Publications by Ross C. Hardison

2007

Giardine B, S. van Baal, P. Kaimakis, C. Riemer, W. Miller, M. Samara, P. Kollia, N. P. Anagnou, D. H. Chui, H. Wajcman, R. C. Hardison, and G. P. Patrinos.  HbVar database of human hemoglobin variants and thalassemia mutations: 2007 update.  Hum. Mutat. 28:206#.

Giardine, B., C. Riemer, T. Hefferon, D. Thomas, F. Hsu, J. Zielenski, Y. Sang, L. Elnitski, G. Cutting, H. Trumbower, A. Kern, R. Kuhn, G. P. Patrinos, J. Hughes, D. Higgs, D. Chui, C. Scriver, M. Phommarinh , S. K. Patnaik, O. Blumenfeld, B. Gottlieb, J. Kent, W. Miller, and R. C. Hardison.  PhenCode: Connecting ENCODE data with mutations and phenotype.  Hum. Mutat. 28:554-562.

Gibbs, R. A. plus 175 authors including R. C. Hardison.  Evolutionary and biomedical insights from the rhesus macaque genome.  Science 316:222-234.  Drs. Miller, Makova and Hardison were three of the 13 analysis leaders; the Penn State group made major contributions to the sections on “Determining ancestral genome structure,” “Gene family expansions,” “Orthologous genes,” “Sex chromosome evolution” and “Human disease orthologs in macaque,” pp. 224-233.

Margulies, E. H., G. M. Cooper, G. Asimenos, D. J. Thomas, and many authors from the ENCODE Multispecies Sequence Analysis Consortium, including from Penn State M. Hou, J. Taylor, R. C. Hardison, and W. Miller.  Analyses of deep mammalian sequence alignments and constraint predictions for 1% of the human genome.  Genome Res. 17:760-774.  The Penn State group provided one of the three major sets of alignments and helped analyze the patterns of conservation and constraint in the several functional classes.

King, D. C., J. Taylor, Y. Zhang, Y. Cheng, H. A. Lawson, J. Martin, ENCODE groups for Transcriptional Regulation and Multispecies Alignment, F. Chiaromonte, W. Miller, and R. C. Hardison.  Finding cis-regulatory elements using comparative genomics: some lessons from ENCODE data.  Genome Res. 17:775-786.

Blankenberg, D., J. Taylor, I. Schenck, J. He, Y. Zhang, M. Ghent, N. Veeraraghavan, I. Albert, W. Miller, K. Makova, R. C. Hardison, and A. Nekrutenko.  A framework for collaborative analysis of ENCODE data: Making large-scale analyses biologist-friendly.  Genome Res. 17:960-964.

Birney, E. and many authors from the ENCODE Project Consortium.  The ENCODE pilot project: identification and analysis of functional elements in 1% of the human genome.  Nature 447:799-816. Authors from Penn State were J. Taylor, R. C. Hardison, D. C. King, M. Hou, J. D. Martin, and W. Miller. They contributed to the sections on “Regulation of transcription” (pp. 804-807) and “Evolutionary constraint and population variability” (pp. 809-812).

Miller, W., K. Rosenbloom, R. C. Hardison, M. Hou, J. Taylor, B. Raney, R. Burhans, D. C. King, R. Baertsch, D. Blankenberg, S. L. Kosakovsky Pond, A. Nekrutenko, B. Giardine, R. S. Harris, S. Tyekucheva, M. Diekhans, T. H. Pringle, W. J. Murphy, A. Lesk, G. M. Weinstock, K. Lindblad-Toh, R. A. Gibbs, E. S. Lander, A. Siepel, D. Haussler, and W. J. Kent.  28-Way vertebrate alignment and conservation track in the UCSC Genome Browser. Genome Res. 17:1797-1808.

2006

Wang, H., Y. Zhang, Y. Cheng, Y. Zhou, D. C. King, J. Taylor, F. Chiaromonte, J. Kasturi, H. Petrykowska, B. Gibb, C. Dorman, W. Miller, L. C. Dore, J. Welch, M. J. Weiss, and R. C. Hardison.  Experimental validation of predicted mammalian erythroid cis-regulatory modules.  Genome Res. 16:1480-1492.

Taylor, J., S. Tyekucheva, D. C. King, R. C. Hardison, W. Miller, and F. Chiaromonte.  ESPERR:  Learning strong and weak signals in genomic sequence alignments to identify functional elements.  Genome Res. 16:1585-1595.

Elnitski, L., D. C. King, and R. C. Hardison.  Computational prediction of cis-regulatory modules from multispecies alignments using galaxy, table browser and GALA.  In:  Gene Mapping, Discovery and Expression, in series Methods in Molecular Biology.  (M. Bina, ed.), pp. 91-103, Humana Press Inc., Totowa, NJ. 

2005

Elnitski, L., B. Giardine, P. Shah, Y. Zhang, C. Riemer, M. Weirauch, R. Burhans, W. Miller, and R. C. Hardison. Improvements to GALA and dbERGEII: databases featuring genomic sequence alignment, annotation and experimental results. Nucleic Acids Res. 33:D466-470.

 
Ovcharenko, I., G. G. Loots, M. A. Nobrega, R. C. Hardison, W. Miller, and L. Stubbs. Evolution and functional classification of vertebrate gene deserts. Genome Res. 15:137-145.
 
Ovcharenko, I., G. G. Loots, B. M. Giardine, M. Hou, J. Ma, R. C. Hardison, L. Stubbs, and W. Miller. Mulan: Multiple-sequence local alignment and visualization for studying function and evolution. Genome Res. 15:184-194.
 
King, D. C., J. Taylor, L. Elnitski, F. Chiaromonte, W. Miller, and R. C. Hardison. Evaluation of regulatory potential and conservation scores for detecting cis-regulatory modules in aligned mammalian genome sequences. Genome Res. 15:1051-1060.
 
Giardine, B., C. Riemer, R. C. Hardison, R. Burhans, L. Elnitski, P. Shah, Y. Zhang, D. Blankenberg, I. Albert, W. Miller, W. J. Kent, and A. Nekrutenko. Galaxy: A platform for interactive large-scale genome analysis. Genome Res. 15:1451-1455.

2004

Ovcharenko, I., G.G. Loots, R.C. Hardison, W. Miller, and L. Stubbs. zPicture: Dynamic alignment and visualization tool for analyzing conservation profiles. Genome Res. 14:472-477.

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. Global predictions and tests of erythroid regulatory regions. In: Cold Spring Harbor Symposia on Quantitative Biology, Volume LXVIII, “The Genome of Homo sapiens.” (B. Stillman, D. Stewart, and J. Ebert, eds.), pp. 335-344, Cold Spring Harbor Press, Cold Spring Harbor, NY.

Gibbs, R.A., G.M. Weinstock, M.L. Metzker, D.M. Muzny, E.J. Sodergren, S. Scherer, G. Scott, D. Steffen, K.C. Worley, P.E. Burch, G. Okwuonu, S. Hines, L. Lewis, C. DeRamo, O. Delgado, S. Dugan-Rocha, G. Miner, M. Morgan, A. Hawes, R. Gill, R.A. Holt, M.D. Adams, P.G. Amanatides, H. Baden-Tillson, M. Barnstead, S. Chin, C.A. Evans, S. Ferriera, C. Fosler, A. Glodek, Z. Gu, D. Jennings, C.L. Kraft, T. Nguyen, C.M. Pfannkoch, C. Sitter, G.G. Sutton, J.C. Venter, T. Woodage, D. Smith, H.M. Lee, E. Gustafson, P. Cahill, A. Kana, L. Doucette-Stamm, K. Weinstock, K. Fechtel, R.B. Weiss, D.M. Dunn, E.D. Green, R.W. Blakesley, G.G. Bouffard, P.J. De Jong, K. Osoegawa, B. Zhu, M. Marra, J. Schein, I. Bosdet, C. Fjell, S. Jones, M. Krzywinski, C. Mathewson, A. Siddiqui, N. Wye, J. McPherson, S. Zhao, C.M. Fraser, J. Shetty, S. Shatsman, K. Geer, Y. Chen, S. Abramzon, W.C. Nierman, P.H. Havlak, R. Chen, K.J. Durbin, A. Egan, Y. Ren, X.Z. Song, B. Li, Y. Liu, X. Qin, S. Cawley, K.C. Worley, A.J. Cooney, L.M. D'Souza, K. Martin, J.Q. Wu, M.L. Gonzalez-Garay, A.R. Jackson, K.J. Kalafus, M.P. McLeod, A. Milosavljevic, D. Virk, A. Volkov, D.A. Wheeler, Z. Zhang, J.A. Bailey, E.E. Eichler, E. Tuzun, E. Birney, E. Mongin, A. Ureta-Vidal, C. Woodwark, E. Zdobnov, P. Bork, M. Suyama, D. Torrents, M. Alexandersson, B.J. Trask, J.M. Young, H. Huang, H. Wang, H. Xing, S. Daniels, D. Gietzen, J. Schmidt, K. Stevens, U. Vitt, J. Wingrove, F. Camara, M. Mar Alba, J.F. Abril, R. Guigo, A. Smit, I. Dubchak, E.M. Rubin, O. Couronne, A. Poliakov, N. Hubner, D. Ganten, C. Goesele, O. Hummel, T. Kreitler, Y.A. Lee, J. Monti, H. Schulz, H. Zimdahl, H. Himmelbauer, H. Lehrach, H.J. Jacob, S. Bromberg, J. Gullings-Handley, M.I. Jensen-Seaman, A.E. Kwitek, J. Lazar, D. Pasko, P.J. Tonellato, S. Twigger, C.P. Ponting, J.M. Duarte, S. Rice, L. Goodstadt, S.A. Beatson, R.D. Emes, E.E. Winter, C. Webber, P. Brandt, G. Nyakatura, M. Adetobi, F. Chiaromonte, L. Elnitski, P. Eswara, R.C. Hardison, M. Hou, D. Kolbe, K. Makova, W. Miller, A. Nekrutenko, C. Riemer, S. Schwartz, J. Taylor, S. Yang, Y. Zhang, K. Lindpaintner, T.D. Andrews, M. Caccamo, M. Clamp, L. Clarke, V. Curwen, R. Durbin, E. Eyras, S.M. Searle, G.M. Cooper, S. Batzoglou, M. Brudno, A. Sidow, E.A. Stone, J.C. Venter, B.A. Payseur, G. Bourque, C. Lopez-Otin, X.S. Puente, K. Chakrabarti, S. Chatterji, C. Dewey, L. Pachter, N. Bray, V.B. Yap, A. Caspi, G. Tesler, P.A. Pevzner, D. Haussler, K.M. Roskin, R. Baertsch, H. Clawson, T.S. Furey, A.S. Hinrichs, D. Karolchik, W.J. Kent, K.R. Rosenbloom, H. Trumbower, M. Weirauch, D.N. Cooper, P.D. Stenson, B. Ma, M. Brent, M. Arumugam, D. Shteynberg, R.R. Copley, M.S. Taylor, H. Riethman, U. Mudunuri, J. Peterson, M. Guyer, A. Felsenfeld, S. Old, S. Mockrin, and F. Collins. Genome sequence of the Brown Norway rat yields insights into mammalian evolution. Nature 428:493-521.

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

Tufarelli, C., R. Hardison, W. Miller, J. Hughes, K. Clark, N. Ventress, A.M. Frischauf, and D.R. Higgs. Comparative analysis of the a-like globin clusters in mouse, rat, and human chromosomes indicates a mechanism underlying breaks in conserved synteny. Genome Res. 14: 623-630.

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

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

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. Global regulation of erythroid gene expression by transcription factor GATA-1. Blood 104:3136-3147.

Feingold, E.A., P.J. Good, M. Guyer, S. Kamholz, L. Liefer, K. Wetterstrand, F.S. Collins, T.R. Gingeras, D. Kampa, E.A. Sekinger, J. Cheng, H. Hirsch, S. Ghosh, Z. Zhu, S. Patel, A. Piccolboni, A. Yang, H. Tammana, S. Bekiranov, P. Kapranov, G. Church, K. Struhl, R. Harrison, B. Ren, T.H. Kim, L.O. Barrera, C. Qu, S. Van Calcar, R. Luna, C.K. Glass, M.G. Rosenfeld, R. Guigo, S. Antonarakis, E. Birney, M. Brent, L. Pachter, A. Reymond, M. Dermitzakis, C. Dewey, D. Keefe, F. Denoeud, J. Lagarde, J. Ashurst, T. Hubbard, J.J. Wesselink, R. Castelo, E. Eyras, R.M. Myers, A. Sidow, S. Batzoglou, N.D. Trinklein, S.J. Hartman, S.F. Aldred, E. Anton, D.I. Schroeder, S.S. Marticke, L. Nguyen, J. Schmutz, J. Grimwood, M. Dickson, G.M. Cooper, E.A. Stone, G. Asimenos, M. Brudno, A. Dutta, N. Karnani, C.M. Taylor, H.K. Kim, G. Robins, G. Stamatoyannopoulos, J.A. Stamatoyannopoulos, M. Dorschner, P. Sabo, M. Hawrylycz, R. Humbert, J. Wallace, M. Yu, P. Navas, M. Olson, M. McArthur, W.S. Noble, I. Dunham, C.M. Koch, R.M. Andrews, G.K. Clelland, S. Wilcox, J.M. Fowler, K.D. James, P. Groth, O.M. Dovey, P.D. Ellis, V.L. Wraight, A.J. Mungall, P. Dhami, H. Fiegler, C.F. Langford, N.P. Carter, D. Vetrie, M. Snyder, G. Euskirchen, A. Urban, U. Nagalakshmi, J. Rinn, G. Popescu, P. Bertone, J. Rozowsky, O. Emanuelsson, T. Royce, S. Chung, M. Gerstein, Z. Lian, J. Lian, Y. Nakayama, S. Weissman, V. Stolc, W. Tongprasit, H. Sethi, S. Jones, M. Marra, H. Shin, J. Schein, M. Clamp, K. Lindblad-Toh, J. Chang, D.B. Jaffe, M. Kamal, E.S. Lander, T. Mikkelson, J. Vinson, M.C. Zody, P.J. de Jong, K. Osoegawa, M. Nefedov, B. Zhu, T.J. Vasicek, D. Zhou, S. Luo, A.D. Baxevanis, T.G. Wolfsberg, I.E. Holt, F.S. Collins, G.E. Crawford, J. Whittle, E.D. Green, G.G. Bouffard, E.H. Margulies, M.E. Portnoy, N.F. Hansen, P.J. Thomas, J.C. McDowell, B. Maskeri, A.C. Young, J.R. Idol, R.W. Blakesley, G. Schuler, W. Miller, R. Hardison, L. Elnitski, P. Shah, S.L. Salzberg, M. Pertea, W.H. Majoros, D. Haussler, D. Thomas, K. Rosenbloom, H. Clawson, A. Siepel, W.J. Kent, Z. Weng, S. Jin, A. Halees, H. Burden, U. Karaoz, Y. Fu, Y. Yu, C. Ding, C.R. Cantor, R.E. Kingston, J. Dennis, R.D. Green, M.A. Singer, T.A. Richmond, J.E. Norton, P.J. Farnham, M.J. Oberley, D.R. Inman, M.R. McCormick, H. Kim, C.L. Middle, M.C. Pirrung, X. D. Fu, Y.S. Kwon, Z. Ye, J. Dekker, T.M. Tabuchi, N. Gheldof, J. Dostie, and S.C. Harvey. The ENCODE (ENCyclopedia of DNA Elements) Project. Science 306:636-640.

Hillier, L.W., W. Miller, E. Birney, W. Warren, R.C. Hardison, C.P. Ponting, P. Bork, D.W. Burt, M.A. Groenen, M.E. Delany, J.B. Dodgson, A.T. Chinwalla, P.F. Cliften, S.W. Clifton, K.D. Delehaunty, C. Fronick, R.S. Fulton, T.A. Graves, C. Kremitzki, D. Layman, V. Magrini, J.D. McPherson, T.L. Miner, P. Minx, W.E. Nash, M.N. Nhan, J.O. Nelson, L.G. Oddy, C.S. Pohl, J. Randall-Maher, S.M. Smith, J.W. Wallis, S.P. Yang, M.N. Romanov, C.M. Rondelli, B. Paton, J. Smith, D. Morrice, L. Daniels, H.G. Tempest, L. Robertson, J.S. Masabanda, D.K. Griffin, A. Vignal, V. Fillon, L. Jacobbson, S. Kerje, L. Andersson, R.P. Crooijmans, J. Aerts, J.J. van der Poel, H. Ellegren, R.B. Caldwell, S.J. Hubbard, D.V. Grafham, A.M. Kierzek, S.R. McLaren, I.M. Overton, H. Arakawa, K.J. Beattie, Y. Bezzubov, P.E. Boardman, J.K. Bonfield, M.D. Croning, R.M. Davies, M.D. Francis, S.J. Humphray, C.E. Scott, R.G. Taylor, C. Tickle, W.R. Brown, J. Rogers, J.M. Buerstedde, S.A. Wilson, L. Stubbs, I. Ovcharenko, L. Gordon, S. Lucas, M.M. Miller, H. Inoko, T. Shiina, J. Kaufman, J. Salomonsen, K. Skjoedt, G.K. Wong, J. Wang, B. Liu, J. Yu, H. Yang, M. Nefedov, M. Koriabine, P.J. Dejong, L. Goodstadt, C. Webber, N.J. Dickens, I. Letunic, M. Suyama, D. Torrents, C. von Mering, E.M. Zdobnov, K. Makova, A. Nekrutenko, L. Elnitski, P. Eswara, D.C. King, S. Yang, S. Tyekucheva, A. Radakrishnan, R.S. Harris, F. Chiaromonte, J. Taylor, J. He, M. Rijnkels, S. Griffiths-Jones, A. Ureta-Vidal, M.M. Hoffman, J. Severin, S.M. Searle, A.S. Law, D. Speed, D. Waddington, Z. Cheng, E. Tuzun, E. Eichler, Z. Bao, P. Flicek, D. D. Shteynberg, M.R. Brent, J.M. Bye, E.J. Huckle, S. Chatterji, C. Dewey, L. Pachter, A. Kouranov, Z. Mourelatos, A.G. Hatzigeorgiou, A.H. Paterson, R. Ivarie, M. Brandstrom, E. Axelsson, N. Backstrom, S. Berlin, M.T. Webster, O. Pourquie, A. Reymond, C. Ucla, S.E. Antonarakis, M. Long, J.J. Emerson, E. Betran, I. Dupanloup, H. Kaessmann, A.S. Hinrichs, G. Bejerano, T.S. Furey, R.A. Harte, B. Raney, A. Siepel, W.J. Kent, D. Haussler, E. Eyras, R. Castelo, J.F. Abril, S. Castellano, F. Camara, G. Parra, R. Guigo, G. Bourque, G. Tesler, P.A. Pevzner, A. Smit, L.A. Fulton, E.R. Mardis, and R.K. Wilson. Sequence and comparative analysis of the chicken genome provide unique perspectives on vertebrate evolution. Nature 432:695-716.

Patrinos, G.P., B. Giardine, C. Riemer, W. Miller, D.H.K. Chui, N.P. Anagnou, H. Wajcman, and R.C. Hardison. Improvements in the HbVar database of human hemoglobin variants and thalassemia mutations for population and sequence variation studies. Nucl. Acids Res. 32:D537-D541.

2003

Frazer, K.A., L. Elnitski, D.M. Church, I. Dubchak, and R.C. Hardison. Cross-species sequence comparisons: A review of methods and available resources. Genome Res. 13:1-12.

Hardison, R.C., K.M. Roskin, S. Yang, M. Diekhans, W.J. Kent, R. Weber, L. Elnitski, J. Li, M. O’Connor, D. Kolbe, S. Schwartz, T.S. Furey, S. Whelan, N. Goldman, A. Smit, W. Miller, F. Chiaromonte, and D. Haussler. Covariation in frequencies of substitution, deletion, transposition, and recombination during eutherian evolution. Genome Res. 13:13-26.

Elnitski, L., R.C. Hardison, J. Li, S. Yang, D. Kolbe, P. Eswara, M.J. O’Connor, S. Schwartz, W. Miller, and F. Chiaromonte. Distinguishing regulatory DNA from neutral sites. Genome Res. 13:64-72.

Schwartz, S., W.J. Kent, A. Smit, Z. Zhang, R. Baertsch, R.C. Hardison, D. Haussler, and W. Miller. Human-mouse alignments with BLASTZ. Genome Res. 13:103-107.

Giardine, B., L. Elnitski, C. Riemer, I. Makalowska, S. Schwartz, W. Miller, and R.C. Hardison. GALA, a database for genomic sequence alignments and annotations. Genome Res. 13:732-741.

Schwartz, S., L. Elnitski, M. Li, M. Weirauch, C. Riemer, A. Smit, NISC Comparative Sequencing Program, E.D. Green, R.C. Hardison, and W. Miller. MultiPipMaker and supporting tools: alignments and analysis of multiple genomic DNA sequences. Nucleic Acids Res. 31:3518-3524.

Bulger, M., D. Schübeler, M.A. Bender, J. Hamilton, C.M. Farrell, R.C. Hardison, and M. Groudine. A complex chromatin landscape revealed by patterns of nuclease sensitivity and histone modification within the mouse b-globin locus. Mol. Cell. Biol. 23:5234-5244.

Hardison, R.C. Primer on comparative genomics. PloS Biol. 1:156-160.

Hardison, R.C. Globin genes: Evolution. In: Encyclopedia of the Human Genome. (D. Cooper and W.-H. Li, eds), pp. 5971-5974, Nature Publishing Group, London.

Hardison, R.C. Fishing for evolutionary clues to globin gene regulation. An “Inside BLOOD” capsule. Blood 101:2451.

2002

Hardison, R.C., D.H.K. Chui, B. Giardine, C. Riemer, G.P. Patrinos, N. Anagnou, W. Miller and H. Wajcman. HbVar: A relational database of human hemoglobin variants and thalassemia mutations at the globin gene server. Hum. Mutat. 19:225-233.

Molete, J.M., H. Petrykowska, M. Sigg, W. Miller, and R. C. Hardison. Functional and binding studies of HS3.2 of the beta-globin locus control region. Gene. 283:185-197.

Elnitski, L., C. Riemer, H. Petrykowska, S. Schwartz, L. Florea, W. Miller, and R.C. Hardison. PipTools: A computational toolkit to annotate and analyze pairwise comparisons of genomic sequences. Genomics. 80:681-690.

Waterston, R.H., K. Lindblad-Toh, E. Birney, J. Rogers, J.F. Abril, P. Agarwal, R. Agarwala, R. Ainscough, M. Alexandersson, P. An, S.E. Antonarakis, J. Attwood, R. Baertsch, J. Bailey, K. Barlow, S. Beck, E. Berry, B. Birren, T. Bloom, P. Bork, M. Botcherby, N. Bray, M.R. Brent, D.G. Brown, S.D. Brown, C. Bult, J. Burton, J. Butler, R.D. Campbell, P. Carninci, S. Cawley, F. Chiaromonte, A.T. Chinwalla, D.M. Church, M. Clamp, C. Clee, F.S. Collins, L.L. Cook, R.R. Copley, A. Coulson, O. Couronne, J. Cuff, V. Curwen, T. Cutts, M. Daly, R. David, J. Davies, K.D. Delehaunty, J. Deri, E.T. Dermitzakis, C. Dewey, N.J. Dickens, M. Diekhans, S. Dodge, I. Dubchak, D.M. Dunn, S.R. Eddy, L. Elnitski, R.D. Emes, P. Eswara, E. Eyras, A. Felsenfeld, G.A. Fewell, P. Flicek, K. Foley, W.N. Frankel, L.A. Fulton, R.S. Fulton, T.S. Furey, D. Gage, R.A. Gibbs, G. Glusman, S. Gnerre, N. Goldman, L. Goodstadt, D. Grafham, T.A. Graves, E.D. Green, S. Gregory, R. Guigo, M. Guyer, R.C. Hardison, D. Haussler, Y. Hayashizaki, L.W. Hillier, A. Hinrichs, W. Hlavina, T. Holzer, F. Hsu, A. Hua, T. Hubbard, A. Hunt, I. Jackson, D.B. Jaffe, L.S. Johnson, M. Jones, T.A. Jones, A. Joy, M. Kamal, E.K. Karlsson, D. Karolchik, A. Kasprzyk, J. Kawai, E. Keibler, C. Kells, W.J. Kent, A. Kirby, D.L. Kolbe, I. Korf, R.S. Kucherlapati, E.J. Kulbokas, D. Kulp, T. Landers, J.P. Leger, S. Leonard, I. Letunic, R. Levine, J. Li, M. Li, C. Lloyd, S. Lucas, B. Ma, D.R. Maglott, E.R. Mardis, L. Matthews, E. Mauceli, J.H. Mayer, M. McCarthy, W.R. McCombie, S. McLaren, K. McLay, J.D. McPherson, J. Meldrim, B. Meredith, J.P. Mesirov, W. Miller, T.L. Miner, E. Mongin, K.T. Montgomery, M. Morgan, R. Mott, J.C. Mullikin, D.M. Muzny, W.E. Nash, J.O. Nelson, M.N. Nhan, R. Nicol, Z. Ning, C. Nusbaum, M.J. O'Connor, Y. Okazaki, K. Oliver, E. Overton-Larty, L. Pachter, G. Parra, K.H. Pepin, J. Peterson, P. Pevzner, R. Plumb, C.S. Pohl, A. Poliakov, T.C. Ponce, C.P. Ponting, S. Potter, M. Quail, A. Reymond, B.A. Roe, K.M. Roskin, E.M. Rubin, A.G. Rust, R. Santos, V. Sapojnikov, B. Schultz, J. Schultz, M.S. Schwartz, S. Schwartz, C. Scott, S. Seaman, S. Searle, T. Sharpe, A. Sheridan, R. Shownkeen, S. Sims, J.B. Singer, G. Slater, A. Smit, D.R. Smith, B. Spencer, A. Stabenau, N. Stange-Thomann, C. Sugnet, M. Suyama, G. Tesler, J. Thompson, D. Torrents, E. Trevaskis, J. Tromp, C. Ucla, A. Ureta-Vidal, J.P. Vinson, A.C. Von Niederhausern, C.M. Wade, M. Wall, R.J. Weber, R.B. Weiss, M.C. Wendl, A.P. West, K. Wetterstrand, R. Wheeler, S. Whelan, J. Wierzbowski, D. Willey, S. Williams, R.K. Wilson, E. Winter, K.C. Worley, D. Wyman, S. Yang, S.P. Yang, E.M. Zdobnov, M.C. Zody, and E.S. Lander. Initial sequencing and comparative analysis of the mouse genome. Nature. 420:520-562.

2001

Tufarelli, C., A.-M. Frischauf, R. Hardison, J. Flint, and D.R. Higgs. Characterization of a widely expressed gene (LUC7-LIKE) defining the centromeric boundary of the human alpha-globin domain. Genomics. 71:307-314.

Flint, J., J. Peden, C.Tufarelli, A.-M. Frischauf, W. Miller, R. Hardison, and D.R. Higgs. Long-range sequence comparisons and regions of conserved synteny in vertebrates defines the alpha-globin domain. Hum. Mol. Genet. 10:371-382.

Hardison, R.C. 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.

Elnitski, L., J. Li, C.T. Noguchi, W. Miller, and R. Hardison. 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.

Molete, J., H. Petrykowska, E. Bouhassira, Y.-Q. Feng, W. Miller, and R. Hardison. Sequences flanking hypersensitive sites of the beta-globin locus control region are required for synergistic enhancement. Mol. Cell. Biol. 21:2969-2980.

Hardison, R.C., D.H.K. Chui, C. Riemer, B. Giardine, H. Lehväslaiho, H. Wajcman, and W. Miller. Databases of human hemoglobin variants and other resources at the globin gene server. Hemoglobin. 25:183-193.

Chiaromonte, F., S. Yang, L. Elnitski, W. Miller, and R.C. Hardison. Association between divergence and interspersed repeats in mammalian noncoding genomic DNA. Proc. Natl. Acad. Sci. USA 98:14503-14508.

2000

Ikonomi, P., C.T. Noguchi, W. Miller, H. Kassahun, R. C. Hardison, and A. Schecter. Levels of GATA1/GATA2 Transcription Factors Modulate Expression of Embryonic and Fetal Hemoglobins. Gene 261:277-287.

Schwartz, S., Z. Zhang, K.A. Frazer, A. Smit, C. Riemer, J. Bouck, R. Gibbs, R.C. Hardison, and W. Miller. PipMaker--A Web Server for Aligning Two Genomic DNA Sequences. Genome Res. 10:577-586.

Florea, L., M. Li, C. Riemer, B. Giardine, W. Miller, and R.C. Hardison. Validating Computer Programs for Functional Genomics in Gene Regulatory Regions. Curr. Genomics 1:11-27.

Hardison, R.C. Conserved Noncoding Sequences are Reliable Guides to Regulatory Elements. Trends Genet. 16:369-372.

Bulger, M., M.A. Bender, J. Hjikke van Doorninck, B. Wertman, C. Farrell, G. Felsenfeld, M. Groudine, and R.C. Hardison. 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.

1999

Elnitski, L. and R. Hardison. Efficient and Reliable Transfection of Mouse Erythroleukemia Cells Using Cationic Lipids. Blood Cell Mol. Dis. 25:299-304.

Hardison, R. 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.

Stojanovic, N., L. Florea, C. Riemer, D.L. Gumucio, J. Slightom, M. Goodman, W. Miller, and R. Hardison. Comparison of Five Methods for Finding Conserved Sequences in Multiple Alignments of Gene Regulatory Regions. Nucleic Acids Res. 27:3899-3910.

1998

Bender, M., A. Reik, J. Close, A. Telling, E. Epner, S. Fiering, R. Hardison, and M. Groudine. Description and Targeted Deletion of 5' Hypersensitive Site 5 and 6 of the Mouse-globin Locus Control Region. Blood 92:4394-4403.

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. An Electronic Database of Human Hemoglobin Variants on the World Wide Web. Blood 91:2643-2644.

Hardison, R. Hemoglobins from Bacteria to Man: Evolution of Different Patterns of Gene Expression. J. Exp. Biol. 201:1099-1117.

Hardison, R., C. Riemer, D.H.K. Chui, T.H.J. Huisman, and W. Miller. Electronic Access to Sequence Alignments, Experimental Results, and Human Mutations as an Aid to Studying Globin Gene Regulation. Genomics 47:429-437.

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. Access to a Syllabus of Human Hemoglobin Variants (1996) via the World Wide Web. Hemoglobin 22:113-127.

Li, J., C.T. Noguchi, W. Miller, R. Hardison, and A. Schechter. Multiple Regulatory Elements in the 5' Flanking Sequence of the Human Epsilon Globin Gene. J. Biol. Chem. 273:10202-10209.

Riemer, C., A. El Sherbini, N. Stojanovic, S. Schwartz, P. Kwitkin, W. Miller, and R. Hardison. A Database of Experimental Results on Globin Gene Expression. Genomics 53:325-337.

1997

Elnitski, L., W. Miller, and R.C. Hardison. Conserved E Boxes Function as Part of the Enhancer in Hypersensitive Site 2 of the b-globin Locus Control Region. J. Biol. Chem. 272:369-378.

Hardison, R.C., J. Oeltjen, and W. Miller. Long Human-Mouse Sequence Alignments Reveal Novel Regulatory Elements: A Reason to Sequence the Mouse Genome. Genome Res. 7:959-966.

Hardison. R.C., J.L. Slightom, D.L. Gumucio, M. Goodman, N. Stojanovic, and W. Miller. Locus Control Regions of Mammalian b-globin Gene Clusters: Combining Phylogenetic Analyses and Experimental Results to Gain Functional Insights. Gene 205:73-94.

Shewchuk, B.M. and R.C. Hardison. CpG Islands from the -Globin Gene Cluster Increase Gene Expression in an Integration-Dependent Manner. Mol. Cell. Biol. 17:5856-5866.

Slightom, J.L., J.H. Bock, D.A. Tagle, D.L. Gumucio, M. Goodman, N. Stojanovic, J. Jackson, W. Miller, and R.C. Hardison. The Complete Sequences of the Galago and Rabbit b-globin Locus Control Regions: Extended Sequence and Functional Conservation Outside the Cores of DNAse Hypersensitive Sites. Genomics 39:90-94.

Stojanovic, N., P. Berman, D. Gumucio, R.C. Hardison, and W. Miller. A Linear-Time Algorithm for the 1-Mismatch Problem. In: Algorithms and Data Structures. (F. Dehne, A. Rau-Chaplin, J.-R. Sack, and R. Tamassia, eds.), pp. 126-135, Springer, New York, N.Y.

Shelton, D.A., L. Stegman, R.C. Hardison, W. Miller, J.H. Bock, J.L. Slightom, M. Goodman, and D.L. Gumucio. Phylogenetic Footprinting of Hypersensitive Site 3 of the b-globin Locus Control Region. Blood 89:3457-3469.

Tang, D.C., D. Ebb, R.C. Hardison, and G.P. Rodgers. Restoration of the CCAAT Box or Insertion of the CACCC Motif Activate d-globin Gene Expression. Blood 90:421-427.

1996

Jackson, J.D., H. Petrykowska, S. Philipsen, W. Miller, and R. Hardison. Role of DNA Sequences Outside the Cores of DNase Hypersensitive Sites (Hss) in Functions of the a-globin Locus Control Region: Domain Opening and Synergism Between HS2 and HS3. J. Biol. Chem. 271:11871-11878.

Hardison, R. A Brief History of Hemoglobins - Plant, Animal, Protist, Bacteria (Commentary). Proc. Natl. Acad Sci. USA 93:5675-5679.

Jackson, J.D., W. Miller, and R. Hardison. Sequences Within and Flanking DNase Hypersensitive Sites 3 and 2 of the a-globin Locus Control Region Required for Synergistic Versus Additive Interactions with the a-globin Gene Promoter. Nucleic Acids Res. 24:4327-4335.

1995

Hardison, R., L. Elnitsky, A. Goldstrohm, A. El Sherbini, C. Riemer, S. Schwartz, N. Stojanovic, and W. Miller. Globin Gene Server: An Aid to Studying the Regulation of Mammalian Globin Genes. In: Molecular Biology of Hemoglobin Switching. (G. Stamatoyannopoulos, ed.), pp. 405-426, Intercept Ltd., Andover, UK.

Jackson, J., A. El Sherbini, C. Riemer, N. Stojanovic, W. Miller, and R. Hardison. Effects of Hypersensitive Sites from the a-Globin LCR on Enhancement in Transfected Cells: Synergism Between HS3 and HS2. In: Molecular Biology of Hemoglobin Switching. (G. Stamatoyannopoulos, ed.), pp. 87-109, Intercept Ltd., Andover, UK.

James-Pederson, M., S. Yost, B. Shewchuk, T. Zeigler, R. Miller, and R. Hardison. Flanking and Intragenic Sequences Regulating the Expression of the Rabbit a-Globin Gene. J. Biol. Chem. 270:3965-3973.

Miller, W., A. El Sherbini, J. Peck, C. Riemer, S. Schwartz, N. Stojanovic, and R. Hardison. A Database for Globin Gene Expression Data. In: Proceedings of the 28th Annual Hawaii Conference on System Sciences. pp. 62-7l, Ieee Press, Philadelphia, PA.

1994

Chao, Z.-M., R.C. Hardison, and W. Miller. Recent Developments in Linear-space Alignment Methods: A Survey. J. Computational Biology l:27l-29l.

Hardison, R., K.-M. Chao, S. Schwartz, N. Stojanovic, M. Ganetsky, and W. Miller. Globin Gene Server: A Prototype E-mail Database Server Featuring Extensive Multiple Alignments and Data Compilation for Electronic Genetic Analysis. Genomics 2l:344-353.

Miller, W., M. Boguski, B. Raghavachari, Z. Zhang, and R.C. Hardison. Constructing Aligned Sequence Blocks. J. Computational Biology 1:51-64.

Miller, W., S. Schwartz, and R.C. Hardison. A Point of Contact Between Computer Science and Molecular Biology. IEEE Computational Science and Engineering. l:69-78.

Richards, C., R. Hardison, and C. Boyer. Expression of the Large Plastid Gene ORF2280 in Tomato Fruit and Flowers. Current Genetics 26:494-496.

Trepicchio, W.L., M.A. Dyer, R.C. Hardison, and M.H. Baron. Upstream Regulatory Region of the Human Embryonic b-like Globin Gene e. DNA Sequence 4:409-412.

Wedler, F., R. Bernlohr, R. Hardison, T.-h. Kao, and M. Tien. Solutions Manual for Principles of Biochemistry (2nd edition). (Textbook by Lehninger, Nelson, and Cox), Worth Publishers, Inc., New York, NY.

Zhang, Z., B. Raghavachari, R. Hardison, and W. Miller. Chaining Multiple-Alignment Blocks. J. Computational Biology 1:2l7-226.

1993

Chao, K.-M., R.C. Hardison, and W. Miller. Constrained Sequence Alignment. Bull. Math. Biol. 55:503-524.

Hardison, R.C. and W. Miller. Use of Long Sequence Alignments to Study the Evolution and Regulation of Mammalian Globin Gene Clusters. Mol. Biol. Evol. l0:73-102.

Hardison, R.C., J. Xu, J. Jackson, J. Mansberger, O. Selifonova, B. Grotch, J. Biesecker, H. Petrykowska, and W. Miller. Comparative Analysis of the Locus Control Region of the Rabbit b-like Globin Gene Cluster. HS3 Increases Transient Expression of an Embryonic e- Globin Gene. Nucleic Acids Res. 2l:1265-1272.

Chao, K.-M., R.C. Hardison, and W. Miller. Locating Well-Conserved Regions Within a Pairwise Alignment. Comput. Appl. Biosci. 9:387-396.

Yost, S., B. Shewchuk, and R.C. Hardison. Nuclear Protein Binding Sites in a Transcriptional Control Region of the Rabbit a-Globin Gene. Mol. Cell Biol. l3:5439-5449.

Hardison, R.C., K.-M. Chao, M. Adamkiewicz, D. Price, J. Jackson, T. Zeigler, and W. Miller. Positive and Negative Regulatory Elements of the Rabbit Embryonic e-Globin Gene Revealed by an Improved Multiple Alignment Program and Functional Analysis. DNA Sequence 4l:l63-176.

1992

Boguski, M.S., R. C. Hardison, S. Schwartz, and W. Miller. 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.

Huang, X., W. Miller, S. Schwartz, and R.C. Hardison. Parallelization of a Local Similarity Algorithm. Comput. Appl. Biosci. 8:155-165.

Price, D.K., J.A. Ayres, D. Pasqualone, C.H. Cabell, W. Miller, and R.C. Hardison. 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.

1991

Hardison, R.C. Evolution of Globin Gene Families. In: Evolution at the Molecular Level. (R.K. Selander, A.G. Clark and T.S. Whittam, eds.), pp. 272-289. Sinauer Assoc., Sunderland, Massachusetts.

Hardison, R.C., D. Krane, D. Vandenbergh, J.-F. Cheng, J. Mansberger, J. Taddie, S. Schwartz, X. Huang, and W. Miller. Sequence and Comparative Analysis of the Rabbit a-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.

Krane, D.E., A.G. Clark, J.-F. Cheng, and R.C. Hardison. Subfamily Relationships and Clustering of Rabbit C Repeats. Mol. Biol. Evol. 8:1-30.

Richards, C.M., S.B. Hinman, C.D. Boyer, and R.C. Hardison. Survey of Plastid RNA Abundance During Tomato Fruit Ripening: The Amounts of RNA from the ORF 2280 Region Increase in Chromoplasts. Plant Mol. Biol. 17:1179-1188.

Schwartz, S., W. Miller, C.-M. Yang, and R.C. Hardison. Software Tools for Analyzing Pairwise Alignments of Long Sequences. Nucleic Acids Res. 19:4663-4667.

Vandenbergh, D.J., M. James-Pederson, and R.C. Hardison. An Apparent Pause Site in the Transcription Unit of the Rabbit a-Globin Gene. J. Mol. Biol. 220:255-270.

Xu, J. and R.C. Hardison. Localization of the a-like Globin Gene Cluster to Region q 12 of Rabbit Chromosome 6 by In Situ Hybridization. Genomics 9:362-365.

Yost, S.E., M. James-Pederson, J. Xu, D. Krane, R. Miller, T. Zeigler, and R.C. Hardison. Intragenic Sequences and Proteins Regulating the Rabbit a-globin Gene. In: The Regulation of Hemoglobin Switching. (G. Stamatoyannopoulos and A. Nienhuis, eds.), pp. 220-234. Johns Hopkins University Press, Baltimore, Maryland.