PAPERS IN REFEREED JOURNALS/BOOK CHAPTERS

(“†” represents equal contributors and “*” co-corresponding authors)

REPRESENTATIVES/SAMPLES

1. Liu, J., Yu, T., Mu, Z., Li^*, G. (2019) TransLiG: a de novo transcriptome assembler that uses line graph iteration, Genome Biology 20 (81) (IF: 14.028; top)  (first author was a student I supervised).

2. Li, Y., Ni, P., Zhang, S., Li^*, G., Su^*, Z. (2019) Ultra-fast and accurate motif finding in large ChIP-seq datasets reveals transcription factor binding patterns, Bioinformatics. (IF: 4.531; top) (first author was a student I supervised).

3. Liu, J., Ren, X., Li^*, G. (2019) scRNAss: a single-cell RNA-seq assembler via saving dropouts and combing junctions. Bioinformatics. (IF: 4.531; top) (first author was a student I supervised).

4. Gao, B., Zhao, Y., Li, Y., Liu, J., Li^*, G., Su,^* Z. (2019). Prediction of driver modules via balancing exclusive coverages of mutations in cancer samples. Advanced Science. (IF: 15.804; top) (first author was a student I supervised).

5. Hou, Y., Gao, B., Li^*, G., Su^*, Z. (2018). MaxMIF: a new method for identifying cancer driver genes through effective data integration. Advanced Science 5 (9) (IF:15.804; top) (first author was a student I supervised).

6. Liu^†, J., Yu^†, T., Jiang, T., Li^†,*, G. (2016). TransComb: an ab initio transcriptome assembler via combing junctions in splicing graphs. Genome      Biology 17（213）(IF: 14.028; top) (first author was a student I supervised).

7. Liu^†, J., Li^†,*, G., Gao, B., Liu, B., McMullen, M., Huang^*, X. (2016). BinPacker: packing-based de novo transcriptome assembly from RNA-seq data, Plos Computational Biology 12(2) (IF: 4.428; top) (first author was a student I supervised).

8. Chang^†, Z., Li^†,*, G., et al., Huang^*_, X. (2015). Bridger: A new framework for de novo transcriptome assembly using RNA sequence data. Genome Biology 16(30) (IF: 14.028; top) (first author was a student I supervised).

9. Li, G., Ma, Q., Mao, X., Yin, Y. Zhu, X., Xu^*, Y. (2011). Integration of Sequence-Similarity and Functional Association Information Can Overcome      Intrinsic Problems in Orthology Mapping across Bacterial Genomes. Nucleic Acids Research 39(22) (IF: 11.147; top)

10. Li^†, G., Liu^†, B., Ma, Q., Xu^*, Y. (2010). A New Framework for Identifying cis Regulatory Motifs in Prokaryotes. Nucleic Acids Research 39(7) (IF: 11.147; top)

11. Li^†, G., Ma^†, Q., Tang, H., Paterson, A. C., Xu^*, Y. (2009). QUBIC: A Qualitative Biclustering Algorithm for Analyses of Gene Expression Data. Nucleic Acids Research 37(15) (IF: 11.147; top)

12. Li^†, G., Liu^†, B., Xu^*, Y. (2009). Accurate Recognition of cis-Regulatory Motifs with the Correct Lengths in Prokaryotic Genomes. Nucleic Acids Research 38(2) (IF: 11.147; top)

13. Che^†, D., Li^†, G., Mao, F., Xu^*, Y. (2006). Detecting Uber-Operons in Microbial Genomes. Nucleic Acids Research 34(8). (IF: 11.147; top)

14. Deng, X., Li, G., Ma, B., Wang, L. (2003). Genetic Design of Drugs without Side-effects, SIAM Journal on Computing 32(4), 1073–1090. (The authors are ordered alphabetically). It solved a long open problem of distinguishing substrings.

15. Li, G., Deng, X. (2009). A Polynomial-Time Approximation Scheme for Embedding Hypergraph in a Cycle, ACM Transactions on Algorithms 412(48), 6786-6793. It solved a long open problem of embedding hypergraph on a ring network.

16. Deng, X., Li, G., Zang, W. (2003). A 2-Approximation Algorithm for Path Coloring on A Restricted Class of Trees of Rings. ACM Transactions on Algorithms (Journal of Algorithms 47(1), 1-13. (The authors are ordered alphabetically). The best performance has been being kept.      

17. Deng, X., Li, G., Zang, W. (2004). Proof of Chvátal’s Conjecture on Maximal Stable Sets and Maximal Cliques in Graphs, Journal of Combinatorial Theory, Series B 91(2), 301-325. (The authors are ordered alphabetically). It proves Chvátal’s Conjecture.

18. Li, G. (2000). Edge Disjoint Hamilton Cycles in Graphs. Journal of Graph Theory 35(1), 8-20. It proves Zhou’s Conjecture.

19. Li, G., Chen, C., Liu, Z. (2005). On Connected [g, f+1]-Factors in Graphs. Combinatorica 25 (4), 393–405. It proves Kano’s Conjecture.

20. Li, G., Liu, G., (1998). (g, f)-Factorizations Orthogonal to Any Subgraph in Graphs, Science in China, Ser. A, Mathematics 41(3), 267-272. It proves Alspach’s Conjecture.

21. Li, S., Li, G. (2005). Minimizing Makespan on A Single Batch Machine with Release Times and Non-identical Job Sizes. Operations Research Letters. 33(2), 157-164. (first author was a student I supervised). The best performance has been being kept.

MISCELLANEOUS

Related to Bioinformatics

22. Qi,E., Wang, D., Li, Yang, Li^*, G., Su^*, Z.,(2019) Revealing favorable and unfavorable residues in cooperative positions in protease cleavage sites, BioMedical & Biophysical Research Communication, 519(4), 19Nov. 714-720. (IF: 2.559)

23. Li, Y., Liu, B., Li, J., Li*, G. (2019) MiMod: a New Algorithm for Mining Biological Network Modules, IEEE Access 7

24. Mu, Z., Yu, T., Qi, E., Liu*, J., Li*, G. (2019) DCGR: Feature extractions from protein sequences based on CGR via remodeling multiple information, BMC Bioinformatics 20:351 (IF:2.213 )

25. Qi, E., Wang, D., Gao, B., Li, Y., Li, G. (2017). Block-based characterization of protease specificity from substrate sequence profile, BMC Bioinformatics 18:438. (IF:2.213 )

26. Gao†, B., Li^†,*, G., Liu,  J., Li, Y., Huang, X., (2017), Identification of driver modules in pan-cancer via coordinating coverage and exclusivity, Oncotarget 8(22) 36115-36126 (IF: 5.1680) (^†equal contributors; ^*corresponding authors)

27. Wang, Z., Zhou, C., Chang, Z., Liu, B., Ma, Q., Li, G. (2017), An insight into species from same descendent aspect and the application into Clostridia, Current Bioinformatics, online. (IF: 0.770)

28. Wang^†,^* Z., Li^†,*, G., Robinson, W. R., Huang^*, X. (2016). UniBic: Sequential row-based biclustering algorithm for analysis of gene expression data. Scientific Report 6: 23466. (^†equal contributors; ^*co-corresponding authors)

29. Liu, B., Zhou, C., Li*, G., Ma*, Q. (2016). Bacterial regulon modeling and prediction based on systematic cis regulatory motif analyses, Scientific Report 6:23030. (^*co-corresponding authors)

30. Liu, B., Zhang, H., Zhou, C., Li, G., Fennell, A., Wang, G., Kang, Y., Liu, Q., Ma, Q. An integrative and applicable phylogenetic footprinting framework for cis-regulatory motifs identification in prokaryotic genomes. BMC Genetics (2016) (IF: 2.40)

31. Yu, X., Ceng, T., Li, G., Integrative enrichment analysis: a new computational method to Detect dysregulated pathways in heterogeneous samples, BMC Genetics (2015)16 (918) (IF: 2.40)  Liu, J., Sun, J., Huang, X., Li, G., Liu, B., Goldindec: A Novel Algorithm for Raman Spectrum Baseline Correction, APPLIED SPECTROSCOPY, (2015) 69(7), 834~842. SCI

32. Yu, X., Zeng T., Wang X., Li*, G., Chen* L., Unravelling personalized dysfunctional gene network of complex diseases based on differential network model, Journal of Translational Medicine (2015) 13(189) (IF: 3.93)

33. Chang, Z, Wang, Z., Li, G., Huang, X., The Impacts of Read Length and Transcriptome Complexity for DeNovo Assembly: A Simulation Study, Plos One (2014) 9(4) (IF:3.534)

34. Zhou, C., Ma, Q., Li, G., Elucidation of Operon Structures across Closely Related BacterialGenomes, Plos One (2014) 9(6) (IF:3.534)

35. Yu, X., Li, G., Chen, L.,（2013）Prediction and early diagnosis of complex diseases byedge-network, Bioinformatics 30(6) (IF:4.981)

36. Liu, J., Duan, X., Sun, J., Yin, Y., Li, G., Wang, L., Liu, B., Bi-factor Analysis based on noise-reduction (BIFANR): A new algorithm for detecting coevolving amino acid sites in proteins, Plos One (2013) (IF: 3.534)

37. Ma, Q., Liu, B., Zhou, C., Yin, Y., Li, G., Xu, Y., An integrated toolkit for accurate prediction and analysis of cis regulatory motifs at a genome scale, Bioinformatics (2013), Vol. 29 (18), p2261 (IF: 4.981)

38. Ma, Q., Yin, Y., Zhang, H., Schell, M. A., Li, G., Xu, Y., Elucidation of the dynamic supercoil structures of folded E. coli chromosome: a computational approach, Nucleic Acids Research (2013), doi:10.1093/nar/gkt261 (IF: 9.112)

39. Zhou, F., Ma, Q., Li, G., Xu, Y., QServer: a biclustering server for prediction and validation of co-expressed gene clusters, PLOS one 7:3 (2012) (IF: 3.534)

40. Chen, Y., Mao, F., Li, G., Xu, Y., Genome-wide discovery of missing genes in biological pathways in prokaryotes, BMC Bioinformatics, 12:51 (2011).

41. Qi, X., Li, G., Li, S., Xu, Y., Sorting genomes by translocations, insertions and deletions, IEEE/ACM Transactions on Computational Biology and Bioinformatics, 7(2) (2010) SCI

42. Li, G., Liu, Z., Guo, J., Xu, Y., An Algorithm for Simultaneous Backbone Threading and Side-Chain Packing, Algorithmica, 51 (2008), 435-450 SCI

43. Chen, Y., Zhou, F., Li, G., Xu, Y., MUST: A system for identification of miniature inverted-repeat transposable elements and applications to nabaena variabilis and Haloquadratum walsbyi, Gene 436 (2009) 1–7 SCI

44. Chen, Y., Li, G., An effective algorithm of motif finding problem, Int. J. Bioinformatics Research and Applications, Vol.4, No.2, 2008, 137-149 SCI

45. Chen, Y., Zhou, F., Li, G., Xu, Y., A recently active MITE, Chunjie, inserted into an operon without disturbing the operon structure in Geobacter uraniireducens Rf4, Genetics 179: 2008, 2219--2297 SCI

46. Li, G., Che, D., Xu, Y., A Universal operon predictor for prokaryotic genomes, Journal of Bioinformatics and Computational Biology, Vol. 7, No. 1 (Y. 2009), 19-38 SCI

47. Chen, Y., Li, G., An effective algorithm of motif finding problem, Int. J. Bioinformatics Research and applications, Vol.4, No.2, 2008, 137-149 SCI

48. Qi, X., Wu, J., Li, S., Li, G., Sorting by transpositions: dealing with length-weighted models, Int. J. Bioinformatics Research and applications, Vol.4, No.2, 2008, 164-171 SCI

49. Li, G., Liu, Z., Guo, J., Xu, Y., An algorithm for simultaneous backbone threading and side-chain packing, Algorithmica (2007)48: 329-342 SCI

50. Li, G., Lu, J., Victor, O., Xu, Y., A highly sensitive algorithm for identification of cis regulatory elements: from cliques to high information content analysis, Journal of Bioinformatics and Computational Biology, Vol.5, Issue 4 (2007), 817-838 SCI

51. Li, G., Qi, X., Wang, X., Zhu, B., A linear-time algorithm for computing translocation distance between signed genomes CPM 2004: 323-332.

52. Deng, X., Li, G., Wang, L., Center and distinguisher for string selection on unbounded alphabet, Journal of Combinatorial Optimization, Vol. 6, 383-400. 2002 SCI

53. Qi, X., Li, G., Xu, Y., An asymptotically optimal algorithm for sorting by reciprocal translocations and deletions/insertions, CSB2006 Conference Proceedings, Stanford CA, 14-18 August 2006.

54. Qi, X., Li, G., Wu, J., Liu, B., Sorting signed permutations by fixed-length reversals, International Journal of Foundations of Computer Science, Vol. 17, No. 4 (2006) 933-948 SCI

55. Qi, X., Li, G., Li, S., A faster algorithm for genomic sorting problem, Math. Appl. 19(2006) N.1, 66-74.

56. Deng, X., Li, G., Li, Z., Ma, B., Wang, L., A PTAS for distinguishing (sub)string selection, Lecture Notes in Computer Science, Vol. 2380, 740-751 (2002).

57. Li, G., X. Qi, X. Wang, A linear-time algorithm for computing translocation distance between signed genomes, Lecture Notes in Computer Science, Vol.3109, 323-332 (2004).

58. Che, D., Li, G., Jensen, S., Liu, J., Xu, Y., PFP: a new approach to phylogenetic footprinting in prokaryotic genomes, Proceedings of International      Symposium on Bioinformatics Research and Applications, pp. 110-121, 2008.

59. Qi, X., Li, S., Li, G., Xu, Y., Sorting genomes by translocations and deletions, Proceedings of CSB2006, pp. 157-166, 2006.

    Related to Graph Theory

60. G. Su, L. Xiong, X. Su, G. Li, Maximally edge-connected graphs and Zeroth-order general Randic Index for α≤ -1. J.Comb. Optim. 31(1)(2016),182-195. SCI

61. A. Dong, Q. Zou, G. Li, Equitable and List Equitable Colorings of Graphs with Bounded Maximum Average Degree, Ars Combinatoria, (2016) 1(124), 303~311. SCI

62. B. Xue, L. Zuo, G. Li, Coloring the square of sierpinski graphs. Graph Combin. 31(1) (2015), 1-10. SCI

63. B. Xue, L. Zuo, G. Wang, G. Li, Shortest paths in Sierpiński graphs, Discrete Applied Mathematics, Vol. 162(10) (2014), 314-321. SCI

64. B. Xue, G. Wang, G. Li, The Linear t-Colorings of SierpiA"ski-Like Graphs, Graphs and Combinatorics, 30(3) (2014), pp 755-767. SCI

65. H. Chen, X. Tan, J. Wu, G. Li, The linear arboricity of planar graphs without 5-, 6-cycles with chords, Graphs and Combinatorics, 29(3) (2013), 373-385. SCI

66. Q. Zou, H. Chen, G. Li, Vertex-disjoint cycles of order eight with chords in a bipartite graph, Bull. Malays. Math. Sci. Soc. (2) 36(1) (2013), 255–262. SCI

67. Y. Gao, G. Li, J. Yan, Notes on Hamiltonian graphs and Hamiltonian connected graphs. Ars Combinatoria 109 (2013), 405-414. SCI

68. Q. Zou, G. Li, Y. Gao: Every cycle-connected multipartite tournament with δ ≥ 2 contains at least two universal arcs.Graphs and Combinatorics 29(4) (2013), 1141-1149. SCI

69. Y. Gao, G. Li, J. Yan: Neighborhood Unions for the Existence of Disjoint Chorded Cycles in Graphs. Graphs and Combinatorics 29(5) (2013), 1337-1345. SCI

70. B. Xue, L. Zuo, G. Li, The Hamiltonicity and path t-coloring of Sierpiński-like graphs, Discrete Appl. Math. 160 (2) (2012), 1822-1836. SCI

71. A. Dong, G. Liu, G. Li,  List edge and list total colorings of planar graphs without 6-cycles with chord, Bulletin of the Korean Mathematical Society, 49 (2012) 359 - 365. SCI

72. A. Dong, G. Li, Equitable coloring and equitable choosability of planar graphs without 6- and 7-cycles, Ars Combinatoria Vol. 103 (2012) 333-352. SCI

73. C. Yang, G. Li, A polynomial time approximation scheme for embedding hypergraph in a weighted cycle, Theoretical Computer Science 412 (2011) 67866793; also Lecture Notes on Computer Sciences 6213, pp. 197–209, 2010.

74. Y. Gao, G. Li, On the maximum number of disjoint chorded cycles in graphs, Ars Combin. 98 (2011). SCI

75. Y. Gao, J. Yan, G. Li, On 2-factors with chorded quadrilaterals in graphs. Ars Combin. 98 (2011). SCI

76. S. Chiba, S. Fujita, Y. Gao, G. Li, On a sharp degree sum condition for disjoint chorded cycles in graphs. Graphs and Combinatorics 26 (2010). SCI

77. Y. Gao, J. Yan, G. Li, On 2-factors with cycles containing specified vertices in a bipartite graph. J. Appl. Math. Comput. 31 (2009), no. 1-2. SCI

78. H. Zhang, G. Li, H. Zhao, A kind of QP-free feasible method, Journal of Computational and Applied Mathematics, Volume 224, Issue 1(2009), 230-241. SCI

79. Y. Gao, G. Li, X. Li, Degree condition for the existence of a k-factor containing a given Hamiltonian cycle. Discrete Mathematics 309(2009), 2373-2381. SCI

80. H. Zhao, G. Li, Batch scheduling with a common due window on a single machine, Journal of Systems Science and Complexity, Vol. 21: 296-303, 2008. SCI

81. H. Kang, J. Wu, G. Li, Removable edges of cycles in 5-connected graphs, J. Appl. Math. Comput. 2008.

82. S. Li, G. Li, Minimizing total weighted completion time on parallel unbounded batch machines, Journal of Software, Vol. 17, No. 10, 2063-2068, 2006.

83. S. Li, G. Li, H. Zhao, Minimizing total completion time of bounded batch scheduling, Math. Appl. (in China) 19(2006), no. 2, 446-454.

84. S. Li, G. Li, S. Zhang , Minimizing makespan on a single batching machine with release times and non-identical job sizes, Discrete Applied Mathematics 148 ( 2005) 127-134. SCI

85. X. Deng, H. Feng, G. Li, B. Shi, A PTAS for semiconductor burn-in scheduling, Journal of of Combinatorial Optimization, Vol. 9, No. 1 (2005) 5-17. SCI

86. S. Li, G. Li, Minimum maximum lateness on identical parallel batch processing machines, COCOO N '04.

87. X. Deng, G. Li, W. Zang, Corrigendum to proof of Chvátal's conjecture on maximal stable sets and maximal cliques in graphs, J. Combin. Theory Ser. B 91 (2004) 301-325.

88. S. Zhang, G. Li, S. Li, A linear time algorithm for the minimum weight feedback vertex set problem in series-parallel graphs, Software Vol.20, No.4 (2004) 1-10.

89. X. Deng, G. Li, A PTAS for embedding hypergraph in a cycle, ICALP'04.

90. M. Wang, G. Li, Packing a tree of order p with a (p, p+1)-graph, J. Syst. Sci. Complex, 16(2003), No. 1, 122-132. SCI

91. G. Li, S. Zhang, Wavelength assignment in all-optical WDM network with ring topology, Acta Mathematicae Applicatae Sinica, Vol. 26, No. 3 (2003), 1-7 . SCI

92. S. Zhang, G. Li, Linear time algorithm for feedback vertex set problem in serial parallel graphs, Computer Science, Vol. 30, No. 8(2003), 122-125.

93. G. Li, G. Liu, A generalization of orthogonal factorizations in graphs, Acta Mathematica Sinica, Vol. 46, No. 4(2003), 715-720. SCI

94. X. Deng, G. Li, L. Wang, Center and distinguisher for strings with unbounded alphabet, Journal of Combinatorial Optimization 6 (4), 2002, 383-400. SCI

95. G. Li et al., Hamiltonicity in 3-connected claw-free graphs, Discrete Mathematics, 250/1-3(2002), pp.137-151. SCI

96. G. Li et al., Orthogonal factorizations of graphs, Discrete Mathematics, Vol. 245, No. 1-3, (2002),      pp.173-194. SCI

97. G. Li et al., Connected [k,k+1]-factors in claw-free graphs, Ars Combinatoria, 62 (2002), pp.207-219. SCI

98. X. Deng, G. Li, A PTAS for minimizing total completion time of bounded batch scheduling, International Journal of foundations of computer science, Vol.   13 No. 6(2002) 817-827. SCI

99. S. Zhang, G. Li, Wavelength conversion in bi-directed networks, J. Software, Vol.13, No.2, 2002, 1899-1904.

100. X. Deng, H. Feng, G. Li, A PTAS for minimizing total completion time of bounded batch scheduling, IPCO'2002.

101. G. Li et al., A generalization of orthogonal factorizations of graphs, Acta Mathematica Sinica, Vol. 17, No. 4 (2001). 669-678. SCI

102. G. Li, W. Zang, Wavelength allocation on a tree of rings, Networks, Vol. 35(4) (2000), 248-252. SCI

103. P. Lin, G. Liu, G. Li, Orthogonal (g,f)-Factorizations in Networks, Networks,  Vol. 35(4) (2000), 274-278. SCI

104. M. Wang, G. Li, A Result of Erdos-Sos conjecture, Ars Combinatoria, Vol. 55 (2000), 123-127. SCI

105. X. Deng, G. Li, et al., A 2-approximation algorithm for path coloring on trees of rings, Letter Notes on computer science, 2000, 144-155.

106. G. Li et al., Disjoint hamiltonian cycles in graphs, Australasian J. Combinatorics, Vol.18(1999), 83-89.

107. G. Li et al., On connected [2, 3]-factors in claw-free graphs, Acta Mathematicae Applicatae Sinica, No. 1(1998). SCI

108. M. Wang, G. Li, A result on Erdos-Sos conjecture, Acta Mathematica Scientia, (1998). SCI

109. G. Li, Factorizations orthogonal to a subgraph in graphs, Advances in Mathematics, No.5 (1997) .

110. G. Li et al., A new result on forbidden graphs and hamiltonicity, Chinese Bulletin, No. 2(1996); 93-99. SCI

111. G. Li et al., Hamiltonicity in 3-connected regular claw-free graphs, Advances in Mathematics, No. 1(1996); 51-57.

POPULAR ARTICALES including

1. Li^†, G., Ma^†, Q., Tang, H., Paterson, A. C., Xu^*, Y. (2009). QUBIC: A Qualitative Biclustering Algorithm for Analyses of Gene Expression Data. Nucleic Acids Research 37(15) (IF: 11.147; top)

2. Chang^†, Z., Li^†,*, G., et al., Huang^*_, X. (2015). Bridger: A new framework for de novo transcriptome assembly using RNA sequence data. Genome Biology 16(30) (IF: 14.028; top) (first author was a student I supervised).

3. Deng, X., Li, G., Ma, B., Wang, L. (2003). Genetic Design of Drugs without Side-effects, SIAM Journal on Computing 32(4), 1073–1090. (The authors are ordered alphabetically). It      solved a long open problem of distinguishing substrings.

4. Deng, X., Li, G., Zang, W. (2004). Proof of Chvátal’s Conjecture on Maximal Stable Sets and Maximal Cliques in Graphs, Journal of Combinatorial Theory, Series B 91(2), 301-325. (The authors are ordered alphabetically). It proves Chvátal’s Conjecture.