├── README.md ├── variant_counts.py ├── LICENSE └── maverefs.tsv /README.md: -------------------------------------------------------------------------------- 1 | # MaveReferences 2 | Welcome to our table of Multiplexed Assay of Variant Effect (MAVE) studies. 3 | To cite this document, please use the citation details for [MaveDB](https://www.mavedb.org/). 4 | 5 | Please click on the `maverefs.tsv` file in the repository file list to view the table in your browser. 6 | 7 | To calculate the total number of mutations scanned per year, run `variant_counts.py`. 8 | This requires [pandas](https://pandas.pydata.org/). 9 | 10 | ## Updating the table 11 | To add or edit a study: 12 | 1. [Fork this repository](https://help.github.com/en/github/getting-started-with-github/fork-a-repo) and create a local clone. 13 | 1. Open `maverefs.tsv` in a spreadsheet program and make your changes. 14 | 1. Save `maverefs.tsv`, making sure it remains a tab-separated text file. 15 | 1. Commit your changes and [please submit a pull request](https://help.github.com/en/github/collaborating-with-issues-and-pull-requests/creating-a-pull-request)! 16 | 17 | You can also submit changes using the [GitHub issue tracker](https://github.com/VariantEffect/MaveReferences/issues). 18 | -------------------------------------------------------------------------------- /variant_counts.py: -------------------------------------------------------------------------------- 1 | # Simple script to calculate the number of variants per year 2 | 3 | import sys 4 | import pandas as pd 5 | 6 | 7 | def get_total(s): 8 | """Convert a semicolon-separated list of integers into the sum of that list. 9 | 10 | Helper function for multi-target papers. 11 | 12 | Returns the integer if only one value is present. 13 | 14 | Returns 0 if the value of s is None or NA. 15 | """ 16 | if s is None or pd.isna(s): 17 | return 0 18 | elif ";" in s: 19 | return sum(int(x) for x in s.split(";")) 20 | else: 21 | return int(s) 22 | 23 | 24 | if __name__ == "__main__": 25 | # read the table 26 | if len(sys.argv) > 1: 27 | infile = sys.argv[1] 28 | else: 29 | infile = "maverefs.tsv" 30 | df = pd.read_csv(infile, sep="\t") 31 | 32 | # calculate and store the number of variants per paper 33 | # keep the maximum of nt and aa variant counts if both are specified 34 | df["Variants (max)"] = 0 35 | for i, r in df.iterrows(): 36 | df.loc[i, "Variants (max)"] = max( 37 | get_total(r["Variants (nt)"]), get_total(r["Variants (aa)"]) 38 | ) 39 | 40 | # calculate the sum of variants for each year 41 | result = df.groupby("Year")["Variants (max)"].sum() 42 | result.index = [ 43 | int(x) for x in result.index 44 | ] # convert years to ints instead of float 45 | result.index.name = "year" 46 | result.name = "variants" 47 | result = pd.DataFrame(result) 48 | result["cumulative_variants"] = result["variants"].cumsum() 49 | 50 | # write the result to stdout 51 | result.to_csv(sys.stdout) 52 | -------------------------------------------------------------------------------- /LICENSE: -------------------------------------------------------------------------------- 1 | Attribution 4.0 International 2 | 3 | ======================================================================= 4 | 5 | Creative Commons Corporation ("Creative Commons") is not a law firm and 6 | does not provide legal services or legal advice. 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For 392 | the avoidance of doubt, this paragraph does not form part of the 393 | public licenses. 394 | 395 | Creative Commons may be contacted at creativecommons.org. 396 | -------------------------------------------------------------------------------- /maverefs.tsv: -------------------------------------------------------------------------------- 1 | PMID Journal DOI Preprint DOI First Author Year Type Target Molecule Target Molecule Size (bp) Variants (nt) Variants (aa) Sequence Origin Assay System Assay Type Mutagenesis Type Sequencing Platform Raw Data Scores in Table MaveDB URN 2 | 18045863 10.1074/jbc.M708536200 Barthelemy 2008 DMS VH domain 180 Human Phage Binding NNS PCR Illumina 3 | 19915551 10.1038/nbt.1589 Patwardhan 2009 MPRA T3 promoter;T7 promoter;SP6 promoter;CMV promoter;HBB promoter;S100A4 promoter 12972 in vitro Transcription microarray synthesis Illumina SRP001721 TXT 4 | 20363230 10.1016/j.jmb.2010.03.058 Dutta 2010 DMS BH3 170 Human Yeast Binding 5 | 20439748 10.1073/pnas.1004290107 Kinney 2010 MPRA lac promoter 220591 E.coli FACS doped oligo synthesis Roche 454 SRA012345 No 6 | 20711194 10.1038/nmeth.1492 Fowler 2010 DMS WW domain 102 362000 human Phage Binding doped oligo synthesis Illumina SRP002725 No urn:mavedb:00000002 7 | 20714644 10.1039/c0mb00061b Ernst 2010 DMS Synthetic PDZ domain 26566 Phage Binding Kunkel Roche 454 No No 8 | 21464309 10.1073/pnas.1016024108 Hietpas 2011 DMS Hsp90 27 200 yeast Yeast Growth NNN PCR Illumina No TXT urn:mavedb:00000011 9 | 21825149 10.1073/pnas.1111218108 Zhang 2011 DMS IgG Human Phage Binding Combinatorial Roche 454 No No 10 | 22325784 10.1016/j.str.2011.11.021 Adkar 2012 DMS Ccdb 306 1176 E. coli E.coli toxin activity PCR with specific codons Roche 454 No XLS urn:mavedb:00000084 11 | 22371081 10.1038/nbt.2136 Patwardhan 2012 MPRA ALDOB enhancer;ECR11 enhancer;LTV1 enhancer 259;620;302 33411;191890;45499 human mouse liver Transcription doped oligo synthesis Illumina SRA049159 TXT urn:mavedb:00000006;urn:mavedb:00000007;urn:mavedb:00000008 12 | 22371084 10.1038/nbt.2137 Melnikov 2012 MPRA cAMP-regulated enhancer;interferon-B enhancer 27000 Human cell culture (HEK239T) Transcription in silico design and synthesis Illumina GSE31982 XLS 13 | 22609971 10.1038/nbt.2205 Sharon 2012 MPRA designed promoters 6500 Yeast Fluorescence;Transcription microarray synthesis Illumina No No 14 | 22634563 10.1038/nbt.2214 Whitehead 2012 DMS Designed influenza binder 1053; 1013 Yeast FACS synthesized Illumina No No 15 | 22665811 10.1073/pnas.1202107109 Schlinkmann 2012 DMS Neurotensin receptor 1 GPCR 6897 Human E.coli FACS NNN PCR Roche 454 No No 16 | 22846908 10.1016/j.jmb.2012.07.017 Traxlmayr 2012 DMS IgG 318 human Yeast FACS error-prone PCR Roche 454 No No urn:mavedb:00000072 17 | 23017428 10.1016/j.jmb.2012.09.014 Deng 2012 DMS TEM1 Beta-lactamase 4997 E.coli Amp resistance NNS Kunkel Roche 454 No XLS 18 | 23035249 10.1073/pnas.1209751109 Araya 2012 DMS WW domain Phage Binding doped oligo synthesis Illumina Yes No 19 | 23041932 10.1038/nature11500 McLaughlin 2012 DMS PSD95 PDZ 249 1578 Human Bacteria Special NNS PCR Illumina No No urn:mavedb:00000090 20 | 23103372 10.1016/j.bbrc.2012.10.066 Fujino 2012 DMS Fab antibody fragment 950 in vitro Ribodisplay PCR with fragments Roche 454 No No 21 | 23152521 10.1128/JVI.01658-12 Wu 2012 DMS Neuraminidase Influenza Human/H1N1 Oseltamivir resistance error prone pcr Roche 454 No No 22 | 23241746 10.1101/gr.144659.112 Liachko 2012 MPRA Autonomously replicating sequences 22000 Yeast Growth doped oligo synthesis Illumina SRA051406 No 23 | 23287719 10.1126/science.1230161 Ernst 2013 DMS Ubiquitin Phage Binding site-directed mutagenesis with doped oligos ELISA No No 24 | 23376099 10.1016/j.jmb.2013.01.032 Roscoe 2013 DMS Ubiquitin 225 4800 1575 yeast Yeast Growth NNN PCR Illumina No XLS urn:mavedb:00000037 25 | 23509263 10.1073/pnas.1303309110 Starita 2013 DMS E4B 309 98299 human Phage Auto-ubiquitination doped oligo synthesis Illumina (barcoded and subassembly) No XLS urn:mavedb:00000004 26 | 23512712 10.1101/gr.144899.112 Kheradpour 2013 MPRA Regulatory motifs for HNF1;HNF4;FOXA;GATA;NFE2L2;GFI1;ZFP161 5418 Human cell culture (K562 and HepG2) Transcription microarray synthesis Illumina GSE33367 TXT 27 | 23625929 10.1074/jbc.M112.447326 Gold 2013 DMS PKA RII 460 Human Phage Binding doped oligo synthesis Illumina No No 28 | 23765106 10.4161/mabs.24979 Forsyth 2013 DMS IgG 1060 Human Human cells FACS NNK PCR Roche 454 No PDF 29 | 23818646 10.1073/pnas.1307449110 White 2013 MPRA Crx target sequences 777 Mouse retina Transcription microarray synthesis Illumina No TXT 30 | 23825969 10.1371/journal.pgen.1003600 Jiang 2013 DMS Hsp90 27 576 189 yeast Yeast Growth NNN PCR Illumina No XLS urn:mavedb:00000039 31 | 23827138 10.1016/j.jmb.2013.06.035 Procko 2013 DMS Designed protein binder 1060 Synthetic (designed) Yeast FACS site-directed mutagenesis and error-prone PCR Illumina No No 32 | 23878237 10.1073/pnas.1215206110 Jacquier 2013 DMS TEM1 Beta-lactamase 2893 E. coli E.coli Amoxicillin resistance single nucleotide random Sanger! No XLS 33 | 23892608 10.1038/ng.2713 Smith 2013 MPRA Synthetic liver enhancers 5000 mouse primary liver;human HepG2 cell line Transcription designed combinations of binding sites Illumina SRP018414 XLS 34 | 23897579 10.1074/mcp.O113.031708 Kim 2013 DMS Yeast degron 30000 S. cerevisiae Yeast Growth doped oligo synthesis Illumina No No 35 | 23921661 10.1101/gr.157891.113 Mogno 2013 MPRA Synthetic promoters 2534 Yeast Transcription Combinatorial Illumina No TXT 36 | 23924614 10.1073/pnas.1301301110 Kosuri 2013 MPRA Synthetic promoters and ribosome binding sites 12563 E.coli Transcription and translation designed combinations of binding sites Illumina No XLS 37 | 24005320 10.1038/nature12443 Tinberg 2013 DMS Designed digoxigenin binder 397 Yeast FACS doped oligo synthesis Illumina No PDF (Counts) 38 | 24064791 10.1261/rna.040709.113 Melamed 2013 DMS Pab1 225 110745 human Yeast Growth doped oligo synthesis Illumina No XLS urn:mavedb:00000010 39 | 24112705 10.1111/pcmr.12171 Wagenaar 2013 DMS BRAF V600E 357 1463 Human Human vemurafenib resistance NNN PCR Illumina No XLS (Partial) urn:mavedb:00000091 40 | 24204297 10.1371/journal.pgen.1003882 Rockah-Shmuel 2012 DMS M.HaeIII E.coli Indel read-through;activity error-prone PCR Illumina No No 41 | 24299404 10.1111/evo.12207 Hietpas 2013 DMS Hsp90 27 189 yeast Yeast Growth NNN PCR Illumina No XLS urn:mavedb:00000040 42 | 24381156 10.1073/pnas.1313605111 Strauch 2014 DMS Designed IgG Synthetic Yeast FACS error-prone PCR Illumina No No 43 | 24449856 10.1073/pnas.1319402111 Ostermaier 2014 DMS ARRB1 1209 403 403 human E. coli Binding PCR - Alanine scan n/a No XLS urn:mavedb:00000082 44 | 24567513 10.1093/molbev/msu081 Firnberg 2014 DMS TEM-1 BL 861 15167 e. coli Bacteria Growth PFunkel Roche 454 No XLS urn:mavedb:00000070 45 | 24603708 10.1371/journal.pgen.1004169 Liachko 2014 MPRA Autonomously replicating sequences 400 P. pastoris Yeast Growth doped oligo synthesis Illumina SRP031760 No 46 | 24633241 10.1038/nbt.2851 Zhao 2014 MPRA 3' UTR 2828 Human cell culture (BEAS-2B;Jurkat or WiDr cells) mRNA stability and protein level microarray synthesis Illumina SRX463338 XLS 47 | 24656821 10.1016/j.celrep.2014.03.001 Oikonomou 2014 MPRA 3' UTR 16332 Human cells (FlpIn293) FACS microarray synthesis Illumina GSE55396 XLS 48 | 24722365 10.1371/journal.ppat.1004064 Qi 2014 DMS NS4B 1806 Human cell culture (Huh-7.5.1) Growth NNK PCR Illumina No XLS 49 | 24820965 10.1038/srep04942 Wu 2014 DMS HA 5100 Influenza 50 | 24859245 10.1093/molbev/msu173 Bloom 2014 DMS influenza nucleoprotein 1494 9980 Influenza Human/H1N1 viral replication NNN PCR Illumina SRP036064 XLS urn:mavedb:00000087 51 | 24862281 10.1016/j.jmb.2014.05.019 Roscoe 2014 DMS Ubiquitin 27;225 yeast Yeast Binding NNN PCR Illumina No XLS urn:mavedb:00000038 52 | 24887409 10.1371/journal.pone.0097817 Shin 2014 DMS flavin mononucleotide binding fluorescent protein 4000 E.coli Fluorescence error-prone PCR Illumina (barcoded) PRJNA242983 XLS 53 | 24914046 10.1093/nar/gku511 Melnikov 2014 DMS APH(3')II 4993 E. coli Bacteria Growth microarray synthesis Illumina SRP042113 TXT 54 | 24965464 10.1128/JVI.01494-14 Wu 2014 DMS NS1 1021 Influenza HEK293T;A549 Growth;Drug Resistance Error prone PCR Illumina 55 | 25006036 10.7554/eLife.03300 Thyagarajan 2014 DMS Hemagglutinin 1692 1000 Influenza Influenza Growth NNN PCR Illumina SRP040983 TXT urn:mavedb:00000092 56 | 25030889 10.1101/gr.168773.113 Sharon 2014 MPRA designed promoters 6500 Yeast Fluorescence;Transcription ? Illumina GSE55346 TXT 57 | 25064858 10.1093/nar/gku689 Gajula 2014 DMS AID 384 Human E.coli Growth NNS PCR Illumina No PDF (Counts) 58 | 25085423 10.1101/gad.245936.114 Guy 2014 DMS tRNA 25491 Yeast FACS doped oligo synthesis Illumina No XLS 59 | 25141179 10.1038/nature13695 Findlay 2014 DMS DBR1 4096 Hap1 Growth CRISPR Illumina SRP044126 XLS 60 | 25170020 10.15252/msb.20145136 Noderer 2014 DMS Start codon efficiency 65536 Mammalian cell culture FACS degenrate PCR Illumina (barcoded) No TXT 61 | 25311858 10.1016/j.jmb.2014.09.025 Reich 2015 DMS BH3 1000 Human Yeast FACS ? Illumina No No 62 | 25371431 10.1093/molbev/msu301 Bank 2015 DMS Hsp90 1015 yeast Yeast Growth NNN PCR Illumina No No 63 | 25451031 10.1016/j.jmb.2014.10.024 Doolan 2015 DMS PrP 1341 Human Yeast FACS site-directed mutagenesis PacBio No No 64 | 25455030 10.1016/j.cub.2014.09.072 Olson 2014 DMS GB1 510747 Streptococcus spp mRNA display Binding NNK PCR Illumina No XLS 65 | 25522661 10.1186/s12977-014-0124-6 Al-Mawsawi 2014 DMS HIV genome 7314 HIV Growth error-prone PCR Illumina PRJNA259391 XLS 66 | 25559584 10.1038/nmeth.3223 Kitzman 2014 DMS Gal4 192 1320 yeast Yeast Growth PALS (array+PCR) Illumina (barcoded and subassembly) PRJNA268398 No urn:mavedb:00000012 67 | 25657251 10.1126/science.1257360 Podgornaia 2015 DMS PhoQ 160000 E. coli Bacteria FACS NNS PCR Illumina No No 68 | 25723163 10.1016/j.cell.2015.01.035 Stiffler 2015 DMS TEM1 B-lactamase 861 4997 E. coli E.coli Growth NNS PCR Illumina No XLS urn:mavedb:00000086 69 | 25823446 10.1534/genetics.115.175802 Starita 2015 DMS BRCA1 909 Yeast;Phage Growth;Binding microarray synthesis Illumina (barcoded and subassembly) No No* urn:mavedb:00000003 70 | 25875337 10.1371/journal.pgen.1005147 Shalem 2015 MPRA 3' UTR 13000 Yeast Fluorescence;Transcription microarray synthesis Illumina No XLS 71 | 26040002 10.1073/pnas.1422285112 Romero 2015 DMS Bgl2 3083 Streptomyces spp Bacteria/microfluidic droplets Activity error-prone PCR Illumina No No 72 | 26088137 10.1074/jbc.M115.662783 Koenig 2015 DMS IgG CDR 1092 Synthetic (antibody FAB) Phage Binding NNK PCR Illumina No No 73 | 26132554 10.1371/journal.pgen.1005310 Wu 2015 DMS Polymerase PA 5280 Influenza Growth error-prone PCR Illumina PRJNA254185 XLS 74 | 26170332 10.1073/pnas.1511328112 Kretz 2015 DMS VWF 219 1286 Phage Binding/cleavage doped oligo synthesis Illumina No XLS 75 | 26226986 10.1093/molbev/msv167 Doud 2015 DMS Nucleoproteins 1494 Influenza Influenza Growth NNN PCR Illumina SRP056028 TXT urn:mavedb:00000088 76 | 26274323 10.1371/journal.pcbi.1004421 Rockah-Shmuel 2015 DMS M.HaeIII 1957 H. aegyptus Bacteria Activity error-prone PCR Illumina No XLS 77 | 26296891 10.1074/jbc.M115.676635 Kowalsky 2015 DMS TNF;PTxS2;TROP2 738;531 3550;4400;4940 Human; B. pertussis; Human Yeast FACS PFunkel Illumina No TXT 78 | 26369947 10.1021/acssynbio.5b00131 Klesmith 2015 DMS LGK 8000 E.coli E.coli Growth PFunkel Illumina No No 79 | 26424794 10.1074/jbc.M115.684035 Mueller 2015 noncoding SMN1-7 54 Human HeLa Transcription (minigene) N PCR Illumina 80 | 26478181 10.1016/j.cell.2015.09.055 Aakre 2015 DMS ParD 8424 bacteria Bacteria Growth ProxiMax Illumina No No 81 | 26496609 10.1016/j.cell.2015.09.054 Rosenberg 2015 MPRA Splice sites 2000000 Synthetic (introns/mini-gene) HEK293 Isoform occurrence degenrate PCR Illumina GSE74070 No 82 | 26576614 10.1101/gr.193789.115 Shen 2016 MPRA Promoters and enhancers 45670 Mouse retina;mouse cortex Transcription capture of existing elements Illumina GSM1463994 XLS 83 | 26626484 10.1016/j.molcel.2015.10.029 Vvedenskaya 2015 MPRA Neuraminidase 16384 Bacteria Transcription MASTER Illumina SRP057850 XLS 84 | 26637602 10.1128/AEM.03074-15 Jin 2015 DMS ACD-1 Bacteria Growth doped oligo synthesis Roche 454 PRJEB11657 No 85 | 26656922 10.1016/j.jmb.2015.11.027 Jiang 2016 DMS neuraminidase (NA) 450 Influenza Growth NNN PCR Illumina PRJNA272490 XLS 86 | 26689263 10.1038/nmeth.3696 Taylor 2016 DMS lac repressor 6000 E. coli Bacteria Growth microarray synthesis Illumina GSE75009 No 87 | 26716404 10.7554/eLife.09532 Sahoo 2015 DMS CcdB;DgkA Bacteria Growth NNN PCR Roche 454 No No 88 | 26754751 10.1186/s12864-015-2358-7 Wu 2016 DMS M segment 1881 Influenza Growth error-prone PCR Illumina PRJNA285135 XLS 89 | 26779844 10.1002/pro.2881 Foight 2016 DMS CD40;TANK Bacteria FACS NNK PCR Illumina No No 90 | 26824389 10.7554/eLife.12125 Elazar 2016 DMS Transmembrane segment 69;72;45 800 e coli Bacteria Growth NNS PCR Illumina No XLS (Counts) urn:mavedb:00000051 91 | 26865697 10.1534/g3.116.027904 Hoggard 2016 MPRA Autonomously replicating sequences Yeast Growth doped oligo synthesis Illumina SRP065331 No 92 | 26936925 10.1534/genetics.116.188037 Rich 2016 MPRA SUL1 promoter 493 29906 yeast Yeast Growth error-prone PCR Illumina (barcoded and subassembly) PRJNA273419 XLS urn:mavedb:00000009 93 | 26941320 10.1126/science.aad6881 Winkelman 2016 MPRA TSS 1000000 E. coli Bacteria Transcription MASTER Illumina No No 94 | 27013733 10.1126/science.aad9195 Jardine 2016 DMS eOD-GT6 (immunogen) 1160 Syntehtic Yeast FACS NNK PCR Illumina No No 95 | 27068472 10.1016/j.celrep.2016.03.046 Mishra 2016 DMS Hsp90 696 12400 yeast Yeast Growth NNN PCR Illumina No XLS urn:mavedb:00000074 96 | 27080103 10.1126/science.aaf0965 Puchta 2016 DMS snoRNA U3 981 yeast inducible covering allele doped oligo synthesis Illumina (barcoded) GSE77709 TXT (Counts) 97 | 27080104 10.1126/science.aae0568 Li 2016 DMS tRNA(Arg-CCU) 65000 yeast yeast tRNA folding stability random single nucleotide Illumina PRJNA311172 No 98 | 27111525 10.7554/eLife.15802 Mavor 2016 DMS Ubiquitin 1475 yeast Yeast Growth NNN PCR Illumina (barcoded) SRR3194828 No 99 | 27147747 10.1128/JVI.00804-16 Salamango 2016 DMS env 2800 MLV 293FT Infection;Fusogenicity;Viral particle incorporation NNN PCR Illumina 100 | 27161764 10.1038/ncomms11558 Julien 2016 MPRA FAS/CD95 63 189 Human Human splicing commercial library cassete ligation collapsing read pairs PRJEB13140 XLS 101 | 27162333 10.1073/pnas.1603271113 Vvedenskaya 2016 MPRA TSS 16000 E. coli in vitro;E.coli Transcription MASTER Illumina SRP071742 No 102 | 27173379 10.1016/j.jmb.2016.04.033 Steinberg 2016 DMS TEM1 Beta-lactamase 858 12815 E. coli E.coli Amp resistance PFunkel Roche 454 No XLS urn:mavedb:00000085 103 | 27193686 10.1038/nature17995 Sarkisyan 2016 DMS GFP 714 56086 Bacteria Activity error-prone PCR Illumina PRJNA282342. TXT urn:mavedb:00000080 104 | 27259153 10.1016/j.cell.2016.04.027 Tewhey 2016 MPRA eQTL peaks 32373 Human cell lines (NA12878;NA19239;HepG22) Transcription microarray synthesis Illumina GSE75661 XLS 105 | 27259154 10.1016/j.cell.2016.04.048 Ulirsch 2016 MPRA GWAS peaks Human cell lines (K562) Transcription microarray synthesis Illumina No No 106 | 27271655 10.3390/v8060155 Doud 2016 DMS Hemagglutinin 10412 Influenza Growth NNN PCR Illumina PRJNA309339 TXT 107 | 27374328 10.1016/j.cell.2016.05.070 Gamble 2016 DMS GFP 35000 A. victoria Yeast FACS NNN/VNN PCR Illumina No No 108 | 27391790 10.7554/eLife.16965 Wu 2016 DMS GB1 160000 mRNA display Binding random single nucleotide Illumina PRJNA278685 XLS 109 | 27461281 10.1002/anie.201605470 Kobori 2016 DMS Self-cleaving ribozyme 10296 Oryza sativa Ribozyme Transcription (ribozyme cleavage) Oligo synthesis Illumina 110 | 27563054 10.1093/molbev/msw182 Tripathi 2016 DMS CcdB 1664 E. coli E.coli Growth NNK PCR Illumina No No 111 | 27681597 10.1074/jbc.M116.748681 Harris 2016 DMS TCR Synthetic (immunogen) Yeast FACS site-directed mutagenesis ? No No 112 | 27699856 10.1002/prot.25175 Kowalsky 2016 DMS dockerin 486;456 2970; 2778 C. thermocellum and C. cellulolyticum Yeast FACS NNN PCR Illumina No TXT urn:mavedb:00000077 113 | 27741319 10.1371/journal.pone.0164296 Gaiotto 2016 DMS HA 98 S. cerevisiae EBY100 Yeast Antibody binding error-prone PCR Illumina (barcoded) PRJEB15301 DOC 114 | 27749844 10.1038/ng.3700 Majithia 2016 DMS PPARG 1515 9595 Human Human cells FACS microarray synthesis Illumina No No 115 | 27760319 10.1016/j.celrep.2016.09.061 Brenan 2016 DMS Mapk1/Erk2 1080 6810 Human Human inhibitor resistance microarray synthesis Illumina No XLS 116 | 27820858 10.1371/journal.ppat.1005988 Duenas-Decamp 2016 DMS Env 380 HIV HIV Growth 117 | 27898685 10.1371/journal.pgen.1006321 Qiu 2016 DMS RNAPII trigger loop 600 yeast Yeast Growth site-directed mutagenesis Illumina PRJNA340979 No 118 | 27959955 10.1371/journal.ppat.1006114 Haddox 2016 DMS Env 10000 HIV Growth NNN PCR Illumina PRJNA320270 TXT 119 | 27974464 10.1074/jbc.M116.764225 van Rosmalen 2017 DMS Cyclic peptide 200 Synthetic (epitope) Yeast FACS site-directed mutagenesis Illumina No No 120 | 27984726 10.1016/j.cell.2016.11.031 Fernandes 2016 DMS Tat;Rev 12928 HIV Growth NNN PCR Illumina E-MTAB-5154 XLS 121 | 28007883 10.1534/genetics.116.196428 Keskin 2017 DMS Fis1p 81 520 yeast Yeast Growth site-directed mutagenesis Illumina 10.5061/dryad.j14r5 XLS (Counts) urn:mavedb:00000076 122 | 28009265 10.1016/j.cels.2016.11.004 Kelsic 2016 DMS infA 4599 Bacteria Growth MAGE amplicon E-MTAB-4020 TXT 123 | 28024160 10.1038/nmeth.4121 Yartseva 2017 MPRA mRNA stability Zebrafish Transcription selected RNA sequences Illumina SRP090954 No 124 | 28035901 10.7554/eLife.23156 Adams 2016 DMS scFV antibody Yeast Yeast display Cassette Ligation Illumina PRJNA344711 CSV 125 | 28057863 10.1073/pnas.1613231114 Koenig 2017 DMS IgG 4360 Human Phage Binding NNK PCR Illumina No No 126 | 28137873 10.1073/pnas.1621150114 Grossman 2017 MPRA natural and synthetic enhancers mouse Transcription microarray synthesis Illumina (barcoded) GSE84888 No 127 | 28196882 10.1073/pnas.1614437114 Klesmith 2017 DMS TEM-1 BL;LGK 12874 E. colo Yeast;Bacteria FACS;Growth NNN PCR Illumina No No 128 | 28204611 10.1093/nar/gkw942 Maricque 2017 MPRA genomic regions Human cells Transcription microarray synthesis Illumina No No 129 | 28212748 10.1016/j.molcel.2017.01.007 Levo 2017 MPRA yeast promoters 1600 Yeast Transcription microarray synthesis Illumina GSE92300 XLS 130 | 28262665 10.1038/ncomms14614 Chan 2017 DMS IGPS 5040 bacteria Yeast Growth NNN PCR Illumina No No 131 | 28288189 10.1371/journal.ppat.1006271 Doud 2017 DMS HA 10000 Influenza Antibody binding NNN PCR Illumina SAMN05789126 TXT 132 | 28335006 10.1093/nar/gkx183 Matreyek 2017 DMS GFP N-terminal codon 3 Human cell lines (HEK293T) FACS oligo synthesis Illumina (barcoded) SRP095490 TXT urn:mavedb:00000042 133 | 28346537 10.1371/journal.ppat.1006288 Ashenberg 2017 DMS NP 1494 Influenza Virus Growth NNN PCR Illumina SRP082554 TXT urn:mavedb:00000089 134 | 28579254 10.1016/j.chom.2017.05.003 Dingens 2017 DMS Env 12559 HIV Antibody binding NNN PCR Illumina (barcoded) SRA: SRX2548567-SRX2548579 TXT 135 | 28585537 10.1038/ncomms15695 Wrenbeck 2017 DMS amiE 42966 E.coli Growth Pfunkel Illumina PRJNA360623 TXT 136 | 28585908 10.1080/19420862.2017.1337618 Koenig 2017 DMS IgG heavy chain 640 Phage Binding NNK PCR Illumina (barcoded) No PDF 137 | 28618270 10.1016/j.chom.2017.05.011 Wu 2017 DMS HA RBS 15679 Human cells Growth NNK PCR amplicon PRJNA353496 XLS 138 | 28652265 10.1158/1541-7786.MCR-17-0245 Bhagavatula 2017 DMS TP53 synonymous 16916 Human HEK293T FACS doped oligo synthesis Illumina PRJNA384242 No 139 | 28686159 10.7554/eLife.27810 Bandaru 2017 DMS Ras 495 3119 human Bacteria activity NNS PCR Illumina No XLS urn:mavedb:00000057 140 | 28902834 10.1038/nature23902 Starr 2017 DMS ancestral RH 160000 Human (ancestrally reconstructed protein) Yeast FACS NNK PCR Illumina PRJNA362734 No 141 | 29039417 10.1038/nmeth.4464 Woodsmith 2017 DMS BBSome 2040 1036 yeast Y2H PALS (array+PCR) simple deep sequencing PRJNA407860 XLS 142 | 29078326 10.1073/pnas.1708268114 Ma 2017 DMS BCR-ABL 180 Human (ongenic fusion) Ba/F3 cells Growth CRISPR Illumina No No 143 | 29097404 10.1101/gr.224964.117 Cuperus 2017 MPRA 5' UTR 500000 Random sequence yeast Growth random oligos Illumina GSE104252 XLS 144 | 29203891 10.1038/s41598-017-17081-y Spencer 2017 DMS Cas9 4173 3248 S. pyogenes Bacteria Growth error-prone PCR Illumina SRP107783 XLS urn:mavedb:00000071 145 | 29225039 10.1016/j.molcel.2017.11.014 Rabani 2017 MPRA 3' UTR 85500 Zebrafish Transcript abundance known UTRs Illumina GSE106677 XLS 146 | 29242188 10.1101/gr.219683.116 Ke 2017 MPRA DHFR exon 1-5 51 5560 human HEK293 splicing microarray synthesis Illumina GSE105785 XLS urn:mavedb:00000083 147 | 29269382 10.15252/msb.20177908 Weile 2017 DMS UBE2I;SUMO1;TPK1;CALM1-3 477;306;585;450 13000 human yeast complementation popcode Barseq+TileSeq (Illumina) PRJNA390305 TXT urn:mavedb:00000001 148 | 29301959 10.1126/science.aao5167 Plesa 2018 DMS PPAT 1152 E.coli Growth ortholog synthesis Illumina SRP126669 XLS 149 | 29410437 10.1038/s41467-018-02980-z Vainberg Slutskin 2018 MPRA microRNA 14000 Synthetic K562 FACS microarray synthesis Illumina SRP128656 No 150 | 29466705 10.1016/j.jmb.2018.02.009 Canale 2018 DMS HA 254 Human/infulenza viral replication ? Illumina No XLS (Counts) 151 | 29525204 10.1016/j.cels.2018.01.015 Staller 2018 DMS Gcn4 132;132 6340 yeast Yeast FACS microarray synthesis Illumina 10.17632/rbfr6m4733.1 TXT urn:mavedb:00000052 152 | 29590010 10.7554/eLife.34420 Haddox 2018 DMS Env 28080 HIV (two different variants) Human/HIV viral replication NNN PCR Illumina (barcoded) PRJNA371844;PRJNA412552 CSV (Counts) 153 | 29638215 10.7554/eLife.32472 Diss 2018 DMS AP-1 96;96 120000 Yeast Growth doped oligo synthesis Illumina GSE102901 XLS 154 | 29643335 10.1038/s41467-018-03783-y Hartman 2018 DMS MS2 phage capsid 2580 Phage MS2 SyMAPS NNN PCR Illumina No XLS 155 | 29643370 10.1038/s41467-018-03665-3 Doud 2018 DMS H1 hemaglutinin 10735 Influenza Growth NNN PCR Illumina SAMN05789126 TXT 156 | 29663315 10.1002/bit.26706 Medina-Cucurella 2018 DMS canine nerve growth factor 1737 Yeast Antibody binding by FACS Pfunkel Illumina SRA (SAMN07693504-SAMN07693526) TSV 157 | 29678950 10.4049/jimmunol.1800343 Heredia 2018 DMS CXCR4;CCR5 1053;1053 7000 human Expi293F FACS;Binding ? Illumina GSE100368 XLS urn:mavedb:00000047;urn:mavedb:00000048 158 | 29706350 10.1016/j.ajhg.2018.03.018 Mighell 2018 DMS PTEN 1212 7244 human Yeast lipid phosphatase activity MITE Illumina SRP134135 XLS urn:mavedb:00000054 159 | 29728462 10.1073/pnas.1722055115 Belliveau 2018 MPRA lacZYA;relBE;marRAB;yebG;purT;xylE;dgoRKADT promoters E. coli E.coli FACS Cassette Ligation Illumina SRP121362 CSV 160 | 29785012 10.1038/s41588-018-0122-z Matreyek 2018 DMS PTEN;TPMT 1212;738 7801 human human Protein stability inverse PCR Illumina (barcoded and subassembly) PRJNA428380 XLS urn:mavedb:00000013 161 | 29813059 10.1371/journal.pgen.1007419 Dandage 2018 DMS GmR 2000 E.coli Gentamicin resistance NNK PCR Illumina (barcoded) PRJNA384918 XLS 162 | 29912470 10.1093/nar/gky255 Atkinson 2018 DMS adenylate kinase Not a DMS E.coli activity Transposon mutagenesis (not substitution) Illumina SRR6327683;SRR6327684 No 163 | 29931269 10.1093/nar/gky550 Mason 2018 DMS CDR 14842 PnP hybridoma cells FACS CRISPR Illumina No No 164 | 29975771 10.1371/journal.ppat.1007159 Dingens 2018 DMS env 12730 HIV-1 SupT1.CCR5 Antibody escape NNN PCR Ilumina 165 | 29979580 10.1021/acssynbio.8b00121 Scott 2018 DMS tetracycline inactivating enzyme 7400 E. Coli Yeast Tetracycline resistance error-prone PCR Illumina No No 166 | 29979965 10.1016/j.molcel.2018.06.012 Kotler 2018 DMS TP53 573 3874 human HEK293T Growth microarray synthesis Illumina GSE115072 XLS urn:mavedb:00000059 167 | 30012625 10.1073/pnas.1803598115 Cantor 2018 DMS EGFR 2600 Human E.coli FACS NNS PCR Illumina No No 168 | 30024376 10.7554/eLife.34300 Salinas 2018 DMS PDZ 57549 Human Bacteria activity NNS PCR Illumina No No 169 | 30037883 10.1242/bio.036103 Mavor 2018 DMS Ubiquitin 1520 Yeast Yeast Growth NNN PCR Illumina (barcoded) SRP070953 No 170 | 30068600 10.1073/pnas.1805882115 Dorrity 2018 DMS Ste12 20000 Yeast Yeast Mating/Invasion doped oligo synthesis Illumina PRJNA379449 XLS 171 | 30078555 10.1016/j.stemcr.2018.07.002 Veerapandian 2018 DMS Sox17;Sox2 8000 Mouse OG2-MEF FACS NNK PCR Illumina 172 | 30079747 10.1164/rccm.201802-0337OC Castaldi 2019 MPRA FAM13A locus 45 Human human; cell line Transcription microarray synthesis Illumina No No 173 | 30104379 10.1073/pnas.1806133115 Lee 2018 DMS HA 10754 Virus Growth NNN PCR Illumina SAMN08102609;SAMN08102610 TXT 174 | 30120239 10.1038/s41467-018-05748-7 Braun 2018 noncoding RON exon 11 680 5200 Human HEK293T Transcription (minigene splicing) Error prone PCR Illumina (barcoded) 175 | 30174293 10.1016/j.molcel.2018.07.033 Wong 2018 MPRA Splice sites 32768 HeLa Transcription ? Illumina SRP135892 No 176 | 30188321 10.7554/eLife.38795 Phillips 2018 DMS HA 36790 Influenza Growth NNN PCR Illumina SRP149672 TXT 177 | 30209399 10.1038/s41586-018-0461-z Findlay 2018 DMS BRCA1 647 3893 Human HAP1 Growth microarray synthesis + CRISPR Illumina No XLS urn:mavedb:00000097 178 | 30219179 10.1016/j.ajhg.2018.07.016 Starita 2018 DMS BRCA1 5589 1056 human human DNA-repair assay NNK PCR Illumina GSE116427 XLS urn:mavedb:00000081 179 | 30224458 10.1073/pnas.1811993115 Blaesi 2018 DMS RNR 380 Bacteria Bacteria Growth NNS PCR Illumina No No 180 | 30224644 10.1038/s41588-018-0204-y Giacomelli 2018 DMS TP53 1182 25217 human human Growth microarray synthesis Illumina No XLS urn:mavedb:00000068 181 | 30227960 10.1016/j.isci.2018.02.005 Gong 2018 DMS env 3849 Zika C6/36;A549;hCMEC/D3 Growth Error prone PCR Illumina 182 | 30258049 10.1038/s41467-018-06403-x Naftaly 2018 DMS APPI 340 Human Yeast FACS NNS PCR Illumina No No 183 | 30478237 10.15252/msb.20188371 Bassalo 2018 DMS Lysine metabolic pathway 16300 Bacteria Growth microarray synthesis Illumina No XLS 184 | 30503770 10.1016/j.molcel.2018.10.037 Cheung 2019 MPRA Splice sites 2198 Human human cells FACS microarray synthesis Illumina GSE120695 No 185 | 30709739 10.1016/j.immuni.2018.12.017 Dingens 2019 DMS Env HIV HIV Antibody binding NNN PCR Illumina (barcoded) SRP15794;PRJNA486029 CSV 186 | 30716072 10.1371/journal.pcbi.1006226 Barnes 2019 MPRA LacI binding site E.coli FACS Cassette Ligation Illumina SRP146291 CSV 187 | 30721031 10.1021/acssynbio.8b00486 Wrenbeck 2019 DMS pyrrolidine ketide synthase;levoglucosan kinase 1143 E.coli VAMP-seq NNN;NNK PCR Illumina SUB4818031 CSV urn:mavedb:00000079 188 | 30723160 10.1074/jbc.RA118.006173 Park 2020 DMS T1R2 16300 Expi293F FACS;surface expression error-prone PCR Illumina GSE115751 XLS 189 | 30761651 10.1002/jmr.2778 Wollacott 2019 DMS Proliferation-inducing ligand 144 960 Human Yeast Binding by FACS NNK PCR Illumina No No 190 | 30778069 10.1038/s41467-019-08777-y Michaels 2019 MPRA microRNA HEK293T polysome profiling degenerate oligos Illumina PRJNA516224 No 191 | 30886357 10.1038/s41564-019-0399-4 Setoh 2019 DMS Zika envelope 3827 Zika Zika viral replication NNN PCR Illumina (barcoded) PRJNA449413 CSV 192 | 30894475 10.1128/JVI.00219-19 Heredia 2019 DMS Env 16332 HIV-1B Expi293F Binding by FACS overlap extension PCR Illumina (barcoded) GSE102276;GSE117328;GSE126136 XLS 193 | 30908907 10.1021/acssynbio.8b00529 McGeachy 2019 DMS RPL28 270000 Yeast Yeast 194 | 30936490 10.1038/s41564-019-0412-y Noda-Garcia 2019 DMS GDH (GudB) 269 Bacillus subtilis Bacillus subtilis Growth NNS PCR Illumina No XLS 195 | 30956043 10.1016/j.molcel.2019.02.003 Ahler 2019 DMS Src 54;750 3506 human Yeast Growth NNK PCR Illumina (barcoded and subassembly) GSE114098 XLS urn:mavedb:00000041 196 | 30969963 10.1371/journal.pgen.1008079 Pokusaeva 2019 DMS IGPD 48198 Yeast Growth ? Illumina GSE99990 TXT 197 | 30977563 10.1002/humu.23762 Wan 2019 DMS rhodopsin 1047 210 Human HEK293T FACS;surface expression site-directed mutagenesis Illumina No XLS urn:mavedb:00000099 198 | 31019050 10.1128/JVI.00161-19 Hom 2019 DMS matrix protein 5040 Influenza Human/influenza A viral replication NNN PCR Illumina (barcoded) SRP144482 CSV 199 | 31034887 10.1016/j.jmb.2019.04.030 Gonzalez 2019 DMS TEM-1 861 4737 XLSX urn:mavedb:00000100 200 | 31038123 10.7554/eLife.45079 Soh 2019 DMS PB2 15180 Influenza Influenza viral replication NNN PCR Illumina (barcoded) PRJNA511556 CSV 201 | 31081325 10.1021/acssynbio.9b00104 Nikoomanzar 2019 DMS Kod DNA polymerase 940 T kodakarensis E.coli activity by DrOPS site-directed mutagenesis Illumina No No 202 | 31096572 10.3390/v11050439 Dingens 2019 DMS env 12730 HIV-1 Growth 203 | 31242389 10.1021/acs.molpharmaceut.9b00418 Klesmith 2019 DMS CD19 816 Synthetic Yeast Binding by FACS NNK PCR Illumina No No 204 | 31267113 10.1038/s41587-019-0164-5 Sample 2019 MPRA 5' UTR 280000 Random human cells polysome profiling random bases Illumina GSE114002 No 205 | 31325330 10.1002/prot.25786 Warszawski 2020 DMS basigin 405 970 Yeast Binding;expression NNS PCR Illumina (barcoded) No XLS 206 | 31371509 10.1073/pnas.1903888116 Nisthal 2019 DMS GB1 1064 Streptococcus 207 | 31395785 10.1126/science.aax3649 Boettcher 2019 DMS TP53 7893 Human K562;MOLM13 No No 208 | 31395865 10.1038/s41467-019-11526-w Kircher 2019 MPRA Multiple mammalian promoters and enhancers 600;303;600;385;187;274;285;451;601;318;591;600;463;470;470;600;600;601;600;259;259;259;259;591;579;486;486 30000 human multiple cell lines Transcription error-prone PCR Illumina GSE126550 TXT urn:mavedb:00000014;urn:mavedb:00000015;urn:mavedb:00000016;urn:mavedb:00000017;urn:mavedb:00000018;urn:mavedb:00000019;urn:mavedb:00000020;urn:mavedb:00000021;urn:mavedb:00000022;urn:mavedb:00000023;urn:mavedb:00000024;urn:mavedb:00000025;urn:mavedb:00000026;urn:mavedb:00000027;urn:mavedb:00000028;urn:mavedb:00000029;urn:mavedb:00000030;urn:mavedb:00000031;urn:mavedb:00000032;urn:mavedb:00000033;urn:mavedb:00000034 209 | 31400199 10.1093/molbev/msz184 Faber 2019 DMS AmiE 6407;6791 Pseudomonas aeruginosa E.coli Growth Pfunkel Illumina (barcoded) SRA SAMN11258744-SAMN11258771 XLS 210 | 31442220 10.1371/journal.pcbi.1007207 Warszawski 2019 DMS IgG Fv targeting lysozyme 8505 Human Yeast Binding;expression NNS PCR Illumina (barcoded) https://www.addgene.org/110212/ XLS 211 | 31452511 10.7554/eLife.49324 Lee 2019 DMS HA Antibody escape 212 | 31467279 10.1038/s41467-019-11735-3 Li 2019 DMS CI 531 213 | 31511387 10.1128/JVI.01291-19 Sourisseau 2019 DMS Zika envelope 1512 9576 Zika Human/Zika viral replication NNN PCR Illumina (barcoded) PRJNA530795 XLS urn:mavedb:00000075 214 | 31519910 10.1038/s41467-019-12101-z Bolognesi 2019 DMS TDP-43 1242 57996 human Yeast Toxicity doped oligo synthesis Illumina No urn:mavedb:00000060 215 | 31530582 10.1101/gr.247312.118 Vainberg Slutskin 2019 MPRA PAS (poly-adenylation site) 12339 HIV1;SVL K562 Expression 216 | 31558564 10.1534/g3.119.400535 Gray 2019 DMS amyloid beta 42 126 791 human Yeast Growth NNK PCR Illumina GSE139122 TSV urn:mavedb:00000058 217 | 31609039 10.15252/embj.2019102145 Kennouche 2019 DMS PilE 1147 Neisseria meningitidis 218 | 31665623 10.1016/j.celrep.2019.09.057 Salamango 2019 DMS HIV-1 Vif 3400 HIV Human cells Enzymatic activity error-prone PCR Illumina E-MTAB-8357 No 219 | 31666291 10.1534/genetics.119.302601 Adney 2019 DMS LINE-1 538 Human 220 | 31697803 10.1182/blood.2019002561 Bridgford 2020 DMS MPL 93 580 human Ba/F3 cells Growth NNN PCR Illumina SRR10193506 TXT urn:mavedb:00000043 221 | 31780559 10.1126/science.aaw2900 Ogden 2019 DMS AAV2 capsid 29400 AAV AAV Production fitness;Infectivity;Thermostability;Antibody neutralization Oligo synthesis Illumina 222 | 31796585 10.1073/pnas.1915562116 McShan 2019 DMS HLA-A*02:01 362 3524 Human Expi293F FACS NNN PCR Illumina 223 | 31808666 10.1021/acschembio.9b00669 Zinkus-Boltz 2019 DMS RAF 117 E.coli Binding error-prone PCR Illumina No XLS urn:mavedb:00000061 224 | 31905288 10.1021/acs.jcim.9b00954 Nutschel 2020 DMS LipA 3439 Bacillus subtilis 225 | 31925410 10.1038/s41594-019-0358-z Persky 2020 DMS CDK4;CDK6 6060;6520 Human Human cells Growth MITE ? PRJNA559517 XLS 226 | 31928070 10.1161/CIRCGEN.119.002786 10.1101/773887 Glazer 2019 DMS SCN5A 36 248 Human urn:mavedb:00000098 227 | 32000841 10.1186/s13073-020-0711-1 Sun 2020 DMS CBS 1656 10323 6879 human Yeast Growth popcode Illumina urn:mavedb:00000005 228 | 32004414 10.1111/cts.12758 Zhang 2020 DMS CYP2C9;CYP2C19 1461;1443 109;121 109;121 human HEK293T VAMP-seq Nicking mutagenesis Illumina No DOC urn:mavedb:00000062 229 | 32094176 10.1073/pnas.1915680117 Suiter 2020 DMS NUDT15 495 3097 human HEK293T VAMP-seq;drug sensitivity Synthesized Illumina No XLS urn:mavedb:00000055 230 | 32094176 10.1073/pnas.1915680117 Yang 2020 DMS NUDT15 489 2935 Human HEK293T Growth;Flow Cytometry Twist Illumina (barcoded) 231 | 32098152 10.3390/v12020241 Roop 2020 DMS env 12559 HIV-1 Macaque 232 | 32129763 10.7554/eLife.53810 Flynn 2020 DMS Hsp90 14570 Yeast Yeast Growth 233 | 32144244 10.1038/s41467-020-15102-5 Wu 2020 DMS HA 576 human Influenza H3N2 Influenza Growth PCR targeted mutagenesis Illumina PRJNA563320 XLS 234 | 32152544 10.1038/s41589-020-0480-6 Newberry 2020 DMS alpha-synuclein 420 2600 Human Yeast Growth Provided Illumina (barcoded) PRJNA564806 XLS 235 | 32175691 10.15252/msb.20199265 Choudhury 2020 DMS rpoB E. coli E.coli Rifampicin resistance error-prone PCR Miseq GSE143629 CSV 236 | 32181350 10.1126/sciadv.aay7505 Penn 2020 DMS rhodopsin 808 Human HEK293T FACS;surface expression NNN PCR Illumina No PDF (Counts) 237 | 32238226 10.1099/mgen.0.000364 Andrews 2020 DMS LamB 1341 413 phage E.coli Growth error prone pcr Illumina PRJNA604031 XLS urn:mavedb:00000064 238 | 32385156 10.1073/pnas.1918680117 Mehlhoff 2020 DMS TEM-1 BL 5428 E. coli E.coli Growth NNN PCR Illumina PRJNA565437 XLS 239 | 32424071 10.1101/gr.260182.119 Kuo 2020 DMS Shine-Dalgarno sequence 262144 E. Coli E. Coli 240 | 32510322 10.7554/eLife.56707 Chen 2020 DMS VIM-2 lactamase 804 5535 E.coli E.coli Antibiotics resistance NNN PCR Illumina PRJNA606894 XLS urn:mavedb:00000073 241 | 32522694 10.1016/j.hrthm.2020.05.041 Kozek 2020 DMS KCNH2 220 Human HEK293T Trafficking 242 | 32531152 10.1021/acssynbio.0c00236 Nikoomanzar 2020 DMS Kod DNA polymerase 7657 E. Coli 243 | 32541028 10.1073/pnas.1920662117 Sharma 2020 DMS 237-CAR 1024 Human T Cells 244 | 32554590 10.1126/science.aaz5143 10.1101/2019.12.30.891135 Wu 2020 DMS HA 6381 Influenza Influenza Growth NNS/NNK PCR Illumina PRJNA510654;PRJNA493101;PRJNA510700 TXT 245 | 32559251 10.1371/journal.ppat.1008647 Park 2020 DMS PDGFRA 3780 Human Binding 246 | 32626892 10.1093/protein/gzaa012 Atkinson 2019 DMS AK Growth 247 | 32698006 10.1016/j.celrep.2020.107928 Jalal 2020 DMS ParB 100000 248 | 32701056 10.7554/eLife.53476 Thompson 2020 DMS DHFR 480 e. coli E.coli Growth NNS PCR Illumina ? CSV urn:mavedb:00000063 249 | 32703877 10.1126/science.aba3304 10.1101/2020.04.01.020487 Russ 2020 DMS CM1 1130 E.coli Growth oligo synthesis Illumina 250 | 32747536 10.1073/pnas.1909634117 Walker 2020 DMS 23S rRNA E. coli SQZ10 E.coli Growth ? Illumina (barcoded) PRJNA511591 No 251 | 32753553 10.1126/science.abc0870 10.1101/2020.03.16.994236 Chan 2020 DMS ACE2 2415 2340 human Expi293F FACS;Binding NNK PCR Illumina GSE147194 XLS urn:mavedb:00000069 252 | 32786289 10.1021/acschembio.0c00339 10.1101/2020.05.01.072884 Newberry 2020 DMS alpha-synuclein 423 2600 human Yeast Compound resistance Provided Illumina (barcoded) PRJNA56480 XLS urn:mavedb:00000045 253 | 32841599 10.1016/j.cell.2020.08.012 10.1101/2020.06.17.157982 Starr 2020 DMS SARS-CoV-2 spike 603 3804 SARS CoV 2 yeast Yeast display NNS PCR Illumina PRJNA639956 TXT urn:mavedb:00000044 254 | 32870157 10.7554/eLife.58026 Chiasson 2020 DMS VKOR 489 2695 human HEK293T VAMP-seq Mutagenesis primer Illumina (barcoded) GSE149922 CSV urn:mavedb:00000078 255 | 32871012 10.1093/molbev/msaa211 Cote-Hammarlof  2021 DMS HSP90 2300 Yeast Yeast Growth NNN PCR Barcoded Illumina PRJNA656157 XLS 256 | 32930662 10.7554/eLife.59988 Tenthorey 2020 DMS Human and Rhesus TRIM5α v1 Loop 231 Human CRFK Viral restriction by FACS NNS PCR Illumina No? CSV 257 | 33084570 10.7554/eLife.54895 10.1101/623108 Jones 2020 DMS ADRB2 1236 7800 HEK293T Receptor activity oligo synthesis Illumina (barcoded) No (preprint) TSV 258 | 33085662 10.1371/journal.pgen.1009009 Zhang 2020 DMS HIV-1 protease 2736 HIV-1 259 | 33202260 10.1016/j.ajhg.2020.10.015 Meitlis 2020 DMS CARD11 429 2580 Human TMD8 Growth Oligo synthesis Illumina 260 | 33259788 10.1016/j.chom.2020.11.007 Greaney 2021 DMS Spike 3804 SARS-CoV-2 Yeast Antibody binding;FACS NNS PCR Illumina PRJNA639956 CSV (GitHub) 261 | 33326746 10.1016/j.cell.2020.11.024 10.1101/2020.09.09.288324 Tycko 2020 DMS transcriptional domains 5731 Human 262 | 33340452 10.1016/j.cels.2020.11.012 10.1101/2020.06.22.165571 Aditham 2021 DMS PHO4 210 Yeast Yeast TF expression;DNA binding QuikChange site-directed mutagenesis Illumina 10.17605/OSF.IO/8QRZP No 263 | 33357406 10.1016/j.ajhg.2020.12.003 10.1101/2020.06.03.133017v2 Jia 2021 DMS MSH2 2805 17746 human HAP1 Growth Illumina GSE162130 MaveDB urn:mavedb:00000050 264 | 33432927 10.7554/eLife.64256 Mattenberger 2021 DMS Capsid 14839 265 | 33522485 10.7554/eLife.63364 Seuma 2021 DMS APP 14483 266 | 33524037 10.1371/journal.pgen.1009353 10.1101/2020.06.06.130575 Soo 2021 DMS 267 | 33574611 10.1038/s41587-020-00793-4 Bryant 2021 DMS AAV2 capsid 201426 AAV AAV Growth 268 | 33620761 10.1002/prot.26067 10.1101/2020.06.26.174375 Nedrud 2020 DMS PSD95 PDZ 249 520743 human E.coli Binding oligo synthesis Illumina PRJNA642160 MaveDB urn:mavedb:00000053 269 | 33658230 10.1124/dmd.120.000264 Zhang 2021 DMS SLCO1B1 137 Human HEK293T 270 | 33846332 10.1038/s41467-021-22489-2 10.1101/840884 Liu 2021 920 271 | 33847559 10.7554/eLife.66181 Subramanian 2021 DMS Polymerase cliding clamp and clamp loader 6015;4278;3492 T4 bacteriophage Phage Growth 272 | 34157285 10.1016/j.jbc.2021.100900 Trenker 2021 DMS CD86 78 520 Human HeLa Flow Cytometry NNN PCR Illumina 273 | 34157285 10.1016/j.jbc.2021.100900 Trenker 2021 DMS MARCH1; MIR2 81 urn:mavedb:00000046 274 | 34214447 10.1016/j.ajhg.2021.05.009 Weile 2021 DMS MTHFR 1971 13776 human Yeast Growth popcode Illumina urn:mavedb:00000049 275 | 34314704 10.1016/j.ajhg.2021.07.001 Amorosi 2021 DMS CYP2C9 1470 6370 Human Yeast and HEK293T Click-seq and VAMP-seq urn:mavedb:00000095 276 | 34408246 10.1038/s42003-021-02490-7 Hamborg 2021 DMS chymotrypsin inhibitor 2 25 Barley E.coli Stability mutagenic PCR Illumina No No 277 | 34431656 10.1021/acschembio.1c00423 10.1101/2020.08.21.261578 Koberstein 2021 DMS biosensors 2304 278 | 34491198 10.7554/eLife.71393 Phillips 2021 DMS bnAbs 65536;2048 Human Yeast Binding 279 | 34497069 10.1261/rna.078954.121 Mouali 2021 DMS ProQ 5000 Salmonella Salmonella Growth 280 | 34552126 10.1038/s41598-021-97871-7 Huttinger 2021 DMS PAI-1 1963 Human Phage Binding error-prone PCR Illumina No TXT 281 | 34638709 10.3390/ijms221910359 Ortiz 2021 DMS HokC 1616 E.coli E.coli Growth pdf 282 | 34649609 10.1186/s13073-021-00984-x Matreyek 2021 DMS PTEN 1212 4112 Human HEK293T VAMP-seq TSV urn:mavedb:00000101;urn:mavedb:00000102 283 | 34756884 10.1016/j.jbc.2021.101359 McKee 2021 DMS Rhodopsin 700 Human HEK293T Plasma membrane expression No PDF 284 | 34871407 10.1093/nar/gkab1172 10.1101/2021.03.11.435011 Carmody 2021 DMS −1PRF 4530 285 | 34919820 10.1016/j.molcel.2021.11.024 10.1101/2021.03.30.437622 Javanmardi 2021 DMS Spike 200 SARS-CoV-2 HEK293T 286 | 35013287 10.1038/s41420-021-00799-0 Roychowdury 2022 DMS CASP3;CASP7 1644; 1772 Activity PRJNA622561 No 287 | 35044296 10.7554/eLife.75555 10.1101/2020.09.08.288233 Katrekar 2022 DMS ADAR2 4958 Human HEK293FT RNA editing activity Oligonucleotide chip synthesis Illumina GSE158656 No;but raw RNA edits are stored in .gz in GSE15856 288 | 35058622 10.1038/s41587-021-01160-7 10.1101/2020.11.16.383307 Ursu 2022 DMS KRAS;TP53 200 Human A549 Perturb-seq Twist 'clonal gene' platform Illumina GSE161824 CSV 289 | 35120642 10.1016/j.cels.2022.01.002 10.1101/2020.10.28.359026 Staller 2022 DMS 7 transcriptional activation domains within VP16;CITED2;HIF1A;P65;STAT3;P53 (2) 3516 Human K562 FACS site-directed mutagenesis Illumina GSE190288 CSV 290 | 35196514 10.1016/j.ajhg.2022.01.019 Adamovich 2022 DMS BRACA1-BRCT 2271 Human HeLa Growth;Drug Resistance NNK PCR Illumina (barcoded) 291 | 35510622 10.7554/eLife.75842 10.1101/2021.12.08.471728 Gonzalez Somermeyer 2021 DMS GFP 140860 Aequorea victoria E.coli Fluorescence error prone PCR 292 | 35639599 10.7554/eLife.76903 10.1101/2022.01.06.475280 Coyote-Maestas 2022 DMS Kir2.1 1305 6898;6944 Human HEK293T FACS targeted domain insertion Illumina PRJNA791691 CSV (GitHub) 293 | 35688148 10.1016/j.ajhg.2022.05.003 10.1101/2021.07.10.451881 Ng 2021 DMS KCNH2 1603;458 Human HEK293T Trafficking;Patch clamp QuikChange Lightning multi site-directed mutagenesis Illumina dryad.zpc866t9x (patch clamp);dryad.dbrv15f3f (trafficking) XLSX (patch clamp) 294 | 35723575 10.7554/eLife.77433 10.1101/2022.01.26.477860 Flynn 2022 DMS Mpro 6042 SARS-CoV-2 Yeast FRET + FACS;Fluorescence;Growth massively parallel oligo synthesis Illumina PRJNA842255 XLSX 295 | unpublished unpublished 10.1101/2020.10.14.338756 Heyne 2020 DMS BPTI 30651 296 | unpublished unpublished 10.1101/2021.04.16.440236 Sinai 2021 DMS AAV2 capsid 22704 AAV AAV Growth 297 | unpublished unpublished 10.1101/2021.04.19.440442 Young 2021 DMS SERT 12000 Expi293F Fluorescence NNN PCR 298 | unpublished unpublished 10.1101/2021.06.06.447205 Trivedi 2021 DMS PAL Anabaena variabilis Activity 299 | unpublished unpublished 10.1101/2021.08.21.457204 Stadelmann 2021 DMS AcrIIA4;AcrIIA5 1740;2800 E.coli 300 | unpublished unpublished 10.1101/2021.09.14.460249 Faure 2021 DMS PSD95-PDZ3 domain;GRB2-SH3 domain 607571 Yeast Growth NNN PCR txt 301 | unpublished unpublished 10.1101/2021.10.01.462730 Meier 2021 DMS EfrCD 1500 302 | unpublished unpublished 10.1101/2021.10.06.463360 Silverstein 2021 DMS GDI1 1344 Yeast Growth popcode Illumina urn:mavedb:00000066 303 | unpublished unpublished 10.1101/2021.10.07.463098 Ding 2021 DMS toxin-antitoxin complex 5796 E.coli Growth 304 | unpublished unpublished 10.1101/2021.12.07.471580 Taft 2021 DMS Spike SARS-CoV-2 305 | unpublished unpublished 10.1101/2022.03.29.486051 Coelho 2022 DMS JAK1 3462 10595 HT-29 and LS-411N CRC Growth Illumina 306 | unpublished unpublished 10.1101/2022.05.04.490571 Gersing 2022 DMS GCK 1395 9003 Human Yeast Growth NNK PCR Illumina 307 | unpublished unpublished 10.1101/2022.06.10.22276179 Radford 2022 DMS DDX3X 1986 6766;1886 Human HAP1 Growth oligo synthesis Illumina No 308 | unpublished unpublished 10.1101/2022.12.06.519132v3 Tsuboyama 2022 DMS synthetic and natural proteins (many) 850000 309 | unpublished unpublished 10.1101/831503 Mavor 2019 DMS Ubiquitin 1520 Yeast Yeast Growth NNN PCR Illumina (barcoded) 310 | unpublished unpublished unpublished DMS HMGCR 2667 Yeast Growth popcode Illumina urn:mavedb:00000035 311 | unpublished unpublished unpublished DMS LDLRAP1 927 Hap1 FACS popcode Illumina urn:mavedb:00000036 312 | unpublished unpublished unpublished DMS NCS1 573 Yeast Growth popcode Illumina urn:mavedb:00000065 313 | unpublished unpublished unpublished DMS TECR 927 Yeast Growth popcode Illumina urn:mavedb:00000067 314 | --------------------------------------------------------------------------------