*corresponding author
Wei,
F., E. Coe, W. Nelson, A. Bharti, F. Engler, E. Butler, H. Kim, J. Goicoechea,
M. Chen, S. Lee, G. Fuks, H. Sanchez-Villeda, S. Schroeder, Z. Fang, M.
McMullen, G. Davis, J. Bowers, A. Paterson, M. Schaeffer, J. Gardiner, K. Cone, J. Messing, C. Soderlund, and R. Wing (2007).
Physical and Genetic Structure of the Maize Genome Reflects its Complex
Evolutionary History. PLoS Genetics. In press
Gowda M., R-C. Venu, H. Li,
C. Jantasuriyarat, S. Chen, M. Bellizzi, V. Pampanwar, H. Kim, R. A. Dean , E.
Stahlberg, R. Wing, C. Soderlund,
G. Wang (2007). Magnaporthe grisea Infection Triggers RNA Variation and
Antisense Transcript Expression in Rice. Plant Physiology, 144: 524-533.
Kim, H., P. San Miguel, W.
Nelson, K. Collura, M. Wissotski, J.G. Walling, J-P. Kim, S. A. Jackson, C.
Soderlund, R. A. Wing (2007).
Comparative physical mapping between O. sativa (AA genome type) and O. punctata
(BB genome type). Genetics. 89:
160-165.
Nelson, W, J. Dvorak, M. Luo,
J. Messing, R. Wing, and C. Soderlund* (2006). Efficacy of clone fingerprinting methodologies. Genomics 89: 160-165..
Soderlund*, C., K.
Haller, V. Pampanwar, D. Ebbole, M. Farman, M. Orbach, G. Wang, R. Wing, J. Xu,
D. Brown, T. Mitchell, R. Dean (2006) MGOS: a resource for studing Magnaporthe
grisea and Oryza Sativa interactions. Mol Plant Microbe Interact 19: 1055-1061.
Soderlund*, C., W. Nelson, A. Shoemaker, A. Paterson.
(2006) SyMAP: A system for discovering and viewing syntenic regions of FPC
maps. Genome Research
16:1159-1168.
Adema, C., M.
Luo, B. Hanelt, L. Hertel, J. Marshall, S. Zhang, R. DeJong, H. Kim, D. Kudrna,
R. Wing, C. Soderlund,
M. Knight, F. Lewis, R. Caldeira,
L. Jannotti-Passos, O. Carvalho, E. Loker (2006) A bacterial artificial
chromosome library for Biomphalaria glabrata, intermediate snail host of Schistosoma
mansoni. Mem Inst
Oswaldo Cruz, Rio de
Janeiro, 101(Suppl. I): 167-177.
Udall, J. A., J. Swanson, K.
Haller, R.A. Rapp, M.E. Sparks, J. Hatfield, Y. Yu, Y. Wu, A.B. Arpat, B.A. Sickler, T.A. Wilkins,
J.-Y. Guo, X.-Y. Chen, J. Scheffler, E. Taliercio, R. Turley, H. McFadden, P. Payton, R. Allen, D. Zhang, C.
Haigler, C. Wilkerson, J. Suo,
S.R. Schulze, M.L. Pierce, M. Essenberg, H. Kim, D.J. Llewellyn, E.S. Dennis,
D. Kudrna, R. Wing, A.H. Paterson, C. Soderlund, and J.F. Wendel1 (2005) A global assembly of cotton
ESTs. Genome Research 16:441-450.
Ammiraju, J., M. Luo, J.
Goicoechea, W. Wang, D. Kudrna, C. Mueller, J. Talag, H. Kim, N. Sisneros, B.
Blackmon, E. Fang, J. Tomkins, D. Brar, D. MacKill, S. McCouch, N. Kurata, G.
Lambert, D. Galbraith, K. Arumuganathan, K. Rao, J. Walling, N. Gill, Y. Yu, P.
SanMiguel, C. Soderlund, S.
Jackson, and RA. Wing (2005) The Oryza bacterial artificial chromosome library
resource: Construction and analysis of 12 deep-coverage large-insert BAC
libraries that represent the 10 genome types of the genus Oryza. Genome
Research 16:140-147.
Bowers J, M. Arias, R.
Asher, J. Avise, R. Ball, G. Brewer, R. Buss, A. Chen, T. Edwards, J. Estill,
H. Exum, V. Goff, K. Herrick, C. Steele, S. Karunakaran, G. Lafayette, C.
Lemke, B. Marler, S. Masters, J. McMillan, L. Nelson, G. Newsome, C. Nwakanma,
R. Odeh, C. Phelps, E. Rarick, C. Rogers, S. Ryan, K. Slaughter, C. Soderlund, H. Tang, R. Wing, A. Paterson (2005) Comparative
physical mapping links conservation of microsynteny to chromosome structure and
recombination in grasses. Proc Natl Acad Sci U S A 102:1320-1321
Nelson, W, A Bharti, E Butler, F Wei, G Fuks, H Kim, R Wing, J Messing, and
C Soderlund* (2005). Whole-Genome
Validation of High-Information-Content Fingerprinting. Plant Physiology, 139:27-38.
Wing, R.A., J.S.S. Ammiraju, M. Luo, H.R. Kim, Y. Yu,
D. Kudrna, J.L. Goicoechea, W.
Wang, W. Nelson, K. Rao, D. Brar, D.J. Mackill, B. Han, C. Soderlund, L. Stein, P. SanMiguel, and S. Jackson. 2005. The Oryza Map Alignment
Project: The Golden Path to
Unlocking the Genetic Potential of Wild Rice Species. Plant Molecular, 59:53-62.
Jantasuriyarat, C, M. Gowda,
K. Haller, J. Hatfield, G. Lu, E. Stahlberg
, B. Zhou, H. Li, H. Kim, Y. Yu, R. Dean, R. Wing, C. Soderlund and G. Wang (2005). Large-scale
identification of ESTs involved in rice and rice blast (Magnaporthe grisea) interaction. Plant Physiology 138: 105-115.
Pampanwar, V., F, Engler, J. Hatfield, S. Blundy, G.
Gupta, and C. Soderlund* (2005). FPC Web tools for rice, maize and
distribution. Plant Physiology 138:116-126.
Messing, J.,
Bharti, A.K., Karlowski, W.M., Gundlach, H., Kim, H.R., Yu, Y., Wei, F., Fuks,
G., Soderlund, C.A., Mayer, K.F.,
and Wing, R.A. (2004). Sequence composition and genome organization of maize. Proc
Natl Acad Sci U S A 101:14349-14354.
Gardiner J, Schroeder S,
Polacco ML, Sanchez-Villeda H, Fang Z, Morgante M, Landewe T, Fengler K, Useche
F, Hanafey M, Tingey S, Chou H, Wing R, Soderlund C, Coe EH. Anchoring 9,3971 maize expressed sequence
tagged unigenes to the bacterial artificial chromosome contig map by
two-dimensional overgo hybridization. Plant Physiology. 2004 134:1317-1326.
Engler, F., J. Hatfield, W. Nelson, and C. Soderlund* (2003). Locating sequence on FPC maps and selecting a minimal tiling
path. Genome Research 13:2152-2163.
Yim, Y., G. Davis, N. Duru, T. Musket, E. Linton,
J. Messing, M. McMullen, C. Soderlund,
M. Polacco, J. Gardiner, and E. Coe, Jr. (2002) Characterization of Three Maize
Bacterial Artificial Chromosome Libraries toward Anchoring of the Physical Map
to the Genetic Map Using High-Density Bacterial Artificial Chromosome Filter
Hybridization. Plant Physiololgy.
130:1686-1696.
Cone, K., M. McMullen, I. Bi, G. Davis, Y. Yim, J. Gardiner, M. Polacco, H. Sanchez-Villeda, Z. Fang, S. Schroeder,
S. Havermann, J.. Bowers, A.
Paterson, C. Soderlund, F.
Engler, R. Wing, and E. Coe, Jr. (2002) Genetic, Physical, and Informatics Resources for
Maize. On the Road to an Integrated Map. Plant Physiol. 130: 1598-1605.
Coe E, Cone K, McMullen M,
Chen S, Davis G, Gardiner J, Liscum E, Polacco M, Paterson A, Sanchez-Villeda H,
Soderlund C, Wing R (2002). Access to
the maize genome: an integrated physical and genetic map. Plant Physiology 128:9-12.
Chen, M., G. Presting, W.
Barbazuk, J. Goicoechea, B. Blackmon, H. Kim, G. Fang, D. Frisch, Y. Yu, S.
Higingbottom, J. Phimphilai, D. Phimphilai, S. Thurmond, B. Gaudette, P. Li, J.
Liu, J. Hatfield, S. Sun, K. Farrar, C. Henderson, L. Barnett, R. Costa, B.
Williams, J. Gilbert, S. Walser, M. Atkins, C. Hall, I. Bancroft, J. Salse, F.
Regad, T. Mohapatra, N. Singh, A. Tyagi, C. Soderlund, R. Dean, R. Wing (2002). An Integrated physical and
genetic map of the rice genome. Plant Cell 14:537-545.
Soderlund*, C., S. Humphrey, A. Dunham and L. French
(2000). Contigs built with
fingerprints, markers and FPC v4.7. Genome Research 10:1772-1787.
Steingruber, H, A. Dunham, A.
Coffey, S. Clegg, g. Howell, G. Maslen, C. Scott, H. Gwilliam, P. Hunt, E. Sotheran, E. Huckle, S. Hunt, P. Dhami, C. Soderlund, M.
Leversha, D. Bentley, M. Ross (1999) High-Resolution Landmark Framework
for the Sequence-Ready Mapping of
Xq23-q26.1. Genome Research
9:751-762.
Soderlund*, C., T. Lau and P. Deloukas (1998). Z extensions to
the RHMAPPER package. Bioinformatics
14:538-539.
Soderlund*, C., I. Longden, and R. Mott (1997). FPC: a system
for building contigs from restriction fingerprinted clones. CABIOS 13:523-535.
Collins, J, C. Cole, L. Smink,
C. Garrett, M. Leversha, C. Soderlund,
G. Maslen, L. Everett, C. Rice, A. Coffey, S. Gregory, R. Gwilliam, A. Dunham,
A. Davies, S. Hassock, C. Todd, H.
Lehrach, T. Hulsebos, J. Weissenbach, B. Morrow, B., R. Kucherlapati, R. Wadey, P. Scambler, U-J. Kim, M. Simon,
N. Carter, R. Durbin, J.
Dumanski, D. Bentley, and I. Dunham, I (1995). High Resolution Integrated Yeast Artificial Chromosome Clone Map
of Human Chromosome 22. Nature 377:367-379
Soderlund*, C. and I. Dunham (1995). SAM: A system for
interactively building marker
maps. CABIOS 11:645-655.
Soderlund*, C. and C. Burks (1993). GRAM and genfragII: solving and testing the single-digest partially-ordered restriction map problem.
CABIOS 10:349-358.
Soderlund*, C., D. Torney, and C. Burks (1993). Calculating
Shared Fragments for the single digest problem. Proceedings of the 26th
Hawaii International Conference on System Sciences: Biotechnology Track, ACM-IEEE, 1:620-629.
Soderlund*, C., P. Shanmugam, O. White, and C. Fields
(1992). gm: A tool for exploratory analysis of DNA sequence. Proceedings
of the 25th Hawaii International Conference on System Science: Biotechnology
Track. 1:653-662.
White, O., C. Soderlund, P. Shanmugam, and C. Fields (1992). Information
contents and dinucleotide compositions of plant intron sequences vary with evolutionary origin. Plant
Molecular Biology 19:1057-1064.
Fields, C. A., J. Newberry,
H. Pfeiffer, C. Soderlund, S.
Kirby, and G. McWilliams (1992).
MERCURY: a heterogeneous system for spatial extrapolation of mesoscale
meteorological data. Int. J. Man - Machines Studies, 36:309-326.
Fields, C. and C. Soderlund (1990).
gm: A practical tool for automated DNA sequence analysis. CABIOS 6:263-270.
McWilliams, G., S. Kirby,
Fields, C., C. Cavendish, M. Coombs, Eskridge, R. Hartley, H. Pfeiffer, and C. Soderlund (1989). Army requirements for an intelligent
interface to a real-time meteorological database. Preprints of the Fifth International Conference on Interactive Information and
Processing Systems for Meteorology, Oceanography, and Hydrology. Boston: American Meteorological Society, pp. 1-2.
Pfeiffer, J. J., Jr. and C.
A. Soderlund (1988). Solid modelling data structures for computer vision. Proceedings of the 22nd Asilomar
Conference on Signals, Systems,
and Computers. New York: Institute of Electrical and
Electronics Engineers, pp.
543-547.
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Sequencing Consortium (2003). In-depth view of structure, activity, and
evolution of rice chromosome 10. Science 300:1566-1569
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Genome Mapping Consortium (2001). A physical map of the human genome. Nature 409:934-941.
Bentley, D. et al. (2001) The
physical maps for sequencing human chromosomes 1, 6, 9, 10, 13, 20 and X. Nature 409:942-943.
Deloukas, P. et al. (2001)
The DNA sequence and comparative analysis of human chromosome 20. Nature 414:865-871.
Dunham, I. et al. (1999).
Sequence of Human Chromosome 22. Nature 402:489-95
Deloukas, P. G. D. Schuler,
G. Gyapay, E. M. Beasley, C. Soderlund et al. (1998). A physical
map of 30,000 human genes. Science
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Schuler, et al. (1996). A
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Rambo, E. Fang, B. Blackmon, J.L. Goicoechea, S. Higingbottom, M. Sasinowski,
J. Tomkins, R.A. Dean, C. Soderlund,
R. McCombie, R. Martienssen, M. de la Bastile, R. Wilson, and D. Johnson
(2001). Sequence tagged connector/DNA fingerprint framework for rice genome
sequencing. In G. Khush, D. Brar, and B. Hardy (ed.). Rice Genetics IV,
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Genome Computing, Academic Press.
Soderlund, C., S. Gregory and I. Dunham (1998). Sequence ready
clones. In Bishop, M.J.(ed) Guide
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Gregory, S., C. Soderlund, and A. Coulson (1997). Contig assembly by
fingerprinting. In Dear, P.H.
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