1. Stojmirović A, Yu YK (2009) ITM Probe: analyzing information flow in protein networks. Bioinformatics, 25: 2447-9.
PMID: 19561335

2. Obolensky OI, Doerr TP, Ray R, Yu YK (2009) Rigorous treatment of electrostatics for spatially varying dielectrics based on energy minimization. Physical review E, Statistical, nonlinear, and soft matter physics, 79: 041907.
PMID: 19518256

3. Stojmirović A, Yu YK (2009) Geometric aspects of biological sequence comparison. J Comput Biol, 16: 579-610.
PMID: 19361329

4. 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

5. 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

6. 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

7. 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

8. 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

9. 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

10. Alves G, Ogurtsov AY, Yu YK (2007) RAId_DbS: peptide identification using database searches with realistic statistics. Biol Direct, 2: 25.
PMID: 17961253

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

12. Stojmirović A, Yu YK (2007) Information flow in interaction networks. J Comput Biol, 14: 1115-43.
PMID: 17985991

13. 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

14. 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

15. 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

16. 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

17. 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

18. Doerr TP, Yu YK (2006) Electrostatics of charged dielectric spheres with application to biological systems. Physical review E, Statistical, nonlinear, and soft matter physics, 73: 061902.
PMID: 16906859

19. 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

20. 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

21. 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. Physical review E, Statistical, nonlinear, and soft matter physics, 72: 061917.
PMID: 16485984

22. 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

23. 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

24. 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

25. Przytycka TM, Yu YK (2004) Scale-free networks versus evolutionary drift. Computational biology and chemistry, 28: 257-64.
PMID: 15548452

26. 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

27. 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. Physical review E, Statistical, nonlinear, and soft matter physics, 69: 061904.
PMID: 15244614

28. Yu YK, Wootton JC, Altschul SF (2003) The compositional adjustment of amino acid substitution matrices. Proc Natl Acad Sci USA, 100: 15688-93.
PMID: 14663142

29. 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