1. Alves G, Hamaneh M, Ogurtsov AY, Yu YK (2026) Taxonomic-Level Protein Quantification in Metaproteomics Using a Biomass-Constrained Expectation-Maximization Approach. J Am Soc Mass Spectrom, 37: 424-439.
DOI: 10.1021/jasms.5c00332

2. Muth T, Karlsson R, Yu YK, Alves G (2025) From Identification to Insight: Making Full Use of the Diagnostic Potential of MS/MS Proteotyping in Clinical Microbiology Using Efficient Bioinformatics. J Proteome Res, 24: 5336-5351.
PMID: 41159248
DOI: 10.1021/acs.jproteome.5c00733

3. Foerster A, Obolensky OI, Huynh BC, Doerr TP, Yu YK (2025) Interaction at pre-bonding distances and bond formation for open p-shell atoms with different orientations of their angular momenta. J Chem Phys, 163: 134308.
PMID: 41055197
DOI: 10.1063/5.0288344

4. Hamaneh MB, Yu YK (2025) FastSpel: A Method for Fast Spectral Library Generation. J Proteome Res, 24: 4952-4964.
PMID: 40864661
DOI: 10.1021/acs.jproteome.5c00279

5. Alves G, Ogurtsov AY, Yu YK (2025) Biological Function Assignment Across Taxonomic Levels in Mass-Spectrometry-Based Metaproteomics via a Modified Expectation Maximization Algorithm. J Proteome Res, 24: 3818-3832.
DOI: 10.1021/acs.jproteome.4c01125

6. Jenson SC, Chu F, Alves G, Ogurtsov AY, Barente AS, Crockett DL, Lamar NC, Merkley ED, Yu YK, Jarman KH (2025) MARLOWE: Taxonomic Characterization of Unknown Samples for Forensics Using De Novo Peptide Identification. bioRxiv: the preprint server for biology, 20240930615220: 1-35.
DOI: 10.1101/2024.09.30.615220

7. Alves G, Ogurtsov AY, Porterfield H, Maity T, Jenkins LM, Sacks D, Yu YK (2024) Multiplexing the Identification of Microorganisms via Tandem Mass Tag Labeling Augmented by Interference Removal through a Novel Modification of the Expectation Maximization Algorithm. J Am Soc Mass Spectrom, 35: 1138-1155.
DOI: 10.1021/jasms.3c00445

8. Hamaneh MB, Ogurtsov AY, Obolensky OI, Yu YK (2024) Systematic Assessment of Deep Learning-Based Predictors of Fragmentation Intensity Profiles. J Proteome Res, 23: 1983-1999.
PMID: 38728051
DOI: 10.1021/acs.jproteome.3c00857

9. Ogurtsov A, Alves G, Rubio A, Joyce B, Andersson B, Karlsson R, Moore ERB, Yu YK (2024) MiCId GUI: The Graphical User Interface for MiCId, a Fast Microorganism Classification and Identification Workflow with Accurate Statistics and High Recall. J Comput Biol, 31: 175-178.
PMID: 38301204
DOI: 10.1089/cmb.2023.0149

10. Hamaneh M, Yu YK (2023) A Simple Method for Robust and Accurate Intrinsic Subtyping of Breast Cancer. Cancer Inform, 22: 11769351231159893.
DOI: 10.1177/11769351231159893

11. Hamaneh M, Yu YK (2022) An 8-Gene Signature for Classifying Major Subtypes of Non-Small-Cell Lung Cancer. Cancer Inform, 21: 11769351221100718.
DOI: 10.1177/11769351221100718

12. Alves G, Ogurtsov A, Karlsson R, Jaén-Luchoro D, Piñeiro-Iglesias B, Salvà-Serra F, Andersson B, Moore ERB, Yu YK (2022) Identification of Antibiotic Resistance Proteins via MiCId's Augmented Workflow. A Mass Spectrometry-Based Proteomics Approach. J Am Soc Mass Spectrom, 33: 917-931.
DOI: 10.1021/jasms.1c00347

13. Obolensky OI, Doerr TP, Yu YK (2021) Rigorous treatment of pairwise and many-body electrostatic interactions among dielectric spheres at the Debye-Hückel level. Eur Phys J E, 44: 129.
DOI: 10.1140/epje/s10189-021-00131-9

14. 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, Karlsson R (2021) Mass Spectrometry Proteotyping-Based Detection and Identification of Staphylococcus aureus, Escherichia coli, and Candida albicans in Blood. Front Cell Infect Microbiol, 11: 634215.
DOI: 10.3389/fcimb.2021.634215

15. Sénécaut N, Alves G, Weisser H, Lignières L, Terrier S, Yang-Crosson L, Poulain P, Lelandais G, Yu YK, Camadro JM (2021) Novel Insights into Quantitative Proteomics from an Innovative Bottom-Up Simple Light Isotope Metabolic (bSLIM) Labeling Data Processing Strategy. J Proteome Res, 20: 1476-1487.
PMID: 33573382
DOI: 10.1021/acs.jproteome.0c00478

16. Yu YK (2020) Electrostatics of charged dielectric spheres with application to biological systems. III. Rigorous ionic screening at the Debye-Hückel level. Phys Rev E, 102: 052404.
PMID: 33327080
DOI: 10.1103/PhysRevE.102.052404

17. Alves G, Yu YK (2020) Robust Accurate Identification and Biomass Estimates of Microorganisms via Tandem Mass Spectrometry. J Am Soc Mass Spectrom, 31: 85-102.
PMID: 32881514
DOI: 10.1021/jasms.9b00035

18. Yu YK (2019) Electrostatics of charged dielectric spheres with application to biological systems. II. A formalism bypassing Wigner rotation matrices. Phys Rev E, 100: 012401.
PMID: 31499794
DOI: 10.1103/PhysRevE.100.012401

19. Hamaneh MB, Yu YK (2019) Exploring induced pluripotency in human fibroblasts via construction, validation, and application of a gene regulatory network. PLoS One, 14: e0220742.
PMID: 31374103
DOI: 10.1371/journal.pone.0220742

20. Ogurtsov AY, Alves G, Yu YK (2019) RAId: Knowledge-Integrated Proteomics Web Service with Accurate Statistical Significance Assignment. Proteomics, 19: e1800367.
PMID: 30908818
DOI: 10.1002/pmic.201800367

21. Wang K, Guzman AK, Yan Z, Zhang S, Hu MY, Hamaneh MB, Yu YK, Tolu S, Zhang J, Kanavy HE, Ye K, Bartholdy B, Bouhassira EE (2019) Ultra-High-Frequency Reprogramming of Individual Long-Term Hematopoietic Stem Cells Yields Low Somatic Variant Induced Pluripotent Stem Cells. Cell Rep, 26: 2580-2592e7.
PMID: 30840883
DOI: 10.1016/j.celrep.2019.02.021

22. Duki SF, Doerr TP, Yu YK (2018) Improving series convergence: the simple pendulum and beyond. Eur J Phys, 39: 065802.
DOI: 10.1088/1361-6404/aad876

23. Buckingham DTW, Neumeier JJ, Masunaga SH, Yu YK (2018) Thermal Expansion of Single-Crystal H_{2}O and D_{2}O Ice Ih. Phys Rev Lett, 121: 185505.
PMID: 30444387
DOI: 10.1103/PhysRevLett.121.185505

24. Duki SF, Yu YK (2018) Robust Hund rule without Coulomb repulsion and exclusion principle in quantum antiferromagnetic chains of composite half spins. J Phys Condens Matter, 30: 435801.
PMID: 30215385
DOI: 10.1088/1361-648X/aae169

25. Alves G, Wang G, Ogurtsov AY, Drake SK, Gucek M, Sacks DB, Yu YK (2018) Rapid Classification and Identification of Multiple Microorganisms with Accurate Statistical Significance via High-Resolution Tandem Mass Spectrometry. J Am Soc Mass Spectrom, 29: 1721-1737.
PMID: 29873019
DOI: 10.1007/s13361-018-1986-y

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

27. Yu YK (2018) Surface charge method for molecular surfaces with curved areal elements I. Spherical triangles. J Phys Condens Matter, 30: 105003.
PMID: 29376832
DOI: 10.1088/1361-648X/aaab2b

28. Doerr TP, Obolensky OI, Yu YK (2017) Extending electrostatics of dielectric spheres to arbitrary charge distributions with applications to biosystems. Phys Rev E, 96: 062414.
PMID: 29347333
DOI: 10.1103/PhysRevE.96.062414

29. Obolensky OI, Doerr TP, Ogurtsov AY, Yu YK (2016) Can dielectric spheres accurately model atomic-scale interactions?. Epl, 116: 24003.
DOI: 10.1209/0295-5075/116/24003

30. Hamaneh MB, Yu YK (2016) Mechanism-based disease similarity. J Rare Dis Res Treat, 1: 1-4.
PMID: 30854526
DOI: 10.29245/2572-9411/2016/3.1044

31. Alves G, Yu YK (2016) Confidence assignment for mass spectrometry based peptide identifications via the extreme value distribution. Bioinformatics, 32: 2642-9.
PMID: 27153659
DOI: 10.1093/bioinformatics/btw225

32. Hamaneh MB, Haber J, Yu YK (2015) Analytical solution and scaling of fluctuations in complex networks traversed by damped, interacting random walkers. Phys Rev E Stat Nonlin Soft Matter Phys, 92: 052803.
PMID: 26651740
DOI: 10.1103/PhysRevE.92.052803

33. Alves G, Wang G, Ogurtsov AY, Drake SK, Gucek M, Suffredini AF, Sacks DB, Yu YK (2016) Identification of Microorganisms by High Resolution Tandem Mass Spectrometry with Accurate Statistical Significance. J Am Soc Mass Spectrom, 27: 194-210.
PMID: 26510657
DOI: 10.1007/s13361-015-1271-2

34. Hamaneh MB, Yu YK (2015) DeCoaD: determining correlations among diseases using protein interaction networks. BMC Res Notes, 8: 226.
PMID: 26047952
DOI: 10.1186/s13104-015-1211-z

35. Alves G, Yu YK (2015) Mass spectrometry-based protein identification with accurate statistical significance assignment. Bioinformatics, 31: 699-706.
PMID: 25362092
DOI: 10.1093/bioinformatics/btu717

36. Hamaneh MB, Yu YK (2014) Relating diseases by integrating gene associations and information flow through protein interaction network. PLoS One, 9: e110936.
PMID: 25360770
DOI: 10.1371/journal.pone.0110936

37. Yu YK, Capra JA, Stojmirović A, Landsman D, Altschul SF (2015) Log-odds sequence logos. Bioinformatics, 31: 324-31.
PMID: 25294922
DOI: 10.1093/bioinformatics/btu634

38. Doerr TP, Yu YK (2014) Electrical interactions in the cell: Asymmetric screening in a watery antiverse. Am J Phys, 82: 460-465.
PMID: 25125701
DOI: 10.1119/1.4869281

39. Stojmirović A, Yu YK (2014) Building a hierarchical organization of protein complexes out of protein association data. PLoS One, 9: e100098.
PMID: 24978199
DOI: 10.1371/journal.pone.0100098

40. Alves G, Yu YK (2014) Accuracy evaluation of the unified P-value from combining correlated P-values. PLoS One, 9: e91225.
PMID: 24663491
DOI: 10.1371/journal.pone.0091225

41. Alves G, Ogurtsov AY, Yu YK (2014) Molecular Isotopic Distribution Analysis (MIDAs) with adjustable mass accuracy. J Am Soc Mass Spectrom, 25: 57-70.
PMID: 24254576
DOI: 10.1007/s13361-013-0733-7

42. Alves G, Yu YK (2013) Improving peptide identification sensitivity in shotgun proteomics by stratification of search space. J Proteome Res, 12: 2571-81.
PMID: 23668635
DOI: 10.1021/pr301139y

43. Obolensky OI, Wu WW, Shen RF, Yu YK (2013) 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 Commun Mass Spectrom, 27: 152-6.
PMID: 23239328
DOI: 10.1002/rcm.6451

44. Stojmirović A, Bliskovsky A, Yu YK (2012) CytoITMprobe: a network information flow plugin for Cytoscape. BMC Res Notes, 5: 237.
PMID: 22587372
DOI: 10.1186/1756-0500-5-237

45. Stojmirović A, Yu YK (2012) Information flow in interaction networks II: channels, path lengths, and potentials. J Comput Biol, 19: 379-403.
PMID: 22409812
DOI: 10.1089/cmb.2010.0228

46. Obolensky OI, Wu WW, Shen RF, Yu YK (2012) Using dissociation energies to predict observability of b- and y-peaks in mass spectra of short peptides. Rapid Commun Mass Spectrom, 26: 915-20.
PMID: 22396027
DOI: 10.1002/rcm.6180

47. Stojmirovic A, Bliskovsky A, Yu YK (2012) CytoSaddleSum: a functional enrichment analysis plugin for Cytoscape based on sum-of-weights scores. Bioinformatics, 28: 893-4.
PMID: 22345616
DOI: 10.1093/bioinformatics/bts041

48. Alves G, Yu YK (2011) 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

49. Stojmirović A, Yu YK (2011) ppiTrim: constructing non-redundant and up-to-date interactomes. Database (Oxford), 2011: bar036.
PMID: 21873645
DOI: 10.1093/database/bar036

50. Yu YK, Altschul SF (2011) The complexity of the dirichlet model for multiple alignment data. J Comput Biol, 18: 925-39.
PMID: 21702692
DOI: 10.1089/cmb.2011.0039

51. Ye X, Yu YK, Altschul SF (2011) On the inference of dirichlet mixture priors for protein sequence comparison. J Comput Biol, 18: 941-54.
PMID: 21702690
DOI: 10.1089/cmb.2011.0040

52. Yu YK (2011) Challenges of information retrieval and evaluation in data-centric biology. OMICS, 15: 239-40.
PMID: 21476849
DOI: 10.1089/omi.2011.0026

53. Ozdemir V, Smith C, Bongiovanni K, Cullen D, Knoppers BM, Lowe A, Peters M, Robbins R, Stewart E, Yee G, Yu YK, Kolker E (2011) Policy and data-intensive scientific discovery in the beginning of the 21st century. OMICS, 15: 221-5.
PMID: 21476845
DOI: 10.1089/omi.2011.0007

54. Ye X, Yu YK, Altschul SF (2010) Compositional adjustment of Dirichlet mixture priors. J Comput Biol, 17: 1607-20.
PMID: 21128852
DOI: 10.1089/cmb.2010.0117

55. Alves G, Ogurtsov AY, Yu YK (2010) 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

56. Alves G, Ogurtsov AY, Yu YK (2011) Assigning statistical significance to proteotypic peptides via database searches. J Proteomics, 74: 199-211.
PMID: 21055489
DOI: 10.1016/j.jprot.2010.10.005

57. Stojmirović A, Yu YK (2010) Robust and accurate data enrichment statistics via distribution function of sum of weights. Bioinformatics, 26: 2752-9.
PMID: 20826881
DOI: 10.1093/bioinformatics/btq511

58. Altschul SF, Wootton JC, Zaslavsky E, Yu YK (2010) The construction and use of log-odds substitution scores for multiple sequence alignment. PLoS Comput Biol, 6: e1000852.
PMID: 20657661
DOI: 10.1371/journal.pcbi.1000852

59. Doerr TP, Yu YK (2010) Simple electrostatic model applicable to biomolecular recognition. Phys Rev E Stat Nonlin Soft Matter Phys, 81: 031925.
PMID: 20365788
DOI: 10.1103/PhysRevE.81.031925

60. Stojmirović A, Yu YK (2009) ITM Probe: analyzing information flow in protein networks. Bioinformatics, 25: 2447-9.
PMID: 19561335
DOI: 10.1093/bioinformatics/btp398

61. Obolensky OI, Doerr TP, Ray R, Yu YK (2009) Rigorous treatment of electrostatics for spatially varying dielectrics based on energy minimization. Phys Rev E Stat Nonlin Soft Matter Phys, 79: 041907.
PMID: 19518256
DOI: 10.1103/PhysRevE.79.041907

62. Stojmirović A, Yu YK (2009) Geometric aspects of biological sequence comparison. J Comput Biol, 16: 579-610.
PMID: 19361329
DOI: 10.1089/cmb.2008.0100

63. Altschul SF, Gertz EM, Agarwala R, Schäffer AA, Yu YK (2009) PSI-BLAST pseudocounts and the minimum description length principle. Nucleic Acids Res, 37: 815-24.
PMID: 19088134
DOI: 10.1093/nar/gkn981

64. Alves G, Yu YK (2008) 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

65. Alves G, Ogurtsov AY, Yu YK (2008) 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

66. Alves G, Ogurtsov AY, Kwok S, Wu WW, Wang G, Shen RF, Yu YK (2008) Detection of co-eluted peptides using database search methods. Biol Direct, 3: 27.
PMID: 18597684
DOI: 10.1186/1745-6150-3-27

67. Stojmirović A, Gertz EM, Altschul SF, Yu YK (2008) The effectiveness of position- and composition-specific gap costs for protein similarity searches. Bioinformatics, 24: i15-23.
PMID: 18586708
DOI: 10.1093/bioinformatics/btn171

68. Alves G, Wu WW, Wang G, Shen RF, Yu YK (2008) Enhancing peptide identification confidence by combining search methods. J Proteome Res, 7: 3102-13.
PMID: 18558733
DOI: 10.1021/pr700798h

69. Alves G, Ogurtsov AY, Wu WW, Wang G, Shen RF, Yu YK (2007) Calibrating E-values for MS2 database search methods. Biol Direct, 2: 26.
PMID: 17983478
DOI: 10.1186/1745-6150-2-26

70. Alves G, Ogurtsov AY, Yu YK (2007) RAId_DbS: peptide identification using database searches with realistic statistics. Biol Direct, 2: 25.
PMID: 17961253
DOI: 10.1186/1745-6150-2-25

71. Zhang YC, Blattner M, Yu YK (2007) Heat conduction process on community networks as a recommendation model. Phys Rev Lett, 99: 154301.
PMID: 17995171
DOI: 10.1103/PhysRevLett.99.154301

72. Stojmirović A, Yu YK (2007) Information flow in interaction networks. J Comput Biol, 14: 1115-43.
PMID: 17985991
DOI: 10.1089/cmb.2007.0069

73. Sardiu ME, Cheung MS, Yu YK (2007) Cysteine-cysteine contact preference leads to target-focusing in protein folding. Biophys J, 93: 938-51.
PMID: 17617551
DOI: 10.1529/biophysj.106.097824

74. Yu YK, Zhang YC, Laureti P, Moret L (2006) Decoding information from noisy, redundant, and intentionally distorted sources. Physica A, 371: 732-44.
DOI: 10.1016/j.physa.2006.04.057

75. Laureti P, Moret L, Zhang YC, Yu YK (2006) Information filtering via Iterative Refinement. Europhys Lett, 75: 1006-12.
DOI: 10.1209/epl/i2006-10204-8

76. Gertz EM, Yu YK, Agarwala R, Schäffer AA, Altschul SF (2006) Composition-based statistics and translated nucleotide searches: improving the TBLASTN module of BLAST. BMC Biol, 4: 41.
PMID: 17156431
DOI: 10.1186/1741-7007-4-41

77. Yu YK, Gertz EM, Agarwala R, Schäffer AA, Altschul SF (2006) Retrieval accuracy, statistical significance and compositional similarity in protein sequence database searches. Nucleic Acids Res, 34: 5966-73.
PMID: 17068079
DOI: 10.1093/nar/gkl731

78. Doerr TP, Yu YK (2006) Electrostatics of charged dielectric spheres with application to biological systems. Phys Rev E Stat Nonlin Soft Matter Phys, 73: 061902.
PMID: 16906859
DOI: 10.1103/PhysRevE.73.061902

79. Doerr TP, Yu YK (2006) Electrostatics of charged dielectric spheres with application to biological systems. Phys Rev E, 73: 061902.
DOI: 10.1103/PhysRevE.73.061902

80. Doerr TP, Alves G, Yu YK (2005) 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, 354: 558-70.
DOI: 10.1016/j.physa.2005.03.004

81. Sardiu ME, Alves G, Yu YK (2005) 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: 061917.
PMID: 16485984
DOI: 10.1103/PhysRevE.72.061917

82. Altschul SF, Wootton JC, Gertz EM, Agarwala R, Morgulis A, Schäffer AA, Yu YK (2005) Protein database searches using compositionally adjusted substitution matrices. FEBS J, 272: 5101-9.
PMID: 16218944
DOI: 10.1111/j.1742-4658.2005.04945.x

83. Alves G, Yu YK (2005) Robust accurate identification of peptides (RAId): deciphering MS2 data using a structured library search with de novo based statistics. Bioinformatics, 21: 3726-32.
PMID: 16105903
DOI: 10.1093/bioinformatics/bti620

84. Yu YK, Altschul SF (2005) The construction of amino acid substitution matrices for the comparison of proteins with non-standard compositions. Bioinformatics, 21: 902-11.
PMID: 15509610
DOI: 10.1093/bioinformatics/bti070

85. Przytycka TM, Yu YK (2004) Scale-free networks versus evolutionary drift. Comput Biol Chem, 28: 257-64.
PMID: 15548452
DOI: 10.1016/j.compbiolchem.2004.07.001

86. Yu YK (2003) On a class of integrals of Legendre polynomials with complicated arguments--with applications in electrostatics and biomolecular modeling. Physica A, 326: 522-33.
PMID: 15759366
DOI: 10.1016/s0378-4371(03)00335-2

87. Yu YK (2004) Replica model for an unusual directed polymer in 1+1 dimensions and prediction of the extremal parameter of gapped sequence alignment statistics. Phys Rev E Stat Nonlin Soft Matter Phys, 69: 061904.
PMID: 15244614
DOI: 10.1103/PhysRevE.69.061904

88. Yu YK, Wootton JC, Altschul SF (2003) The compositional adjustment of amino acid substitution matrices. Proc Natl Acad Sci U S A, 100: 15688-93.
PMID: 14663142
DOI: 10.1073/pnas.2533904100

89. Yu YK, Bundschuh R, Hwa T (2002) Statistical significance and extremal ensemble of gapped local hybrid alignment. Lecture Notes in Physics, Springer Berlin/Heidelberg, 585: 3-21.
DOI: 10.1007/3-540-45692-9_1