DRAFT 2 Functions of the Arabidopsis microRNA and siRNA Systems (2008)
Michael Snyder, Heng Zhu, Christine Horak, Anuj Kumar, Ghia Euskirchen, Rebecca Goetsch, ...
The genomes of a wide variety of organisms have now been sequenced; a major challenge ahead is to identify genes and their encoded projects and to understand their function and regulation. For the...
Paul Bertone, Bhaskar Dasgupta, Mark Gerstein, Ming-yang Kao, Michael Snyder
A preliminary version of this paper appeared in the 2 nd Workshop on Algorithms in Bioinformatics,
Fast Optimal Genome Tiling with Applications to Microarray Design and Homology Search (2007)
Piotr Berman, Paul Bertone, Bhaskar Dasgupta, Mark Gerstein, Ming-yang Kao, Michael Snyder
In this paper we consider several variations of the following basic tiling problem: given a sequence of real numbers with two size bound parameters, we want to find a set of tiles such that they...
Design optimization methods for genomic DNA tiling arrays (2006)
Paul Bertone, Valery Trifonov, Joel S. Rozowsky, Falk Schubert, Olof Emanuelsson, John Karro, ...
A recent development in microarray construction entails the unbiased coverage, or tiling, of non-repetitive genomic DNA for the experimental identification of unannotated transcribed sequences and...
Target hub proteins serve as master regulators of development in yeast (2006)
Borneman, Anthony R., Leigh-Bell, Justine A., Yu, Haiyuan, Bertone, Paul, Gerstein, Mark, Snyder, Michael
To understand the organization of the transcriptional networks that govern cell differentiation, we have investigated the transcriptional circuitry controlling pseudohyphal development in...
Hartman, Stephen E., Bertone, Paul, Nath, Anjali K., Royce, Thomas E., Gerstein, Mark, Weissman, Sherman, ...
The STAT (signal transducer and activator of transcription) proteins play a crucial role in the regulation of gene expression, but their targets and the manner in which they select them remain...
Hartman, Stephen E., Bertone, Paul, Nath, Anjali K., Royce, Thomas E., Gerstein, Mark, Weissman, Sherman, ...
The STAT (signal transducer and activator of transcription) proteins play a crucial role in the regulation of gene expression, but their targets and the manner in which they select them remain...
Gilad, Yoav, Rifkin, Scott A., Bertone, Paul, Gerstein, Mark, White, Kevin P.
Interspecies comparisons of gene expression levels will increase our understanding of the evolution of transcriptional mechanisms and help to identify targets of natural selection. This approach...
Design optimization methods for genomic DNA tiling arrays (2005)
Bertone, Paul, Trifonov, Valery, Rozowsky, Joel S., Schubert, Falk, Emanuelsson, Olof, Karro, John, ...
A recent development in microarray research entails the unbiased coverage, or tiling, of genomic DNA for the large-scale identification of transcribed sequences and regulatory elements. A central...
Hartman, Stephen E., Bertone, Paul, Nath, Anjali K., Royce, Thomas E., Gerstein, Mark, Weissman, Sherman, ...
The STAT (signal transducer and activator of transcription) proteins play a crucial role in the regulation of gene expression, but their targets and the manner in which they select them remain...
Chern-sing Goh, Ning Lan, Nathaniel Echols, Shawn M. Douglas, Duncan Milburn, Paul Bertone, ...
We present version 2 of the SPINE system for structural proteomics. SPINE is available over the web at
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, ...
Identification of pseudogenes in the Drosophila melanogaster genome (2003)
Harrison, Paul M., Milburn, Duncan, Zhang, Zhaolei, Bertone, Paul, Gerstein, Mark
Pseudogenes are copies of genes that cannot produce a protein. They can be detected from disruptions to their apparent coding sequence, caused by frameshifts and premature stop codons. They are...
Goh, Chern-Sing, Lan, Ning, Echols, Nathaniel, Douglas, Shawn M., Milburn, Duncan, Bertone, Paul, ...
We present version 2 of the SPINE system for structural proteomics. SPINE is available over the web at http://nesg.org. It serves as the central hub for the Northeast Structural Genomics Consortium,...
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.
Fast optimal genome tiling with applications to microarray design and homology search (2002)
Piotr Berman, Paul Bertone, Bhaskar Dasgupta, Mark Gerstein, Ming-yang Kao, Michael Snyder
In this paper we consider several variations of the following basic tiling problem: given a sequence of real numbers with two size bound parameters, we want to find a set of tiles of maximum total...
Fast optimal genome tiling with applications to microarray design and homology search (2002)
Piotr Berman, Paul Bertone, Bhaskar Dasgupta, Mark Gerstein, Ming-yang Kao, Michael Snyder, ...
Abstract. In this paper we consider several variations of the following basic tiling problem: given a sequence of real numbers with two size bound parameters, we want to nd a set of tiles such that...
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, ...
Bertone, Paul, Kluger, Yuval, Lan, Ning, Zheng, Deyou, Christendat, Dinesh, Yee, Adelinda, ...
High-throughput structural proteomics is expected to generate considerable amounts of data on the progress of structure determination for many proteins. For each protein this includes information...
Bertone, Paul, Kluger, Yuval, Lan, Ning, Zheng, Deyou, Christendat, Dinesh, Yee, Adelinda, ...
High-throughput structural proteomics is expected to generate considerable amounts of data on the progress of structure determination for many proteins. For each protein this includes information...
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...
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.
Identification of pseudogenes in the Drosophila melanogaster genome
Harrison, Paul M., Milburn, Duncan, Zhang, Zhaolei, Bertone, Paul, Gerstein, Mark
Pseudogenes are copies of genes that cannot produce a protein. They can be detected from disruptions to their apparent coding sequence, caused by frameshifts and premature stop codons. They are...
SPINE 2: a system for collaborative structural proteomics within a federated database framework
Goh, Chern-Sing, Lan, Ning, Echols, Nathaniel, Douglas, Shawn M., Milburn, Duncan, Bertone, Paul, ...
We present version 2 of the SPINE system for structural proteomics. SPINE is available over the web at http://nesg.org. It serves as the central hub for the Northeast Structural Genomics Consortium,...
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...
Multi-species microarrays reveal the effect of sequence divergence on gene expression profiles
Gilad, Yoav, Rifkin, Scott A., Bertone, Paul, Gerstein, Mark, White, Kevin P.
Interspecies comparisons of gene expression levels will increase our understanding of the evolution of transcriptional mechanisms and help to identify targets of natural selection. This approach...
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...
Global changes in STAT target selection and transcription regulation upon interferon treatments
Hartman, Stephen E., Bertone, Paul, Nath, Anjali K., Royce, Thomas E., Gerstein, Mark, Weissman, Sherman, ...
The STAT (signal transducer and activator of transcription) proteins play a crucial role in the regulation of gene expression, but their targets and the manner in which they select them remain...
Design optimization methods for genomic DNA tiling arrays
Bertone, Paul, Trifonov, Valery, Rozowsky, Joel S., Schubert, Falk, Emanuelsson, Olof, Karro, John, ...
A recent development in microarray research entails the unbiased coverage, or tiling, of genomic DNA for the large-scale identification of transcribed sequences and regulatory elements. A central...
Target hub proteins serve as master regulators of development in yeast
Borneman, Anthony R., Leigh-Bell, Justine A., Yu, Haiyuan, Bertone, Paul, Gerstein, Mark, Snyder, Michael
To understand the organization of the transcriptional networks that govern cell differentiation, we have investigated the transcriptional circuitry controlling pseudohyphal development in...
Bertone, Paul, Kluger, Yuval, Lan, Ning, Zheng, Deyou, Christendat, Dinesh, Yee, Adelinda, ...
High-throughput structural proteomics is expected to generate considerable amounts of data on the progress of structure determination for many proteins. For each protein this includes information...
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...
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.
Identification of pseudogenes in the Drosophila melanogaster genome
Harrison, Paul M., Milburn, Duncan, Zhang, Zhaolei, Bertone, Paul, Gerstein, Mark
Pseudogenes are copies of genes that cannot produce a protein. They can be detected from disruptions to their apparent coding sequence, caused by frameshifts and premature stop codons. They are...
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...
SPINE 2: a system for collaborative structural proteomics within a federated database framework
Goh, Chern-Sing, Lan, Ning, Echols, Nathaniel, Douglas, Shawn M., Milburn, Duncan, Bertone, Paul, ...
We present version 2 of the SPINE system for structural proteomics. SPINE is available over the web at http://nesg.org. It serves as the central hub for the Northeast Structural Genomics Consortium,...
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...
Multi-species microarrays reveal the effect of sequence divergence on gene expression profiles
Gilad, Yoav, Rifkin, Scott A., Bertone, Paul, Gerstein, Mark, White, Kevin P.
Interspecies comparisons of gene expression levels will increase our understanding of the evolution of transcriptional mechanisms and help to identify targets of natural selection. This approach...
Global changes in STAT target selection and transcription regulation upon interferon treatments
Hartman, Stephen E., Bertone, Paul, Nath, Anjali K., Royce, Thomas E., Gerstein, Mark, Weissman, Sherman, ...
The STAT (signal transducer and activator of transcription) proteins play a crucial role in the regulation of gene expression, but their targets and the manner in which they select them remain...
Design optimization methods for genomic DNA tiling arrays
Bertone, Paul, Trifonov, Valery, Rozowsky, Joel S., Schubert, Falk, Emanuelsson, Olof, Karro, John, ...
A recent development in microarray research entails the unbiased coverage, or tiling, of genomic DNA for the large-scale identification of transcribed sequences and regulatory elements. A central...
Target hub proteins serve as master regulators of development in yeast
Borneman, Anthony R., Leigh-Bell, Justine A., Yu, Haiyuan, Bertone, Paul, Gerstein, Mark, Snyder, Michael
To understand the organization of the transcriptional networks that govern cell differentiation, we have investigated the transcriptional circuitry controlling pseudohyphal development in...