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65
deepBase: a database for deeply annotating and mining deep sequencing data
- Nucleic Acids Research
, 2010
"... Advances in high-throughput next-generation sequencing technology have reshaped the transcriptomic research landscape. However, explo-ration of these massive data remains a daunting challenge. In this study, we describe a novel database, deepBase, which we have developed to facilitate the comprehens ..."
Abstract
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Cited by 26 (2 self)
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Advances in high-throughput next-generation sequencing technology have reshaped the transcriptomic research landscape. However, explo-ration of these massive data remains a daunting challenge. In this study, we describe a novel database, deepBase, which we have developed to facilitate
Probability landscapes for integrative genomics
, 2008
"... Background: The comprehension of the gene regulatory code in eukaryotes is one of the major challenges of systems biology, and is a requirement for the development of novel therapeutic strategies for multifactorial diseases. Its bi-fold degeneration precludes brute force and statistical approaches b ..."
Abstract
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and increasing numbers of genome sequences and empirical sequence annotations are under continual discovery-driven change. Furthermore, given the complexity of the question, a decade(s) long multi-laboratory effort needs to be envisioned. These constraints need to be considered in the creation of a framework
Identification of protein–protein interaction sites from docking energy landscapes
- J. Mol. Biol
, 2004
"... Protein recognition is one of the most challenging and intriguing pro-blems in structural biology. Despite all the available structural, sequence and biophysical information about protein–protein complexes, the phy-sico-chemical patterns, if any, that make a protein surface likely to be involved in ..."
Abstract
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Cited by 25 (1 self)
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in protein–protein interactions, remain elusive. Here, we apply protein docking simulations and analysis of the interaction energy land-scapes to identify protein–protein interaction sites. The new protocol for global docking based on multi-start global energy optimization of an all-atom model of the ligand
COMPUTATIONAL ANALYSIS OF THE MAMMALIAN CIS-REGULATORY LANDSCAPE
"... Improvements in DNA sequencing technologies have made it possible to determine the genetic makeup of many organisms. Computational analyses of the massive amounts of sequence data available have produced many insights into evolutionary and developmental biology. For example, comparison of the full g ..."
Abstract
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be produced. This dissertation describes three major contributions to the computational analysis of regulatory elements. First, I describe the Genomic Regions Enrichment of Annotations Tool (GREAT), a novel statistical method and associated web-based tool developed to infer the biological functions
Functional genome annotation through phylogenomic mapping.
- Nat Biotechnol
, 2005
"... Accurate determination of functional interactions among proteins at the genome level remains a challenge for genomic research. Here we introduce a genome-scale approach to functional protein annotation-phylogenomic mapping-that requires only sequence data, can be applied equally well to both finish ..."
Abstract
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Cited by 9 (3 self)
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Accurate determination of functional interactions among proteins at the genome level remains a challenge for genomic research. Here we introduce a genome-scale approach to functional protein annotation-phylogenomic mapping-that requires only sequence data, can be applied equally well to both
investigAtion Variants of CARD14 gene and psoriasis vulgaris in southern Chinese cohort
"... Abstract: Background: Recent mutation analysis identified several missense mutations in CARD14 in psoriasis. oBJectIves: We performed the genomic sequence analysis on CARD14 in southern Chinese Han Cantonese with Psoriasis Vulgaris (PsV) to reveal more causative missense mutations. Methods: A total ..."
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Abstract: Background: Recent mutation analysis identified several missense mutations in CARD14 in psoriasis. oBJectIves: We performed the genomic sequence analysis on CARD14 in southern Chinese Han Cantonese with Psoriasis Vulgaris (PsV) to reveal more causative missense mutations. Methods: A
The fast changing landscape of sequencing technologies and their impact on microbial genome assemblies and annotation. PLoS One. 2012;7:e48837. Lau et al
- Standards in Genomic Sciences (2015) 10:51 Page 8 of 817. Vaas LAI, Marheine M, Sikorski J, Göker M, Schumacher M. Impacts
"... Background: The emergence of next generation sequencing (NGS) has provided the means for rapid and high throughput sequencing and data generation at low cost, while concomitantly creating a new set of challenges. The number of available assembled microbial genomes continues to grow rapidly and their ..."
Abstract
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Cited by 4 (0 self)
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and their quality reflects the quality of the sequencing technology used, but also of the analysis software employed for assembly and annotation. Methodology/Principal Findings: In this work, we have explored the quality of the microbial draft genomes across various sequencing technologies. We have compared
The Genomic Landscape of TP53 and p53 Annotated High Grade Ovarian Serous Carcinomas from a Defined Founder Population Associated with Patient Outcome
"... Abstract High-grade ovarian serous carcinomas (HGSC) are characterized by TP53 mutations and non-random patterns of chromosomal anomalies, where the nature of the TP53 mutation may correlate with clinical outcome. However, the frequency of common somatic genomic events occurring in HGSCs from demog ..."
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comparative analysis of genomic landscapes revealed a significant enrichment of gains involving 1q, 8q, and 12p intervals in the subgroup expressing mutant p53 protein as compared with the p53 protein null subgroup. Although the findings show that the frequency of TP53 mutations and the genomic landscapes
Open Access The transcriptional landscape of Chlamydia pneumoniae
"... Background: Gene function analysis of the obligate intracellular bacterium Chlamydia pneumoniae is hampered by the facts that this organism is inaccessible to genetic manipulations and not cultivable outside the host. The genomes of several strains have been sequenced; however, very little informati ..."
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transcriptional start sites of annotated genes and novel transcripts were mapped. Analysis of adjacent genes for cotranscription revealed 246 polycistronic transcripts. In total, a distinct transcription start site or an affiliation to an operon could be assigned to 862 out of 1,074 annotated protein coding genes
Defining the transcriptomic landscape of Candida glabrata by RNA-Seq
, 2014
"... Candida glabrata is the second most common pathogenic Candida species and has emerged as a leading cause of nosocomial fungal infections. Its reduced susceptibility to antifungal drugs and its close relationship to Saccharomyces cerevisiae make it an interesting research focus. Although its genome s ..."
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sequence was published in 2004, little is known about its transcriptional dynamics. Here, we provide a detailed RNA-Seq-based analysis of the transcriptomic landscape of C. glabrata in nutrient-rich media, as well as under nitrosative stress and during pH shift. Using RNA-Seq data together with state
Results 1 - 10
of
65
