SAGA: a subgraph matching tool for biological graphs von Tian, Yuanyuan, McEachin, Richard C., Santos, Carlos, States, David J., Patel, Jignesh M.

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Literature-based discovery of diabetes- and ROS-related targets von Hur, Junguk, Sullivan, Kelli A, Schuyler, Adam D, Hong, Yu, Pande, Manjusha, States, David J, Jagadish, H V, Feldman, Eva L

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Profiles of Growth Hormone (GH)-regulated Genes Reveal Time-dependent Responses and Identify a Mechanism for Regulation of Activating Transcription Factor 3 By GH von Huo, Jeffrey S., McEachin, Richard C., Cui, Tracy Xiao, Duggal, Nisha K., Hai, Tsonwin, States, David J., Schwartz, Jessica

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Data management and preliminary data analysis in the pilot phase of the HUPO Plasma Proteome Project von Adamski, Marcin, Blackwell, Thomas, Menon, Rajasree, Martens, Lennart, Hermjakob, Henning, Taylor, Chris, Omenn, Gilbert S., States, David J.

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SciMiner: web-based literature mining tool for target identification and functional enrichment analysis von Hur, Junguk, Schuyler, Adam D., States, David J., Feldman, Eva L.

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Wnt pathway curation using automated natural language processing: combining statistical methods with partial and full parse for knowledge extraction von Santos, Carlos, Eggle, Daniela, States, David. J.

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Cytoscape ESP: simple search of complex biological networks von Ashkenazi, Maital, Bader, Gary D., Kuchinsky, Allan, Moshelion, Menachem, States, David J.

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CLO: The cell line ontology von Sarntivijai, Sirarat, Lin, Yu, Xiang, Zuoshuang, Meehan, Terrence F, Diehl, Alexander D, Vempati, Uma D, Schürer, Stephan C, Pang, Chao, Malone, James, Parkinson, Helen, Liu, Yue, Takatsuki, Terue, Saijo, Kaoru, Masuya, Hiroshi, Nakamura, Yukio, Brush, Matthew H, Haendel, Melissa A, Zheng, Jie, Stoeckert, Christian J, Peters, Bjoern, Mungall, Christopher J, Carey, Thomas E, States, David J, Athey, Brian D, He, Yongqun

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Gene structure prediction and alternative splicing analysis using genomically aligned ESTs von Kan, Z, Rouchka, E C, Gish, W R, States, D J

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Linear Discriminant Analysis-Based Estimation of the False Discovery Rate for Phosphopeptide Identifications von Du, Xiuxia, Yang, Feng, Manes, Nathan P, Stenoien, David L, Monroe, Matthew E, Adkins, Joshua N, States, David J, Purvine, Samuel O, Camp, II, David G, Smith, Richard D

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Supplementary data need to be kept in public repositories von Santos, Carlos, Blake, Judith, States, David J

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Consensus promoter identification in the human genome utilizing expressed gene markers and gene modeling von Liu, Rongxiang, States, David J

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Conformational model for binding site recognition by the E.coli MetJ transcription factor von Liu, Rongxiang, Blackwell, Thomas W., States, David J.

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The Cell Line Ontology and its use in tagging cell line names in biomedical text von Sarntivijai, Sirarat, Ade, Alexander S, Athey, Brian D, States, David J

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Inferring Time-Varying Network Topologies from Gene Expression Data von Rao, Arvind, Hero III, Alfred O., States, David J., Engel, James Douglas

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Simplifying access to a Clinical Data Repository using schema summarization von Yu, Cong, Hanauer, David A, Athey, Brian D, Jagadish, Hosagrahar V, States, David J

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CHARMM: A program for macromolecular energy, minimization, and dynamics calculations von Brooks, Bernard R., Bruccoleri, Robert E., Olafson, Barry D., States, David J., Swaminathan, S., Karplus, Martin

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Probabilistic approaches to the use of higher order clone relationships in physical map assembly von States, David J., Nowotny, Volker, Blackwell, Thomas W.

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Systematic Definition and Evolutionary Analsis of Macrophage Genes: Evidence for Novel Host Defense Genes von MacDonald, Jennifer J., Lee, Angel W., States, David J.

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A functional annotation of subproteomes in human plasma von Ping, Peipei, Vondriska, Thomas M., Creighton, Chad J., Gandhi, TKB, Yang, Ziping, Menon, Rajasree, Kwon, Min-Seok, Cho, Sang Yun, Drwal, Garry, Kellmann, Markus, Peri, Suraj, Suresh, Shubha, Gronborg, Mads, Molina, Henrik, Chaerkady, Raghothama, Rekha, B., Shet, Arun S., Gerszten, Robert E., Wu, Haifeng, Raftery, Mark, Wasinger, Valerie, Schulz-Knappe, Peter, Hanash, Samir M., Paik, Young-ki, Hancock, William S., States, David J., Omenn, Gilbert S., Pandey, Akhilesh

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