C. Soderlund

发表

CHAPTER THIRTY-FOUR – Stochastic Optimization Tools for Genomic Sequence Assembly

C. Burks, S. Forrest, M. Engle, 1994 .

Sequence composition and genome organization of maize.

R. Wing, Yeisoo Yu, Hyeran Kim, 2004, Proceedings of the National Academy of Sciences of the United States of America.

The B73 Maize Genome: Complexity, Diversity, and Dynamics

Dawn H. Nagel, Kevin L. Schneider, Thomas K. Wolfgruber, 2009, Science.

An elm EST database for identifying leaf beetle egg-induced defense genes

J. Gershenzon, C. Soderlund, D. Gang, 2012, BMC Genomics.

Anchoring 9,371 Maize Expressed Sequence Tagged Unigenes to the Bacterial Artificial Chromosome Contig Map by Two-Dimensional Overgo Hybridization1

Steven G. Schroeder, R. Wing, M. Morgante, 2004, Plant Physiology.

SyMAP: A system for discovering and viewing syntenic regions of FPC maps.

C. Soderlund, William M. Nelson, A. Shoemaker, 2006, Genome research.

Draft genome sequence of chickpea (Cicer arietinum) provides a resource for trait improvement

James K. Hane, Jun Wang, J. Wang, 2013, Nature Biotechnology.

An Integrated Physical and Genetic Map of the Rice Genome

B. Williams, R. Dean, G. Presting, 2002, The Plant Cell Online.

Genetic, Physical, and Informatics Resources for Maize. On the Road to an Integrated Map1

Steven G. Schroeder, Seth A. Havermann, A. Paterson, 2002, Plant Physiology.

Physical and Genetic Structure of the Maize Genome Reflects Its Complex Evolutionary History

Steven G. Schroeder, A. Paterson, R. Wing, 2007, PLoS genetics.

MGOS: development of a community annotation database for Magnaporthe oryzae.

Carol Soderlund, Barbara Valent, C. Soderlund, 2012, Molecular plant-microbe interactions : MPMI.

Comparison of Potato and Asian Citrus Psyllid Adult and Nymph Transcriptomes Identified Vector Transcripts with Potential Involvement in Circulative, Propagative Liberibacter Transmission

Mark Willer, C. Soderlund, D. Gang, 2014, Pathogens.

Large-Scale Identification of Expressed Sequence Tags Involved in Rice and Rice Blast Fungus Interaction1

R. Dean, R. Wing, Yeisoo Yu, 2005, Plant Physiology.

Allele Workbench: Transcriptome Pipeline and Interactive Graphics for Allele-Specific Expression

S. Goff, C. Soderlund, William M. Nelson, 2014, PloS one.

A systems-wide comparison of red rice (Oryza longistaminata) tissues identifies rhizome specific genes and proteins that are targets for cultivated rice improvement

G. May, C. Soderlund, D. Gang, 2014, BMC Plant Biology.

Next-generation sequencing-based transcriptomic and proteomic analysis of the common reed, Phragmites australis (Poaceae), reveals genes involved in invasiveness and rhizome specificity.

G. May, C. Soderlund, D. Gang, 2012, American journal of botany.

Asian Citrus Psyllid Expression Profiles Suggest Candidatus Liberibacter Asiaticus-Mediated Alteration of Adult Nutrition and Metabolism, and of Nymphal Development and Immunity

C. Soderlund, D. Gang, R. He, 2015, PloS one.

6 – Radiation Hybrid Mapping

C. Soderlund, L. McCarthy, 1998 .

A physical map of the human genome

D. Haussler, B. Trask, R. Wilson, 2001, Nature.

Bioinformatics Whole-Genome Validation of High-Information-Content Fingerprinting 1

R. Wing, Hyeran Kim, C. Soderlund, 2005 .

Sequence-tagged connector/DNA fingerprint framework for rice genome sequencing.

R. Wilson, R. Dean, W. McCombie, 2001 .

7 – Sequence Ready Clone Maps

I. Dunham, S. Gregory, C. Soderlund, 1998 .

Life at the hyperarid margin: novel bacterial diversity in arid soils of the Atacama Desert, Chile

R. Wing, J. Betancourt, C. Soderlund, 2012, Extremophiles.

Methylation-sensitive linking libraries enhance gene-enriched sequencing of complex genomes and map DNA methylation domains

J. Bennetzen, R. Wing, Hyeran Kim, 2008, BMC Genomics.

PAVE: Program for assembling and viewing ESTs

C. Soderlund, A. Descour, Matthew Bomhoff, 2009, BMC Genomics.

Translating Anatomical Structures and Functional Genomics of Candidatus Liberibacter asiaticus and solanacearum Into Circulative, Propagative Vector-Mediated Transmission Processes

C. Soderlund, D. Gang, R. He, 2014 .

Ginger and turmeric expressed sequence tags identify signature genes for rhizome identity and development and the biosynthesis of curcuminoids, gingerols and terpenoids

R. Wing, Yeisoo Yu, Hyeran Kim, 2013, BMC Plant Biology.

Profiling Bacterial Diversity and Taxonomic Composition on Speleothem Surfaces in Kartchner Caverns, AZ

R. Wing, Yeisoo Yu, C. Soderlund, 2012, Microbial Ecology.

Assessing Fungal Community Structure from Mineral Surfaces in Kartchner Caverns Using Multiplexed 454 Pyrosequencing

C. Soderlund, R. Maier, William M. Nelson, 2015, Microbial Ecology.

Making a living while starving in the dark: metagenomic insights into the energy dynamics of a carbonate cave

R. Wing, C. Soderlund, R. Maier, 2013, The ISME Journal.

Construction, alignment and analysis of twelve framework physical maps that represent the ten genome types of the genus Oryza

L. Stein, J. Mullikin, C. Maher, 2008, Genome Biology.

A BAC-based physical map of Brachypodium distachyon and its comparative analysis with rice and wheat

J. Dvorak, C. Soderlund, M. Luo, 2009, BMC Genomics.

Comparative Physical Mapping Between Oryza sativa (AA Genome Type) and O. punctata (BB Genome Type)

S. Jackson, R. Wing, Hyeran Kim, 2007, Genetics.

gm: a practical tool for automating DNA sequence analysis

Chris A. Fields, C. A. Soderlund, C. Soderlund, 1990, Comput. Appl. Biosci..

Locating sequence on FPC maps and selecting a minimal tiling path.

William Nelson, C. Soderlund, William M. Nelson, 2003, Genome research.

SAM: a system for iteratively building marker maps

Carol Soderlund, I. Dunham, I. Dunham, 1995, Comput. Appl. Biosci..

Integrating sequence with FPC fingerprint maps

Carol Soderlund, William Nelson, C. Soderlund, 2009, Nucleic acids research.

Efficacy of clone fingerprinting methodologies.

R. Wing, J. Dvorak, C. Soderlund, 2007, Genomics.

Information contents and dinucleotide compositions of plant intron sequences vary with evolutionary origin

Carol Soderlund, Owen White, Chris Fields, 1992, Plant Molecular Biology.

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 Hybridization1

Ngozi A. Duru, G. Davis, M. McMullen, 2002, Plant Physiology.

Sequencing, Mapping, and Analysis of 27,455 Maize Full-Length cDNAs

Carol Soderlund, Virginia Walbot, Lomax Boyd, 2009, PLoS genetics.

Comparative physical mapping links conservation of microsynteny to chromosome structure and recombination in grasses.

Gene A. Brewer, Haibao Tang, A. Paterson, 2005, Proceedings of the National Academy of Sciences of the United States of America.

FPC: a system for building contigs from restriction fingerprinted clones

Carol Soderlund, Richard Mott, Ian Longden, 1997, Comput. Appl. Biosci..

Comparative Functional Genomic Analysis of Solanum Glandular Trichome Types1[W][OA]

Anthony L. Schilmiller, A. D. Jones, E. Pichersky, 2010, Plant Physiology.

Next-Generation Sequencing-Based Transcriptional Profiling of Sacred Lotus “China Antique”

C. Soderlund, D. Gang, Min-Jeong Kim, 2013, Tropical Plant Biology.

SyMAP v3.4: a turnkey synteny system with application to plant genomes

Carol Soderlund, Matthew Bomhoff, C. Soderlund, 2011, Nucleic acids research.

Whole-Genome Validation of High-Information-Content Fingerprinting1

Galina Fuks, Joachim Messing, Rod A Wing, 2005, Plant Physiology.

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.

S. Jackson, D. Galbraith, R. Wing, 2005, Genome research.

Sequence, annotation, and analysis of synteny between rice chromosome 3 and diverged grass species.

Rod A Wing, Wei Zhu, Carol Soderlund, 2005, Genome research.

FPC Web Tools for Rice, Maize, and Distribution1

Carol Soderlund, Gaurav Gupta, Vishal Pampanwar, 2005, Plant Physiology.

Oryza libraries that represent the 10 genome types of the genus Construction and analysis of 12 deep-coverage large-insert BAC bacterial artificial chromosome library resource : Oryza The Material Supplemental

S. Jackson, D. Galbraith, R. Wing, 2005 .

Update on Map Resources for Maize Genetic , Physical , and Informatics Resources for Maize . On the Road to an Integrated Map 1

Seth A. Havermann, A. Paterson, R. Wing, 2002 .

Mapping Sequence to Rice FPC

Carol Soderlund, James Hatfield, Fred Engler, 2003, Computational Biology and Genome Informatics.

Computational techniques for elucidating plant-pathogen interactions from large-scale experiments on fungi and oomycetes

Carol Soderlund, C. Soderlund, 2009, Briefings Bioinform..

MGOS: A resource for studying Magnaporthe grisea and Oryza sativa interactions.

Carol Soderlund, Vishal Pampanwar, Guo-Liang Wang, 2006, Molecular plant-microbe interactions : MPMI.

Transcriptome computational workbench (TCW): analysis of single and comparative transcriptomes

Carol Soderlund, C. Soderlund, 2019, bioRxiv.

Comparative proteomic analysis of developing rhizomes of the ancient vascular plant Equisetum hyemale and different monocot species.

C. Soderlund, D. Gang, J. Thelen, 2015, Journal of proteome research.

Profiling Bacterial Diversity and Taxonomic Composition on Speleothem Surfaces in Kartchner Caverns, AZ

R. Wing, Yeisoo Yu, C. Soderlund, 2012, Microbial Ecology.

Magnaporthe grisea Oryza sativa (MGOS) Interaction Database: Community Annotation

Carol Soderlund, Kevin A. Greer, C. Soderlund, 2009 .

Use of robust-long serial analysis of gene expression to identify novel fungal and plant genes involved in host-pathogen interactions.

C. Soderlund, E. Stahlberg, Guo‐Liang Wang, 2007, Methods in molecular biology.

Software for Restriction Fragment Physical Maps

Carol Soderlund, William Nelson, C. Soderlund, 2005 .

The DNA sequence of human chromosome 22

Melanie E. Goward, Antony V. Cox, R. Durbin, 1999, Nature.

Contigs built with fingerprints, markers, and FPC V4.7.

C. Soderlund, S. Humphray, A. Dunham, 2000, Genome research.

Next-Generation Sequencing-Based Transcriptional Profiling of Sacred Lotus “China Antique”

C. Soderlund, D. Gang, Min-Jeong Kim, 2013, Tropical Plant Biology.

TCW: Transcriptome Computational Workbench

Carol Soderlund, William Nelson, Mark Willer, 2013, PloS one.

The physical maps for sequencing human chromosomes 1, 6, 9, 10, 13, 20 and X

P. Deloukas, R. Durbin, J. Sulston, 2001, Nature.

Z extensions to the RHMAPPER package

Carol Soderlund, Panagiotis Deloukas, Timun Lau, 1998, Bioinform..