1. Alves G, Ogurtsov AY, Porterfield H, Maity T, Jenkins LM, Sacks D, and YKY (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, XX: X-X.
DOI: 10.1021/jasms.3c00445

2. Hamaneh MB, Ogurtsov AY, Obolensky OI, Yu YK (2024) Systematic Assessment of Deep Learning-Based Predictors of Fragmentation Intensity Profiles. J Proteome Res, May 10; [Epub ahead of print].
PMID: 38728051

3. 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: 31.
PMID: 38301204

4. 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

5. 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

6. 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

7. 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

8. 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: 11.
DOI: 10.3389/fcimb.2021.634215

9. 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: 20.
PMID: 33573382

10. 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: 102.
PMID: 33327080

11. Alves G, Yu YK (2020) Robust Accurate Identification and Biomass Estimates of Microorganisms via Tandem Mass Spectrometry. J Am Soc Mass Spectrom, 31: 31.
PMID: 32881514

12. Yu YK (2019) Electrostatics of charged dielectric spheres with application to biological systems. II. A formalism bypassing Wigner rotation matrices. Phys Rev E, 100: 100.
PMID: 31499794

13. Hamaneh MB, Yu YK (2019) Exploring induced pluripotency in human fibroblasts via construction, validation, and application of a gene regulatory network. PLoS One, 14: 14.
PMID: 31374103

14. Ogurtsov AY, Alves G, Yu YK (2019) RAId: Knowledge-Integrated Proteomics Web Service with Accurate Statistical Significance Assignment. Proteomics, 19: 19.
PMID: 30908818

15. 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: 26.
PMID: 30840883

16. 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

17. 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: 121.
PMID: 30444387

18. 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: 30.
PMID: 30215385

19. 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: 29.
PMID: 29873019

20. 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: 11.
PMID: 29544540

21. Yu YK (2018) Surface charge method for molecular surfaces with curved areal elements I. Spherical triangles. J Phys Condens Matter, 30: 30.
PMID: 29376832

22. Doerr TP, Obolensky OI, Yu YK (2017) Extending electrostatics of dielectric spheres to arbitrary charge distributions with applications to biosystems. Phys Rev E, 96: 96.
PMID: 29347333

23. 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

24. Hamaneh MB, Yu YK (2016) Mechanism-based disease similarity. J Rare Dis Res Treat, 1: 1.
PMID: 30854526

25. Alves G, Yu YK (2016) Confidence assignment for mass spectrometry based peptide identifications via the extreme value distribution. Bioinformatics, 32: 32.
PMID: 27153659

26. 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: 92.
PMID: 26651740

27. 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: 27.
PMID: 26510657

28. Hamaneh MB, Yu YK (2015) DeCoaD: determining correlations among diseases using protein interaction networks. BMC Res Notes, 8: 8.
PMID: 26047952

29. Alves G, Yu YK (2015) Mass spectrometry-based protein identification with accurate statistical significance assignment. Bioinformatics, 31: 31.
PMID: 25362092

30. Hamaneh MB, Yu YK (2014) Relating diseases by integrating gene associations and information flow through protein interaction network. PLoS One, 9: 9.
PMID: 25360770

31. Yu YK, Capra JA, Stojmirović A, Landsman D, Altschul SF (2015) Log-odds sequence logos. Bioinformatics, 31: 31.
PMID: 25294922

32. Doerr TP, Yu YK (2014) Electrical interactions in the cell: Asymmetric screening in a watery antiverse. Am J Phys, 82: 82.
PMID: 25125701

33. Stojmirović A, Yu YK (2014) Building a hierarchical organization of protein complexes out of protein association data. PLoS One, 9: 9.
PMID: 24978199

34. Alves G, Yu YK (2014) Accuracy evaluation of the unified P-value from combining correlated P-values. PLoS One, 9: 9.
PMID: 24663491

35. Alves G, Ogurtsov AY, Yu YK (2014) Molecular Isotopic Distribution Analysis (MIDAs) with adjustable mass accuracy. J Am Soc Mass Spectrom, 25: 25.
PMID: 24254576

36. Alves G, Yu YK (2013) Improving peptide identification sensitivity in shotgun proteomics by stratification of search space. J Proteome Res, 12: 12.
PMID: 23668635

37. 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: 27.
PMID: 23239328

38. Stojmirović A, Bliskovsky A, Yu YK (2012) CytoITMprobe: a network information flow plugin for Cytoscape. BMC Res Notes, 5: 5.
PMID: 22587372

39. Stojmirović A, Yu YK (2012) Information flow in interaction networks II: channels, path lengths, and potentials. J Comput Biol, 19: 19.
PMID: 22409812

40. 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: 26.
PMID: 22396027

41. Stojmirovic A, Bliskovsky A, Yu YK (2012) CytoSaddleSum: a functional enrichment analysis plugin for Cytoscape based on sum-of-weights scores. Bioinformatics, 28: 28.
PMID: 22345616

42. Alves G, Yu YK (2011) Combining independent, weighted P-values: achieving computational stability by a systematic expansion with controllable accuracy. PLoS One, 6: 6.
PMID: 21912585

43. Stojmirović A, Yu YK (2011) ppiTrim: constructing non-redundant and up-to-date interactomes. Database (Oxford), 2011: 2011.
PMID: 21873645

44. Yu YK, Altschul SF (2011) The complexity of the dirichlet model for multiple alignment data. J Comput Biol, 18: 18.
PMID: 21702692

45. Ye X, Yu YK, Altschul SF (2011) On the inference of dirichlet mixture priors for protein sequence comparison. J Comput Biol, 18: 18.
PMID: 21702690

46. Yu YK (2011) Challenges of information retrieval and evaluation in data-centric biology. OMICS, 15: 15.
PMID: 21476849

47. 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: 15.
PMID: 21476845

48. Ye X, Yu YK, Altschul SF (2010) Compositional adjustment of Dirichlet mixture priors. J Comput Biol, 17: 17.
PMID: 21128852

49. Alves G, Ogurtsov AY, Yu YK (2010) RAId_aPS: MS/MS analysis with multiple scoring functions and spectrum-specific statistics. PLoS One, 5: 5.
PMID: 21103371

50. Alves G, Ogurtsov AY, Yu YK (2011) Assigning statistical significance to proteotypic peptides via database searches. J Proteomics, 74: 74.
PMID: 21055489

51. Stojmirović A, Yu YK (2010) Robust and accurate data enrichment statistics via distribution function of sum of weights. Bioinformatics, 26: 26.
PMID: 20826881

52. 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: 6.
PMID: 20657661

53. Doerr TP, Yu YK (2010) Simple electrostatic model applicable to biomolecular recognition. Phys Rev E Stat Nonlin Soft Matter Phys, 81: 81.
PMID: 20365788

54. Stojmirović A, Yu YK (2009) ITM Probe: analyzing information flow in protein networks. Bioinformatics, 25: 25.
PMID: 19561335

55. 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: 79.
PMID: 19518256

56. Stojmirović A, Yu YK (2009) Geometric aspects of biological sequence comparison. J Comput Biol, 16: 16.
PMID: 19361329

57. Altschul SF, Gertz EM, Agarwala R, Schäffer AA, Yu YK (2009) PSI-BLAST pseudocounts and the minimum description length principle. Nucleic Acids Res, 37: 37.
PMID: 19088134

58. 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: 387.
PMID: 19918268

59. Alves G, Ogurtsov AY, Yu YK (2008) RAId_DbS: mass-spectrometry based peptide identification web server with knowledge integration. BMC Genomics, 9: 9.
PMID: 18954448

60. 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: 3.
PMID: 18597684

61. Stojmirović A, Gertz EM, Altschul SF, Yu YK (2008) The effectiveness of position- and composition-specific gap costs for protein similarity searches. Bioinformatics, 24: 24.
PMID: 18586708

62. Alves G, Wu WW, Wang G, Shen RF, Yu YK (2008) Enhancing peptide identification confidence by combining search methods. J Proteome Res, 7: 7.
PMID: 18558733

63. Alves G, Ogurtsov AY, Wu WW, Wang G, Shen RF, Yu YK (2007) Calibrating E-values for MS2 database search methods. Biol Direct, 2: 2.
PMID: 17983478

64. Alves G, Ogurtsov AY, Yu YK (2007) RAId_DbS: peptide identification using database searches with realistic statistics. Biol Direct, 2: 2.
PMID: 17961253

65. Zhang YC, Blattner M, Yu YK (2007) Heat conduction process on community networks as a recommendation model. Phys Rev Lett, 99: 99.
PMID: 17995171

66. Stojmirović A, Yu YK (2007) Information flow in interaction networks. J Comput Biol, 14: 14.
PMID: 17985991

67. Sardiu ME, Cheung MS, Yu YK (2007) Cysteine-cysteine contact preference leads to target-focusing in protein folding. Biophys J, 93: 93.
PMID: 17617551

68. 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

69. 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

70. 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: 4.
PMID: 17156431

71. 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: 34.
PMID: 17068079

72. Doerr TP, Yu YK (2006) Electrostatics of charged dielectric spheres with application to biological systems. Phys Rev E Stat Nonlin Soft Matter Phys, 73: 73.
PMID: 16906859

73. 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

74. 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

75. 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: 72.
PMID: 16485984

76. 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: 272.
PMID: 16218944

77. 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: 21.
PMID: 16105903

78. Yu YK, Altschul SF (2005) The construction of amino acid substitution matrices for the comparison of proteins with non-standard compositions. Bioinformatics, 21: 21.
PMID: 15509610

79. Przytycka TM, Yu YK (2004) Scale-free networks versus evolutionary drift. Comput Biol Chem, 28: 28.
PMID: 15548452

80. Yu YK (2003) On a class of integrals of Legendre polynomials with complicated arguments--with applications in electrostatics and biomolecular modeling. Physica A, 326: 326.
PMID: 15759366

81. 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: 69.
PMID: 15244614

82. Yu YK, Wootton JC, Altschul SF (2003) The compositional adjustment of amino acid substitution matrices. Proc Natl Acad Sci U S A, 100: 100.
PMID: 14663142

83. 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