1) Hardison, R. C., Eichner, M. E. and Chalkley, R. (1975) An approach to histone nearest neighbors in extended chromatin. Nucleic Acids Res. 2, 1751-1770.
2) Smith, H. E., Neergaard, J. R., Burrows, E. P., Hardison, R. C. and Smith, R. G. (1975) Synthesis of affinity labels for steroid-receptor proteins. In Methods in Enzymology , Vol. XXXVI, B. W. O'Malley and J. G. Hardman, eds. (Academic Press, NY) pp. 411-426.
3) Hardison, R. C., Zeitler, D. P., Murphy, J. M. and Chalkley, R. (1977) Histone neighbors in nuclei and extended chromatin. Cell 12, 417-427.
4) Jackson, V., Hoffman, P., Hardison, R. C., Murphy, J., Eichner, M. E. and Chalkley, R. (1977) Some problems in dealing with chromatin structure. In The Molecular Biology of the Mammalian Genetic Apparatus , Vol. 1, P.T'so, ed. (Elsevier/North-Holland Biomedical Press, Amsterdam) pp. 281-300.
5) Gaubatz, J., Hardison, R. C., Murphy, J., Eichner, M. E. and Chalkley, R. (1977) The organization of H1 histone on chromosomes. In Molecular Human Cytogenetics , ICN-UCLA Symposium on Molecular and Cellular Biology, Vol. VII, R. Sparkes, D. Comings and C. F. Fox, eds. (Academic Press, NY) pp.139-157.
6) Gaubatz, J., Hardison, R. C., Murphy, J., Eichner, M. E. and Chalkley, R. (1978) The role of H1 in the structure of chromatin.In Chromatin , Cold Spring Harbor Symposia on Quant. Biol., Vol. XLII, Part 1 (Cold Spring Harbor Laboratory, NY) pp. 265-271.
7) Maniatis, T., Hardison, R. C., Lacy, E., Lauer, J., O'Connell, C., Quon, D., Sim, G. K. and Efstratiadis, A. (1978) The isolation of structural genes from libraries of eukaryotic DNA. Cell 15, 687-70l.
8) Hardison, R. C. and Chalkley, R. (1978) Polyacrylamide gel electrophoretic fractionation of histones. In Methods in Cell Biology , Vol. 17, G. Stein, J. Stein and L. Kleinsmith, eds. (Academic Press, NY) pp. 235-251.
9) Lacy, E., Hardison, R. C., Quon, D. and Maniatis, T. (1979) The linkage arrangement of four rabbit beta-like globin genes. Cell 18, 1273-1283.
10) Hardison, R. C., Butler, E. III, Lacy, E., Maniatis, T., Rosenthal, N. and Efstratiadis, A. (1979) The structure and transcription of four linked rabbit beta-like globin genes. Cell 18, 1285-1297.
11) Lacy, E., Lawn, R., Fritsch, E., Hardison, R. C., Parker, R. and Maniatis, T. (1979) Isolation and characterization of mammalian globin genes. In Cellular and Molecular regulation of Hemoglobin Switching, G. Stamatoyannopoulos and A. Nienhuis, eds. (Grune and Stratton, NY) pp. 501-519.
12) Maniatis, T., Butler, E. III, Fritsch, E., Hardison, R. C., Lacy, E., Lawn, R., Parker, R. and Shen, C.-K. J. (1979) The linkage arrangement of mammalian beta-like globin genes. In Eukaryotic Gene Regulation, ICN-UCLA Symposium on Molecular and Cellular Biology, Vol. XIV, R. Axel, T. Maniatis and C. F. Fox, eds. (Academic Press, NY) 317-333.
13) Hardison, R. C. (1981) The nucleotide sequence of the rabbit embryonic globin gene beta3. J. Biol. Chem. 256, 11780-11786.
14) Hardison, R. C., Lacy, E., Shen, C.-K. J., Butler, E. III and Maniatis T. (1981) The beta-like globin gene family of rabbits. In Organization and Expression of Globin Genes , G. Stamatoyannopoulos and A. Nienhuis, eds. (Alan R. Liss, Inc., NY) pp. 89-99.
15) Hardison, R. C., Rohrbaugh, M. and Morrison, J. (1981) Expression of beta-like globin genes during rabbit embryogenesis. In Developmental Biology Using Purified Genes , ICN-UCLA Symposia on Molecular and Cellular Biology, Vol. XXIII, D. Brown and C. F. Fox, eds. (Academic Press, NY) 51-60.
16) Rohrbaugh, M. L. and Hardison, R. C. (1983) Analysis of rabbit beta-like globin gene transcripts during development. J. Mol. Biol . 164, 395-417.
17) Hardison, R. C. (1983) The nucleotide sequence of the rabbit embryonic globin gene beta4. J. Biol. Chem. 258, 8739-8744.
18) Cheng, J.-F., Printz, R., Callaghan, T., Shuey, D. and Hardison, R. (1984) The rabbit C family of short, interspersed repeats: Nucleotide sequence determination and transcriptional analysis. J. Mol. Biol. 176, 1-20.
19) Hardison, R. C. and Margot, J. (1984) Rabbit globin pseudogene psi beta2 is a hybrid of delta- and beta-globin gene sequences. Molec. Biol. and Evol. 1, 302-316.
20) Hardison, R. C. (1984) Comparison of the beta-like globin gene families of rabbits and humans indicates that the gene cluster 5'-epsilon-gamma-delta-beta-3'predates the mammalian radiation. Molec. Biol. and Evol. 1, 390-410.
21) Hardison, R. C. (1984) A review of Hemoglobin: Structure, Function, Evolution and Pathology by R. E. Dickerson and I. Geis. Molec. Biol. and Evol. 1, 435-437.
22) Rohrbaugh, M. L., Johnson, J. E., III., James, M. D. and Hardison, R. C. (1985) The transcription unit of the rabbit beta1 globin gene. Mol. Cell. Biol . 5, 147-160.
23) Hardison, R. C. and Printz, R. (1985) Variability within the rabbit C repeats and sequences shared with other SINES. Nucleic Acids Res. 13, 1073-1088.
24) Margot, J. B. and Hardison, R. C. (1985) DNase I and nuclease S1 sensitivity of the rabbit beta1 globin gene in nuclei and in supercoiled plasmids. J. Mol. Biol. 184, 195-210.
25) Cheng, J. F., Raid, L. and Hardison, R. C. (1986) Isolation and nucleotide sequence of the rabbit globin gene cluster psi zeta - alpha1 - psi alpha : Absence of a pair ofalpha-globin genes evolving in concert. J. Biol. Chem. 261, 839-848.
26) Demers, G. W., Brech, K. and Hardison, R. C. (1986) Long interspersed L1 repeats in rabbit DNA are homologous to L1 repeats of mouse and human in a open reading frame region. Mol. Biol. and Evol. 3, 179-190.
27) Hardison, R. C., Sawada, I., Cheng, J.-F., C.-K. J. Shen, and Schmid, C. (1986) A previously undetected pseudogene in the human alpha-like globin gene cluster. Nucleic Acids Res. 14, 1903-1911.
28) Hardison, R. C. and Gelinas, R. (1986) Assignment of orthologous relationships among mammalian alpha-like globin genes by examining flanking regions reveals a rapid rate of evolution. Mol. Biol. and Evol. 3, 243-261.
29) Hunt, C., Hardison, R. C. and Boyer, C. D. (1986) Restriction enzyme analysis of tomato chloroplast and chromoplast DNA. Plant Physiology 82, 1145-1147.
30) Hardison, R. C., Cheng, J.-F., Demers, G. W., and Margot, J. (1987) Rabbit alpha-like and beta-like globin gene clusters: Comparisons among mammalian globin gene clusters, volume on Developmental Control of Globin Gene Expression, G. Stamatoyannopoulos and A. Nienhuis, eds. (A. R. Liss, NY), Progress in Clinical and Biological Research 251: 91-105.
31) Cheng, J. F., Raid, L. and Hardison, R. C. (1987) Block duplications of a zeta-zeta-alpha-theta gene set in the rabbit alpha-like globin gene cluster. J. Biol. Chem. 262, 5414-5421.
32) Cheng, J.-F., Krane, D., and Hardison, R. C. (1988) Nucleotide sequence and expression of rabbit globin genes zeta1, zeta2 and zeta3: Pseudogenes generated by block duplications are transcriptionally competent. J. Biol. Chem. 263, 9981-9993.
33) Cheng, J.-F. and Hardison, R. C. (1988) The rabbit alpha-like globin gene cluster is polymorphic both in the sizes of BamHI fragments and in the numbers of duplicated sets of genes. Mol. Biol. and Evol. 5, 486-498.
34) Margot, J. B., Demers, G. W. and Hardison, R. C. (1989) Complete nucleotide sequence of the rabbit beta-like globin gene cluster: Analysis of intergenic sequences and comparison with the human beta-like globin gene cluster. J. Mol. Biol. 205, 15-40.
35) Demers, G. W., Matunis, M. J. and Hardison, R. C. (1989) The L1 family of long interspersed repetitive DNA in rabbits: Sequence, copy number, conserved open reading frames, and homology to keratin. J. Mol. Evol. 29, 3-19.
36) Kim, J.-H., Yu, C.-Y., Bailey, A., Hardison, R. and Shen, C.-K. J. (1989) Unique sequence organization and erythroid cell-specific nuclear factor-binding of mammalian theta1-globin promoters. Nucleic Acids Res. 17, 5687-5700.
37) Xu, J. and Hardison, R. C. (1989) Localization of the beta-like globin gene cluster and the genes for parathyroid hormone and c-Harvey-ras 1 to region q14-q21 of rabbit chromosome 1 by in situ hybridization. Cytogenetics and Cell Genetics 52, 157-161.
38) Hardison, R. C., Margot, J. and Demers, G. W. (1989) Complete nucleotide sequence of the rabbit beta-like globin gene cluster: Insights into evolution and regulation, volume on Hemoglobin Switching, Part B: Cellular and Molecular Mechanisms, G. Stamatoyannopoulos and A. Nienhuis, eds. (A. R. Liss, NY), Progress in Clinical and Biological Research 316B: 1-17.
39) Richards, C., Hinman, S., Boyer, C. and Hardison, R. C. (1989) Variation in the patterns of plastid RNA accumulation during fruit ripening in different cultivars of tomato. In Physiology, Biochemistry and Genetics of Nongreen Plastids , C. D. Boyer, J. C. Shannon and R. C. Hardison, eds., (Amer. Soc. Plant Physiol.) 281-283.
40) Lim, H. T., Gounaris, I., Hardison, R. and Boyer, C. (1989) Organization of the plastid DNA of Cucurbita pepo L. In Physiology, Biochemistry and Genetics of Nongreen Plastids , C. D. Boyer, J. C. Shannon and R. C. Hardison, eds. (Amer. Soc. Plant Physiol.) 269-273.
41) Krane, D. E. and Hardison, R. C. (1990) Short interspersed repeats in rabbit DNA can provide functional polyadenylation signals. Mol. Biol. and Evol. 7, 1-8.
42) Lim, H., Gounaris, I., Hardison, R. C. and Boyer, C. D. (1990) Restriction site and genetic map of Cucurbita pepo chloroplast DNA. Current Genetics 18, 273-275.
43) Huang, X., Hardison, R., and Miller, W. (1990) A space-efficient algorithm for local similarities. Computer Applications in the Biosciences 6, 373-381.
44) Krane, D. E., Clark, A. G., Cheng, J.-F., and Hardison, R. C. (1991) Subfamily relationships and clustering of rabbit C repeats. Mol. Biol. and Evol. 8, 1-30.
45) Xu, J. and Hardison, R. C. (1991) Localization of the alpha-like globin gene cluster to region q 12 of rabbit chromosome 6 by in situ hybridization. Genomics 9, 362-365.
46) Vandenbergh, D. J., James-Pederson, M., and Hardison, R. C. (1991) An apparent pause site in the transcription unit of the rabbit alpha-globin gene. J. Mol. Biol. 220, 255-270.
47) Schwartz, S., Miller, W., Yang, C.-M. and Hardison, R. C. (1991) Software tools for analyzing pairwise alignments of long sequences. Nucleic Acids Res. 19, 4663-4667.
48) Hardison, R., Krane, D., Vandenbergh, D., Cheng, J.-F., 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.
49) Richards, C. M., Hinman, S. B., Boyer, C. D. and Hardison, R. C. (1991) Survey of plastid RNA abundance during tomato fruit ripening: the amounts of RNA from the ORF 2280 region increase in chromoplasts. Plant Molecular Biol. 17, 1179-1188.
50) Hardison, R. C. (1991) Evolution of globin gene families. In Evolution at the Molecular Level , R. K. Selander, A. G. Clark and T. S. Whittam, eds. (Sinauer Assoc., Sunderland, MA) 272-289.
51) Yost, S. E., James-Pederson, M., Xu, J., Krane, D., Miller, R., Zeigler, T. and Hardison, R. (1991) Intragenic sequences and proteins regulating the rabbit alpha-globin gene. In The Regulation of Hemoglobin Switching . G. Stamatoyannopoulos and A. Nienhuis, eds. (Johns Hopkins University Press, Baltimore, MD) 220-234.
52) Boguski, M. S., Hardison, R. C., 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. The New Biologist 4, 247-260.
53) Huang, X., Miller, W., Schwartz, S. and Hardison, R. C. (1992) Parallelization of a local similarity algorithm. Computer Applications in the Biosciences 8, 155-165.
54) Price, D. K., Ayres, J. A., Pasqualone, D., Cabell, C. H., Miller, W. and Hardison, R. C. (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.
55) Chao, K.-M., Hardison, R. C., and Miller, W. (1993) Constrained sequence alignment. Bulletin of Mathematical Biology 55, 503-524.
56) Hardison, R. and Miller, W. (1993) Use of long sequence alignments to study the evolution and regulation of mammalian globin gene clusters. Mol. Biol. and Evol. 10, 73-102.
57) 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 globin gene cluster: HS3 increases transient expression of an embryonic epsilon-globin gene. Nucleic Acids Res. 21 : 1265-1272. Full text.
58) Chao, K.-M., Hardison, R. C. and Miller, W. (1993) Locating well-conserved regions within a pairwise alignment. Computer Applications in the Biosciences 9, 387-396.
59) 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.
60) Hardison, R., Chao, K.-M., Adamkiewicz, M., Price, D., Jackson, J., Zeigler, T. 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 Sequence 4, 163-176.
61) Miller, W., Schwartz, S. and Hardison, R. C. (1994) A point of contact between computer science and molecular biology. IEEE Computational Science and Engineering 1, 69-78.
62) Miller, W., Boguski, M., Raghavachari, B., Zhang, Z., and Hardison, R. C. (1994). Constructing aligned sequence blocks. Journal of Computational Biology 1, 51-64.
63) Trepicchio, W.L., Dyer, M.A., Hardison, R.C., and Baron, M.H. (1994) Upstream regulatory region of the human embryonic beta-like globin gene, epsilon. DNA Sequence 4, 409-412.
64) 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.
65) Richards, C., Hardison, R. and Boyer, C. (1994) Expression of the large plastid gene ORF2280 in tomato fruit and flowers. Current Genetics 26, 494-496.
66) Zhang, Z., Raghavachari, B., Hardison, R. and Miller, W. (1994) Chaining multiple-alignment blocks. J. Computational Biology 1, 217-226.
67) Chao, K.-M., Hardison, R.C., and Miller, W. (1994) Recent developments in linear-space alignment methods: A survey. Journal of Computational Biology 1, 271-291.
68) 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.
69) Miller, W., El Sherbini, A., Peck, J., Riemer, C., Schwartz, S., Stojanovic, N. and Hardison, R. (1995) A database for globin gene expression data. Proceedings of the 28th Annual Hawaii Conference on System Sciences 62-71.
70) Jackson, J., El Sherbini, A., Riemer, C., Stojanovic, N., Miller, W. and Hardison, R. (1995) Effects of hypersensitive sites from the beta-globin LCR on enhancement in transfected cells: Synergism between HS3 and HS2. Molecular Biology of Hemoglobin Switching , Ed., G. Stamatoyannopoulos, (Intercept Ltd., Andover, UK) pp. 87-109.
71) Hardison, R., Elnitski, L., Goldstrohm, A., El Sherbini, A., Riemer, C., Schwartz, S., Stojanovic, N. and Miller, W. (1995) Globin Gene Server: An aid to studying the regulation of mammalian globin genes. Molecular Biology of Hemoglobin Switching, Ed., G. Stamatoyannopoulos, (Intercept Ltd., Andover, UK) pp. 405-426.
72) Jackson, J. D., 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. Full text.
73) Hardison, R. (1996) A brief history of hemoglobins - Plant, animal, protist, bacteria. Commentary to Proc. Natl. Acad. of Sci., USA 93 : 5675-5679. Full text.
74) Jackson, J. D., Miller, W. and Hardison, R. (1996) Sequences within and flanking DNase hypersensitive sites 3 and 2 of the beta-globin locus control region required for synergistic versus additive interactions with the epsilon-globin gene promoter. Nucleic Acids Res. 24 : 4327-4335. Full text.
75) 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. Full text.
76) Slightom, J., Bock, J., Tagle, D. A., Gumucio, D. L., 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. Full text.
77) Shelton, D. A., Stegman, L., Hardison, R., Miller, W., Slightom, J. L., Goodman, M. and Gumucio, D. L. (1997) Phylogenetic footprinting of hypersensitive site 3 of the beta-globin locus control region. Blood 89 : 3457-3469. Full text.
78) Tang, D. C., Ebb, D., Hardison, R. C. and Rodgers, G. P. (1997) Restoration of the CCAAT box and insertion of the CACCC motif activate delta-globin gene expression. Blood 90 : 421-427. Full text.
79) Stojanovic, N., P. Berman, D. Gumucio, R. Hardison and W. Miller (1997) A linear-time algorithm for the 1-mismatch problem. Algorithms and Data Structures, F. Dehne, A. Rau-Chaplin, J.-R. Sack and R. Tamassia, ed. (Springer, New York) 126-135.
80) Shewchuk, B. M. and R. C. Hardison (1997) CpG islands from the alpha-globin gene cluster increase gene expression in an integration-dependent manner. Mol. Cell. Biol. 17: 5856-5866. Full text.
81) Hardison, R. C., J. Oeltjen, and W. Miller (1997) Long human-mouse sequence alignments reveal novel regulatory elements: A reason to sequence the mouse genome. Genome Research 7: 959-966. Full text.
82) Hardison, R., J. L. Slightom, D. L. Gumucio, M. Goodman, N. Stojanovic, and W. Miller (1997) Locus control regions of mammalian beta-globin gene clusters: Combining phylogenetic analyses and experimental results to gain functional insights. Gene 205, 73-94.
83) Chui, D. H. K., R. Hardison, C. Riemer, W. Miller, M. F. H. Carver, T. P. Molchanova, G. D. Efremov and T. H. J. Huisman (1998) An electronic database of human hemoglobin variants on the World Wide Web. Blood 91 : 2643-2644. Full text.
84) Hardison, R., C. Riemer, D. H. K. Chui, T. H. J. Huisman and W. Miller (1998) Electronic access to sequence alignments, experimental results, and human mutations as an aid to studying globin gene regulation. Genomics 47, 429-437.
85) Li, J., C.T. Noguchi, W. Miller, R. Hardison, and A. Schechter (1998) Multiple regulatory elements in the 5' flanking sequence of the human epsilon globin gene, J. Biol. Chem. 273 : 10202-10209. Full text.
86) Hardison, R. (1998) Hemoglobins from bacteria to man: Evolution of different patterns of gene expression. J. Experimental Biology 201 : 1099-1117. Full text.
87) Hardison, R. C., D. H. K. Chui, C. R. Riemer, W. Miller, M. F. H. Carver, T. P. Molchanova, G. D. Efremov and T. H. J. Huisman (1998) Access to A Syllabus of Human Hemoglobin Variants (1996) via the World Wide Web. Hemoglobin 22, 113-127.
88) Riemer, C., A. ElSherbini, N. Stojanovic, S. Schwartz, P. Kwitkin, W. Miller, and R. Hardison (1998) A database of experimental results on globin gene expression. Genomics 53, 325-337.
89) Bender, M., A. Reik, J. Close, A. Telling, E. Epner, S. Fiering, R. Hardison, and M. Groudine (1998) Description and targeted deletion of 5' hypersensitive site 5 and 6 of the mouse beta-globin locus control region. Blood 92 : 4394-4403. Full text.
90) Stojanovic, N., L. Florea, C. Riemer, D. L. Gumucio, J. Slightom, M. Goodman, W. Miller and R. Hardison (1999) Comparison of five methods for finding conserved sequences in multiple alignments of gene regulatory regions. Nucleic Acids Research 27 : 3899-3910. Full text. , associated materials and software, test servers
91) Elnitski, L. and R. Hardison (1999) Efficient and reliable transfection of mouse erythroleukemia cells using cationic lipids. Blood Cells, Molecules and Diseases 25 : 299-304. Full text.
92) 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. American Scientist , 87, 126-137 (March-April issue). Full text.
93) Hardison, R. (1999) A review of The Biotech Century by Jeremy Rifkin, Bulletin of Science and Technology, & Society 19: 68-72.
94) Schwartz, S., Z. Zhang, K. A. Frazer, A. Smit, C. Riemer, J. Bouck, R. Gibbs, R. Hardison, and W. Miller (2000) PipMaker - A web server for aligning two genomic DNA sequences, Genome Research 10: 577-586. publication
95) Florea, L., M. Li, C. Riemer, B. Giardine, W. Miller, and R. Hardison (2000) Validating computer programs for functional genomics in gene regulatory regions, Current Genomics 1 : 11-27. Full text.
96) Hardison, R. C. (2000) Conserved noncoding sequences are reliable guides to regulatory elements, Trends in Genetics 16 :369-372. Full text.
97) Bulger, M., M. A. Bender, J. Hjikke van Doorninck, B. Wertman, C. Farrell, G. Felsenfeld, M. Groudine, and R. Hardison (2000) Comparative structural and functional analysis of the olfactory receptor genes flanking the human and mouse beta-globin gene clusters. Proc. Natl. Acad. Sci., USA 97:14560-14565. publication, supplement
98) Ikonomi, P., C. T. Noguchi, W. Miller, H. Kassahun, R. Hardison, and A. Schechter (2000) Levels of GATA1/GATA2 transcription factors modulate expression of embryonic and fetal hemoglobins, Gene , 261:277-287.
99) Tufarelli, C., A.-M. Frischauf, R. Hardison, J. Flint, and D. R. Higgs (2001) Characterisation of a widely expressed gene (LUC7-LIKE) defining the centromeric boundary of the human alpha- globin domain. Genomics 71:307-314. Full text.
100) Flint, J., J. Peden, C.Tufarelli, A.-M. Frischauf, W. Miller, R. Hardison, and D. R. Higgs (2001) Long-range sequence comparisons and regions of conserved synteny in vertebrates defines the alpha globin domain. Human Molecular Genetics 10 :371-382. Full text.
101) Hardison, R. C. (2001) New views of evolution and regulation of vertebrate beta-like globin gene clusters from an orphaned gene in marsupials. Proc. Natl. Acad. Sci., USA 98:1327-1329.
102) Elnitski, L., J. Li, C. T. Noguchi, W. Miller, and R. Hardison (2001) A negative cis-element regulates the level of enhancement by hypersensitive site 2 of the beta-globin locus control region. J. Biol. Chem. >276 :6289-6298. Full text.
103) Molete, J., H. Petrykowska, E. Bouhassira, Y.-Q. Feng, W. Miller and R. Hardison (2001) Sequences flanking hypersensitive sites of the beta-globin locus control region are required for synergistic enhancement, Molec. Cell. Biol. 21:2969-2980. publication
104) Hardison, R. C., D. H. K. Chui, C. Riemer, B. Giardine, H. Lehvaslaiho, H. Wajcman, and W. Miller (2001) Databases of Human Hemoglobin Variants and Other Resources at the Globin Gene Server, Hemoglobin, 25:183-193.
105) Chiaromonte, F., S. Yang, L. Elnitski, W. Miller and R. C. Hardison (2001) Association between divergence and interspersed repeats in mammalian noncoding genomic DNA. Proc. Natl. Acad. Sci., USA 98:14503-14508. publication
106) Hardison, R. (2001) "Organization, evolution and regulation of the globin genes" in Disorders of Hemoglobin: Genetics, Pathophysiology, and Clinical Management , eds. M.H. Steinberg, B.G. Forget, D.R. Higgs, R.L. Nagel (Cambridge University Press, Cambridge, UK) pp. 95-116. The new version of this book (2007 or 2008) omits most of this material, so I am providing it here as an html file and as a pdf file
107) Hardison, R. (2001) "Evolution of the Haemoglobins" in the Encyclopedia of Genetics, ed. Dr. Eric C.R. Reeve (Fitzroy Dearborn, Publishers, London), 401-411.
108) Hardison, R. (2002) "Globin Gene Clusters" in the Encyclopedia of Molecular Medicine , ed. Dr. Thomas Creighton (John Wiley & Sons, New York), 1427-1430.
109) Hardison, R. C., D. H. K. Chui, B. Giardine, C. Riemer, G. P. Patrinos, N. Anagnou, W. Miller and H. Wajcman (2002) HbVar: A Relational Database of Human Hemoglobin Variants and Thalassemia Mutations at the Globin Gene Server. Human Mutation , 19 : 225-233. publication
110) Molete, Joseph M., Hanna Petrykowska, Martin Sigg, Webb Miller and Ross Hardison (2002) Functional and binding studies of HS3.2 of the beta-globin locus control region, Gene 283 : 185-197. publication
111) Elnitski, L., C. Riemer, H. Petrykowska, S. Schwartz, L. Florea, W. Miller and R. Hardison (2002) PipTools: A computational toolkit to annotate and analyze pairwise comparisons of genomic sequences. Genomics 80 : 681-690. publication
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113) Frazer, K.A., L. Elnitski, D. Church, I. Dubchak and R.C. Hardison (2003) Cross-species Sequence Comparisons: A Review of Methods and Available Resources. Genome Res. 13 : 1-12. publication
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125) Hardison, R.C., F. Chiaromonte, D. Kolbe, H. Wang, H. Petrykowska, L. Elnitski, S. Yang, B. Giardine, Y. Zhang, C. Riemer, S. Schwartz, D. Haussler, K.M. Roskin, R.J. Weber, M. Diekhans, W.J. Kent, M.J. Weiss, J. Welch, and W. Miller (2003) Global Predictions and Tests of Erythroid Regulatory Regions. In The Genome of Homo sapiens, Cold Spring Harbor Symposium on Quantitative Biology LXVIII: 335-344, (Cold Spring Harbor Press, Cold Spring Harbor, NY). publication
126) Ovcharenko, I., G.G. Loots, R.C. Hardison, W. Miller, and L. Stubbs. (2004) zPicture: Dynamic alignment and visualization tool for analyzing conservation profiles. Genome Res. 14: 472-477. publication
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129) Tufarelli, C., R.C. Hardison, W. Miller, J. Hughes, K. Clark, N. Ventress, A.M. Frischauf, and D. Higgs. (2004) Comparative analysis of the alpha-like globin clusters in mouse, rat and human chromosomes indicates a mechanism underlying breaks in conserved synteny. Genome Res. 14 : 623-630. publication
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131) Miller, W., K. D. Makova, A. Nekrutenko and R. C. Hardison (2004) Comparative genomics. Annu Rev Genomics Hum Genet 5 : 15-56. publication
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135) Elnitski L., B. Giardine, P. Shah, Y. Zhang, C. Riemer, M. Weirauch, R. Burhan, W. Miller, and R. C. Hardison (2005) Improvements to GALA and dbERGEII: databases featuring genomic sequence alignment, annotation and experimental results. Nucleic Acids Res. 33 Database Issue:D466-470. Full text of publication.
136) Ovcharenko, I., G. G. Loots, M. A. Nobrega, R. C. Hardison, W. Miller and L. Stubbs (2005) Evolution and functional classification of vertebrate gene deserts. Genome Res. 15 : 137-145 publication
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140) Elnitski, L., David C. King, and Ross C. Hardison (2006) Computational Prediction of cis-Regulatory Modules from Multispecies Alignments Using Galaxy, Table Browser and GALA, in Gene Mapping, Discovery and Expression, ed. Minou Bina, series Methods in Molecular Biology (Humana Press Inc., Totowa, N.J.) pp. 91-103. Preprint of publication.
141) Hao Wang, Ying Zhang, Yong Cheng, Yuepin Zhou, David C. King, James Taylor, Francesca Chiaromonte, Jyotsna Kasturi, Hanna Petrykowska, Bryan Gibb, Christine Dorman, Webb Miller, Louis C. Dore, John Welch, Mitchell J. Weiss, Ross C. Hardison (2006) Experimental Validation of Predicted Mammalian Erythroid Cis-Regulatory Modules. Genome Res. 16 : 1480-1492. Full text of publication.
142) James Taylor, Svitlana Tyekucheva, David C. King, Ross C. Hardison, Webb Miller and Francesca Chiaromonte (2006) ESPERR: Learning strong and weak signals in genomic sequence alignments to identify functional elements. Genome Res. 16 : 1596-1604. Full text of publication.
143) Belinda Giardine, Cathy Riemer, Tim Hefferon, Daryl Thomas, Fan Hsu, Julian Zielenski, Yunhua Sang, Laura Elnitski, Garry Cutting, Heather Trumbower, Andrew Kern, Robert Kuhn, George P. Patrinos, Jim Hughes, Doug Higgs, David Chui, Charles Scriver, Manyphong Phommarinh, Santosh K. Patnaik, Olga Blumenfeld, Bruce Gottlieb, Mauno Vihinen, Jouni Valiaho, Jim Kent, Webb Miller, Ross C. Hardison (2007) PhenCode: Connecting ENCODE Data with Mutations and Phenotype. Human Mutation. 28 : 554-562. Full text
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145) Rhesus Macaque Genome Sequencing and Analysis Consortium: Richard A. Gibbs, Jeffrey Rogers, Michael G. Katze, Roger Bumgarner, George M. Weinstock, Elaine R. Mardis, Karin A. Remington, Robert L. Strausberg, J. Craig Venter, Richard K. Wilson, Mark A. Batzer, Carlos D. Bustamante, Evan E. Eichler, Matthew W. Hahn, Ross C. Hardison, Kateryna D. Makova, Webb Miller, Aleksandar Milosavljevic, Robert E. Palermo, Adam Siepel, James M. Sikela, Tony Attaway, Stephanie Bell, Kelly E. Bernard, Christian J. Buhay, Mimi N. Chandrabose, Marvin Dao, Clay Davis, Kimberly D. Delehaunty, Yan Ding, Huyen H. Dinh, Shannon Dugan-Rocha, Lucinda A. Fulton, Ramatu Ayiesha Gabisi, Toni T. Garner, Jennifer Godfrey, Alicia C. Hawes, Judith Hernandez, Sandra Hines, Michael Holder, Jennifer Hume, Shalini N. Jhangiani, Vandita Joshi, Ziad Mohid Khan, Ewen F. Kirkness, Andrew Cree, R. Gerald Fowler, Sandra Lee, Lora R. Lewis, Zhangwan Li, Yih-shin Liu, Stephanie M. Moore, Donna Muzny, Lynne V. Nazareth, Dinh Ngoc Ngo, Geoffrey O. Okwuonu, Grace Pai, David Parker, Heidie A. Paul, Cynthia Pfannkoch, Craig S. Pohl, Yu-Hui Rogers, San Juana Ruiz, Aniko Sabo, Jireh Santibanez, Brian W. Schneider, Scott M. Smith, Erica Sodergren, Amanda F. Svatek, Teresa R. Utterback, Selina Vattathil, Wesley Warren, Courtney Sherell White, Asif T. Chinwalla, Yucheng Feng, Aaron L. Halpern, LaDeana W. Hillier, Xiaoqiu Huang, Pat Minx, Joanne O. Nelson, Kymberlie H. Pepin, Xiang Qin, Granger G. Sutton, Eli Venter, Brian P. Walenz, John W. Wallis, Kim C. Worley, Shiaw-Pyng Yang, Steven M. Jones, Marco A. Marra, Mariano Rocchi, Jacqueline E. Schein, Robert Baertsch, Laura Clarke, Miklos Csuros, Jarret Glasscock, R. Alan Harris, Paul Havlak, Andrew R. Jackson, Huaiyang Jiang, Yue Liu, David N. Messina, Yufeng Shen, Henry Xing-Zhi Song, Todd Wylie, Lan Zhang, Ewan Birney, Kyudong Han, Miriam K. Konkel, Jungnam Lee, Arian F. A. Smit, Brygg Ullmer, Hui Wang, Jinchuan Xing, Richard Burhans, Ze Cheng, John E. Karro, Jian Ma, Brian Raney, Xinwei She, Michael J. Cox, Jeffery P. Demuth, Laura J. Dumas, Sang-Gook Han, Janet Hopkins, Anis Karimpour-Fard, Young H. Kim, Jonathan R. Pollack, Tomas Vinar, Charles Addo-Quaye, Jeremiah Degenhardt, Alexandra Denby, Melissa J. Hubisz, Amit Indap, Carolin Kosiol, Bruce T. Lahn, Heather A. Lawson, Alison Marklein, Rasmus Nielsen, Eric J. Vallender, Andrew G. Clark, Betsy Ferguson, Ryan D. Hernandez, Kashif Hirani, Hildegard Kehrer-Sawatzki, Jessica Kolb, Shobha Patil, Ling-Ling Pu, Yanru Ren, David Glenn Smith, David A. Wheeler, Ian Schenck, Edward V. Ball, Rui Chen, David N. Cooper, Belinda Giardine, Fan Hsu, W. James Kent, Arthur Lesk, David L. Nelson, William E. O'Brien, Kay Prufer, Peter D. Stenson, James C. Wallace, Hui Ke, Xiao-Ming Liu, Peng Wang, Andy Peng Xiang, Fan Yang, Galt P. Barber, David Haussler, Donna Karolchik, Andy D. Kern, Robert M. Kuhn, Kayla E. Smith, Ann S. Zwieg (2007) Evolutionary and Biomedical Insights from the Rhesus Macaque Genome. Science 13 April 136 :222-234. Full text.
146) Elliott H. Margulies, Gregory M. Cooper, George Asimenos, Daryl J. Thomas, Colin N. Dewey, Adam Siepel, Ewan Birney, Damian Keefe, Ariel S. Schwartz, Minmei Hou, James Taylor, Sergey Nikolaev, Juan I. Montoya-Burgos, Ari Loytynoja, Simon Whelan, Fabio Pardi, Tim Massingham, James B. Brown, Peter Bickel, Ian Holmes, James C. Mullikin, Abel Ureta-Vidal, Benedict Paten, Greg Schuler, Deanna Church, Kate R. Rosenbloom, W. James Kent, NISC Comparative Sequencing Program, Baylor College of Medicine Human Genome Sequencing Center, Washington University Genome Sequencing Center, Broad Institute, UCSC Genome Browser Team, British Columbia Cancer Agency Genome Sciences Center, Stylianos E. Antonarakis, Serafim Batzoglou, Nick Goldman, Ross Hardison, David Haussler, Webb Miller, Lior Pachter, Eric D. Green, and Arend Sidow, and the ENCODE Consortium (2007) Analyses of deep mammalian sequence alingments and constraint predictions for 1% of the human genome. Genome Res. 17 : 760-764. Full text.
147) David C. King, James Taylor, Ying Zhang, Yong Cheng, Heather A. Lawson, Joel Martin, ENCODE groups for Transcriptional Regulation and Multispecies Alignment, Francesca Chiaromonte, Webb Miller, and Ross C. Hardison (2007) Finding cis-regulatory elements using comparative genomics: some lessons from ENCODE data. Genome Research 17 : 775-786. Full text.
148) Blankenberg, Daniel, James Taylor, Ian Schenck, Jianbin He, Yi Zhang, Matthew Ghent, Narayanan Veeraraghavan, Istvan Albert, Webb Miller, Kateryna Makova, Ross C. Hardison, and Anton Nekrutenko (2007) A framework for collaborative analysis of ENCODE data: Making large-scale analyses biologist-friendly. Genome Res., 17 : 960-964. Full text.
149) ENCODE Project Consortium, Birney E, Stamatoyannopoulos JA, Dutta A, Guigo R, Gingeras TR, Margulies EH, Weng Z, Snyder M, Dermitzakis ET, Thurman RE, Kuehn MS, Taylor CM, Neph S, Koch CM, Asthana S, Malhotra A, Adzhubei I, Greenbaum JA, Andrews RM, Flicek P, Boyle PJ, Cao H, Carter NP, Clelland GK, Davis S, Day N, Dhami P, Dillon SC, Dorschner MO, Fiegler H, Giresi PG, Goldy J, Hawrylycz M, Haydock A, Humbert R, James KD, Johnson BE, Johnson EM, Frum TT, Rosenzweig ER, Karnani N, Lee K, Lefebvre GC, Navas PA, Neri F, Parker SC, Sabo PJ, Sandstrom R, Shafer A, Vetrie D, Weaver M, Wilcox S, Yu M, Collins FS, Dekker J, Lieb JD, Tullius TD, Crawford GE, Sunyaev S, Noble WS, Dunham I, Denoeud F, Reymond A, Kapranov P, Rozowsky J, Zheng D, Castelo R, Frankish A, Harrow J, Ghosh S, Sandelin A, Hofacker IL, Baertsch R, Keefe D, Dike S, Cheng J, Hirsch HA, Sekinger EA, Lagarde J, Abril JF, Shahab A, Flamm C, Fried C, Hackermuller J, Hertel J, Lindemeyer M, Missal K, Tanzer A, Washietl S, Korbel J, Emanuelsson O, Pedersen JS, Holroyd N, Taylor R, Swarbreck D, Matthews N, Dickson MC, Thomas DJ, Weirauch MT, Gilbert J, Drenkow J, Bell I, Zhao X, Srinivasan KG, Sung WK, Ooi HS, Chiu KP, Foissac S, Alioto T, Brent M, Pachter L, Tress ML, Valencia A, Choo SW, Choo CY, Ucla C, Manzano C, Wyss C, Cheung E, Clark TG, Brown JB, Ganesh M, Patel S, Tammana H, Chrast J, Henrichsen CN, Kai C, Kawai J, Nagalakshmi U, Wu J, Lian Z, Lian J, Newburger P, Zhang X, Bickel P, Mattick JS, Carninci P, Hayashizaki Y, Weissman S, Hubbard T, Myers RM, Rogers J, Stadler PF, Lowe TM, Wei CL, Ruan Y, Struhl K, Gerstein M, Antonarakis SE, Fu Y, Green ED, Karaoz U, Siepel A, Taylor J, Liefer LA, Wetterstrand KA, Good PJ, Feingold EA, Guyer MS, Cooper GM, Asimenos G, Dewey CN, Hou M, Nikolaev S, Montoya-Burgos JI, Loytynoja A, Whelan S, Pardi F, Massingham T, Huang H, Zhang NR, Holmes I, Mullikin JC, Ureta-Vidal A, Paten B, Seringhaus M, Church D, Rosenbloom K, Kent WJ, Stone EA; NISC Comparative Sequencing Program; Baylor College of Medicine Human Genome Sequencing Center; Washington University Genome Sequencing Center; Broad Institute; Children's Hospital Oakland Research Institute, Batzoglou S, Goldman N, Hardison RC, Haussler D, Miller W, Sidow A, Trinklein ND, Zhang ZD, Barrera L, Stuart R, King DC, Ameur A, Enroth S, Bieda MC, Kim J, Bhinge AA, Jiang N, Liu J, Yao F, Vega VB, Lee CW, Ng P, Shahab A, Yang A, Moqtaderi Z, Zhu Z, Xu X, Squazzo S, Oberley MJ, Inman D, Singer MA, Richmond TA, Munn KJ, Rada-Iglesias A, Wallerman O, Komorowski J, Fowler JC, Couttet P, Bruce AW, Dovey OM, Ellis PD, Langford CF, Nix DA, Euskirchen G, Hartman S, Urban AE, Kraus P, Van Calcar S, Heintzman N, Kim TH, Wang K, Qu C, Hon G, Luna R, Glass CK, Rosenfeld MG, Aldred SF, Cooper SJ, Halees A, Lin JM, Shulha HP, Zhang X, Xu M, Haidar JN, Yu Y, Ruan Y, Iyer VR, Green RD, Wadelius C, Farnham PJ, Ren B, Harte RA, Hinrichs AS, Trumbower H, Clawson H, Hillman-Jackson J, Zweig AS, Smith K, Thakkapallayil A, Barber G, Kuhn RM, Karolchik D, Armengol L, Bird CP, de Bakker PI, Kern AD, Lopez-Bigas N, Martin JD, Stranger BE, Woodroffe A, Davydov E, Dimas A, Eyras E, Hallgrimsdottir IB, Huppert J, Zody MC, Abecasis GR, Estivill X, Bouffard GG, Guan X, Hansen NF, Idol JR, Maduro VV, Maskeri B, McDowell JC, Park M, Thomas PJ, Young AC, Blakesley RW, Muzny DM, Sodergren E, Wheeler DA, Worley KC, Jiang H, Weinstock GM, Gibbs RA, Graves T, Fulton R, Mardis ER, Wilson RK, Clamp M, Cuff J, Gnerre S, Jaffe DB, Chang JL, Lindblad-Toh K, Lander ES, Koriabine M, Nefedov M, Osoegawa K, Yoshinaga Y, Zhu B, de Jong PJ. (2007) Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project. Nature 447 : 799-816. Full text.
150) Miller W, Rosenbloom K, Hardison RC, Hou M, Taylor J, Raney B, Burhans R, King DC, Baertsch R, Blankenberg D, Kosakovsky Pond SL, Nekrutenko A, Giardine B, Harris RS, Tyekucheva S, Diekhans M, Pringle TH, Murphy WJ, Lesk A, Weinstock GM, Lindblad-Toh K, Gibbs RA, Lander ES, Siepel A, Haussler D, Kent WJ. (2007) 28-Way vertebrate alignment and conservation track in the UCSC Genome Browser. Genome Res. 17 : Nov 5; Epub ahead of print. Full text.
151) Obi L. Griffith, Stephen B. Montgomery, Bridget Bernier, Bryan Chu, Katayoon Kasaian, Stein Aerts, Shaun Mahony, Monica C. Sleumer, Mikhail Bilenky, Maximilian Haeussler, Malachi Griffith, Steven M. Gallo, Belinda Giardine, Bart Hooghe, Peter Van Loo, Enrique Blanco, Amy Ticoll, Stuart Lithwick, Elodie Portales-Casamar, Ian J. Donaldson, Gordon Robertson, Claes Wadelius, Pieter De Bleser, Dominique Vlieghe, Marc S. Halfon, Wyeth Wasserman, Ross Hardison, Casey M. Bergman, Steven J.M. Jones, The Open Regulatory Annotation Consortium (2007) ORegAnno: an open-access community-driven resource for regulatory annotation. Nucleic Acids Research 36(Database Issue) : D107-D113 (doi: 10.1093/nar/gkm967). Full text.
152) Karro, John E., Peifer, Martin, Hardison, Ross C., Kollmannm M. and von Gruenberg, Hennig H. (2008) Exponential decay of GC-content detected by strand-symmetric substitution rates influences the evolution of isochore structure. Molecular Biology and Evolution 25 : 362-374 Full text.
153) Dore LC, Amigo JD, Dos Santos CO, Zhang Z, Gai X, Tobias JW, Yu D, Klein AM, Dorman C, Wu W, Hardison RC, Paw BH, Weiss MJ. (2008) A GATA-1-regulated microRNA locus essential for erythropoiesis. Proc Natl Acad Sci U S A. 105 : 3333-3338. Full text.
154) Hardison, Ross C. (2008) Comparative Genomics , a chapter in the textbook Human Genetics - Principles and Approaches - 4th Edition, Editors: Friedrich Vogel, Arno Motulsky, Stylianos Antonarakis, and Michael Speicher, Springer Publishing, in press. Preprint.
155) Forget, Bernard G. and Hardison, Ross C. (2008) The Normal Structure and Regulation of Human Globin Gene Clusters , Chapter 3 in the book Disorders of Hemoglobins: Genetics, Pathophysiology, and Clinical Management - 2nd Edition, Editors:
156) Heather A. Lawson, Joel Martin, David C. King, Belinda Giardine, Webb Miller, Ross C. Hardison (2007) Recent natural selection in human noncoding sequences. : Under revision. Version submitted. Supplement submitted., Excel file
Hardison, R.C. (1977) Histone Neighbors and the Structure of Chromatin Ph.D. thesis, University of Iowa, Dept. of Biochemistry, supervised by Professor Roger Chalkley.
Boyer, C. D., Shannon, J. C. and Hardison, R. C. (1989) Physiology, Biochemistry and Genetics of Nongreen Plastids Current Topics in Plant Physiology, Vol. 2 (Amer. Soc. Plant Physiol, Rockville, MD).
Wedler, F., Bernlohr, R., Hardison, R., Kao, T.-h., and Tien, M. (1994) Solutions Manual for Principles of Biochemistry, 2nd Edition (Textbook by Lehninger, Nelson and Cox) (Worth Publishers, Inc., New York, NY).
Hardison, Ross C. (2005) Working with Molecular Genetics. This is a textbook for an advanced course in molecular genetics, with a heavy emphasis on solving problems. It is self-published and freely available online here.