Publications of Ross C. Hardison

T. Ming Chu Professor of Biochemistry and Molecular Biology, Penn State University

A. Articles

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. PMC343543 Full text.

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. Full text.

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. Full text.

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.

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). Publication.

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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128) Yang, S., A.F. Smit, S. Schwartz, F. Chiaromonte, K.M. Roskin, D. Haussler, W. Miller, and R.C. Hardison. (2004) Patterns of insertions and their covariation with substitutions in the rat, mouse and human genomes. Genome Res. 14 : 517-527. publication

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

130) Kolbe, D., J. Taylor, L. Elnitski, P. Eswara, J. Li, W. Miller, R. Hardison, and F. Chiaromonte. (2004) Regulatory potential scores from genome-wide three-way alignments of human, mouse and rat. Genome Res. 14 : 700-707. publication

131) Miller, W., K. D. Makova, A. Nekrutenko and R. C. Hardison (2004) Comparative genomics. Annu Rev Genomics Hum Genet 5 : 15-56. publication

132) Welch, J. J., J. A. Watts, C. R. Vakoc, Y. Yao, H. Wang, R. C. Hardison, G. A. Blobel, L. A. Chodosh and M. J. Weiss (2004). Global regulation of erythroid gene expression by transcription factor GATA-1. BLOOD 104 : 3136-3147. 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

137) Ovcharenko, I., G. G. Loots, B. M. Giardine, M. Hou, J. Ma, R. C. Hardison, L. Stubbs and W. Miller (2005) Mulan: Multiple-sequence local alignment and visualization for studying function and evolution. Genome Res. 15 : 184-194. publication

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139) Giardine, Belinda, Cathy Riemer, Ross C. Hardison, Richard Burhans, Laura Elnitski, Prachi Shah, Yi Zhang, Daniel Blankenberg, Istvan Albert, Webb Miller, W. James Kent, and Anton Nekrutenko (2005) Galaxy: A platform for interactive large-scale genome analysis. Genome Res. 15 : 1451-1455. Full text of publication.

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

144) Giardine B, van Baal S, Kaimakis P, Riemer C, Miller W, Samara M, Kollia P, Anagnou NP, Chui DH, Wajcman H, Hardison RC, and Patrinos GP. (2007) HbVar database of human hemoglobin variants and thalassemia mutations: 2007 update. Hum Mutat. Feb 28(2):206. Online publication.

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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 : 1797-1808 Full text.

151) Griffith OL, Montgomery SB, Bernier B, Chu B, Kasaian K, Aerts S, Mahony S, Sleumer MC, Bilenky M, Haeussler M, Griffith M, Gallo SM, Giardine B, Hooghe B, Van Loo P, Blanco E, Ticoll A, Lithwick S, Portales-Casamar E, Donaldson IJ, Robertson G, Wadelius C, De Bleser P, Vlieghe D, Halfon MS, Wasserman W, Hardison R, Bergman CM, Jones SJ; Open Regulatory Annotation Consortium. (2008) 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) Chen Z, Luo HY, Basran RK, Hsu TH, Mang DW, Nuntakarn L, Rosenfield CG, Patrinos GP, Hardison RC, Steinberg MH, Chui DH. (2008) A T-to-G transversion at nucleotide -567 upstream of HBG2 in a GATA-1 binding motif is associated with elevated hemoglobin F. Mol Cell Biol. 28:4386-4393. Full text.

155) Tyekucheva S, Makova KD, Karro JE, Hardison RC, Miller W, Chiaromonte F. (2008) Human-macaque comparisons illuminate variation in neutral substitution rates. Genome Biol. 9:R76. PMID: 18447906 Full text.

156) Warren WC, Hillier LW, Marshall Graves JA, Birney E, Ponting CP, Grutzner F, Belov K, Miller W, Clarke L, Chinwalla AT, Yang SP, Heger A, Locke DP, Miethke P, Waters PD, Veyrunes F, Fulton L, Fulton B, Graves T, Wallis J, Puente XS, Lopez-Otin C, Ordonez GR, Eichler EE, Chen L, Cheng Z, Deakin JE, Alsop A, Thompson K, Kirby P, Papenfuss AT, Wakefield MJ, Olender T, Lancet D, Huttley GA, Smit AF, Pask A, Temple-Smith P, Batzer MA, Walker JA, Konkel MK, Harris RS, Whittington CM, Wong ES, Gemmell NJ, Buschiazzo E, Vargas Jentzsch IM, Merkel A, Schmitz J, Zemann A, Churakov G, Kriegs JO, Brosius J, Murchison EP, Sachidanandam R, Smith C, Hannon GJ, Tsend-Ayush E, McMillan D, Attenborough R, Rens W, Ferguson-Smith M, Lefevre CM, Sharp JA, Nicholas KR, Ray DA, Kube M, Reinhardt R, Pringle TH, Taylor J, Jones RC, Nixon B, Dacheux JL, Niwa H, Sekita Y, Huang X, Stark A, Kheradpour P, Kellis M, Flicek P, Chen Y, Webber C, Hardison R, Nelson J, Hallsworth-Pepin K, Delehaunty K, Markovic C, Minx P, Feng Y, Kremitzki C, Mitreva M, Glasscock J, Wylie T, Wohldmann P, Thiru P, Nhan MN, Pohl CS, Smith SM, Hou S, Renfree MB, Mardis ER, Wilson RK. (2008) Genome analysis of the platypus reveals unique signatures of evolution. Nature 453:175-183. PMID: 18464734 Full text.

157) Dos Santos CO, Dore LC, Valentine E, Shelat SG, Hardison RC, Ghosh M, Wang W, Eisenstein RS, Costa FF, Weiss MJ. (2008) An iron responsive element-like stem-loop regulates alpha hemoglobin stabilizing protein mRNA. J Biol Chem. 283:26956-26964. Aug 2. [Epub ahead of print] PMID: 18676996 Full text.

158) Cheng Y, King DC, Dore LC, Zhang X, Zhou Y, Zhang Y, Dorman C, Abebe D, Kumar S, Chiaromonte F, Miller W, Green RD, Weiss MJ, Hardison RC (2008) Transcriptional enhancement by GATA1-occupied DNA segments is strongly associated with evolutionary constraint on the binding site motif. Genome Res. 18:1896-1905. PMID: 18818370 Full text.

159) Hardison, Ross C. (2008) Globin genes on the move. Minireview for Journal of Biology (BioMed Central) 7:35. PMID: 19040770 Full text.

160) Tripic T, Deng W, Cheng Y, Zhang Y, Vakoc CR, Gregory GD, Hardison RC, Blobel GA. (2009) SCL and associated proteins distinguish active from repressive GATA transcription factor complexes. Blood 113:2191-2201. PMID: 19011221, PMCID: PMC2652367 Full text.

161) den Dunnen JT, Sijmons RH, Andersen PS, Vihinen M, Beckmann JS, Rossetti S, Talbot CC Jr, Hardison RC, Povey S, Cotton RG. (2009) Sharing data between LSDBs and central repositories. Hum. Mutat. 30:493-495. PMID: 19306393 Full text.

162) Kaput J, Cotton RG, Hardman L, Watson M, Al Aqeel AI, Al-Aama JY, Al-Mulla F, Alonso S, Aretz S, Auerbach AD, Bapat B, Bernstein IT, Bhak J, Bleoo SL, Blocker H, Brenner SE, Burn J, Bustamante M, Calzone R, Cambon-Thomsen A, Cargill M, Carrera P, Cavedon L, Cho YS, Chung YJ, Claustres M, Cutting G, Dalgleish R, den Dunnen JT, Diaz C, Dobrowolski S, dos Santos MR, Ekong R, Flanagan SB, Flicek P, Furukawa Y, Genuardi M, Ghang H, Golubenko MV, Greenblatt MS, Hamosh A, HancockJM, Hardison R, Harrison TM, Hoffmann R, Horaitis R, Howard HJ, Barash CI, Izagirre N, Jung J, Kojima T, Laradi S, Lee YS, Lee JY, Gil-da-Silva-Lopes VL, Macrae FA, Maglott D, Marafie MJ, Marsh SG, Matsubara Y, Messiaen LM, Moslein G, Netea MG, Norton ML, Oefner PJ, Oetting WS, O'Leary JC, de Ramirez AM, Paalman MH, Parboosingh J, Patrinos GP, Perozzi G, Phillips IR, Povey S, Prasad S, Qi M, Quin DJ, Ramesar RS, Richards CS, Savige J, Scheible DG, Scott RJ, Seminara D, Shephard EA, Sijmons RH, Smith TD, Sobrido MJ, Tanaka T, Tavtigian SV, Taylor GR, Teague J, Topel T, Ullman-Cullere M, Utsunomiya J, van Kranen HJ, Vihinen M, Webb E, Weber TK, Yeager M, Yeom YI, Yim SH, Yoo HS; Contributors to the Human Variome Project Planning Meeting. (2009) Planning the human variome project: the Spain report. Hum. Mutat. 30:496-510 PMID: 19306394 Full text.

163) 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: Martin Steinberg, Bernard Forget, Douglas Higgs, and Ronald Nagel. Cambridge Publishing, pp. 46-61. Preprint.

164) Hardison, Ross C. (2009) It takes (LMO) two to tango (An Inside Blood commentary). BLOOD 114: 5693. Full text.

165) Chou ST, Khandros E, Bailey LC, Nichols KE, Vakoc C, Yao Y, Huang Z, Crispino JD, Hardison RC, Blobel GA, Weiss MJ. (2009) Graded repression of PU.1/Sfpi1 gene transcription by GATA factors regulates hematopoietic cell fate. BLOOD 114: 983-994. [Epub ahead of print Jun 2., 2009] PMID: 19491391. Full text.

166) Zhang, Ying, Weisheng Wu, Yong Cheng, David C. King, Robert S. Harris, James Taylor, Francesca Chiaromonte, Ross C. Hardison, (2009) Primary sequence and epigenetic determinants of in vivo occupancy of genomic DNA by GATA1. Nucleic Acids Res. 37: 7024-7038 (published online ahead of print, September 18, 2009). Full text.

167) Cheng, Yong, Weisheng Wu, Swathi Ashok Kumar, Duonan Yu, Wulan Deng, Tamara Tripic, David C. King, Kuan-Bei Chen, Ying Zhang, Daniela Drautz, Belinda Giardine, Stephan C. Schuster, Webb Miller, Francesca Chiaromonte, Yu Zhang, Gerd A. Blobel, Mitchell J. Weiss, and Ross C. Hardison (2009) Erythroid GATA1 function revealed by genome-wide analysis of transcription factor occupancy, histone modifications and mRNA expression. Genome Res. 19: 2172-2184 (published online ahead of print, November 03, 2009). Full text. and Supplementary Material.

168) Yu M, Riva L, Xie H, Schindler Y, Moran TB, Cheng Y, Yu D, Hardison R, Weiss MJ, Orkin SH, Bernstein BE, Fraenkel E, Cantor AB. (2009) Insights into GATA-1-mediated gene activation versus repression via genome-wide chromatin occupancy analysis. Molecular Cell 36: 682-695. PubMed PMID: 19941827; PubMed Central PMCID:PMC2800995. Full text.

169) Schuster SC, Miller W, Ratan A, Tomsho LP, Giardine B, Kasson LR, Harris RS, Petersen DC, Zhao F, Qi J, Alkan C, Kidd JM, Sun Y, Drautz DI, Bouffard P, Muzny DM, Reid JG, Nazareth LV, Wang Q, Burhans R, Riemer C, Wittekindt NE, Moorjani P, Tindall EA, Danko CG, Teo WS, Buboltz AM, Zhang Z, Ma Q, Oosthuysen A, Steenkamp AW, Oostuisen H, Venter P, Gajewski J, Zhang Y, Pugh BF, Makova KD, Nekrutenko A, Mardis ER, Patterson N, Pringle TH, Chiaromonte F, Mullikin JC, Eichler EE, Hardison RC, Gibbs RA, Harkins TT, Hayes VM. (2010) Complete Khoisan and Bantu genomes from southern Africa. Nature 463: 943-947. PubMed PMID: 20164927. Full text.

170) Hardison, Ross C. (2010) Comparative Genomics , a chapter in the textbook Vogel and Motulsky's Human Genetics: Principles and Approaches - 4th Edition, Editors: Michael Speicher, Stylianos Antonarakis, and Arno Motulsky. Springer Publishing, pp. 557-587. Full text.

171) Hardison, Ross C. (2010) Variable evolutionary signatures at the heart of enhancers. Nature Genetics (News and Views) 42: 734-735 Full text.

172) Hsu CH, Zhang Y, Hardison RC; NISC Comparative Sequencing Program, Green ED, Miller W. An effective method for detecting gene conversion events in whole genomes. (2010) J Comput Biol. 17:1281-1297. PubMed PMID: 20874409. Full text.

173) Giardine, B., Borg, J., Higgs, D.R., Peterson, K.R., Maglott, D., Basak, A.N., Clark, B., Faustino, P., Felice, A.E., Francina, A., Gallivan, M.V.E., Georgitsi, M., Gibbons, R.J., Giordano, P.C. Harteveld, C.L., Joly, P., Kanavakis, E., Kollia, P., Menzel, S., Miller, W., Moradkhani, K., Old, J., Papachatzopoulou, A., Papadakis, M.N., Papadopoulos, P., Pavlovic, S., Philipsen, S., Radmilovic, M., Riemer, C., Schrijver, I., Stojiljkovic, M., Thein, S.L., Traeger-Synodinos, J., Tully, R., Wada, T., Waye, J., Wiemann, C., Zukic, B., Chui, D.H.K., Wajcman, H., Hardison, R.C., Patrinos, G.P. (2011) Systematic documentation and analysis of human genetic variation using the microattribution approach. Nature Genetics 43: 295-301. Full text. Roles: Patrinos and Hardison conceived of the project; Patrinos led the project to completion with Hardison directing the database developer (Giardine) and helping interpret the results. An editorial about this paper, Crowdsourcing human mutations, was published in Nature Genetics 43: 279 (2011) Full text.

174) Myers, Richard M., Stamatoyannopoulos, J., Snyder, M., Dunham, I., Hardison, R.C., Bernstein, B.E., Gingeras, T.R., Kent, W.J., Birney, E., Wold, B., Crawford, G.E. and The ENCODE Project Consortium (2011) A User's Guide to the Encyclopedia of DNA Elements (ENCODE). PLoS Biology 9: e1001046. doi:10.1371/journal.pbio.1001046 Full text. Role: Hardison was part of the writing group (named above) and was part of the Data Analysis Group.

175) Lamonica, J., Deng, W., Kadauke, S., Campbell, A., Gamsjaeger, R., Wang, H., Cheng, Y., Billin, A., Hardison, R.C., Mackay, J. and Blobel, G.A. (2011) The Bromodomain Protein Brd3 Associates with Acetylated GATA1 to Promote its Chromatin Occupancy at Erythroid Target Genes. Proc Natl Acad Sci USA 108 : E159-68. Published online before print May 2, 2011, doi: 10.1073/pnas.1102140108. PubMed PMID: 21536911; PubMed Central PMCID: PMC3107332 Full text.

176) Wu W, Cheng Y, Keller CA, Ernst J, Kumar SA, Mishra T, Morrissey C, Dorman CM, Chen KB, Drautz D, Giardine B, Shibata Y, Song L, Pimkin M, Crawford GE, Furey TS, Kellis M, Miller W, Taylor J, Schuster SC, Zhang Y, Chiaromonte F, Blobel GA, Weiss MJ, Hardison RC. (2011) Dynamics of the epigenetic landscape during erythroid differentiation after GATA1 restoration. Genome Res. 21:1659-1671. doi: 10.1101/gr.125088.111. Epub 2011 Jul 27. PubMed PMID:21795386; PubMed Central PMCID: PMC3202283. Full text.

177) Song G, Hsu CH, Riemer C, Zhang Y, Kim HL, Hoffmann F, Zhang L, Hardison RC, NISC Comparative Sequencing Program, Green ED, Miller W. (2011) Conversion events in gene clusters. BMC Evol Biol. 11 : 226. PubMed PMID: 21798034; PubMed Central PMCID: PMC3161012. Full text.

178) Ponting CP, Hardison R. (2011) What fraction of the human genome is functional? Genome Res. 21 :1769-1776. [2011 Aug 29 Epub ahead of print] PubMed PMID: 21875934; PubMed Central PMCID: PMC3161012. Full text.

179) Pilon AM, Ajay SS, Kumar SA, Steiner LA, Cherukuri PF, Wincovitch S, Anderson SM, Comparative Sequencing Program N, Mullikin JC, Gallagher PG, Hardison RC, Margulies EH, Bodine DM. (2011) Genome-wide ChIP-Seq reveals a dramatic shift in the binding of the transcription factor erythroid Kruppel-like factor during erythrocyte differentiation. Blood 118 :e139-48. [2011 Sep 6 Epub ahead of print] PubMed PMID: 21900194; PubMed Central PMCID: PMC3208289. Full text.

180) Song G, Riemer C, Dickins B, Kim HL, Zhang L, Zhang Y, Hsu CH, Hardison RC, NISC Comparative Sequencing Program, Green ED, Miller W. (2012) Revealing mammalian evolutionary relationships by comparative analysis of gene clusters. Genome Biol Evol. 4:586-601. doi: 10.1093/gbe/evs032. Epub 2012 Mar 27. PubMed PMID:22454131; PubMed Central PMCID: PMC3342878. Full text.

181) Hardison RC, Taylor J. (2012) Genomic approaches towards finding cis-regulatory modules in animals. Nat Rev Genet. 13: 469-483. doi:10.1038/nrg3242. Review. PubMed PMID: 22705667; PubMed Central PMCID: PMC3541939. Full text.

182) Mouse ENCODE Consortium, Stamatoyannopoulos JA, Snyder M, Hardison R, Ren B, Gingeras T, Gilbert DM, Groudine M, Bender M, Kaul R, Canfield T, Giste E, Johnson A, Zhang M, Balasundaram G, Byron R, Roach V, Sabo PJ, Sandstrom R, Stehling AS, Thurman RE, Weissman SM, Cayting P, Hariharan M, Lian J, Cheng Y, Landt SG, Ma Z, Wold BJ, Dekker J, Crawford GE, Keller CA, Wu W, Morrissey C, Kumar SA, Mishra T, Jain D, Byrska-Bishop M, Blankenberg D, Lajoie1 BR, Jain G, Sanyal A, Chen KB, Denas O, Taylor J, Blobel GA, Weiss MJ, Pimkin M, Deng W, Marinov GK, Williams BA, Fisher-Aylor KI, Desalvo G, Kiralusha A, Trout D, Amrhein H, Mortazavi A, Edsall L, McCleary D, Kuan S, Shen Y, Yue F, Ye Z, Davis CA, Zaleski C, Jha S, Xue C, Dobin A, Lin W, Fastuca M, Wang H, Guigo R, Djebali S, Lagarde J, Ryba T, Sasaki T, Malladi VS, Cline MS, Kirkup VM, Learned K, Rosenbloom KR, Kent WJ, Feingold EA, Good PJ, Pazin M, Lowdon RF, Adams LB. (2012) An encyclopedia of mouse DNA elements (Mouse ENCODE). Genome Biol. 13: 418. [Epub ahead of print] PubMed PMID: 22889292; PubMed Central PMCID: PMC3491367. Full text.

183) Kadauke S, Udugama MI, Pawlicki JM, Achtman JC, Jain DP, Cheng Y, Hardison RC, Blobel GA. (2012) Tissue-specific mitotic bookmarking by hematopoietic transcription factor GATA1. Cell 150: 725-737. doi: 10.1016/j.cell.2012.06.038. PubMed PMID: 22901805; PubMed Central PMCID: PMC3425057. Full text.

184) Hardison RC. (2012) Genome-wide epigenetic data facilitate understanding of disease susceptibility association studies. J Biol Chem. 287:30932-30940. doi: 10.1074/jbc.R112.352427. Epub 2012 Sep 5. Review. PubMed PMID: 22952232; PubMed Central PMCID: PMC3438926. Full text.

185) ENCODE Project Consortium, Dunham I, Kundaje A, Aldred SF, Collins PJ, Davis CA, Doyle F, Epstein CB, Frietze S, Harrow J, Kaul R, Khatun J, Lajoie BR, Landt SG, Lee BK, Pauli F, Rosenbloom KR, Sabo P, Safi A, Sanyal A, Shoresh N, Simon JM, Song L, Trinklein ND, Altshuler RC, Birney E, Brown JB, Cheng C, Djebali S, Dong X, Dunham I, Ernst J, Furey TS, Gerstein M, Giardine B, Greven M, Hardison RC, Harris RS, Herrero J, Hoffman MM, Iyer S, Kelllis M, Khatun J, Kheradpour P, Kundaje A, Lassman T, Li Q, Lin X, Marinov GK, Merkel A, Mortazavi A, Parker SC, Reddy TE, Rozowsky J, Schlesinger F, Thurman RE, Wang J, Ward LD, Whitfield TW, Wilder SP, Wu W, Xi HS, Yip KY, Zhuang J, Bernstein BE, Birney E, Dunham I, Green ED, Gunter C, Snyder M, Pazin MJ, Lowdon RF, Dillon LA, Adams LB, Kelly CJ, Zhang J, Wexler JR, Green ED, Good PJ, Feingold EA, Bernstein BE, Birney E, Crawford GE, Dekker J, Elinitski L, Farnham PJ, Gerstein M, Giddings MC, Gingeras TR, Green ED, Guigo R, Hardison RC, Hubbard TJ, Kellis M, Kent WJ, Lieb JD, Margulies EH, Myers RM, Snyder M, Stamatoyannopoulos JA, Tennebaum SA, Weng Z, White KP, Wold B, Khatun J, Yu Y, Wrobel J, Risk BA, Gunawardena HP, Kuiper HC, Maier CW, Xie L, Chen X, Giddings MC, Bernstein BE, Epstein CB, Shoresh N, Ernst J, Kheradpour P, Mikkelsen TS, Gillespie S, Goren A, Ram O, Zhang X, Wang L, Issner R, Coyne MJ, Durham T, Ku M, Truong T, Ward LD, Altshuler RC, Eaton ML, Kellis M, Djebali S, Davis CA, Merkel A, Dobin A, Lassmann T, Mortazavi A, Tanzer A, Lagarde J, Lin W, Schlesinger F, Xue C, Marinov GK, Khatun J, Williams BA, Zaleski C, Rozowsky J, Roder M, Kokocinski F, Abdelhamid RF, Alioto T, Antoshechkin I, Baer MT, Batut P, Bell I, Bell K, Chakrabortty S, Chen X, Chrast J, Curado J, Derrien T, Drenkow J, Dumais E, Dumais J, Duttagupta R, Fastuca M, Fejes-Toth K, Ferreira P, Foissac S, Fullwood MJ, Gao H, Gonzalez D, Gordon A, Gunawardena HP, Howald C, Jha S, Johnson R, Kapranov P, King B, Kingswood C, Li G, Luo OJ, Park E, Preall JB, Presaud K, Ribeca P, Risk BA, Robyr D, Ruan X, Sammeth M, Sandu KS, Schaeffer L, See LH, Shahab A, Skancke J, Suzuki AM, Takahashi H, Tilgner H, Trout D, Walters N, Wang H, Wrobel J, Yu Y, Hayashizaki Y, Harrow J, Gerstein M, Hubbard TJ, Reymond A, Antonarakis SE, Hannon GJ, Giddings MC, Ruan Y, Wold B, Carninci P, Guigo R, Gingeras TR, Rosenbloom KR, Sloan CA, Learned K, Malladi VS, Wong MC, Barber GP, Cline MS, Dreszer TR, Heitner SG, Karolchik D, Kent WJ, Kirkup VM, Meyer LR, Long JC, Maddren M, Raney BJ, Furey TS, Song L, Grasfeder LL, Giresi PG, Lee BK, Battenhouse A, Sheffield NC, Simon JM, Showers KA, Safi A, London D, Bhinge AA, Shestak C, Schaner MR, Kim SK, Zhang ZZ, Mieczkowski PA, Mieczkowska JO, Liu Z, McDaniell RM, Ni Y, Rashid NU, Kim MJ, Adar S, Zhang Z, Wang T, Winter D, Keefe D, Birney E, Iyer VR, Lieb JD, Crawford GE, Li G, Sandhu KS, Zheng M, Wang P, Luo OJ, Shahab A, Fullwood MJ, Ruan X, Ruan Y, Myers RM, Pauli F, Williams BA, Gertz J, Marinov GK, Reddy TE, Vielmetter J, Partridge EC, Trout D, Varley KE, Gasper C, Bansal A, Pepke S, Jain P, Amrhein H, Bowling KM, Anaya M, Cross MK, King B, Muratet MA, Antoshechkin I, Newberry KM, McCue K, Nesmith AS, Fisher-Aylor KI, Pusey B, DeSalvo G, Parker SL, Balasubramanian S, Davis NS, Meadows SK, Eggleston T, Gunter C, Newberry JS, Levy SE, Absher DM, Mortazavi A, Wong WH, Wold B, Blow MJ, Visel A, Pennachio LA, Elnitski L, Margulies EH, Parker SC, Petrykowska HM, Abyzov A, Aken B, Barrell D, Barson G, Berry A, Bignell A, Boychenko V, Bussotti G, Chrast J, Davidson C, Derrien T, Despacio-Reyes G, Diekhans M, Ezkurdia I, Frankish A, Gilbert J, Gonzalez JM, Griffiths E, Harte R, Hendrix DA, Howald C, Hunt T, Jungreis I, Kay M, Khurana E, Kokocinski F, Leng J, Lin MF, Loveland J, Lu Z, Manthravadi D, Mariotti M, Mudge J, Mukherjee G, Notredame C, Pei B, Rodriguez JM, Saunders G, Sboner A, Searle S, Sisu C, Snow C, Steward C, Tanzer A, Tapanari E, Tress ML, van Baren MJ, Walters N, Washieti S, Wilming L, Zadissa A, Zhengdong Z, Brent M, Haussler D, Kellis M, Valencia A, Gerstein M, Raymond A, Guigo R, Harrow J, Hubbard TJ, Landt SG, Frietze S, Abyzov A, Addleman N, Alexander RP, Auerbach RK, Balasubramanian S, Bettinger K, Bhardwaj N, Boyle AP, Cao AR, Cayting P, Charos A, Cheng Y, Cheng C, Eastman C, Euskirchen G, Fleming JD, Grubert F, Habegger L, Hariharan M, Harmanci A, Iyenger S, Jin VX, Karczewski KJ, Kasowski M, Lacroute P, Lam H, Larnarre-Vincent N, Leng J, Lian J, Lindahl-Allen M, Min R, Miotto B, Monahan H, Moqtaderi Z, Mu XJ, O'Geen H, Ouyang Z, Patacsil D, Pei B, Raha D, Ramirez L, Reed B, Rozowsky J, Sboner A, Shi M, Sisu C, Slifer T, Witt H, Wu L, Xu X, Yan KK, Yang X, Yip KY, Zhang Z, Struhl K, Weissman SM, Gerstein M, Farnham PJ, Snyder M, Tenebaum SA, Penalva LO, Doyle F, Karmakar S, Landt SG, Bhanvadia RR, Choudhury A, Domanus M, Ma L, Moran J, Patacsil D, Slifer T, Victorsen A, Yang X, Snyder M, White KP, Auer T, Centarin L, Eichenlaub M, Gruhl F, Heerman S, Hoeckendorf B, Inoue D, Kellner T, Kirchmaier S, Mueller C, Reinhardt R, Schertel L, Schneider S, Sinn R, Wittbrodt B, Wittbrodt J, Weng Z, Whitfield TW, Wang J, Collins PJ, Aldred SF, Trinklein ND, Partridge EC, Myers RM, Dekker J, Jain G, Lajoie BR, Sanyal A, Balasundaram G, Bates DL, Byron R, Canfield TK, Diegel MJ, Dunn D, Ebersol AK, Ebersol AK, Frum T, Garg K, Gist E, Hansen RS, Boatman L, Haugen E, Humbert R, Jain G, Johnson AK, Johnson EM, Kutyavin TM, Lajoie BR, Lee K, Lotakis D, Maurano MT, Neph SJ, Neri FV, Nguyen ED, Qu H, Reynolds AP, Roach V, Rynes E, Sabo P, Sanchez ME, Sandstrom RS, Sanyal A, Shafer AO, Stergachis AB, Thomas S, Thurman RE, Vernot B, Vierstra J, Vong S, Wang H, Weaver MA, Yan Y, Zhang M, Akey JA, Bender M, Dorschner MO, Groudine M, MacCoss MJ, Navas P, Stamatoyannopoulos G, Kaul R, Dekker J, Stamatoyannopoulos JA, Dunham I, Beal K, Brazma A, Flicek P, Herrero J, Johnson N, Keefe D, Lukk M, Luscombe NM, Sobral D, Vaquerizas JM, Wilder SP, Batzoglou S, Sidow A, Hussami N, Kyriazopoulou-Panagiotopoulou S, Libbrecht MW, Schaub MA, Kundaje A, Hardison RC, Miller W, Giardine B, Harris RS, Wu W, Bickel PJ, Banfai B, Boley NP, Brown JB, Huang H, Li Q, Li JJ, Noble WS, Bilmes JA, Buske OJ, Hoffman MM, Sahu AO, Kharchenko PV, Park PJ, Baker D, Taylor J, Weng Z, Iyer S, Dong X, Greven M, Lin X, Wang J, Xi HS, Zhuang J, Gerstein M, Alexander RP, Balasubramanian S, Cheng C, Harmanci A, Lochovsky L, Min R, Mu XJ, Rozowsky J, Yan KK, Yip KY, Birney E. (2012) An integrated encyclopedia of DNA elements in the human genome. Nature 489: 57-74. doi: 10.1038/nature11247. PubMed PMID: 22955616; PubMed Central PMCID: PMC3439153. Roles: Hardison helped direct the analysis of association of phenotype-associated variants with epigenetic signatures of activity; all authors from Penn State worked on multiple analyses. Full text.

186) Chou ST, Byrska-Bishop M, Tober JM, Yao Y, Vandorn D, Opalinska JB, Mills JA, Choi JK, Speck NA, Gadue P, Hardison RC, Nemiroff RL, French DL, Weiss MJ. (2012) Trisomy 21-associated defects in human primitive hematopoiesis revealed through induced pluripotent stem cells. Proc Natl Acad Sci U S A 109: 17573-17578. doi: 10.1073/pnas.1211175109. Epub 2012 Oct 8. PubMed PMID:23045704; PubMed Central PMCID: PMC3491490. Full text.

187) Hardison RC. (2012) Evolution of hemoglobin and its genes. Cold Spring Harb Perspect Med. 2:a011627. doi: 10.1101/cshperspect.a011627. PubMed PMID:23209182. PMCID: PMC3543078 Full text.

188) Hoffman MM, Ernst J, Wilder SP, Kundaje A, Harris RS, Libbrecht M, Giardine B, Ellenbogen PM, Bilmes JA, Birney E, Hardison RC, Dunham I, Kellis M, Noble WS. (2013) Integrative annotation of chromatin elements from ENCODE data. Nucleic Acids Res. 41:827-841. doi: 10.1093/nar/gks1284. Epub 2012 Dec 5. PubMed PMID:23221638; PubMed Central PMCID: PMC3553955. Full text.

189) Su MY, Steiner LA, Bogardus H, Mishra T, Schulz VP, Hardison RC, Gallagher PG. (2013) Identification of biologically relevant enhancers in human erythroid cells. J Biol Chem. 288:8433-8444. doi: 10.1074/jbc.M112.413260. Epub 2013 Jan 22. PubMed PMID: 23341446; PubMed Central PMCID: PMC3605659. Full text.

190) Zheng R, Rebolledo-Jaramillo B, Zong Y, Wang L, Russo P, Hancock W, Stanger BZ, Hardison RC, Blobel GA. (2013) Function of GATA factors in the adult mouse liver. PLoS One. 8:e83723. doi: 10.1371/journal.pone.0083723. eCollection 2013. PubMed PMID: 24367609; PubMed Central PMCID: PMC3867416. Full text.

191) Blobel GA, Hardison RC. (2013) A cluster to remember. Cell. 154:718-720. doi: 10.1016/j.cell.2013.07.041. PubMed PMID: 23953105; PubMed Central PMCID: PMC3878159. Full text.

192) Hardison RC, Blobel GA. (2013) Genetics. GWAS to therapy by genome edits? Science. 342:206-207. doi: 10.1126/science.1245813. PubMed PMID: 24115432. Full text.

193) Mortazavi A, Pepke S, Jansen C, Marinov GK, Ernst J, Kellis M, Hardison RC, Myers RM, Wold BJ. (2013) Integrating and mining the chromatin landscape of cell-type specificity using self-organizing maps. Genome Res. 23:2136-2148. doi:10.1101/gr.158261.113. Epub 2013 Oct 29. PubMed PMID: 24170599; PubMed Central PMCID: PMC3847782. Full text.

194) Giardine B, Borg J, Viennas E, Pavlidis C, Moradkhani K, Joly P, Bartsakoulia M, Riemer C, Miller W, Tzimas G, Wajcman H, Hardison RC, Patrinos GP. (2014) Updates of the HbVar database of human hemoglobin variants and thalassemia mutations. Nucleic Acids Res. 42(Database issue):D1063-9. doi: 10.1093/nar/gkt911. Epub 2013 Oct 16. PubMed PMID: 24137000; PubMed Central PMCID: PMC3964999. Full text.

195) Paralkar VR, Mishra T, Luan J, Yao Y, Kossenkov AV, Anderson SM, Dunagin M, Pimkin M, Gore M, Sun D, Konuthula N, Raj A, An X, Mohandas N, Bodine DM, Hardison RC, Weiss MJ. (2014) Lineage and species-specific long noncoding RNAs during erythro-megakaryocytic development. Blood. Mar 20;123:1927-37. doi:10.1182/blood-2013-12-544494. Epub 2014 Feb 4. PubMed PMID: 24497530; PubMed Central PMCID: PMC3962165. Full text.

196) Kellis M, Wold B, Snyder MP, Bernstein BE, Kundaje A, Marinov GK, Ward LD, Birney E, Crawford GE, Dekker J, Dunham I, Elnitski LL, Farnham PJ, Feingold EA, Gerstein M, Giddings MC, Gilbert DM, Gingeras TR, Green ED, Guigo R, Hubbard T, Kent J, Lieb JD, Myers RM, Pazin MJ, Ren B, Stamatoyannopoulos JA, Weng Z, White KP, Hardison RC. (2014) Defining functional DNA elements in the human genome. Proc Natl Acad Sci U S A. 111:6131-8. doi: 10.1073/pnas.1318948111. Epub 2014 Apr 21. Review. PubMed PMID: 24753594; PubMed Central PMCID: PMC4035993. Full text.

197) Hardison RC. Discovering enhancers directly by activity. (2014) Nat Methods. 11:491-492. doi: 10.1038/nmeth.2933. PubMed PMID: 24781321. Full text.

198) Lee Y, Ghosh D, Hardison RC, Zhang Y. (2014) MRHMMs: multivariate regression hidden Markov models and the variantS. Bioinformatics. 30:1755-1756. doi:10.1093/bioinformatics/btu070. Epub 2014 Feb 19. PubMed PMID: 24558116; PubMed Central PMCID: PMC4058941. Full text.

199) Chang GS, Chen XA, Park B, Rhee HS, Li P, Han KH, Mishra T, Chan-Salis KY, Li Y, Hardison RC, Wang Y, Pugh BF. (2014) A Comprehensive and High-Resolution Genome-wide Response of p53 to Stress. Cell Rep. 8:514-527. doi:10.1016/j.celrep.2014.06.030. Epub 2014 Jul 17. PubMed PMID: 25043190; PubMed Central PMCID: PMC4113076.[Available on 2015/7/24]

200) Pimkin M, Kossenkov AV, Mishra T, Morrissey CS, Wu W, Keller CA, Blobel GA, Lee D, Beer MA, Hardison RC, Weiss MJ. (2014) Divergent functions of hematopoietic transcription factors in lineage priming and differentiation during erythro-megakaryopoiesis. Genome Res. 24:1932-1944. doi: 10.1101/gr.164178.113. Epub 2014 Oct 15. PubMed PMID: 25319996; PubMed Central PMCID: PMC4248311. Full text.

201) Wu W, Morrissey CS, Keller CA, Mishra T, Pimkin M, Blobel GA, Weiss MJ, Hardison RC. (2014) Dynamic shifts in occupancy by TAL1 are guided by GATA factors and drive large-scale reprogramming of gene expression during hematopoiesis. Genome Res. 24:1945-62. doi: 10.1101/gr.164830.113. Epub 2014 Oct 15. PubMed PMID: 25319994; PubMed Central PMCID: PMC4248312. Full text.

202) Hsiung CC, Morrissey CS, Udugama M, Frank CL, Keller CA, Baek S, Giardine B, Crawford GE, Sung M, Hardison RC, Blobel GA. (2014) Genome accessibility is widely preserved and locally modulated during mitosis. Genome Res. 2014 Nov 4. pii:gr.180646.114. [Epub ahead of print] PubMed PMID: 25373146. Full text.

203) Yue F, Cheng Y, Breschi A, Vierstra J, Wu W, Ryba T, Sandstrom R, Ma Z, Davis C, Pope BD, Shen Y, Pervouchine DD, Djebali S, Thurman RE, Kaul R, Rynes E, Kirilusha A, Marinov GK, Williams BA, Trout D, Amrhein H, Fisher-Aylor K, Antoshechkin I, DeSalvo G, See LH, Fastuca M, Drenkow J, Zaleski C, Dobin A, Prieto P, Lagarde J, Bussotti G, Tanzer A, Denas O, Li K, Bender MA, Zhang M, Byron R, Groudine MT, McCleary D, Pham L, Ye Z, Kuan S, Edsall L, Wu YC, Rasmussen MD, Bansal MS, Kellis M, Keller CA, Morrissey CS, Mishra T, Jain D, Dogan N, Harris RS, Cayting P, Kawli T, Boyle AP, Euskirchen G, Kundaje A, Lin S, Lin Y, Jansen C, Malladi VS, Cline MS, Erickson DT, Kirkup VM, Learned K, Sloan CA, Rosenbloom KR, Lacerda de Sousa B, Beal K, Pignatelli M, Flicek P, Lian J, Kahveci T, Lee D, Kent WJ, Ramalho Santos M, Herrero J, Notredame C, Johnson A, Vong S, Lee K, Bates D, Neri F, Diegel M, Canfield T, Sabo PJ, Wilken MS, Reh TA, Giste E, Shafer A, Kutyavin T, Haugen E, Dunn D, Reynolds AP, Neph S, Humbert R, Hansen RS, De Bruijn M, Selleri L, Rudensky A, Josefowicz S, Samstein R, Eichler EE, Orkin SH, Levasseur D, Papayannopoulou T, Chang KH, Skoultchi A, Gosh S, Disteche C, Treuting P, Wang Y, Weiss MJ, Blobel GA, Cao X, Zhong S, Wang T, Good PJ, Lowdon RF, Adams LB, Zhou XQ, Pazin MJ, Feingold EA, Wold B, Taylor J, Mortazavi A, Weissman SM, Stamatoyannopoulos JA, Snyder MP, Guigo R, Gingeras TR, Gilbert DM, Hardison RC, Beer MA, Ren B; Mouse ENCODE Consortium. (2014) A comparative encyclopedia of DNA elements in the mouse genome. Nature. 515:355-364. doi: 10.1038/nature13992. Hardison is one of the co-corresponding authors. PubMed PMID: 25409824; PubMed Central PMCID: PMC4266106. Full text.

204) Cheng Y, Ma Z, Kim BH, Wu W, Cayting P, Boyle AP, Sundaram V, Xing X, Dogan N, Li J, Euskirchen G, Lin S, Lin Y, Visel A, Kawli T, Yang X, Patacsil D, Keller CA, Giardine B; Mouse ENCODE Consortium, Kundaje A, Wang T, Pennacchio LA, Weng Z, Hardison RC, Snyder MP. (2014) Principles of regulatory information conservation between mouse and human. Nature. 515:371-375. Hardison and Snyder are co-corresponding authors. doi:10.1038/nature13985. PubMed PMID: 25409826. Full text.

205) Pope BD, Ryba T, Dileep V, Yue F, Wu W, Denas O, Vera DL, Wang Y, Hansen RS, Canfield TK, Thurman RE, Cheng Y, Gulsoy G, Dennis JH, Snyder MP, Stamatoyannopoulos JA, Taylor J, Hardison RC, Kahveci T, Ren B, Gilbert DM. (2014) Topologically associating domains are stable units of replication-timing regulation. Nature. 515:402-405. doi: 10.1038/nature13986. PubMed PMID: 25409831; PubMed Central PMCID: PMC4251741. Full text.

206) Chen KB, Hardison R, Zhang Y. (2014) dCaP: detecting differential binding events in multiple conditions and proteins. BMC Genomics. 15 Suppl 9:S12. doi:10.1186/1471-2164-15-S9-S12. Epub 2014 Dec 8. PubMed PMID: 25522020. Full text.

207) Olgert Denas, Richard Sandstrom, Yong Cheng, Kathryn Beal, Javier Herrero, Ross C. Hardison, and James Taylor (2015) Genome-wide comparative analysis reveals human-mouse regulatory landscape and evolution. BMC Genomics. 16:87. doi: 10.1186/s12864-015-1245-6. Full text.. Also deposited in bioRxiv: doi:

208) Marta Byrska-Bishop, Daniel VanDorn, Amy E. Campbell, Marisol Betensky, Philip R. Arca, Yu Yao, Paul Gadue, Fernando F. Cost, Richard L. Nemiroff, Gerd A. Blobel, Deborah L. French, Ross C. Hardison, Mitchell J. Weiss, Stella T. Chou (2015) Pluripotent stem cells reveal novel erythroid activities of the GATA1 N-terminus. Journal of Clinical Investigation. 125:993-1005. PMID: 25621499. Full text.

209) Aaron J. Stonestrom, Sarah C. Hsu, Kristen S. Jahn, Peng Huang, Stephan Kadauke, Amy E. Campbell, Cheryl A. Keller, Belinda Giardine, Ross C. Hardison, and Gerd A. Blobel (2015) Function of BET proteins in GATA1-mediated transcriptional activation. Blood 125:2825-2834. Epub 2015 Feb 18. PMCID: PMC4424630. Full text. PMCID: PMC4424630

210) Deepti Jain, Tejaswini Mishra, Belinda M. Giardine, Cheryl A. Keller, Christapher S. Morrissey, Susan Magargee, Christine M. Dorman, Maria Long, Mitchell J.Weiss, and Ross C. Hardison (2015) Dynamics of GATA1 binding and expression response in a GATA1-induced erythroid differentiation system. Genomics Data 4:1-7. PMCID: PMC4338950. Full text. PMCID: PMC4338950.

211) Kateryna D. Makova and Ross C. Hardison (2015) The Effects of Chromatin Organization on Variation in Mutation Rates in the Genome. Nature Reviews Genetics. 16:213-223. Full text. PMCID: PMC4500049.

212) Nergiz Dogan, Weisheng Wu, Christapher S. Morrissey, Kuan-Bei Chen, Aaron Stonestrom, Maria Long, Cheryl A. Keller, Yong Cheng, Deepti Jain, Axel Visel, Len A. Pennacchio, Mitchell J. Weiss, Gerd A. Blobel, Ross C. Hardison (2015) Occupancy by key transcription factors is a more accurate predictor of enhancer activity than histone modifications or chromatin accessibility. Epigenetics and Chromatin 8:16. Full text. PMCID: PMC4432502.

213) G. Celine Han, Vinesh Vinayachandran, Alain R. Bataille, Bongsoo Park, Ka Yim Chan-Salis, Cheryl A. Keller, Maria Long, Shaun Mahony, Ross C. Hardison, B. Franklin Pugh (2016) Genome-wide organization of GATA1 and TAL1 determined at high resolution. Mol. Cell. Biol. 36:157-172. Full text. PMCID: PMC4702602.

214) Jens Lichtenberg, Elisabeth F. Heuston, Tejaswini Mishra, Cheryl A. Keller, Ross C. Hardison, David M. Bodine (2016) SBR-Blood: Systems biology repository for hematopoietic cells. Nucleic Acids Res. 44(D1):D925-D931. Full text. PMCID: PMC4702891.

215) Vikram R. Paralkar, Cristian C. Taborda, Peng Huang, Yu Yao, Andrew V. Kossenkov, Rishi Prasad, Jing Luan, James O. J. Davies, Jim R. Hughes, Ross C. Hardison, Gerd A. Blobel, Mitchell J. Weiss (2016) Unlinking an lncRNA from its associated cis element. Molecular Cell 62:104-110. Full text. PMCID: PMC4877494.

216) Yu Zhang, Lin An, Feng Yue, Ross C. Hardison (2016) Jointly characterizing epigenetic dynamics across multiple human cell types. Nucleic Acids Res. 44:6721-6731. PMID: 27095202. Full text. Preprint deposited in bioRxiv (2015) entitled "Bayesian modeling of epigenetic variation in multiple human cell types" doi:

217) Ross C. Hardison (2016) Finding partners to play the music of regulation. Inside Blood essay. Blood 127:1624-1626. Full text. PMCID: PMC4817306.

218) Chris C.-S. Hsiung, Caroline Bartman, Peng Huang, Paul Ginart, Aaron J. Stonestrom, Cheryl A. Keller, Carolyne Face, Kristen S. Jahn, Perry Evans, Laavanya Sankaranarayanan, Belinda Giardine, Ross C. Hardison, Arjun Raj, and Gerd A. Blobel (2016) A hyperactive transcriptional state marks genome reactivation at the mitosis-G1 transition. Genes & Development 30:1423-1439. Full text. PMCID: PMC4926865.

219) Ross C. Hardison (2016) A guide to translation of research results from model organisms to human. Genome Biology 17:161. Full text. PMCID: PMC4962550.

220) Traxler EA, Yao Y, Wang YD, Woodard KJ, Kurita R, Nakamura Y, Hughes JR, Hardison RC, Blobel GA, Li C, Weiss MJ. (2016) A genome-editing strategy to treat beta-hemoglobinopathies that recapitulates a mutation associated with a benign genetic condition. Nature Medicine 22:987-990. PMID: 27525524. Full text.

221) Sarah C. Hsu, Caroline R. Bartman, Thomas G. Gilgenast, Christopher R. Edwards, Aaron J. Stonestrom, Peng Huang, Daniel Emerson, Michael T. Werner, Kristen S. Jahn, Cheryl A. Keller, Belinda Giardine, Ross C. Hardison, Arjun Raj, Jennifer E. Phillips-Cremins and Gerd A. Blobel (2017) The BET protein BRD2 cooperates with CTCF to enforce transcriptional and architectural boundaries. Molecular Cell 66:102-116.e7. PMID: 28388437. Full text.

222) Tao Yang, Feipeng Zhang, Galip Gurkan Yardimci, Ross C. Hardison, William Stafford Noble, Feng Yue, Qunhua Li (2017) HiCRep: Assessing the reproducibility of Hi-C data using a stratum-adjusted correlation coefficient. Genome Research. Accepted. Preprint is on bioRxiv. Full text.

223) Yu Zhang, Ross C. Hardison (2017) Accurate and reproducible functional maps in 127 human cell types via 2D genome segmentation. Nucleic Acids Res. Accepted. Preprint is on bioRxiv. Full text.

224) Sjaak Philipsen and Ross C. Hardison (2017) Evolution of hemoglobin loci and their regulatory elements. Refereed review in Special Issue on Globins. Blood Cells, Molecules, and Diseases. Accepted. Full text. Preprint is available here without restriction.

225) A. Marieke Oudelaar, Lars L. P. Hanssen, Ross C. Hardison, Jim R. Hughes and Douglas R. Higgs (2017) Between form and function: the complexity of genome folding. Human Molecular Genetics, in press.

B. Submitted or Under Revision

x) Heather A. Lawson, Joel Martin, David C. King, Belinda Giardine, Webb Miller, Ross C. Hardison (200?) Recent natural selection in human noncoding sequences. Version submitted. Supplement submitted., Excel file

226) Jesse Dixon, Jie Xu, Vishnu Dileep, Ye Zhan, Fan Song, Victoria T. Le, Galip Gurkan Yardimci, Abhijit Chakraborty, Darrin V. Bann, Yanli Wang, Royden Clark, Lijun Zhang, Hongbo Yang, Tingting Liu, Sriranga Iyyanki, Lin An, Christopher Pool, Takayo Sasaki, Juan Carlos Rivera Mulia, Hakan Ozadam, Bryan R. Lajoie, Rajinder Kaul, Michael Buckley, Kristen Lee, Morgan Diegel, Dubravka Pezic, Christina Ernst, Suzana Hadjur, Duncan T. Odom, John A. Stamatoyannopoulos, James R. Broach, Ross Hardison, Ferhat Ay, William Stafford Noble, Job Dekker, David M Gilbert, Feng Yue (2017) An integrative framework for detecting structural variations in cancer genomes; submitted manuscript being revised. Preprint is on bioRxiv 119651.

227) Yanli Wang, Bo Zhang, Lijun Zhang, Lin An, Jie Xu, Daofeng Li, Mayank NK Choudhary, Yun Li, Ming Hu, Ross Hardison, Ting Wang, Feng Yue (2017) The 3D Genome Browser: a web-based browser for visualizing 3D genome organization and long-range chromatin interactions. Manuscript under review. Preprint is on bioRxiv 112268.

C. Ph.D. Thesis

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.

D. Books

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.