User:SMian/Selected publications

1. Spyres, L., Hedge, V., Wang, M., Mian, I.S. and Deutsch, W.A. The high affinity of human ribosomal protein S3 to 7,8-dihydro-8-oxoguanine is abrogated by a single amino acid change, DNA Repair, In press (2006)

2. Huang S. et al, The spectrum of WRN mutations in Werner Syndrome patients. Human Mutation, In press (2006)

3. Blei DM, Franks K, Jordan MI and Mian IS. Statistical modeling of biomedical corpora: mining the Caenorhabditis Genetic Center Bibliography for genes related to aging, BMC Bioinformatics, In press (2006)

4. Semeiks JR, Rizki A, Bissell MJ, and Mian IS. Ensemble attribute profile clustering: discovering and characterizing groups of genes with similar patterns of biological features. BMC Bioinformatics. 2006 Mar 16;7:147. DOI:10.1186/1471-2105-7-147 |
5. Patil CK, Mian IS, and Campisi J. The thorny path linking cellular senescence to organismal aging. Mech Ageing Dev. 2005 Oct;126(10):1040-5. DOI:10.1016/j.mad.2005.08.001 |
6. Wu W, Xing EP, Myers C, Mian IS, and Bissell MJ. Evaluation of normalization methods for cDNA microarray data by k-NN classification. BMC Bioinformatics. 2005 Jul 26;6:191. DOI:10.1186/1471-2105-6-191 |
7. Reed JA, Lin Q, Chen D, Mian IS, and Medrano EE. SKI pathways inducing progression of human melanoma. Cancer Metastasis Rev. 2005 Jun;24(2):265-72. DOI:10.1007/s10555-005-1576-x |
8. Nakayama Y, Mian IS, Kohwi-Shigematsu T, and Ogawa T. A nuclear targeting determinant for SATB1, a genome organizer in the T cell lineage. Cell Cycle. 2005 Aug;4(8):1099-106.
9. Semeiks JR, Grate LR, and Mian IS. Text-based analysis of genes, proteins, aging, and cancer. Mech Ageing Dev. 2005 Jan;126(1):193-208. DOI:10.1016/j.mad.2004.09.028 |
10. Bhattacharyya C, Grate LR, Jordan MI, El Ghaoui L, and Mian IS. Robust sparse hyperplane classifiers: application to uncertain molecular profiling data. J Comput Biol. 2004;11(6):1073-89. DOI:10.1089/cmb.2004.11.1073 |
11. Abad PC, Mian IS, Plachot C, Nelpurackal A, Bator-Kelly C, and Lelièvre SA. The C terminus of the nuclear protein NuMA: phylogenetic distribution and structure. Protein Sci. 2004 Oct;13(10):2573-7. DOI:10.1110/ps.04906804 |

12. Semeiks JR, Grate LR and Mian IS. Networks of genetic loci and the scientific literature. International Conference on Complex Systems (ICCS) (2004) PDF

13. Loguinov AV, Mian IS, and Vulpe CD. Exploratory differential gene expression analysis in microarray experiments with no or limited replication. Genome Biol. 2004;5(3):R18. DOI:10.1186/gb-2004-5-3-r18 |

14. Chen D, Lin Q, Mian IS, Reed J and Medrano EE. The multiple roles of the oncogenic protein SKI in human malignant melanoma. In "From Melanocytes to Malignant Melanoma". Eds. Hearing V and Leong S. Human Press (2004)

15. Bissell MJ, Rizki A, and Mian IS. Tissue architecture: the ultimate regulator of breast epithelial function. Curr Opin Cell Biol. 2003 Dec;15(6):753-62. DOI:10.1016/j.ceb.2003.10.016 |
16. Lue NF, Lin YC, and Mian IS. A conserved telomerase motif within the catalytic domain of telomerase reverse transcriptase is specifically required for repeat addition processivity. Mol Cell Biol. 2003 Dec;23(23):8440-9. DOI:10.1128/MCB.23.23.8440-8449.2003 |
17. Worthey EA, Schnaufer A, Mian IS, Stuart K, and Salavati R. Comparative analysis of editosome proteins in trypanosomatids. Nucleic Acids Res. 2003 Nov 15;31(22):6392-408. DOI:10.1093/nar/gkg870 |
18. Chen L, Lee L, Kudlow BA, Dos Santos HG, Sletvold O, Shafeghati Y, Botha EG, Garg A, Hanson NB, Martin GM, Mian IS, Kennedy BK, and Oshima J. LMNA mutations in atypical Werner's syndrome. Lancet. 2003 Aug 9;362(9382):440-5. DOI:10.1016/S0140-6736(03)14069-X |
19. Grate LR, Bhattacharyya C, Jordan MI, and Mian IS. Integrated analysis of transcript profiling and protein sequence data. Mech Ageing Dev. 2003 Jan;124(1):109-14. DOI:10.1016/s0047-6374(02)00174-4 |
20. Bosoy D, Peng Y, Mian IS, and Lue NF. Conserved N-terminal motifs of telomerase reverse transcriptase required for ribonucleoprotein assembly in vivo. J Biol Chem. 2003 Feb 7;278(6):3882-90. DOI:10.1074/jbc.M210645200 |

21. Bhattacharyya C. Grate LR, Rizki A, Radisky DC, Molina FJ, Jordan MI, Bissell MJ and Mian IS. Simultaneous relevant feature identification and classification in high-dimensional spaces. Signal Processing 83:729-743 (2003)

22. Grate LR, Bhattacharyya C, Jordan MI and Mian IS. Simultaneous relevant feature identification and classification in high-dimensional spaces. Workshop on Algorithms in Bioinformatics (WABI 2002), Springer (2002). PDF

23. Singh SM, Steinberg-Neifach O, Mian IS, and Lue NF. Analysis of telomerase in Candida albicans: potential role in telomere end protection. Eukaryot Cell. 2002 Dec;1(6):967-77. DOI:10.1128/EC.1.6.967-977.2002 |
24. Earl AM, Mohundro MM, Mian IS, and Battista JR. The IrrE protein of Deinococcus radiodurans R1 is a novel regulator of recA expression. J Bacteriol. 2002 Nov;184(22):6216-24. DOI:10.1128/JB.184.22.6216-6224.2002 |
25. Holley WR, Mian IS, Park SJ, Rydberg B, and Chatterjee A. A model for interphase chromosomes and evaluation of radiation-induced aberrations. Radiat Res. 2002 Nov;158(5):568-80. DOI:10.1667/0033-7587(2002)158[0568:amfica]2.0.co;2 |
26. Everly DN Jr, Feng P, Mian IS, and Read GS. mRNA degradation by the virion host shutoff (Vhs) protein of herpes simplex virus: genetic and biochemical evidence that Vhs is a nuclease. J Virol. 2002 Sep;76(17):8560-71. DOI:10.1128/jvi.76.17.8560-8571.2002 |
27. Chekanova JA, Dutko JA, Mian IS, and Belostotsky DA. Arabidopsis thaliana exosome subunit AtRrp4p is a hydrolytic 3'-->5' exonuclease containing S1 and KH RNA-binding domains. Nucleic Acids Res. 2002 Feb 1;30(3):695-700. DOI:10.1093/nar/30.3.695 |
28. Arking DE, Krebsova A, Macek M Sr, Macek M Jr, Arking A, Mian IS, Fried L, Hamosh A, Dey S, McIntosh I, and Dietz HC. Association of human aging with a functional variant of klotho. Proc Natl Acad Sci U S A. 2002 Jan 22;99(2):856-61. DOI:10.1073/pnas.022484299 |
29. Lim CS, Mian IS, Dernburg AF, and Campisi J. C. elegans clk-2, a gene that limits life span, encodes a telomere length regulator similar to yeast telomere binding protein Tel2p. Curr Biol. 2001 Oct 30;11(21):1706-10. DOI:10.1016/s0960-9822(01)00526-7 |

30. Bissell MJ, Mian IS, Radisky D and Turley E. Tissue-specificity: Structural cues allow diverse phenotypes from a constant genotype. In "Origination of Organismal Form: Toward a postgenomic synthesis". Eds Newman SA, Muiller GB. Vienna Series in Theoretical Biology. MIT Press (2001)

31. Peng Y, Mian IS, and Lue NF. Analysis of telomerase processivity: mechanistic similarity to HIV-1 reverse transcriptase and role in telomere maintenance. Mol Cell. 2001 Jun;7(6):1201-11. DOI:10.1016/s1097-2765(01)00268-4 |
32. Galande S, Dickinson LA, Mian IS, Sikorska M, and Kohwi-Shigematsu T. SATB1 cleavage by caspase 6 disrupts PDZ domain-mediated dimerization, causing detachment from chromatin early in T-cell apoptosis. Mol Cell Biol. 2001 Aug;21(16):5591-604. DOI:10.1128/MCB.21.16.5591-5604.2001 |
33. Hegde V, Kelley MR, Xu Y, Mian IS, and Deutsch WA. Conversion of the bifunctional 8-oxoguanine/beta-delta apurinic/apyrimidinic DNA repair activities of Drosophila ribosomal protein S3 into the human S3 monofunctional beta-elimination catalyst through a single amino acid change. J Biol Chem. 2001 Jul 20;276(29):27591-6. DOI:10.1074/jbc.M101213200 |
34. Dance GS, Beemiller P, Yang Y, Mater DV, Mian IS, and Smith HC. Identification of the yeast cytidine deaminase CDD1 as an orphan C-->U RNA editase. Nucleic Acids Res. 2001 Apr 15;29(8):1772-80. DOI:10.1093/nar/29.8.1772 |
35. Chow ML, Moler EJ, and Mian IS. Identifying marker genes in transcription profiling data using a mixture of feature relevance experts. Physiol Genomics. 2001 Mar 8;5(2):99-111. DOI:10.1152/physiolgenomics.2001.5.2.99 |
36. Bengtsson H, Calder B, Mian IS, Callow M, Rubin E, and Speed TP. Identifying differentially expressed genes in cDNA microarray experiments authors. Sci Aging Knowledge Environ. 2001 Dec 19;2001(12):vp8. DOI:10.1126/sageke.2001.12.vp8 |
37. Moler EJ, Radisky DC, and Mian IS. Integrating naive Bayes models and external knowledge to examine copper and iron homeostasis in S. cerevisiae. Physiol Genomics. 2000 Dec 18;4(2):127-135. DOI:10.1152/physiolgenomics.2000.4.2.127 |
38. Mian IS and Dubchak I. Representing and reasoning about protein families using generative and discriminative methods. J Comput Biol. 2000;7(6):849-62. DOI:10.1089/10665270050514972 |
39. Moler EJ, Chow ML, and Mian IS. Analysis of molecular profile data using generative and discriminative methods. Physiol Genomics. 2000 Dec 18;4(2):109-126. DOI:10.1152/physiolgenomics.2000.4.2.109 |
40. Xia J, Peng Y, Mian IS, and Lue NF. Identification of functionally important domains in the N-terminal region of telomerase reverse transcriptase. Mol Cell Biol. 2000 Jul;20(14):5196-207. DOI:10.1128/MCB.20.14.5196-5207.2000 |
41. Chen HM, Schmeichel KL, Mian IS, Lelièvre S, Petersen OW, and Bissell MJ. AZU-1: a candidate breast tumor suppressor and biomarker for tumor progression. Mol Biol Cell. 2000 Apr;11(4):1357-67. DOI:10.1091/mbc.11.4.1357 |
42. Gross EA, Li GR, Lin ZY, Ruuska SE, Boatright JH, Mian IS, and Nickerson JM. Prediction of structural and functional relationships of Repeat 1 of human interphotoreceptor retinoid-binding protein (IRBP) with other proteins. Mol Vis. 2000 Apr 7;6:30-9.
42. Gross EA, Li GR, Ruuska SE, Boatright JH, Mian IS, and Nickerson JM. Effects of dispersed point substitutions in Repeat 1 of human interphotoreceptor retinoid binding protein (IRBP). Mol Vis. 2000 Apr 7;6:40-50.

43. Murphy, K and Mian, S. Modelling Gene Expression Data using Dynamic Bayesian Networks, Technical Report Department of Computer Science, University of California Berkeley (1999)

44. Rydberg B, Holley WR, Mian IS, and Chatterjee A. Chromatin conformation in living cells: support for a zig-zag model of the 30 nm chromatin fiber. J Mol Biol. 1998 Nov 20;284(1):71-84. DOI:10.1006/jmbi.1998.2150 |

45. Holley WR, Chatterjee A, Mian IS, and Rydberg B. Theoretical modeling of radiation effects. In "Proceedings Theoretical modeling of radiation effects". Eds Sharan RN, Forschungszentrum Julich GmbH (1998)

46. Huang S, Li B, Gray MD, Oshima J, Mian IS, and Campisi J. The premature ageing syndrome protein, WRN, is a 3'-->5' exonuclease. Nat Genet. 1998 Oct;20(2):114-6. DOI:10.1038/2410 |
47. Mian IS and Moser MJ. The Fanconi anemia complementation group A protein contains a peroxidase domain. Mol Genet Metab. 1998 Mar;63(3):230-4. DOI:10.1006/mgme.1997.2652 |
48. Mian IS. Sequence, structural, functional, and phylogenetic analyses of three glycosidase families. Blood Cells Mol Dis. 1998 Jun;24(2):83-100. DOI:10.1006/bcmd.1998.9998 |
49. Mian IS, Moser MJ, Holley WR, and Chatterjee A. Statistical modelling and phylogenetic analysis of a deaminase domain. J Comput Biol. 1998 Spring;5(1):57-72. DOI:10.1089/cmb.1998.5.57 |
50. Moser MJ, Holley WR, Chatterjee A, and Mian IS. The proofreading domain of Escherichia coli DNA polymerase I and other DNA and/or RNA exonuclease domains. Nucleic Acids Res. 1997 Dec 15;25(24):5110-8. DOI:10.1093/nar/25.24.5110 |
51. Dalgaard JZ, Klar AJ, Moser MJ, Holley WR, Chatterjee A, and Mian IS. Statistical modeling and analysis of the LAGLIDADG family of site-specific endonucleases and identification of an intein that encodes a site-specific endonuclease of the HNH family. Nucleic Acids Res. 1997 Nov 15;25(22):4626-38. DOI:10.1093/nar/25.22.4626 |
52. Martin GM and Mian IS. Ageing. New mice for old questions. Nature. 1997 Nov 6;390(6655):18-9. DOI:10.1038/36210 |
53. Mian IS. Comparative sequence analysis of ribonucleases HII, III, II PH and D. Nucleic Acids Res. 1997 Aug 15;25(16):3187-95. DOI:10.1093/nar/25.16.3187 |
54. Herbert A, Alfken J, Kim YG, Mian IS, Nishikura K, and Rich A. A Z-DNA binding domain present in the human editing enzyme, double-stranded RNA adenosine deaminase. Proc Natl Acad Sci U S A. 1997 Aug 5;94(16):8421-6. DOI:10.1073/pnas.94.16.8421 |
55. Dalgaard JZ, Moser MJ, Hughey R, and Mian IS. Statistical modeling, phylogenetic analysis and structure prediction of a protein splicing domain common to inteins and hedgehog proteins. J Comput Biol. 1997 Summer;4(2):193-214. DOI:10.1089/cmb.1997.4.193 |
56. Sjölander K, Karplus K, Brown M, Hughey R, Krogh A, Mian IS, and Haussler D. Dirichlet mixtures: a method for improved detection of weak but significant protein sequence homology. Comput Appl Biosci. 1996 Aug;12(4):327-45. DOI:10.1093/bioinformatics/12.4.327 |
57. Sakakibara Y, Brown M, Hughey R, Mian IS, Sjölander K, Underwood RC, and Haussler D. Stochastic context-free grammars for tRNA modeling. Nucleic Acids Res. 1994 Nov 25;22(23):5112-20. DOI:10.1093/nar/22.23.5112 |
58. Krogh A, Mian IS, and Haussler D. A hidden Markov model that finds genes in E. coli DNA. Nucleic Acids Res. 1994 Nov 11;22(22):4768-78. DOI:10.1093/nar/22.22.4768 |
59. Krogh A, Brown M, Mian IS, Sjölander K, and Haussler D. Hidden Markov models in computational biology. Applications to protein modeling. J Mol Biol. 1994 Feb 4;235(5):1501-31. DOI:10.1006/jmbi.1994.1104 |
60. Grate L, Herbster M, Hughey R, Haussler D, Mian IS, and Noller H. RNA modeling using Gibbs sampling and stochastic context free grammars. Proc Int Conf Intell Syst Mol Biol. 1994;2:138-46.
61. Brown M, Hughey R, Krogh A, Mian IS, Sjölander K, and Haussler D. Using Dirichlet mixture priors to derive hidden Markov models for protein families. Proc Int Conf Intell Syst Mol Biol. 1993;1:47-55.
62. Mian IS. Sequence similarities between cell regulation factors, heat shock proteins and RNA helicases. Trends Biochem Sci. 1993 Apr;18(4):125-7.
63. Ellenberger DL, Pieniazek NJ, Mian IS, Eberhard ML, and Lammie PJ. Cloning and characterization of the Wuchereria bancrofti S15 ribosomal protein. Mol Biochem Parasitol. 1992 May;52(1):131-5. DOI:10.1016/0166-6851(92)90043-j |
64. Mian IS, Bradwell AR, and Olson AJ. Structure, function and properties of antibody binding sites. J Mol Biol. 1991 Jan 5;217(1):133-51. DOI:10.1016/0022-2836(91)90617-f |

65. Goodsell DS, Mian IS, Olson AJ. Rendering of volumetric data in molecular systems. J. Molecular Graphics, 7:41-47 (1989)

66. Mian IS and Richards WG. Theoretical binding energies of inhibitors to enzymes. Biochim Biophys Acta. 1986 Mar 7;870(1):177-9. DOI:10.1016/0167-4838(86)90022-1 |