Principles of transcriptional regulation and evolution of the metabolic system in E. coli (2009)
Seshasayee, Aswin S.N., Fraser, Gillian M., Babu, M. Madan, Luscombe, Nicholas M.
Organisms must adapt to make optimal use of the metabolic system in response to environmental changes. In the long-term, this involves evolution of the genomic repertoire of enzymes; in the...
Dov Greenbaum, Nicholas M. Luscombe, Ronald Jansen, Jiang Qian, Mark Gerstein
With the completion of genome sequences, the current challenge for biology is to determine the functions of all gene products and to understand how they contribute in making an organism viable. For...
Annotation Transfer Between Genomes: (2008)
Protein–protein Interologs, Haiyuan Yu, Nicholas M. Luscombe, Hao Xin Lu, Xiaowei Zhu, ...
this paper, we present results from both approaches
Transcriptional networking (2005)
Teichmann, Sarah A, Bornberg-Bauer, Erich, Luscombe, Nicholas M
Abstract A report on the European Science Foundation workshop 'Transcription Networks: A Global View', Madrid, Spain, 26-28 May 2005.
Annotation Transfer Between Genomes: Protein-Protein Interologs and Protein-DNA Regulogs (2004)
Yu, Haiyuan, Luscombe, Nicholas M., Lu, Hao Xin, Zhu, Xiaowei, Xia, Yu, Han, Jing-Dong J., ...
Proteins function mainly through interactions, especially with DNA and other proteins. While some large-scale interaction networks are now available for a number of model organisms, their...
ExpressYourself: a modular platform for processing and visualizing microarray data (2003)
Luscombe, Nicholas M., Royce, Thomas E., Bertone, Paul, Echols, Nathaniel, Horak, Christine E., Chang, Joseph T., ...
DNA microarrays are widely used in biological research; by analyzing differential hybridization on a single microarray slide, one can detect changes in mRNA expression levels, increases in DNA copy...
The transcriptional activity of human Chromosome 22 (2003)
Rinn, John L., Euskirchen, Ghia, Bertone, Paul, Martone, Rebecca, Luscombe, Nicholas M., Hartman, Stephen, ...
Qian, Jiang, Lin, Jimmy, Luscombe, Nicholas M., Yu, Haiyuan, Gerstein, Mark
Motivation: Defining regulatory networks, linking transcription factors (TFs) to their targets, is a central problem in post-genomic biology. One might imagine one could readily determine these...
Luscombe, Nicholas M, Qian, Jiang, Zhang, Zhaolei, Johnson, Ted, Gerstein, Mark
Abstract Background The sequencing of genomes provides us with an inventory of the 'molecular parts' in nature, such as protein families and folds, and their functions in living organisms. Through...
Structural genomics: a new era for pharmaceutical research (2002)
Liu, Yang, Luscombe, Nicholas M, Alexandrov, Vadim, Bertone, Paul, Harrison, Paul, Zhang, Zhaolei, ...
A report on the 15th Annual Center for Advanced Biotechnology and Medicine Symposium on structural genomics in pharmaceutical design, Princeton, USA, 24-25 October 2001.
Complex transcriptional circuitry at the G1/S transition in Saccharomyces cerevisiae (2002)
Horak, Christine E., Luscombe, Nicholas M., Qian, Jiang, Bertone, Paul, Piccirrillo, Stacy, Gerstein, Mark, ...
Echols, Nathaniel, Harrison, Paul, Balasubramanian, Suganthi, Luscombe, Nicholas M., Bertone, Paul, Zhang, Zhaolei, ...
Based on searches for disabled homologs to known proteins, we have identified a large population of pseudogenes in four sequenced eukaryotic genomes—the worm, yeast, fly and human (chromosomes 21...
Harrison, Paul M., Hegyi, Hedi, Balasubramanian, Suganthi, Luscombe, Nicholas M., Bertone, Paul, Echols, Nathaniel, ...
Protein-RNA interactions: a structural analysis (2001)
Jones, Susan, Daley, David T. A., Luscombe, Nicholas M., Berman, Helen M., Thornton, Janet M.
A detailed computational analysis of 32 protein–RNA complexes is presented. A number of physical and chemical properties of the intermolecular interfaces are calculated and compared with those...
Luscombe, Nicholas M., Laskowski, Roman A., Thornton, Janet M.
To assess whether there are universal rules that govern amino acid–base recognition, we investigate hydrogen bonds, van der Waals contacts and water-mediated bonds in 129 protein–DNA complex...
An overview of the structures of protein-DNA complexes (2000)
Luscombe, Nicholas M, Austin, Susan E, Berman, Helen M, Thornton, Janet M
Abstract On the basis of a structural analysis of 240 protein-DNA complexes contained in the Protein Data Bank (PDB), we have classified the DNA-binding proteins involved into eight different...
Review An overview of the structures of protein-DNA complexes (2000)
Nicholas M Luscombe, Susan E Austin, Helen M Berman, Correspondence Janet, M Thornton
The electronic version of this article is the complete one and can be
Protein clefts in molecular recognition and function (1996)
Downloaded From, R. A. Laskowski, Roman A. Laskowski, Nicholas M. Luscombe, Mark B. Swindells, ...
Article cited in:
Protein–RNA interactions: a structural analysis
Jones, Susan, Daley, David T. A., Luscombe, Nicholas M., Berman, Helen M., Thornton, Janet M.
A detailed computational analysis of 32 protein–RNA complexes is presented. A number of physical and chemical properties of the intermolecular interfaces are calculated and compared with those...
Luscombe, Nicholas M., Laskowski, Roman A., Thornton, Janet M.
To assess whether there are universal rules that govern amino acid–base recognition, we investigate hydrogen bonds, van der Waals contacts and water-mediated bonds in 129 protein–DNA complex...
Echols, Nathaniel, Harrison, Paul, Balasubramanian, Suganthi, Luscombe, Nicholas M., Bertone, Paul, Zhang, Zhaolei, ...
Based on searches for disabled homologs to known proteins, we have identified a large population of pseudogenes in four sequenced eukaryotic genomes—the worm, yeast, fly and human (chromosomes 21...
GATA-1 binding sites mapped in the β-globin locus by using mammalian chIp-chip analysis
Horak, Christine E., Mahajan, Milind C., Luscombe, Nicholas M., Gerstein, Mark, Weissman, Sherman M., Snyder, Michael
The expression of the β-like globin genes is intricately regulated by a series of both general and tissue-restricted transcription factors. The hemapoietic lineage-specific transcription factor...
Luscombe, Nicholas M, Qian, Jiang, Zhang, Zhaolei, Johnson, Ted, Gerstein, Mark
The sequencing of genomes provides us with an inventory of the 'molecular parts' in nature, such as protein families and folds, and their functions in living organisms. The genomic occurrence of...
An overview of the structures of protein-DNA complexes
Luscombe, Nicholas M, Austin, Susan E, Berman , Helen M, Thornton, Janet M
On the basis of a structural analysis of 240 protein-DNA complexes contained in the Protein Data Bank (PDB), we have classified the DNA-binding proteins involved into eight different...
Structural genomics: a new era for pharmaceutical research
Liu, Yang, Luscombe, Nicholas M, Alexandrov, Vadim, Bertone, Paul, Harrison, Paul, Zhang, Zhaolei, ...
A report on the 15th Annual Center for Advanced Biotechnology and Medicine Symposium on structural genomics in pharmaceutical design, Princeton, USA, 24-25 October 2001.
ExpressYourself: a modular platform for processing and visualizing microarray data
Luscombe, Nicholas M., Royce, Thomas E., Bertone, Paul, Echols, Nathaniel, Horak, Christine E., Chang, Joseph T., ...
DNA microarrays are widely used in biological research; by analyzing differential hybridization on a single microarray slide, one can detect changes in mRNA expression levels, increases in DNA copy...
Complex transcriptional circuitry at the G1/S transition in Saccharomyces cerevisiae
Horak, Christine E., Luscombe, Nicholas M., Qian, Jiang, Bertone, Paul, Piccirrillo, Stacy, Gerstein, Mark, ...
In the yeast Saccharomyces cerevisiae, SBF (Swi4–Swi6 cell cycle box binding factor) and MBF (MluI binding factor) are the major transcription factors regulating the START of the cell cycle, a time...
The transcriptional activity of human Chromosome 22
Rinn, John L., Euskirchen, Ghia, Bertone, Paul, Martone, Rebecca, Luscombe, Nicholas M., Hartman, Stephen, ...
A DNA microarray representing nearly all of the unique sequences of human Chromosome 22 was constructed and used to measure global-transcriptional activity in placental poly(A)+ RNA. We found that...
Distribution of NF-κB-binding sites across human chromosome 22
Martone, Rebecca, Euskirchen, Ghia, Bertone, Paul, Hartman, Stephen, Royce, Thomas E., Luscombe, Nicholas M., ...
We have mapped the chromosomal binding site distribution of a transcription factor in human cells. The NF-κB family of transcription factors plays an essential role in regulating the induction of...
CREB Binds to Multiple Loci on Human Chromosome 22
Euskirchen, Ghia, Royce, Thomas E., Bertone, Paul, Martone, Rebecca, Rinn, John L., Nelson, F. Kenneth, ...
The cyclic AMP-responsive element-binding protein (CREB) is an important transcription factor that can be activated by hormonal stimulation and regulates neuronal function and development. An...
Annotation Transfer Between Genomes: Protein–Protein Interologs and Protein–DNA Regulogs
Yu, Haiyuan, Luscombe, Nicholas M., Lu, Hao Xin, Zhu, Xiaowei, Xia, Yu, Han, Jing-Dong J., ...
Proteins function mainly through interactions, especially with DNA and other proteins. While some large-scale interaction networks are now available for a number of model organisms, their...
Teichmann, Sarah A, Bornberg-Bauer, Erich, Luscombe, Nicholas M
A report on the European Science Foundation workshop ‘Transcription Networks: A Global View’, Madrid, Spain, 26-28 May 2005.
Harrison, Paul M., Hegyi, Hedi, Balasubramanian, Suganthi, Luscombe, Nicholas M., Bertone, Paul, Echols, Nathaniel, ...
We have developed an initial approach for annotating and surveying pseudogenes in the human genome. We search human genomic DNA for regions that are similar to known protein sequences and contain...
Protein–RNA interactions: a structural analysis
Jones, Susan, Daley, David T. A., Luscombe, Nicholas M., Berman, Helen M., Thornton, Janet M.
A detailed computational analysis of 32 protein–RNA complexes is presented. A number of physical and chemical properties of the intermolecular interfaces are calculated and compared with those...
Luscombe, Nicholas M., Laskowski, Roman A., Thornton, Janet M.
To assess whether there are universal rules that govern amino acid–base recognition, we investigate hydrogen bonds, van der Waals contacts and water-mediated bonds in 129 protein–DNA complex...
Echols, Nathaniel, Harrison, Paul, Balasubramanian, Suganthi, Luscombe, Nicholas M., Bertone, Paul, Zhang, Zhaolei, ...
Based on searches for disabled homologs to known proteins, we have identified a large population of pseudogenes in four sequenced eukaryotic genomes—the worm, yeast, fly and human (chromosomes 21...
GATA-1 binding sites mapped in the β-globin locus by using mammalian chIp-chip analysis
Horak, Christine E., Mahajan, Milind C., Luscombe, Nicholas M., Gerstein, Mark, Weissman, Sherman M., Snyder, Michael
The expression of the β-like globin genes is intricately regulated by a series of both general and tissue-restricted transcription factors. The hemapoietic lineage-specific transcription factor...
Luscombe, Nicholas M, Qian, Jiang, Zhang, Zhaolei, Johnson, Ted, Gerstein, Mark
The sequencing of genomes provides us with an inventory of the 'molecular parts' in nature, such as protein families and folds, and their functions in living organisms. The genomic occurrence of...
An overview of the structures of protein-DNA complexes
Luscombe, Nicholas M, Austin, Susan E, Berman , Helen M, Thornton, Janet M
On the basis of a structural analysis of 240 protein-DNA complexes contained in the Protein Data Bank (PDB), we have classified the DNA-binding proteins involved into eight different...
Structural genomics: a new era for pharmaceutical research
Liu, Yang, Luscombe, Nicholas M, Alexandrov, Vadim, Bertone, Paul, Harrison, Paul, Zhang, Zhaolei, ...
A report on the 15th Annual Center for Advanced Biotechnology and Medicine Symposium on structural genomics in pharmaceutical design, Princeton, USA, 24-25 October 2001.
Harrison, Paul M., Hegyi, Hedi, Balasubramanian, Suganthi, Luscombe, Nicholas M., Bertone, Paul, Echols, Nathaniel, ...
We have developed an initial approach for annotating and surveying pseudogenes in the human genome. We search human genomic DNA for regions that are similar to known protein sequences and contain...
ExpressYourself: a modular platform for processing and visualizing microarray data
Luscombe, Nicholas M., Royce, Thomas E., Bertone, Paul, Echols, Nathaniel, Horak, Christine E., Chang, Joseph T., ...
DNA microarrays are widely used in biological research; by analyzing differential hybridization on a single microarray slide, one can detect changes in mRNA expression levels, increases in DNA copy...
Complex transcriptional circuitry at the G1/S transition in Saccharomyces cerevisiae
Horak, Christine E., Luscombe, Nicholas M., Qian, Jiang, Bertone, Paul, Piccirrillo, Stacy, Gerstein, Mark, ...
In the yeast Saccharomyces cerevisiae, SBF (Swi4–Swi6 cell cycle box binding factor) and MBF (MluI binding factor) are the major transcription factors regulating the START of the cell cycle, a time...
The transcriptional activity of human Chromosome 22
Rinn, John L., Euskirchen, Ghia, Bertone, Paul, Martone, Rebecca, Luscombe, Nicholas M., Hartman, Stephen, ...
A DNA microarray representing nearly all of the unique sequences of human Chromosome 22 was constructed and used to measure global-transcriptional activity in placental poly(A)+ RNA. We found that...
Distribution of NF-κB-binding sites across human chromosome 22
Martone, Rebecca, Euskirchen, Ghia, Bertone, Paul, Hartman, Stephen, Royce, Thomas E., Luscombe, Nicholas M., ...
We have mapped the chromosomal binding site distribution of a transcription factor in human cells. The NF-κB family of transcription factors plays an essential role in regulating the induction of...
CREB Binds to Multiple Loci on Human Chromosome 22
Euskirchen, Ghia, Royce, Thomas E., Bertone, Paul, Martone, Rebecca, Rinn, John L., Nelson, F. Kenneth, ...
The cyclic AMP-responsive element-binding protein (CREB) is an important transcription factor that can be activated by hormonal stimulation and regulates neuronal function and development. An...
Annotation Transfer Between Genomes: Protein–Protein Interologs and Protein–DNA Regulogs
Yu, Haiyuan, Luscombe, Nicholas M., Lu, Hao Xin, Zhu, Xiaowei, Xia, Yu, Han, Jing-Dong J., ...
Proteins function mainly through interactions, especially with DNA and other proteins. While some large-scale interaction networks are now available for a number of model organisms, their...
Teichmann, Sarah A, Bornberg-Bauer, Erich, Luscombe, Nicholas M
A report on the European Science Foundation workshop ‘Transcription Networks: A Global View’, Madrid, Spain, 26-28 May 2005.
Transcriptomics and adaptive genomics of the asymptomatic bacteriuria Escherichia coli strain 83972
Hancock, Viktoria, Seshasayee, Aswin S., Ussery, David W., Luscombe, Nicholas M., Klemm, Per
Escherichia coli strains are the major cause of urinary tract infections in humans. Such strains can be divided into virulent, UPEC strains causing symptomatic infections, and asymptomatic,...
Pearson, Melanie M., Sebaihia, Mohammed, Churcher, Carol, Quail, Michael A., Seshasayee, Aswin S., Luscombe, Nicholas M., ...
The gram-negative enteric bacterium Proteus mirabilis is a frequent cause of urinary tract infections in individuals with long-term indwelling catheters or with complicated urinary tracts (e.g., due...
Principles of transcriptional regulation and evolution of the metabolic system in E. coli
Seshasayee, Aswin S.N., Fraser, Gillian M., Babu, M. Madan, Luscombe, Nicholas M.
Organisms must adapt to make optimal use of the metabolic system in response to environmental changes. In the long-term, this involves evolution of the genomic repertoire of enzymes; in the...