Browsing by Author "Bing Zhang"
Now showing items 1-13 of 13
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Harrell, Morgan Rachel (2014-07-22)Department: Biomedical InformaticsGene fusions are instances where two discrete genes incorrectly join together. They are common mutations in cancer, and, since the advent of next generation sequencing technology, many gene fusions in cancer tissues have ...
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Ma, Zeqiang (2012-03-28)Department: Biomedical InformaticsTandem mass spectrometry-based shotgun proteomics has become a widespread technology for analyzing complex protein mixtures. Assessing the full information content of shotgun proteomics experiments has motivated a series ...
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Wang, Dong (2012-11-05)Department: Biomedical InformaticsIn shotgun proteomics, database search algorithms rely on fragmentation models to predict fragment ions that should be observed for a given peptide sequence. The most widely used strategy (Naïve model) is oversimplified, ...
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Federspiel, Joel Davis (2016-04-06)Department: BiochemistryApoptosis signal-regulating kinase 1 (ASK1) is a critical sensor of cellular stress that is capable of integrating several chemically distinct signals into a single response pathway and is believed to play a role in several ...
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Straub, Peter Steven (2010-12-06)Department: Biomedical InformaticsShotgun liquid chromatography/tandem mass spectrometry (LC-MS/MS) technology provides data sets rich in the type of information required proteomic quantitation; however, these data are not fully exploited by existing tools. ...
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Greer, Michael J. (2017-11-21)Department: Biomedical InformaticsThe reduced cost of sequencing has made it feasible to acquire multi-tissue site expression data from the same patient. In the field of cancer research, this has caused an accumulation of cancer type specific tumor with ...
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Jourquin, Jerome (2010-04-12)Department: Biomedical InformaticsAnswering questions such as “Which genes are related to breast cancer?” usually requires retrieving relevant publications through the PubMed search engine, reading these publications, and manually creating gene lists. This ...
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Kochen, Michael Allen (2015-07-06)Department: Biomedical InformaticsLipid identification from data sets produced with high-throughput technologies is essential to discovery in lipidomics experiments. A number of software tools for making lipid identifications from tandem spectra have been ...
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Ma, Zeqiang (2009-07-15)Department: Biomedical InformaticsTandem mass spectrometry-based shotgun proteomics has become a widespread technology for analyzing complex protein mixtures. A number of database searching algorithms have been developed to assign peptide sequences to ...
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Chambers, Matthew Chase (2016-08-05)Department: Biomedical InformaticsProteomics allows us to see post-translational modifications and expression patterns that we cannot see with genomics and transcriptomics alone. By itself, proteomics has limited sensitivity to detect genetic variation ...
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Castellanos, Jason Alfred (2016-06-15)Department: Biomedical InformaticsColorectal Cancer (CRC) remains a leading cause of cancer-related mortality in the United States. A key therapeutic dilemma in the treatment of CRC is whether patients with stage II and stage III disease require adjuvant ...
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Chen, Yao-Yi (2012-05-15)Department: Biomedical InformaticsSpectral counting has become a widely used approach for comparing protein abundance in label-free shotgun proteomics. However, when analyzing complex samples, the ambiguity of matching between peptides and proteins greatly ...
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Savage, Sara Renee (2018-07-26)Department: Biomedical InformaticsAltered kinase signaling is one of the hallmarks of cancer that has previously been studied at the genomic and transcriptomic level. However, phosphoproteomic data are an increasingly popular way to study global cell ...