25 Result(s)

Article

Assessing the impact of comparative genomic sequence data on the functional annotation of the Drosophilagenome

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 comparison remain to be de...

Casey M Bergman, Barret D Pfeiffer, Diego E Rincón-Limas, Roger A Hoskins… in Genome Biology (2002)

Article

Correction: Corrigendum: DNA sequence and analysis of human chromosome 18

Nature 437, 551–555 (2005) doi:10.1038/nature03983 The name of Keith O'Neill was accidentally omitted from the published author list. He is at the first affiliation in the address list.

Chad Nusbaum, Michael C. Zody, Mark L. Borowsky, Michael Kamal… in Nature (2005)

Article

Insights from the genome of the biotrophic fungal plant pathogen Ustilago maydis

Ustilago maydis is an important fungal pathogen of maize, causing corn smut. It is well adapted to its host and proliferates in living plant tissue without inducing a defence response. The genome sequence of U. m...

Jörg Kämper, Regine Kahmann, Michael Bölker, Li-Jun Ma, Thomas Brefort… in Nature (2006)

Article

ALLPATHS 2: small genomes assembled accurately and with high continuity from short paired reads

We demonstrate that genome sequences approaching finished quality can be generated from short paired reads. Using 36 base (fragment) and 26 base (jum**) reads from five microbial genomes of varied GC composi...

Iain MacCallum, Dariusz Przybylski, Sante Gnerre, Joshua Burton… in Genome Biology (2009)

Article

Targeted next-generation sequencing of a cancer transcriptome enhances detection of sequence variants and novel fusion transcripts

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 hybridization to oligo...

Joshua Z Levin, Michael F Berger, **an Adiconis, Peter Rogov… in Genome Biology (2009)

Article

Correction: Corrigendum: Ab initio reconstruction of cell type–specific transcriptomes in mouse reveals the conserved multi-exonic structure of lincRNAs

Nat. Biotechnol. 28, 503–510 (2010); published online 02 May 2010; corrected after print 9 July 2010 In the version of this article initially published, the fourth sentence in the Online Methods section “RNA e...

Mitchell Guttman, Manuel Garber, Joshua Z Levin, Julie Donaghey… in Nature Biotechnology (2010)

Article

Strand-specific RNA sequencing reveals extensive regulated long antisense transcripts that are conserved across yeast species

Recent studies in budding yeast have shown that antisense transcription occurs at many loci. However, the functional role of antisense transcripts has been demonstrated only in a few cases and it has been sugg...

Moran Yassour, Jenna Pfiffner, Joshua Z Levin, **an Adiconis… in Genome Biology (2010)

Article

Development and evaluation of RNA-seq methods

Joshua Levin, **an Adiconis, Moran Yassour, Dawn Thompson… in Genome Biology (2010)

Article

Analyzing and minimizing bias in Illumina sequencing libraries

Daniel Aird, Wei-Shen Chen, Michael Ross, Kristen Connolly, Jim Meldrim… in Genome Biology (2010)

Article

Evaluation of bacterial ribosomal RNA (rRNA) depletion methods for sequencing microbial community transcriptomes

Dawn Ciulla, Georgia Giannoukos, Ashlee Earl, Michael Feldgarden… in Genome Biology (2010)

Article

Analyzing and minimizing PCR amplification bias in Illumina sequencing libraries

Despite the ever-increasing output of Illumina sequencing data, loci with extreme base compositions are often under-represented or absent. To evaluate sources of base-composition bias, we traced genomic sequen...

Daniel Aird, Michael G Ross, Wei-Sheng Chen, Maxwell Danielsson… in Genome Biology (2011)

Article

Hybrid selection for sequencing pathogen genomes from clinical samples

We have adapted a solution hybrid selection protocol to enrich pathogen DNA in clinical samples dominated by human genetic material. Using mock mixtures of human and Plasmodium falciparum malaria parasite DNA as ...

Alexandre Melnikov, Kevin Galinsky, Peter Rogov, Timothy Fennell… in Genome Biology (2011)

Article

RNA-Seq methods for imperfect samples: development, evaluation and applications

**an Adiconis, Lin Fan, David DeLuca, Andrey Sivachenko, Nathalie Pochet… in Genome Biology (2011)

Article

RNA-Seq methods for imperfect samples: development, evaluation and applications

**an Adiconis, Lin Fan, David DeLuca, Andrey Sivachenko, Nathalie Pochet… in Genome Biology (2011)

Article

Efficient and robust RNA-seq process for cultured bacteria and complex community transcriptomes

We have developed a process for transcriptome analysis of bacterial communities that accommodates both intact and fragmented starting RNA and combines efficient rRNA removal with strand-specific RNA-seq. We ap...

Georgia Giannoukos, Dawn M Ciulla, Katherine Huang, Brian J Haas… in Genome Biology (2012)

Article

Gel-free multiplexed reduced representation bisulfite sequencing for large-scale DNA methylation profiling

Sequencing-based approaches have led to new insights about DNA methylation. While many different techniques for genome-scale map** of DNA methylation have been employed, throughput has been a key limitation ...

Patrick Boyle, Kendell Clement, Hongcang Gu, Zachary D Smith… in Genome Biology (2012)

Article

The African coelacanth genome provides insights into tetrapod evolution

The discovery of a living coelacanth specimen in 1938 was remarkable, as this lineage of lobe-finned fish was thought to have become extinct 70 million years ago. The modern coelacanth looks remarkably similar...

Chris T. Amemiya, Jessica Alföldi, Alison P. Lee, Shaohua Fan, Hervé Philippe… in Nature (2013)

Article

Correction: Corrigendum: Comparative analysis of RNA sequencing methods for degraded or low-input samples

Nat. Methods 10, 623–629 (2013); published online 19 May 2013; corrected after 2 December 2013 In the version of this article initially published, in the Online Methods “RNase H libraries” section, the sentenc...

**an Adiconis, Diego Borges-Rivera, Rahul Satija, David S DeLuca… in Nature Methods (2014)

Article

Enhanced methods for unbiased deep sequencing of Lassa and Ebola RNA viruses from clinical and biological samples

We have developed a robust RNA sequencing method for generating complete de novo assemblies with intra-host variant calls of Lassa and Ebola virus genomes in clinical and biological samples. Our method uses targe...

Christian B Matranga, Kristian G Andersen, Sarah Winnicki, Michele Busby… in Genome Biology (2014)

Article

Transcription factor binding dynamics during human ES cell differentiation

Pluripotent stem cells provide a powerful system to dissect the underlying molecular dynamics that regulate cell fate changes during mammalian development. Here we report the integrative analysis of genome-wid...

Alexander M. Tsankov, Hongcang Gu, Veronika Akopian, Michael J. Ziller… in Nature (2015)