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JBrowse 2: a modular genome browser with views of synteny and structural variation

https://doi.org/10.1186/s13059-023-02914-z

Diesh, Colin; Stevens, Garrett J; Xie, Peter; De Jesus Martinez, Teresa; Hershberg, Elliot A.; Leung, Angel; Guo, Emma; Dider, Shihab; Zhang, Junjun; Bridge, Caroline; et al (December 2023, Genome Biology)

Abstract We present JBrowse 2, a general-purpose genome annotation browser offering enhanced visualization of complex structural variation and evolutionary relationships. It retains core features of JBrowse while adding new views for synteny, dotplots, breakpoints, gene fusions, and whole-genome overviews. It allows users to share sessions, open multiple genomes, and navigate between views. It can be embedded in a web page, used as a standalone application, or run from Jupyter notebooks or R sessions. These improvements are enabled by a ground-up redesign using modern web technology. We describe application functionality, use cases, performance benchmarks, and implementation notes for web administrators and developers.
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Ensemble Inference Methods for Models With Noisy and Expensive Likelihoods

https://doi.org/10.1137/21M1410853

Dunbar, Oliver R.; Duncan, Andrew B.; Stuart, Andrew M.; Wolfram, Marie-Therese (June 2022, SIAM Journal on Applied Dynamical Systems)

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Topochemical Synthesis of Single-Crystalline Hydrogen-Bonded Cross-Linked Organic Frameworks and Their Guest-Induced Elastic Expansion

https://doi.org/10.1021/jacs.9b05232

Jiang, Xuanfeng; Cui, Xunzhe; Duncan, Andrew J.; Li, Liang; Hughes, Russell P.; Staples, Richard J.; Alexandrov, Eugeny V.; Proserpio, Davide M.; Wu, Yuyang; Ke, Chenfeng (June 2019, Journal of the American Chemical Society)

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Putting Cocrystal Stoichiometry to Work: A Reactive Hydrogen-Bonded “Superassembly” Enables Nanoscale Enlargement of a Metal–Organic Rhomboid via a Solid-State Photocycloaddition

https://doi.org/10.1021/jacs.8b01775

Chu, Qianli; Duncan, Andrew J.; Papaefstathiou, Giannis S.; Hamilton, Tamara D.; Atkinson, Manza B.; Mariappan, S. V.; MacGillivray, Leonard R. (April 2018, Journal of the American Chemical Society)

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Advanced Polymer Designs for Direct‐Ink‐Write 3D Printing

https://doi.org/10.1002/chem.201900975

Li, Longyu; Lin, Qianming; Tang, Miao; Duncan, Andrew J. E.; Ke, Chenfeng (July 2019, Chemistry – A European Journal)

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