On-line Documentation

• The current dbERGE schema
• Understanding the dbERGE schema
• Writing Genie queries

Publications

	1999
	Berman P, Zhang Z, Wolf Y, Koonin E, and Miller W (1999). Winnowing sequences from a database search. RECOMB '99: 50-58.
	Elnitski L, Li J, Noguchi C, Miller W, and Hardison R (1999). Cell type-specific positive and negative cis-elements regulate the level of enhancement by hypersensitive site 2 of the beta-globin locus control region. Re-submitted.
	Endrizzi M, Huang S, Scharf J, Kelter A-R, Wirth B, Kunkel L, Miller W, and Dietrich W (1999). Comparative sequence analysis of the mouse and human Lgn1/SMA interval. Genomics 60: 137-151.   PubMed
	Florea L, Li M, Riemer C, Giardine B, Miller W, and Hardison R (19__). Validating computer programs for functional genomics in gene regulatory regions. Submitted.
	Hardison R (1999). The evolution of hemoglobin: studies of a very ancient protein suggest that changes in gene regulation are an important part of the evolutionary story. Am Sci 87: 126-137.   Abstract
	Hwang S-Y, Oh B, Zhang Z, Miller W, Solter D, and Knowles B (1999). The mouse cornichon gene family. Dev Genes Evol 209: 120-125.   PubMed
	Ikonomi P, Kassahum H, Noguchi C, Hardison R, and Schechter A (1999). Levels of GATA1/GATA2 transcription factors modulate expression of embryonic and fetal hemoglobins. Submitted.
	Jang W, Hua A, Spilson S, Miller W, Roe B, and Meisler M (1999). Comparative sequence of human and mouse BAC clones from the mnd2 region of chromosome 2p13. Genome Res 9: 53-61.   PubMed
	Liang Y, Wang A, Belyantseva I, Anderson D, Probst F, Barber T, Miller W, Touchman J, Jin L, Sullivan S, Sellers J, Camper S, Lloyd R, Kachar B, Friedman T, and Fridell R (1999). Characterization of the human and mouse unconventional myosin XV genes responsible for hereditary deafness DFNB3 and shaker 2. Genomics 61: 243-258.   PubMed
	Liu X, Dangel A, Kelley R, Zhao W, Denny P, Botcherby M, Cattanach B, Peters J, Hunsicker P, Mallon A-M, Strivens M, Bate R, Miller W, Rhodes M, Brown S, and Herman G (1999). The gene mutated in bare patches and striated mice encodes a novel 3beta-hydroxysteroid dehydrogenase. Nat Genet 22: 182-187.   PubMed
	Schwartz S, Zhang Z, Frazer K, Smit A, Riemer C, Bouck J, Gibbs R, Hardison R, and Miller W (19__). PipMaker - a web server for aligning two genomic DNA sequences. Submitted.
	Stojanovic N, Florea L, Riemer C, Gumucio D, Slightom J, Goodman M, Miller W, and Hardison R (1999). Comparison of five methods for finding conserved sequences in multiple alignments of gene regulatory regions. Nucleic Acids Res 27: 3899-3910.   PubMed Reprint   (Reproduced with permission from NAR Online)
	Zhang Z, Berman P, Wiehe T, and Miller W (1999). Post-processing long pairwise alignments. To appear in Bioinformatics.
	Zhang Z, Schwartz S, Wagner L, and Miller W (1999). A greedy algorithm for aligning DNA sequences. To appear in J Comput Biol.
	1998
	Ansari-Lari M, Oeltjen J, Schwartz S, Zhang Z, Muzny D, Lu J, Gorrell J, Chinault A, Belmont J, Miller W, and Gibbs R (1998). Comparative sequence analysis of a gene-rich cluster at human chromosome 12p13 and its syntenic region in mouse chromosome 6. Genome Res 8: 29-40.   PubMed
	Bender M, Reik A, Close J, Telling A, Epner E, Fiering S, Hardison R, and Groudine M (1998). Description and targeted deletion of 5' hypersensitive site 5 and 6 of the mouse beta-globin locus control region. Blood 92: 4394-4403.   PubMed
	Bouck J, Miller W, Gorrell J, Muzny D, and Gibbs R (1998). Analysis of the quality and utility of random shotgun sequencing at low redundancies. Genome Res 8: 1074-1084.   PubMed
	Chui DHK, Hardison R, Riemer C, Miller W, Carver M, Molchanova T, Efremov G, and Huisman THJ (1998). An electronic database of human hemoglobin variants on the World Wide Web. Blood 91: 2643-2644.   PubMed
	Florea L, Hartzell G, Zhang Z, Rubin G, and Miller W (1998). A computer program for aligning a cDNA sequence with a genomic DNA sequence. Genome Res 8: 967-974.   PubMed
	Hardison R (1998). Hemoglobins from bacteria to man: evolution of different patterns of gene expression. J Exp Biol 201: 1099-1117.   PubMed
	Hardison R (1998). Organization and evolution of the globin genes. In ``Disorders of Hemoglobin'' (B Forget, D Higgs, R Nagel, and M Steinberg, eds.), Cambridge University Press, Cambridge, UK. In press.
	Hardison R, Chui DHK, Riemer C, Miller W, Carver M, Molchanova T, Efremov G, and Huisman THJ (1998). Access to ``A Syllabus of Human Hemoglobin Variants (1996)'' via the World Wide Web. Hemoglobin 22: 113-127.   PubMed
	Hardison R, Riemer C, Chui DHK, Huisman THJ, and Miller W (1998). Electronic access to sequence alignments, experimental results and human mutations as an aid to studying globin gene regulation. Genomics 47: 429-437.   PubMed
	Li J, Noguchi C, Miller W, Hardison R, Schechter A (1998). Multiple regulatory elements in the 5'-flanking sequence of the human epsilon-globin gene. J Biol Chem 273: 10202-10209.   PubMed
	Riemer C, ElSherbini A, Stojanovic N, Schwartz S, Kwitkin P, Miller W, and Hardison R (1998). A database of experimental results on globin gene expression. Genomics 53: 325-337.   PubMed
	Zhang Z, Berman P, and Miller W (1998). Alignments without low-scoring regions. J Comput Biol 5: 197-210.   PubMed
	Zhang Z, Schaffer A, Miller W, Madden T, Lipman D, Koonin E, and Altschul S (1998). Protein sequence similarity searches using patterns as seeds. Nucleic Acids Res 26: 3986-3990.   PubMed
	1997
	Altschul S, Madden T, Schaffer A, Zhang J, Zhang Z, Miller W, and Lipman D (1997). Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res 25: 3389-3402.   PubMed
	Chao K-M, Zhang J, Ostell J, and Miller W (1997). A tool for aligning very similar DNA sequences. Comput Appl Biosci 13: 75-80.   PubMed
	Elnitski L, Miller W, and Hardison R (1997). Conserved E boxes function as part of the enhancer in hypersensitive site 2 of the beta-globin locus control region: role of basic helix-loop-helix proteins. J Biol Chem 272: 369-378.   PubMed
	Hardison R (1997). Locus control regions of globin gene domains and hemoglobin switching: phylogenetic analysis and mechanism of action. In ``Production of Human Hemoglobin in Transgenic Swine: The Hunt for the Red Blood Cell Substitute'' (R Kumar, ed.) RG Landes Publishing Co, Georgetown, TX.
	Hardison R, Oeltjen J, and Miller W (1997). Long human-mouse sequence alignments reveal novel regulatory elements: a reason to sequence the mouse genome. Genome Res 7: 959-966.   PubMed
	Hardison R, Slightom J, Gumucio D, Goodman M, Stojanovic N, and Miller W (1997). Locus control regions of mammalian beta-globin gene clusters: combining phylogenetic analyses and experimental results to gain functional insights. Gene 205: 73-94.   PubMed
	Oeltjen J, Malley T, Muzny D, Miller W, Gibbs R, and Belmont J (1997). Large scale comparative sequence analysis of the human and murine Bruton's tyrosine kinase loci reveals conserved regulatory domains. Genome Res 7: 315-329.   PubMed
	Pearson W, Wood T, Zhang Z, and Miller W (1997). Comparison of DNA sequences with protein sequences. Genomics 46: 24-36.   PubMed
	Shelton D, Stegman L, Hardison R, Miller W, Slightom J, Goodman M, and Gumucio D (1997). Phylogenetic footprinting of hypersensitive site 3 of the beta-globin locus control region. Blood 89: 3457-3469.   PubMed
	Shewchuk B and Hardison R (1997). CpG islands from the alpha-globin gene cluster increase gene expression in an integration-dependent manner. Mol Cell Biol 17: 5856-5866.   PubMed
	Slightom J, Bock J, Tagle D, Gumucio D, Goodman M, Stojanovic N, Jackson J, Miller W, and Hardison R (1997). The complete sequences of the galago and rabbit beta-globin locus control regions: extended sequence and functional conservation outside the cores of DNase hypersensitive sites. Genomics 39: 90-94.   PubMed
	Stojanovic N, Berman P, Gumucio D, Hardison R, and Miller W (1997). A linear-time algorithm for the 1-mismatch problem. In ``Algorithms and Data Structures'' (F Dehne, A Rau-Chaplin, J Sack, and R Tamassia, eds.), Lecture Notes in Computer Science 1272: 126-135, Springer.
	Tang D, Ebb D, Hardison R, and Rodgers G (1997). Restoration of the CCAAT box or insertion of the CACCC motif activates delta-globin gene expression. Blood 90: 421-427.   PubMed
	Zhang Z, Pearson W, and Miller W (1997). Aligning a DNA sequence with a protein sequence. J Comput Biol 4: 339-349.   PubMed
	1996
	Fürer M and Miller W (1996). Alignment-to-alignment editing with ``move gap'' operations. Intl J Foundations Comput Sci 7: 23-41.
	Hardison R (1996). A brief history of hemoglobins: plant, animal, protist and bacteria. Proc Natl Acad Sci U S A 93: 5675-5679.   PubMed
	Jackson J, Miller W, and Hardison R (1996). Sequences within and flanking hypersensitive sites 3 and 2 of the beta-globin locus control region required for synergistic versus additive interaction with the epsilon-globin gene promoter. Nucleic Acids Res 24: 4327-4335.   PubMed
	Jackson J, Petrykowska H, Philipsen S, Miller W, and Hardison R (1996). Role of DNA sequences outside the cores of DNase hypersensitive sites (HSs) in functions of the beta-globin locus control region. Domain opening and synergism between HS2 and HS3. J Biol Chem 271: 11871-11878.   PubMed
	Myers G, Selznick S, Zhang Z, and Miller W (1996). Progressive multiple alignment with constraints. J Comput Biol 3: 563-572.   PubMed
	Zhang Z, He B, and Miller W (1996). Local multiple alignment via subgraph enumeration. Discr Appl Math 71: 337-365.
	1995
	Chao K-M and Miller W (1995). Linear-space algorithms that build local alignments from fragments. Algorithmica 13: 106-134.
	Chao K-M, Zhang J, Ostell J, and Miller W (1995). A local alignment tool for very long DNA sequences. Comput Appl Biosci 11: 147-153.   PubMed
	Hardison R, Elnitski L, ElSherbini A, Goldstrohm A, Jackson J, Peck J, Riemer C, Schwartz S, Stojanovic N, and Miller W (1995). The Globin Gene Server: an aid to studying the regulation of mammalian globin gene clusters. In ``Molecular Biology of Hemoglobin Switching: Volume 1 of the Proceedings of the 9th Conference on Hemoglobin Switching'' (G Stamatoyannopoulos, ed.), pp 405-426, Intercept Ltd, Andover, UK.
	Jackson J, ElSherbini A, Riemer C, Stojanovic N, Miller W, and Hardison R (1995). Effects of hypersensitive sites from beta-globin LCR on enhancement in transfected cells: synergism between HS3 and HS2. In ``Molecular Biology of Hemoglobin Switching: Volume 1 of the Proceedings of the 9th Conference on Hemoglobin Switching'' (G Stamatoyannopoulos, ed.), pp 87-109, Intercept Ltd, Andover, UK.
	James-Pederson M, Yost S, Shewchuk B, Zeigler T, Miller R, and Hardison R (1995). Flanking and intragenic sequences regulating the expression of the rabbit alpha-globin gene. J Biol Chem 270: 3965-3973.   PubMed
	Miller W, ElSherbini A, Peck J, Riemer C, Schwartz S, Stojanovic N, and Hardison R (1995). A database for globin gene expression data. In ``Proceedings of the 28th Annual Hawaii International Conference on Computer and System Sciences'', pp 62-71.   Complete paper
	Myers E and Miller W (1995). Chaining multiple-alignment fragments in sub-quadratic time. In ``Proceedings of the Sixth Annual ACM-SIAM Symposium on Discrete Algorithms'', pp 38-47.
	1994
	Chao K-M, Hardison R, and Miller W (1994). Recent developments in linear-space alignment methods: a survey. J Comput Biol 1: 271-291.   PubMed
	Hardison R, Chao K-M, Schwartz S, Stojanovic N, Ganetsky M, and Miller W (1994). Globin Gene Server: a prototype e-mail database server featuring extensive multiple alignments and data compilation for electronic genetic analysis. Genomics 21: 344-353.   PubMed
	Huang X, Pevzner P, and Miller W (1994). Parametric recomputing in alignment graphs. In ``Combinatorial Pattern Matching'', Lecture Notes in Computer Science 807: 87-101, Springer.
	Miller W and Boguski M (1994). A note about computing all local alignments. Comput Appl Biosci 10: 455-456.   PubMed
	Miller W, Boguski M, Raghavachari B, Zhang Z, and Hardison R (1994). Constructing aligned sequence blocks. J Comput Biol 1: 51-64.   PubMed
	Miller W, Schwartz S, and Hardison R (1994). A point of contact between computer science and molecular biology. Comput Sci Engineering 1: 69-78.
	Richards C, Hardison R, and Boyer C (1994). Expression of the large plastid gene, ORF2280, in tomato fruits and flowers. Curr Genet 26: 494-496.   PubMed
	Trepicchio W, Dyer M, Hardison R, and Baron M (1994). Upstream regulatory region of the human embryonic beta-like globin gene, epsilon. DNA Seq 4: 409-412.   PubMed
	Zhang Z, Raghavachari B, Hardison R, and Miller W (1994). Chaining multiple-alignment blocks. J Comput Biol 1: 217-226.   PubMed
	1993
	Chao K-M, Hardison R, and Miller W (1993). Constrained sequence alignment. Bull Math Biol 55: 503-524.   PubMed
	Chao K-M, Hardison R, and Miller W (1993). Locating well-conserved regions within a pairwise alignment. Comput Appl Biosci 9: 387-396.   PubMed
	Hardison R, Chao K-M, Adamkiewicz M, Price D, Jackson J, Zeigler T, Stojanovic N, and Miller W (1993). Positive and negative regulatory elements of the rabbit embryonic epsilon-globin gene revealed by an improved multiple alignment program and functional analysis. DNA Seq 4: 163-176.   PubMed
	Hardison R and Miller W (1993). Use of long sequence alignments to study the evolution and regulation of mammalian globin gene clusters. Mol Biol Evol 10: 73-102.   PubMed
	Hardison R, Xu J, Jackson J, Mansberger J, Selifonova O, Grotch B, Biesecker J, Petrykowska H, and Miller W (1993). Comparative analysis of the locus control region of the rabbit beta-like gene cluster: HS3 increases transient expression of an embryonic epsilon-globin gene. Nucleic Acids Res 21: 1265-1272.   PubMed
	Miller W (1993). Building multiple alignments from pairwise alignments. Comput Appl Biosci 9: 169-176.   PubMed
	Yost S, Shewchuk B, and Hardison R (1993). Nuclear protein-binding sites in a transcriptional control region of the rabbit alpha-globin gene. Mol Cell Biol 13: 5439-5449.   PubMed
	1992
	Boguski M, Hardison R, Schwartz S, and Miller W (1992). Analysis of conserved domains and sequence motifs in cellular regulatory proteins and locus control regions using new software tools for multiple alignment and visualization. New Biol 4: 247-260.   PubMed
	Chao K-M, Pearson W, and Miller W (1992). Aligning two sequences within a specified diagonal band. Comput Appl Biosci 8: 481-487.   PubMed
	Huang X, Miller W, Schwartz S, and Hardison R (1992). Parallelization of a local similarity algorithm. Comput Appl Biosci 8: 155-165.   PubMed
	Pearson W and Miller W (1992). Dynamic programming algorithms for biological sequence comparison. Methods Enzymol 210: 575-601.   PubMed
	Price D, Ayres J, Pasqualone D, Cabell C, Miller W, and Hardison R (1992). The 5' ends of LINE1 repeats in rabbit DNA define subfamilies and reveal a short sequence conserved between rabbits and humans. Genomics 14: 320-331.   PubMed
	Rudd K, Bouffard G, and Miller W (1992). Computer analysis of Escherichia coli restriction maps. In ``Strategies for Physical Mapping, Vol. 4'' (K Davies and S Tilghman, eds.), pp 1-38, Cold Spring Harbor Laboratory Press.
	1991
	Hardison R, Krane D, Vandenbergh D, Cheng J, Mansberger J, Taddie J, Schwartz S, Huang X, and Miller W (1991). Sequence and comparative analysis of the rabbit alpha-like globin gene cluster reveals a rapid mode of evolution in a G+C-rich region of mammalian genomes. J Mol Biol 222: 233-249.   PubMed
	Huang X and Miller W (1991). A time-efficient, linear-space local similarity algorithm. Advances Appl Math 12: 337-357.
	Krane D, Clark A, Cheng J, and Hardison R (1991). Subfamily relationships and clustering of rabbit C repeats. Mol Biol Evol 8: 1-30.   PubMed
	Miller W, Barr J, and Rudd K (1991). Improved algorithms for searching restriction maps. Comput Appl Biosci 7: 447-456.   PubMed
	Richards C, Hinman S, Boyer C, and Hardison R (1991). Survey of plastid RNA abundance during tomato fruit ripening: the amounts of RNA from the ORF 2280 region increase in chromoplasts. Plant Mol Biol 17: 1179-1188.   PubMed
	Rudd K, Miller W, Werner C, Ostell J, Tolstoshev C, and Satterfield S (1991). Mapping sequenced E. coli genes by computer: software, strategies and examples. Nucleic Acids Res 19: 637-647.   PubMed
	Schwartz S, Miller W, Yang C, and Hardison R (1991). Software tools for analyzing pairwise alignments of long sequences. Nucleic Acids Res 19: 4663-4667.   PubMed
	Vandenbergh D, James-Pederson M, and Hardison R (1991). An apparent pause site in the transcription unit of the rabbit alpha-globin gene. J Mol Biol 220: 255-270.   PubMed
	Xu J and Hardison R (1991). Localization of the alpha-like globin gene cluster to region q12 of rabbit chromosome 6 by in situ hybridization. Genomics 9: 362-365.   PubMed
	1990
	Altschul S, Gish W, Miller W, Myers E, and Lipman D (1990). A basic local alignment search tool. J Mol Biol 215: 403-410.   PubMed
	Huang X, Hardison R, and Miller W (1990). A space-efficient algorithm for local similarities. Comput Appl Biosci 6: 373-381.   PubMed
	Krane D and Hardison R (1990). Short interspersed repeats in rabbit DNA can provide functional polyadenylation signals. Mol Biol Evol 7: 1-8.   PubMed
	Lim H, Gounaris I, Hardison R, and Boyer C (1990). Restriction site and genetic map of Cucurbita pepo chloroplast DNA. Curr Genet 18: 273-275.   PubMed
	Miller W, Ostell J, Rudd K (1990). An algorithm for searching restriction maps. Comput Appl Biosci 6: 247-252.   PubMed
	Rudd K, Miller W, Ostell J, and Benson D (1990). Alignment of Escherichia coli K12 DNA sequence to a genomic restriction map. Nucleic Acids Res 18: 313-321.   PubMed
	Wu S, Manber U, Myers E, and Miller W (1990). An O(NP) sequence comparison algorithm. Info Processing Letters 35: 317-323.