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Publications

View and download our up-to-date publications from the following resources:

Here is a list - not updated very often:

1. Community cyberinfrastructure for Advanced Microbial Ecology Research and Analysis: the CAMERA resource
Author(s): Sun, S. L.; Chen, J.; Li, W. Z.; et al.
Source: Nucleic Acids Research Volume: 39 Pages: D546-D551 Published: 2011
Times Cited: 8
DOI: 10.1093/nar/gkq1102

2. FR-HIT, a very fast program to recruit metagenomic reads to homologous reference genomes
Author(s): Niu, B. F.; Zhu, Z. W.; Fu, L. M.; et al.
Source: Bioinformatics Volume: 27 Issue: 12 Pages: 1704-1705 Published: 2011
Times Cited: 2
DOI: 10.1093/bioinformatics/btr252

3. Metagenome Plasticity of the Bovine Abomasal Microbiota in Immune Animals in Response to Ostertagia Ostertagi Infection
Author(s): Li, R. W.; Wu, S. T.; Li, W. Z.; et al.
Source: Plos One Volume: 6 Issue: 9 Published: 2011
Times Cited: 0
DOI: e2441710.1371/journal.pone.0024417

4. WebMGA: a customizable web server for fast metagenomic sequence analysis
Author(s): Wu, Sitao; Zhu, Zhengwei; Fu, Liming; et al.
Source: Bmc Genomics Volume: 12 Published: 2011
Times Cited: 0
DOI: 44410.1186/1471-2164-12-444

5. Artificial and natural duplicates in pyrosequencing reads of metagenomic data
Author(s): Niu, B. F.; Fu, L. M.; Sun, S. L.; et al.
Source: Bmc Bioinformatics Volume: 11 Pages: 11 Published: 2010
Times Cited: 19
DOI: 18710.1186/1471-2105-11-187

6. CD-HIT Suite: a web server for clustering and comparing biological sequences
Author(s): HUANG, Y; NIU, BF; GAO, Y; et al.
Source: BIOINFORMATICS Volume: 26 Issue: 5 Pages: 680-682 Published: 2010
Times Cited: 25
DOI: 10.1093/bioinformatics/btq003

7. Expansion of the Protein Repertoire in Newly Explored Environments: Human Gut Microbiome Specific Protein Families
Author(s): Ellrott, K.; Jaroszewski, L.; Li, W. Z.; et al.
Source: Plos Computational Biology Volume: 6 Issue: 6 Pages: 11 Published: 2010
Times Cited: 7
DOI: e100079810.1371/journal.pcbi.1000798

8. Analysis and comparison of very large metagenomes with fast clustering and functional annotation
Author(s): LI, WZ
Source: BMC BIOINFORMATICS Volume: 10 Published: 2009
Times Cited: 18
DOI: 10.1186/1471-2105-10-359

9. Identification of ribosomal RNA genes in metagenomic fragments
Author(s): HUANG, Y; GILNA, P; LI, WZ
Source: BIOINFORMATICS Volume: 25 Issue: 10 Pages: 1338-1340 Published: 2009
Times Cited: 13
DOI: 10.1093/bioinformatics/btp161

10. Occurrence of phosphate acquisition genes in Prochlorococcus cells from different ocean regions
Author(s): MARTINY, AC; HUANG, Y; LI, WZ
Source: ENVIRONMENTAL MICROBIOLOGY Volume: 11 Issue: 6 Pages: 1340-1347 Published: 2009
Times Cited: 22
DOI: 10.1111/j.1462-2920.2009.01860.x

11. Detection of Large Numbers of Novel Sequences in the Metatranscriptomes of Complex Marine Microbial Communities
Author(s): Gilbert, J. A.; Field, D.; Huang, Y.; et al.
Source: Plos One Volume: 3 Issue: 8 Pages: 13 Published: 2008
Times Cited: 83
DOI: e304210.1371/journal.pone.0003042

14-Jan-11
12. Gene identification and protein classification in microbial metagenomic sequence data via incremental clustering
Author(s): YOOSEPH, S; LI, WZ; SUTTON, G
Source: BMC BIOINFORMATICS Volume: 9 Published: 2008
Times Cited: 13
DOI: 10.1186/1471-2105-9-182

13. Probing Metagenomics by Rapid Cluster Analysis of Very Large Datasets
Author(s): LI, WZ; WOOLEY, JC; GODZIK, A
Source: PLOS ONE Volume: 3 Issue: 10 Published: 2008
Times Cited: 11
DOI: 10.1371/journal.pone.0003375

14. Crystal structure of the tetrameric inositol 1-phosphate phosphatase (TM1415) from the hyperthermophile, Thermotoga maritima
Author(s): STIEGLITZ, KA; ROBERTS, MF; LI, WZ; et al.
Source: FEBS JOURNAL Volume: 274 Issue: 10 Pages: 2461-2469 Published: MAY 2007
Times Cited: 4
DOI: 10.1111/j.1742-4658.2007.05779.x

15. The Sorcerer II Global Ocean Sampling expedition: Expanding the universe of protein families
Author(s): YOOSEPH, S; SUTTON, G; RUSCH, DB; et al.
Source: PLOS BIOLOGY Volume: 5 Issue: 3 Pages: 432-466 Published: 2007
Times Cited: 254
DOI: 10.1371/journal.pbio.0050016

16. A fast clustering algorithm for analyzing highly similar compounds of very large libraries
Author(s): LI, WZ
Source: JOURNAL OF CHEMICAL INFORMATION AND MODELING Volume: 46 Issue: 5 Pages: 1919-1923 Published: SEP 25 2006
Times Cited: 7
DOI: 10.1021/ci0600859

17. Cd-hit: a fast program for clustering and comparing large sets of protein or nucleotide sequences
Author(s): LI, WZ; GODZIK, A
Source: BIOINFORMATICS Volume: 22 Issue: 13 Pages: 1658-1659 Published: JUL 1 2006
Times Cited: 487
DOI: 10.1093/bioinformatics/btl158

18. VISSA: a program to visualize structural features from structure sequence alignment
Author(s): LI, WZ; GODZIK, A
Source: BIOINFORMATICS Volume: 22 Issue: 7 Pages: 887-888 Published: APR 1 2006
Times Cited: 6
DOI: 10.1093/bioinformatics/btl019

19. FFAS03: a server for profile-profile sequence alignments
Author(s): JAROSZEWSKI, L; RYCHLEWSKI, L; LI, ZW; et al.
Source: NUCLEIC ACIDS RESEARCH Volume: 33 Pages: W284-W288 Published: JUL 1 2005
Times Cited: 171
DOI: 10.1093/nar/gki418

20. A residue in the S-2 subsite controls substrate selectivity of matrix metalloproteinase-2 and matrix metalloproteinase-9
Author(s): CHEN, EI; LI, WZ; GODZIK, A; et al.
Source: JOURNAL OF BIOLOGICAL CHEMISTRY Volume: 278 Issue: 19 Pages: 17158-17163 Published: MAY 9 2003
Times Cited: 20
DOI: 10.1074/jbc.M210324200

21. A segment alignment approach to protein comparison
Author(s): YE, YZ; JAROSZEWSKI, L; LI, WZ; et al.
Source: BIOINFORMATICS Volume: 19 Issue: 6 Pages: 742-749 Published: APR 12 2003
Times Cited: 15
DOI: 10.1093/bioinformatics/btg073

22. Homotypic secretory vesicle fusion induced by the protein tyrosine phosphatase MEG2 depends on polyphosphoinositides in T cells
Author(s): Huynh, H.; Wang, X. D.; Li, W. H.; et al.
Source: Journal of Immunology Volume: 171 Issue: 12 Pages: 6661-6671 Published: 2003
Times Cited: 22

23. A unique substrate binding mode discriminates membrane type-1 matrix metalloproteinase from other matrix metalloproteinases
Author(s): KRIDEL, SJ; SAWAI, H; RATNIKOV, BI; et al.
Source: JOURNAL OF BIOLOGICAL CHEMISTRY Volume: 277 Issue: 26 Pages: 23788-23793 Published: JUN 28 2002
Times Cited: 45
DOI: 10.1074/jbc.M111574200

24. A unique substrate recognition profile for matrix metalloproteinase-2
Author(s): CHEN, EI; KRIDEL, SJ; HOWARD, EW; et al.
Source: JOURNAL OF BIOLOGICAL CHEMISTRY Volume: 277 Issue: 6 Pages: 4485-4491 Published: FEB 8 2002
Times Cited: 56
DOI: 10.1074/jbc.M109469200

25. Cloning and characterization of glucose transporter 11, a novel sugar transporter that is alternatively spliced in various tissues
Author(s): WU, XH; LI, WZ; SHARMA, V; et al.
Source: MOLECULAR GENETICS AND METABOLISM Volume: 76 Issue: 1 Pages: 37-45 Published: MAY 2002
Times Cited: 20

26. Cysteine regulation of protein function - as exemplified by NMDA-receptor modulation
Author(s): LIPTON, SA; CHOI, YB; TAKAHASHI, H; et al.
Source: TRENDS IN NEUROSCIENCES Volume: 25 Issue: 9 Pages: 474-480 Published: SEP 2002
Times Cited: 130

27. Discovering new genes with advanced homology detection
Author(s): LI, WZ; GODZIK, A
Source: TRENDS IN BIOTECHNOLOGY Volume: 20 Issue: 8 Pages: 315-316 Published: AUG 2002
Times Cited: 5

28. In search for more accurate alignments in the twilight zone
Author(s): JAROSZEWSKI, L; LI, WZ; GODZIK, A
Source: PROTEIN SCIENCE Volume: 11 Issue: 7 Pages: 1702-1713 Published: JUL 2002
Times Cited: 60
DOI: 10.1110/ps.4820102

29. Sequence clustering strategies improve remote homology recognitions while reducing search times
Author(s): LI, WZ; JAROSZEWSKI, L; GODZIK, A
Source: PROTEIN ENGINEERING Volume: 15 Issue: 8 Pages: 643-649 Published: AUG 2002
Times Cited: 34

30. Tolerating some redundancy significantly speeds up clustering of large protein databases
Author(s): LI, WZ; JAROSZEWSKI, L; GODZIK, A
Source: BIOINFORMATICS Volume: 18 Issue: 1 Pages: 77-82 Published: JAN 2002
Times Cited: 111

31. Clustering of highly homologous sequences to reduce the size of large protein databases
Author(s): LI, WZ; JAROSZEWSKI, L; GODZIK, A
Source: BIOINFORMATICS Volume: 17 Issue: 3 Pages: 282-283 Published: MAR 2001
Times Cited: 271

32. Modeling the third loop of short-chain snake venom neurotoxins: Roles of the short-range and long-range interactions
Author(s): LIU, ZJ; LI, WZ; ZHANG, HY; et al.
Source: PROTEINS-STRUCTURE FUNCTION AND GENETICS Volume: 42 Issue: 1 Pages: 6-16 Published: JAN 1 2001
Times Cited: 3

33. Calculation of protein surface loops using Monte-Carlo simulated annealing simulation
Author(s): LIU, ZJ; MAO, FL; LI, WZ; et al.
Source: JOURNAL OF MOLECULAR MODELING Volume: 6 Issue: 1 Pages: 1-8 Published: 2000
Times Cited: 47

34. Comparison of sequence profiles. Strategies for structural predictions using sequence information
Author(s): RYCHLEWSKI, L; JAROSZEWSKI, L; LI, WZ; et al.
Source: PROTEIN SCIENCE Volume: 9 Issue: 2 Pages: 232-241 Published: FEB 2000
Times Cited: 352

35. Conformational changes accompanying with the binding of protein and ligand
Author(s): LIU, ZJ; JIANG, L; LI, WZ; et al.
Source: ACTA CHIMICA SINICA Volume: 58 Issue: 7 Pages: 772-776 Published: 2000
Times Cited: 0

36. Construction of protein binding sites in scaffold structures
Author(s): LIANG, SD; LIU, ZJ; LI, WZ; et al.
Source: BIOPOLYMERS Volume: 54 Issue: 7 Pages: 515-523 Published: DEC 2000
Times Cited: 14

37. Grafting of protein-protein interaction epitope
Author(s): LIANG, SD; LI, WZ; XIAO, L; et al.
Source: JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS Volume: 17 Issue: 5 Pages: 821-828 Published: APR 2000
Times Cited: 6

38. Saturated BLAST: an automated multiple intermediate sequence search used to detect distant homology
Author(s): LI, WZ; PIO, F; PAWLOWSKI, K; et al.
Source: BIOINFORMATICS Volume: 16 Issue: 12 Pages: 1105-1110 Published: DEC 2000
Times Cited: 34

39. A quantum and docking study of substituted deoxyuridines
Author(s): SUN, M; LI, WZ; YU, M; et al.
Source: ACTA PHYSICO-CHIMICA SINICA Volume: 15 Issue: 9 Pages: 834-837 Published: SEP 1999
Times Cited: 0

40. Exploring the conformational diversity of loops on conserved frameworks
Author(s): LI, WZ; LIANG, S; WANG, RX; et al.
Source: PROTEIN ENGINEERING Volume: 12 Issue: 12 Pages: 1075-1086 Published: DEC 1999
Times Cited: 12

41. Progress of bioinformatics database services
Author(s): LI, WZ; WANG, RX; LIN, DW; et al.
Source: PROGRESS IN BIOCHEMISTRY AND BIOPHYSICS Volume: 26 Issue: 1 Pages: 22-26 Published: FEB 1999
Times Cited: 1

42. Protein loops on structurally similar scaffolds: Database and conformational analysis
Author(s): LI, WZ; LIU, ZJ; LAI, LH
Source: BIOPOLYMERS Volume: 49 Issue: 6 Pages: 481-495 Published: MAY 1999
Times Cited: 21

43. Rational screening in combinatorial peptide libraries of protein functional loop
Author(s): LI, WZ; LIU, ZJ; LIANG, SD; et al.
Source: CHINESE SCIENCE BULLETIN Volume: 44 Issue: 23 Pages: 2150-2154 Published: DEC 1999
Times Cited: 0

44. Estimating binding affinities for enzyme-ligand complexes
Author(s): Wang, R. X.; Li, W. Z.; Lai, L. H.; et al.
Source: Acta Physico-Chimica Sinica Volume: 14 Issue: 9 Pages: 826-832 Published: 1998
Times Cited: 1

45. Solvation interaction and stability of modified superoxide dismutase
Author(s): Li, W. Z.; Miao, F. M.
Source: Acta Physico-Chimica Sinica Volume: 14 Issue: 4 Pages: 289-292 Published: 1998
Times Cited: 0

46. 1,4,10,13-tetrathia-7,16-diazacycloocta-decanenickel(II) nitrate hydrate
Author(s): LI, WZ; WANG, JL; MIAO, XS; et al.
Source: ACTA CRYSTALLOGRAPHICA SECTION C-CRYSTAL STRUCTURE COMMUNICATIONS Volume: 52 Pages: 555-557 Published: 1996
Times Cited: 2

47. Electrostatics and stability of modified copper, zinc superoxide dismutase
Author(s): Li, W. Z.; Miao, F. M.
Source: Progress in Biochemistry and Biophysics Volume: 23 Issue: 6 Pages: 537-541 Published: 1996
Times Cited: 0

48. DIMETHYL [ALPHA(BENZYLAMINO)-P-CHLORO-BENZYL]PHOSPHONATE
Author(s): LIU, XL; ZHOU, Y; LI, WZ; et al.
Source: ACTA CRYSTALLOGRAPHICA SECTION C-CRYSTAL STRUCTURE COMMUNICATIONS Volume: 51 Pages: 2350-2352 Published: NOV 15 1995
Times Cited: 6