Advanced search    

Search: authors:"Dong Zhang"

25 papers found.
Use AND, OR, NOT, +word, -word, "long phrase", (parentheses) to fine-tune your search.

Expression of minichromosome maintenance genes in renal cell carcinoma

Expression of minichromosome maintenance genes in renal cell carcinoma Hongbin Zhong,1,* Bin Chen,1,* Henrique Neves,2 Jinchun Xing,1 Youxin Ye,1 Ying Lin,1 Guohong Zhuang,3 Shu-Dong Zhang,4 Jiyi

A gene-signature progression approach to identifying candidate small-molecule cancer therapeutics with connectivity mapping

, UK 1 Centre for Cancer Research and Cell Biology (CCRCB), Queen's University Belfast , Belfast , UK 2 Peter W. Hamilton and Shu-Dong Zhang are joint senior authors 3 Scientific Computing Department

The prognostic significance of DAPK1 in bladder cancer

Bladder cancer is one of the leading causes of cancer-related death in men, however, there was only limited effective treatment for invasive bladder cancer. DAPK1 has been shown to play important role in apoptosis and autophagy to suppress cancer progression. Previous results have shown that DAPK1 promoter was hypermethylated in the majority of bladder cancer specimens, however...

Computational cancer biology: education is a natural key to many locks

Background Oncology is a field that profits tremendously from the genomic data generated by high-throughput technologies, including next-generation sequencing. However, in order to exploit, integrate, visualize and interpret such high-dimensional data efficiently, non-trivial computational and statistical analysis methods are required that need to be developed in a problem...

QUADrATiC: scalable gene expression connectivity mapping for repurposing FDA-approved therapeutics

contributor. Ken I. Mills and Shu-Dong Zhang are joint senior authors Background: Gene expression connectivity mapping has proven to be a powerful and flexible tool for research. Its application has been shown

The significance of combining VEGFA, FLT1, and KDR expressions in colon cancer patient prognosis and predicting response to bevacizumab

The significance of combining VEGFA, FLT1, and KDR expressions in colon cancer patient prognosis and predicting response to bevacizumab Shu-Dong Zhang,1,2,* Cian M McCrudden,3,* Chen Meng,4 Yao Lin,4 ... ; angiogenesis; survival - open access to scientific and medical research O r i g i n a l r e s e a r c h shu-Dong Zhang 1,2,* cian M Mccrudden 3,* chen Meng 4 Yao lin 4 hang Fai Kwok 1,3 *These authors

Dry computational approaches for wet medical problems

This is a report on the 4th international conference in ‘Quantitative Biology and Bioinformatics in Modern Medicine’ held in Belfast (UK), 19–20 September 2013. The aim of the conference was to bring together leading experts from a variety of different areas that are key for Systems Medicine to exchange novel findings and promote interdisciplinary ideas and collaborations.

Analysis of Gene Expression in 3D Spheroids Highlights a Survival Role for ASS1 in Mesothelioma

To investigate the underlying causes of chemoresistance in malignant pleural mesothelioma, we have studied mesothelioma cell lines as 3D spheroids, which acquire increased chemoresistance compared to 2D monolayers. We asked whether the gene expression of 3D spheroids would reveal mechanisms of resistance. To address this, we measured gene expression of three mesothelioma cell...

Connectivity mapping using a combined gene signature from multiple colorectal cancer datasets identified candidate drugs including existing chemotherapies

Background While the discovery of new drugs is a complex, lengthy and costly process, identifying new uses for existing drugs is a cost-effective approach to therapeutic discovery. Connectivity mapping integrates gene expression profiling with advanced algorithms to connect genes, diseases and small molecule compounds and has been applied in a large number of studies to identify...

Towards Accurate Estimation of the Proportion of True Null Hypotheses in Multiple Testing

Background Biomedical researchers are now often faced with situations where it is necessary to test a large number of hypotheses simultaneously, eg, in comparative gene expression studies using high-throughput microarray technology. To properly control false positive errors the FDR (false discovery rate) approach has become widely used in multiple testing. The accurate estimation...

Identification of Candidate Small-Molecule Therapeutics to Cancer by Gene-Signature Perturbation in Connectivity Mapping

Connectivity mapping is a recently developed technique for discovering the underlying connections between different biological states based on gene-expression similarities. The sscMap method has been shown to provide enhanced sensitivity in mapping meaningful connections leading to testable biological hypotheses and in identifying drug candidates with particular pharmacological...

cudaMap: a GPU accelerated program for gene expression connectivity mapping

Darragh G McArt 0 Peter Bankhead 0 Philip D Dunne Manuel Salto-Tellez Peter Hamilton Shu-Dong Zhang 0 Equal contributors Centre for Cancer Research and Cell Biology (CCRCB), Queen's University

Néstor-Guillermo Progeria Syndrome: a biochemical insight into Barrier-to-Autointegration Factor 1, alanine 12 threonine mutation

Background Premature aging syndromes recapitulate many aspects of natural aging and provide an insight into this phenomenon at a molecular and cellular level. The progeria syndromes appear to cause rapid aging through disruption of normal nuclear structure. Recently, a coding mutation (c.34G > A [p.A12T]) in the Barrier to Autointegration Factor 1 (BANF1) gene was identified as...

Connectivity Mapping for Candidate Therapeutics Identification Using Next Generation Sequencing RNA-Seq Data

Peter W. Hamilton 0 Shu-Dong Zhang 0 Knut Stieger, Justus-Liebig-University Giessen, Germany 0 Centre for Cancer Research and Cell Biology(CCRCB), Queen's University Belfast , Belfast , United Kingdom

A simple and robust method for connecting small-molecule drugs using gene-expression signatures

Background Interaction of a drug or chemical with a biological system can result in a gene-expression profile or signature characteristic of the event. Using a suitably robust algorithm these signatures can potentially be used to connect molecules with similar pharmacological or toxicological properties by gene expression profile. Lamb et al first proposed the Connectivity Map...

Simultaneously Hermaphroditic Shrimp Use Lipophilic Cuticular Hydrocarbons as Contact Sex Pheromones

Successful mating is essentially a consequence of making the right choices at the correct time. Animals use specific strategies to gain information about a potential mate, which is then applied to decision-making processes. Amongst the many informative signals, odor cues such as sex pheromones play important ecological roles in coordinating mating behavior, enabling mate and kin...

TAZ Expression as a Prognostic Indicator in Colorectal Cancer

The Hippo pathway restricts the activity of transcriptional coactivators TAZ (WWTR1) and YAP. TAZ and YAP are reported to be overexpressed in various cancers, however, their prognostic significance in colorectal cancers remains unstudied. The expression levels of TAZ and YAP, and their downstream transcriptional targets, AXL and CTGF, were extracted from two independent colon...

Gene Expression Meta-Analysis Identifies VDAC1 as a Predictor of Poor Outcome in Early Stage Non-Small Cell Lung Cancer

Background The bioenergetic status of non-small cell lung cancer correlates with tumour aggressiveness. The voltage dependent anion channel type 1 (VDAC1) is a component of the mitochondrial permeability transition pore, regulates mitochondrial ATP/ADP exchange suggesting that its over-expression could be associated with energy dependent processes including increased...

Effect of pooling samples on the efficiency of comparative studies using microarrays

Shu-Dong Zhang 0 Timothy W. Gant 0 0 MRC Toxicology Unit , Hodgkin Building, Lancaster Road , University of Leicester , Leicester , UK Motivation: Many biomedical experiments are carried out by