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Cited In for PubMed (Select 19682367)


Integrated microRNA, mRNA, and protein expression profiling reveals microRNA regulatory networks in rat kidney treated with a carcinogenic dose of aristolochic acid.

Li Z, Qin T, Wang K, Hackenberg M, Yan J, Gao Y, Yu LR, Shi L, Su Z, Chen T.

BMC Genomics. 2015 May 8;16:365. doi: 10.1186/s12864-015-1516-2.


Evaluating intra- and inter-individual variation in the human placental transcriptome.

Hughes DA, Kircher M, He Z, Guo S, Fairbrother GL, Moreno CS, Khaitovich P, Stoneking M.

Genome Biol. 2015 Mar 19;16:54. doi: 10.1186/s13059-015-0627-z.


Transcriptome analysis of thermophilic methylotrophic Bacillus methanolicus MGA3 using RNA-sequencing provides detailed insights into its previously uncharted transcriptional landscape.

Irla M, Neshat A, Brautaset T, Rückert C, Kalinowski J, Wendisch VF.

BMC Genomics. 2015 Feb 14;16:73. doi: 10.1186/s12864-015-1239-4.


Extensive tissue-related and allele-related mtDNA heteroplasmy suggests positive selection for somatic mutations.

Li M, Schröder R, Ni S, Madea B, Stoneking M.

Proc Natl Acad Sci U S A. 2015 Feb 24;112(8):2491-6. doi: 10.1073/pnas.1419651112. Epub 2015 Feb 9.


Insight into biases and sequencing errors for amplicon sequencing with the Illumina MiSeq platform.

Schirmer M, Ijaz UZ, D'Amore R, Hall N, Sloan WT, Quince C.

Nucleic Acids Res. 2015 Mar 31;43(6):e37. doi: 10.1093/nar/gku1341. Epub 2015 Jan 13.


Estimating genotype error rates from high-coverage next-generation sequence data.

Wall JD, Tang LF, Zerbe B, Kvale MN, Kwok PY, Schaefer C, Risch N.

Genome Res. 2014 Nov;24(11):1734-9. doi: 10.1101/gr.168393.113. Epub 2014 Oct 10.


Human paternal and maternal demographic histories: insights from high-resolution Y chromosome and mtDNA sequences.

Lippold S, Xu H, Ko A, Li M, Renaud G, Butthof A, Schröder R, Stoneking M.

Investig Genet. 2014 Sep 24;5:13. doi: 10.1186/2041-2223-5-13. eCollection 2014.


First ancient mitochondrial human genome from a prepastoralist southern African.

Morris AG, Heinze A, Chan EK, Smith AB, Hayes VM.

Genome Biol Evol. 2014 Sep 10;6(10):2647-53. doi: 10.1093/gbe/evu202.


A Polychaete's powerful punch: venom gland transcriptomics of Glycera reveals a complex cocktail of toxin homologs.

von Reumont BM, Campbell LI, Richter S, Hering L, Sykes D, Hetmank J, Jenner RA, Bleidorn C.

Genome Biol Evol. 2014 Sep 5;6(9):2406-23. doi: 10.1093/gbe/evu190.


Genetic influences on brain gene expression in rats selected for tameness and aggression.

Heyne HO, Lautenschläger S, Nelson R, Besnier F, Rotival M, Cagan A, Kozhemyakina R, Plyusnina IZ, Trut L, Carlborg Ö, Petretto E, Kruglyak L, Pääbo S, Schöneberg T, Albert FW.

Genetics. 2014 Nov;198(3):1277-90. doi: 10.1534/genetics.114.168948. Epub 2014 Sep 3.


The genomic architecture of population divergence between subspecies of the European rabbit.

Carneiro M, Albert FW, Afonso S, Pereira RJ, Burbano H, Campos R, Melo-Ferreira J, Blanco-Aguiar JA, Villafuerte R, Nachman MW, Good JM, Ferrand N.

PLoS Genet. 2014 Aug 28;10(8):e1003519. doi: 10.1371/journal.pgen.1003519. eCollection 2014 Aug.


Comparative analysis of functional metagenomic annotation and the mappability of short reads.

Carr R, Borenstein E.

PLoS One. 2014 Aug 22;9(8):e105776. doi: 10.1371/journal.pone.0105776. eCollection 2014.


Transmission from centenarians to their offspring of mtDNA heteroplasmy revealed by ultra-deep sequencing.

Giuliani C, Barbieri C, Li M, Bucci L, Monti D, Passarino G, Luiselli D, Franceschi C, Stoneking M, Garagnani P.

Aging (Albany NY). 2014 Jun;6(6):454-67.


Impact of next-generation sequencing error on analysis of barcoded plasmid libraries of known complexity and sequence.

Deakin CT, Deakin JJ, Ginn SL, Young P, Humphreys D, Suter CM, Alexander IE, Hallwirth CV.

Nucleic Acids Res. 2014;42(16):e129. doi: 10.1093/nar/gku607. Epub 2014 Jul 10.


Analysis of plant microbe interactions in the era of next generation sequencing technologies.

Knief C.

Front Plant Sci. 2014 May 21;5:216. doi: 10.3389/fpls.2014.00216. eCollection 2014. Review.


MOIRAI: a compact workflow system for CAGE analysis.

Hasegawa A, Daub C, Carninci P, Hayashizaki Y, Lassmann T.

BMC Bioinformatics. 2014 May 16;15:144. doi: 10.1186/1471-2105-15-144.


A simple method for gene phasing using mate pair sequencing.

Cradic KW, Murphy SJ, Drucker TM, Sikkink RA, Eberhardt NL, Neuhauser C, Vasmatzis G, Grebe SK.

BMC Med Genet. 2014 Feb 6;15:19. doi: 10.1186/1471-2350-15-19.


Visualization and probability-based scoring of structural variants within repetitive sequences.

Halper-Stromberg E, Steranka J, Burns KH, Sabunciyan S, Irizarry RA.

Bioinformatics. 2014 Jun 1;30(11):1514-21. doi: 10.1093/bioinformatics/btu054. Epub 2014 Feb 4.


Comprehensive analysis to improve the validation rate for single nucleotide variants detected by next-generation sequencing.

Park MH, Rhee H, Park JH, Woo HM, Choi BO, Kim BY, Chung KW, Cho YB, Kim HJ, Jung JW, Koo SK.

PLoS One. 2014 Jan 29;9(1):e86664. doi: 10.1371/journal.pone.0086664. eCollection 2014.


Separating endogenous ancient DNA from modern day contamination in a Siberian Neandertal.

Skoglund P, Northoff BH, Shunkov MV, Derevianko AP, Pääbo S, Krause J, Jakobsson M.

Proc Natl Acad Sci U S A. 2014 Feb 11;111(6):2229-34. doi: 10.1073/pnas.1318934111. Epub 2014 Jan 27.

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