79 Result(s)

Article

Global nucleosome occupancy in yeast

Although eukaryotic genomes are generally thought to be entirely chromatin-associated, the activated PHO5 promoter in yeast is largely devoid of nucleosomes. We systematically evaluated nucleosome occupancy in ye...

Bradley E Bernstein, Chih Long Liu, Emily L Humphrey, Ethan O Perlstein… in Genome Biology (2004)

Article

Network security and data integrity in academia: an assessment and a proposal for large-scale archiving

Andrew Smith, Dov Greenbaum, Shawn M Douglas, Morrow Long, Mark Gerstein in Genome Biology (2005)

Article

A low-cost open-source SNP genoty** platform for association map** applications

Association map** aimed at identifying DNA polymorphisms that contribute to variation in complex traits entails genoty** a large number of single-nucleotide polymorphisms (SNPs) in a very large panel of in...

Stuart J Macdonald, Tomi Pastinen, Anne Genissel, Theodore W Cornforth… in Genome Biology (2005)

Article

Fine scale structural variants distinguish the genomes of Drosophila melanogaster and D. pseudoobscura

A primary objective of comparative genomics is to identify genomic elements of functional significance that contribute to phenotypic diversity. Complex changes in genome structure (insertions, duplications, re...

Stuart J Macdonald, Anthony D Long in Genome Biology (2006)

Article

Large-scale analysis of transcriptional cis-regulatory modules reveals both common features and distinct subclasses

Transcriptional cis-regulatory modules (for example, enhancers) play a critical role in regulating gene expression. While many individual regulatory elements have been characterized, they have never been analyzed...

Long Li, Qianqian Zhu, **n He, Saurabh Sinha, Marc S Halfon in Genome Biology (2007)

Article

RNA polymerase map** during stress responses reveals widespread nonproductive transcription in yeast

The use of genome-wide RNA abundance profiling by microarrays and deep sequencing has spurred a revolution in our understanding of transcriptional control. However, changes in mRNA abundance reflect the combin...

Tae Soo Kim, Chih Long Liu, Moran Yassour, John Holik, Nir Friedman… in Genome Biology (2010)

Article

Deep sequencing on genome-wide scale reveals the unique composition and expression patterns of microRNAs in develo** pollen of Oryza sativa

Pollen development in flowering plants requires strict control of the gene expression program and genetic information stability by mechanisms possibly including the miRNA pathway. However, our understanding of...

Li Qin Wei, Long Feng Yan, Tai Wang in Genome Biology (2011)

Article

Why rodent pseudogenes refuse to retire

A new study in this issue of Genome Biology sheds light on why some pseudogenes persist in rodent, and other mammalian, genomes.

Manyuan Long, Li Zhang in Genome Biology (2012)

Article

Genome of the long-living sacred lotus (Nelumbo nucifera Gaertn.)

Sacred lotus is a basal eudicot with agricultural, medicinal, cultural and religious importance. It was domesticated in Asia about 7,000 years ago, and cultivated for its rhizomes and seeds as a food crop. It ...

Ray Ming, Robert VanBuren, Yanling Liu, Mei Yang, Yuepeng Han… in Genome Biology (2013)

Article

Architecture of epigenetic reprogramming following Twist1-mediated epithelial-mesenchymal transition

Epithelial-mesenchymal transition (EMT) is known to impart metastasis and stemness characteristics in breast cancer. To characterize the epigenetic reprogramming following Twist1-induced EMT, we characterized ...

Gabriel G Malouf, Joseph H Taube, Yue Lu, Tapasree Roysarkar… in Genome Biology (2013)

Article

Genome-wide analysis of light-regulated alternative splicing mediated by photoreceptors in Physcomitrella patens

Light is one of the most important factors regulating plant growth and development. Light-sensing photoreceptors tightly regulate gene expression to control photomorphogenic responses. Although many levels of ...

Hshin-** Wu, Yi-shin Su, Hsiu-Chen Chen, Yu-Rong Chen, Chia-Chen Wu… in Genome Biology (2014)

Article

New genes drive the evolution of gene interaction networks in the human and mouse genomes

The origin of new genes with novel functions creates genetic and phenotypic diversity in organisms. To acquire functional roles, new genes must integrate into ancestral gene-gene interaction (GGI) networks. Th...

Wenyu Zhang, Patrick Landback, Andrea R. Gschwend, Bairong Shen… in Genome Biology (2015)

Article

Genomic legacy of the African cheetah, Acinonyx jubatus

Patterns of genetic and genomic variance are informative in inferring population history for human, model species and endangered populations.

Pavel Dobrynin, Shi** Liu, Gaik Tamazian, Zijun **ong… in Genome Biology (2015)

Article

Challenges and emerging directions in single-cell analysis

Single-cell analysis is a rapidly evolving approach to characterize genome-scale molecular information at the individual cell level. Development of single-cell technologies and computational methods has enable...

Guo-Cheng Yuan, Long Cai, Michael Elowitz, Tariq Enver, Guo** Fan… in Genome Biology (2017)

Article

Data normalization considerations for digital tumor dissection

In a recently published article in Genome Biology, Li and colleagues introduced TIMER, a gene expression deconvolution approach for studying tumor-infiltrating leukocytes (TILs) in 23 cancer types profiled by The...

Aaron M. Newman, Andrew J. Gentles, Chih Long Liu, Maximilian Diehn… in Genome Biology (2017)