Taking U out, with two nucleases? (2006)
Mian, I Saira, Worthey, Elizabeth A, Salavati, Reza
Abstract Background REX1 and REX2 are protein components of the RNA editing complex (the editosome) and function as exouridylylases. The exact roles of REX1 and REX2 in the editosome are unclear and...
Huang, Shurong, Lee, Lin, Hanson, Nancy B., Lenaerts, Catherine, Hoehn, Holger, Poot, Martin, ...
The International Registry of Werner syndrome ( www.wernersyndrome.org ) has been providing molecular diagnosis of the Werner syndrome (WS) for the past decade. The present communication summarizes,...
Evaluation of normalization methods for cDNA microarray data by k-NN classification (2005)
Wu, Wei, Xing, Eric P, Myers, Connie, Mian, I Saira, Bissell, Mina J
Abstract Background Non-biological factors give rise to unwanted variations in cDNA microarray data. There are many normalization methods designed to remove such variations. However, to date there...
Loguinov, Alexander V, Mian, I Saira, Vulpe, Chris D
Abstract We describe an exploratory, data-oriented approach for identifying candidates for differential gene expression in cDNA microarray experiments in terms of α -outliers and outlier regions,...
Anders Krogh, Michael Brown, I. Saira Mian, Kimmen Sjolander
Hidden Markov Models (HMMs) are applied to the problems of statistical modeling, database searching and multiple sequence alignment of protein families and protein domains. These methods are...
Stochastic Context-Free Grammars for tRNA Modeling (2000)
Yasubumi Sakakibara, Michael Brown, Richard Hughey, I. Saira Mian, Kimmen Sjolander, Rebecca C. Underwood
Stochastic context-free grammars (SCFGs) are applied to the problems of folding, aligning and modeling families of tRNA sequences. SCFGs capture the sequences' common primary and secondary structure...
Kimmen Sjolander, Kevin Karplus, Michael Brown, Richard Hughey, Anders Krogh, I. Saira Mian, ...
This paper presents the mathematical foundations of Dirichlet mixtures, which have been used to improve database search results for homologous sequences, when a variable number of sequences from a...
A Hidden Markov Model that finds genes in (2000)
Anders Krogh, I. Saira Mian, David Haussler, Em Algorithm
A hidden Markov model (HMM) has been developed to find protein coding genes in E. coli DNA using E. coli genome DNA sequence from the EcoSeq6 database maintained by Kenn Rudd. This HMM includes...
Kimmen Sjolander, Kevin Karplus, Michael Brown, Richard Hughey, Anders Krogh, I. Saira Mian, ...
This paper presents the mathematical foundations of Dirichlet mixtures, which have been used to improve database search results for homologous sequences, when a variable number of sequences from a...
Kimmen Sjolander, Kevin Karplus, Michael Brown, Richard Hughey, Anders Krogh, I. Saira Mian, ...
This paper presents the mathematical foundations of Dirichlet mixtures, which have been used to improve database search results for homologous sequences, when a variable number of sequences from a...
Kimmen Sjolander, Kevin Karplus, Michael Brown, Richard Hughey, Anders Krogh, I. Saira Mian, ...
This paper presents the mathematical foundations of Dirichlet mixtures, which have been used to improve database search results for homologous sequences, when a variable number of sequences from a...
Kimmen Sjolander, Kevin Karplus, Michael Brown, Richard Hughey, Anders Krogh, I. Saira Mian, ...
We present a method for condensing the information in multiple alignments of proteins into a mixture of Dirichlet densities over amino acid distributions. Dirichlet mixture densities are designed to...
Kimmen Sjolander, Kevin Karplus, Michael Brown, Richard Hughey, Anders Krogh, I. Saira Mian, ...
We present a method for condensing the information in multiple alignments of proteins into a mixture of Dirichlet densities over amino acid distributions. Dirichlet mixture densities are designed to...
Kimmen Sjolander, Kevin Karplus, Michael Brown, Richard Hughey, Anders Krogh, I. Saira Mian, ...
We present a method for condensing the information in multiple alignments of proteins into a mixture of Dirichlet densities over amino acid distributions. Dirichlet mixture densities are designed to...
Kevin Karplus, Michael Brown, Richard Hughey, Anders Krogh, I. Saira Mian, David Haussler
This paper presents the mathematical foundations of Dirichlet mixtures, which have been used to improve database search results for homologous sequences, when a variable number of sequences from a...
Kevin Karplus, Michael Brown, Richard Hughey, Anders Krogh, I. Saira Mian, David Haussler
This paper presents the mathematical foundations of Dirichlet mixtures, which have been used to improve database search results for homologous sequences, when a variable number of sequences from a...
A Hidden Markov Model that finds genes in (1995)
Anders Krogh, I. Saira Mian, David Haussler
A hidden Markov model (HMM) has been developed to find protein coding genes in E. coli DNA using E. coli genome DNA sequence from the EcoSeq6 database maintained by Kenn Rudd. This HMM includes...
A Hidden Markov Model that finds genes in (1995)
Anders Krogh, I. Saira Mian, David Haussler
A hidden Markov model (HMM) has been developed to find protein coding genes in E. coli DNA using E. coli genome DNA sequence from the EcoSeq6 database maintained by Kenn Rudd. This HMM includes...
Using Dirichlet Mixture Priors to Derive Hidden Markov Models for Protein Families (1995)
Michael Brown, Richard Hughey, Anders Krogh, I. Saira Mian, Kimmen Sjolander, David Haussler
A Bayesian method for estimating the amino acid distributions in the states of a hidden Markov model (HMM) for a protein family or the columns of a multiple alignment of that family is introduced....
Using Dirichlet Mixture Priors to Derive Hidden Markov Models for Protein Families (1994)
Michael Brown, Richard Hughey, Anders Krogh, I. Saira Mian, Kimmen Sjolander, David Haussler
A Bayesian method for estimating the amino acid distributions in the states of a hidden Markov model (HMM) for a protein family or the columns of a multiple alignment of that family is introduced....
Anders Krogh, Michael Brown, I. Saira Mian, Kimmen Sjolander
Hidden Markov Models (HMMs) are applied to the problems of statistical modeling, database searching and multiple sequence alignment of protein families and protein domains. These methods are...
Anders Krogh, Michael Brown, I. Saira Mian, Kimmen Sjolander
Hidden Markov Models (HMMs) are applied to the problems of statistical modeling, database searching and multiple sequence alignment of protein families and protein domains. These methods are...
Stochastic Context-Free Grammars for tRNA Modeling (1994)
Yasubumi Sakakibara, Michael Brown, Richard Hughey, I. Saira Mian, Rebecca C. Underwood
Stochastic context-free grammars (SCFGs) are applied to the problems of folding, aligning and modeling families of tRNA sequences. SCFGs capture the sequences' common primary and secondary structure...
Recent Methods for RNA Modeling Using Stochastic Context-Free Grammars (1994)
Yasubumi Sakakibara, Michael Brown, Richard Hughey, I. Saira Mian, Kimmen Sjolander, Rebecca C. Underwood, ...
Stochastic context-free grammars (SCFGs) can be applied to the problems of folding, aligning and modeling families of homologous RNA sequences. SCFGs capture the sequences' common primary and...
A Hidden Markov Model that finds genes in E. coli DNA (1994)
Anders Krogh, I. Saira Mian, David Haussler
A hidden Markov model (HMM) has been developed to find protein coding genes in E. coli DNA using E. coli genome DNA sequence from the EcoSeq6 database maintained by Kenn Rudd. This HMM includes...
A Hidden Markov Model that finds genes in (1994)
Anders Krogh, I. Saira Mian, David Haussler
A hidden Markov model (HMM) has been developed to find protein coding genes in E. coli DNA using E. coli genome DNA sequence from the EcoSeq6 database maintained by Kenn Rudd. This HMM includes...
Yasubumi Sakakibara, Michael Brown, Richard Hughey, I. Saira Mian, Kimmen Sjolander, Rebecca C. Underwood
Stochastic context-free grammars (SCFGs) are applied to the problems of folding, aligning and modeling families of homologous RNA sequences. SCFGs capture the sequences' common primary and secondary...
Stochastic Context-Free Grammars for tRNA Modeling (1994)
Yasubumi Sakakibara, Michael Brown, Richard Hughey, I. Saira Mian, Kimmen Sjolander, Rebecca C. Underwood
Stochastic context-free grammars (SCFGs) are applied to the problems of folding, aligning and modeling families of tRNA sequences. SCFGs capture the sequences' common primary and secondary structure...
Stochastic Context-Free Grammars for Modeling RNA (1993)
Yasubumi Sakakibara, Michael Brown, Rebecca C. Underwood, I. Saira Mian
Stochastic context-free grammars (SCFGs) are used to fold, align and model a family of homologous RNA sequences. SCFGs capture the sequences' common primary and secondary structure and generalize the...
Anders Krogh, Michael Brown, I. Saira Mian, Kimmen Sjolander
Hidden Markov Models (HMMs) are applied to the problems of statistical modeling, database searching and multiple sequence alignment of protein families and protein domains. These methods are...
Hidden Markov Models in Computational Biology: Applications to Protein Modeling (1993)
Anders Krogh, Michael Brown, I. Saira Mian, Kimmen Sjolander
Hidden Markov Models (HMMs) are applied to the problems of statistical modeling, database searching and multiple sequence alignment of protein families and protein domains. These methods are...
Anders Krogh, Michael Brown, I. Saira Mian
Hidden Markov Models (HMMs) are applied to the problems of statistical modeling, database searching and multiple sequence alignment of protein families and protein domains. These methods are...
Stochastic Context-Free Grammars for Modeling RNA (1993)
Yasubumi Sakakibara, Michael Brown, Rebecca C. Underwood, I. Saira Mian, David Haussler
this paper, we apply stochastic context-free grammars (SCFGs) to the problems of statistical modeling, database searching, multiple alignment, and prediction of the secondary structure of RNA...
Protein Modeling using Hidden Markov Models: Analysis of Globins (1992)
David Haussler, Anders Krogh, I. Saira Mian
We apply Hidden Markov Models (HMMs) to the problem of statistical modeling and multiple sequence alignment of protein families. A variant of the Expectation Maximization (EM) algorithm known as the...
AZU-1: A Candidate Breast Tumor Suppressor and Biomarker for Tumor Progression
Chen, Huei-Mei, Schmeichel, Karen L., Mian, I. Saira, Lelièvre, Sophie, Petersen, Ole W., Bissell, Mina J.
To identify genes misregulated in the final stages of breast carcinogenesis, we performed differential display to compare the gene expression patterns of the human tumorigenic mammary epithelial...
A Z-DNA binding domain present in the human editing enzyme, double-stranded RNA adenosine deaminase
Herbert, Alan, Alfken, Jens, Kim, Yang-Gyun, Mian, I. Saira, Nishikura, Kazuko, Rich, Alexander
Editing of RNA changes the read-out of information from DNA by altering the nucleotide sequence of a transcript. One type of RNA editing found in all metazoans uses double-stranded RNA (dsRNA) as a...
Identification of the yeast cytidine deaminase CDD1 as an orphan C→U RNA editase
Dance, Geoffrey S. C., Beemiller, Peter, Yang, Yan, Mater, David Van, Mian, I. Saira, Smith, Harold C.
Yeast co-expressing rat APOBEC-1 and a fragment of human apolipoprotein B (apoB) mRNA assembled functional editosomes and deaminated C6666 to U in a mooring sequence-dependent fashion. The occurrence...
Xia, Jinqiang, Peng, Yun, Mian, I. Saira, Lue, Neal F.
Telomerase is a ribonucleoprotein reverse transcriptase responsible for the maintenance of one strand of telomere terminal repeats. The key protein subunit of the telomerase complex, known as TERT,...
Galande, Sanjeev, Dickinson, Liliane A., Mian, I. Saira, Sikorska, Marianna, Kohwi-Shigematsu, Terumi
SATB1 is expressed primarily in thymocytes and orchestrates temporal and spatial expression of a large number of genes in the T-cell lineage. SATB1 binds to the bases of chromatin loop domains in...
Chekanova, Julia A., Dutko, James A., Mian, I. Saira, Belostotsky, Dmitry A.
The exosome, an evolutionarily conserved complex of multiple 3′→5′ exoribonucleases, is responsible for a variety of RNA processing and degradation events in eukaryotes. In this report...
Association of human aging with a functional variant of klotho
Arking, Dan E., Krebsova, Alice, Macek, Milan, Macek, Milan, Arking, Albert, Mian, I. Saira, ...
Mice deficient in Klotho gene expression exhibit a syndrome resembling premature human aging. To determine whether variation in the human KLOTHO locus contributes to survival, we applied two newly...
Feng, Pinghui, Mian, I. Saira, Read, G. Sullivan
During lytic infections, the virion host shutoff (Vhs) protein (UL41) of herpes simplex virus destabilizes both host and viral mRNAs. By accelerating the decay of all mRNAs, it helps redirect the...
Analysis of Telomerase in Candida albicans: Potential Role in Telomere End Protection
Singh, Sunitha M., Steinberg-Neifach, Olga, Mian, I. Saira, Lue, Neal F.
Telomerase is a ribonucleoprotein reverse transcriptase responsible for the maintenance of one strand of telomere terminal repeats. Analysis of the telomerase complex in the budding yeast...
The IrrE Protein of Deinococcus radiodurans R1 Is a Novel Regulator of recA Expression
Earl, Ashlee M., Mohundro, Michael M., Mian, I. Saira, Battista, John R.
IRS24 is a DNA damage-sensitive strain of Deinococcus radiodurans strain 302 carrying a mutation in an uncharacterized locus designated irrE. Five overlapping cosmids capable of restoring ionizing...
Lue, Neal F., Lin, You-Chin, Mian, I. Saira
Telomerase is a ribonucleoprotein reverse transcriptase responsible for the maintenance of one strand of the telomere terminal repeats. The catalytic protein subunit of the telomerase complex, known...
SURVEY AND SUMMARY: Comparative analysis of editosome proteins in trypanosomatids
Worthey, Elizabeth A., Schnaufer, Achim, Mian, I. Saira, Stuart, Kenneth, Salavati, Reza
Detailed comparisons of 16 editosome proteins from Trypanosoma brucei, Trypanosoma cruzi and Leishmania major identified protein motifs associated with catalysis and protein or nucleic acid...
Loguinov, Alexander V, Mian, I Saira, Vulpe, Chris D
An exploratory, data-oriented approach is described for identifying candidates for differential gene expression in cDNA microarray experiments in terms of α-outliers and outlier regions, using...
Evaluation of normalization methods for cDNA microarray data by k-NN classification
Wu, Wei, Xing, Eric P, Myers, Connie, Mian, I Saira, Bissell, Mina J
AZU-1: A Candidate Breast Tumor Suppressor and Biomarker for Tumor Progression
Chen, Huei-Mei, Schmeichel, Karen L., Mian, I. Saira, Lelièvre, Sophie, Petersen, Ole W., Bissell, Mina J.
To identify genes misregulated in the final stages of breast carcinogenesis, we performed differential display to compare the gene expression patterns of the human tumorigenic mammary epithelial...
A Z-DNA binding domain present in the human editing enzyme, double-stranded RNA adenosine deaminase
Herbert, Alan, Alfken, Jens, Kim, Yang-Gyun, Mian, I. Saira, Nishikura, Kazuko, Rich, Alexander
Editing of RNA changes the read-out of information from DNA by altering the nucleotide sequence of a transcript. One type of RNA editing found in all metazoans uses double-stranded RNA (dsRNA) as a...
Identification of the yeast cytidine deaminase CDD1 as an orphan C→U RNA editase
Dance, Geoffrey S. C., Beemiller, Peter, Yang, Yan, Mater, David Van, Mian, I. Saira, Smith, Harold C.
Yeast co-expressing rat APOBEC-1 and a fragment of human apolipoprotein B (apoB) mRNA assembled functional editosomes and deaminated C6666 to U in a mooring sequence-dependent fashion. The occurrence...
Xia, Jinqiang, Peng, Yun, Mian, I. Saira, Lue, Neal F.
Telomerase is a ribonucleoprotein reverse transcriptase responsible for the maintenance of one strand of telomere terminal repeats. The key protein subunit of the telomerase complex, known as TERT,...
Galande, Sanjeev, Dickinson, Liliane A., Mian, I. Saira, Sikorska, Marianna, Kohwi-Shigematsu, Terumi
SATB1 is expressed primarily in thymocytes and orchestrates temporal and spatial expression of a large number of genes in the T-cell lineage. SATB1 binds to the bases of chromatin loop domains in...
Chekanova, Julia A., Dutko, James A., Mian, I. Saira, Belostotsky, Dmitry A.
The exosome, an evolutionarily conserved complex of multiple 3′→5′ exoribonucleases, is responsible for a variety of RNA processing and degradation events in eukaryotes. In this report...
Association of human aging with a functional variant of klotho
Arking, Dan E., Krebsova, Alice, Macek, Milan, Macek, Milan, Arking, Albert, Mian, I. Saira, ...
Mice deficient in Klotho gene expression exhibit a syndrome resembling premature human aging. To determine whether variation in the human KLOTHO locus contributes to survival, we applied two newly...
Feng, Pinghui, Mian, I. Saira, Read, G. Sullivan
During lytic infections, the virion host shutoff (Vhs) protein (UL41) of herpes simplex virus destabilizes both host and viral mRNAs. By accelerating the decay of all mRNAs, it helps redirect the...
Analysis of Telomerase in Candida albicans: Potential Role in Telomere End Protection
Singh, Sunitha M., Steinberg-Neifach, Olga, Mian, I. Saira, Lue, Neal F.
Telomerase is a ribonucleoprotein reverse transcriptase responsible for the maintenance of one strand of telomere terminal repeats. Analysis of the telomerase complex in the budding yeast...
The IrrE Protein of Deinococcus radiodurans R1 Is a Novel Regulator of recA Expression
Earl, Ashlee M., Mohundro, Michael M., Mian, I. Saira, Battista, John R.
IRS24 is a DNA damage-sensitive strain of Deinococcus radiodurans strain 302 carrying a mutation in an uncharacterized locus designated irrE. Five overlapping cosmids capable of restoring ionizing...
Lue, Neal F., Lin, You-Chin, Mian, I. Saira
Telomerase is a ribonucleoprotein reverse transcriptase responsible for the maintenance of one strand of the telomere terminal repeats. The catalytic protein subunit of the telomerase complex, known...
SURVEY AND SUMMARY: Comparative analysis of editosome proteins in trypanosomatids
Worthey, Elizabeth A., Schnaufer, Achim, Mian, I. Saira, Stuart, Kenneth, Salavati, Reza
Detailed comparisons of 16 editosome proteins from Trypanosoma brucei, Trypanosoma cruzi and Leishmania major identified protein motifs associated with catalysis and protein or nucleic acid...
Loguinov, Alexander V, Mian, I Saira, Vulpe, Chris D
An exploratory, data-oriented approach is described for identifying candidates for differential gene expression in cDNA microarray experiments in terms of α-outliers and outlier regions, using...
Evaluation of normalization methods for cDNA microarray data by k-NN classification
Wu, Wei, Xing, Eric P, Myers, Connie, Mian, I Saira, Bissell, Mina J
NuMA Influences Higher Order Chromatin Organization in Human Mammary Epithelium
Abad, Patricia C., Lewis, Jason, Mian, I. Saira, Knowles, David W., Sturgis, Jennifer, Badve, Sunil, ...
The coiled-coil protein NuMA is an important contributor to mitotic spindle formation and stabilization. A potential role for NuMA in nuclear organization or gene regulation is suggested by the...