GLay: community structure analysis of biological networks von Su, Gang, Kuchinsky, Allan, Morris, John H., States, David J., Meng, Fan

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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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Identification of Novel Alternative Splice Isoforms of Circulating Proteins in a Mouse Model of Human Pancreatic Cancer von MENON, Rajasree, QING ZHANG, YAN ZHANG, FERMIN, Damian, BARDEESY, Nabeel, DEPINHO, Ronald A, CHUNXIA LU, HANASH, Samir M, OMENN, Gilbert S, STATES, David J

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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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Identification of protein coding regions by database similarity search von Gish, W, States, D.J

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A bioinformatics analysis of the cell line nomenclature von Sarntivijai, Sirarat, Ade, Alexander S., Athey, Brian D., States, David J.

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Challenges in deriving high-confidence protein identifications from data gathered by a HUPO plasma proteome collaborative study von Hanash, Samir M, States, David J, Omenn, Gilbert S, Blackwell, Thomas W, Fermin, Damian, Eng, Jimmy, Speicher, David W

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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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Integration of genome and chromatin structure with gene expression profiles to predict c-MYC recognition site binding and function von Chen, Yili, Blackwell, Thomas W, Chen, Ji, Gao, Jing, Lee, Angel W, States, David J

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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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Integrating and annotating the interactome using the MiMI plugin for cytoscape von Gao, Jing, Ade, Alex S., Tarcea, V. Glenn, Weymouth, Terry E., Mirel, Barbara R., Jagadish, H.V., States, David J.

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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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Computational and Functional Analysis of Growth Hormone (GH)-Regulated Genes Identifies the Transcriptional Repressor B-Cell Lymphoma 6 (Bc16) as a Participant in GH-Regulated Tran... von Chen, Yili, Lin, Grace, Huo, Jeffrey S, Barney, Deborah, Wang, Zhenni, Livshiz, Tamara, States, David J, Qin, Zhaohui S, Schwartz, Jessica

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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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MiSearch adaptive pubMed search tool von States, David J., Ade, Alex S., Wright, Zachary C., Bookvich, Aaron V., Athey, Brian 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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