25 Result(s)

Article

Compound NSC84167 selectively targets NRF2-activated pancreatic cancer by inhibiting asparagine synthesis pathway

Nuclear factor erythroid 2-related factor 2 (NRF2) is aberrantly activated in about 93% of pancreatic cancers. Activated NRF2 regulates multiple downstream molecules involved in cancer cell metabolic reprogram...

Bingbing Dai, Jithesh J. Augustine, Ya’an Kang, David Roife… in Cell Death & Disease (2021)

Article

ElemCor: accurate data analysis and enrichment calculation for high-resolution LC-MS stable isotope labeling experiments

The investigation of intracellular metabolism is the mainstay in the biotechnology and physiology settings. Intracellular metabolic rates are commonly evaluated using labeling pattern of the identified metabol...

Di Du, Lin Tan, Yumeng Wang, Bo Peng, John N. Weinstein… in BMC Bioinformatics (2019)

Article

Global analysis of tRNA and translation factor expression reveals a dynamic landscape of translational regulation in human cancers

The protein translational system, including transfer RNAs (tRNAs) and several categories of enzymes, plays a key role in regulating cell proliferation. Translation dysregulation also contributes to cancer deve...

Zhao Zhang, Youqiong Ye, **g Gong, Hang Ruan, Chun-Jie Liu… in Communications Biology (2018)

Article

Genes suppressed by DNA methylation in non-small cell lung cancer reveal the epigenetics of epithelial–mesenchymal transition

DNA methylation is associated with aberrant gene expression in cancer, and has been shown to correlate with therapeutic response and disease prognosis in some types of cancer. We sought to investigate the biol...

Steven H Lin, **g Wang, Pierre Saintigny, Chia-Chin Wu, Uma Giri… in BMC Genomics (2014)

Article

Targeted metabolomic analysis of amino acid response to L-asparaginase in adherent cells

L-asparaginase (L-ASP) is a therapeutic enzyme used clinically for the treatment of childhood acute lymphoblastic leukemia. L-ASP’s anticancer activity is believed to be associated primarily with depletion of ...

Preeti Purwaha, Philip L. Lorenzi, Leslie P. Silva, David H. Hawke… in Metabolomics (2014)

Article

TCPA: a resource for cancer functional proteomics data

Jun Li, Yiling Lu, Rehan Akbani, Zhenlin Ju, Paul L Roebuck, Wenbin Liu… in Nature Methods (2013)

Article

RedundancyMiner: De-replication of redundant GO categories in microarray and proteomics analysis

The Gene Ontology (GO) Consortium organizes genes into hierarchical categories based on biological process, molecular function and subcellular localization. Tools such as GoMiner can leverage GO to perform ont...

Barry R Zeeberg, Hongfang Liu, Ari B Kahn, Martin Ehler… in BMC Bioinformatics (2011)

Article

CellMiner: a relational database and query tool for the NCI-60 cancer cell lines

Advances in the high-throughput omic technologies have made it possible to profile cells in a large number of ways at the DNA, RNA, protein, chromosomal, functional, and pharmacological levels. A persistent pr...

Uma T Shankavaram, Sudhir Varma, David Kane, Margot Sunshine… in BMC Genomics (2009)

Article

SpliceCenter: A suite of web-based bioinformatic applications for evaluating the impact of alternative splicing on RT-PCR, RNAi, microarray, and peptide-based studies

Over 60% of protein-coding genes in vertebrates express mRNAs that undergo alternative splicing. The resulting collection of transcript isoforms poses significant challenges for contemporary biological assays....

Michael C Ryan, Barry R Zeeberg, Natasha J Caplen, James A Cleland… in BMC Bioinformatics (2008)

Article

VennMaster: Area-proportional Euler diagrams for functional GO analysis of microarrays

Microarray experiments generate vast amounts of data. The functional context of differentially expressed genes can be assessed by querying the Gene Ontology (GO) database via GoMiner. Directed acyclic graph re...

Hans A Kestler, André Müller, Johann M Kraus, Malte Buchholz… in BMC Bioinformatics (2008)

Article

The LeFE algorithm: embracing the complexity of gene expression in the interpretation of microarray data

Interpretation of microarray data remains a challenge, and most methods fail to consider the complex, nonlinear regulation of gene expression. To address that limitation, we introduce Learner of Functional Enr...

Gabriel S Eichler, Mark Reimers, David Kane, John N Weinstein in Genome Biology (2007)

Article

SpliceMiner: a high-throughput database implementation of the NCBI Evidence Viewer for microarray splice variant analysis

There are many fewer genes in the human genome than there are expressed transcripts. Alternative splicing is the reason. Alternatively spliced transcripts are often specific to tissue type, developmental stage...

Ari B Kahn, Michael C Ryan, Hongfang Liu, Barry R Zeeberg… in BMC Bioinformatics (2007)

Article

AbMiner: A bioinformatic resource on available monoclonal antibodies and corresponding gene identifiers for genomic, proteomic, and immunologic studies

Monoclonal antibodies are used extensively throughout the biomedical sciences for detection of antigens, either in vitro or in vivo. We, for example, have used them for quantitation of proteins on "reverse-phase"...

Sylvia M Major, Satoshi Nishizuka, Daisaku Morita, Rick Rowland… in BMC Bioinformatics (2006)

Article

High-Throughput GoMiner, an 'industrial-strength' integrative gene ontology tool for interpretation of multiple-microarray experiments, with application to studies of Common Variable Immune Deficiency (CVID)

We previously developed GoMiner, an application that organizes lists of 'interesting' genes (for example, under-and overexpressed genes from a microarray experiment) for biological interpretation in the contex...

Barry R Zeeberg, Haiying Qin, Sudarshan Narasimhan, Margot Sunshine… in BMC Bioinformatics (2005)

Article

Quality assessment of microarrays: Visualization of spatial artifacts and quantitation of regional biases

Quality-control is an important issue in the analysis of gene expression microarrays. One type of problem is regional bias, in which one region of a chip shows artifactually high or low intensities (or ratios ...

Mark Reimers, John N Weinstein in BMC Bioinformatics (2005)