| Year |
Citation |
Score |
| 2024 |
Ogurtsov A, Alves G, Rubio A, Joyce B, Andersson B, Karlsson R, Moore ERB, Yu YK. MiCId GUI: The Graphical User Interface for MiCId, a Fast Microorganism Classification and Identification Workflow with Accurate Statistics and High Recall. Journal of Computational Biology : a Journal of Computational Molecular Cell Biology. PMID 38301204 DOI: 10.1089/cmb.2023.0149 |
0.603 |
|
| 2022 |
Alves G, Ogurtsov A, Karlsson R, Jaén-Luchoro D, Piñeiro-Iglesias B, Salvà-Serra F, Andersson B, Moore ERB, Yu YK. Identification of Antibiotic Resistance Proteins via MiCId's Augmented Workflow. A Mass Spectrometry-Based Proteomics Approach. Journal of the American Society For Mass Spectrometry. PMID 35500907 DOI: 10.1021/jasms.1c00347 |
0.563 |
|
| 2021 |
Kondori N, Kurtovic A, Piñeiro-Iglesias B, Salvà-Serra F, Jaén-Luchoro D, Andersson B, Alves G, Ogurtsov A, Thorsell A, Fuchs J, Tunovic T, Kamenska N, Karlsson A, Yu YK, Moore ERB, et al. Mass Spectrometry Proteotyping-Based Detection and Identification of , , and in Blood. Frontiers in Cellular and Infection Microbiology. 11: 634215. PMID 34381737 DOI: 10.3389/fcimb.2021.634215 |
0.554 |
|
| 2021 |
Sénécaut N, Alves G, Weisser H, Lignières L, Terrier S, Yang-Crosson L, Poulain P, Lelandais G, Yu YK, Camadro JM. Novel Insights into Quantitative Proteomics from an Innovative Bottom-Up Simple Light Isotope Metabolic (bSLIM) Labeling Data Processing Strategy. Journal of Proteome Research. PMID 33573382 DOI: 10.1021/acs.jproteome.0c00478 |
0.583 |
|
| 2020 |
Alves G, Yu YK. Robust Accurate Identification and Biomass Estimates of Miroorganisms via Tandem Mass Spectrometry. Journal of the American Society For Mass Spectrometry. 31: 85-102. PMID 32881514 DOI: 10.1021/Jasms.9B00035 |
0.629 |
|
| 2019 |
Ogurtsov AY, Alves G, Yu YK. RAId: Knowledge Integrated Proteomics Web Service with Accurate Statistical Significance Assignment. Proteomics. e1800367. PMID 30908818 DOI: 10.1002/Pmic.201800367 |
0.653 |
|
| 2019 |
Alves G, Yu Y. Robust Accurate Identification and Biomass Estimates of Miroorganisms via Tandem Mass Spectrometry Journal of the American Society For Mass Spectrometry. 31: 85-102. DOI: 10.1021/jasms.9b00035 |
0.547 |
|
| 2018 |
Alves G, Wang G, Ogurtsov AY, Drake SK, Gucek M, Sacks DB, Yu YK. Rapid Classification and Identification of Multiple Microorganisms with Accurate Statistical Significance via High-Resolution Tandem Mass Spectrometry. Journal of the American Society For Mass Spectrometry. PMID 29873019 DOI: 10.1007/S13361-018-1986-Y |
0.639 |
|
| 2018 |
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 Research Notes. 11: 182. PMID 29544540 DOI: 10.1186/S13104-018-3289-6 |
0.642 |
|
| 2016 |
Alves G, Yu YK. Confidence assignment for mass spectrometry based peptide identifications via the extreme value distribution. Bioinformatics (Oxford, England). PMID 27153659 DOI: 10.1093/Bioinformatics/Btw225 |
0.668 |
|
| 2015 |
Alves G, Wang G, Ogurtsov AY, Drake SK, Gucek M, Suffredini AF, Sacks DB, Yu YK. Identification of Microorganisms by High Resolution Tandem Mass Spectrometry with Accurate Statistical Significance. Journal of the American Society For Mass Spectrometry. PMID 26510657 DOI: 10.1007/S13361-015-1271-2 |
0.644 |
|
| 2015 |
Alves G, Yu YK. Mass spectrometry-based protein identification with accurate statistical significance assignment. Bioinformatics (Oxford, England). 31: 699-706. PMID 25362092 DOI: 10.1093/Bioinformatics/Btu717 |
0.659 |
|
| 2014 |
Alves G, Yu YK. Accuracy evaluation of the unified P-value from combining correlated P-values. Plos One. 9: e91225. PMID 24663491 DOI: 10.1371/Journal.Pone.0091225 |
0.588 |
|
| 2014 |
Alves G, Ogurtsov AY, Yu YK. Molecular Isotopic Distribution Analysis (MIDAs) with adjustable mass accuracy. Journal of the American Society For Mass Spectrometry. 25: 57-70. PMID 24254576 DOI: 10.1007/S13361-013-0733-7 |
0.571 |
|
| 2014 |
Alves G, Yu YK. Correction: Accuracy evaluation of the unified P-value from combining correlated P-values (PLoS ONE (2014) 9, 7 (e103662) DOI: 10.1371/journal.pone. 0103662) Plos One. 9. DOI: 10.1371/journal.pone.0103662 |
0.518 |
|
| 2013 |
Alves G, Yu YK. Improving peptide identification sensitivity in shotgun proteomics by stratification of search space. Journal of Proteome Research. 12: 2571-81. PMID 23668635 DOI: 10.1021/Pr301139Y |
0.639 |
|
| 2013 |
Obolensky OI, Wu WW, Shen RF, Yu YK. Using dissociation energies to predict observability of b- and y-peaks in mass spectra of short peptides. II. Results for hexapeptides with non-polar side chains. Rapid Communications in Mass Spectrometry : Rcm. 27: 152-6. PMID 23239328 DOI: 10.1002/Rcm.6451 |
0.349 |
|
| 2012 |
Obolensky OI, Wu WW, Shen RF, Yu YK. Using dissociation energies to predict observability of b- and y-peaks in mass spectra of short peptides. Rapid Communications in Mass Spectrometry : Rcm. 26: 915-20. PMID 22396027 DOI: 10.1002/Rcm.6180 |
0.367 |
|
| 2012 |
Stojmirovic A, Bliskovsky A, Yu YK. CytoSaddleSum: a functional enrichment analysis plugin for Cytoscape based on sum-of-weights scores. Bioinformatics (Oxford, England). 28: 893-4. PMID 22345616 DOI: 10.1093/Bioinformatics/Bts041 |
0.316 |
|
| 2011 |
Alves G, Yu YK. Combining independent, weighted P-values: achieving computational stability by a systematic expansion with controllable accuracy. Plos One. 6: e22647. PMID 21912585 DOI: 10.1371/Journal.Pone.0022647 |
0.591 |
|
| 2011 |
Stojmirović A, Yu YK. ppiTrim: constructing non-redundant and up-to-date interactomes. Database : the Journal of Biological Databases and Curation. 2011: bar036. PMID 21873645 DOI: 10.1093/Database/Bar036 |
0.309 |
|
| 2011 |
Ye X, Yu YK, Altschul SF. On the inference of dirichlet mixture priors for protein sequence comparison. Journal of Computational Biology : a Journal of Computational Molecular Cell Biology. 18: 941-54. PMID 21702690 DOI: 10.1089/Cmb.2011.0040 |
0.354 |
|
| 2011 |
Alves G, Ogurtsov AY, Yu YK. Assigning statistical significance to proteotypic peptides via database searches. Journal of Proteomics. 74: 199-211. PMID 21055489 DOI: 10.1016/J.Jprot.2010.10.005 |
0.665 |
|
| 2010 |
Ye X, Yu YK, Altschul SF. Compositional adjustment of Dirichlet mixture priors. Journal of Computational Biology : a Journal of Computational Molecular Cell Biology. 17: 1607-20. PMID 21128852 DOI: 10.1089/Cmb.2010.0117 |
0.336 |
|
| 2010 |
Alves G, Ogurtsov AY, Yu YK. RAId_aPS: MS/MS analysis with multiple scoring functions and spectrum-specific statistics. Plos One. 5: e15438. PMID 21103371 DOI: 10.1371/Journal.Pone.0015438 |
0.66 |
|
| 2010 |
Stojmirović A, Yu YK. Robust and accurate data enrichment statistics via distribution function of sum of weights. Bioinformatics (Oxford, England). 26: 2752-9. PMID 20826881 DOI: 10.1093/Bioinformatics/Btq511 |
0.359 |
|
| 2010 |
Altschul SF, Wootton JC, Zaslavsky E, Yu YK. The construction and use of log-odds substitution scores for multiple sequence alignment. Plos Computational Biology. 6: e1000852. PMID 20657661 DOI: 10.1371/Journal.Pcbi.1000852 |
0.347 |
|
| 2009 |
Stojmirović A, Yu YK. Geometric aspects of biological sequence comparison. Journal of Computational Biology : a Journal of Computational Molecular Cell Biology. 16: 579-610. PMID 19361329 DOI: 10.1089/Cmb.2008.0100 |
0.319 |
|
| 2009 |
Altschul SF, Gertz EM, Agarwala R, Schäffer AA, Yu YK. PSI-BLAST pseudocounts and the minimum description length principle. Nucleic Acids Research. 37: 815-24. PMID 19088134 DOI: 10.1093/Nar/Gkn981 |
0.367 |
|
| 2008 |
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: 6538-6544. PMID 19918268 DOI: 10.1016/J.Physa.2008.08.024 |
0.624 |
|
| 2008 |
Alves G, Ogurtsov AY, Yu YK. RAId_DbS: mass-spectrometry based peptide identification web server with knowledge integration. Bmc Genomics. 9: 505. PMID 18954448 DOI: 10.1186/1471-2164-9-505 |
0.63 |
|
| 2008 |
Alves G, Ogurtsov AY, Kwok S, Wu WW, Wang G, Shen RF, Yu YK. Detection of co-eluted peptides using database search methods. Biology Direct. 3: 27. PMID 18597684 DOI: 10.1186/1745-6150-3-27 |
0.652 |
|
| 2008 |
Alves G, Wu WW, Wang G, Shen RF, Yu YK. Enhancing peptide identification confidence by combining search methods. Journal of Proteome Research. 7: 3102-13. PMID 18558733 DOI: 10.1021/Pr700798H |
0.656 |
|
| 2007 |
Alves G, Ogurtsov AY, Wu WW, Wang G, Shen RF, Yu YK. Calibrating E-values for MS2 database search methods. Biology Direct. 2: 26. PMID 17983478 DOI: 10.1186/1745-6150-2-26 |
0.662 |
|
| 2007 |
Alves G, Ogurtsov AY, Yu YK. RAId_DbS: peptide identification using database searches with realistic statistics. Biology Direct. 2: 25. PMID 17961253 DOI: 10.1186/1745-6150-2-25 |
0.661 |
|
| 2007 |
Sardiu ME, Cheung MS, Yu YK. Cysteine-cysteine contact preference leads to target-focusing in protein folding. Biophysical Journal. 93: 938-51. PMID 17617551 DOI: 10.1529/Biophysj.106.097824 |
0.621 |
|
| 2007 |
Yu Y. A metric measure for weight matrices of variable lengths—with applications to clustering and classification of hidden Markov models Physica a: Statistical Mechanics and Its Applications. 375: 212-220. DOI: 10.1016/J.Physa.2006.08.061 |
0.3 |
|
| 2006 |
Gertz EM, Yu YK, Agarwala R, Schäffer AA, Altschul SF. Composition-based statistics and translated nucleotide searches: improving the TBLASTN module of BLAST. Bmc Biology. 4: 41. PMID 17156431 DOI: 10.1186/1741-7007-4-41 |
0.351 |
|
| 2006 |
Yu YK, Gertz EM, Agarwala R, Schäffer AA, Altschul SF. Retrieval accuracy, statistical significance and compositional similarity in protein sequence database searches. Nucleic Acids Research. 34: 5966-73. PMID 17068079 DOI: 10.1093/Nar/Gkl731 |
0.354 |
|
| 2005 |
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. Physical Review. E, Statistical, Nonlinear, and Soft Matter Physics. 72: 061917. PMID 16485984 DOI: 10.1103/Physreve.72.061917 |
0.724 |
|
| 2005 |
Altschul SF, Wootton JC, Gertz EM, Agarwala R, Morgulis A, Schäffer AA, Yu YK. Protein database searches using compositionally adjusted substitution matrices. The Febs Journal. 272: 5101-9. PMID 16218944 DOI: 10.1111/J.1742-4658.2005.04945.X |
0.358 |
|
| 2005 |
Alves G, Yu YK. Robust accurate identification of peptides (RAId): deciphering MS2 data using a structured library search with de novo based statistics. Bioinformatics (Oxford, England). 21: 3726-32. PMID 16105903 DOI: 10.1093/Bioinformatics/Bti620 |
0.657 |
|
| 2005 |
Doerr TP, Alves G, Yu YK. 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 Physica a: Statistical Mechanics and Its Applications. 354: 558-570. DOI: 10.1016/J.Physa.2005.03.004 |
0.611 |
|
| 2004 |
Yu YK. Replica model for an unusual directed polymer in 1+1 dimensions and prediction of the extremal parameter of gapped sequence alignment statistics. Physical Review. E, Statistical, Nonlinear, and Soft Matter Physics. 69: 061904. PMID 15244614 DOI: 10.1103/Physreve.69.061904 |
0.333 |
|
| 2002 |
Yu YK, Bundschuh R, Hwa T. Hybrid alignment: High-performance with universal statistics Bioinformatics. 18: 864-872. PMID 12075022 DOI: 10.1093/Bioinformatics/18.6.864 |
0.354 |
|
| 2001 |
Yu YK, Hwa T. Statistical significance of probabilistic sequence alignment and related local hidden Markov models. Journal of Computational Biology : a Journal of Computational Molecular Cell Biology. 8: 249-82. PMID 11535176 DOI: 10.1089/10665270152530845 |
0.358 |
|
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