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Soo-Yon Rhee
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26
Shafer, Robert
12
Fessel, Jeffrey
9
Reiser, Leonore
8
Mueller, Lukas
7
Zhang, Peifen
7
Liu, Tommy
5
Gonzales, Matthew
5
Huala, Eva
5
Weems, Dan
5
Taylor, Jonathan
4
Paley, Suzanne
4
Winters, Mark
4
Yoo, Danny
4
Zolopa, Andrew
4
Hurley, Leo
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All Publications
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2009: Varghese Vici; Shahriar Rajin; Rhee Soo-Yon; Liu Tommy; Simen Birgitte B; Egholm Michael; Hanczaruk Bozena; Blake Lisbeth A; Gharizadeh Baback; Babrzadeh Farbod; Bachmann Michael H; Fessel W Jeffrey; Shafer Robert W
Minority variants associated with transmitted and acquired HIV-1 nonnucleoside reverse transcriptase inhibitor resistance: implications for the use of second-generation nonnucleoside reverse transcriptase inhibitors.
Journal of acquired immune deficiency syndromes (1999) 2009;52(3):309-15.
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2009: Shahriar Rajin; Rhee Soo-Yon; Liu Tommy F; Fessel W Jeffrey; Scarsella Anthony; Towner William; Holmes Susan P; Zolopa Andrew R; Shafer Robert W
Nonpolymorphic human immunodeficiency virus type 1 protease and reverse transcriptase treatment-selected mutations.
Antimicrobial agents and chemotherapy 2009;53(11):4869-78.
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2009: Rhee Soo-Yon; Fessel W Jeffrey; Liu Tommy F; Marlowe Natalia M; Rowland Charles M; Rode Richard A; Vandamme Anne-Mieke; Van Laethem Kristel; Brun-Vezinet Françoise; Calvez Vincent; Taylor Jonathan; Hurley Leo; Horberg Michael; Shafer Robert W
Predictive value of HIV-1 genotypic resistance test interpretation algorithms.
The Journal of infectious diseases 2009;200(3):453-63.
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2009: Gifford Robert J; Liu Tommy F; Rhee Soo-Yon; Kiuchi Mark; Hue Stephane; Pillay Deenan; Shafer Robert W
The calibrated population resistance tool: standardized genotypic estimation of transmitted HIV-1 drug resistance.
Bioinformatics (Oxford, England) 2009;25(9):1197-8.
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2009: Altmann André; Däumer Martin; Beerenwinkel Niko; Peres Yardena; Schülter Eugen; Büch Joachim; Rhee Soo-Yon; Sönnerborg Anders; Fessel W Jeffrey; Shafer Robert W; Zazzi Maurizio; Kaiser Rolf; Lengauer Thomas
Predicting the response to combination antiretroviral therapy: retrospective validation of geno2pheno-THEO on a large clinical database.
The Journal of infectious diseases 2009;199(7):999-1006.
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2009: Bembom Oliver; Petersen Maya L; Rhee Soo-Yon; Fessel W Jeffrey; Sinisi Sandra E; Shafer Robert W; van der Laan Mark J
Biomarker discovery using targeted maximum-likelihood estimation: application to the treatment of antiretroviral-resistant HIV infection.
Statistics in medicine 2009;28(1):152-72.
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2009: Altmann André; Sing Tobias; Vermeiren Hans; Winters Bart; Van Craenenbroeck Elke; Van der Borght Koen; Rhee Soo-Yon; Shafer Robert W; Schülter Eugen; Kaiser Rolf; Peres Yardena; Sönnerborg Anders; Fessel W Jeffrey; Incardona Francesca; Zazzi Maurizio; Bacheler Lee; Van Vlijmen Herman; Lengauer Thomas
Advantages of predicted phenotypes and statistical learning models in inferring virological response to antiretroviral therapy from HIV genotype.
Antiviral therapy 2009;14(2):273-83.
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2009: Bennett Diane E; Camacho Ricardo J; Otelea Dan; Kuritzkes Daniel R; Fleury Hervé; Kiuchi Mark; Heneine Walid; Kantor Rami; Jordan Michael R; Schapiro Jonathan M; Vandamme Anne-Mieke; Sandstrom Paul; Boucher Charles A B; van de Vijver David; Rhee Soo-Yon; Liu Tommy F; Pillay Deenan; Shafer Robert W
Drug resistance mutations for surveillance of transmitted HIV-1 drug-resistance: 2009 update.
PloS one 2009;4(3):e4724.
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2008: Eriksson Nicholas; Pachter Lior; Mitsuya Yumi; Rhee Soo-Yon; Wang Chunlin; Gharizadeh Baback; Ronaghi Mostafa; Shafer Robert W; Beerenwinkel Niko
Viral population estimation using pyrosequencing.
PLoS computational biology 2008;4(4):e1000074.
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2008: Gifford Robert J; Rhee Soo-Yon; Eriksson Nicolas; Liu Tommy F; Kiuchi Mark; Das Amar K; Shafer Robert W
Sequence editing by Apolipoprotein B RNA-editing catalytic component [corrected] and epidemiological surveillance of transmitted HIV-1 drug resistance.
AIDS (London, England) 2008;22(6):717-25.
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2008: Lalonde Sylvie; Ehrhardt David W; Loqué Dominique; Chen Jin; Rhee Seung Y; Frommer Wolf B
Molecular and cellular approaches for the detection of protein-protein interactions: latest techniques and current limitations.
The Plant journal : for cell and molecular biology 2008;53(4):610-35.
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2008: Avraham Shulamit; Tung Chih-Wei; Ilic Katica; Jaiswal Pankaj; Kellogg Elizabeth A; McCouch Susan; Pujar Anuradha; Reiser Leonore; Rhee Seung Y; Sachs Martin M; Schaeffer Mary; Stein Lincoln; Stevens Peter; Vincent Leszek; Zapata Felipe; Ware Doreen
The Plant Ontology Database: a community resource for plant structure and developmental stages controlled vocabulary and annotations.
Nucleic acids research 2008;36(Database issue):D449-54.
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2008: Caspi Ron; Foerster Hartmut; Fulcher Carol A; Kaipa Pallavi; Krummenacker Markus; Latendresse Mario; Paley Suzanne; Rhee Seung Y; Shearer Alexander G; Tissier Christophe; Walk Thomas C; Zhang Peifen; Karp Peter D
The MetaCyc Database of metabolic pathways and enzymes and the BioCyc collection of Pathway/Genome Databases.
Nucleic acids research 2008;36(Database issue):D623-31.
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2008: Rhee Soo-Yon; Liu Tommy F; Kiuchi Mark; Zioni Rafael; Gifford Robert J; Holmes Susan P; Shafer Robert W
Natural variation of HIV-1 group M integrase: implications for a new class of antiretroviral inhibitors.
Retrovirology 2008;5():74.
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2008: Shafer Robert W; Rhee Soo-Yon; Bennett Diane E
Consensus drug resistance mutations for epidemiological surveillance: basic principles and potential controversies.
Antiviral therapy 2008;13 Suppl 2():59-68.
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2008: Kapoor Amit; Shapiro Beth; Shafer Robert W; Shulman Nancy; Rhee Soo-Yon; Delwart Eric L
Multiple independent origins of a protease inhibitor resistance mutation in salvage therapy patients.
Retrovirology 2008;5():7.
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2007: Mitsuya Yumi; Liu Tommy F; Rhee Soo-Yon; Fessel W Jeffrey; Shafer Robert W
Prevalence of darunavir resistance-associated mutations: patterns of occurrence and association with past treatment.
The Journal of infectious diseases 2007;196(8):1177-9.
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2007: Petersen Maya L; Wang Yue; van der Laan Mark J; Rhee Soo-Yon; Shafer Robert W; Fessel W Jeffrey
Virologic efficacy of boosted double versus boosted single protease inhibitor therapy.
AIDS (London, England) 2007;21(12):1547-54.
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2007: Rhee Soo-Yon; Liu Tommy F; Holmes Susan P; Shafer Robert W
HIV-1 subtype B protease and reverse transcriptase amino acid covariation.
PLoS computational biology 2007;3(5):e87.
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2007: Ilic Katica; Kellogg Elizabeth A; Jaiswal Pankaj; Zapata Felipe; Stevens Peter F; Vincent Leszek P; Avraham Shulamit; Reiser Leonore; Pujar Anuradha; Sachs Martin M; Whitman Noah T; McCouch Susan R; Schaeffer Mary L; Ware Doreen H; Stein Lincoln D; Rhee Seung Y
The plant structure ontology, a unified vocabulary of anatomy and morphology of a flowering plant.
Plant physiology 2007;143(2):587-99.
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2007: Shafer Robert W; Rhee Soo-Yon; Pillay Deenan; Miller Veronica; Sandstrom Paul; Schapiro Jonathan M; Kuritzkes Daniel R; Bennett Diane
HIV-1 protease and reverse transcriptase mutations for drug resistance surveillance.
AIDS (London, England) 2007;21(2):215-23.
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2007: Hernandez Genaro; Rhee Soo-Yon; Shafer Robert W; Das Amar K
Knowledge integration of software for HIV drug resistance research.
AMIA ... Annual Symposium proceedings / AMIA Symposium. AMIA Symposium 2007;():973.
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2007: Altmann Andre; Beerenwinkel Niko; Sing Tobias; Savenkov Igor; Doumer Martin; Kaiser Rolf; Rhee Soo-Yon; Fessel W Jeffrey; Shafer Robert W; Lengauer Thomas
Improved prediction of response to antiretroviral combination therapy using the genetic barrier to drug resistance.
Antiviral therapy 2007;12(2):169-78.
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2007: Sinisi Sandra E; Polley Eric C; Petersen Maya L; Rhee Soo-Yon; van der Laan Mark J
Super learning: an application to the prediction of HIV-1 drug resistance.
Statistical applications in genetics and molecular biology 2007;6():Article7.
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2006: Mitsuya Yumi; Winters Mark A; Fessel W Jeffrey; Rhee Soo-Yon; Hurley Leo; Horberg Michael; Schiffer Celia A; Zolopa Andrew R; Shafer Robert W
N88D facilitates the co-occurrence of D30N and L90M and the development of multidrug resistance in HIV type 1 protease following nelfinavir treatment failure.
AIDS research and human retroviruses 2006;22(12):1300-5.
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2006: Rhee Soo-Yon; Taylor Jonathan; Wadhera Gauhar; Ben-Hur Asa; Brutlag Douglas L; Shafer Robert W
Genotypic predictors of human immunodeficiency virus type 1 drug resistance.
Proceedings of the National Academy of Sciences of the United States of America 2006;103(46):17355-60.
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2006: Pujar Anuradha; Jaiswal Pankaj; Kellogg Elizabeth A; Ilic Katica; Vincent Leszek; Avraham Shulamit; Stevens Peter; Zapata Felipe; Reiser Leonore; Rhee Seung Y; Sachs Martin M; Schaeffer Mary; Stein Lincoln; Ware Doreen; McCouch Susan
Whole-plant growth stage ontology for angiosperms and its application in plant biology.
Plant physiology 2006;142(2):414-28.
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2006: Mitsuya Yumi; Winters Mark A; Fessel W Jeffrey; Rhee Soo-Yon; Slome Sally; Flamm Jason; Horberg Michael; Hurley Leo; Klein Daniel; Shafer Robert W
HIV-1 drug resistance genotype results in patients with plasma samples with HIV-1 RNA levels less than 75 copies/mL.
Journal of acquired immune deficiency syndromes (1999) 2006;43(1):56-9.
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2006: Li Shijun; Ehrhardt David W; Rhee Seung Y
Systematic analysis of Arabidopsis organelles and a protein localization database for facilitating fluorescent tagging of full-length Arabidopsis proteins.
Plant physiology 2006;141(2):527-39.
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2006: Rhee Soo-Yon; Kantor Rami; Katzenstein David A; Camacho Ricardo; Morris Lynn; Sirivichayakul Sunee; Jorgensen Louise; Brigido Luis F; Schapiro Jonathan M; Shafer Robert W;
HIV-1 pol mutation frequency by subtype and treatment experience: extension of the HIVseq program to seven non-B subtypes.
AIDS (London, England) 2006;20(5):643-51.
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2006: Caspi Ron; Foerster Hartmut; Fulcher Carol A; Hopkinson Rebecca; Ingraham John; Kaipa Pallavi; Krummenacker Markus; Paley Suzanne; Pick John; Rhee Seung Y; Tissier Christophe; Zhang Peifen; Karp Peter D
MetaCyc: a multiorganism database of metabolic pathways and enzymes.
Nucleic acids research 2006;34(Database issue):D511-6.
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2006: Lin Ray S; Rhee Soo-Yon; Shafer Robert W; Das Amar K
A combined data mining approach for infrequent events: analyzing HIV mutation changes based on treatment history.
Computational systems bioinformatics / Life Sciences Society. Computational Systems Bioinformatics Conference 2006;():385-8.
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2006: Lin Ray S; Rhee Soo-Yon; Shafer Robert W; Das Amar K
Prediction of HIV mutation changes based on treatment history.
AMIA ... Annual Symposium proceedings / AMIA Symposium. AMIA Symposium 2006;():1011.
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2006: Leebens-Mack Jim; Vision Todd; Brenner Eric; Bowers John E; Cannon Steven; Clement Mark J; Cunningham Clifford W; dePamphilis Claude; deSalle Rob; Doyle Jeff J; Eisen Jonathan A; Gu Xun; Harshman John; Jansen Robert K; Kellogg Elizabeth A; Koonin Eugene V; Mishler Brent D; Philippe Hervé; Pires J Chris; Qiu Yin-Long; Rhee Seung Y; Sjölander Kimmen; Soltis Douglas E; Soltis Pamela S; Stevenson Dennis W; Wall Kerr; Warnow Tandy; Zmasek Christian
Taking the first steps towards a standard for reporting on phylogenies: Minimum Information About a Phylogenetic Analysis (MIAPA).
Omics : a journal of integrative biology 2006;10(2):231-7.
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2006: Rhee Seung Yon; Dickerson Julie; Xu Dong
Bioinformatics and its applications in plant biology.
Annual review of plant biology 2006;57():335-60.
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2005: Rhee Soo-Yon; Fessel W Jeffrey; Zolopa Andrew R; Hurley Leo; Liu Tommy; Taylor Jonathan; Nguyen Dong Phuong; Slome Sally; Klein Daniel; Horberg Michael; Flamm Jason; Follansbee Stephen; Schapiro Jonathan M; Shafer Robert W
HIV-1 Protease and reverse-transcriptase mutations: correlations with antiretroviral therapy in subtype B isolates and implications for drug-resistance surveillance.
The Journal of infectious diseases 2005;192(3):456-65.
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2005: Yan Thomas; Yoo Danny; Berardini Tanya Z; Mueller Lukas A; Weems Dan C; Weng Shuai; Cherry J Michael; Rhee Seung Y
PatMatch: a program for finding patterns in peptide and nucleotide sequences.
Nucleic acids research 2005;33(Web Server issue):W262-6.
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2005: Rhee Seung Yon
Bioinformatics. Current limitations and insights for the future.
Plant physiology 2005;138(2):569-70.
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2005: Zhang Peifen; Foerster Hartmut; Tissier Christophe P; Mueller Lukas; Paley Suzanne; Karp Peter D; Rhee Seung Y
MetaCyc and AraCyc. Metabolic pathway databases for plant research.
Plant physiology 2005;138(1):27-37.
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2005: Johnston Elizabeth; Dupnik Kathryn M; Gonzales Matthew J; Winters Mark A; Rhee Soo-Yon; Imamichi Tomozumi; Shafer Robert W
Panel of prototypical infectious molecular HIV-1 clones containing multiple nucleoside reverse transcriptase inhibitor resistance mutations.
AIDS (London, England) 2005;19(7):731-3.
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2005: Zhang Jie; Rhee Soo-Yon; Taylor Jonathan; Shafer Robert W
Comparison of the precision and sensitivity of the Antivirogram and PhenoSense HIV drug susceptibility assays.
Journal of acquired immune deficiency syndromes (1999) 2005;38(4):439-44.
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2005: Schlueter Shannon D; Wilkerson Matthew D; Huala Eva; Rhee Seung Y; Brendel Volker
Community-based gene structure annotation.
Trends in plant science 2005;10(1):9-14.
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2005: Bard Jonathan; Rhee Seung Y; Ashburner Michael
An ontology for cell types.
Genome biology 2005;6(2):R21.
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2004: Johnston Elizabeth; Winters Mark A; Rhee Soo-Yon; Merigan Thomas C; Schiffer Celia A; Shafer Robert W
Association of a novel human immunodeficiency virus type 1 protease substrate cleft mutation, L23I, with protease inhibitor therapy and in vitro drug resistance.
Antimicrobial agents and chemotherapy 2004;48(12):4864-8.
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2004: Zhang Xin; Fowler Sarah G; Cheng Hongmei; Lou Yigong; Rhee Seung Y; Stockinger Eric J; Thomashow Michael F
Freezing-sensitive tomato has a functional CBF cold response pathway, but a CBF regulon that differs from that of freezing-tolerant Arabidopsis.
The Plant journal : for cell and molecular biology 2004;39(6):905-19.
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2004: Rhee Soo-Yon; Liu Tommy; Ravela Jaideep; Gonzales Matthew J; Shafer Robert W
Distribution of human immunodeficiency virus type 1 protease and reverse transcriptase mutation patterns in 4,183 persons undergoing genotypic resistance testing.
Antimicrobial agents and chemotherapy 2004;48(8):3122-6.
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2004: Kapoor Amit; Jones Morris; Shafer R W; Rhee Soo-Yon; Kazanjian Powel; Delwart Eric L
Sequencing-based detection of low-frequency human immunodeficiency virus type 1 drug-resistant mutants by an RNA/DNA heteroduplex generator-tracking assay.
Journal of virology 2004;78(13):7112-23.
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2004: Berardini Tanya Z; Mundodi Suparna; Reiser Leonore; Huala Eva; Garcia-Hernandez Margarita; Zhang Peifen; Mueller Lukas A; Yoon Jungwoon; Doyle Aisling; Lander Gabriel; Moseyko Nick; Yoo Danny; Xu Iris; Zoeckler Brandon; Montoya Mary; Miller Neil; Weems Dan; Rhee Seung Y
Functional annotation of the Arabidopsis genome using controlled vocabularies.
Plant physiology 2004;135(2):745-55.
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2004: Tian Guo-Wei; Mohanty Amitabh; Chary S Narasimha; Li Shijun; Paap Brigitte; Drakakaki Georgia; Kopec Charles D; Li Jianxiong; Ehrhardt David; Jackson David; Rhee Seung Y; Raikhel Natasha V; Citovsky Vitaly
High-throughput fluorescent tagging of full-length Arabidopsis gene products in planta.
Plant physiology 2004;135(1):25-38.
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2004: Dolan Erin L; Soots Barbara E; Lemaux Peggy G; Rhee Seung Y; Reiser Leonore
Strategies for avoiding reinventing the precollege education and outreach wheel.
Genetics 2004;166(4):1601-9.
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2004: Thimm Oliver; Bläsing Oliver; Gibon Yves; Nagel Axel; Meyer Svenja; Krüger Peter; Selbig Joachim; Müller Lukas A; Rhee Seung Y; Stitt Mark
MAPMAN: a user-driven tool to display genomics data sets onto diagrams of metabolic pathways and other biological processes.
The Plant journal : for cell and molecular biology 2004;37(6):914-39.
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2004: Bard Jonathan B L; Rhee Seung Y
Ontologies in biology: design, applications and future challenges.
Nature reviews. Genetics 2004;5(3):213-22.
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2004: Rhee Seung Yon
Carpe diem. Retooling the publish or perish model into the share and survive model.
Plant physiology 2004;134(2):543-7.
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2004: Krieger Cynthia J; Zhang Peifen; Mueller Lukas A; Wang Alfred; Paley Suzanne; Arnaud Martha; Pick John; Rhee Seung Y; Karp Peter D
MetaCyc: a multiorganism database of metabolic pathways and enzymes.
Nucleic acids research 2004;32(Database issue):D438-42.
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2003: Rhee Seung Y; Osborne Erin; Poindexter Patricia D; Somerville Chris R
Microspore separation in the quartet 3 mutants of Arabidopsis is impaired by a defect in a developmentally regulated polygalacturonase required for pollen mother cell wall degradation.
Plant physiology 2003;133(3):1170-80.
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2003: Gonzales Matthew J; Belitskaya Ilana; Dupnik Kathryn M; Rhee Soo-Yon; Shafer Robert W
Protease and reverse transcriptase mutation patterns in HIV type 1 isolates from heavily treated persons: comparison of isolates from Northern California with isolates from other regions.
AIDS research and human retroviruses 2003;19(10):909-15.
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2003: Gonzales Matthew J; Delwart Eric; Rhee Soo-Yon; Tsui Rose; Zolopa Andrew R; Taylor Jonathan; Shafer Robert W
Lack of detectable human immunodeficiency virus type 1 superinfection during 1072 person-years of observation.
The Journal of infectious diseases 2003;188(3):397-405.
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2003: Mueller Lukas A; Zhang Peifen; Rhee Seung Y
AraCyc: a biochemical pathway database for Arabidopsis.
Plant physiology 2003;132(2):453-60.
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2003: Clarke Bryan; Lambrecht Mark; Rhee Seung Y
Arabidopsis genomic information for interpreting wheat EST sequences.
Functional & integrative genomics 2003;3(1-2):33-8.
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2003: Rhee Soo-Yon; Gonzales Matthew J; Kantor Rami; Betts Bradley J; Ravela Jaideep; Shafer Robert W
Human immunodeficiency virus reverse transcriptase and protease sequence database.
Nucleic acids research 2003;31(1):298-303.
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2003: Rhee Seung Yon; Beavis William; Berardini Tanya Z; Chen Guanghong; Dixon David; Doyle Aisling; Garcia-Hernandez Margarita; Huala Eva; Lander Gabriel; Montoya Mary; Miller Neil; Mueller Lukas A; Mundodi Suparna; Reiser Leonore; Tacklind Julie; Weems Dan C; Wu Yihe; Xu Iris; Yoo Daniel; Yoon Jungwon; Zhang Peifen
The Arabidopsis Information Resource (TAIR): a model organism database providing a centralized, curated gateway to Arabidopsis biology, research materials and community.
Nucleic acids research 2003;31(1):224-8.
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2002: Garcia-Hernandez Margarita; Berardini Tanya Z; Chen Guanghong; Crist Debbie; Doyle Aisling; Huala Eva; Knee Emma; Lambrecht Mark; Miller Neil; Mueller Lukas A; Mundodi Suparna; Reiser Leonore; Rhee Seung Y; Scholl Randy; Tacklind Julie; Weems Dan C; Wu Yihe; Xu Iris; Yoo Daniel; Yoon Jungwon; Zhang Peifen
TAIR: a resource for integrated Arabidopsis data.
Functional & integrative genomics 2002;2(6):239-53.
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2002: Reiser Leonore; Mueller Lukas A; Rhee Seung Yon
Surviving in a sea of data: a survey of plant genome data resources and issues in building data management systems.
Plant molecular biology 2002;48(1-2):59-74.
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2001: Huala E; Dickerman A W; Garcia-Hernandez M; Weems D; Reiser L; LaFond F; Hanley D; Kiphart D; Zhuang M; Huang W; Mueller L A; Bhattacharyya D; Bhaya D; Sobral B W; Beavis W; Meinke D W; Town C D; Somerville C; Rhee S Y
The Arabidopsis Information Resource (TAIR): a comprehensive database and web-based information retrieval, analysis, and visualization system for a model plant.
Nucleic acids research 2001;29(1):102-5.
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1999: Rhee S Y; Weng S; Bongard-Pierce D K; García-Hernández M; Malekian A; Flanders D J; Cherry J M
Unified display of Arabidopsis thaliana physical maps from AtDB, the A.thaliana database.
Nucleic acids research 1999;27(1):79-84.
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1998: Rhee S Y; Weng S; Flanders D; Cherry J M; Dean C; Lister C; Anderson M; Koornneef M; Meinke D W; Nickle T; Smith K; Rounsley S D
Genome maps 9. Arabidopsis thaliana. Wall chart.
Science (New York, N.Y.) 1998;282(5389):663-7.
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1998: Rhee S Y; Somerville C R
Tetrad pollen formation in quartet mutants of Arabidopsis thaliana is associated with persistence of pectic polysaccharides of the pollen mother cell wall.
The Plant journal : for cell and molecular biology 1998;15(1):79-88.
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1994: Preuss D; Rhee S Y; Davis R W
Tetrad analysis possible in Arabidopsis with mutation of the QUARTET (QRT) genes.
Science (New York, N.Y.) 1994;264(5164):1458-60.
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