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Implementation in rehabilitation: a roadmap for practitioners and researchers.

Morris JH, Bernhardsson S, Bird ML, Connell L, Lynch E, Jarvis K, Kayes NM, Miller K, Mudge S, Fisher R.

Disabil Rehabil. 2019 Apr 12:1-10. doi: 10.1080/09638288.2019.1587013. [Epub ahead of print]


Dynamic Lycra® orthoses as an adjunct to arm rehabilitation after stroke: a single-blind, two-arm parallel group, randomized controlled feasibility trial.

Morris JH, John A, Wedderburn L, Rauchhaus P, Donnan PT.

Clin Rehabil. 2019 Aug;33(8):1331-1343. doi: 10.1177/0269215519840403. Epub 2019 Apr 12.


Exercise Training and Heart Failure: A Review of the Literature.

Morris JH, Chen L.

Card Fail Rev. 2019 Feb;5(1):57-61. doi: 10.15420/cfr.2018.31.1. Review.


STRING v11: protein-protein association networks with increased coverage, supporting functional discovery in genome-wide experimental datasets.

Szklarczyk D, Gable AL, Lyon D, Junge A, Wyder S, Huerta-Cepas J, Simonovic M, Doncheva NT, Morris JH, Bork P, Jensen LJ, Mering CV.

Nucleic Acids Res. 2019 Jan 8;47(D1):D607-D613. doi: 10.1093/nar/gky1131.


Cytoscape StringApp: Network Analysis and Visualization of Proteomics Data.

Doncheva NT, Morris JH, Gorodkin J, Jensen LJ.

J Proteome Res. 2019 Feb 1;18(2):623-632. doi: 10.1021/acs.jproteome.8b00702. Epub 2018 Dec 5.


aMatReader: Importing adjacency matrices via Cytoscape Automation.

Settle B, Otasek D, Morris JH, Demchak B.

Version 2. F1000Res. 2018 Jun 21 [revised 2018 Jan 1];7. pii: ISCB Comm J-823. doi: 10.12688/f1000research.15146.2. eCollection 2018.


Copycat Layout: Network layout alignment via Cytoscape Automation.

Settle B, Otasek D, Morris JH, Demchak B.

Version 2. F1000Res. 2018 Jun 21 [revised 2018 Jan 1];7. pii: ISCB Comm J-822. doi: 10.12688/f1000research.15144.2. eCollection 2018.


The Cytoscape Automation app article collection.

Demchak B, Otasek D, Pico AR, Bader GD, Ono K, Settle B, Sage E, Morris JH, Longabaugh W, Lopes C, Kucera M, Treister A, Schwikowski B, Molenaar P, Ideker T.

F1000Res. 2018 Jun 20;7:800. doi: 10.12688/f1000research.15355.1. eCollection 2018.


Rapidity of Correction of Hyponatremia Due to Syndrome of Inappropriate Secretion of Antidiuretic Hormone Following Tolvaptan.

Morris JH, Bohm NM, Nemecek BD, Crawford R, Kelley D, Bhasin B, Nietert PJ, Velez JCQ.

Am J Kidney Dis. 2018 Jun;71(6):772-782. doi: 10.1053/j.ajkd.2017.12.002. Epub 2018 Feb 23.


Prediction of enzymatic pathways by integrative pathway mapping.

Calhoun S, Korczynska M, Wichelecki DJ, San Francisco B, Zhao S, Rodionov DA, Vetting MW, Al-Obaidi NF, Lin H, O'Meara MJ, Scott DA, Morris JH, Russel D, Almo SC, Osterman AL, Gerlt JA, Jacobson MP, Shoichet BK, Sali A.

Elife. 2018 Jan 29;7. pii: e31097. doi: 10.7554/eLife.31097.


Art participation for psychosocial wellbeing during stroke rehabilitation: a feasibility randomised controlled trial.

Morris JH, Kelly C, Joice S, Kroll T, Mead G, Donnan P, Toma M, Williams B.

Disabil Rehabil. 2019 Jan;41(1):9-18. doi: 10.1080/09638288.2017.1370499. Epub 2017 Aug 30.


UCSF ChimeraX: Meeting modern challenges in visualization and analysis.

Goddard TD, Huang CC, Meng EC, Pettersen EF, Couch GS, Morris JH, Ferrin TE.

Protein Sci. 2018 Jan;27(1):14-25. doi: 10.1002/pro.3235. Epub 2017 Sep 6.


Masked Hypertension: Finding Trouble Under the Disguise.

Morris JH, Bisognano JD.

Circ Cardiovasc Qual Outcomes. 2017 Jul;10(7). pii: e003945. doi: 10.1161/CIRCOUTCOMES.117.003945. No abstract available.


Biocuration in the structure-function linkage database: the anatomy of a superfamily.

Holliday GL, Brown SD, Akiva E, Mischel D, Hicks MA, Morris JH, Huang CC, Meng EC, Pegg SC, Ferrin TE, Babbitt PC.

Database (Oxford). 2017 Jan 1;2017. doi: 10.1093/database/bax045. No abstract available.


Biocuration in the structure-function linkage database: the anatomy of a superfamily.

Holliday GL, Brown SD, Akiva E, Mischel D, Hicks MA, Morris JH, Huang CC, Meng EC, Pegg SC, Ferrin TE, Babbitt PC.

Database (Oxford). 2017 Jan 1;2017(1). doi: 10.1093/database/bax006. Erratum in: Database (Oxford). 2017 Jan 1;2017:null.


Acute Aortic Syndromes: Update in Current Medical Management.

Morris JH, Mix D, Cameron SJ.

Curr Treat Options Cardiovasc Med. 2017 Apr;19(4):29. doi: 10.1007/s11936-017-0523-9. Review.


An Atlas of Peroxiredoxins Created Using an Active Site Profile-Based Approach to Functionally Relevant Clustering of Proteins.

Harper AF, Leuthaeuser JB, Babbitt PC, Morris JH, Ferrin TE, Poole LB, Fetrow JS.

PLoS Comput Biol. 2017 Feb 10;13(2):e1005284. doi: 10.1371/journal.pcbi.1005284. eCollection 2017 Feb.


An approach to functionally relevant clustering of the protein universe: Active site profile-based clustering of protein structures and sequences.

Knutson ST, Westwood BM, Leuthaeuser JB, Turner BE, Nguyendac D, Shea G, Kumar K, Hayden JD, Harper AF, Brown SD, Morris JH, Ferrin TE, Babbitt PC, Fetrow JS.

Protein Sci. 2017 Apr;26(4):677-699. doi: 10.1002/pro.3112. Epub 2017 Mar 8.


The STRING database in 2017: quality-controlled protein-protein association networks, made broadly accessible.

Szklarczyk D, Morris JH, Cook H, Kuhn M, Wyder S, Simonovic M, Santos A, Doncheva NT, Roth A, Bork P, Jensen LJ, von Mering C.

Nucleic Acids Res. 2017 Jan 4;45(D1):D362-D368. doi: 10.1093/nar/gkw937. Epub 2016 Oct 18.


DASP3: identification of protein sequences belonging to functionally relevant groups.

Leuthaeuser JB, Morris JH, Harper AF, Ferrin TE, Babbitt PC, Fetrow JS.

BMC Bioinformatics. 2016 Nov 11;17(1):458.


Physical activity participation in community dwelling stroke survivors: synergy and dissonance between motivation and capability. A qualitative study.

Morris JH, Oliver T, Kroll T, Joice S, Williams B.

Physiotherapy. 2017 Sep;103(3):311-321. doi: 10.1016/ Epub 2016 May 11.


Soluble Factors Secreted by Endothelial Cells Allow for Productive and Latent HIV-1 Infection in Resting CD4+ T Cells.

Morris JH 3rd, Nguyen T, Nwadike A, Geels ML, Kamp DL, Kim BR, Boyer JD, Shen A.

AIDS Res Hum Retroviruses. 2017 Feb;33(2):110-120. doi: 10.1089/AID.2016.0058. Epub 2016 Oct 5.


The Cytoscape app article collection.

Pico AR, Bader GD, Demchak B, Guitart Pla O, Hull T, Longabaugh W, Lopes C, Lotia S, Molenaar P, Montojo J, Morris JH, Ono K, Schwikowski B, Welker D, Ideker T.

F1000Res. 2014 Jul 1;3:138. doi: 10.12688/f1000research.4642.1. eCollection 2014.


CyAnimator: Simple Animations of Cytoscape Networks.

Morris JH, Vijay D, Federowicz S, Pico AR, Ferrin TE.

Version 2. F1000Res. 2015 Aug 5 [revised 2015 Jan 1];4:482. doi: 10.12688/f1000research.6852.2. eCollection 2015.


What is orthopaedic triage? A systematic review.

Morris JH, James RE, Davey R, Waddington G.

J Eval Clin Pract. 2015 Feb;21(1):128-36. doi: 10.1111/jep.12260. Epub 2014 Nov 20. Review.


setsApp for Cytoscape: Set operations for Cytoscape Nodes and Edges.

Morris JH, Lotia S, Wu A, Doncheva NT, Albrecht M, Pico AR, Ferrin TE.

Version 2. F1000Res. 2014 Jul 1 [revised 2015 Jan 1];3:149. doi: 10.12688/f1000research.4392.2. eCollection 2014.


enhancedGraphics: a Cytoscape app for enhanced node graphics.

Morris JH, Kuchinsky A, Ferrin TE, Pico AR.

F1000Res. 2014 Jul 1;3:147. doi: 10.12688/f1000research.4460.1. eCollection 2014.


Affinity purification-mass spectrometry and network analysis to understand protein-protein interactions.

Morris JH, Knudsen GM, Verschueren E, Johnson JR, Cimermancic P, Greninger AL, Pico AR.

Nat Protoc. 2014 Nov;9(11):2539-54. doi: 10.1038/nprot.2014.164. Epub 2014 Oct 2.


Integrative visual analysis of protein sequence mutations.

Doncheva NT, Klein K, Morris JH, Wybrow M, Domingues FS, Albrecht M.

BMC Proc. 2014 Aug 28;8(Suppl 2 Proceedings of the 3rd Annual Symposium on Biologica):S2. doi: 10.1186/1753-6561-8-S2-S2. eCollection 2014.


cddApp: a Cytoscape app for accessing the NCBI conserved domain database.

Morris JH, Wu A, Yamashita RA, Marchler-Bauer A, Ferrin TE.

Bioinformatics. 2015 Jan 1;31(1):134-6. doi: 10.1093/bioinformatics/btu605. Epub 2014 Sep 10.


Biological network exploration with Cytoscape 3.

Su G, Morris JH, Demchak B, Bader GD.

Curr Protoc Bioinformatics. 2014 Sep 8;47:8.13.1-24. doi: 10.1002/0471250953.bi0813s47.


Enhancing UCSF Chimera through web services.

Huang CC, Meng EC, Morris JH, Pettersen EF, Ferrin TE.

Nucleic Acids Res. 2014 Jul;42(Web Server issue):W478-84. doi: 10.1093/nar/gku377. Epub 2014 May 26.


Interventions to promote long-term participation in physical activity after stroke: a systematic review of the literature.

Morris JH, Macgillivray S, McFarlane S.

Arch Phys Med Rehabil. 2014 May;95(5):956-67. doi: 10.1016/j.apmr.2013.12.016. Epub 2014 Jan 1. Review.


The Structure-Function Linkage Database.

Akiva E, Brown S, Almonacid DE, Barber AE 2nd, Custer AF, Hicks MA, Huang CC, Lauck F, Mashiyama ST, Meng EC, Mischel D, Morris JH, Ojha S, Schnoes AM, Stryke D, Yunes JM, Ferrin TE, Holliday GL, Babbitt PC.

Nucleic Acids Res. 2014 Jan;42(Database issue):D521-30. doi: 10.1093/nar/gkt1130. Epub 2013 Nov 23.


From structure to systems: high-resolution, quantitative genetic analysis of RNA polymerase II.

Braberg H, Jin H, Moehle EA, Chan YA, Wang S, Shales M, Benschop JJ, Morris JH, Qiu C, Hu F, Tang LK, Fraser JS, Holstege FC, Hieter P, Guthrie C, Kaplan CD, Krogan NJ.

Cell. 2013 Aug 15;154(4):775-88. doi: 10.1016/j.cell.2013.07.033. Epub 2013 Aug 8.


Non-medical prescribing by physiotherapists: issues reported in the current evidence.

Morris JH, Grimmer K.

Man Ther. 2014 Feb;19(1):82-6. doi: 10.1016/j.math.2013.04.003. Epub 2013 May 10. Review.


Predicting health related quality of life 6 months after stroke: the role of anxiety and upper limb dysfunction.

Morris JH, van Wijck F, Joice S, Donaghy M.

Disabil Rehabil. 2013 Feb;35(4):291-9. doi: 10.3109/09638288.2012.691942. Epub 2012 Jun 12.


Responses of the less affected arm to bilateral upper limb task training in early rehabilitation after stroke: a randomized controlled trial.

Morris JH, Van Wijck F.

Arch Phys Med Rehabil. 2012 Jul;93(7):1129-37. doi: 10.1016/j.apmr.2012.02.025. Epub 2012 Mar 12.


Global landscape of HIV-human protein complexes.

Jäger S, Cimermancic P, Gulbahce N, Johnson JR, McGovern KE, Clarke SC, Shales M, Mercenne G, Pache L, Li K, Hernandez H, Jang GM, Roth SL, Akiva E, Marlett J, Stephens M, D'Orso I, Fernandes J, Fahey M, Mahon C, O'Donoghue AJ, Todorovic A, Morris JH, Maltby DA, Alber T, Cagney G, Bushman FD, Young JA, Chanda SK, Sundquist WI, Kortemme T, Hernandez RD, Craik CS, Burlingame A, Sali A, Frankel AD, Krogan NJ.

Nature. 2011 Dec 21;481(7381):365-70. doi: 10.1038/nature10719.


clusterMaker: a multi-algorithm clustering plugin for Cytoscape.

Morris JH, Apeltsin L, Newman AM, Baumbach J, Wittkop T, Su G, Bader GD, Ferrin TE.

BMC Bioinformatics. 2011 Nov 9;12:436. doi: 10.1186/1471-2105-12-436.


GLay: community structure analysis of biological networks.

Su G, Kuchinsky A, Morris JH, States DJ, Meng F.

Bioinformatics. 2010 Dec 15;26(24):3135-7. doi: 10.1093/bioinformatics/btq596.


Improving the quality of protein similarity network clustering algorithms using the network edge weight distribution.

Apeltsin L, Morris JH, Babbitt PC, Ferrin TE.

Bioinformatics. 2011 Feb 1;27(3):326-33. doi: 10.1093/bioinformatics/btq655. Epub 2010 Nov 29.


Protein network prediction and topological analysis in Leishmania major as a tool for drug target selection.

Flórez AF, Park D, Bhak J, Kim BC, Kuchinsky A, Morris JH, Espinosa J, Muskus C.

BMC Bioinformatics. 2010 Sep 27;11:484. doi: 10.1186/1471-2105-11-484.


Computational tools for the interactive exploration of proteomic and structural data.

Morris JH, Meng EC, Ferrin TE.

Mol Cell Proteomics. 2010 Aug;9(8):1703-15. doi: 10.1074/mcp.R000007-MCP201. Epub 2010 Jun 4.


Partitioning biological data with transitivity clustering.

Wittkop T, Emig D, Lange S, Rahmann S, Albrecht M, Morris JH, Böcker S, Stoye J, Baumbach J.

Nat Methods. 2010 Jun;7(6):419-20. doi: 10.1038/nmeth0610-419. No abstract available.


Optimising long-term participation in physical activities after stroke: exploring new ways of working for physiotherapists.

Morris JH, Williams B.

Physiotherapy. 2009 Sep;95(3):228-34. doi: 10.1016/ Epub 2009 Jan 29.


Using sequence similarity networks for visualization of relationships across diverse protein superfamilies.

Atkinson HJ, Morris JH, Ferrin TE, Babbitt PC.

PLoS One. 2009;4(2):e4345. doi: 10.1371/journal.pone.0004345. Epub 2009 Feb 3.


A comparison of bilateral and unilateral upper-limb task training in early poststroke rehabilitation: a randomized controlled trial.

Morris JH, van Wijck F, Joice S, Ogston SA, Cole I, MacWalter RS.

Arch Phys Med Rehabil. 2008 Jul;89(7):1237-45. doi: 10.1016/j.apmr.2007.11.039.


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