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3 results on '"Navarro, J Daniel"'

1. Human protein reference database as a discovery resource for proteomics

Author

Peri, Suraj, Navarro, J. Daniel, Kristiansen, Troels Z., Amanchy, Ramars, Surendranath, Vineeth, Muthusamy, Babylakshmi, Gandhi, T.K.B., Chandrika, K.N., Deshpande, Nandan, Suresh, Shubha, Rashmi, B.P., Shanker, K., Padma, N., Niranjan, Vidya, Harsha, H.C., Talreja, Naveen, Vrushabendra, B.M., Ramya, M.A., Yatish, A.J., Joy, Mary, Shivashankar, H.N., Kavitha, M.P., Menezes, Minal, Choudhury, Dipanwita Roy, Ghosh, Neelanjana, Saravana, R., Chandran, Sreenath, Mohan, Sujatha, Jonnalagadda, Chandra Kiran, Prasad, C.K., Kumar-Sinha, Chandan, Deshpande, Krishna S., Pandey, Akhilesh, Peri, Suraj, Navarro, J. Daniel, Kristiansen, Troels Z., Amanchy, Ramars, Surendranath, Vineeth, Muthusamy, Babylakshmi, Gandhi, T.K.B., Chandrika, K.N., Deshpande, Nandan, Suresh, Shubha, Rashmi, B.P., Shanker, K., Padma, N., Niranjan, Vidya, Harsha, H.C., Talreja, Naveen, Vrushabendra, B.M., Ramya, M.A., Yatish, A.J., Joy, Mary, Shivashankar, H.N., Kavitha, M.P., Menezes, Minal, Choudhury, Dipanwita Roy, Ghosh, Neelanjana, Saravana, R., Chandran, Sreenath, Mohan, Sujatha, Jonnalagadda, Chandra Kiran, Prasad, C.K., Kumar-Sinha, Chandan, Deshpande, Krishna S., and Pandey, Akhilesh

Abstract

The rapid pace at which genomic and proteomic data is being generated necessitates the development of tools and resources for managing data that allow integration of information from disparate sources. The Human Protein Reference Database (http://www.hprd.org) is a web-based resource based on open source technologies for protein information about several aspects of human proteins including protein-protein interactions, post-translational modifications, enzyme-substrate relationships and disease associations. This information was derived manually by a critical reading of the published literature by expert biologists and through bioinformatics analyses of the protein sequence. This database will assist in biomedical discoveries by serving as a resource of genomic and proteomic information and providing an integrated view of sequence, structure, function and protein networks in health and disease.

Published
2004

2. Development of human protein reference database as an initial platform for approaching systems biology in humans.

Author

UCL - SSS/DDUV - Institut de Duve, Peri, Suraj, Navarro, J Daniel, Amanchy, Ramars, Kristiansen, Troels Z, Jonnalagadda, Chandra Kiran, Surendranath, Vineeth, Niranjan, Vidya, Muthusamy, Babylakshmi, Gandhi, T K B, Gronborg, Mads, Ibarrola, Nieves, Deshpande, Nandan, Shanker, K, Shivashankar, H N, Rashmi, B P, Ramya, M A, Zhao, Zhixing, Chandrika, K N, Padma, N, Harsha, H C, Yatish, A J, Kavitha, M P, Menezes, Minal, Choudhury, Dipanwita Roy, Suresh, Shubha, Ghosh, Neelanjana, Saravana, R, Chandran, Sreenath, Krishna, Subhalakshmi, Joy, Mary, Anand, Sanjeev K, Madavan, V, Joseph, Ansamma, Wong, Guang W, Schiemann, William P, Constantinescu, Stefan N., Huang, Lily, Khosravi-Far, Roya, Steen, Hanno, Tewari, Muneesh, Ghaffari, Saghi, Blobe, Gerard C, Dang, Chi V, Garcia, Joe G N, Pevsner, Jonathan, Jensen, Ole N, Roepstorff, Peter, Deshpande, Krishna S, Chinnaiyan, Arul M, Hamosh, Ada, Chakravarti, Aravinda, Pandey, Akhilesh, UCL - SSS/DDUV - Institut de Duve, Peri, Suraj, Navarro, J Daniel, Amanchy, Ramars, Kristiansen, Troels Z, Jonnalagadda, Chandra Kiran, Surendranath, Vineeth, Niranjan, Vidya, Muthusamy, Babylakshmi, Gandhi, T K B, Gronborg, Mads, Ibarrola, Nieves, Deshpande, Nandan, Shanker, K, Shivashankar, H N, Rashmi, B P, Ramya, M A, Zhao, Zhixing, Chandrika, K N, Padma, N, Harsha, H C, Yatish, A J, Kavitha, M P, Menezes, Minal, Choudhury, Dipanwita Roy, Suresh, Shubha, Ghosh, Neelanjana, Saravana, R, Chandran, Sreenath, Krishna, Subhalakshmi, Joy, Mary, Anand, Sanjeev K, Madavan, V, Joseph, Ansamma, Wong, Guang W, Schiemann, William P, Constantinescu, Stefan N., Huang, Lily, Khosravi-Far, Roya, Steen, Hanno, Tewari, Muneesh, Ghaffari, Saghi, Blobe, Gerard C, Dang, Chi V, Garcia, Joe G N, Pevsner, Jonathan, Jensen, Ole N, Roepstorff, Peter, Deshpande, Krishna S, Chinnaiyan, Arul M, Hamosh, Ada, Chakravarti, Aravinda, and Pandey, Akhilesh

Abstract

Human Protein Reference Database (HPRD) is an object database that integrates a wealth of information relevant to the function of human proteins in health and disease. Data pertaining to thousands of protein-protein interactions, posttranslational modifications, enzyme/substrate relationships, disease associations, tissue expression, and subcellular localization were extracted from the literature for a nonredundant set of 2750 human proteins. Almost all the information was obtained manually by biologists who read and interpreted >300,000 published articles during the annotation process. This database, which has an intuitive query interface allowing easy access to all the features of proteins, was built by using open source technologies and will be freely available at http://www.hprd.org to the academic community. This unified bioinformatics platform will be useful in cataloging and mining the large number of proteomic interactions and alterations that will be discovered in the postgenomic era.

Published
2003

3. Human Proteinpedia enables sharing of human protein data

Author

Mathivanan, Suresh, Ahmed, Mukhtar, Ahn, Natalie G, Alexandre, Hainard, Amanchy, Ramars, Andrews, Philip C, Bader, Joel S, Balgley, Brian M, Bantscheff, Marcus, Bennett, Keiryn L, Björling, Erik, Blagoev, Blagoy, Bose, Ron, Brahmachari, Samir K, Burlingame, Alma S, Bustelo, Xosé R, Cagney, Gerard, Cantin, Greg T, Cardasis, Helene L, Celis, Julio E, Chaerkady, Raghothama, Chu, Feixia, Cole, Philip A, Costello, Catherine E, Cotter, Robert J, Crockett, David, DeLany, James P, De Marzo, Angelo M, DeSouza, Leroi V, Deutsch, Eric W, Dransfield, Eric, Drewes, Gerard, Droit, Arnaud, Dunn, Michael J, Elenitoba-Johnson, Kojo, Ewing, Rob M, Eyk, Jennifer Van, Faca, Vitor, Falkner, Jayson, Fang, Xiangming, Fenselau, Catherine, Figeys, Daniel, Gagné, Pierre, Gelfi, Cecilia, Gevaert, Kris, Gimble, Jeffrey M, Gnad, Florian, Goel, Renu, Gromov, Pavel, Hanash, Samir M, Hancock, William S, Harsha, HC, Hart, Gerald, Hays, Faith, He, Fuchu, Hebbar, Prashantha, Helsens, Kenny, Hermeking, Heiko, Hide, Winston, Hjernø, Karin, Hochstrasser, Denis F, Hofmann, Oliver, Horn, David M, Hruban, Ralph H, Ibarrola, Nieves, James, Peter, Jensen, Ole N, Jensen, Pia Hønnerup, Jung, Peter, Kandasamy, Kumaran, Kheterpal, Indu, Kikuno, Reiko F, Korf, Ulrike, Körner, Roman, Kuster, Bernhard, Kwon, Min-Seok, Lee, Hyoung-Joo, Lee, Young-Jin, Lefevre, Michael, Lehvaslaiho, Minna, Lescuyer, Pierre, Levander, Fredrik, Lim, Megan S, Löbke, Christian, Loo, Joseph A, Mann, Matthias, Martens, Lennart, Martinez-Heredia, Juan, McComb, Mark, McRedmond, James, Mehrle, Alexander, Menon, Rajasree, Miller, Christine A, Mischak, Harald, Mohan, S Sujatha, Mohmood, Riaz, Molina, Henrik, Moran, Michael F, Morgan, James D, Moritz, Robert, Morzel, Martine, Muddiman, David C, Nalli, Anuradha, Navarro, J Daniel, Neubert, Thomas A, Ohara, Osamu, Oliva, Rafael, Omenn, Gilbert S, Oyama, Masaaki, Paik, Young-Ki, Pennington, Kyla, Pepperkok, Rainer, Periaswamy, Balamurugan, Petricoin, Emanuel F, Poirier, Guy G, Prasad, T S Keshava, Purvine, Samuel O, Rahiman, B Abdul, Ramachandran, Prasanna, Ramachandra, Y L, Rice, Robert H, Rick, Jens, Ronnholm, Ragna H, Salonen, Johanna, Sanchez, Jean-Charles, Sayd, Thierry, Seshi, Beerelli, Shankari, Kripa, Sheng, Shi Jun, Shetty, Vivekananda, Shivakumar, K, Simpson, Richard J, Sirdeshmukh, Ravi, Michael Siu, K W, Smith, Jeffrey C, Smith, Richard D, States, David J, Sugano, Sumio, Sullivan, Matthew, Superti-Furga, Giulio, Takatalo, Maarit, Thongboonkerd, Visith, Trinidad, Jonathan C, Uhlen, Mathias, Vandekerckhove, Joël, Vasilescu, Julian, Veenstra, Timothy D, Vidal-Taboada, José-Manuel, Vihinen, Mauno, Wait, Robin, Wang, Xiaoyue, Wiemann, Stefan, Wu, Billy, Xu, Tao, Yates, John R, Zhong, Jun, Zhou, Ming, Zhu, Yunping, Zurbig, Petra, Pandey, Akhilesh, Mathivanan, Suresh, Ahmed, Mukhtar, Ahn, Natalie G, Alexandre, Hainard, Amanchy, Ramars, Andrews, Philip C, Bader, Joel S, Balgley, Brian M, Bantscheff, Marcus, Bennett, Keiryn L, Björling, Erik, Blagoev, Blagoy, Bose, Ron, Brahmachari, Samir K, Burlingame, Alma S, Bustelo, Xosé R, Cagney, Gerard, Cantin, Greg T, Cardasis, Helene L, Celis, Julio E, Chaerkady, Raghothama, Chu, Feixia, Cole, Philip A, Costello, Catherine E, Cotter, Robert J, Crockett, David, DeLany, James P, De Marzo, Angelo M, DeSouza, Leroi V, Deutsch, Eric W, Dransfield, Eric, Drewes, Gerard, Droit, Arnaud, Dunn, Michael J, Elenitoba-Johnson, Kojo, Ewing, Rob M, Eyk, Jennifer Van, Faca, Vitor, Falkner, Jayson, Fang, Xiangming, Fenselau, Catherine, Figeys, Daniel, Gagné, Pierre, Gelfi, Cecilia, Gevaert, Kris, Gimble, Jeffrey M, Gnad, Florian, Goel, Renu, Gromov, Pavel, Hanash, Samir M, Hancock, William S, Harsha, HC, Hart, Gerald, Hays, Faith, He, Fuchu, Hebbar, Prashantha, Helsens, Kenny, Hermeking, Heiko, Hide, Winston, Hjernø, Karin, Hochstrasser, Denis F, Hofmann, Oliver, Horn, David M, Hruban, Ralph H, Ibarrola, Nieves, James, Peter, Jensen, Ole N, Jensen, Pia Hønnerup, Jung, Peter, Kandasamy, Kumaran, Kheterpal, Indu, Kikuno, Reiko F, Korf, Ulrike, Körner, Roman, Kuster, Bernhard, Kwon, Min-Seok, Lee, Hyoung-Joo, Lee, Young-Jin, Lefevre, Michael, Lehvaslaiho, Minna, Lescuyer, Pierre, Levander, Fredrik, Lim, Megan S, Löbke, Christian, Loo, Joseph A, Mann, Matthias, Martens, Lennart, Martinez-Heredia, Juan, McComb, Mark, McRedmond, James, Mehrle, Alexander, Menon, Rajasree, Miller, Christine A, Mischak, Harald, Mohan, S Sujatha, Mohmood, Riaz, Molina, Henrik, Moran, Michael F, Morgan, James D, Moritz, Robert, Morzel, Martine, Muddiman, David C, Nalli, Anuradha, Navarro, J Daniel, Neubert, Thomas A, Ohara, Osamu, Oliva, Rafael, Omenn, Gilbert S, Oyama, Masaaki, Paik, Young-Ki, Pennington, Kyla, Pepperkok, Rainer, Periaswamy, Balamurugan, Petricoin, Emanuel F, Poirier, Guy G, Prasad, T S Keshava, Purvine, Samuel O, Rahiman, B Abdul, Ramachandran, Prasanna, Ramachandra, Y L, Rice, Robert H, Rick, Jens, Ronnholm, Ragna H, Salonen, Johanna, Sanchez, Jean-Charles, Sayd, Thierry, Seshi, Beerelli, Shankari, Kripa, Sheng, Shi Jun, Shetty, Vivekananda, Shivakumar, K, Simpson, Richard J, Sirdeshmukh, Ravi, Michael Siu, K W, Smith, Jeffrey C, Smith, Richard D, States, David J, Sugano, Sumio, Sullivan, Matthew, Superti-Furga, Giulio, Takatalo, Maarit, Thongboonkerd, Visith, Trinidad, Jonathan C, Uhlen, Mathias, Vandekerckhove, Joël, Vasilescu, Julian, Veenstra, Timothy D, Vidal-Taboada, José-Manuel, Vihinen, Mauno, Wait, Robin, Wang, Xiaoyue, Wiemann, Stefan, Wu, Billy, Xu, Tao, Yates, John R, Zhong, Jun, Zhou, Ming, Zhu, Yunping, Zurbig, Petra, and Pandey, Akhilesh

Abstract

Proteomic technologies, such as yeast two-hybrid, mass spectrometry (MS), protein/peptide arrays and fluorescence microscopy, yield multi-dimensional data sets, which are often quite large and either not published or published as supplementary information that is not easily searchable. Without a system in place for standardizing and sharing data, it is not fruitful for the biomedical community to contribute these types of data to centralized repositories.

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