A citation-based method for searching scientific literature

Claire N Bedbrook, Austin J Rice, Kevin K Yang, Xiaozhe Ding, Siyuan Chen, Emily M LeProust, Viviana Gradinaru, Frances H Arnold. Proc Natl Acad Sci U S A 2017
Times Cited: 26







List of co-cited articles
141 articles co-cited >1



Times Cited
  Times     Co-cited
Similarity


Protein building blocks preserved by recombination.
Christopher A Voigt, Carlos Martinez, Zhen-Gang Wang, Stephen L Mayo, Frances H Arnold. Nat Struct Biol 2002
229
26

Machine learning to design integral membrane channelrhodopsins for efficient eukaryotic expression and plasma membrane localization.
Claire N Bedbrook, Kevin K Yang, Austin J Rice, Viviana Gradinaru, Frances H Arnold. PLoS Comput Biol 2017
34
23

Independent optical excitation of distinct neural populations.
Nathan C Klapoetke, Yasunobu Murata, Sung Soo Kim, Stefan R Pulver, Amanda Birdsey-Benson, Yong Ku Cho, Tania K Morimoto, Amy S Chuong, Eric J Carpenter, Zhijian Tian,[...]. Nat Methods 2014
892
19

A diverse family of thermostable cytochrome P450s created by recombination of stabilizing fragments.
Yougen Li, D Allan Drummond, Andrew M Sawayama, Christopher D Snow, Jesse D Bloom, Frances H Arnold. Nat Biotechnol 2007
88
19

Crystal structure of the channelrhodopsin light-gated cation channel.
Hideaki E Kato, Feng Zhang, Ofer Yizhar, Charu Ramakrishnan, Tomohiro Nishizawa, Kunio Hirata, Jumpei Ito, Yusuke Aita, Tomoya Tsukazaki, Shigehiko Hayashi,[...]. Nature 2012
305
19

Navigating the protein fitness landscape with Gaussian processes.
Philip A Romero, Andreas Krause, Frances H Arnold. Proc Natl Acad Sci U S A 2013
87
19

Biocatalytic asymmetric synthesis of chiral amines from ketones applied to sitagliptin manufacture.
Christopher K Savile, Jacob M Janey, Emily C Mundorff, Jeffrey C Moore, Sarena Tam, William R Jarvis, Jeffrey C Colbeck, Anke Krebber, Fred J Fleitz, Jos Brands,[...]. Science 2010
555
19

Synthetic biology for the directed evolution of protein biocatalysts: navigating sequence space intelligently.
Andrew Currin, Neil Swainston, Philip J Day, Douglas B Kell. Chem Soc Rev 2015
165
19

Improving and repurposing biocatalysts via directed evolution.
Carl A Denard, Hengqian Ren, Huimin Zhao. Curr Opin Chem Biol 2015
113
15

The coming of age of de novo protein design.
Po-Ssu Huang, Scott E Boyken, David Baker. Nature 2016
490
15

Ultrahigh-throughput-directed enzyme evolution by absorbance-activated droplet sorting (AADS).
Fabrice Gielen, Raphaelle Hours, Stephane Emond, Martin Fischlechner, Ursula Schell, Florian Hollfelder. Proc Natl Acad Sci U S A 2016
108
15

Iterative saturation mutagenesis: a powerful approach to engineer proteins by systematically simulating Darwinian evolution.
Carlos G Acevedo-Rocha, Sabrina Hoebenreich, Manfred T Reetz. Methods Mol Biol 2014
48
15

Methods for the directed evolution of proteins.
Michael S Packer, David R Liu. Nat Rev Genet 2015
349
15

Structure-guided recombination creates an artificial family of cytochromes P450.
Christopher R Otey, Marco Landwehr, Jeffrey B Endelman, Kaori Hiraga, Jesse D Bloom, Frances H Arnold. PLoS Biol 2006
99
15

Machine-learning-guided directed evolution for protein engineering.
Kevin K Yang, Zachary Wu, Frances H Arnold. Nat Methods 2019
142
15

Exploring protein fitness landscapes by directed evolution.
Philip A Romero, Frances H Arnold. Nat Rev Mol Cell Biol 2009
492
11

SCHEMA-designed variants of human Arginase I and II reveal sequence elements important to stability and catalysis.
Philip A Romero, Everett Stone, Candice Lamb, Lynne Chantranupong, Andreas Krause, Aleksandr E Miklos, Randall A Hughes, Blake Fechtel, Andrew D Ellington, Frances H Arnold,[...]. ACS Synth Biol 2012
34
11

Genetically Encoded Spy Peptide Fusion System to Detect Plasma Membrane-Localized Proteins In Vivo.
Claire N Bedbrook, Mihoko Kato, Sripriya Ravindra Kumar, Anupama Lakshmanan, Ravi D Nath, Fei Sun, Paul W Sternberg, Frances H Arnold, Viviana Gradinaru. Chem Biol 2015
35
11

Periscope: quantitative prediction of soluble protein expression in the periplasm of Escherichia coli.
Catherine Ching Han Chang, Chen Li, Geoffrey I Webb, BengTi Tey, Jiangning Song, Ramakrishnan Nagasundara Ramanan. Sci Rep 2016
9
33

Chimeragenesis of distantly-related proteins by noncontiguous recombination.
Matthew A Smith, Philip A Romero, Timothy Wu, Eric M Brustad, Frances H Arnold. Protein Sci 2013
23
13

Millisecond-timescale, genetically targeted optical control of neural activity.
Edward S Boyden, Feng Zhang, Ernst Bamberg, Georg Nagel, Karl Deisseroth. Nat Neurosci 2005
11

Reducing codon redundancy and screening effort of combinatorial protein libraries created by saturation mutagenesis.
Sabrina Kille, Carlos G Acevedo-Rocha, Loreto P Parra, Zhi-Gang Zhang, Diederik J Opperman, Manfred T Reetz, Juan Pablo Acevedo. ACS Synth Biol 2013
115
11

Improving enzyme properties: when are closer mutations better?
Krista L Morley, Romas J Kazlauskas. Trends Biotechnol 2005
251
11

Enzyme engineering by targeted libraries.
Moshe Goldsmith, Dan S Tawfik. Methods Enzymol 2013
59
11

Synthetic DNA Synthesis and Assembly: Putting the Synthetic in Synthetic Biology.
Randall A Hughes, Andrew D Ellington. Cold Spring Harb Perspect Biol 2017
106
11

Evolving strategies for enzyme engineering.
Jesse D Bloom, Michelle M Meyer, Peter Meinhold, Christopher R Otey, Derek MacMillan, Frances H Arnold. Curr Opin Struct Biol 2005
210
11

Economical analysis of saturation mutagenesis experiments.
Carlos G Acevedo-Rocha, Manfred T Reetz, Yuval Nov. Sci Rep 2015
26
11

Speeding up directed evolution: Combining the advantages of solid-phase combinatorial gene synthesis with statistically guided reduction of screening effort.
Sabrina Hoebenreich, Felipe E Zilly, Carlos G Acevedo-Rocha, Matías Zilly, Manfred T Reetz. ACS Synth Biol 2015
25
12


SCHEMA recombination of a fungal cellulase uncovers a single mutation that contributes markedly to stability.
Pete Heinzelman, Christopher D Snow, Matthew A Smith, Xinlin Yu, Arvind Kannan, Kevin Boulware, Alan Villalobos, Sridhar Govindarajan, Jeremy Minshull, Frances H Arnold. J Biol Chem 2009
68
11

Improving catalytic function by ProSAR-driven enzyme evolution.
Richard J Fox, S Christopher Davis, Emily C Mundorff, Lisa M Newman, Vesna Gavrilovic, Steven K Ma, Loleta M Chung, Charlene Ching, Sarena Tam, Sheela Muley,[...]. Nat Biotechnol 2007
224
11

Global analysis of protein folding using massively parallel design, synthesis, and testing.
Gabriel J Rocklin, Tamuka M Chidyausiku, Inna Goreshnik, Alex Ford, Scott Houliston, Alexander Lemak, Lauren Carter, Rashmi Ravichandran, Vikram K Mulligan, Aaron Chevalier,[...]. Science 2017
162
11

Computational tools for designing and engineering enzymes.
Jiri Damborsky, Jan Brezovsky. Curr Opin Chem Biol 2014
91
11

Massively parallel de novo protein design for targeted therapeutics.
Aaron Chevalier, Daniel-Adriano Silva, Gabriel J Rocklin, Derrick R Hicks, Renan Vergara, Patience Murapa, Steffen M Bernard, Lu Zhang, Kwok-Ho Lam, Guorui Yao,[...]. Nature 2017
162
11

Enzyme engineering in biomimetic compartments.
Pierre-Yves Colin, Anastasia Zinchenko, Florian Hollfelder. Curr Opin Struct Biol 2015
37
11

Expanding the range of substrate acceptance of enzymes: combinatorial active-site saturation test.
Manfred T Reetz, Marco Bocola, José Daniel Carballeira, Dongxing Zha, Andreas Vogel. Angew Chem Int Ed Engl 2005
207
11

Directed Evolution of Protein Catalysts.
Cathleen Zeymer, Donald Hilvert. Annu Rev Biochem 2018
133
11

SWISS-MODEL: homology modelling of protein structures and complexes.
Andrew Waterhouse, Martino Bertoni, Stefan Bienert, Gabriel Studer, Gerardo Tauriello, Rafal Gumienny, Florian T Heer, Tjaart A P de Beer, Christine Rempfer, Lorenza Bordoli,[...]. Nucleic Acids Res 2018
11

Structure-guided SCHEMA recombination of distantly related beta-lactamases.
Michelle M Meyer, Lisa Hochrein, Frances H Arnold. Protein Eng Des Sel 2006
65
11

Principles for applying optogenetic tools derived from direct comparative analysis of microbial opsins.
Joanna Mattis, Kay M Tye, Emily A Ferenczi, Charu Ramakrishnan, Daniel J O'Shea, Rohit Prakash, Lisa A Gunaydin, Minsuk Hyun, Lief E Fenno, Viviana Gradinaru,[...]. Nat Methods 2011
426
11

ReaChR: a red-shifted variant of channelrhodopsin enables deep transcranial optogenetic excitation.
John Y Lin, Per Magne Knutsen, Arnaud Muller, David Kleinfeld, Roger Y Tsien. Nat Neurosci 2013
414
11

Characterization of engineered channelrhodopsin variants with improved properties and kinetics.
John Y Lin, Michael Z Lin, Paul Steinbach, Roger Y Tsien. Biophys J 2009
408
11


Retinylidene proteins: structures and functions from archaea to humans.
J L Spudich, C S Yang, K H Jung, E N Spudich. Annu Rev Cell Dev Biol 2000
406
7

Optogenetics in neural systems.
Ofer Yizhar, Lief E Fenno, Thomas J Davidson, Murtaza Mogri, Karl Deisseroth. Neuron 2011
973
7

All-optical electrophysiology in mammalian neurons using engineered microbial rhodopsins.
Daniel R Hochbaum, Yongxin Zhao, Samouil L Farhi, Nathan Klapoetke, Christopher A Werley, Vikrant Kapoor, Peng Zou, Joel M Kralj, Dougal Maclaurin, Niklas Smedemark-Margulies,[...]. Nat Methods 2014
383
7

Biophysics of Channelrhodopsin.
Franziska Schneider, Christiane Grimm, Peter Hegemann. Annu Rev Biophys 2015
99
7

A review of machine learning methods to predict the solubility of overexpressed recombinant proteins in Escherichia coli.
Narjeskhatoon Habibi, Siti Z Mohd Hashim, Alireza Norouzi, Mohammed Razip Samian. BMC Bioinformatics 2014
21
9

Energetics of membrane protein folding.
Karen G Fleming. Annu Rev Biophys 2014
43
7

A large-scale evaluation of computational protein function prediction.
Predrag Radivojac, Wyatt T Clark, Tal Ronnen Oron, Alexandra M Schnoes, Tobias Wittkop, Artem Sokolov, Kiley Graim, Christopher Funk, Karin Verspoor, Asa Ben-Hur,[...]. Nat Methods 2013
454
7


Co-cited is the co-citation frequency, indicating how many articles cite the article together with the query article. Similarity is the co-citation as percentage of the times cited of the query article or the article in the search results, whichever is the lowest. These numbers are calculated for the last 100 citations when articles are cited more than 100 times.