Research Topics
Genomes and Genes
| Andreas D BaxevanisSummaryAffiliation: National Institutes of Health Country: USA Publications
| Collaborators
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Detail Information
Publications
Characterization of the CHD family of proteinsT Woodage
Laboratory of Gene Transfer, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA
Proc Natl Acad Sci U S A 94:11472-7. 1997....- The Molecular Biology Database Collection: 2003 updateAndreas D Baxevanis
Genome Technology Branch, National Human Genome Research Institute, National Institutes of Health, Building 50, Room 5222, Bethesda, MD 20892 8002, USA
Nucleic Acids Res 31:1-12. 2003..Short, searchable summaries and updates for each of the databases included in this Collection are available through the Nucleic Acids Research Web site at http://nar.oupjournals.org... - The DNA-binding region of RAG 1 is not a homeodomainSharmila Banerjee-Basu
Genome Technology Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892-4470, USA
Genome Biol 3:INTERACTIONS1004. 2002..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 discussed... - The molecular biology database collection: an online compilation of relevant database resourcesA D Baxevanis
Genome Technology Branch, National Human Genome Research Institute, National Institutes of Health, Building 49, Room 4A 22, Bethesda, MD 20892 4470, USA
Nucleic Acids Res 28:1-7. 2000..An emphasis has also been placed on including databases where new value is added to the underlying data by virtue of curation, new data connections, or other innovative approaches... 
Homology model building of Hho1p supports its role as a yeast histone H1 proteinA D Baxevanis
Genome Technology Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland 20892, USA
In Silico Biol 1:5-11. 1998..These findings support the proposal that Hho1p acts as an "H1 dimer" and could be responsible for the decreased linker DNA length observed between nucleosomal core particles...- The Molecular Biology Database Collection: an updated compilation of biological database resourcesA D Baxevanis
Genome Technology Branch, National Human Genome Research Institute, National Institutes of Health, Building 49, Room 4A 22, Bethesda, MD 20892 4470, USA
Nucleic Acids Res 29:1-10. 2001..Short, searchable summaries of each of the databases included in the Collection are available through the Nucleic Acids Research Web site, at http://www. nar.oupjournals.org... - The Molecular Biology Database Collection: 2002 updateAndreas D Baxevanis
Genome Technology Branch, National Human Genome Research Institute, National Institutes of Health, Building 50, Room 5222, Bethesda, MD 20892 8002, USA
Nucleic Acids Res 30:1-12. 2002..Short, searchable summaries and updates for each of the databases included in the Collection are available through the Nucleic Acids Research Web site at http://nar.oupjournals.org... - Using genomic databases for sequence-based biological discoveryAndreas D Baxevanis
Genome Technology Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland 20852, USA
Mol Med 9:185-92. 2003..An overview of the types of information available through each of these front-ends is given, as well as information on tutorials and other documentation intended to increase the reader's familiarity with these tools... - The homeodomain complement of the ctenophore Mnemiopsis leidyi suggests that Ctenophora and Porifera diverged prior to the ParaHoxozoaJoseph F Ryan
Genome Technology Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
Evodevo 1:9. 2010..The homeobox superfamily of genes is particularly suited for these kinds of gene content comparisons, since it is large, diverse, and features a highly conserved domain... - The Histone Database: an integrated resource for histones and histone fold-containing proteinsLeonardo Mariño-Ramírez
Computational Biology Branch, National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, 8600 Rockville Pike, MSC 6075, Bethesda, MD 20894 6075, USA
Database (Oxford) 2011:bar048. 2011..The Histone Sequence Database is an inclusive resource for the analysis of chromatin structure and function focused on histones and histone fold-containing proteins... - Structural analysis of disease-causing mutations in the P-subfamily of forkhead transcription factorsSharmila Banerjee-Basu
Genome Technology Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland 20892 8002, USA
Proteins 54:639-47. 2004..The missense mutations R553H in FOXP2 and R397W in FOXP3 dramatically alter the electrostatic potentials of the molecular surface of their respective forkhead domains... - The ENCODEdb portal: simplified access to ENCODE Consortium dataLaura L Elnitski
Genome Technology Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland 20892, USA
Genome Res 17:954-9. 2007..The ENCODEdb portal is freely accessible at http://research.nhgri.nih.gov/ENCODEdb... - The Histone Database: a comprehensive resource for histones and histone fold-containing proteinsLeonardo Mariño-Ramírez
Computational Biology Branch, National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland 20894 6075, USA
Proteins 62:838-42. 2006..The Histone Database is a comprehensive bioinformatics resource for the study of structure and function of histones and histone fold-containing proteins. The database is available at http://research.nhgri.nih.gov/histones/... - Characteristics of users of online personalized genomic risk assessments: implications for physician-patient interactionsColleen M McBride
Social and Behavioral Research Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland 20892, USA
Genet Med 11:582-7. 2009..To evaluate what psychological and behavioral factors predict who is likely to seek SNP-based genetic tests for multiple common health conditions where feedback can be used to motivate primary prevention... - Searching Online Mendelian Inheritance in Man (OMIM) for information for genetic loci involved in human diseaseAndreas D Baxevanis
National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland, USA
Curr Protoc Bioinformatics . 2002..This unit gives an overview of the OMIM database, the layout of the records, and the information that is available within each entry... - Consumers' use of web-based information and their decisions about multiplex genetic susceptibility testingKimberly A Kaphingst
Social and Behavioral Research Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
J Med Internet Res 12:e41. 2010.... - Searching Online Mendelian Inheritance in Man (OMIM) for information for genetic loci involved in human diseaseAndreas D Baxevanis
National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland, USA
Curr Protoc Hum Genet . 2003.... - An overview of gene identification: approaches, strategies, and considerationsAndreas D Baxevanis
National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland, USA
Curr Protoc Bioinformatics . 2004..This unit offers an overview of many of the gene prediction methods that are currently available and offers a general assessment of how well the methods work for various problems... - Molecular evolution of the homeodomain family of transcription factorsS Banerjee-Basu
Genome Technology Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892-4470, USA
Nucleic Acids Res 29:3258-69. 2001..The phylogenetic analysis, coupled with the chromosomal localization of these genes, provides powerful clues as to how each of these classes arose from the ancestral homeodomain... - The Homeodomain Resource: 2003 updateSharmila Banerjee-Basu
Genome Technology Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA
Nucleic Acids Res 31:304-6. 2003..All entries are cross-linked for easy retrieval of the original records from source databases. The Homeodomain Resource is freely available through the World Wide Web at http://research.nhgri.nih.gov/homeodomain/... - The Histone DatabaseSteven Sullivan
Computational Biology Branch, National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Building 45, Room 6AN12J, 45 Center Drive, MSC 6510, Bethesda, MD 20892-6510, USA
Nucleic Acids Res 30:341-2. 2002..The database also provides summaries of current information on solved histone fold structures, post-translational modifications of histones, and the human histone gene complement... - A 6-Mb high-resolution physical and transcription map encompassing the hereditary prostate cancer 1 (HPC1) regionJ D Carpten
Cancer Genetics Branch, Bethesda, Maryland 20892, USA
Genomics 64:1-14. 2000..An additional 11 known genes and ESTs have been placed within the larger 1q24-q31 interval. These transcription units represent candidate genes for multiple hereditary diseases, including HPC1... - The human RGL (RalGDS-like) gene: cloning, expression analysis and genomic organizationR Sood
Cancer Genetics Branch, National Human Genome Research Institute, National Institutes of Health, Building 36, Room 3D05, 9000 Rockville Pike, Bethesda, MD, USA
Biochim Biophys Acta 1491:285-8. 2000..Northern blot analysis shows that human RGL is expressed in a wide variety of tissues with strong expression being seen in the heart, brain, kidney, spleen and testis... - Cloning and characterization of 13 novel transcripts and the human RGS8 gene from the 1q25 region encompassing the hereditary prostate cancer (HPC1) locusR Sood
Cancer Genetics Branch, National Human Genome Research Institute, Bethesda, MD 20892, USA
Genomics 73:211-22. 2001..Overall, data on 13 novel transcripts and the human RGS8 gene (homologue of the rat RGS8 gene) are presented in this paper. Ten of the 13 novel transcripts are expressed in prostate tissue and represent positional candidates for HPC1... - GeneLink: a database to facilitate genetic studies of complex traitsElizabeth M Gillanders
Cancer Genetics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892 8000, USA
BMC Genomics 5:81. 2004..To minimize the difficulties inherent in complex trait studies, we have developed GeneLink, a Web-accessible, password-protected Sybase database... - Putting science over supposition in the arena of personalized genomicsColleen M McBride
Social and Behavioral Research Branch, National Genome Research Institute, National Institutes of Health, Bethesda, Maryland 20892, USA
Nat Genet 40:939-42. 2008..They also outline one element of this agenda, the Multiplex Initiative, which has been underway since 2006... - Power to the people. A User's Guide to the Human Genome. ForewardAndreas D Baxevanis
National Human Genome Research Institute, USA
Nat Genet 35:2. 2003 - A user's guide to the human genomeTyra G Wolfsberg
National Human Genome Research Institute, NIH, Bethesda, Maryland 20892, USA
Nat Genet 32:1-79. 2002 - A variety of DNA-binding and multimeric proteins contain the histone fold motifA D Baxevanis
National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
Nucleic Acids Res 23:2685-91. 1995..It is proposed that these proteins may share a similar three-dimensional conformation despite the lack of significant sequence similarity... - Pendred syndrome is caused by mutations in a putative sulphate transporter gene (PDS)L A Everett
Genome Technology Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland 20892, USA
Nat Genet 17:411-22. 1997.... - Genomic organization, evolution, and expression of photoprotein and opsin genes in Mnemiopsis leidyi: a new view of ctenophore photocytesChristine E Schnitzler
National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA
BMC Biol 10:107. 2012..We combined our genomic survey with gene trees, developmental expression patterns, and functional protein assays of photoproteins and opsins to provide a comprehensive view of light production and light reception in Mnemiopsis... - The diversification of the LIM superclass at the base of the metazoa increased subcellular complexity and promoted multicellular specializationBernard J Koch
Genome Technology Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland, United States of America
PLoS ONE 7:e33261. 2012..Despite their fundamental roles in cellular processes and human disease, little is known about the evolution of the LIM superclass... - Molecular modeling of mutations in the DNA-binding domain of the oncoprotein QinSharmila Banerjee-Basu
Genome Technology Branch, National Human Genome Research Institute, NIH, Bethesda, Maryland 20892-4470, USA
Mol Cancer Ther 1:1237-41. 2002..The mutated proteins form the overall structure of the forkhead domain, but the mutations do interfere with DNA binding... - Cumulative ligand activity of NODAL mutations and modifiers are linked to human heart defects and holoprosencephalyErich Roessler
Medical Genetics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892 3717, USA
Mol Genet Metab 98:225-34. 2009.... - Hox, Wnt, and the evolution of the primary body axis: insights from the early-divergent phylaJoseph F Ryan
Genome Technology Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA
Biol Direct 2:37. 2007.... - Identification of six novel genes by experimental validation of GeneMachine predicted genesIzabela Makalowska
Genome Technology Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
Gene 284:203-13. 2002..Our studies support the feasibility of identifying novel genes from regions of interest using draft human genome sequence... 
Internet basicsA D Baxevanis
National Human Genome Research Institute, NIH, Bethesda, Maryland, USA
Curr Protoc Protein Sci . 2001..Finally, one of the most common problems that has arisen with the proliferation of Web pages throughout the world is addressed--i.e., finding useful information on the World Wide Web...- MLH3: a DNA mismatch repair gene associated with mammalian microsatellite instabilityS M Lipkin
Genetics Branch, National Human Genome Research Institute, Bethesda, Maryland, USA
Nat Genet 24:27-35. 2000..Functional redundancy among Mlh3, Pms1 and Pms2 may explain why neither Pms1 nor Pms2 mutant mice develop colon cancer, and why PMS1 and PMS2 mutations are only rarely found in HNPCC families... - GeneMachine: gene prediction and sequence annotationI Makalowska
Genome Technology Branch, National Human Genome Research Institute, National Institutes of Health, Building 49, Room 4A-22, Bethesda, MD 20892, USA
Bioinformatics 17:843-4. 2001..nhgri.nih.gov. The Web supplement to this paper may be found at http://genome.nhgri.nih.gov/genemachine/supplement/... - MicroRNAs and essential components of the microRNA processing machinery are not encoded in the genome of the ctenophore Mnemiopsis leidyiEvan K Maxwell
Genome Technology Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA
BMC Genomics 13:714. 2012..The genomic repertoires of metazoan microRNAs have become increasingly endorsed as phylogenetic characters and drivers of biological complexity... - Physical and transcript map of the hereditary prostate cancer region at xq27Dietrich A Stephan
Cancer Genetics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA
Genomics 79:41-50. 2002..These transcriptional units represent candidate genes for HPCX and multiple other hereditary diseases at Xq26.3-q27.3... - The HMG-1 box protein family: classification and functional relationshipsA D Baxevanis
National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
Nucleic Acids Res 23:1604-13. 1995..The HMG-1 box provides an excellent example of how a specific protein motif, with slight alteration, can be used to recognize DNA in a variety of functional contexts... - Progressive juvenile-onset punctate cataracts caused by mutation of the gammaD-crystallin geneD A Stephan
Cancer Genetics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA
Proc Natl Acad Sci U S A 96:1008-12. 1999..This is the first gene defect shown to be responsible for a noncongenital progressive cataract, and studying the defective protein should teach us more about the mechanisms underlying cataract formation... - Internet basics for biologistsA D Baxevanis
National Human Genome Research Institute, NIH, Bethesda, Maryland, USA
Curr Protoc Cell Biol . 2001..This unit provides an introduction to the internet-how it is organized, how you connect to it, using email and file transfer protocols, and finding your way around the Web... - Internet basics for biologistsA D Baxevanis
National Human Genome Research Institute, NIH, Bethesda, Maryland, USA
Curr Protoc Hum Genet . 2001..Finally, one of the most common problems that has arisen with the proliferation of Web pages throughout the worldWith the explosion of sequence and structural information available to researchers, the field of bioinformatics is playing... - Internet basics for biologistsA D Baxevanis
National Human Genome Research Institute, NIH, Bethesda, Maryland, USA
Curr Protoc Mol Biol . 2001..Finally, one of the most common problems that has arisen with the proliferation of Web pages throughout the world is addressed, i.e., finding useful information on the World Wide Web... - Gene identification: methods and considerationsA D Baxevanis
National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland, USA
Curr Protoc Hum Genet . 2001..This unit introduces readers to some of the more commonly used techniques for gene identification... - Comparative analyses of the Dominant megacolon-SOX10 genomic interval in mouse and humanE M Southard-Smith
Genetic Disease Research Branch, National Human Genome Research Institute, National Institutes of Health, 49 Convent Dr, Bethesda, Maryland 20892-4470, USA
Mamm Genome 10:744-9. 1999 - Mutation of a gene encoding a putative chaperonin causes McKusick-Kaufman syndromeD L Stone
Genetic Diseases Research Branch, National Human Genome Research Institute, NIH, Bethesda, Maryland, USA
Nat Genet 25:79-82. 2000..We believe that this is the first description of a human disorder caused by mutations affecting a putative chaperonin molecule... - The Sox10(Dom) mouse: modeling the genetic variation of Waardenburg-Shah (WS4) syndromeE M Southard-Smith
Genetic Disease Research Branch, National Human Genome Research Institute, National Institutes of Health NIH, Bethesda, Maryland 20892 4472 USA
Genome Res 9:215-25. 1999..Structural analysis of the HMG DNA-binding domain was performed to evaluate the effect of human mutations in this region... - Loss-of-function mutations in growth differentiation factor-1 (GDF1) are associated with congenital heart defects in humansJ D Karkera
Medical Genetics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA
Am J Hum Genet 81:987-94. 2007..These findings implicate perturbations of the TGF- beta signaling pathway in the causation of a major subclass of human CHDs... - The importance of biological databases in biological discoveryAndreas D Baxevanis
Curr Protoc Bioinformatics . 2006..Non-sequence-centric databases such as Online Mendelian Inheritance in Man (OMIM), the Protein Data Bank (PDB), and the Kyoto Encyclopedia of Genes and Genomes (KEGG) are also discussed... - Searching the NCBI databases using EntrezAndreas D Baxevanis
Curr Protoc Hum Genet . 2006..The Support Protocol reviews how to save frequently-issued queries. Finally, Cn3D, a structure visualization tool, is also discussed... - Searching the NCBI databases using EntrezAndreas D Baxevanis
Curr Protoc Bioinformatics . 2006..The Support Protocol reviews how to save frequently-issued queries. Finally, Cn3D, a structure visualization tool, is also discussed... - Common file formatsShonda A Leonard
IBM Life Sciences, St Leonards, NSW, Australia
Curr Protoc Bioinformatics . 2007..Specifically, it reviews the rules for generating FASTA files and provides guidance for interpreting NCBI descriptor lines, commonly found in FASTA files. In addition, it reviews the construction of GenBank, Phylip, MSF and Nexus files... - Gaucher mutation N188S is associated with myoclonic epilepsyLaurence Kowarz
Hum Mutat 26:271-3; author reply 274-5. 2005..quot; Our clinical experience with patients carrying this mutation and preliminary protein modeling data lead us to dispute this conclusion...