotic DNA breakpoints reveals association with actively transcribed genes and gene translocations.
Fullwood MJ, Lee J, Lin L, Li G, et al.
PLoS One. 2011;6(11):e26054.

Direct, genome-wide assessment of DNA mutations in single cells.
Gundry M, Li W, Maqbool SB, Vijg J.
Nucleic Acids Res. 2011 Nov 15. [Epub ahead of print]

The SEQanswers wiki: a wiki database of tools for high-throughput sequencing analysis.
Li JW, Robison K, Martin M, Sjödin A, et al.
Nucleic Acids Res. 2011 Nov 15. [Epub ahead of print]

IMG/M: the integrated metagenome data management and comparative analysis system.
Markowitz VM, Chen IM, Chu K, Szeto E, et al.
Nucleic Acids Res. 2011 Nov 15. [Epub ahead of print]

Whole genome resequencing of Black Angus and Holstein cattle for SNP and CNV discovery.
Stothard P, Choi JW, Basu U, Sumner-Thomson JM, et al.
BMC Genomics. 2011 Nov 15;12(1):559.

OmniMapFree: A unified tool to visualise and explore sequenced genomes.
Antoniw J, Beacham AM, Baldwin TK, Urban M, et al.
BMC Bioinformatics. 2011 Nov 15;12(1):447.

Jaguc — a software package for environmental diversity analyses.
Nebel ME, Wild S, Holzhauser M, Hüttenberger L, et al.
J Bioinform Comput Biol. 2011 Dec;9(6):749-73.

Whole mitochondrial genome sequencing of domestic horses reveals incorporation of extensive wild horse diversity during domestication.
Lippold S, Matzke NJ, Reissmann M, Hofreiter M.
BMC Evol Biol. 2011 Nov 14;11(1):328.

The Scan

Quality Improvement Study Compares Molecular Tumor Boards, Central Consensus Recommendations

With 50 simulated cancer cases, researchers in JAMA Network Open compared molecular tumor board recommendations with central consensus plans at a dozen centers in Japan.

Lupus Heterogeneity Highlighted With Single-Cell Transcriptomes

Using single-cell RNA sequencing, researchers in Nature Communications tracked down immune and non-immune cell differences between discoid lupus erythematosus and systemic lupus erythematosus.

Rare Disease Clues Gleaned From Mobile Element Insertions in Exome Sequences

With an approach called MELT, researchers in the European Journal of Human Genetics uncovered mobile element insertions in exomes from 3,232 individuals with or without developmental or neurological abnormalities.

Team Tracks Down Potential Blood Plasma Markers Linked to Heart Failure in Atrial Fibrillation Patients

Researchers in BMC Genomics found 10 differentially expressed proteins or metabolites that marked atrial fibrillation with heart failure cases.