Update paper

paper/README.md

@@ -23,4 +23,4 @@ pandoc -s paper.md --citeproc \
 -o paper.pdf
 ```
 
-The format is dictated by the `template.tex` file, which is a spliced together combo of the default Pandoc template with some additions to deal with authors and affiliations in the metadata format JOSS requires.
+The format is dictated by the `template.tex` file, which is a spliced-together combo of the default Pandoc template with some additions to deal with authors and affiliations in the metadata format JOSS requires.

paper/paper.bib

@@ -1,5 +1,5 @@
 @article{bloomFitnessEffectsMutations2023,
-  title = {Fitness Effects of~Mutations to {{SARS-CoV-2}} Proteins},
+  title = {Fitness Effects of Mutations to {{SARS-CoV-2}} Proteins},
   author = {Bloom, Jesse D. and Neher, Richard A.},
   year = {2023},
   journal = {Virus Evolution},
@@ -17,20 +17,20 @@ @article{bloomFitnessEffectsMutations2023
 
 @misc{bobyOpenScienceDiscovery2023,
   title = {Open {{Science Discovery}} of {{Potent Non-Covalent SARS-CoV-2 Main Protease Inhibitors}}},
-  author = {Boby, Melissa L. and Fearon, Daren and Ferla, Matteo and Filep, Mihajlo and Koekemoer, Lizb{\'e} and Robinson, Matthew C. and Consortium, The COVID Moonshot and Chodera, John D. and Lee, Alpha A. and London, Nir and von Delft, Annette and von Delft, Frank},
+  author = {Boby, Melissa L. and Fearon, Daren and Ferla, Matteo and Filep, Mihajlo and Koekemoer, Lizb{\'e} and Robinson, Matthew C. and Consortium, The COVID Moonshot and Chodera, John D. and Lee, Alpha A. and London, Nir and {von Delft}, Annette and {von Delft}, Frank},
   year = {2023},
   month = sep,
-  primaryclass = {New Results},
+  eprintclass = {New Results},
   pages = {2020.10.29.339317},
   publisher = {{bioRxiv}},
   doi = {10.1101/2020.10.29.339317},
   urldate = {2023-10-24},
   abstract = {We report the results of the COVID Moonshot, a fully open-science, crowd sourced, structure-enabled drug discovery campaign targeting the SARS-CoV-2 main protease. We discovered a non-covalent, non-peptidic inhibitor scaffold with lead-like properties that is differentiated from current main protease inhibitors. Our approach leveraged crowdsourcing, machine learning, exascale molecular simulations, and high-throughput structural biology and chemistry. We generated a detailed map of the structural plasticity of the SARS-CoV-2 main protease, extensive structure-activity relationships for multiple chemotypes, and a wealth of biochemical activity data. All compound designs ({$>$}18,000 designs), crystallographic data ({$>$}840 ligand-bound X-ray structures), assay data ({$>$}10,000 measurements), and synthesized molecules ({$>$}2,400 compounds) for this campaign were shared rapidly and openly, creating a rich open and IP-free knowledgebase for future anti-coronavirus drug discovery.},
   archiveprefix = {bioRxiv},
   chapter = {New Results},
-  copyright = {\textcopyright{} 2023, Posted by Cold Spring Harbor Laboratory. This pre-print is available under a Creative Commons License (Attribution 4.0 International), CC BY 4.0, as described at http://creativecommons.org/licenses/by/4.0/},
+  copyright = {{\textcopyright} 2023, Posted by Cold Spring Harbor Laboratory. This pre-print is available under a Creative Commons License (Attribution 4.0 International), CC BY 4.0, as described at http://creativecommons.org/licenses/by/4.0/},
   langid = {english},
-  file = {/Users/will/Zotero/storage/ZWLEJESD/Boby et al. - 2023 - Open Science Discovery of Potent Non-Covalent SARS.pdf}
+  file = {/Users/will/Zotero/storage/EAESIVEC/Boby et al. - 2023 - Open Science Discovery of Potent Non-Covalent SARS.pdf}
 }
 
 @article{dadonaitePseudovirusSystemEnables2023,
@@ -49,7 +49,64 @@ @article{dadonaitePseudovirusSystemEnables2023
   pmcid = {PMC9922669},
   pmid = {36868218},
   keywords = {{Antibodies, Neutralizing},{Antibodies, Viral},antibody escape,antibody neutralization,BA.1,COVID-19,deep mutational scanning,Delta,Humans,Mutation,Omicron,pseudovirus,RNA Viruses,SARS-CoV-2,spike},
-  file = {/Users/will/Zotero/storage/GMCE8CNL/Dadonaite et al. - 2023 - A pseudovirus system enables deep mutational scann.pdf}
+  file = {/Users/will/Zotero/storage/L338TZXJ/Dadonaite et al. - 2023 - A pseudovirus system enables deep mutational scann.pdf}
+}
+
+@article{espositoMaveDBOpensourcePlatform2019,
+  title = {{{MaveDB}}: An Open-Source Platform to Distribute and Interpret Data from Multiplexed Assays of Variant Effect},
+  shorttitle = {{{MaveDB}}},
+  author = {Esposito, Daniel and Weile, Jochen and Shendure, Jay and Starita, Lea M. and Papenfuss, Anthony T. and Roth, Frederick P. and Fowler, Douglas M. and Rubin, Alan F.},
+  year = {2019},
+  month = nov,
+  journal = {Genome Biology},
+  volume = {20},
+  number = {1},
+  pages = {223},
+  issn = {1474-760X},
+  doi = {10.1186/s13059-019-1845-6},
+  urldate = {2024-05-15},
+  abstract = {Multiplex assays of variant effect (MAVEs), such as deep mutational scans and massively parallel reporter assays, test thousands of sequence variants in a single experiment. Despite the importance of MAVE data for basic and clinical research, there is no standard resource for their discovery and distribution. Here, we present MaveDB (https://www.mavedb.org), a public repository for large-scale measurements of sequence variant impact, designed for interoperability with applications to interpret these datasets. We also describe the first such application, MaveVis, which retrieves, visualizes, and contextualizes variant effect maps. Together, the database and applications will empower the community to mine these powerful datasets.},
+  keywords = {Deep mutational scanning,Genome interpretation,Large-scale mutagenesis,Massively parallel reporter assays,MAVE,Multiplexed assay of variant effect,Personalized medicine},
+  file = {/Users/will/Zotero/storage/6SZKBKAH/Esposito et al. - 2019 - MaveDB an open-source platform to distribute and .pdf;/Users/will/Zotero/storage/558JQB6R/s13059-019-1845-6.html}
+}
+
+@article{fowlerAtlasVariantEffects2023,
+  title = {An {{Atlas}} of {{Variant Effects}} to Understand the Genome at Nucleotide Resolution},
+  author = {Fowler, Douglas M. and Adams, David J. and Gloyn, Anna L. and Hahn, William C. and Marks, Debora S. and Muffley, Lara A. and Neal, James T. and Roth, Frederick P. and Rubin, Alan F. and Starita, Lea M. and Hurles, Matthew E.},
+  year = {2023},
+  month = jul,
+  journal = {Genome Biology},
+  volume = {24},
+  number = {1},
+  pages = {147},
+  issn = {1474-760X},
+  doi = {10.1186/s13059-023-02986-x},
+  abstract = {Sequencing has revealed hundreds of millions of human genetic variants, and continued efforts will only add to this variant avalanche. Insufficient information exists to interpret the effects of most variants, limiting opportunities for precision medicine and comprehension of genome function. A solution lies in experimental assessment of the functional effect of variants, which can reveal their biological and clinical impact. However, variant effect assays have generally been undertaken reactively for individual variants only after and, in most cases long after, their first observation. Now, multiplexed assays of variant effect can characterise massive numbers of variants simultaneously, yielding variant effect maps that reveal the function of every possible single nucleotide change in a gene or regulatory element. Generating maps for every protein encoding gene and regulatory element in the human genome would create an 'Atlas' of variant effect maps and transform our understanding of genetics and usher in a new era of nucleotide-resolution functional knowledge of the genome. An Atlas would reveal the fundamental biology of the human genome, inform human evolution, empower the development and use of therapeutics and maximize the utility of genomics for diagnosing and treating disease. The Atlas of Variant Effects Alliance is an international collaborative group comprising hundreds of researchers, technologists and clinicians dedicated to realising an Atlas of Variant Effects to help deliver on the promise of genomics.},
+  langid = {english},
+  pmcid = {PMC10316620},
+  pmid = {37394429},
+  keywords = {Functional genomics,Genetic Variation,Genome interpretation,{Genome, Human},Genomics,Global alliance,High-Throughput Nucleotide Sequencing,Humans,Multiplexed assay of variant effect,Precision Medicine,Saturation mutagenesis,Variant effect},
+  file = {/Users/will/Zotero/storage/493P75CG/Fowler et al. - 2023 - An Atlas of Variant Effects to understand the geno.pdf}
+}
+
+@article{fowlerDeepMutationalScanning2014,
+  title = {Deep Mutational Scanning: A New Style of Protein Science},
+  shorttitle = {Deep Mutational Scanning},
+  author = {Fowler, Douglas M. and Fields, Stanley},
+  year = {2014},
+  month = aug,
+  journal = {Nature Methods},
+  volume = {11},
+  number = {8},
+  pages = {801--807},
+  issn = {1548-7105},
+  doi = {10.1038/nmeth.3027},
+  abstract = {Mutagenesis provides insight into proteins, but only recently have assays that couple genotype to phenotype been used to assess the activities of as many as 1 million mutant versions of a protein in a single experiment. This approach-'deep mutational scanning'-yields large-scale data sets that can reveal intrinsic protein properties, protein behavior within cells and the consequences of human genetic variation. Deep mutational scanning is transforming the study of proteins, but many challenges must be tackled for it to fulfill its promise.},
+  langid = {english},
+  pmcid = {PMC4410700},
+  pmid = {25075907},
+  keywords = {Genetic Variation,Humans,Mutation,Protein Engineering,Proteins},
+  file = {/Users/will/Zotero/storage/NM3KM8L8/Fowler and Fields - 2014 - Deep mutational scanning a new style of protein s.pdf}
 }
 
 @article{hiltonDmsviewInteractiveVisualization2020,
@@ -66,25 +123,45 @@ @article{hiltonDmsviewInteractiveVisualization2020
   langid = {english},
   pmcid = {PMC8237788},
   pmid = {34189395},
-  file = {/Users/will/Zotero/storage/5UVNCHTV/Hilton et al. - 2020 - dms-view Interactive visualization tool for deep .pdf}
+  file = {/Users/will/Zotero/storage/JVH8BCLB/Hilton et al. - 2020 - dms-view Interactive visualization tool for deep .pdf}
 }
 
 @misc{liDeepMutationalScanning2023,
   title = {Deep Mutational Scanning Reveals the Functional Constraints and Evolutionary Potential of the Influenza {{A}} Virus {{PB1}} Protein},
-  author = {Li, Yuan and Arcos, Sarah and Sabsay, Kimberly R. and te Velthuis, Aartjan J. W. and Lauring, Adam S.},
+  author = {Li, Yuan and Arcos, Sarah and Sabsay, Kimberly R. and {te Velthuis}, Aartjan J. W. and Lauring, Adam S.},
   year = {2023},
   month = aug,
-  primaryclass = {New Results},
+  eprintclass = {New Results},
   pages = {2023.08.27.554986},
   publisher = {{bioRxiv}},
   doi = {10.1101/2023.08.27.554986},
   urldate = {2023-10-14},
   abstract = {The influenza virus polymerase is central to influenza virus evolution. Adaptive mutations within the polymerase are often a prerequisite for efficient spread of novel animal-derived viruses in human populations. The polymerase also determines fidelity, and therefore the rate at which the virus will acquire mutations that lead to host range expansion, drug resistance, or antigenic drift. Despite its importance to viral replication and evolution, our understanding of the mutational effects and associated constraints on the influenza RNA-dependent RNA polymerase (RdRp) is relatively limited. We performed deep mutational scanning of the A/WSN/1933(H1N1) PB1, generating a library of 95.4\% of amino acid substitutions at 757 sites. After accuracy filters, we were able to measure replicative fitness for 13,354 (84\%) of all possible amino acid substitutions, and 16 were validated by results from pairwise competition assays. Functional and structural constraints were better revealed by individual sites involved in RNA or protein interactions than by major subdomains defined by sequence conservation. Mutational tolerance, as defined by site entropy, was correlated with evolutionary potential, as captured by diversity in available H1N1 sequences. Of 29 beneficial sites, many have either been identified in the natural evolution of PB1 or shown experimentally to have important impacts on replication and adaptation. Accessibility of amino acid substitutions by single nucleotide mutation was a key factor in determining whether mutations appeared in natural PB1 evolution. Our work provides a comprehensive map of mutational effects on a viral RdRp and a valuable resource for subsequent studies of influenza replication and evolution.},
   archiveprefix = {bioRxiv},
   chapter = {New Results},
-  copyright = {\textcopyright{} 2023, Posted by Cold Spring Harbor Laboratory. This pre-print is available under a Creative Commons License (Attribution-NonCommercial-NoDerivs 4.0 International), CC BY-NC-ND 4.0, as described at http://creativecommons.org/licenses/by-nc-nd/4.0/},
+  copyright = {{\textcopyright} 2023, Posted by Cold Spring Harbor Laboratory. This pre-print is available under a Creative Commons License (Attribution-NonCommercial-NoDerivs 4.0 International), CC BY-NC-ND 4.0, as described at http://creativecommons.org/licenses/by-nc-nd/4.0/},
+  langid = {english},
+  file = {/Users/will/Zotero/storage/S68YYPN6/Li et al. - 2023 - Deep mutational scanning reveals the functional co.pdf}
+}
+
+@article{matreyekMultiplexAssessmentProtein2018,
+  title = {Multiplex Assessment of Protein Variant Abundance by Massively Parallel Sequencing},
+  author = {Matreyek, Kenneth A. and Starita, Lea M. and Stephany, Jason J. and Martin, Beth and Chiasson, Melissa A. and Gray, Vanessa E. and Kircher, Martin and Khechaduri, Arineh and Dines, Jennifer N. and Hause, Ronald J. and Bhatia, Smita and Evans, William E. and Relling, Mary V. and Yang, Wenjian and Shendure, Jay and Fowler, Douglas M.},
+  year = {2018},
+  month = jun,
+  journal = {Nature Genetics},
+  volume = {50},
+  number = {6},
+  pages = {874--882},
+  publisher = {{Nature Publishing Group}},
+  issn = {1546-1718},
+  doi = {10.1038/s41588-018-0122-z},
+  urldate = {2024-05-15},
+  abstract = {Determining the pathogenicity of genetic variants is a critical challenge, and functional assessment is often the only option. Experimentally characterizing millions of possible missense variants in thousands of clinically important genes requires generalizable, scalable assays. We describe variant abundance by massively parallel sequencing (VAMP-seq), which measures the effects of thousands of missense variants of a protein on intracellular abundance simultaneously. We apply VAMP-seq to quantify the abundance of 7,801 single-amino-acid variants of PTEN and TPMT, proteins in which functional variants are clinically actionable. We identify 1,138 PTEN and 777 TPMT variants that result in low protein abundance, and may be pathogenic or alter drug metabolism, respectively. We observe selection for low-abundance PTEN variants in cancer, and show that p.Pro38Ser, which accounts for {\textasciitilde}10\% of PTEN missense variants in melanoma, functions via a dominant-negative mechanism. Finally, we demonstrate that VAMP-seq is applicable to other genes, highlighting its generalizability.},
+  copyright = {2018 The Author(s)},
   langid = {english},
-  file = {/Users/will/Zotero/storage/XKGTYKHM/Li et al. - 2023 - Deep mutational scanning reveals the functional co.pdf}
+  keywords = {Medical genetics,Mutagenesis,Pharmacogenomics},
+  file = {/Users/will/Zotero/storage/7PINB29L/Matreyek et al. - 2018 - Multiplex assessment of protein variant abundance .pdf}
 }
 
 @article{radfordMappingNeutralizingSpecificity2023,
@@ -102,12 +179,12 @@ @article{radfordMappingNeutralizingSpecificity2023
   langid = {english},
   pmcid = {PMC10351223},
   pmid = {37327779},
-  keywords = {1\textendash 18,{Antibodies, Monoclonal},{Antibodies, Neutralizing},CD4 binding site,deep mutational scanning,{env Gene Products, Human Immunodeficiency Virus},Epitopes,HIV,HIV Antibodies,HIV envelope,HIV Envelope Protein gp120,HIV Infections,HIV-1,Humans,Mutation,mutational antigenic profiling,N276 glycan},
-  file = {/Users/will/Zotero/storage/E8CM5IYU/Radford et al. - 2023 - Mapping the neutralizing specificity of human anti.pdf}
+  keywords = {1{\textendash}18,{Antibodies, Monoclonal},{Antibodies, Neutralizing},CD4 binding site,deep mutational scanning,{env Gene Products, Human Immunodeficiency Virus},Epitopes,HIV,HIV Antibodies,HIV envelope,HIV Envelope Protein gp120,HIV Infections,HIV-1,Humans,Mutation,mutational antigenic profiling,N276 glycan},
+  file = {/Users/will/Zotero/storage/SEXNM9L4/Radford et al. - 2023 - Mapping the neutralizing specificity of human anti.pdf}
 }
 
 @article{roseNGLViewerWebbased2018,
-  title = {{{NGL}} Viewer: Web-Based Molecular Graphics for Large Complexes},
+  title = {{{NGL}} Viewer: {{Web-based}} Molecular Graphics for Large Complexes},
   shorttitle = {{{NGL}} Viewer},
   author = {Rose, Alexander S. and Bradley, Anthony R. and Valasatava, Yana and Duarte, Jose M. and Prlic, Andreas and Rose, Peter W.},
   year = {2018},
@@ -123,7 +200,7 @@ @article{roseNGLViewerWebbased2018
   pmcid = {PMC6198858},
   pmid = {29850778},
   keywords = {Computer Graphics,Internet,Macromolecular Substances,Software},
-  file = {/Users/will/Zotero/storage/SPF3FIGU/Rose et al. - 2018 - NGL viewer web-based molecular graphics for large.pdf}
+  file = {/Users/will/Zotero/storage/5UPL6NQ5/Rose et al. - 2018 - NGL viewer web-based molecular graphics for large.pdf}
 }
 
 @article{starrDeepMutationalScanning2020,
@@ -142,7 +219,7 @@ @article{starrDeepMutationalScanning2020
   pmcid = {PMC7418704},
   pmid = {32841599},
   keywords = {ACE2,Angiotensin-Converting Enzyme 2,Binding Sites,deep mutational scanning,HEK293 Cells,Humans,Molecular Docking Simulation,Mutation,Peptidyl-Dipeptidase A,Phenotype,Protein Binding,Protein Folding,receptor-binding domain,Saccharomyces cerevisiae,SARS-CoV-2,{Spike Glycoprotein, Coronavirus}},
-  file = {/Users/will/Zotero/storage/D5JYKJYB/Starr et al. - 2020 - Deep Mutational Scanning of SARS-CoV-2 Receptor Bi.pdf}
+  file = {/Users/will/Zotero/storage/L2RAWF6V/Starr et al. - 2020 - Deep Mutational Scanning of SARS-CoV-2 Receptor Bi.pdf}
 }
 
 @article{starrProspectiveMappingViral2021,
@@ -161,7 +238,7 @@ @article{starrProspectiveMappingViral2021
   pmcid = {PMC7963219},
   pmid = {33495308},
   keywords = {Amino Acid Substitution,Angiotensin-Converting Enzyme 2,{Antibodies, Monoclonal, Humanized},{Antibodies, Viral},{Cells, Cultured},COVID-19,COVID-19 Serotherapy,Drug Combinations,Humans,{Immunization, Passive},Mutation,Protein Binding,Protein Domains,{Receptors, Coronavirus},SARS-CoV-2,{Spike Glycoprotein, Coronavirus}},
-  file = {/Users/will/Zotero/storage/R9R2T8ED/Starr et al. - 2021 - Prospective mapping of viral mutations that escape.pdf}
+  file = {/Users/will/Zotero/storage/8DIJYPGC/Starr et al. - 2021 - Prospective mapping of viral mutations that escape.pdf}
 }
 
 @article{yuBiophysicalModelViral2022,
@@ -179,5 +256,5 @@ @article{yuBiophysicalModelViral2022
   pmcid = {PMC9793855},
   pmid = {36582502},
   keywords = {antibody epitope,biophysical model,deep mutational scanning,epistasis,viral escape},
-  file = {/Users/will/Zotero/storage/6BW92S8Q/Yu et al. - 2022 - A biophysical model of viral escape from polyclona.pdf}
+  file = {/Users/will/Zotero/storage/3ZGVVB9T/Yu et al. - 2022 - A biophysical model of viral escape from polyclona.pdf}
 }