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- Gelio Alves, Aleksey Y. Ogurtsov, Yi-Kuo Yu
- PloS one
- 2010

Statistically meaningful comparison/combination of peptide identification results from various search methods is impeded by the lack of a universal statistical standard. Providing an E-value calibration protocol, we demonstrated earlier the feasibility of translating either the score or heuristic E-value reported by any method into the textbook-defined… (More)

- Gelio Alves, Wells W. Wu, Guanghui Wang, Rong-Fong Shen, Yi-Kuo Yu
- Journal of proteome research
- 2008

Confident peptide identification is one of the most important components in mass-spectrometry-based proteomics. We propose a method to properly combine the results from different database search methods to enhance the accuracy of peptide identifications. The database search methods included in our analysis are SEQUEST (v27 rev12), ProbID (v1.0), InsPecT… (More)

- Gelio Alves, Yi-Kuo Yu
- Bioinformatics
- 2005

MOTIVATION
The key to MS -based proteomics is peptide sequencing. The major challenge in peptide sequencing, whether library search or de novo, is to better infer statistical significance and better attain noise reduction. Since the noise in a spectrum depends on experimental conditions, the instrument used and many other factors, it cannot be predicted… (More)

- Gelio Alves, Aleksey Y. Ogurtsov, Yi-Kuo Yu
- Biology Direct
- 2007

The key to mass-spectrometry-based proteomics is peptide identification. A major challenge in peptide identification is to obtain realistic E-values when assigning statistical significance to candidate peptides. Using a simple scoring scheme, we propose a database search method with theoretically characterized statistics. Taking into account possible… (More)

- Gelio Alves, Aleksey Y. Ogurtsov, Wells W. Wu, Guanghui Wang, Rong-Fong Shen, Yi-Kuo Yu
- Biology Direct
- 2007

The key to mass-spectrometry-based proteomics is peptide identification, which relies on software analysis of tandem mass spectra. Although each search engine has its strength, combining the strengths of various search engines is not yet realizable largely due to the lack of a unified statistical framework that is applicable to any method. We have developed… (More)

- Gelio Alves, Yi-Kuo Yu
- PloS one
- 2011

Given the expanding availability of scientific data and tools to analyze them, combining different assessments of the same piece of information has become increasingly important for social, biological, and even physical sciences. This task demands, to begin with, a method-independent standard, such as the P-value, that can be used to assess the reliability… (More)

- Gelio Alves, Yi-Kuo Yu
- Bioinformatics
- 2015

MOTIVATION
Assigning statistical significance accurately has become increasingly important as metadata of many types, often assembled in hierarchies, are constructed and combined for further biological analyses. Statistical inaccuracy of metadata at any level may propagate to downstream analyses, undermining the validity of scientific conclusions thus… (More)

- Gelio Alves, Yi-Kuo Yu
- Physica A
- 2008

We provide a complete thermodynamic solution of a 1D hopping model in the presence of a random potential by obtaining the density of states. Since the partition function is related to the density of states by a Laplace transform, the density of states determines completely the thermodynamic behavior of the system. We have also shown that the transfer matrix… (More)

- Gelio Alves, Yi-Kuo Yu
- PloS one
- 2014

Meta-analysis methods that combine P-values into a single unified P-value are frequently employed to improve confidence in hypothesis testing. An assumption made by most meta-analysis methods is that the P-values to be combined are independent, which may not always be true. To investigate the accuracy of the unified P-value from combining correlated… (More)

- Gelio Alves, Aleksey Y. Ogurtsov, Yi-Kuo Yu
- BMC Genomics
- 2008

Existing scientific literature is a rich source of biological information such as disease markers. Integration of this information with data analysis may help researchers to identify possible controversies and to form useful hypotheses for further validations. In the context of proteomics studies, individualized proteomics era may be approached through… (More)