Topic

Proteomics; Mass spectrometry; Proteomics experiment

Details

Publications

Joyce B, Lee D, Rubio A, Ogurtsov A, Alves G, Yu YK "A graphical user interface for RAId, a knowledge integrated proteomics analysis suite with accurate statistics." BMC Res Notes 2018; 11(1):182 https://doi.org/10.1186/s13104-018-3289-6
PMID: 29544540
PMCID: PMC5856202

Alves G, Ogurtsov AY, Yu YK "Assigning statistical significance to proteotypic peptides via database searches." J Proteomics 74(2): 199-211. https://doi.org/10.1016/j.jprot.2010.10.005
PMID: 21055489
PMCID: PMC3186061

Alves G, Yu YK "Statistical Characterization of a 1D Random Potential Problem - with applications in score statistics of MS-based peptide sequencing." Physica A 387(26): 6538-6544. https://doi.org/10.1016/j.physa.2008.08.024
PMID: 19918268
PMCID: PMC2702782

Alves G, Wu WW, Wang G, Shen RF, Yu YK "Enhancing peptide identification confidence by combining search methods." J Proteome Res 7(8): 3102-13. https://doi.org/10.1021/pr700798h
PMID: 18558733
PMCID: PMC2658881

Alves G, Yu YK "Robust accurate identification of peptides (RAId): deciphering MS2 data using a structured library search with de novo based statistics." Bioinformatics 21(19): 3726-32. https://doi.org/10.1093/bioinformatics/bti620
PMID: 16105903

Alves G, Yu YK "Mass spectrometry-based protein identification with accurate statistical significance assignment." Bioinformatics 31(5): 699-706. https://doi.org/10.1093/bioinformatics/btu717
PMID: 25362092
PMCID: PMC4341067

Alves G, Yu YK "Confidence assignment for mass spectrometry based peptide identifications via the extreme value distribution." Bioinformatics 32(17): 2642-9. https://doi.org/10.1093/bioinformatics/btw225
PMID: 27153659
PMCID: PMC5939896

Sardiu ME, Alves G, Yu YK "Score statistics of global sequence alignment from the energy distribution of a modified directed polymer and directed percolation problem." Phys Rev E Stat Nonlin Soft Matter Phys 72(6 Pt 1): 061917. https://doi.org/10.1103/PhysRevE.72.061917
PMID: 16485984

Alves G, Ogurtsov AY, Yu YK "RAId_DbS: mass-spectrometry based peptide identification web server with knowledge integration." BMC Genomics 9: 505. https://doi.org/10.1186/1471-2164-9-505
PMID: 18954448
PMCID: PMC2605478

Alves G, Ogurtsov AY, Yu YK "RAId_DbS: peptide identification using database searches with realistic statistics." Biol Direct 2: 25. https://doi.org/10.1186/1745-6150-2-25
PMID: 17961253
PMCID: PMC2211744

Alves G, Ogurtsov AY, Wu WW, Wang G, Shen RF, Yu YK "Calibrating E-values for MS2 database search methods." Biol Direct 2: 26. https://doi.org/10.1186/1745-6150-2-26
PMID: 17983478
PMCID: PMC2206012

Alves G, Ogurtsov AY, Kwok S, Wu WW, Wang G, Shen RF, Yu YK "Detection of co-eluted peptides using database search methods." Biol Direct 3: 27. https://doi.org/10.1186/1745-6150-3-27
PMID: 18597684
PMCID: PMC2483259

Alves G, Ogurtsov AY, Yu YK "RAId_aPS: MS/MS analysis with multiple scoring functions and spectrum-specific statistics." PLoS One 5(11): e15438. https://doi.org/10.1371/journal.pone.0015438
PMID: 21103371
PMCID: PMC2982831

Alves G, Yu YK "Combining independent, weighted P-values: achieving computational stability by a systematic expansion with controllable accuracy." PLoS One 6(8): e22647. https://doi.org/10.1371/journal.pone.0022647
PMID: 21912585
PMCID: PMC3166143

Alves G, Yu YK "Accuracy evaluation of the unified P-value from combining correlated P-values." PLoS One 9(3): e91225. https://doi.org/10.1371/journal.pone.0091225
PMID: 24663491
PMCID: PMC3963868

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