Publication List (by toptic)

List by year; Back to Liang Lab

  • Publications related to retrotransposons and the associated genomic variations in human

    1. Callinan PA*, Wang J*, Herke SW*, Garber RK, Liang P, Batzer MA. Alu retrotransposition-mediated deletion. J Mol Biol 348:791-800, 2005. (*co-first authors). PubMed Abstract, PDF, Supplemental Materials.
    2. Wang J*, Song L*, Gonder MK, Azrak S, Ray DA, Batzer MA, Tishkoff SA, Liang P. Whole genome computational comparative genomics: a fruitful approach for ascertaining Alu insertion polymorphisms. Gene 365:11-20, 2006. PubMed Abstract, , PDF, Supplemental Data (*co-first authors)
    3. Han K*, Sen SK*, Wang J*, Callinan PA, Lee J, Cordaux R, Liang P, Batzer MA. Genomic rearrangements by LINE-1 insertion-mediated deletion in the human and chimpanzee lineages. Nucleic Acids Res 33:4040-4052, 2005. (*co-first authors) PubMed Abstract; Supplemental Data1; Supplemental Data2
    4. Charbonnier F, Baert-Desurmont S, Liang P, Di Fiore F, Martin C, Frerot S, Olschwang S, Wang Q, Buisine MP, Gilbert B, Nilbert M, Lindblom A, Frebourg T. The 5' region of the MSH2 gene involved in hereditary non-polyposis colorectal cancer contains a high density of recombinogenic sequences. Hum Mutat 26:255-261, 2005. PubMed Abstract, PDF
    5. Wang, J.*, L. Song*, D. Grover*, S. Azrak, M. A. Batzer, Liang P. dbRIP: A Highly Integrated Database of Retrotransposon Insertion Polymorphism in Human. Human Mutat 27:323-329,2006. PubMed Abstract; PDF (*co-first authors).
    6. Li L, McVety S, Younan R, Liang P, DuSart D, Gordon P, Hutter P, Hogervorst FB, Chong G, and Foulkes WD. Distinct patterns of Germ-Line Deletions in MLH1 and MSH2 in hereditary non-polyposiscolorectal cancer families: the role of Alu sequences. Human Mutat 27:388, 2006. PubMed Abstract
    7. Sen SK*, Han K, Wang J, Lee J, Wang H, Callinan PA, Dyer M, Cordaux R, Liang P, Batzer MA.Human genomic deletions mediated by recombination between Alu elements. Am J Hum Genet 79:41-53, 2006. PubMed Abstract , PDF
    8. Lee, J, Cordaux R, Han K, Wang J, Hedges DJ, Batzer MA*, Liang P*. Different evolutionary fates of recently integrated human and chimpanzee LI NE-1 retrotransposons. Gene 390:18-27, 2007. PubMed Abstract. (*co-senior authors)
    9. Konkel M*, Wang J*, Liang P, Batzer MA. Identification and characterization of novel polymorphic LINE-1 insertions through comparison of two Human genome sequence assemblies. Gene 390:28-38, 2007. PubMed Abstract (*co-first authors)
    10. Han K, Lee J, Meyer TJ, Wang J, Sen SK, Srikanta D, Liang P, Batzer MA. Chimpanzee-specific structural variation deriv ed from Alu recombination-mediated deletions. PLOS Genetics 3:1939-1949, 2007. Open Access at PLOS Genetics.

  • Publications related to gene/genome annotations & bioinformatics analyses

    1. Jiang Z*, Liang P*, Leng R, Guo Z, Liu Y, Liu X, Bubnic S, Keating A, Murray D, Goss P, Zacksenhaus E. E2F1 and p53 are dispensable, whereas p21Waf1/Cip1 cooperates with Rb to restrict endoreduplication and apoptosis during skeletal myogenesis. Dev Biol 227: 28-41, 2000. (*co-first authors) PubMed Abstract, PDF
    2. Ng WV, Kennedy SP, Mahairas GG, Berquist B, Pan M, Shukla HD, Lasky SR, Baliga NS, Thorsson V, Sbrogna J, Swartzell S, Weir D, Hall J, Dahl TA, Welti R, Goo YA, Leithauser B, Keller K, Cruz R, Danson MJ, Hough DW, Maddocks DG, Jablonski PE, Krebs MP, Angevine CM, Dale H, Isenbarger TA, Peck RF, Pohlschroder M, Spudich JL, Jung KW, Alam M, Freitas T, Hou S, Daniels CJ, Dennis PP, Omer AD, Ebhardt H, Lowe TM, Liang P, Riley M, Hood L, DasSarma S. Genome sequence of a genetically tractable and extremely halophilic archaeon. PNAS 97: 11677-12388, 2000. PubMed Abstract , PDF
    3. Liang P, and M. Riley. Comparative genomics approach for studying ancestral proteins and evolution. Adv Appl Microbiol 50: 39-72, 2001. PubMed Abstract
    4. Liang P, LabedanB, Riley M. Physiological genomics of E. coli protein families. Physiol Genomics 9:15-26, 2002. PubMed Abstract , PDF
    5. Serres M, Gopal S, Nahum LA, Liang P, Gaasterland T, Riley M. A functional update of the Escherichia coli K-12 genome. Genome Biol 2: Research0035.1-7,2002. PubMed Abstract , PDF
    6. Still IH, Vettaikkorumakankauv AK, DiMatteo A, Liang P. Structure-function evolution of the transforming acidic coiled coil genes revealed by analysis of phylogenetically diverse organisms. BMC Evol Biol 4:16, 2004. PubMed Abstract , PDF
    7. Chen Y, Vujcic S, Liang P, Diegelman P, Kramer DL, Porter CL. Genomic identification and biochemical characterization of a second spermidine/spermine n1-acetyltransferase. Biochem J 373:661-667, 2003. PubMed Abstract , PDF
    8. Wang J, Liang P. Digi-Northern digital expression analysis of query genes based on ESTs. Bioinformatics 19:653-654, 2003. PubMed Abstract , PDF
    9. Vujcic S, Liang P, Diegelman P, Kramer DL, Porter CL. Genomic identification and biochemical characterization of the mammalian polyamine oxidase involved in polyamine back-convertion. Biochem J 370:19-28, 2003. PubMed Abstract , PDF
    10. Zhang Q, Zhao B, Li W, Oiso N, Novak EK, Rusiniak ME, Gautam R, Chintala S, O'Brien EP, Zhang Y, Roe BA, Elliott RW, Eicher EM, Liang P, Kratz C, Legius E, Spritz RA, O'Sullivan TN, Copeland NG, Jenkins NA, Swank RT. Ru2 and Ru encode mouse orthologs of the genes mutated in human Hermansky-Pudlak syndromes type 5 and 6. Nature Genet 33:145-153, 2003. PubMed Abstract , PDF
    11. Ghadersohi A, Odunsi K, Winston JS, Lele S, Collins Y, Greco WR, Liang P, Sood AK. Prostate derived Ets transcription factor shows better tumor-association than other cancer-associated molecules. Oncology Reports 11:453-458, 2004. PubMed Abstract
    12. Charbonnier F, Baert-Desurmont S, Liang P, Di Fiore F, Martin C, Frerot S, Olschwang S, Wang Q, Buisine MP, Gilbert B, Nilbert M, Lindblom A, Frebourg T. The 5' region of the MSH2 gene involved in hereditary non-polyposis colorectal cancer contains a high density of recombinogenic sequences. Hum Mutat 2005 Aug 5;26(3):255-261. PubMed Abstract, PDF
    13. Li L, McVety S, Younan R, Liang P, DuSart D, Gordon P, Hutter P, Hogervorst FB, Chong G, and Foulkes WD. Distinct patterns of Germ-Line Deletions in MLH1 and MSH2 in hereditary non-polyposiscolorectal cancer families: the role of Alu sequences. Human Mutat 27:388, 2006. PubMed Abstract
    14. Liang P*, Jones CA*, Bisgrove BW, Song L, Glenn ST, Yost HJ, Gross KW. Genomic characterization and expression analysis of the first non-mammalian renin genes from zebrafish and pufferfish. Physiol Genomics 16:314-322, 2004. (*co-first authors) PubMed Abstract , PDF, Supplemental Materials,
    15. Wu J, Ling X, Pan D, Apontes P, Song L, Liang P, Altieri DC, Beerman T, Li F. Molecular mechanism of inhibition of survivin transcription by the GC-rich sequence-selective DNA binding antitumor agent, hedamycin: evidence of survivin down-regulation associated with drug sensitivity. J Biol Chem 280:9745-9751, 2005. PubMed Abstract, PDF
    16. Chen H, Wang J, Liang P, Karsay-Klein M, James AA, Brazeau D, Yan G.Microarray analysis for identification of Plasmodium-refractoriness candidate genes in mosquitoes. Genome 6:1061-1070, 2004. PubMed Abstract, PDF
    17. Liang P*, Nair JR, Song L, McGuire JJ, Dolnick BJ*. Comparative genomic analysis reveals a novel mitochondrial isoform of human rTS protein and unusual phylogenetic distribution of the rTS gene. BMC Genomics 6:126, 2005 (*co-senior authors) PubMed Abstract, PDF
    18. Laun P, Ramachandran L, Jarolim S, Herker E, Liang P, Wang J, Weinberger W, Burhans DT, Suter B, Madeo F, Burhans WC, Breitenbach M. A comparison of the aging and apoptotic transcriptome of Saccharomyces cerevisiae. FEMS Yeast Res (2005 in press).
    19. Shankar G, Rossi1 MR, McQuaid DE, Conroy JM, Gaile DP, Cowell JK, Nowak NJ, Liang P. 2006. aCGHViewer: a generic visualization tool for aCGH data. Cancer Informatics 2:36-43, 2006.
    20. Li W, He M, Zhou H, Bourne J, Liang P. Mutation Data Integration in Gene-Oriented Files of Hermansky-Pudlak Syndrome Database. Human Mutat (in press) PubMed Abstract.
    21. Ramachandran L, Burhans DT, Laun P, Wang J, Liang P,Weinberger M, Wissing S, Jarolim S, Madeo SB, Breitenbach M, Burhans WC. Evidence for ORC-dependent repression of budding yeast genes induced by starvation and other stresses. FEMS Yeast (in press).
    22. Burhans DT, Ramachandran L, Weinberger M, Wang J, Liang P, Patterton HG, Breitenbach M, Burhans WC. Non-random clustering of stress-related genes during evolution of the S. Cerevisiae Genome. BMC Evolutionary Biology (in press)
    23. Shen L, Zhang C, Wang T, Brooks S, Ford RJ, Lin-Lee YC, Kasianowicz A, Kumar V, Martin L, Liang P, Cowell JC, Ambrus Jr JL. Development of Autoimmunity in Interleukin 14alpha Transgenic Mice. J Immunol 177:5676-5686, 2006. PubMed Abstract
    24. Chattopadhyay S, Tracy E, Liang P, Robledo O, Rose-John S, Baumann H. Interleukin-31 and oncostatin-m mediate distinct signaling reactions and response patterns in lung epithelial cells. J Biol Chem 282:3014-3026, 2007.PubMed Abstract.
    25. Rossetti S, Hoogeveen AT, Liang P, Stanciu C, Spek P, Sacchi N. Epigenetic regulation of novel AML1 targets iden tified by bioinformatic survey of microarray gene expression data. BMC Genomics 8:38, 2007. link to PDF file.
    26. Kim YJ, Ahn JY, Liang P, Ip C, Zhang Y, Park YM. 2007. Human prx1 gene is a target of Nrf2 and is up-regulated by hypoxia/reoxygenation. Cancer Res 67:546-554. PubMed Abstract.
    27. Blickwedeh J, McEvoy S, Wong I, Kousis P, Clements J, Elliott R, Cresswell P, Liang P, Bangia N. Proteasomes and proteasome activat or 200kd (pa200) accumulate on chromatin in response to ionizing radiation. Radiation Res 167: 663-674, 2007. PubMe Abstract
    28. Wu J, Pan D, Song L, Liang P, Yang L, Li F. Molecular mechanism of upregulation of survivin transcription by the AT-rich DNA-binding antitumor agent, Hoechst33342: evidence for survivin involvement in drug resistance. Nuc Acid Res 35:2390-402, 2007. PubMed Abstract
    29. Lo K, Shankar G, Rossi M, Burkhardt T, Liang P, Cowell JK. 2007. Overlay tool for aCGHViewer: an analysis module built for aCGHViewer used to combine different microarray platforms for visualization. Cancer Informatics 3:309-319, 2007.
    30. Glenn ST, Jones CA, Liang P, Kaushik D, Gross KW, Kim HL. Expression profiling of renal tumors by quantitative PCR using frozen and archival tissue. Biotechniques 43:639-647, 2007.
    31. Smiraglia D, Kazhiyur-Mannar R, Oakes C, Wu Y, Liang P, Ansari T, Su J, Rush L, Smith L, Yu L, Liu C, Dai Z, Chen S, Wang S, Costello JF, Ioshikhes I, Dawson D, Hong J, Teitell M, Szafranek A. A Restriction Landmark Genomic Scanning (RLGS) spot identification by second generation virtual RLGS in multiple genomes with multiple enzyme combinations. BMC Genomics 8:446, 2007.
    32. Cotton RGH, Beckmann J, Blumenfeld O, Brookes A, Brown AF, Carrera P, Cox D, den Dunnen JT, Gottlieb B, Greenblatt B, Hilbert P, Lehvaslaiho H, Liang P, Marsh S, Nebert D, Rossetti D, Scriver C, Summar M, Tolan D, Verma I, Vihinen M. Definitions of locus Specific databases and their curation. Human Mutations 29:2-25, 2008.
    33. Kim JH, Bogner PN, Baek SH, Ramnath N, Liang P, Kim HR, Andrews C, Park YM, 2008. Up-regulation of peroxiredoxin 1 in lung cancer and its implicationi as prognostic and therapeutic target. J Clin Can Res 14:2326-2333, 2008.

  • Publications related to small heat shock proteins and tubulins

    1. Clegg JS, Jackson SA, Liang P, MacRae TH. Nuclear-cytoplasmic translocations of protein p26 during aerobic-anoxic transitions in embryos of Artemia franciscana. Exp Cell Res 219:1-7, 1995. PubMed Abstract, PDF
    2. Liang P, Amons R, Clegg JS, MacRae TH. Molecular characterization of a small heat shock/alpha-crystallin protein in encysted Artemia embryos. J Biol Chem 272:19051-19058, 1997. PubMed Abstract; , PDF
    3. Liang P, MacRae TH. Molecular chaperones and the cytoskeleton. J Cell Sci 110: 1431-1440, 1997. PubMed Abstract, PDF, Highly cited (details at JCS).
    4. Liang P, Amons R, MacRae TH, Clegg JS. Purification, structure and in vitro molecular-chaperone activity in vitro of Artemia p26, a small heat shock/alpha-crystallin protein. Eur J Biochem 243: 225-232, 1997. PubMed Abstract
    5. Zheng Y, Roy P, Liang P, MacRae TH. Cloning and sequencing of an alpha-tubulin cDNA from Artemia franciscana: evidence for translational regulation of alpha-tubulin synthesis. Biochim Biophys Acta 1442:419-426, 1998. PubMed Abstract, PDF
    6. MacRae TH, Liang P. Molecular characterization of p26, a cyst-specific, small heat shock/alpha-crystallin protein from Artemia franciscana. Arch Hydrobiol Spec Issues Advanc Limnol 52:393-409, 1998.
    7. Liang P, MacRae TH. The synthesis of a small heat shock/alpha-crystallin protein in Artemia and its relationship to stress tolerance during development. Dev Biol 207:445-456, 1999. PubMed Abstract, PDF
    8. Oulton MM, Amons R, Liang P, MacRae TH. A 49kDA microtubule cross-linking protein from Artemia franciscana is a coenzyme A-transferase. Eur J Biochem 270:4962-4972, 2003. PubMed Abstract , PDF

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    Last modified: Tuesday, 22-Apr-2008 09:12:07 EDT.