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| 2008 |
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Joann Mudge, Neil A. Miller, Irina Khrebtukova,
Ingrid E. Lindquist, Gregory D. May, Jim J. Huntley,
Shujun Luo, Lu Zhang, Jennifer C. van Velkinburgh, Andrew D. Farmer,
Sharon Lewis, William D. Beavis, Faye D. Schilkey, Selene M. Virk, C. Forrest Black,
M. Kathy Myers, Lar C. Madar, Ray J. Langley, John P. Utsey, Ryan W. Kim,
Rosalinda C. Roberts, Sat Kirpal Khalsa, Meredith Garcia, Victoria Ambriz-Griffith,
Richard Harlan, Wendy Czika, Stanton Martin, Russel D. Wolfinger, Nora I. Perrone-Bizzozero,
Gary P. Schroth, Stephen F. Kingsmore (2008)
Genomic Convergence Analysis of Schizophrenia: mRNA Sequencing Reveals Altered Synaptic
Vesicular Transport in Post-Mortem Cerebellum
PLos One 2008
[Abstract]
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Wang ET, Sandbery R, Luo S, Khrebtukova I, Zhang L, Mayr C, Kingsmore SF,
Schroth GP, Burge CB. (2008)
Alternative isoform regulation in human tissue transcriptomes
Nature 2008
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Salsbury Jr FR, Crowder MW, Kingsmore SF, Huntley JJA. (2008)
Molecular dynamic simulations of the metallo-beta-lactamase from Bacteroides fragilis in presence and absence of a tight-binding inhibitor.
J Mol Model 2008
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Kingsmore SF, Kennedy N, Halliday HL, Van Velkinburgh JC, Zhong S, Gabriel V, Grant J, Beavis WD, Tchernev VT, Perlee L, Lejnine S, Grimwade B, Sorette M, Edgar JDM. (2008)
Identification of diagnostic biomarkers for infection in premature neonates
Mol Cell Proteomics. Jul 13, 2008
PMID: 18622029
[Abstract]
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Woods CW, Feezor RJ, Kingsmore SF. (2008)
Sepsis and the Genomic Revolution: Risk, Diagnosis, Prognosis, and Therapeutics.
Genomic and Personalized Medicine,eds.Willard H and Ginsburg G. Elsevier. 2008
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Kingsmore SF, Lindquist IE, Mudge J, Gessler DD, Beavis WD. (2008)
Genome-wide association studies: progress and potential for drug discovery and development.
Nat Rev Drug Discov. 2008 Mar;7(3):221-30. Review.
PMID: 18274536
[Abstract]
[PubMed - indexed for MEDLINE]
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Sugarbaker DJ, Richards WG, Gordon GJ, Dong L, De Rienzo A, Maulik G, Glickman JN, Chirieac LR, Hartman ML, Taillon BE, Du L, Bouffard P, Kingsmore SF, Miller NA, Farmer AD, Jensen RV, Gullans SR, Bueno R.
(2008)
Transcriptome sequencing of malignant pleural mesothelioma tumors.
Proc Natl Acad Sci U S A. 2008 Mar 4;105(9):3521-6. Epub 2008 Feb 26.
PMID: 18303113
[Abstract ]
[PubMed - in process]
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Pendleton, R., Kitchen, S., Mudge, J., and McArthur, E.D.
(2008)
Origin of the Flax Cultivar 'Appar' and Its Position within the Linum perenne Complex.
International Journal of Plant Sciences 169, 445-453.
[Abstract]
[Full Text]
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Mudge, J., Farmer, A.D., and May, G.D.
The Long and the Short of it: Uniqueness of short DNA sequences in plants.
Plant & Animal Genomes XVI Conference, January 12-16, 2008, San Diego, CA
[Abstract]
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Mian MA, Zhang Y, Wang ZY, Zhang JY, Cheng X, Chen L, Chekhovskiy K, Dai X, Mao C, Cheung F, Zhao X, He J, Scott AD, Town CD, May, GD
(2008)
Analysis of tall fescue ESTs representing different abiotic stresses, tissue types and developmental stages.
BMC Plant Biol. 2008 Mar 4;8:27.
PMID: 18318913
[Abstract]
[Full Text]
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Schilkey, F.D., Miller, N.A., Mudge, J., Mader, L.C., Weems, D.,Virk, S.M., Black, C.F., Myers, M.K., Rice, M., Gomez, T., et al.
Alpheus: A Web Software Tool for Variant Detection using Next-Generation Sequencing Technologies.
Plant & Animal Genomes XVI Conference, January 12-16, 2008, San Diego, CA
[Abstract]
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| 2007 |
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Stephen F. Kingsmore, Ingrid E. Lindquist, Joann Mudge and William D. Beavis
(2007)
Genome-Wide Association Studies: Progress in Identifying Genetic Biomarkers in Common, Complex Diseases
Biomarker Insights 2007:2 283.292
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Retzel EF, Johnson JE, Crow JA, Lamblin AF, Paule CE
(2007)
Legume Resources: MtDB and Medicago.Org.
Methods Mol Biol. 2007;406:261-74
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Dixon, R.A., Bouton, J.H., Narasimhamoorthy, B., Saha, M., Wang, Z.-Y., and May, G.D.
(2007)
Beyond structural genomics for plant science.
Advances in Agronomy 95, 77-161.
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Naoumkina M, Torres-Jerez I, Allen S, He J, Zhao PX, Dixon RA, May, GD
(2007)
Analysis of cDNA libraries from developing seeds of guar (Cyamopsis tetragonoloba (L.) Taub).
BMC Plant Biol. 2007 Nov 23;7:62.
PMID: 18034910
[Abstract]
[Full Text]
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Joslyn CA, KM Verspoor, DDG Gessler (2007)
Knowledge Integration in Open Worlds: Utilizing the Mathematics of Hierarchical Structure.
Proc. IEEE Int. Conf. Semantic Computing (ICSC 07), Irvine, IEEE Computer Society, pp. 105-112.
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DDG Gessler, Verspoor K, Joslyn C, Koester B, Schmidt S. (2007)
Integrating Semantic Data Sources for Disease-implicated Gene Discovery.
Keynote speech at the Fifth Rocky Mountain Bioinformatics Conference [delivered by K Verspoor], Nov 30 - Dec 2, Snowmass, CO, p. 13.
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Mudge, J., Kingsmore, S.F., Miller, N.A., Kamoun, S., Lamour, K.H., Richardson, P.M., Platt, D., Grigoriev, I., Kuo, A., May, G.D., et al.
De novo Hybrid 454/Sanger Genome Assembly of Phytophthora capsici. (2007)
Paper presented at: Finishing in the Future, Santa Fe, NM
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| 2006 |
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Stacey G, Libault M, Brechenmacher L, Wan J, May GD (2006)
Genetics and functional genomics of legume nodulation. Curr. Opin. Plant Biol. 9(2):110-21
PMID: 16458572
[Abstract]
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Saha MC, Cooper JD, Mian MA, Chekhovskiy K, May GD,(2006)
Tall fescue genomic SSR markers: development and transferability across multiple grass species.
Theor. Appl. Genet. 113(8):1449-58.
PMID: 16947059
[Abstract]
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Cheung F, Haas BJ, Goldberg SM, May GD, Xiao Y, Town CD (2006)
Sequencing Medicago truncatula expressed sequenced tags using 454 Life Sciences technology.
BMC Genomics. 7:272.
PMID: 17062153
[Abstract]
[Full Text]
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Cannon SB, Sterck L, Rombauts S, Sato S, Cheung F, Gouzy J, Wang X,Mudge, J,
Vasdewani J, Schiex T, Spannagl M, Monaghan E, Nicholson C, Humphray SJ, Schoof H, Mayer KF, Rogers J, Quétier F, Oldroyd GE, Debellé F, Cook DR, Retzel EF, Roe BA, Town CD, Tabata S, Van de Peer Y, Young ND.
(2006)
Legume genome evolution viewed through the Medicago truncatula and Lotus
japonicus genomes.
Proc Natl Acad Sci U S A. 2006 Oct 3;103(40):14959-64. Epub 2006 Sep 26. Erratum in: Proc Natl Acad Sci U S A. 2006 Nov 21;103(47):18026. Scheix, Thomas
[corrected to Schiex, Thomas].
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Jackson SA, Wing RA, Stacey G, May GD, Shoemaker RC
(2006)
SoyMap: an integrated map of soybean for resolution and dissection of multiple genome duplication events.
Soybean Gen. Newsletter. Vol 37.
[Abstract]
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Baxter SM, Day SW, Fetrow JS, Reisinger S
(2006)
Scientific Software Development Is Not an Oxymoron.
PLoS Comput Biol 2(9): e87.
PMID: 16965174
[Full Text]
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McKinney BA, Reif DM, Rock MT, Edwards KM, Kingsmore SF, Moore JH, Crowe JE Jr.
(2006)
Cytokine Expression Patterns Associated with Systemic Adverse Events following Smallpox Immunization.
The Journal of infectious diseases.
194(4):444-53.
PMID: 16845627
[Abstract]
[Full Text]
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Gessler D, Dye C, Farmer P, Murray M, Navin T, Reves R, Shinnick T, Small PM, Yates T, Simpson G.
(2006)
Public health. A National Tuberculosis Archive.
Science. 311(5765):1245-6.
PMID: 16513968
[Abstract]
[Full Text]
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Kaukola T, Herva R, Perhomaa M, Pääkkö E, Kingsmore S, Vainionpää L, Hallman M.
(2006)
Population cohort associating chorioamnionitis, cord inflammatory cytokines and neurologic outcome in very preterm, extremely low birth weight infants.
Pediatr Res. 2006 Mar 59(3):478-83
PMID: 16492993
[Abstract]
[PubMed - indexed for MEDLINE]
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Zuev SM, Kingsmore SF, Gessler DD.
(2006)
Sepsis progression and outcome: a dynamical model.
Theoretical biology & medical modelling [electronic resource].
3(1):8.
PMID: 16480490
[Full Text]
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Kingsmore SF.
Multiplexed protein measurement: Technologies and Applications of Antibody Arrays.
Nat Rev Drug Discovery (in press).
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Gajendran K, Gonzales MD, Farmer A, Archuleta E, Win J, Waugh ME, Kamoun S.
(2006)
Phytophthora functional genomics database (PFGD): functional genomics of phytophthora-plant interactions.
Nucleic acids research.
34(Database issue):D465-70.
PMID: 16381913
[Full Text]
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Zuev SM, Kingsmore SF, Gessler DD
(2006)
Sepsis progression and outcome: a dynamical model. Theoretical biology & medical modelling.
Feb 15;3:8. PMID: 16480490
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DDG Gessler, Joslyn CA, Verspoor KM, Schmidt SE
(2006)
Deconstruction, Reconstruction, and Ontogenesis for Large, Monolithic, Legacy Ontologies in Semantic Web Service Applications.
Los Alamos Technical Report 06-5859
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Joslyn CA, DDG Gessler, SE Schmidt, KM Verspoor
(2006)
Distributed Representations of Bio-Ontologies for Semantic Web Services, Joint BioLINK and 9th Bio-Ontologies Meeting
Joint BioLINK and 9th Bio-Ontologies Meeting (JBB 06), ISMB 06
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Stein L, Beavis W, Gessler D, Rhee S, Rokhsar D, Main D, Mueller L, Huala E, Lawrence C
(2005)
The Plant Genome Databases Working Group. Plant Biology Databases: A Needs Assessment.
Commissioned report by the National Science Foundation. Available at
www.gramene.org/resources/plant_databases.pdf.
Resulted in the publication:
Stein L, Beavis W, Gessler D, Rhee S, Rokhsar D, Main D, Mueller L, Huala E, Lawrence C
The Plant Genome Database Working Group. Save our Data!
(2006)
The Scientist 20(4): 24-25
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| 2005 |
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Kaukola T, Herva R, Perhomaa M, Paakko E, Kingsmore S, Vainionpaa L, Hallman M
(2005)
Chorioamnionitis and Cord Serum Proinflammatory Cytokines: Lack of Association with Brain Damage and Neurologic Outcome in Very Preterm Infants.
Pediatric research. 2005 Sep 23.
PMID: 16183807
[Full Text]
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Kader HA, Tchernev VT, Satyaraj E, Lejnine S, Kotler G, Kingsmore SF, Patel DD
(2005)
Protein microarray analysis of disease activity in pediatric inflammatory bowel disease demonstrates elevated serum PLGF, IL-7, TGF-beta1, and IL-12p40 levels in Crohn's disease and ulcerative colitis patients in remission versus active disease.
The American journal of gastroenterology. 100(2):414-23.
PMID: 15667502
[Full Text]
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Yan T, Yoo D, Berardini TZ, Mueller LA, Weems DC, Weng S, Cherry JM, Rhee SY
(2005)
PatMatch: a program for finding patterns in peptide and nucleotide sequences.
Nucleic acids research. 33(Web Server issue):W262-6.
PMID: 15980466
[Full Text]
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Munneke B, Schlauch KA, Simonsen KL, Beavis WD, Doerge RW
(2005)
Adding confidence to gene expression clustering.
Genetics. 170(4):2003-11.
PMID: 15944369
[Full Text]
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Kevin M. Bailey, Lorenzo Ciannelli, Nicholas A. Bond, Andrea Belgrano, Nils Chr. Stenseth.
(5)
Recruitment of walleye pollock in a physically and biologically complex ecosystem: A new perspective.
Progress In Oceanography.
67(1-2):24-42.
[Abstract]
[Full Text]
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| 2004 |
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Arpat AB, Waugh M, Sullivan JP, Gonzales M, Frisch D, Main D, Wood T, Leslie A, Wing RA, Wilkins TA.
(2004)
Functional genomics of cell elongation in developing cotton fibers.
Plant molecular biology.
54(6):911-29.
PMID: 15604659
[Full Text]
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Belgrano A.
(2004)
Emergent properties of complex marine systems: a macroecological perspective
Marine Ecology Progress Series.
273: 281-289.
[Full Text]
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Belgrano A, Lima M, Stenseth N, Lindahl O.
(2004)
Community Ecology: Phytoplankton. In Ecological effects of climatic variations in the North Atlantic. Eds: Stenseth N, Ottersen G, Hurrell J, Belgrano A.
Oxford University Press.
2004.
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Almo Farina, Andrea Belgrano.
(4)
The eco-field: A new paradigm for landscape ecology.
Ecological Research.
Volume 19 Issue 1.
[Abstract]
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Huitema E, Bos JI, Tian M, Win J, Waugh ME, Kamoun S.
(2004)
Linking sequence to phenotype in Phytophthora-plant interactions.
Trends in microbiology.
12(4):193-200.
PMID: 15051070
[Full Text]
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Belgrano A, Lima M, Stenseth NC.
(2004)
Non-linear dynamics in marine-phytoplankton population systems.
Marine Ecology Progress Series.
273:281-28.
[Abstract]
[Full Text]
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Berardini TZ, Mundodi S, Reiser L, Huala E, Garcia-Hernandez M, Zhang P, Mueller LA, Yoon J, Doyle A, Lander G, Moseyko N, Yoo D, Xu I, Zoeckler B, Montoya M, Miller N, Weems D, Rhee SY.
(2004)
Functional annotation of the Arabidopsis genome using controlled vocabularies.
Plant physiology.
135(2):745-55.
PMID: 15173566
[Full Text]
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Farmer A. Explorations into the client-side of the semantic web: ISYS. W3C Workshop on Semantic Web for Life Sciences (2004).
[Full Text]
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Fernández-Pavía S, Biles C, Waugh M, Waugh
K, Rodríguez-Alvarado G, Liddell C. 2004. Characterization
of southern New Mexico Phytophthora capsici isolates from pepper. Revista
Mexicana de Fitopatologia. 22:1.
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Hagberg J, Tunberg B, Wieking G, Kröncke I, Belgrano
A. Community Ecology: Benthos. In Ecological effects of
climatic variations in the North Atlantic. Eds: Stenseth N,
Ottersen G, Hurrell J, Belgrano. Oxford University Press.
(2004)
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Kamoun S, Waugh M 2004. Comparative and functional genomics
of pathogenic oomycetes. In Applied Mycology and Biotechnology, Elsevier
Scientific Publishers. (in press)
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Sawkins M, Farmer A, Hoisington D, Sullivan J, Tolopko A, Jiang Z, Ribaut J. 2004. Comparative map and trait viewer (CMTV): an integrated bioinformatic tool to construct consensus maps and compare QTL and functional genomics data across genomes and experiments. Plant Molecular Biology. Oct;56(3):465-80.
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Schiltz G, Gessler D, Stein L. Semantic MOBY. Position Paper, W3C Workshop on Semantic Web for Life Sciences (2004). [Full Text]
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Smayda T, Borkman D, Beaugrand G, Belgrano A. Ecological effects of climatic
variations in the North Atlantic. Eds: Stenseth N, Ottersen G, Hurrell J, Belgrano A. Oxford University Press. (2004)
Smayda T, Borkman D, Beaugrand G, Belgrano A. Plankton Populations: Phytoplankton. In Ecological effects of climatic
variations in the North Atlantic. Eds: Stenseth N, Ottersen G,
Hurrell J, Belgrano. Oxford University Press. (2004)
Thro A, Parrott W, Udall J, Beavis W. 2004. Genomics and Plant
Breeding: The Experience of the Initiative for Future Agricultural and
Food Systems. Crop Science (accepted).
Weems D, Miller N, Garcia-Hernandez M,
Huala E, Rhee S. 2004. Design, implementation and maintenance of a
model organism database for Arabidopsis thaliana. Comparative
Genomics 5:362-369.
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| 2003 |
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Jansen R,
Jannink J, Beavis W. 2003. Mapping quantitative trait loci in plant
breeding populations: use of parental haplotype sharing. Crop Science
43: 829-834.
Rhee S, Beavis W, Berardini T, Chen G, Dixon D, Doyle
A, Garcia-Hernandez M, Huala E, Lander G, Montoya M, Miller N, Mueller L, Mundodi S, Reiser L, Tacklind J, Weems D, Wu Y, Xu I, Yoo D, Yoon J, Zhang P. 2003. The Arabidopsis
Information Resource (TAIR): a model organism database providing
a centralized, curated gateway to Arabidopsis biology, research
materials and community. Nucleic Acids Research 31:224.
Tuggle C, Green J, Fitzsimmons C, Woods R, Prather R, Malchenko S,
Bento-Soares M, Kucaba T, Crouch K, Smith C, Tack D, Robinson N,
O’Leary B, Scheetz T, Casavant T, Pomp D, Edeal J, Zhang Y,
Rothschild M, Garwood K, Beavis W. 2003. EST-Based Discovery in Pig:
Virtual Expression Patterns and Comparative Mapping to Human. Mammalian
Genome 14: 565-579.
Wilkinson M, Gessler D, Farmer A, Stein L. 2003. The BioMOBY
project explores open-source, simple, extensible protocols for enabling
biological database Interoperability. Proc Virt Conf Genom and Bioinf
(3):16-26. (ISSN 1547-383X). [pdf file] [Conf Proc]
Wlodek D, Gonzales M. Decreased energy levels can cause and sustain
obesity. Journal of Theoretical Biology. 2003. 225:33-44.
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| 2002 |
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Beavis W. 2002. QTL
Mapping in Plant Breeding Populations. US Patent (US 6399855 B1).
Gessler D. 2002. ISYS (Integrated SYStem): a platform for integrating
heterogeneous bioinformatic resources. Comparative and Functional Genomics 3:169-175.
Lee M, Sharopova N, Beavis W, Grant D, Katt M, Blair D, Hallauer A. 2002.
Expanding the genetic map of maize with the intermated B73 x Mo17 (IBM) population.
Plant Molecular Biology. 48:453-61.
Vigouroux Y, Jaqueth J, Matsuoka Y, Smith O, Beavis W, Smith J,
Doebley J. 2002. Rate and pattern of mutation at microsatellite loci in maize. Mol Biol Evol 19:1251-1260.
Waugh M, Anderson W, Bell C, Inman J,
Schilkey F, Sullivan J, May, GD. 2002.
The Medicago Genome Initiative: improved analysis, annotation, storage and retrieval of model legume data.
Nucleic Acids Research.
Waugh M, Tyler B, Mitchell T, Houfek T, Dean R, Anderson W,
Inman J, Schilkey F, Sullivan J and Bell C. 2002. The
Phytophthora Genome Consortium database: significant advances in
automated analysis and annotation to support distributed pathogenomic
research. Nucleic Acids Research.
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2008