I Saira Mian

Summary

Affiliation: Lawrence Berkeley National Laboratory
Country: USA

Publications

  1. pmc MPHASYS: a mouse phenotype analysis system
    R Brent Calder
    Buck Institute for Age Research, Novato, California, USA
    BMC Bioinformatics 8:183. 2007
  2. pmc Statistical modeling of biomedical corpora: mining the Caenorhabditis Genetic Center Bibliography for genes related to life span
    D M Blei
    Computer Science Department, Princeton University, Princeton, New Jersey 08540 USA
    BMC Bioinformatics 7:250. 2006
  3. pmc Ensemble attribute profile clustering: discovering and characterizing groups of genes with similar patterns of biological features
    J R Semeiks
    Life Sciences Division MS 977 225A, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA 94720, USA
    BMC Bioinformatics 7:147. 2006
  4. pmc A linear programming approach for estimating the structure of a sparse linear genetic network from transcript profiling data
    Sahely Bhadra
    Department of Computer Science and Automation, Indian Institute of Science, Bangalore, Karnataka, India
    Algorithms Mol Biol 4:5. 2009
  5. pmc Comparative sequence analysis of ribonucleases HII, III, II PH and D
    I S Mian
    Sinsheimer Laboratories, University of California Santa Cruz, Santa Cruz, CA 95064, USA
    Nucleic Acids Res 25:3187-95. 1997
  6. pmc Taking U out, with two nucleases?
    I Saira Mian
    Life Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720 8265, USA
    BMC Bioinformatics 7:305. 2006
  7. doi request reprint Communication theory and multicellular biology
    I S Mian
    Life Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
    Integr Biol (Camb) 3:350-67. 2011
  8. ncbi request reprint Sequence, structural, functional, and phylogenetic analyses of three glycosidase families
    I S Mian
    Life Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
    Blood Cells Mol Dis 24:83-100. 1998
  9. ncbi request reprint Statistical modelling and phylogenetic analysis of a deaminase domain
    I S Mian
    Life Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
    J Comput Biol 5:57-72. 1998
  10. pmc The proofreading domain of Escherichia coli DNA polymerase I and other DNA and/or RNA exonuclease domains
    M J Moser
    Life Sciences Division Mail Stop 29 100, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA 94720, USA
    Nucleic Acids Res 25:5110-8. 1997

Collaborators

Detail Information

Publications25

  1. pmc MPHASYS: a mouse phenotype analysis system
    R Brent Calder
    Buck Institute for Age Research, Novato, California, USA
    BMC Bioinformatics 8:183. 2007
    ..Additionally, the lack of integrated, standardized ontologies and methodologies for data exchange has inhibited scientific collaboration and discovery...
  2. pmc Statistical modeling of biomedical corpora: mining the Caenorhabditis Genetic Center Bibliography for genes related to life span
    D M Blei
    Computer Science Department, Princeton University, Princeton, New Jersey 08540 USA
    BMC Bioinformatics 7:250. 2006
    ..LDA is a hierarchical Bayesian model which represents a document as a random mixture over latent topics; each topic is characterized by a distribution over words...
  3. pmc Ensemble attribute profile clustering: discovering and characterizing groups of genes with similar patterns of biological features
    J R Semeiks
    Life Sciences Division MS 977 225A, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA 94720, USA
    BMC Bioinformatics 7:147. 2006
    ....
  4. pmc A linear programming approach for estimating the structure of a sparse linear genetic network from transcript profiling data
    Sahely Bhadra
    Department of Computer Science and Automation, Indian Institute of Science, Bangalore, Karnataka, India
    Algorithms Mol Biol 4:5. 2009
    ..The LP-based solutions of the sparse linear regression problem described here may provide a method for learning the structure of transcription factor networks from transcript profiling and transcription factor binding motif data...
  5. pmc Comparative sequence analysis of ribonucleases HII, III, II PH and D
    I S Mian
    Sinsheimer Laboratories, University of California Santa Cruz, Santa Cruz, CA 95064, USA
    Nucleic Acids Res 25:3187-95. 1997
    ..Examination of HMM-generated multiple sequences alignments for each family suggest amino acids that may be important for their structure, substrate binding and/or catalysis...
  6. pmc Taking U out, with two nucleases?
    I Saira Mian
    Life Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720 8265, USA
    BMC Bioinformatics 7:305. 2006
    ..Here, a variety of computational studies were performed to enhance understanding of the structure and function of REX proteins in Trypanosoma and Leishmania species...
  7. doi request reprint Communication theory and multicellular biology
    I S Mian
    Life Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
    Integr Biol (Camb) 3:350-67. 2011
    ....
  8. ncbi request reprint Sequence, structural, functional, and phylogenetic analyses of three glycosidase families
    I S Mian
    Life Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
    Blood Cells Mol Dis 24:83-100. 1998
    ..Similarities in the reactions catalyzed by families 30 and 59 are reflected in the presence of a structurally and functionally related (beta/alpha)8 barrel fold related to that in family 1...
  9. ncbi request reprint Statistical modelling and phylogenetic analysis of a deaminase domain
    I S Mian
    Life Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
    J Comput Biol 5:57-72. 1998
    ..Some bacterial and eucaryotic DM domains form distinct branches in the phylogenetic tree suggesting the existence of common, novel substrates...
  10. pmc The proofreading domain of Escherichia coli DNA polymerase I and other DNA and/or RNA exonuclease domains
    M J Moser
    Life Sciences Division Mail Stop 29 100, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA 94720, USA
    Nucleic Acids Res 25:5110-8. 1997
    ..Examination of a multiple sequence alignment and two three-dimensional structures of proofreading domains has allowed definition of the core sequence, structural and functional elements of this exonuclease domain...
  11. pmc Evaluation of normalization methods for cDNA microarray data by k-NN classification
    Wei Wu
    Life Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
    BMC Bioinformatics 6:191. 2005
    ..However, to date there have been few published systematic evaluations of these techniques for removing variations arising from dye biases in the context of downstream, higher-order analytical tasks such as classification...
  12. ncbi request reprint A nuclear targeting determinant for SATB1, a genome organizer in the T cell lineage
    Yuji Nakayama
    Lawrence Berkeley National Laboratory, University of California, Berkeley, California 94720, USA
    Cell Cycle 4:1099-106. 2005
    ..Our results indicate that SATB1 N-terminal residues 20-40 represent a novel determinant of nuclear targeting...
  13. pmc Tissue architecture: the ultimate regulator of breast epithelial function
    Mina J Bissell
    Department of Cell and Molecular Biology, Life Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
    Curr Opin Cell Biol 15:753-62. 2003
  14. pmc A human breast cell model of preinvasive to invasive transition
    Aylin Rizki
    Life Sciences Division, Ernest Orlando Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
    Cancer Res 68:1378-87. 2008
    ..This model provides a new tool for dissection of mechanisms by which preinvasive breast cells could acquire invasiveness in a metaplastic context...
  15. pmc Exploratory differential gene expression analysis in microarray experiments with no or limited replication
    Alexander V Loguinov
    Department of Nutritional Sciences and Toxicology, University of California at Berkeley, Morgan Hall, Berkeley, CA 94720, USA
    Genome Biol 5:R18. 2004
    ..We demonstrate the improved performance of our approach over existing single-slide methods using public datasets and simulation studies...
  16. ncbi request reprint The thorny path linking cellular senescence to organismal aging
    Christopher K Patil
    Life Sciences Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA 94720, USA
    Mech Ageing Dev 126:1040-5. 2005
  17. ncbi request reprint Integrated analysis of transcript profiling and protein sequence data
    L R Grate
    Life Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
    Mech Ageing Dev 124:109-14. 2003
    ..One family member is a potential biomarker identified recently from a retrospective analysis of transcript profiles for sporadic breast cancer samples from patients with poor and good prognosis, Signal Process. (in press)...
  18. pmc AZU-1: a candidate breast tumor suppressor and biomarker for tumor progression
    H M Chen
    Lawrence Berkeley National Laboratory, Life Sciences Division, Berkeley, California 94720, USA
    Mol Biol Cell 11:1357-67. 2000
    ..These results indicate that AZU-1 is a candidate breast tumor suppressor that may exert its effects by promoting correct tissue morphogenesis...
  19. ncbi request reprint C. elegans clk-2, a gene that limits life span, encodes a telomere length regulator similar to yeast telomere binding protein Tel2p
    C S Lim
    Life Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
    Curr Biol 11:1706-10. 2001
    ..In mammals, telomere length and structure can influence cellular, and possibly organismal, aging. Here, we show that clk-2 encodes a regulator of telomere length in C. elegans...
  20. ncbi request reprint The high binding affinity of human ribosomal protein S3 to 7,8-dihydro-8-oxoguanine is abrogated by a single amino acid change
    Vijay Hegde
    Pennington Biomedical Research Center, Louisiana State University System, Baton Rouge, 70808, USA
    DNA Repair (Amst) 5:810-5. 2006
    ..Overall, the ability of OGG1 to repair 8-oxoG is compromised when hS3 is bound to 8-oxoG sites. Conversely, in the absence of DNA binding, hS3 interacts positively with OGG1 to produce a more robust removal of 8-oxoG residues in DNA...
  21. pmc NuMA influences higher order chromatin organization in human mammary epithelium
    Patricia C Abad
    Department of Basic Medical Sciences and Cancer Center, Purdue University, West Lafayette, IN 47907 2026, USA
    Mol Biol Cell 18:348-61. 2007
    ..These findings suggest that NuMA has a role in mammary epithelial differentiation by influencing the organization of chromatin...
  22. pmc Arabidopsis thaliana exosome subunit AtRrp4p is a hydrolytic 3'-->5' exonuclease containing S1 and KH RNA-binding domains
    Julia A Chekanova
    Department of Biological Sciences, State University of New York at Albany, 1400 Washington Avenue, Albany, NY 12222, USA
    Nucleic Acids Res 30:695-700. 2002
    ..However, only the full-length protein is capable of degrading RNA and interacting with AtRrp41p...
  23. pmc Comparative analysis of editosome proteins in trypanosomatids
    Elizabeth A Worthey
    Seattle Biomedical Research Institute, Seattle, WA 98109, USA
    Nucleic Acids Res 31:6392-408. 2003
    ..These domains are generally conserved within other protein families, but some are found in novel combinations in the editosome proteins...
  24. ncbi request reprint LMNA mutations in atypical Werner's syndrome
    Lishan Chen
    Department of Pathology, University of Washington, Seattle, WA 98195 7470, USA
    Lancet 362:440-5. 2003
    ..Some features of this disorder are also present in laminopathies caused by mutant LMNA encoding nuclear lamin A/C. Because of this similarity, we sequenced LMNA in individuals with atypical Werner's syndrome (wild-type WRN)...
  25. pmc The C terminus of the nuclear protein NuMA: phylogenetic distribution and structure
    Patricia C Abad
    Department of Basic Medical Sciences, Purdue University, 625 Harrison Street, Lynn, West Lafayette, IN 47907 2026, USA
    Protein Sci 13:2573-7. 2004
    ..These data indicate that NuMA-CTDP may represent an important functional sequence conserved in vertebrates, where it may act as a receptor to coordinate cellular events...