BA: CorreLogo: an online server for 3D sequence logos (2008)
Eckart Bindewald, Thomas D. Schneider, Bruce A. Shapiro
We present an online server that generates a 3D representation of properties of user-submitted RNA or DNA alignments. The visualized properties are information of single alignment columns, mutual...
Discovery of novel tumor suppressor p53 response elements using information theory (2008)
Lyakhov, Ilya G., Krishnamachari, Annangarachari, Schneider, Thomas D.
An accurate method for locating genes under tumor suppressor p53 control that is based on a well-established mathematical theory and built using naturally occurring, experimentally proven p53 sites...
Edited by Sankar Adhya Supplemental information: (2007)
Information theory was introduced in the late 1940s by Claude Shannon for the study of communications systems[1, 2]. With this mathematical tool, information passing through a telephone or computer...
Thomas D. Schneider, David N. Mastronarde
An information theory based multiple alignment ("Malign") method was used to align the DNA binding sequences of the OxyR and Fis proteins, whose sequence conservation is so spread out that...
This primer is written for molecular biologists who are unfamiliar with information theory. Its purpose is to introduce you to these ideas so that you can understand how to apply them to binding...
Shultzaberger, Ryan K., Roberts, Lindsey R., Lyakhov, Ilya G., Sidorov, Igor A., Stephen, Andrew G., Fisher, Robert J., ...
Individual protein binding sites on DNA can be measured in bits of information. This information is related to the free energy of binding by the second law of thermodynamics, but binding kinetics...
Anatomy of Escherichia coli {sigma}70 promoters (2007)
Shultzaberger, Ryan K., Chen, Zehua, Lewis, Karen A., Schneider, Thomas D.
Information theory was used to build a promoter model that accounts for the −10, the −35 and the uncertainty of the gap between them on a common scale. Helical face assignment indicated that base...
CorreLogo: an online server for 3D sequence logos of RNA and DNA alignments (2006)
Bindewald, Eckart, Schneider, Thomas D., Shapiro, Bruce A.
We present an online server that generates a 3D representation of properties of user-submitted RNA or DNA alignments. The visualized properties are information of single alignment columns, mutual...
Chen, Zehua, Schneider, Thomas D.
Based on molecular information theory, 10 T7-like promoter models were built for the T7 group of phages and used to scan their host genomes and closely related genomes. 38 genomes were scanned and 12...
Anatomy of Escherichia coli {sigma}70 promoters (2006)
Shultzaberger, Ryan K., Chen, Zehua, Lewis, Karen A., Schneider, Thomas D.
Information theory was used to build a promoter model that accounts for the −10, the −35 and the uncertainty of the gap between them on a common scale. Helical face assignment indicated that base...
Anatomy of Escherichia coli {sigma}70 promoters (2006)
Shultzaberger, Ryan K., Chen, Zehua, Lewis, Karen A., Schneider, Thomas D.
Information theory was used to build a promoter model that accounts for the −10, the −35 and the uncertainty of the gap between them on a common scale. Helical face assignment indicated that base...
Molecular flip-flops formed by overlapping Fis sites (2003)
Hengen, Paul N., Lyakhov, Ilya G., Stewart, Lisa E., Schneider, Thomas D.
The DNA‐binding protein Fis frequently uses pairs of sites 7 or 11 base pairs (bp) apart. Two overlapping Fis sites separated by 11 bp are found in the Escherichia coli origin of chromosomal...
Khan, Sikandar G., Metin, Ahmet, Gozukara, Engin, Inui, Hiroki, Shahlavi, Tala, Muniz-Medina, Vanessa, ...
The lariat branch point sequence (BPS) is crucial for splicing of human nuclear pre-mRNA yet BPS mutations have infrequently been reported to cause human disease. Using an inverse RT-PCR technique we...
Khan, Sikandar G., Metin, Ahmet, Gozukara, Engin, Inui, Hiroki, Shahlavi, Tala, Muniz-Medina, Vanessa, ...
The lariat branch point sequence (BPS) is crucial for splicing of human nuclear pre-mRNA yet BPS mutations have infrequently been reported to cause human disease. Using an inverse RT-PCR technique we...
Khan, Sikandar G., Muniz-Medina, Vanessa, Shahlavi, Tala, Baker, Carl C., Inui, Hiroki, Ueda, Takahiro, ...
XPC DNA repair gene mutations result in the cancer‐prone disorder xeroderma pigmentosum. The XPC gene spans 33 kb and has 16 exons (82–882 bp) and 15 introns (0.08–5.4 kb). A 1.6 kb intron...
Computation-Directed Identification of OxyR DNA Binding Sites in Escherichia coli (2001)
Ming Zheng, Xunde Wang, Bernard Doan, Karen A. Lewis, Thomas D. Schneider, Gisela Storz
A computational search was carried out to identify additional targets for the Escherichia coli OxyR transcription factor. This approach predicted OxyR binding sites upstream of dsbG, encoding a...
Evolution of Biological Information (2001)
Thomas D. Schneider, Thomas Schneider
How do genetic systems gain information by evolutionary processes? Answering this question precisely requires a robust, quantitative measure of information. Fortunately, fty years ago Claude Shannon...
Emmert, Steffen, Schneider, Thomas D., Khan, Sikandar G., Kraemer, Kenneth H.
Defects in the XPG DNA repair endonuclease gene can result in the cancer-prone disorders xeroderma pigmentosum (XP) or the XP–Cockayne syndrome complex. While the XPG cDNA sequence was known,...
Kannan, N, Schneider, Thomas D, Vishveshwara, S
A protein sequence can be classified into one of four structural classes, namely $\alpha, \beta, \alpha + \beta \hspace{2mm} and \hspace{2mm} \alpha/\beta$, based on its amino-acid composition. The...
Kannan, N, Schneider, Thomas D, Vishveshwara, S
A protein sequence can be classified into one of four structural classes, namely $\alpha, \beta, \alpha + \beta \hspace{2mm} and \hspace{2mm} \alpha/\beta$, based on its amino-acid composition. The...
Evolution Of Biological Information (2000)
How do genetic systems gain information by evolutionary processes? Answering this question precisely requires a robust, quantitative measure of information. Fortunately, 50 years ago Claude Shannon...
Evolution of biological information (2000)
key words: evolution, information theory, sequence logo. Nucleic Acids Res, 28(14): 2794-2799, 2000
Evolution of biological information (2000)
How do genetic systems gain information by evolutionary processes? Answering this question precisely requires a robust, quantitative measure of information. Fortunately, 50 years ago Claude Shannon...
Information Theory Primer (1999)
this document cannot be copyrighted. Tom Schneider's Information Theory Primer 2 Information and Uncertainty
New Approaches in Mathematical Biology: Information Theory and Molecular Machines (1996)
Thomas Schneider, Thomas D. Schneider
. My research uses classical information theory to study genetic systems. Information theory, founded by Claude Shannon in the 1940's, has had an enormous impact on communications engineering...
Quantitative analysis of ribosome binding sites in E.coli (1994)
Barrick, Doug, Villanueba, Keith, Childs, John, Kalil, Rhonda, Schneider, Thomas D., Lawrence, Charles E., ...
185 clones with randomized ribosome binding sites, from position −11 to 0 preceding the coding region of β-galactosidase, were selected and sequenced. The translatlonal yield of each clone was...
The Brunn-Minkowski theory (1993)
This primer is written for molecular biologists who are unfamiliar with information theory. Its purpose is to introduce you to these ideas so that you can understand how to apply them to binding...
Sequence logos: A new way to display consensus sequences (1990)
Thomas D. Schneider, R. Michael Stephens
A graphical method is presented for displaying the patterns in a set of aligned sequences. The characters representing the sequence are stacked on top of each other for each position in the aligned...
Sequence logos: a new way to display consensus sequences (1990)
Schneider, Thomas D., Stephens, R.Michael
A graphical method is presented for displaying the patterns in a set of aligned sequences. The characters representing the sequence are stacked on top of each other for each position in the aligned...
Schneider, Thomas D., Stormo, Gary D.
In our previous analysis of the information at binding sites on nucleic acids, we found that most of the sites examined contain the amount of information expected from their frequency in the genome....
Quantitative analysis of the relationship between nucleotide sequence and functional activity (1986)
Stormo, Gary D., Schneider, Thomas D., Gold, Larry
Matrices can be used to evaluate sequences for functional activity. Multiple regression can solve for the matrix that gives the best fit between sequence evaluations and quantitative activities. This...
Characterization of translational initiation sites in E. coli (1982)
Stormo, Gary D., Schneider, Thomas D., Gold, Larry M.
We characterize the Shine and Dalgarno sequence of 124 known gene beginnings This information is used to make “rules” which help distinguish gene beginning from other sites in a library of over...
Use of the 'Perceptron' algorithm to distinguish translational initiation sites in E. coli (1982)
Stormo, Gary D., Schneider, Thomas D., Gold, Larry, Ehrenfeucht, Andrzej
We have used a “Perceptron” algorithm to find a weighting function which distinguishes E. coli translational initiation sites from all other sites in a library of over 78,000 nucleotides of mRNA...
A design for computer nucleic-acid-sequence storage, retrieval, and manipulation (1982)
Schneider, Thomas D., Stormo, Gary D., Haemer, Jeffrey S., Gold, Larry
He have designed and built a data-base system for the storage of nucleic-acid sequences. The system consists of a data base (“the library”) and software that manages and provides access to that...
The human XPG gene: gene architecture, alternative splicing and single nucleotide polymorphisms
Emmert, Steffen, Schneider, Thomas D., Khan, Sikandar G., Kraemer, Kenneth H.
Defects in the XPG DNA repair endonuclease gene can result in the cancer-prone disorders xeroderma pigmentosum (XP) or the XP–Cockayne syndrome complex. While the XPG cDNA sequence was known,...
Computation-Directed Identification of OxyR DNA Binding Sites in Escherichia coli
Zheng, Ming, Wang, Xunde, Doan, Bernard, Lewis, Karen A., Schneider, Thomas D., Storz, Gisela
A computational search was carried out to identify additional targets for the Escherichia coli OxyR transcription factor. This approach predicted OxyR binding sites upstream of dsbG, encoding a...
The sequence logo for DNA binding sites of the bacteriophage P1 replication protein RepA shows unusually high sequence conservation (∼2 bits) at a minor groove that faces RepA. However, B-form DNA...
Lyakhov, Ilya G., Hengen, Paul N., Rubens, Denise, Schneider, Thomas D.
The RepA protein from bacteriophage P1 binds DNA to initiate replication. RepA covers one face of the DNA and the binding site has a completely conserved T that directly faces RepA from the minor...
Evolution of biological information
How do genetic systems gain information by evolutionary processes? Answering this question precisely requires a robust, quantitative measure of information. Fortunately, 50 years ago Claude Shannon...
OxyR and SoxRS Regulation of fur
Zheng, Ming, Doan, Bernard, Schneider, Thomas D., Storz, Gisela
The cytotoxic effects of reactive oxygen species are largely mediated by iron. Hydrogen peroxide reacts with iron to form the extremely reactive and damaging hydroxyl radical via the Fenton reaction....
Matten, Sharlene R., Schneider, Thomas D., Ringquist, Steven, Brusilow, William S. A.
The uncB gene codes for the a subunit of the Fo proton channel sector of the Escherichia coli F1 Fo ATPase. Control of expression of uncB appears to be exerted at some step after translational...
Khan, Sikandar G., Muniz-Medina, Vanessa, Shahlavi, Tala, Baker, Carl C., Inui, Hiroki, Ueda, Takahiro, ...
XPC DNA repair gene mutations result in the cancer-prone disorder xeroderma pigmentosum. The XPC gene spans 33 kb and has 16 exons (82–882 bp) and 15 introns (0.08–5.4 kb). A 1.6 kb intron was...
Molecular flip–flops formed by overlapping Fis sites
Hengen, Paul N., Lyakhov, Ilya G., Stewart, Lisa E., Schneider, Thomas D.
The DNA-binding protein Fis frequently uses pairs of sites 7 or 11 base pairs (bp) apart. Two overlapping Fis sites separated by 11 bp are found in the Escherichia coli origin of chromosomal...
A design for computer nucleic-acid-sequence storage, retrieval, and manipulation
Schneider, Thomas D., Stormo, Gary D., Haemer, Jeffrey S., Gold, Larry
We have designed and built a data-base system for the storage of nucleic-acid sequences. The system consists of a data base (“the library”) and software that manages and provides access to that...
Chen, Zehua, Schneider, Thomas D.
Molecular information theory was used to create sequence logos and promoter models for eight phages of the T7 group: T7, φA1122, T3, φYeO3-12, SP6, K1-5, gh-1 and K11. When these models were used...
Chen, Zehua, Schneider, Thomas D.
Based on molecular information theory, 10 T7-like promoter models were built for the T7 group of phages and used to scan their host genomes and closely related genomes. 38 genomes were scanned and 12...
CorreLogo: an online server for 3D sequence logos of RNA and DNA alignments
Bindewald, Eckart, Schneider, Thomas D., Shapiro, Bruce A.
We present an online server that generates a 3D representation of properties of user-submitted RNA or DNA alignments. The visualized properties are information of single alignment columns, mutual...
The human XPG gene: gene architecture, alternative splicing and single nucleotide polymorphisms
Emmert, Steffen, Schneider, Thomas D., Khan, Sikandar G., Kraemer, Kenneth H.
Defects in the XPG DNA repair endonuclease gene can result in the cancer-prone disorders xeroderma pigmentosum (XP) or the XP–Cockayne syndrome complex. While the XPG cDNA sequence was known,...
Computation-Directed Identification of OxyR DNA Binding Sites in Escherichia coli
Zheng, Ming, Wang, Xunde, Doan, Bernard, Lewis, Karen A., Schneider, Thomas D., Storz, Gisela
A computational search was carried out to identify additional targets for the Escherichia coli OxyR transcription factor. This approach predicted OxyR binding sites upstream of dsbG, encoding a...
The sequence logo for DNA binding sites of the bacteriophage P1 replication protein RepA shows unusually high sequence conservation (∼2 bits) at a minor groove that faces RepA. However, B-form DNA...
Lyakhov, Ilya G., Hengen, Paul N., Rubens, Denise, Schneider, Thomas D.
The RepA protein from bacteriophage P1 binds DNA to initiate replication. RepA covers one face of the DNA and the binding site has a completely conserved T that directly faces RepA from the minor...
Evolution of biological information
How do genetic systems gain information by evolutionary processes? Answering this question precisely requires a robust, quantitative measure of information. Fortunately, 50 years ago Claude Shannon...
OxyR and SoxRS Regulation of fur
Zheng, Ming, Doan, Bernard, Schneider, Thomas D., Storz, Gisela
The cytotoxic effects of reactive oxygen species are largely mediated by iron. Hydrogen peroxide reacts with iron to form the extremely reactive and damaging hydroxyl radical via the Fenton reaction....
Matten, Sharlene R., Schneider, Thomas D., Ringquist, Steven, Brusilow, William S. A.
The uncB gene codes for the a subunit of the Fo proton channel sector of the Escherichia coli F1 Fo ATPase. Control of expression of uncB appears to be exerted at some step after translational...
Khan, Sikandar G., Muniz-Medina, Vanessa, Shahlavi, Tala, Baker, Carl C., Inui, Hiroki, Ueda, Takahiro, ...
XPC DNA repair gene mutations result in the cancer-prone disorder xeroderma pigmentosum. The XPC gene spans 33 kb and has 16 exons (82–882 bp) and 15 introns (0.08–5.4 kb). A 1.6 kb intron was...
Molecular flip–flops formed by overlapping Fis sites
Hengen, Paul N., Lyakhov, Ilya G., Stewart, Lisa E., Schneider, Thomas D.
The DNA-binding protein Fis frequently uses pairs of sites 7 or 11 base pairs (bp) apart. Two overlapping Fis sites separated by 11 bp are found in the Escherichia coli origin of chromosomal...
A design for computer nucleic-acid-sequence storage, retrieval, and manipulation
Schneider, Thomas D., Stormo, Gary D., Haemer, Jeffrey S., Gold, Larry
We have designed and built a data-base system for the storage of nucleic-acid sequences. The system consists of a data base (“the library”) and software that manages and provides access to that...
Chen, Zehua, Schneider, Thomas D.
Molecular information theory was used to create sequence logos and promoter models for eight phages of the T7 group: T7, φA1122, T3, φYeO3-12, SP6, K1-5, gh-1 and K11. When these models were used...
Chen, Zehua, Schneider, Thomas D.
Based on molecular information theory, 10 T7-like promoter models were built for the T7 group of phages and used to scan their host genomes and closely related genomes. 38 genomes were scanned and 12...
CorreLogo: an online server for 3D sequence logos of RNA and DNA alignments
Bindewald, Eckart, Schneider, Thomas D., Shapiro, Bruce A.
We present an online server that generates a 3D representation of properties of user-submitted RNA or DNA alignments. The visualized properties are information of single alignment columns, mutual...
Anatomy of Escherichia coli σ70 promoters
Shultzaberger, Ryan K., Chen, Zehua, Lewis, Karen A., Schneider, Thomas D.
Information theory was used to build a promoter model that accounts for the −10, the −35 and the uncertainty of the gap between them on a common scale. Helical face assignment indicated that base...
Correlation between binding rate constants and individual information of E. coli Fis binding sites
Shultzaberger, Ryan K., Roberts, Lindsey R., Lyakhov, Ilya G., Sidorov, Igor A., Stephen, Andrew G., Fisher, Robert J., ...
Individual protein binding sites on DNA can be measured in bits of information. This information is related to the free energy of binding by the second law of thermodynamics, but binding kinetics...
Discovery of Fur binding site clusters in Escherichia coli by information theory models
Chen, Zehua, Lewis, Karen A., Shultzaberger, Ryan K., Lyakhov, Ilya G., Zheng, Ming, Doan, Bernard, ...
Fur is a DNA binding protein that represses bacterial iron uptake systems. Eleven footprinted Escherichia coli Fur binding sites were used to create an initial information theory model of Fur...
Discovery of novel tumor suppressor p53 response elements using information theory
Lyakhov, Ilya G., Krishnamachari, Annangarachari, Schneider, Thomas D.
An accurate method for locating genes under tumor suppressor p53 control that is based on a well-established mathematical theory and built using naturally occurring, experimentally proven p53 sites...