Search Results - "Knight, James D."

A Dynamic Protein Interaction Landscape of the Human Centrosome-Cilium Interface by Gupta, Gagan D., Coyaud, Étienne, Gonçalves, João, Mojarad, Bahareh A., Liu, Yi, Wu, Qianzhu, Gheiratmand, Ladan, Comartin, David, Tkach, Johnny M., Cheung, Sally W.T., Bashkurov, Mikhail, Hasegan, Monica, Knight, James D., Lin, Zhen-Yuan, Schueler, Markus, Hildebrandt, Friedhelm, Moffat, Jason, Gingras, Anne-Claude, Raught, Brian, Pelletier, Laurence

“…The centrosome is the primary microtubule organizing center of the cells and templates the formation of cilia, thereby operating at a nexus of…”
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ProHits-viz: a suite of web tools for visualizing interaction proteomics data by Knight, James D R, Choi, Hyungwon, Gupta, Gagan D, Pelletier, Laurence, Raught, Brian, Nesvizhskii, Alexey I, Gingras, Anne-Claude

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MOB1 Mediated Phospho-recognition in the Core Mammalian Hippo Pathway by Couzens, Amber L., Xiong, Shawn, Knight, James D.R., Mao, Daniel Y., Guettler, Sebastian, Picaud, Sarah, Kurinov, Igor, Filippakopoulos, Panagis, Sicheri, Frank, Gingras, Anne-Claude

“…The Hippo tumor suppressor pathway regulates organ size and tissue homoeostasis in response to diverse signaling inputs. The core of the pathway consists of a…”
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The GATOR–Rag GTPase pathway inhibits mTORC1 activation by lysosome-derived amino acids by Hesketh, Geoffrey G., Papazotos, Fotini, Pawling, Judy, Rajendran, Dushyandi, Knight, James D. R., Martinez, Sebastien, Taipale, Mikko, Schramek, Daniel, Dennis, James W., Gingras, Anne-Claude

“…Intricacies of amino acid sensing The way in which cells sense amino acids derived from external proteins taken up by micropinocytosis and then degraded in the…”
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Protein interaction network of the mammalian Hippo pathway reveals mechanisms of kinase-phosphatase interactions by Couzens, Amber L, Knight, James D R, Kean, Michelle J, Teo, Guoci, Weiss, Alexander, Dunham, Wade H, Lin, Zhen-Yuan, Bagshaw, Richard D, Sicheri, Frank, Pawson, Tony, Wrana, Jeffrey L, Choi, Hyungwon, Gingras, Anne-Claude

“…The Hippo pathway regulates organ size and tissue homeostasis in response to multiple stimuli, including cell density and mechanotransduction. Pharmacological…”
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A web-tool for visualizing quantitative protein-protein interaction data by Knight, James D. R., Liu, Guomin, Zhang, Jian Ping, Pasculescu, Adrian, Choi, Hyungwon, Gingras, Anne-Claude

“…Quantitative interaction proteomics data can be a challenge to efficiently analyze and subsequently present to an audience in a simple and easy to understand…”
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SAINTq: Scoring protein-protein interactions in affinity purification - mass spectrometry experiments with fragment or peptide intensity data by Teo, Guoci, Koh, Hiromi, Fermin, Damian, Lambert, Jean-Philippe, Knight, James D.R., Gingras, Anne-Claude, Choi, Hyungwon

“…SAINT (Significance Analysis of INTeractome) is a probabilistic method for scoring bait‐prey interactions against negative controls in affinity purification –…”
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Conservation, variability and the modeling of active protein kinases by Knight, James D R, Qian, Bin, Baker, David, Kothary, Rashmi

“…The human proteome is rich with protein kinases, and this richness has made the kinase of crucial importance in initiating and maintaining cell behavior…”
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Properties of Stress Granule and P-Body Proteomes by Youn, Ji-Young, Dyakov, Boris J.A., Zhang, Jianping, Knight, James D.R., Vernon, Robert M., Forman-Kay, Julie D., Gingras, Anne-Claude

“…Stress granules and P-bodies are cytosolic biomolecular condensates that dynamically form by the phase separation of RNAs and proteins. They participate in…”
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A proximity-dependent biotinylation map of a human cell by Go, Christopher D., Knight, James D. R., Rajasekharan, Archita, Rathod, Bhavisha, Hesketh, Geoffrey G., Abe, Kento T., Youn, Ji-Young, Samavarchi-Tehrani, Payman, Zhang, Hui, Zhu, Lucie Y., Popiel, Evelyn, Lambert, Jean-Philippe, Coyaud, Étienne, Cheung, Sally W. T., Rajendran, Dushyandi, Wong, Cassandra J., Antonicka, Hana, Pelletier, Laurence, Palazzo, Alexander F., Shoubridge, Eric A., Raught, Brian, Gingras, Anne-Claude

“…Compartmentalization is a defining characteristic of eukaryotic cells, and partitions distinct biochemical processes into discrete subcellular locations…”
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High-Density Proximity Mapping Reveals the Subcellular Organization of mRNA-Associated Granules and Bodies by Youn, Ji-Young, Dunham, Wade H., Hong, Seo Jung, Knight, James D.R., Bashkurov, Mikhail, Chen, Ginny I., Bagci, Halil, Rathod, Bhavisha, MacLeod, Graham, Eng, Simon W.M., Angers, Stéphane, Morris, Quaid, Fabian, Marc, Côté, Jean-François, Gingras, Anne-Claude

“…mRNA processing, transport, translation, and ultimately degradation involve a series of dedicated protein complexes that often assemble into large membraneless…”
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The role of conserved water molecules in the catalytic domain of protein kinases by Knight, James D. R., Hamelberg, Donald, McCammon, J. Andrew, Kothary, Rashmi

“…Protein kinases are essential signaling molecules with a characteristic bilobal shape that has been studied for over 15 years. Despite the number of crystal…”
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Proximity biotinylation and affinity purification are complementary approaches for the interactome mapping of chromatin-associated protein complexes by Lambert, Jean-Philippe, Tucholska, Monika, Go, Christopher, Knight, James D.R., Gingras, Anne-Claude

“…Mapping protein–protein interactions for chromatin-associated proteins remains challenging. Here we explore the use of BioID, a proximity biotinylation…”
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MSPLIT-DIA: sensitive peptide identification for data-independent acquisition by Wang, Jian, Tucholska, Monika, Knight, James D R, Lambert, Jean-Philippe, Tate, Stephen, Larsen, Brett, Gingras, Anne-Claude, Bandeira, Nuno

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Interactome Rewiring Following Pharmacological Targeting of BET Bromodomains by Lambert, Jean-Philippe, Picaud, Sarah, Fujisawa, Takao, Hou, Huayun, Savitsky, Pavel, Uusküla-Reimand, Liis, Gupta, Gagan D., Abdouni, Hala, Lin, Zhen-Yuan, Tucholska, Monika, Knight, James D.R., Gonzalez-Badillo, Beatriz, St-Denis, Nicole, Newman, Joseph A., Stucki, Manuel, Pelletier, Laurence, Bandeira, Nuno, Wilson, Michael D., Filippakopoulos, Panagis, Gingras, Anne-Claude

“…Targeting bromodomains (BRDs) of the bromo-and-extra-terminal (BET) family offers opportunities for therapeutic intervention in cancer and other diseases…”
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Proximity‐dependent sensors for signaling by Gingras, Anne‐Claude, Martin, Claire, Hesketh, Geoffrey, Al Mismar, Rasha, Knight, James D., Go, Christopher, Dionne, Ugo

“…Understanding dynamic subcellular organization in living cells is key to unravelling mechanisms of intracellular signaling that goes awry in disease. Using…”
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Biochemical, proteomic, structural, and thermodynamic characterizations of integrin-linked kinase (ILK): cross-validation of the pseudokinase by Fukuda, Koichi, Knight, James D R, Piszczek, Grzegorz, Kothary, Rashmi, Qin, Jun

“…Integrin-linked kinase (ILK) is one of the few evolutionarily conserved focal adhesion proteins involved in diverse cell adhesion-dependent physiological and…”
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Gene Information eXtension (GIX): effortless retrieval of gene product information on any website by Knight, James D. R., Samavarchi-Tehrani, Payman, Tyers, Mike, Gingras, Anne-Claude

“…Retrieving information about genes is a continuous and time-consuming aspect of systems biology. While there are resources that can fulfill this need, they…”
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CCM-3/STRIPAK promotes seamless tube extension through endocytic recycling by Lant, Benjamin, Yu, Bin, Goudreault, Marilyn, Holmyard, Doug, Knight, James D.R., Xu, Peter, Zhao, Linda, Chin, Kelly, Wallace, Evan, Zhen, Mei, Gingras, Anne-Claude, Derry, W Brent

“…The mechanisms governing apical membrane assembly during biological tube development are poorly understood. Here, we show that extension of the C. elegans…”
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Phenotypic and Interaction Profiling of the Human Phosphatases Identifies Diverse Mitotic Regulators by St-Denis, Nicole, Gupta, Gagan D., Lin, Zhen Yuan, Gonzalez-Badillo, Beatriz, Veri, Amanda O., Knight, James D.R., Rajendran, Dushyandi, Couzens, Amber L., Currie, Ko W., Tkach, Johnny M., Cheung, Sally W.T., Pelletier, Laurence, Gingras, Anne-Claude

“…Reversible phosphorylation is a fundamental regulatory mechanism, intricately coordinated by kinases and phosphatases, two classes of enzymes widely disrupted…”
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