User:Wanjun Gu

Contact Info

Wanjun Gu (an artistic interpretation)

• Wanjun Gu
• Research Center of Learning Sciences
• Southeast University
• Sipailou #2
• Nanjing, Jiangsu, China.
• Email: Wanjun.Gu@Gmail.com
• Email me through OpenWetWare

Education

• 2006-2008, PostDoc, University of Colorado Denver @[Pollock Lab]http://www.evolutionarygenomics.com
• 2004-2006, PostDoc, Louisiana State University @[Pollock Lab]http://www.evolutionarygenomics.com
• 2001-2004, PhD, Southeast University
• 1998-2001, MS, Southeast University
• 1994-1998, BS, Southeast University

Research interests

1. Computational Biology
2. Evolutionary Biology
3. Molecular Evolution
4. Next Generation Sequencing

Publications

1. Gu W, Xu Y, Xie X, Wang T, Ko JH, and Zhou T. The role of RNA structure at 5' untranslated region in microRNA-mediated gene regulation. RNA. 2014 Sep;20(9):1369-75. DOI:10.1261/rna.044792.114 |
2. Gu W, Li M, Xu Y, Wang T, Ko JH, and Zhou T. The impact of RNA structure on coding sequence evolution in both bacteria and eukaryotes. BMC Evol Biol. 2014 Apr 23;14:87. DOI:10.1186/1471-2148-14-87 |
3. Ko JH, Gu W, Lim I, Bang H, Ko EA, and Zhou T. Ion channel gene expression in lung adenocarcinoma: potential role in prognosis and diagnosis. PLoS One. 2014;9(1):e86569. DOI:10.1371/journal.pone.0086569 |
4. Castoe TA, de Koning AP, Hall KT, Card DC, Schield DR, Fujita MK, Ruggiero RP, Degner JF, Daza JM, Gu W, Reyes-Velasco J, Shaney KJ, Castoe JM, Fox SE, Poole AW, Polanco D, Dobry J, Vandewege MW, Li Q, Schott RK, Kapusta A, Minx P, Feschotte C, Uetz P, Ray DA, Hoffmann FG, Bogden R, Smith EN, Chang BS, Vonk FJ, Casewell NR, Henkel CV, Richardson MK, Mackessy SP, Bronikowski AM, Yandell M, Warren WC, Secor SM, and Pollock DD. The Burmese python genome reveals the molecular basis for extreme adaptation in snakes. Proc Natl Acad Sci U S A. 2013 Dec 17;110(51):20645-50. DOI:10.1073/pnas.1314475110 |
5. Ko JH, Ko EA, Gu W, Lim I, Bang H, and Zhou T. Expression profiling of ion channel genes predicts clinical outcome in breast cancer. Mol Cancer. 2013 Sep 22;12(1):106. DOI:10.1186/1476-4598-12-106 |
6. Gu W, Wang X, Zhai C, Zhou T, and Xie X. Biological basis of miRNA action when their targets are located in human protein coding region. PLoS One. 2013;8(5):e63403. DOI:10.1371/journal.pone.0063403 |
7. Zhou T, Ko EA, Gu W, Lim I, Bang H, and Ko JH. Non-silent story on synonymous sites in voltage-gated ion channel genes. PLoS One. 2012;7(10):e48541. DOI:10.1371/journal.pone.0048541 |
8. Gu W, Zhai C, Wang X, Xie X, Parinandi G, and Zhou T. Translation Efficiency in Upstream Region of microRNA Targets in Arabidopsis thaliana. Evol Bioinform Online. 2012;8:565-74. DOI:10.4137/EBO.S10362 |
9. de Koning AP, Gu W, Castoe TA, and Pollock DD. Phylogenetics, likelihood, evolution and complexity. Bioinformatics. 2012 Nov 15;28(22):2989-90. DOI:10.1093/bioinformatics/bts555 |
10. Gu W, Wang X, Zhai C, Xie X, and Zhou T. Selection on synonymous sites for increased accessibility around miRNA binding sites in plants. Mol Biol Evol. 2012 Oct;29(10):3037-44. DOI:10.1093/molbev/mss109 |
11. de Koning AP, Gu W, Castoe TA, Batzer MA, and Pollock DD. Repetitive elements may comprise over two-thirds of the human genome. PLoS Genet. 2011 Dec;7(12):e1002384. DOI:10.1371/journal.pgen.1002384 |
12. Castoe TA, de Koning JA, Hall KT, Yokoyama KD, Gu W, Smith EN, Feschotte C, Uetz P, Ray DA, Dobry J, Bogden R, Mackessy SP, Bronikowski AM, Warren WC, Secor SM, and Pollock DD. Sequencing the genome of the Burmese python (Python molurus bivittatus) as a model for studying extreme adaptations in snakes. Genome Biol. 2011 Jul 28;12(7):406. DOI:10.1186/gb-2011-12-7-406 |
13. Guo L, Yang Q, Lu J, Li H, Ge Q, Gu W, Bai Y, and Lu Z. A comprehensive survey of miRNA repertoire and 3' addition events in the placentas of patients with pre-eclampsia from high-throughput sequencing. PLoS One. 2011;6(6):e21072. DOI:10.1371/journal.pone.0021072 |
14. Guo L, Liang T, Gu W, Xu Y, Bai Y, and Lu Z. Cross-mapping events in miRNAs reveal potential miRNA-mimics and evolutionary implications. PLoS One. 2011;6(5):e20517. DOI:10.1371/journal.pone.0020517 |
15. Guo L, Li H, Lu J, Yang Q, Ge Q, Gu W, Bai Y, and Lu Z. Tracking miRNA precursor metabolic products and processing sites through completely analyzing high-throughput sequencing data. Mol Biol Rep. 2012 Feb;39(2):2031-8. DOI:10.1007/s11033-011-0950-8 |
16. Castoe TA, Hall KT, Guibotsy Mboulas ML, Gu W, de Koning AP, Fox SE, Poole AW, Vemulapalli V, Daza JM, Mockler T, Smith EN, Feschotte C, and Pollock DD. Discovery of highly divergent repeat landscapes in snake genomes using high-throughput sequencing. Genome Biol Evol. 2011;3:641-53. DOI:10.1093/gbe/evr043 |
17. Warren WC, Clayton DF, Ellegren H, Arnold AP, Hillier LW, Künstner A, Searle S, White S, Vilella AJ, Fairley S, Heger A, Kong L, Ponting CP, Jarvis ED, Mello CV, Minx P, Lovell P, Velho TA, Ferris M, Balakrishnan CN, Sinha S, Blatti C, London SE, Li Y, Lin YC, George J, Sweedler J, Southey B, Gunaratne P, Watson M, Nam K, Backström N, Smeds L, Nabholz B, Itoh Y, Whitney O, Pfenning AR, Howard J, Völker M, Skinner BM, Griffin DK, Ye L, McLaren WM, Flicek P, Quesada V, Velasco G, Lopez-Otin C, Puente XS, Olender T, Lancet D, Smit AF, Hubley R, Konkel MK, Walker JA, Batzer MA, Gu W, Pollock DD, Chen L, Cheng Z, Eichler EE, Stapley J, Slate J, Ekblom R, Birkhead T, Burke T, Burt D, Scharff C, Adam I, Richard H, Sultan M, Soldatov A, Lehrach H, Edwards SV, Yang SP, Li X, Graves T, Fulton L, Nelson J, Chinwalla A, Hou S, Mardis ER, and Wilson RK. The genome of a songbird. Nature. 2010 Apr 1;464(7289):757-62. DOI:10.1038/nature08819 |
18. Zhou T, Gu W, and Wilke CO. Detecting positive and purifying selection at synonymous sites in yeast and worm. Mol Biol Evol. 2010 Aug;27(8):1912-22. DOI:10.1093/molbev/msq077 |
19. Castoe TA, Poole AW, Gu W, Jason de Koning AP, Daza JM, Smith EN, and Pollock DD. Rapid identification of thousands of copperhead snake (Agkistrodon contortrix) microsatellite loci from modest amounts of 454 shotgun genome sequence. Mol Ecol Resour. 2010 Mar;10(2):341-7. DOI:10.1111/j.1755-0998.2009.02750.x |
20. Gu W, Zhou T, and Wilke CO. A universal trend of reduced mRNA stability near the translation-initiation site in prokaryotes and eukaryotes. PLoS Comput Biol. 2010 Feb 5;6(2):e1000664. DOI:10.1371/journal.pcbi.1000664 |
21. Li R, Fan W, Tian G, Zhu H, He L, Cai J, Huang Q, Cai Q, Li B, Bai Y, Zhang Z, Zhang Y, Wang W, Li J, Wei F, Li H, Jian M, Li J, Zhang Z, Nielsen R, Li D, Gu W, Yang Z, Xuan Z, Ryder OA, Leung FC, Zhou Y, Cao J, Sun X, Fu Y, Fang X, Guo X, Wang B, Hou R, Shen F, Mu B, Ni P, Lin R, Qian W, Wang G, Yu C, Nie W, Wang J, Wu Z, Liang H, Min J, Wu Q, Cheng S, Ruan J, Wang M, Shi Z, Wen M, Liu B, Ren X, Zheng H, Dong D, Cook K, Shan G, Zhang H, Kosiol C, Xie X, Lu Z, Zheng H, Li Y, Steiner CC, Lam TT, Lin S, Zhang Q, Li G, Tian J, Gong T, Liu H, Zhang D, Fang L, Ye C, Zhang J, Hu W, Xu A, Ren Y, Zhang G, Bruford MW, Li Q, Ma L, Guo Y, An N, Hu Y, Zheng Y, Shi Y, Li Z, Liu Q, Chen Y, Zhao J, Qu N, Zhao S, Tian F, Wang X, Wang H, Xu L, Liu X, Vinar T, Wang Y, Lam TW, Yiu SM, Liu S, Zhang H, Li D, Huang Y, Wang X, Yang G, Jiang Z, Wang J, Qin N, Li L, Li J, Bolund L, Kristiansen K, Wong GK, Olson M, Zhang X, Li S, Yang H, Wang J, and Wang J. The sequence and de novo assembly of the giant panda genome. Nature. 2010 Jan 21;463(7279):311-7. DOI:10.1038/nature08696 |
22. de Koning AP, Gu W, and Pollock DD. Rapid likelihood analysis on large phylogenies using partial sampling of substitution histories. Mol Biol Evol. 2010 Feb;27(2):249-65. DOI:10.1093/molbev/msp228 |
23. Castoe TA, de Koning AP, Kim HM, Gu W, Noonan BP, Naylor G, Jiang ZJ, Parkinson CL, and Pollock DD. Evidence for an ancient adaptive episode of convergent molecular evolution. Proc Natl Acad Sci U S A. 2009 Jun 2;106(22):8986-91. DOI:10.1073/pnas.0900233106 |
24. Gu W, Castoe TA, Hedges DJ, Batzer MA, and Pollock DD. Identification of repeat structure in large genomes using repeat probability clouds. Anal Biochem. 2008 Sep 1;380(1):77-83. DOI:10.1016/j.ab.2008.05.015 |
25. Castoe TA, Jiang ZJ, Gu W, Wang ZO, and Pollock DD. Adaptive evolution and functional redesign of core metabolic proteins in snakes. PLoS One. 2008 May 21;3(5):e2201. DOI:10.1371/journal.pone.0002201 |
26. Thai V, Renesto P, Fowler CA, Brown DJ, Davis T, Gu W, Pollock DD, Kern D, Raoult D, and Eisenmesser EZ. Structural, biochemical, and in vivo characterization of the first virally encoded cyclophilin from the Mimivirus. J Mol Biol. 2008 Apr 18;378(1):71-86. DOI:10.1016/j.jmb.2007.08.051 |
27. Mikkelsen TS, Wakefield MJ, Aken B, Amemiya CT, Chang JL, Duke S, Garber M, Gentles AJ, Goodstadt L, Heger A, Jurka J, Kamal M, Mauceli E, Searle SM, Sharpe T, Baker ML, Batzer MA, Benos PV, Belov K, Clamp M, Cook A, Cuff J, Das R, Davidow L, Deakin JE, Fazzari MJ, Glass JL, Grabherr M, Greally JM, Gu W, Hore TA, Huttley GA, Kleber M, Jirtle RL, Koina E, Lee JT, Mahony S, Marra MA, Miller RD, Nicholls RD, Oda M, Papenfuss AT, Parra ZE, Pollock DD, Ray DA, Schein JE, Speed TP, Thompson K, VandeBerg JL, Wade CM, Walker JA, Waters PD, Webber C, Weidman JR, Xie X, Zody MC, Broad Institute Genome Sequencing Platform, Broad Institute Whole Genome Assembly Team, Graves JA, Ponting CP, Breen M, Samollow PB, Lander ES, and Lindblad-Toh K. Genome of the marsupial Monodelphis domestica reveals innovation in non-coding sequences. Nature. 2007 May 10;447(7141):167-77. DOI:10.1038/nature05805 |
28. Gentles AJ, Wakefield MJ, Kohany O, Gu W, Batzer MA, Pollock DD, and Jurka J. Evolutionary dynamics of transposable elements in the short-tailed opossum Monodelphis domestica. Genome Res. 2007 Jul;17(7):992-1004. DOI:10.1101/gr.6070707 |
29. Gu W, Ray DA, Walker JA, Barnes EW, Gentles AJ, Samollow PB, Jurka J, Batzer MA, and Pollock DD. SINEs, evolution and genome structure in the opossum. Gene. 2007 Jul 1;396(1):46-58. DOI:10.1016/j.gene.2007.02.028 |
30. Zhou T, Gu W, Ma J, Sun X, and Lu Z. Analysis of synonymous codon usage in H5N1 virus and other influenza A viruses. Biosystems. 2005 Jul;81(1):77-86. DOI:10.1016/j.biosystems.2005.03.002 |
31. Gu W, Zhou T, Ma J, Sun X, and Lu Z. Folding type specific secondary structure propensities of synonymous codons. IEEE Trans Nanobioscience. 2003 Sep;2(3):150-7. DOI:10.1109/tnb.2003.817024 |
32. Gu W, Zhou T, Ma J, Sun X, and Lu Z. Analysis of synonymous codon usage in SARS Coronavirus and other viruses in the Nidovirales. Virus Res. 2004 May;101(2):155-61. DOI:10.1016/j.virusres.2004.01.006 |
33. Gu W, Zhou T, Ma J, Sun X, and Lu Z. The relationship between synonymous codon usage and protein structure in Escherichia coli and Homo sapiens. Biosystems. 2004 Feb;73(2):89-97. DOI:10.1016/j.biosystems.2003.10.001 |
34. Ma J, Zhou T, Gu W, Sun X, and Lu Z. Cluster analysis of the codon use frequency of MHC genes from different species. Biosystems. 2002 Mar-May;65(2-3):199-207. DOI:10.1016/s0303-2647(02)00016-3 |

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