High-Quality Binary Protein Interaction Map of the Yeast Interactome Network
Yu, Haiyuan, Braun, Pascal, Yıldırım, Muhammed A., Lemmens, Irma, Venkatesan, Kavitha, Sahalie, Julie, Hirozane-Kishikawa, Tomoko, Gebreab, Fana, Li, Na, Simonis, Nicolas, Hao, Tong, Rual, Jean-François, Dricot, Amélie, Vazquez, Alexei, Murray, Ryan R., Simon, Christophe, Tardivo, Leah, Tam, Stanley, Svrzikapa, Nenad, Fan, Changyu, de Smet, Anne-Sophie, Motyl, Adriana, Hudson, Michael E., Park, Juyong, Xin, Xiaofeng, Cusick, Michael E., Moore, Troy, Boone, Charlie, Snyder, Michael, Roth, Frederick P., Barabási, Albert-László, Tavernier, Jan, Hill, David E., Vidal, Marc·2008·Science
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- From Midbody Protein−Protein Interaction Network Construction to Novel Regulators in CytokinesisTzu-Chi Chen, Sheng‐An Lee, Tse-Ming Hong, Jin‐Yuan Shih, Jin-Mei Lai, Hsin-Ying Chiou, Shuenn‐Chen Yang, Chen‐hsiung Chan, Cheng-Yan Kao, Pan‐Chyr Yang et al. · 2009 · Journal of Proteome Research
- A Survey of Statistical Network ModelsAnna Goldenberg · 2009 · now publishers, Inc. eBooks
- Proteomic Analysis of Cellular SystemsMarco Y. Hein, Kirti Sharma, Jürgen Cox, Matthias Mann · 2012 · Elsevier eBooks
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- Inferring high-confidence human protein-protein interactionsXueping Yu, Anders Wallqvist, Jaques Reifman A · 2012 · BMC Bioinformatics
- Linking the proteins—Elucidation of proteome‐scale networks using mass spectrometryDelphine Pflieger, Florence Gonnet, Sergio de la Fuente van Bentem, Heribert Hirt, Alberto de la Fuente · 2010 · Mass Spectrometry Reviews
- Human interactome resource and gene set linkage analysis for the functional interpretation of biologically meaningful gene setsXi Fa Zhou, Pengcheng Chen, Qiang Wei, Xueling Shen, Xin Chen · 2013 · Bioinformatics
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