Bioinformatics application/database development

Back to Bioinformatics Core

[authors in Bold print are members of the Core and/or Liang lab]

1. Wang J, Liang P. Digi-Northern digital expression analysis of query genes based on ESTs. Bioinformatics 19:653-654, 2003. PubMed Abstract , PDF
2. Wang, J.*, L. Song*, D. Grover*, Azrak S, 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).
3. Li W, He M, Zhou H, Bourne J, Liang P. Mutation Data Integration in Gene-Oriented Files of Hermansky-Pudlak Syndrome Database. Human Mutat 27:402-407,2006. PDF, PubMed Abstract.
4. Shankar G, Rossi MR, McQuaid DE, Conroy JM, Gaile DP, Cowell JK, Nowak NJ, Liang P. 2006. aCGHViewer: a generic visualization tool for aCGH data. Cancer Informatics 2:36-42, 2006, PDF.
5. Lo K, Shankar G, Rossi M, Burkhardt T, Liang P, Cowell JK. Overlay tool for aCGHViewer: an analysis module built for aCGHViewer used to combine different microarray platforms for visualization. Cancer Informatics 3:309-319, 2007.  

 

Bioinformatics data analysis

6. 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
7. 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
8. 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
9. 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
10. 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
11. 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,
12. 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
13. 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
14. 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 5:1262-1271, 2005. PubMed Abstract
15. 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.
16. 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
17. 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
18. 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
19. 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
20. 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)
21. 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
22. 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
23. 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 6:763-776, 2006. PubMed Abstract
24. 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 6:58, 2006. PubMed Abstract
25. 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
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. 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.
28. Rossetti S, Hoogeveen AT, Liang P, Stanciu C, Spek P, Sacchi N. Epigenetic regulation of novel AML1 targets identified by bioinformatic survey of microarray gene expression data. BMC Genomics 8:38, 2007. link to PDF file.
29. Lee, J, Cordaux R, Han K, Wang J, Hedges DJ, Batzer MA*, Liang P*. Different evolutionary fates of recently integrated human and chimpanzee LINE-1 retrotransposons. Gene 390:18-27, 2007. PubMed Abstract. (*co-senior authors)
30. 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
31. 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
32. Blickwedeh J, McEvoy S, Wong I, Kousis P, Clements J, Elliott R, Cresswell P, Liang P, Bangia N. Proteasomes and proteasome activator 200kd (pa200) accumulate on chromatin in response to ionizing radiation. Radiation Res 167: 663-674, 2007. PubMed Abstract

33. 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 43:5:639-647, 2007.

34. 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.

35. Kim JH, Bogner PN, Baek SH, Ramnath N, Liang P, Kim HR, Adrews C, Park YM. 2008. Up-regulation of Peroxiredoxin 1 in Lung Cancer and Its Implication as Prognostic and Therapeutic Target. J Clin Can Res. (in press).

. Back to Bioinformatics Core