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1

A graphical user interface for RAId, a knowledge integrated proteomics analysis suite with accurate statistics

Joyce, Brendan, Lee, Danny, Rubio, Alex, Ogurtsov, Aleksey, Alves, Gelio, Yu, Yi-Kuo

Journal:

BMC Research Notes

Year:

2018

Language:

english

File:

PDF, 4.34 MB

english, 2018

2

Ranked solutions to a class of combinatorial optimizations—with applications in mass spectrometry based peptide sequencing and a variant of directed paths in random media

Timothy P. Doerr, Gelio Alves, Yi-Kuo Yu

Journal:

Physica A: Statistical Mechanics and its Applications

Year:

2005

Language:

english

File:

PDF, 400 KB

english, 2005

3

Assigning statistical significance to proteotypic peptides via database searches

Gelio Alves, Aleksey Y. Ogurtsov, Yi-Kuo Yu

Journal:

Journal of Proteomics

Year:

2011

Language:

english

File:

PDF, 1.08 MB

english, 2011

4

Statistical characterization of a 1D random potential problem—With applications in score statistics of MS-based peptide sequencing

Gelio Alves, Yi-Kuo Yu

Journal:

Physica A: Statistical Mechanics and its Applications

Year:

2008

Language:

english

File:

PDF, 423 KB

english, 2008

5

RAId_DbS: mass-spectrometry based peptide identification web server with knowledge integration

Gelio Alves, Aleksey Y Ogurtsov, Yi-Kuo Yu

Journal:

Year:

2008

Language:

english

File:

PDF, 581 KB

english, 2008

6

Calibrating E-values for MS2database search methods

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

Journal:

Year:

2007

Language:

english

File:

PDF, 893 KB

english, 2007

7

RAId_DbS: Peptide Identification using Database Searches with Realistic Statistics

Gelio Alves, Aleksey Y Ogurtsov, Yi-Kuo Yu

Journal:

Year:

2007

Language:

english

File:

PDF, 1.21 MB

english, 2007

8

Detection of co-eluted peptides using database search methods

Gelio Alves, Aleksey Y Ogurtsov, Siwei Kwok, Wells W Wu, Guanghui Wang, Rong-Fong Shen, Yi-Kuo Yu

Journal:

Year:

2008

Language:

english

File:

PDF, 1.13 MB

english, 2008

9

Improving Peptide Identification Sensitivity in Shotgun Proteomics by Stratification of Search Space

Alves, Gelio, Yu, Yi-Kuo

Journal:

Journal of Proteome Research

Year:

2013

Language:

english

File:

PDF, 1.10 MB

english, 2013

10

Molecular Isotopic Distribution Analysis (MIDAs) with Adjustable Mass Accuracy

Alves, Gelio, Ogurtsov, Aleksey Y., Yu, Yi-Kuo

Journal:

Journal of the American Society for Mass Spectrometry

Year:

2014

Language:

english

File:

PDF, 549 KB

english, 2014

11

Enhancing Peptide Identification Confidence by Combining Search Methods

Alves, Gelio, Wu, Wells W., Wang, Guanghui, Shen, Rong-Fong, Yu, Yi-Kuo

Journal:

Journal of Proteome Research

Year:

2008

Language:

english

File:

PDF, 2.96 MB

english, 2008

12

Score statistics of global sequence alignment from the energy distribution of a modified directed polymer and directed percolation problem

Sardiu, Mihaela, Alves, Gelio, Yu, Yi-Kuo

Journal:

Physical Review E

Year:

2005

Language:

english

File:

PDF, 1.73 MB

english, 2005

13

Identification of Microorganisms by High Resolution Tandem Mass Spectrometry with Accurate Statistical Significance

Alves, Gelio, Wang, Guanghui, Ogurtsov, Aleksey Y., Drake, Steven K., Gucek, Marjan, Suffredini, Anthony F., Sacks, David B., Yu, Yi-Kuo

Journal:

Journal of the American Society for Mass Spectrometry

Year:

2016

Language:

english

File:

PDF, 3.78 MB

english, 2016

14

Confidence assignment for mass spectrometry based peptide identifications via the extreme value distribution

Alves, Gelio, Yu, Yi-Kuo

Journal:

Year:

2016

Language:

english

File:

PDF, 253 KB

english, 2016

15

Understanding the Association of Fatigue With Other Symptoms of Fibromyalgia: Development of a Cluster Model

Lukkahatai, Nada, Walitt, Brian, Espina, Alexandra, Gelio, Alves, Saligan, Leorey N.

Journal:

Arthritis Care & Research

Year:

2016

Language:

english

File:

PDF, 305 KB

english, 2016

16

Rapid Classification and Identification of Multiple Microorganisms with Accurate Statistical Significance via High-Resolution Tandem Mass Spectrometry

Alves, Gelio, Wang, Guanghui, Ogurtsov, Aleksey Y., Drake, Steven K., Gucek, Marjan, Sacks, David B., Yu, Yi-Kuo

Journal:

Journal of the American Society for Mass Spectrometry

Year:

2018

Language:

english

File:

PDF, 1.09 MB

english, 2018

17

Combining Independent, Weighted P-Values: Achieving Computational Stability by a Systematic Expansion with Controllable Accuracy

Alves, Gelio, Yu, Yi-Kuo, Rapallo, Fabio

Journal:

Year:

2011

Language:

english

File:

PDF, 134 KB

english, 2011

18

Accuracy Evaluation of the Unified P-Value from Combining Correlated P-Values

Alves, Gelio, Yu, Yi-Kuo, Emmert-Streib, Frank

Journal:

Year:

2014

Language:

english

File:

PDF, 1.23 MB

english, 2014

19

RAId: Knowledge Integrated Proteomics Web Service with Accurate Statistical Significance Assignment

Ogurtsov, Aleksey Y., Alves, Gelio, Yu, Yi‐Kuo

Journal:

Year:

2019

Language:

english

File:

PDF, 165 KB

english, 2019