Journal Publications

Vyas, M, TW Fisher, R He, W Nelson, G Yin, JM Cicero, M Willer, R Kim, R Kramer, GA May, JA Crow, CA Soderlund, DR Gang and JK Brown. Expression profiling of adult and nymph Asian citrus psyllids infected by Candidatus Liberibacter asiaticus: decided effects on nymphal immunity and development, and on adult energy metabolism and nutritional exploitation. PLoS One. 2015; 10(6): e0130328.

Salvato F, TS Balbuena, W Nelson, RSP Rao, R He, CA Soderlund, DR Gang, JJ Thelen (2015). Comparative proteomic analysis of developing rhizomes of the ancient vascular plant Equisetum hyemale and different monocot species. Journal of Proteome Research, 14 (4), pp 1779-1791

Vaughn MJ, W Nelson, C Soderlund, RM Maier, B. Pryor (2015). Assessing Fungal Community Structure from Mineral Surfaces in Kartchner Caverns Using Multiplexed 454 Pyrosequencing. Microb. Ecol. (Jan 23)

Soderlund, C, WM Nelson, SA Goff (2014) Allele Workbench: transcriptome pipeline and interactive graphics for allele-specific expression. PLoS ONE 9(12): e115740. doi: 10.1371/journal.pone.0115740

Fisher, TW, M Vyas, R He, W Nelson, JM Cicero, M Willer, R Kim, R Kramer, GA May, JA Crow, CA Soderlund, DR Gang and JK Brown (2014) Comparison of Potato and Asian Citrus Psyllid Adult and Nymph Transcriptomes Identified Vector Transcripts with Potential Involvement in Circulative, Propagative Liberibacter Transmission. Pathogens 3(4), 875-907; doi:10.3390/pathogens3040875.

Ortiz M, Legatzki A, Neilson JW, Fryslie B, Nelson WM, Wing RA, Soderlund CA, Pryor BM, Maier RM (2014) Making a living while starving in the dark: metagenomic insights into the energy dynamics of a carbonate cave. ISME J 8: 478-491.

He R, Salvato F, Park JJ, Kim MJ, Nelson W, Balbuena TS, Willer M, Crow JA, May GD, Soderlund CA, Thelen JJ, Gang DR (2014) A systems-wide comparison of red rice (Oryza longistaminata) tissues identifies rhizome specific genes and proteins that are targets for cultivated rice improvement. BMC Plant Biol 14: 46.

Kim MJ, Nelson W, Soderlund C, and D Gang (2013) Next-generation sequencing-based transcriptional profiling of sacred lotus "China antique". Tropical Plant Biology 6: 161-179

Soderlund, C., W. Nelson, M. Willer, and D. Gang (2013) TCW: Transcriptome Computational Workbench. PLOS ONE 10.1371/journal.pone.0069401.

Fisher T, Nelson W, Vyas M, He R, Willer M, Gang DR, Soderlund C, Brown JK (2013) Publicly available website for the identification of psyllid-'Ca. Liberibacter' interactors using comparative transcriptome analysis. Phytopathology 103: 44-44.

Varshney RK, Song C, Saxena RK, Azam S, Yu S, Sharpe AG, Cannon S, Baek J, Rosen BD, Tar'an B, Millan T, Zhang X, Ramsay LD, Iwata A, Wang Y, Nelson W, Farmer AD, Gaur PM, Soderlund C, Penmetsa RV, Xu C, Bharti AK, He W, Winter P, Zhao S, Hane JK, Carrasquilla-Garcia N, Condie JA, Upadhyaya HD, Luo MC, Thudi M, Gowda CL, Singh NP, Lichtenzveig J, Gali KK, Rubio J, Nadarajan N, Dolezel J, Bansal KC, Xu X, Edwards D, Zhang G, Kahl G, Gil J, Singh KB, Datta SK, Jackson SA, Wang J, Cook DR (2013) Draft genome sequence of chickpea (Cicer arietinum) provides a resource for trait improvement. Nature Biotechnol 31: 240-246.

Koo HJ, McDowell ET, Ma X, Greer KA, Kapteyn J, Xie Z, Descour A, Kim H, Yu Y, Kudrna D, Wing RA, Soderlund CA, Gang DR (2013) Ginger and turmeric expressed sequence tags identify signature genes for rhizome identity and development and the biosynthesis of curcuminoids, gingerols and terpenoids. BMC Plant Biol 13: 27.

Ortiz, M., J. Neilson, W. Nelson, A. Legatzke, A. Byrne, Y.Yu, C. Soderlund, B. Pryor, L. Pierson, R. Maier (2013). Profiling Bacterial Diversity and Taxonomic Composition on Speleothem Surfaces in Kartchner Caverns, AZ. Microbial Ecology 65:371-383.

Buechel, K., E. McDowell, W. Nelson, A. Descour, M. Hilker, J. Gershenzon, T. Fenning, C. Soderlund, D. R. Gang and T. Meiners. (2012) An elm EST databases for detection of leaf beetle oviposition-induced defense genes. BMC Genomics 13:242.

Neilson, J., J. Quade, M. Ortiz, W. M. Nelson, A. Legatzki, F. Tian, M. LaComb, J. Betancourt, R.Wing, C. Soderlund, R. Maier (2012). Life at the hyperarid margin: novel bacterial diversity in arid soils of the Atacama Desert, Chile. Extremophiles 16:553-566.

He, R., M-J Kim, W. Nelson, T. Balbuena, R. Kim, J. Crow, G. May, J. Thelen, C. Soderlund, D. R. Gang (2012) Next generation sequencing based transcriptomic and proteomic analysis of the common reed, Phragmites australis (Poaceae), reveals genes involved in invasiveness and rhizome specificity. Am J Bot, 99:232-247.

Kour, A., K. Greer, B. Valent, M. Orbach, C. Soderlund (2012) MGOS: Development of a community annotation database for Magnaporthe oryzae . Mol Plant Microbe Interact. 25: 271-278.

Soderlund, C, M. Bomhoff, and W. Nelson (2011) SyMAP v3.4: a turnkey synteny system with application to plant genomes. Nucleic Acids Research 10.1093/nar/gkr123.

McDowell, E. T., J. Kapteyn, A. Schmidt, C. Li, J. Kang, A. Descour, F. Shi, M. Larson, A. Schilmiller, L. An, A. Jones, E. Pichersky, C. Soderlund, and D.R. Gang (2011) Comparative functional genomic analysis of Solanum glandular trichome types. Plant Physiololgy 155: 524-539.

Soderlund, C, A. Descour, D. Kudrna, M. Bomhoff, L. Boyd, J. Currie, A. Angelova, K. Collura, M. Wissotski, E. Ashley, D. Morrow, J. Fernandes, V. Walbot, and Y. Yu (2009) Sequencing, Mapping and Analysis of 27,455 Maize Full-length cDNAs. PLoS Genetics 5:e1000740

Soderlund, C (2009) Large-scale experiments for elucidating plant-pathogen interactions for fungi and oomycetes. Briefing in Bioinformatics, 10: 654-663.

Soderlund, C, E. Johnson, M. Bomhoff, and A. Descour (2009) PAVE: Program for assembling and viewing ESTs. BMC Genomics 10:400.

Gu, Y, Y. Ma, N. Huo, J.P. Vogel, F.M. You, G. R. Lazo, D. M. Hayden, W. M. Nelson, C. Soderlund, J. Dvorak, O. D. Anderson, M-C Luo (2009) A BAC-based physical map of Brachypodium distachyon and its comparative analysis with rice and wheat. BMC Genomics, 10: 496.

Nelson, W. and C. Soderlund (2009). Integrating Sequence with FPC Fingerprinted Maps. Nucleic Acids Research 1-11 doi:10.1093/nar/gkp034.

Nelson, W., Luo, M., Ma, J., Haller, K., Bharti, A., Messing, J., Wing, R., San Miguel, P., Bennetzen, J., and Soderlund, C. (2008) Methylation-sensitive linking libraries enhance gene-enriched sequencing of complex genomes and map DNA methylation domains. BMC Genomics, 9:621doi:10.1186/1471-2164-9-621

Kim, H., B. Hurwitz, Y. Yu, K. Collura, N. Gill, P. SanMiguel, J.C. Mullikin, C. Maher, W. Nelson, M. Wissotski, M. Braidotti, D. Kudrna, J.L. Goicoechea, L. Stein, D. Ware, S.A. Jackson, C. Soderlund, and R.A. Wing (2008). Construction, alignment and analysis of twelve framework physical maps that represent the ten genome types of the genus Oryza. Genome Biol 9: R45.

Wei, F., E. Coe, W. Nelson, A.K. Bharti, F. Engler, E. Butler, H. Kim, J.L. Goicoechea, M. Chen, S. Lee, G. Fuks, H. Sanchez-Villeda, S. Schroeder, Z. Fang, M. McMullen, G. Davis, J.E. Bowers, A.H. Paterson, M. Schaeffer, J. Gardiner, K. Cone, J. Messing, C. Soderlund, and R.A. Wing (2007). Physical and genetic structure of the maize genome reflects its complex evolutionary history. PLoS Genet 3: e123.

Nelson, W.M., J. Dvorak, M.C. Luo, J. Messing, R.A. Wing, and C. Soderlund (2007). Efficacy of clone fingerprinting methodologies. Genomics 89: 160-165.

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, and G.L. Wang (2007). Magnaporthe grisea infection triggers RNA variation and antisense transcript expression in rice. Plant Physiol 144: 524-533.

Gowda, M., R.C. Venu, Y. Jia, E. Stahlberg, V. Pampanwar, C. Soderlund, and G.L. Wang (2007). Use of robust-long serial analysis of gene expression to identify novel fungal and plant genes involved in host-pathogen interactions. Methods Mol Biol 354: 131-144. Kim, H., P. San Miguel, W. Nelson, K. Collura, M. Wissotski, J.G. Walling, J.P. Kim, S.A. Jackson, C. Soderlund, and R.A. Wing (2007). Comparative physical mapping between Oryza sativa (AA genome type) and O. punctata (BB genome type). Genetics 176: 379-390.

Soderlund, C., K. Haller, V. Pampanwar, D. Ebbole, M. Farman, M.J. Orbach, G.L. Wang, R. Wing, J.R. Xu, D. Brown, T. Mitchell, and R. Dean (2006). MGOS: A resource for studying 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 (2006) 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.

Donofrio N, R. Rajagopalon, D. Brown, S. Diener, D. Windham, S. Nolin, A. Floyd, T. Mitchell, N. Galadima, S. Tucker, M. Orbach, G. Patel, M. Farman, V. Pampanwar, C. Soderlund, Y. H. Lee, and R. A. Dean (2005) PACLIMS: a component LIM system for high-throughput functional genomic analysis. BMC Bioinformatics 6:94.

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.

Consortium Publications

The Rice Chromosome 3 Sequencing Consortium (2005). Sequence, annotation, and analysis of synteny between rice chromosome 3 and diverged grass species. Genome Research 15:1284-1291.

The International Rice Genome Sequencing Project (2005). The map-based sequencing of the rice genome. Nature 436:793-800. The Rice Chromosome 10 Sequencing Consortium (2003). In-depth view of structure, activity, and evolution of rice chromosome 10. Science 300:1566-1569

The International Human 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 282:744-746.

Mungall AJ, Humphray SJ, Ranby SA et al. (1997) From long range mapping to sequence-ready contigs on human chromosome 6, DNA Seq 8:151-154.

Schuler, et al. (1996). A gene map of the human genome. Science 274:540-546.

Book Chapters

Greer, K. and C. Soderlund (2009). Magnaporthe grisea Oryza sativa (MGOS): community annotation. G.L. Wang and B. Valent (ed). Collection: Advances in Genetics,Genomics and Control of Rice Blast Disease. Springer.

Soderlund, C (2004) Restriction fragment fingerprinting software. In M. Dunn, L. Jorde, P. Little, S. Subramaniam (ed). Encyclopedia of Genomics, Proteomics and Bioinformatics. John Wiley and Son.

Nelson, W. and C. Soderlund (2005) Software for restriction fragment physical maps. In K. Meksem, G. Kahl (ed) The Handbook of Genome Mapping: Genetic and Physical Mapping, Wiley-VCH, pp. 285-306.

Engler, F., and C. Soderlund (2003). Building physical maps with FPC. In Ian Dunham (ed). Genomic Mapping and Sequencing. Horizon Press.pp. 20-236.

Soderlund, C., F. Engler, J. Hatfield, S. Blundy, M. Chen, Y.Yu, and R. Wing (2002). Mapping Sequence to FPC Rice Map. In C.Wu, P. Wang, and J. Wang (ed). Computational Biology and Genome Informatics. Selected papers from CBGI 2001. World Scientific Publishing. pp 59-79.

Wing, R.A., Y. Yu, G. Presting, D. Frisch, T. Wood, S-S. Woo, M.A. Budiman, L. Mao, H.R., Kim, T. 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, International Rice Institute, Science Publishers.

McCarthy, L., and C. Soderlund (1998). Radiation Hybrid Mapping. In Bishop, M.J.(ed) Guide to Human Genome Computing, Academic Press.

Soderlund, C., S. Gregory and I. Dunham (1998). Sequence ready clones. In Bishop, M.J.(ed) Guide to Human Genome Computing, Academic Press.

Gregory, S., C. Soderlund, and A. Coulson (1997). Contig assembly by fingerprinting. In Dear, P.H. (ed), Genome Mapping: A Practical Approach.

Burks, C., M. Engle, S. Forest, R. Parsons, C. Soderlund, and P. Storlz (1993). Stochastic optimization tools for genomic sequence assembly. Automated DNA Sequencing and analysis techniques, Venter, J.C., Ed., Academic Press, London