Cytoscape Automation: empowering workflow-based network analysis von Otasek, David, Morris, John H, Bouças, Jorge, Pico, Alexander R, Demchak, Barry

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Cytoscape StringApp: Network Analysis and Visualization of Proteomics Data von Doncheva, Nadezhda T, Morris, John H, Gorodkin, Jan, Jensen, Lars J

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UCSF ChimeraX: Tools for structure building and analysis von Meng, Elaine C., Goddard, Thomas D., Pettersen, Eric F., Couch, Greg S., Pearson, Zach J., Morris, John H., Ferrin, Thomas E.

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UCSF ChimeraX: Structure visualization for researchers, educators, and developers von Pettersen, Eric F., Goddard, Thomas D., Huang, Conrad C., Meng, Elaine C., Couch, Gregory S., Croll, Tristan I., Morris, John H., Ferrin, Thomas E.

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UCSF ChimeraX: Meeting modern challenges in visualization and analysis von Goddard, Thomas D., Huang, Conrad C., Meng, Elaine C., Pettersen, Eric F., Couch, Gregory S., Morris, John H., Ferrin, Thomas E.

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The STRING database in 2017: quality-controlled protein-protein association networks, made broadly accessible von Szklarczyk, Damian, Morris, John H, Cook, Helen, Kuhn, Michael, Wyder, Stefan, Simonovic, Milan, Santos, Alberto, Doncheva, Nadezhda T, Roth, Alexander, Bork, Peer, Jensen, Lars J, von Mering, Christian

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clusterMaker2: a major update to clusterMaker, a multi-algorithm clustering app for Cytoscape von Utriainen, Maija, Morris, John H

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clusterMaker: a multi-algorithm clustering plugin for Cytoscape von Morris, John H, Apeltsin, Leonard, Newman, Aaron M, Baumbach, Jan, Wittkop, Tobias, Su, Gang, Bader, Gary D, Ferrin, Thomas E

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Using sequence similarity networks for visualization of relationships across diverse protein superfamilies von Atkinson, Holly J, Morris, John H, Ferrin, Thomas E, Babbitt, Patricia C

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Visualize omics data on networks with Omics Visualizer, a Cytoscape App [version 1; peer review: 2 approved] von Legeay, Marc, Doncheva, Nadezhda T., Morris, John H., Jensen, Lars Juhl

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

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Affinity purification–mass spectrometry and network analysis to understand protein-protein interactions von Morris, John H, Knudsen, Giselle M, Verschueren, Erik, Johnson, Jeffrey R, Cimermancic, Peter, Greninger, Alexander L, Pico, Alexander R

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From Structure to Systems: High-Resolution, Quantitative Genetic Analysis of RNA Polymerase II von Braberg, Hannes, Jin, Huiyan, Moehle, Erica A., Chan, Yujia A., Wang, Shuyi, Shales, Michael, Benschop, Joris J., Morris, John H., Qiu, Chenxi, Hu, Fuqu, Tang, Leung K., Fraser, James S., Holstege, Frank C.P., Hieter, Philip, Guthrie, Christine, Kaplan, Craig D., Krogan, Nevan J.

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Ten simple rules to create biological network figures for communication von Marai, G Elisabeta, Pinaud, Bruno, Bühler, Katja, Lex, Alexander, Morris, John H

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Low-density lipoprotein receptor-related protein 1 (LRP1) is a novel receptor for apolipoprotein A4 (APOA4) in adipose tissue von Qu, Jie, Fourman, Sarah, Fitzgerald, Maureen, Liu, Min, Nair, Supna, Oses-Prieto, Juan, Burlingame, Alma, Morris, John H., Davidson, W. Sean, Tso, Patrick, Bhargava, Aditi

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Biological Network Exploration with Cytoscape 3 von Su, Gang, Morris, John H., Demchak, Barry, Bader, Gary D.

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Protein network prediction and topological analysis in Leishmania major as a tool for drug target selection von Flórez, Andrés F, Park, Daeui, Bhak, Jong, Kim, Byoung-Chul, Kuchinsky, Allan, Morris, John H, Espinosa, Jairo, Muskus, Carlos

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Evaluation of methods to assign cell type labels to cell clusters from single-cell RNA-sequencing data [version 2; peer review: 1 approved, 2 approved with reservations] von Diaz-Mejia, J. Javier, Meng, Elaine C, Pico, Alexander R, MacParland, Sonya A, Ketela, Troy, Pugh, Trevor J, Bader, Gary D, Morris, John H

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STRING v11: protein–protein association networks with increased coverage, supporting functional discovery in genome-wide experimental datasets von Szklarczyk, Damian, Gable, Annika L, Lyon, David, Junge, Alexander, Wyder, Stefan, Huerta-Cepas, Jaime, Simonovic, Milan, Doncheva, Nadezhda T, Morris, John H, Bork, Peer, Jensen, Lars J, Mering, Christian von

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Translating desktop success to the web in the cytoscape project von Pratt, Dexter, Pillich, Rudolf T, Morris, John H

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