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Your search keyword '"Sahalie, Julie"' showing total 7 results
Start Over Author "Sahalie, Julie" Journal nature methods
7 results on '"Sahalie, Julie"'

1. Next-generation sequencing to generate interactome datasets

Author

Yu, Haiyuan, primary, Tardivo, Leah, additional, Tam, Stanley, additional, Weiner, Evan, additional, Gebreab, Fana, additional, Fan, Changyu, additional, Svrzikapa, Nenad, additional, Hirozane-Kishikawa, Tomoko, additional, Rietman, Edward, additional, Yang, Xinping, additional, Sahalie, Julie, additional, Salehi-Ashtiani, Kourosh, additional, Hao, Tong, additional, Cusick, Michael E, additional, Hill, David E, additional, Roth, Frederick P, additional, Braun, Pascal, additional, and Vidal, Marc, additional

Published
2011
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2. Empirically controlled mapping of the Caenorhabditis elegans protein-protein interactome network

Author

Simonis, Nicolas, primary, Rual, Jean-François, additional, Carvunis, Anne-Ruxandra, additional, Tasan, Murat, additional, Lemmens, Irma, additional, Hirozane-Kishikawa, Tomoko, additional, Hao, Tong, additional, Sahalie, Julie M, additional, Venkatesan, Kavitha, additional, Gebreab, Fana, additional, Cevik, Sebiha, additional, Klitgord, Niels, additional, Fan, Changyu, additional, Braun, Pascal, additional, Li, Ning, additional, Ayivi-Guedehoussou, Nono, additional, Dann, Elizabeth, additional, Bertin, Nicolas, additional, Szeto, David, additional, Dricot, Amélie, additional, Yildirim, Muhammed A, additional, Lin, Chenwei, additional, de Smet, Anne-Sophie, additional, Kao, Huey-Ling, additional, Simon, Christophe, additional, Smolyar, Alex, additional, Ahn, Jin Sook, additional, Tewari, Muneesh, additional, Boxem, Mike, additional, Milstein, Stuart, additional, Yu, Haiyuan, additional, Dreze, Matija, additional, Vandenhaute, Jean, additional, Gunsalus, Kristin C, additional, Cusick, Michael E, additional, Hill, David E, additional, Tavernier, Jan, additional, Roth, Frederick P, additional, and Vidal, Marc, additional

Published
2008
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3. An experimentally derived confidence score for binary protein-protein interactions

Author

Braun, Pascal, primary, Tasan, Murat, additional, Dreze, Matija, additional, Barrios-Rodiles, Miriam, additional, Lemmens, Irma, additional, Yu, Haiyuan, additional, Sahalie, Julie M, additional, Murray, Ryan R, additional, Roncari, Luba, additional, de Smet, Anne-Sophie, additional, Venkatesan, Kavitha, additional, Rual, Jean-François, additional, Vandenhaute, Jean, additional, Cusick, Michael E, additional, Pawson, Tony, additional, Hill, David E, additional, Tavernier, Jan, additional, Wrana, Jeffrey L, additional, Roth, Frederick P, additional, and Vidal, Marc, additional

Published
2008
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4. An empirical framework for binary interactome mapping

Author

Venkatesan, Kavitha, primary, Rual, Jean-François, additional, Vazquez, Alexei, additional, Stelzl, Ulrich, additional, Lemmens, Irma, additional, Hirozane-Kishikawa, Tomoko, additional, Hao, Tong, additional, Zenkner, Martina, additional, Xin, Xiaofeng, additional, Goh, Kwang-Il, additional, Yildirim, Muhammed A, additional, Simonis, Nicolas, additional, Heinzmann, Kathrin, additional, Gebreab, Fana, additional, Sahalie, Julie M, additional, Cevik, Sebiha, additional, Simon, Christophe, additional, de Smet, Anne-Sophie, additional, Dann, Elizabeth, additional, Smolyar, Alex, additional, Vinayagam, Arunachalam, additional, Yu, Haiyuan, additional, Szeto, David, additional, Borick, Heather, additional, Dricot, Amélie, additional, Klitgord, Niels, additional, Murray, Ryan R, additional, Lin, Chenwei, additional, Lalowski, Maciej, additional, Timm, Jan, additional, Rau, Kirstin, additional, Boone, Charles, additional, Braun, Pascal, additional, Cusick, Michael E, additional, Roth, Frederick P, additional, Hill, David E, additional, Tavernier, Jan, additional, Wanker, Erich E, additional, Barabási, Albert-László, additional, and Vidal, Marc, additional

Published
2008
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5. Empirically controlled mapping of the Caenorhabditis elegans protein-protein interactome network.

Author

Simonis, Nicolas, Rual, Jean-François, Carvunis, Anne-Ruxandra, Tasan, Murat, Lemmens, Irma, Hirozane-Kishikawa, Tomoko, Tong Hao, Sahalie, Julie M., Venkatesan, Kavitha, Gebreab, Fana, Cevik, Sebiha, Klitgord, Niels, Changyu Fan, Braun, Pascal, Ning Li, Ayivi-Guedehoussou, Nono, Dann, Elizabeth, Bertin, Nicolas, Szeto, David, and Dricot, Amélie

Subjects
PROTEIN-protein interactions, CAENORHABDITIS elegans, QUALITY standards, GENES, PROTEINS, CELL physiology
Abstract

To provide accurate biological hypotheses and elucidate global properties of cellular networks, systematic identification of protein-protein interactions must meet high quality standards. We present an expanded C. elegans protein-protein interaction network, or 'interactome' map, derived from testing a matrix of ∼10,000 × ∼10,000 proteins using a highly specific, high-throughput yeast two-hybrid system. Through a new empirical quality control framework, we show that the resulting data set (Worm Interactome 2007, or WI-2007) was similar in quality to low-throughput data curated from the literature. We filtered previous interaction data sets and integrated them with WI-2007 to generate a high-confidence consolidated map (Worm Interactome version 8, or WI8). This work allowed us to estimate the size of the worm interactome at ∼116,000 interactions. Comparison with other types of functional genomic data shows the complementarity of distinct experimental approaches in predicting different functional relationships between genes or proteins. [ABSTRACT FROM AUTHOR]

Published
2009
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6. An experimentally derived confidence score for binary protein-protein interactions.

Author

Braun, Pascal, Tasan, Murat, Dreze, Matija, Barrios-Rodiles, Miriam, Lemmens, Irma, Haiyuan Yu, Sahalie, Julie M., Murray, Ryan R., Roncari, Luba, de Smet, Anne-Sophie, Venkatesan, Kavitha, Rual, Jean-François, Vandenhaute, Jean, Cusick, Michael E., Pawson, Tony, Hill, David E., Tavernier, Jan, Wrana, Jeffrey L., Roth, Frederick P., and Vidal, Marc

Subjects
PROTEIN-protein interactions, PROTEIN analysis, CELL physiology, BIOPHYSICAL labeling, MEDICAL research
Abstract

Information on protein-protein interactions is of central importance for many areas of biomedical research. At present no method exists to systematically and experimentally assess the quality of individual interactions reported in interaction mapping experiments. To provide a standardized confidence-scoring method that can be applied to tens of thousands of protein interactions, we have developed an interaction tool kit consisting of four complementary, high-throughput protein interaction assays. We benchmarked these assays against positive and random reference sets consisting of well documented pairs of interacting human proteins and randomly chosen protein pairs, respectively. A logistic regression model was trained using the data from these reference sets to combine the assay outputs and calculate the probability that any newly identified interaction pair is a true biophysical interaction once it has been tested in the tool kit. This general approach will allow a systematic and empirical assignment of confidence scores to all individual protein-protein interactions in interactome networks. [ABSTRACT FROM AUTHOR]

Published
2009
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7. An empirical framework for binary interactome mapping.

Author

Venkatesan, Kavitha, Rual, Jean-François, Vazquez, Alexei, Stelzl, Ulrich, Lemmens, Irma, Hirozane-Kishikawa, Tomoko, Tong Hao, Zenkner, Martina, Xiaofeng Xin, Kwang-Il Goh, Yildirim, Muhammed A., Simonis, Nicolas, Heinzmann, Kathrin, Gebreab, Fana, Sahalie, Julie M., Cevik, Sebiha, Simon, Christophe, de Smet, Anne-Sophie, Dann, Elizabeth, and Smolyar, Alex

Subjects
PROTEIN-protein interactions, NUCLEOTIDE sequence, HUMAN gene mapping, DNA, HUMAN genome
Abstract

Several attempts have been made to systematically map protein-protein interaction, or 'interactome', networks. However, it remains difficult to assess the quality and coverage of existing data sets. Here we describe a framework that uses an empirically-based approach to rigorously dissect quality parameters of currently available human interactome maps. Our results indicate that high-throughput yeast two-hybrid (HT-Y2H) interactions for human proteins are more precise than literature-curated interactions supported by a single publication, suggesting that HT-Y2H is suitable to map a significant portion of the human interactome. We estimate that the human interactome contains ∼130,000 binary interactions, most of which remain to be mapped. Similar to estimates of DNA sequence data quality and genome size early in the Human Genome Project, estimates of protein interaction data quality and interactome size are crucial to establish the magnitude of the task of comprehensive human interactome mapping and to elucidate a path toward this goal. [ABSTRACT FROM AUTHOR]

Published
2009
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