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- False discovery rate (1)
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Articles 1 - 5 of 5
Full-Text Articles in Life Sciences
State-Of-The-Art Approaches For Sequencing, Assembling And Annotating Naphthenic Acid Degrading Bacterial Metagenomes, Henry H. Say
State-Of-The-Art Approaches For Sequencing, Assembling And Annotating Naphthenic Acid Degrading Bacterial Metagenomes, Henry H. Say
Electronic Thesis and Dissertation Repository
Naphthenic acids (NAs) are the main toxic component of oil refinery wastewater and require special processes to be removed. Harnessing bacterial biodegradation for NA removal has the potential to be effective, yet NA-degrading bacteria and pathways are poorly understood and uncharacterized. To improve our understanding of NA degradation, I characterize the metagenomes of novel NA-degrading bacterial communities seeded in NA-enriched granulated activated carbon (GAC) filters. I demonstrate methods that maximize the throughput of extraction, sequencing, and annotation of novel metagenomes - producing 72 MAGs and other 5432 circular contigs - 226 of which were putative phages. I also include state-of-the-art …
Evolution Of Overlapping Reading Frames In Virus Genomes, Laura Muñoz Baena
Evolution Of Overlapping Reading Frames In Virus Genomes, Laura Muñoz Baena
Electronic Thesis and Dissertation Repository
Viruses are formidable pathogens that represent the majority of biological entities in our planet, and their genomes are a source of interesting enigmas. One feature in which virus genomes are usually rich, is the presence of overlapping reading frames (OvRFs) — portions of the genome where the same nucleotide sequence encodes more than one protein. OvRFs are hypothesized to be used by viruses to encode proteins more compactly and to regulate transcription. In addition, OvRFs might be a source of gene novelty, facilitating the creation of new open reading frames (ORF) within the transcriptional context of existing ones.
To characterize …
Decoy-Target Database Strategy And False Discovery Rate Analysis For Glycan Identification, Xiaoou Li
Decoy-Target Database Strategy And False Discovery Rate Analysis For Glycan Identification, Xiaoou Li
Electronic Thesis and Dissertation Repository
In recent years, the technology of glycopeptide sequencing through MS/MS mass spectrometry data has achieved remarkable progress. Various software tools have been developed and widely used for protein identification. Estimation of false discovery rate (FDR) has become an essential method for evaluating the performance of glycopeptide scoring algorithms. The target-decoy strategy, which involves constructing decoy databases, is currently the most popular utilized method for FDR calculation. In this study, we applied various decoy construction algorithms to generate decoy glycan databases and proposed a novel approach to calculate the FDR by using the EM algorithm and mixture model.
Exploration Of The Immune Landscape Of Ebv-Associated Gastric Cancers, Mikhail Salnikov
Exploration Of The Immune Landscape Of Ebv-Associated Gastric Cancers, Mikhail Salnikov
Electronic Thesis and Dissertation Repository
Epstein–Barr virus (EBV) is a gammaherpesvirus associated with 9% of all gastric cancers (GCs). EBV-associated GCs (EBVaGCs) are pathologically and clinically distinct entities from EBV-negative GCs (EBVnGCs), with EBVaGCs exhibiting differential molecular pathology and patient prognosis. The purpose of this thesis is to investigate the tumor microenvironment (TME) of EBVaGCs, which has not been explored in-depth. We hypothesize that EBVaGCs and EBVnGCs are also distinct in terms of the molecular immune landscape. We employed over 400 stomach adenocarcinoma (STAD) samples from The Cancer Genome Atlas (TCGA), as well as a single cell dataset, for the construction of a web suite …
De Novo Sequencing Of Multiple Tandem Mass Spectra Of Peptide Containing Silac Labeling, Fang Han
De Novo Sequencing Of Multiple Tandem Mass Spectra Of Peptide Containing Silac Labeling, Fang Han
Electronic Thesis and Dissertation Repository
The systematic studies of proteins has gradually become fundamental in the research related to molecular biology. Shotgun proteomics use bottom-up proteomics techniques in identifying proteins contained in complex mixtures using a combination of high performance liquid chromatography coupled with mass spectrometry technology. Current mass spectrometers equipped with high sensitivity and accuracy can produce thousands of tandem mass spectrometry (MS/MS) spectra in a single run. The large amount of data collected in a single LC-MS/MS run requires effective computational approaches to automate the process of spectra interpretation. De novo peptide sequencing from tandem mass spectrometry (MS/MS) has emerged as an important …