86 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

Quantitative trait locus analysis identifies Gabra3 as a regulator of behavioral despair in mice

The Tail Suspension Test (TST), which measures behavioral despair, is widely used as an animal model of human depressive disorders and antidepressant efficacy. In order to identify novel genes involved in the ...

Brooke H. Miller, Laura E. Schultz, Bradley C. Long, Mathew T. Pletcher in Mammalian Genome (2010)

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

Expression of human FUS/TLS in yeast leads to protein aggregation and cytotoxicity, recapitulating key features of FUS proteinopathy

Mutations in the fused in sarcoma/translocated in liposarcoma (FUS/TLS) gene have been associated with amyotrophic lateral sclerosis (ALS). FUS-positive neuropathology is reported in a range of neurodegenerati...

Kazuo Fushimi, Charles Long, Neha Jayaram, ** Chen, Liming Li… in Protein & Cell (2011)

Article

APP and APLP1 are degraded through autophagy in response to proteasome inhibition in neuronal cells

Amyloid beta (Aβ) precursor protein (APP) is a key protein in the pathogenesis of Alzheimer’s disease (AD). Both APP and its paralogue APLP1 (amyloid beta precursor-like protein 1) have multiple functions in c...

Fangfang Zhou, Theo van Laar, Huizhe Huang, Long Zhang in Protein & Cell (2011)

Article

Conserved arginine residue in the membrane-spanning domain of HIV-1 gp41 is required for efficient membrane fusion

Despite the high mutation rate of HIV-1, the amino acid sequences of the membrane-spanning domain (MSD) of HIV-1 gp41 are well conserved. Arginine residues are rarely found in single membrane-spanning domains,...

Yufei Long, Fanxia Meng, Naoyuki Kondo, Aikichi Iwamoto, Zene Matsuda in Protein & Cell (2011)

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

A proteomic approach for the identification of novel lysine methyltransferase substrates

Signaling via protein lysine methylation has been proposed to play a central role in the regulation of many physiologic and pathologic programs. In contrast to other post-translational modifications such as ph...

Dan Levy, Chih Long Liu, Ze Yang, Aaron M Newman, Ash A Alizadeh… in Epigenetics & Chromatin (2011)

Article

Bisindoylmaleimide I enhances osteogenic differentiation

The Wnt/β-catenin and bone morphogenetic proteins (BMPs) pathways play important roles in controlling osteogenesis. Using a cell-based kinase inhibitor screening assay, we identified the compound bisindoylmale...

Fangfang Zhou, Huizhe Huang, Long Zhang in Protein & Cell (2012)

Article

The potential link between PML NBs and ICP0 in regulating lytic and latent infection of HSV-1

Herpes simplex virus type 1 (HSV-1) is a common human pathogen causing cold sores and even more serious diseases. It can establish a latent stage in sensory ganglia after primary epithelial infections, and rea...

Shuai Wang, **g Long, Chun-fu Zheng in Protein & Cell (2012)

Article

Suppression of GSK3β by ERK mediates lipopolysaccharide induced cell migration in macrophage through β-catenin signaling

We investigate the role of β-catenin signaling in the response of macrophage to lipopolysaccharide (LPS) using RAW264.7 cells. LPS rapidly stimulated cytosolic β-catenin accumulation. β-catenin-mediated transc...

Kai Gong, Fangfang Zhou, Huizhe Huang, Yandao Gong, Long Zhang in Protein & Cell (2012)

Article

Transformation: how do nematode sperm become activated and crawl?

Nematode sperm undergo a drastic physiological change during spermiogenesis (sperm activation). Unlike mammalian flagellated sperm, nematode sperm are amoeboid cells and their motility is driven by the dynamic...

Xuan Ma, Yanmei Zhao, Wei Sun, Katsuya Shimabukuro, Long Miao in Protein & Cell (2012)

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

Induction of human lampbrush chromosomes

We previously demonstrated that sperm heads from amphibians (Xenopus and Rana) and zebrafish (Danio) could form giant lampbrush chromosomes when injected into the nucleus of amphibian oocytes. However, similar ex...

Ji-Long Liu, Joseph G. Gall in Chromosome Research (2012)

Article

A closer look into DNase I hypersensitivity

Housheng Hansen He, Clifford A Meyer, Henry Long, X Shirley Liu… in Epigenetics & Chromatin (2013)

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)