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Papers of Note: Nov 30, 2010


Whole-exome-sequencing-based discovery of human FADD deficiency.
Bolze A, Byun M, McDonald D, Morgan NV, et al.
Am J Hum Genet. 2010 Nov 23. [Epub ahead of print]

Systematic detection of putative tumor suppressor genes through the combined use of exome and transcriptome sequencing.
Zhao Q, Kirkness EF, Caballero OL, Galante PA, et al.
Genome Biol. 2010 Nov 25;11(11):R114.

Accurate inference of transcription factor binding from DNA sequence and chromatin accessibility data.
Pique-Regi R, Degner JF, Pai AA, Gaffney DJ, Gilad Y, Pritchard JK.
Genome Res. 2010 Nov 24. [Epub ahead of print]

Pathology tissue-chromatin immunoprecipitation, coupled with high-throughput sequencing, allows the epigenetic profiling of patient samples.
Fanelli M, Amatori S, Barozzi I, Soncini M, et al.
Proc Natl Acad Sci U S A. 2010 Nov 24. [Epub ahead of print]

TGM6 identified as a novel causative gene of spinocerebellar ataxias using exome sequencing.
Wang JL, Yang X, Xia K, Hu ZM, et al.
Brain. 2010 Nov 23. [Epub ahead of print]

Rnnotator: an automated de novo transcriptome assembly pipeline from stranded RNA-seq reads.
Martin J, Bruno VM, Fang Z, Meng X, et al.
BMC Genomics. 2010 Nov 24;11(1):663.

Real-time monitoring of DNA polymerase function and stepwise single-nucleotide DNA strand translocation through a protein nanopore.
Chu J, González-López M, Cockroft SL, Amorin M, Ghadiri MR.
Angew Chem Int Ed Engl. 2010 Nov 23. [Epub ahead of print]

High-throughput DNA sequencing beyond the four-letter code: epigenetic modifications revealed by single-molecule bypass kinetics.
Summerer D.
Chembiochem. 2010 Nov 19. [Epub ahead of print]

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Experiences with array-based sequence capture; toward clinical applications.
Almomani R, van der Heijden J, Ariyurek Y, Lai Y, et al.
Eur J Hum Genet. 2010 Nov 24. [Epub ahead of print]

RNA sequencing shows no dosage compensation of the active X-chromosome.
Xiong Y, Chen X, Chen Z, Wang X, et al.
Nat Genet. 2010 Nov 21. [Epub ahead of print]

Genetic and structural variation in the gastric cancer kinome revealed through targeted deep sequencing.
Zang ZJ, Ong CK, Cutcutache I, Yu W, et al.
Cancer Res. 2010 Nov 19. [Epub ahead of print]

An integrated, low noise patch-clamp amplifier for biological nanopore applications.
Wang G, Dunbar WB.
Conf Proc IEEE Eng Med Biol Soc. 2010;1:2718-21.

Targeted next-generation sequencing of a 12.5 Mb homozygous region reveals ANO10 mutations in patients with autosomal-recessive cerebellar ataxia.
Vermeer S, Hoischen A, Meijer RP, Gilissen C, et al.
Am J Hum Genet. 2010 Nov 17. [Epub ahead of print]

Pash 3.0: A versatile software package for read mapping and integrative analysis of genomic and epigenomic variation using massively parallel DNA sequencing.
Coarfa C, Yu F, Miller CA, Chen Z, et al.
BMC Bioinformatics. 2010 Nov 23;11(1):572.

Electrochemical characterization of thin film electrodes toward developing a DNA transistor.
Harrer S, Ahmed S, Afzali-Ardakani A, Luan B, et al.
Langmuir. 2010 Nov 22. [Epub ahead of print]

Anatomy of a hash-based long read sequence mapping algorithm for next generation DNA sequencing.
Misra S, Agrawal A, Liao WK, Choudhary A.
Bioinformatics. 2010 Nov 18. [Epub ahead of print]

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SAMStat: monitoring biases in next generation sequencing data.
Lassmann T, Hayashizaki Y, Daub CO.
Bioinformatics. 2010 Nov 18. [Epub ahead of print]

The DNA methylome of human peripheral blood mononuclear cells.
Li Y, Zhu J, Tian G, Li N, et al.
PLoS Biol. 2010 Nov 9;8(11):e1000533.

Whole genome sequencing highlights genetic changes associated with laboratory domestication of C. elegans.
Weber KP, De S, Kozarewa I, Turner DJ, et al.
PLoS One. 2010 Nov 11;5(11):e13922.

Systematic inference of copy-number genotypes from personal genome sequencing data reveals extensive olfactory receptor gene content diversity.
Waszak SM, Hasin Y, Zichner T, Olender T, et al.
PLoS Comput Biol. 2010 Nov 11;6(11):e1000988.

Formation, regulation and evolution of Caenorhabditis elegans 3'UTRs.
Jan CH, Friedman RC, Ruby JG, Bartel DP.
Nature. 2010 Nov 17. [Epub ahead of print]

High-throughput sequencing reveals a simple model of nucleosome energetics.
Locke G, Tolkunov D, Moqtaderi Z, Struhl K, Morozov AV.
Proc Natl Acad Sci U S A. 2010 Nov 17. [Epub ahead of print]

In vitro selection of clinically-relevant bevirimat resistance mutations revealed by "deep" sequencing of serially-passaged, quasispecies-containing recombinant HIV-1.
Knapp DJ, Harrigan PR, Poon AF, Brumme ZL, et al.
J Clin Microbiol. 2010 Nov 17. [Epub ahead of print]

SESAME (SEquence Sorter & AMplicon Explorer): Genotyping based on high-throughput multiplex amplicon sequencing.
Meglécz E, Piry S, Desmarais E, Galan M, et al.
Bioinformatics. 2010 Nov 16. [Epub ahead of print]

Combining target enrichment with barcode multiplexing for high throughput SNP discovery.
Cummings N, King R, Rickers A, Kaspi A, et al.
BMC Genomics. 2010 Nov 18;11(1):641.

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GimmeMotifs: a de novo motif prediction pipeline for ChIP-sequencing experiments.
van Heeringen SJ, Veenstra GJ.
Bioinformatics. 2010 Nov 15. [Epub ahead of print]

Control-free calling of copy number alterations in deep-sequencing data using GC-content normalization.
Boeva V, Zinovyev A, Bleakley K, Vert JP, et al.
Bioinformatics. 2010 Nov 15. [Epub ahead of print]

Empirical Bayes analysis of sequencing-based transcriptional profiling without replicates.
Wu Z, Jenkins BD, Rynearson TA, Dyhrman ST, et al.
BMC Bioinformatics. 2010 Nov 16;11(1):564.

Improved detection of rare genetic variants for diseases.
Zhang L, Pei YF, Li J, Papasian CJ, Deng HW.
PLoS One. 2010 Nov 8;5(11):e13857.

C. elegans mutant identification with a one-step whole-genome-sequencing and SNP mapping strategy.
Doitsidou M, Poole RJ, Sarin S, Bigelow H, Hobert O.
PLoS One. 2010 Nov 8;5(11):e15435.

HMMSplicer: a tool for efficient and sensitive discovery of known and novel splice junctions in RNA-seq data.
Dimon MT, Sorber K, Derisi JL.
PLoS One. 2010 Nov 8;5(11):e13875.

Comprehensive genetic testing for hereditary hearing loss using massively parallel sequencing.
Shearer AE, Deluca AP, Hildebrand MS, Taylor KR, et al.
Proc Natl Acad Sci U S A. 2010 Nov 15. [Epub ahead of print]

Targeted massively parallel sequencing of maternal plasma DNA permits efficient and unbiased detection of fetal alleles.
Liao GJ, Lun FM, Zheng YW, Chan KC, et al.
Clin Chem. 2010 Nov 15. [Epub ahead of print]

Efficient parallel and out of core algorithms for constructing large bi-directed de Bruijn graphs.
Kundeti VK, Rajasekaran S, Dinh H, Vaughn M, Thapar V.
BMC Bioinformatics. 2010 Nov 15;11(1):560.

The Scan

Genetic Risk Factors for Hypertension Can Help Identify Those at Risk for Cardiovascular Disease

Genetically predicted high blood pressure risk is also associated with increased cardiovascular disease risk, a new JAMA Cardiology study says.

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.