Research Topics
| I Saira MianSummaryAffiliation: Lawrence Berkeley National Laboratory Country: USA Publications
| Collaborators
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Detail Information
Publications
MPHASYS: a mouse phenotype analysis systemR 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...- Statistical modeling of biomedical corpora: mining the Caenorhabditis Genetic Center Bibliography for genes related to life spanD 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... - Ensemble attribute profile clustering: discovering and characterizing groups of genes with similar patterns of biological featuresJ R Semeiks
Life Sciences Division MS 977 225A, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA 94720, USA
BMC Bioinformatics 7:147. 2006.... - A linear programming approach for estimating the structure of a sparse linear genetic network from transcript profiling dataSahely 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... - Comparative sequence analysis of ribonucleases HII, III, II PH and DI 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... - 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... 
Communication theory and multicellular biologyI S Mian
Life Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
Integr Biol (Camb) 3:350-67. 2011....
Sequence, structural, functional, and phylogenetic analyses of three glycosidase familiesI 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...- Statistical modelling and phylogenetic analysis of a deaminase domainI 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... - The proofreading domain of Escherichia coli DNA polymerase I and other DNA and/or RNA exonuclease domainsM 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... - Evaluation of normalization methods for cDNA microarray data by k-NN classificationWei 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... - A nuclear targeting determinant for SATB1, a genome organizer in the T cell lineageYuji 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... - Tissue architecture: the ultimate regulator of breast epithelial functionMina 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 - A human breast cell model of preinvasive to invasive transitionAylin 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... - Exploratory differential gene expression analysis in microarray experiments with no or limited replicationAlexander 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... - The thorny path linking cellular senescence to organismal agingChristopher K Patil
Life Sciences Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA 94720, USA
Mech Ageing Dev 126:1040-5. 2005 - Integrated analysis of transcript profiling and protein sequence dataL 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)... - AZU-1: a candidate breast tumor suppressor and biomarker for tumor progressionH 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... - C. elegans clk-2, a gene that limits life span, encodes a telomere length regulator similar to yeast telomere binding protein Tel2pC 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... - The high binding affinity of human ribosomal protein S3 to 7,8-dihydro-8-oxoguanine is abrogated by a single amino acid changeVijay 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... - NuMA influences higher order chromatin organization in human mammary epitheliumPatricia 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... - Arabidopsis thaliana exosome subunit AtRrp4p is a hydrolytic 3'-->5' exonuclease containing S1 and KH RNA-binding domainsJulia 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... - Comparative analysis of editosome proteins in trypanosomatidsElizabeth 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... - LMNA mutations in atypical Werner's syndromeLishan 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)... - The C terminus of the nuclear protein NuMA: phylogenetic distribution and structurePatricia 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...