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. Phys Rev E Stat Nonlin Soft Matter Phys, 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