Levin, Joshua Z, Berger, Michael F, Adiconis, Xian, Rogov, Peter, Melnikov, Alexandre, Fennell, Timothy, ...
Abstract Targeted RNA-Seq combines next-generation sequencing with capture of sequences from a relevant subset of a transcriptome. When testing by capturing sequences from a tumor cDNA library by...
MacCallum, Iain, Przybylski, Dariusz, Gnerre, Sante, Burton, Joshua, Shlyakhter, Ilya, Gnirke, Andreas, ...
Abstract We demonstrate that genome sequences approaching finished quality can be generated from short paired reads. Using 36 base (fragment) and 26 base (jumping) reads from five microbial genomes...
The genome of the model beetle and pest Tribolium castaneum (2008)
Gibbs, Richard A, Weinstock, George M, Brown, Susan J, Denell, Robin, Beeman, Richard W, ...
Tribolium castaneum is a member of the most species-rich eukaryotic order, a powerful model organism for the study of generalized insect development, and an important pest of stored agricultural...
The genome of the model beetle and pest Tribolium castaneum (2008)
Gibbs, Richard A., Weinstock, George M., Brown, Susan J., Denell, Robin, Beeman, Richard W., ...
Tribolium castaneum is a member of the most species-rich eukaryotic order, a powerful model organism for the study of generalized insect development, and an important pest of stored agricultural...
Insights from the genome of the biotrophic fungal plant pathogen Ustilago maydis (2006)
Kahmann, Regine, Bölker, Michael, Ma, Li-Jun, Brefort, Thomas, Saville, Barry J, ...
Ustilago maydis is a ubiquitous pathogen of maize and a well-established model organism for the study of plant-microbe interactions. This basidiomycete fungus does not use aggressive virulence...
Meissner, Alexander, Gnirke, Andreas, Bell, George W., Ramsahoye, Bernard, Lander, Eric S., Jaenisch, Rudolf
We describe a large-scale random approach termed reduced representation bisulfite sequencing (RRBS) for analyzing and comparing genomic methylation patterns. BglII restriction fragments were...
Bergman, Casey M, Pfeiffer, Barret D, Rincón-Limas, Diego E, Hoskins, Roger A, Gnirke, Andreas, Mungall, Chris J, ...
Abstract Background It is widely accepted that comparative sequence data can aid the functional annotation of genome sequences; however, the most informative species and features of genome evolution...
the functional annotation of the (2002)
Reviews Reports Deposited, Barret D Pfeiffer, Roger A, Andreas Gnirke, Chris J Mungall, ...
Background: It is widely accepted that comparative sequence data can aid the functional annotation of genome sequences; however, the most informative species and features of genome evolution for...
Lauer, Peter, Meyer, Nicole C., Prass, Cynthia E., Starnes, Steven M., Wolff, Roger K., Gnirke, Andreas
Mikroreprod. e. Ms. 175 Bl. : graph. Darst.
Lauer, Peter, Schneider, Sandra S., Gnirke, Andreas
RecA-assisted restriction endonuclease (RARE) cleavage is an “Achilles’ heel” approach to restriction mapping whereby a RecA-protein–oligodeoxynucleotide complex protects an individual...
Fluorescence energy transfer detection as a homogeneous DNA diagnostic method
Chen, Xiangning, Zehnbauer, Barbara, Gnirke, Andreas, Kwok, Pui-Yan
A homogeneous DNA diagnostic assay based on template-directed primer extension detected by fluorescence resonance energy transfer, named template-directed dye-terminator incorporation (TDI) assay,...
Bergman, Casey M, Pfeiffer, Barret D, Rincón-Limas, Diego E, Hoskins, Roger A, Gnirke, Andreas, Mungall, Chris J, ...
Analysis of conservation in eight genomic regions (apterous, even-skipped, fushi tarazu, twist, and Rhodopsins 1, 2, 3 and 4) from four Drosophila species (D. erecta, D. pseudoobscura, D. willistoni,...
Reduced representation bisulfite sequencing for comparative high-resolution DNA methylation analysis
Meissner, Alexander, Gnirke, Andreas, Bell, George W., Ramsahoye, Bernard, Lander, Eric S., Jaenisch, Rudolf
We describe a large-scale random approach termed reduced representation bisulfite sequencing (RRBS) for analyzing and comparing genomic methylation patterns. BglII restriction fragments were...
Lauer, Peter, Schneider, Sandra S., Gnirke, Andreas
RecA-assisted restriction endonuclease (RARE) cleavage is an “Achilles’ heel” approach to restriction mapping whereby a RecA-protein–oligodeoxynucleotide complex protects an individual...
Fluorescence energy transfer detection as a homogeneous DNA diagnostic method
Chen, Xiangning, Zehnbauer, Barbara, Gnirke, Andreas, Kwok, Pui-Yan
A homogeneous DNA diagnostic assay based on template-directed primer extension detected by fluorescence resonance energy transfer, named template-directed dye-terminator incorporation (TDI) assay,...
Bergman, Casey M, Pfeiffer, Barret D, Rincón-Limas, Diego E, Hoskins, Roger A, Gnirke, Andreas, Mungall, Chris J, ...
Analysis of conservation in eight genomic regions (apterous, even-skipped, fushi tarazu, twist, and Rhodopsins 1, 2, 3 and 4) from four Drosophila species (D. erecta, D. pseudoobscura, D. willistoni,...
Reduced representation bisulfite sequencing for comparative high-resolution DNA methylation analysis
Meissner, Alexander, Gnirke, Andreas, Bell, George W., Ramsahoye, Bernard, Lander, Eric S., Jaenisch, Rudolf
We describe a large-scale random approach termed reduced representation bisulfite sequencing (RRBS) for analyzing and comparing genomic methylation patterns. BglII restriction fragments were...
Xie, Xiaohui, Mikkelsen, Tarjei S., Gnirke, Andreas, Lindblad-Toh, Kerstin, Kellis, Manolis, Lander, Eric S.
Conserved noncoding elements (CNEs) constitute the majority of sequences under purifying selection in the human genome, yet their function remains largely unknown. Experimental evidence suggests that...
The maternal-effect, selfish genetic element Medea is associated with a composite Tc1 transposon
Lorenzen, Marcé D., Gnirke, Andreas, Margolis, Jonathan, Garnes, Jeffrey, Campbell, Margie, Stuart, Jeffrey J., ...
Maternal-Effect Dominant Embryonic Arrest (“Medea”) factors are selfish nuclear elements that combine maternal-lethal and zygotic-rescue activities to gain a postzygotic survival advantage. We...
Ab initio construction of a eukaryotic transcriptome by massively parallel mRNA sequencing
Yassour, Moran, Kaplan, Tommy, Fraser, Hunter B., Levin, Joshua Z., Pfiffner, Jenna, Adiconis, Xian, ...
Defining the transcriptome, the repertoire of transcribed regions encoded in the genome, is a challenging experimental task. Current approaches, relying on sequencing of ESTs or cDNA libraries, are...