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The TIGR Plant Transcript Assemblies database.
Published in:
Nucleic Acids Research, 2007, v. 35, p. d846, doi. 10.1093/nar/gkl785
By:
- Childs, Kevin L.;
- Hamilton, John P.;
- Zhu, Wei;
- Ly, Eugene;
- Cheung, Foo;
- Wu, Hank;
- Rabinowicz, Pablo D.;
- Town, Chris D.;
- Buell, C. Robin;
- Chan, Agnes P.
Publication type:
Article
Draft genome sequence of the oilseed species Ricinus communis.
Published in:
Nature Biotechnology, 2010, v. 28, n. 9, p. 951, doi. 10.1038/nbt.1674
By:
- Chan, Agnes P.;
- Crabtree, Jonathan;
- Zhao, Qi;
- Lorenzi, Hernan;
- Orvis, Joshua;
- Puiu, Daniela;
- Melake-Berhan, Admasu;
- Jones, Kristine M.;
- Redman, Julia;
- Chen, Grace;
- Cahoon, Edgar B.;
- Gedil, Melaku;
- Stanke, Mario;
- Haas, Brian J.;
- Wortman, Jennifer R.;
- Fraser-Liggett, Claire M.;
- Ravel, Jacques;
- Rabinowicz, Pablo D.
Publication type:
Article
Comparison of phasing strategies for whole human genomes.
Published in:
PLoS Genetics, 2018, v. 14, n. 4, p. 1, doi. 10.1371/journal.pgen.1007308
By:
- Choi, Yongwook;
- Chan, Agnes P.;
- Kirkness, Ewen;
- Telenti, Amalio;
- Schork, Nicholas J.
Publication type:
Article
An 'eFP‐Seq Browser' for visualizing and exploring RNA sequencing data.
Published in:
Plant Journal, 2019, v. 100, n. 3, p. 641, doi. 10.1111/tpj.14468
By:
- Sullivan, Alexander;
- Purohit, Priyank K.;
- Freese, Nowlan H.;
- Pasha, Asher;
- Esteban, Eddi;
- Waese, Jamie;
- Wu, Alison;
- Chen, Michelle;
- Chin, Chih Y.;
- Song, Richard;
- Watharkar, Sneha R.;
- Chan, Agnes P.;
- Krishnakumar, Vivek;
- Vaughn, Matthew W.;
- Town, Chris;
- Loraine, Ann E.;
- Provart, Nicholas J.
Publication type:
Article
Araport11: a complete reannotation of the Arabidopsis thaliana reference genome.
Published in:
Plant Journal, 2017, v. 89, n. 4, p. 789, doi. 10.1111/tpj.13415
By:
- Cheng, Chia‐Yi;
- Krishnakumar, Vivek;
- Chan, Agnes P.;
- Thibaud‐Nissen, Françoise;
- Schobel, Seth;
- Town, Christopher D.
Publication type:
Article
Insular Organization of Gene Space in Grass Genomes.
Published in:
PLoS ONE, 2013, v. 8, n. 1, p. 1, doi. 10.1371/journal.pone.0054101
By:
- Gottlieb, Andrea;
- Müller, Hans-Georg;
- Massa, Alicia N.;
- Wanjugi, Humphrey;
- Deal, Karin R.;
- You, Frank M.;
- Xiangyang Xu;
- Gu, Yong Q.;
- Ming-Cheng Luo;
- Anderson, Olin D.;
- Chan, Agnes P.;
- Rabinowicz, Pablo;
- Devos, Katrien M.;
- Dvorak, Jan
Publication type:
Article
Predicting the Functional Effect of Amino Acid Substitutions and Indels.
Published in:
PLoS ONE, 2012, v. 7, n. 10, p. 1, doi. 10.1371/journal.pone.0046688
By:
- Yongwook Choi;
- Sims, Gregory E.;
- Murphy, Sean;
- Miller, Jason R.;
- Chan, Agnes P.
Publication type:
Article
Castor Bean Organelle Genome Sequencing and Worldwide Genetic Diversity Analysis.
Published in:
PLoS ONE, 2011, v. 6, n. 7, p. 1, doi. 10.1371/journal.pone.0021743
By:
- Rivarola, Maximo;
- Foster, Jeffrey T.;
- Chan, Agnes P.;
- Williams, Amber L.;
- Rice, Danny W.;
- Xinyue Liu;
- Melake-Berhan, Admasu;
- Creasy, Heather Huot;
- Puiu, Daniela;
- Rosovitz, M. J.;
- Khouri, Hoda M.;
- Beckstrom-Sternberg, Stephen M.;
- Allan, Gerard J.;
- Keim, Paul;
- Ravel, Jacques;
- Rabinowicz, Pablo D.
Publication type:
Article
Single nucleotide polymorphisms for assessing genetic diversity in castor bean (Ricinus communis).
Published in:
BMC Plant Biology, 2010, v. 10, p. 13, doi. 10.1186/1471-2229-10-13
By:
- Foster, Jeffrey T.;
- Allan, Gerard J.;
- Chan, Agnes P.;
- Rabinowicz, Pablo D.;
- Ravel, Jacques;
- Jackson, Paul J.;
- Keim, Paul
Publication type:
Article
The highest-copy repeats are methylated in the small genome of the early divergent vascular plant Selaginella moellendorffii.
Published in:
BMC Genomics, 2008, v. 9, p. 1, doi. 10.1186/1471-2164-9-282
By:
- Chan, Agnes P.;
- Melake-Berhan, Admasu;
- O'Brien, Kimberly;
- Buckley, Stephanie;
- Hui Quan;
- Chen, Dan;
- Lewis, Matthew;
- Banks, Jo Ann;
- Rabinowicz, Pablo D.
Publication type:
Article
Co-occurrence of Anaerobes in Human Chronic Wounds.
Published in:
Microbial Ecology, 2019, v. 77, n. 3, p. 808, doi. 10.1007/s00248-018-1231-z
By:
- Choi, Yongwook;
- Banerjee, Anirban;
- McNish, Sean;
- Couch, Kara S.;
- Torralba, Manolito G.;
- Lucas, Sarah;
- Tovchigrechko, Andrey;
- Madupu, Ramana;
- Yooseph, Shibu;
- Nelson, Karen E.;
- Shanmugam, Victoria K.;
- Chan, Agnes P.
Publication type:
Article
The TIGR Maize Database.
Published in:
Nucleic Acids Research, 2006, v. 34, n. suppl 1, p. d771, doi. 10.1093/nar/gkj072
By:
- Chan, Agnes P.;
- Pertea, Geo;
- Cheung, Foo;
- Lee, Dan;
- Zheng, Li;
- Whitelaw, Cathy;
- Pontaroli, Ana C.;
- SanMiguel, Phillip;
- Yuan, Yinan;
- Bennetzen, Jeffrey;
- Barbazuk, William Brad;
- Quackenbush, John;
- Rabinowicz, Pablo D.
Publication type:
Article
Nonadditive gene expression is correlated with nonadditive phenotypic expression in interspecific triploid hybrids of willow (Salix spp.).
Published in:
G3: Genes | Genomes | Genetics, 2022, v. 12, n. 3, p. 1, doi. 10.1093/g3journal/jkab436
By:
- Carlson, Craig H.;
- Yongwook Choi;
- Chan, Agnes P.;
- Town, Christopher D.;
- Smart, Lawrence B.
Publication type:
Article
ThaleMine: A Warehouse for Arabidopsis Data Integration and Discovery.
Published in:
Plant & Cell Physiology, 2017, v. 58, n. 1, p. 1, doi. 10.1093/pcp/pcw200
By:
- Krishnakumar, Vivek;
- Contrino, Sergio;
- Chia-Yi Cheng;
- Belyaeva, Irina;
- Ferlanti, Erik S.;
- Miller, Jason R.;
- Vaughn, Matthew W.;
- Micklem, Gos;
- Town, Christopher D.;
- Chan, Agnes P.
Publication type:
Article
A Maize Database Resource that Captures Tissue-Specific and Subcellular-Localized Gene Expression, via Fluorescent Tags and Confocal Imaging (Maize Cell Genomics Database).
Published in:
Plant & Cell Physiology, 2015, v. 56, n. 1, p. e12, doi. 10.1093/pcp/pcu178
By:
- Krishnakumar, Vivek;
- Choi, Yongwook;
- Beck, Erin;
- Wu, Qingyu;
- Luo, Anding;
- Sylvester, Anne;
- Jackson, David;
- Chan, Agnes P.
Publication type:
Article
A novel method of consensus panchromosome assembly and large-scale comparative analysis reveal the highly flexible pan-genome of Acinetobacter baumannii.
Published in:
Genome Biology, 2015, v. 16, n. 1, p. 143, doi. 10.1186/s13059-015-0701-6
By:
- Chan, Agnes P.;
- Sutton, Granger;
- DePew, Jessica;
- Krishnakumar, Radha;
- Choi, Yongwook;
- Huang, Xiao-Zhe;
- Beck, Erin;
- Harkins, Derek M.;
- Kim, Maria;
- Lesho, Emil P.;
- Nikolich, Mikeljon P.;
- Fouts, Derrick E.
Publication type:
Article
Dominance and Sexual Dimorphism Pervade the Salix purpurea L. Transcriptome.
Published in:
Genome Biology & Evolution, 2017, v. 9, n. 9, p. 2377, doi. 10.1093/gbe/evx174
By:
- Carlson, Craig H.;
- Yongwook Choi;
- Chan, Agnes P.;
- Serapiglia, Michelle J.;
- Town, Christopher D.;
- Smart, Lawrence B.
Publication type:
Article
Complete reannotation of the Arabidopsis genome: methods, tools, protocols and the final release.
Published in:
BMC Biology, 2005, v. 3, p. 1, doi. 10.1186/1741-7007-3-7
By:
- Haas, Brian J.;
- Wortman, Jennifer R.;
- Ronning, Catherine M.;
- Hannick, Linda I.;
- Smith Jr., Roger K.;
- Maiti, Rama;
- Chan, Agnes P.;
- Chunhui Yu;
- Farzad, Maryam;
- Dongying Wu;
- White, Owen;
- Town, Christopher D.
Publication type:
Article
Predicting antimicrobial mechanism-of-action from transcriptomes: A generalizable explainable artificial intelligence approach.
Published in:
PLoS Computational Biology, 2021, v. 17, n. 3, p. 1, doi. 10.1371/journal.pcbi.1008857
By:
- Espinoza, Josh L.;
- Dupont, Chris L.;
- O'Rourke, Aubrie;
- Beyhan, Sinem;
- Morales, Pavel;
- Spoering, Amy;
- Meyer, Kirsten J.;
- Chan, Agnes P.;
- Choi, Yongwook;
- Nierman, William C.;
- Lewis, Kim;
- Nelson, Karen E.
Publication type:
Article
AbGRI4, a novel antibiotic resistance island in multiply antibiotic-resistant Acinetobacter baumannii clinical isolates.
Published in:
2020
By:
- Chan, Agnes P;
- Choi, Yongwook;
- Clarke, Thomas H;
- Brinkac, Lauren M;
- White, Richard C;
- Jacobs, Michael R;
- Bonomo, Robert A;
- Adams, Mark D;
- Fouts, Derrick E
Publication type:
journal article
PROVEAN web server: a tool to predict the functional effect of amino acid substitutions and indels.
Published in:
2015
By:
- Yongwook Choi;
- Chan, Agnes P.
Publication type:
Product Review

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