SHORT COMMUNICATION The Histone Database: A Comprehensive Resource for Histones and Histone (2008)
Fold-containing Proteins, Leonardo Mariño-ramírez, Benjamin Hsu, Andreas D. Baxevanis, David L
and searchable collection of full-length sequences and structures of histones and nonhistone proteins containing histone-like folds, compiled from major public databases. Several new histone...
Hox, Wnt, and the evolution of the primary body axis: insights from the early-divergent phyla (2007)
Ryan, Joseph F, Baxevanis, Andreas D
Abstract The subkingdom Bilateria encompasses the overwhelming majority of animals, including all but four early-branching phyla: Porifera, Ctenophora, Placozoa, and Cnidaria. On average, these...
The ENCODEdb portal: Simplified access to ENCODE Consortium data (2007)
Elnitski, Laura L., Shah, Prachi, Moreland, R. Travis, Umayam, Lowell, Wolfsberg, Tyra G., Baxevanis, Andreas D.
The Encyclopedia of DNA Elements (ENCODE) project aims to identify and characterize all functional elements in a representative chromosomal sample comprising 1% of the human genome. Data generated by...
GeneLink: a database to facilitate genetic studies of complex traits (2004)
Gillanders, Elizabeth M, Masiello, Anthony, Gildea, Derek, Umayam, Lowell, Duggal, Priya, Jones, Mary, ...
Abstract Background In contrast to gene-mapping studies of simple Mendelian disorders, genetic analyses of complex traits are far more challenging, and high quality data management systems are often...
The Molecular Biology Database Collection: 2003 update (2003)
The Molecular Biology Database Collection is an online resource listing key databases of value to the biological community. This Collection is intended to bring fellow scientists' attention to...
The Homeodomain Resource: 2003 update (2003)
Banerjee-Basu, Sharmila, Moreland, Travis, Hsu, Benjamin J., Trout, Kenneth L., Baxevanis, Andreas D.
The Homeodomain Resource is a searchable, curated collection of information for the homeodomain protein family. The resource is organized in a compact form and provides user-friendly interfaces for...
Saleem, Ramsey A., Banerjee-Basu, Sharmila, Berry, Fred B., Baxevanis, Andreas D., Walter, Michael A.
Five missense mutations (P79L, P79T, I91S, I91T and R127H) within the forkhead DNA-binding domain of the FOXC1 transcription factor, identified in patients with Axenfeld–Rieger (AR) malformations,...
The DNA-binding region of RAG 1 is not a homeodomain (2002)
Banerjee-Basu, Sharmila, Baxevanis, Andreas D
No abstract available.
DOI: 10.1093/nar/gkg118 The Homeodomain Resource: 2003 update (2002)
Sharmila Banerjee-basu, Travis Morel, Benjamin J. Hsu, Kenneth L. Trout, Andreas D. Baxevanis
The Homeodomain Resource is a searchable, curated collection of information for the homeodomain protein family. The resource is organized in a compact form and provides user-friendly interfaces for...
The Molecular Biology Database Collection: 2002 update (2002)
The Molecular Biology Database Collection is an online resource listing key databases of value to the biological community. This Collection is intended to bring fellow scientists’ attention to...
Sullivan, Steven, Sink, Daniel W., Trout, Kenneth L., Makalowska, Izabela, Taylor, Patrick M., Baxevanis, Andreas D., ...
Histone proteins are often noted for their high degree of sequence conservation. It is less often recognized that the histones are a heterogeneous protein family. Furthermore, several classes of...
Molecular evolution of the homeodomain family of transcription factors (2001)
Banerjee-Basu, Sharmila, Baxevanis, Andreas D.
The homeodomain family of transcription factors plays a fundamental role in a diverse set of functions that include body plan specification, pattern formation and cell fate determination during...
The Molecular Biology Database Collection is an online resource listing key databases of value to the biological community. This Collection is intended to bring fellow scientists’ attention to...
The Homeodomain Resource: sequences, structures, DNA binding sites and genomic information (2001)
Banerjee-Basu, Sharmila, Sink, Daniel W., Baxevanis, Andreas D.
The Homeodomain Resource is an annotated collection of non-redundant protein sequences, three-dimensional structures and genomic information for the homeodomain protein family. Release 3.0 contains...
GeneMachine: gene prediction and sequence annotation (2001)
Makalowska, Izabela, Ryan, Joseph F., Baxevanis, Andreas D.
Motivation: A number of free-standing programs have been developed in order to help researchers find potential coding regions and deduce gene structure for long stretches of what is essentially...
The Molecular Biology Database Collection represents an effort geared at making molecular biology database resources more accessible to biologists. This online resource, available at...
Sullivan, Steven A., Aravind, L., Makalowska, Izabela, Baxevanis, Andreas D., Landsman, David
The Histone Database (HDB) is an annotated and searchable collection of all full-length sequences and structures of histone and non-histone proteins containing the histone fold motif. These sequences...
The Homeodomain Resource: a prototype database for a large protein family (2000)
Banerjee-Basu, Sharmila, Ryan, Joseph F., Baxevanis, Andreas D.
The Homeodomain Resource is an annotated collection of non-redundant protein sequences, three-dimensional structures and genomic information for the homeodomain protein family. Release 2.0 contains...
The Sox10Dom Mouse: Modeling the Genetic Variation of Waardenburg-Shah (WS4) Syndrome (1999)
Southard-Smith, E. Michelle, Angrist, Misha, Ellison, Jane S., Agarwala, Richa, Baxevanis, Andreas D., Chakravarti, Aravinda, ...
Histone Sequence Database: new histone fold family members (1998)
Searches of the major public protein databases with core and linker chicken and human histone sequences have resulted in the compilation of an annotated set of histone protein sequences. In addition,...
Predictive methods using protein sequences (1998)
Andreas D. Baxevanis, Sharmila Banerjee-basu, Genome Technology Branch, Andreas D. Baxevanis, Genome Technology Branch
The discussions of databases and information retrieval in earlier chapters of this book document the tremendous explosion in the amount of sequence information available in a variety of public...
Histone Sequence Database: new histone fold family members (1998)
Andreas D. Baxevanis, David Landsman, David L
Searches of the major public protein databases with core and linker chicken and human histone sequences have resulted in the compilation of an annotated set of histone protein sequences. In addition,...
Histone Sequence Database: a compilation of highly-conserved nucleoprotein sequences (1995)
By searching the current protein sequence databases using sequences from human and chicken histones H1/H5, H2A, H2B, H3 and H4, a database of aligned histone protein sequences with statistically...
The HMG-1 box protein family: classification and functional relationships (1995)
Baxevanis, Andreas D., Landsman, David
The abundant and highly-conserved nucleoprotelns comprising the high mobility group−1/−2 (HMG−1/−2) family contains two homologous basic domains of about 75 amino acids. These basic domains,...
Homology model building of the HMG-1 box structural domain (1995)
Baxevanis, Andreas D., Bryant, Stephen H., Landsman, David
Nucleoproteins belonging to the HMG-1/-2 family possess homologous domains ∼75 amino acids in length. These domains, termed HMG-1 boxes, are highly structured, compact, and mediate the interaction...
A variety of DNA-binding and multimeric proteins contain the histone fold motif (1995)
Baxevanis, Andreas D., Arents, Gina, Moudrianakis, Evangelos N., Landsman, David
The histone fold motif has previously been Identified as a structural feature common to all four core histones and is involved In both histone-histone and histone- DNA Interactions. Through the use...
Vita.
Progressive juvenile-onset punctate cataracts caused by mutation of the γD-crystallin gene
Stephan, Dietrich A., Gillanders, Elizabeth, Vanderveen, Deborah, Freas-Lutz, Diana, Wistow, Graeme, Baxevanis, Andreas D., ...
Cataracts are a significant public health problem. Here, we describe the genetic alteration responsible for a progressive form of cataract, segregating as an autosomal dominant trait in a...
Characterization of the CHD family of proteins
Woodage, Trevor, Basrai, Munira A., Baxevanis, Andreas D., Hieter, Philip, Collins, Francis S.
The murine gene CHD1 (MmCHD1) was previously isolated in a search for proteins that bound a DNA promoter element. The presence of chromo (chromatin organization modifier) domains and an SNF2-related...
The Homeodomain Resource: sequences, structures, DNA binding sites and genomic information
Banerjee-Basu, Sharmila, Sink, Daniel W., Baxevanis, Andreas D.
The Homeodomain Resource is an annotated collection of non-redundant protein sequences, three-dimensional structures and genomic information for the homeodomain protein family. Release 3.0 contains...
The Molecular Biology Database Collection: an updated compilation of biological database resources
The Molecular Biology Database Collection is an online resource listing key databases of value to the biological community. This Collection is intended to bring fellow scientists’ attention to...
Molecular evolution of the homeodomain family of transcription factors
Banerjee-Basu, Sharmila, Baxevanis, Andreas D.
The homeodomain family of transcription factors plays a fundamental role in a diverse set of functions that include body plan specification, pattern formation and cell fate determination during...
Sullivan, Steven, Sink, Daniel W., Trout, Kenneth L., Makalowska, Izabela, Taylor, Patrick M., Baxevanis, Andreas D., ...
Histone proteins are often noted for their high degree of sequence conservation. It is less often recognized that the histones are a heterogeneous protein family. Furthermore, several classes of...
The Molecular Biology Database Collection: 2002 update
The Molecular Biology Database Collection is an online resource listing key databases of value to the biological community. This Collection is intended to bring fellow scientists’ attention to...
The Histone Database: a comprehensive WWW resource for histones and histone fold-containing proteins
Sullivan, Steven A., Aravind, L., Makalowska, Izabela, Baxevanis, Andreas D., Landsman, David
The Histone Database (HDB) is an annotated and searchable collection of all full-length sequences and structures of histone and non-histone proteins containing the histone fold motif. These sequences...
The Homeodomain Resource: a prototype database for a large protein family
Banerjee-Basu, Sharmila, Ryan, Joseph F., Baxevanis, Andreas D.
The Homeodomain Resource is an annotated collection of non-redundant protein sequences, three-dimensional structures and genomic information for the homeodomain protein family. Release 2.0 contains...
The Molecular Biology Database Collection: an online compilation of relevant database resources
The Molecular Biology Database Collection represents an effort geared at making molecular biology database resources more accessible to biologists. This online resource, available at...
The DNA-binding region of RAG 1 is not a homeodomain
Banerjee-Basu, Sharmila, Baxevanis, Andreas D
Functional annotation is used to catalog information that would be of value in experimental design and analysis but annotations in public databases are often incorrect. Here, one such case is...
The Homeodomain Resource: 2003 update
Banerjee-Basu, Sharmila, Moreland, Travis, Hsu, Benjamin J., Trout, Kenneth L., Baxevanis, Andreas D.
The Homeodomain Resource is a searchable, curated collection of information for the homeodomain protein family. The resource is organized in a compact form and provides user-friendly interfaces for...
The Molecular Biology Database Collection: 2003 update
The Molecular Biology Database Collection is an online resource listing key databases of value to the biological community. This Collection is intended to bring fellow scientists' attention to...
GeneLink: a database to facilitate genetic studies of complex traits
Gillanders, Elizabeth M, Masiello, Anthony, Gildea, Derek, Umayam, Lowell, Duggal, Priya, Jones, Mary Pat, ...
Saleem, Ramsey A., Banerjee-Basu, Sharmila, Berry, Fred B., Baxevanis, Andreas D., Walter, Michael A.
Five missense mutations of the winged-helix FOXC1 transcription factor, found in patients with Axenfeld-Rieger (AR) malformations, were investigated for their effects on FOXC1 structure and function....
Using Genomic Databases for Sequence-Based Biological Discovery
The inherent potential underlying the sequence data produced by the International Human Genome Sequencing Consortium and other systematic sequencing projects is, obviously, tremendous. As such, it...
Progressive juvenile-onset punctate cataracts caused by mutation of the γD-crystallin gene
Stephan, Dietrich A., Gillanders, Elizabeth, Vanderveen, Deborah, Freas-Lutz, Diana, Wistow, Graeme, Baxevanis, Andreas D., ...
Cataracts are a significant public health problem. Here, we describe the genetic alteration responsible for a progressive form of cataract, segregating as an autosomal dominant trait in a...
Characterization of the CHD family of proteins
Woodage, Trevor, Basrai, Munira A., Baxevanis, Andreas D., Hieter, Philip, Collins, Francis S.
The murine gene CHD1 (MmCHD1) was previously isolated in a search for proteins that bound a DNA promoter element. The presence of chromo (chromatin organization modifier) domains and an SNF2-related...
The Homeodomain Resource: sequences, structures, DNA binding sites and genomic information
Banerjee-Basu, Sharmila, Sink, Daniel W., Baxevanis, Andreas D.
The Homeodomain Resource is an annotated collection of non-redundant protein sequences, three-dimensional structures and genomic information for the homeodomain protein family. Release 3.0 contains...
The Molecular Biology Database Collection: an updated compilation of biological database resources
The Molecular Biology Database Collection is an online resource listing key databases of value to the biological community. This Collection is intended to bring fellow scientists’ attention to...
Molecular evolution of the homeodomain family of transcription factors
Banerjee-Basu, Sharmila, Baxevanis, Andreas D.
The homeodomain family of transcription factors plays a fundamental role in a diverse set of functions that include body plan specification, pattern formation and cell fate determination during...
Sullivan, Steven, Sink, Daniel W., Trout, Kenneth L., Makalowska, Izabela, Taylor, Patrick M., Baxevanis, Andreas D., ...
Histone proteins are often noted for their high degree of sequence conservation. It is less often recognized that the histones are a heterogeneous protein family. Furthermore, several classes of...
The Molecular Biology Database Collection: 2002 update
The Molecular Biology Database Collection is an online resource listing key databases of value to the biological community. This Collection is intended to bring fellow scientists’ attention to...
The Histone Database: a comprehensive WWW resource for histones and histone fold-containing proteins
Sullivan, Steven A., Aravind, L., Makalowska, Izabela, Baxevanis, Andreas D., Landsman, David
The Histone Database (HDB) is an annotated and searchable collection of all full-length sequences and structures of histone and non-histone proteins containing the histone fold motif. These sequences...
The Homeodomain Resource: a prototype database for a large protein family
Banerjee-Basu, Sharmila, Ryan, Joseph F., Baxevanis, Andreas D.
The Homeodomain Resource is an annotated collection of non-redundant protein sequences, three-dimensional structures and genomic information for the homeodomain protein family. Release 2.0 contains...
The Molecular Biology Database Collection: an online compilation of relevant database resources
The Molecular Biology Database Collection represents an effort geared at making molecular biology database resources more accessible to biologists. This online resource, available at...
The DNA-binding region of RAG 1 is not a homeodomain
Banerjee-Basu, Sharmila, Baxevanis, Andreas D
Functional annotation is used to catalog information that would be of value in experimental design and analysis but annotations in public databases are often incorrect. Here, one such case is...
The Homeodomain Resource: 2003 update
Banerjee-Basu, Sharmila, Moreland, Travis, Hsu, Benjamin J., Trout, Kenneth L., Baxevanis, Andreas D.
The Homeodomain Resource is a searchable, curated collection of information for the homeodomain protein family. The resource is organized in a compact form and provides user-friendly interfaces for...
The Molecular Biology Database Collection: 2003 update
The Molecular Biology Database Collection is an online resource listing key databases of value to the biological community. This Collection is intended to bring fellow scientists' attention to...
GeneLink: a database to facilitate genetic studies of complex traits
Gillanders, Elizabeth M, Masiello, Anthony, Gildea, Derek, Umayam, Lowell, Duggal, Priya, Jones, Mary Pat, ...
Saleem, Ramsey A., Banerjee-Basu, Sharmila, Berry, Fred B., Baxevanis, Andreas D., Walter, Michael A.
Five missense mutations of the winged-helix FOXC1 transcription factor, found in patients with Axenfeld-Rieger (AR) malformations, were investigated for their effects on FOXC1 structure and function....
Using Genomic Databases for Sequence-Based Biological Discovery
The inherent potential underlying the sequence data produced by the International Human Genome Sequencing Consortium and other systematic sequencing projects is, obviously, tremendous. As such, it...
Ryan, Joseph F., Mazza, Maureen E., Pang, Kevin, Matus, David Q., Baxevanis, Andreas D., Martindale, Mark Q., ...
The ENCODEdb portal: Simplified access to ENCODE Consortium data
Elnitski, Laura L., Shah, Prachi, Moreland, R. Travis, Umayam, Lowell, Wolfsberg, Tyra G., Baxevanis, Andreas D.
The Encyclopedia of DNA Elements (ENCODE) project aims to identify and characterize all functional elements in a representative chromosomal sample comprising 1% of the human genome. Data generated by...
Hox, Wnt, and the evolution of the primary body axis: insights from the early-divergent phyla
Ryan, Joseph F, Baxevanis, Andreas D
The subkingdom Bilateria encompasses the overwhelming majority of animals, including all but four early-branching phyla: Porifera, Ctenophora, Placozoa, and Cnidaria. On average, these...