MaveReferences

Welcome to our table of Multiplexed Assay of Variant Effect (MAVE) studies. To cite this document, please use the citation details for MaveDB.

Updating the table

As of release version 0.2.0, the references are now stored in a the tab-separated file 'maverefs.tsv' and formatted for the README using the 'format.py' script.

To add or edit a study:

1. Fork this repository and create a local clone.
2. Open 'maverefs.tsv' in a spreadsheet program and make your changes.
3. Save 'maverefs.tsv', making sure it remains a tab-separated text file.
4. Run python format.py in the MaveReferences directory to re-format the README. Note that this script requires the idutils package (pip install idutils) for link formatting.
5. Commit your changes and please submit a pull request!

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Table of references

PMID	DOI	First author	Year	Type	Molecule	Model	Selection Type	Mutagenesis Type	Sequencing Platform	Raw Data	Scores in Table
19915551	10.1038/nbt.1589	Patwardhan	2009	MPRA	T3 promoter, T7 promoter, SP6 promoter, CMV promoter, HBB promoter, S100A4 promoter	in vitro	Transcription	microarray synthesis	Illumina	SRP001721	TXT
20439748	10.1073/pnas.1004290107	Kinney	2010	MPRA	lac promoter	E.coli	FACS	doped oligo synthesis	Roche 454	SRA012345	No
20711194	10.1038/nmeth.1492	Fowler	2010	DMS	WW domain	Phage	Binding	doped oligo synthesis	Illumina	SRP002725	No
20714644	10.1039/c0mb00061b	Ernst	2010	DMS	Synthetic PDZ domain	Phage	Binding	Kunkel	Roche 454	No	No
21464309	10.1073/pnas.1016024108	Hietpas	2011	DMS	Hsp90	Yeast	Growth	NNN PCR	Illumina	No	TXT
21825149	10.1073/pnas.1111218108	Zhang	2011	DMS	IgG	Phage	Binding	Combinatorial	Roche 454	No	No
22325784	10.1016/j.str.2011.11.021	Adkar	2012	DMS	Ccdb	E.coli	toxin activity	PCR with specific codons	Roche 454	No	XLS
22371081	10.1038/nbt.2136	Patwardhan	2012	MPRA	ALDOB enhancer, ECR11 enhancer, LTV1 enhancer	mouse liver	Transcription	doped oligo synthesis	Illumina	SRA049159	TXT
22371084	10.1038/nbt.2137	Melnikov	2012	MPRA	cAMP-regulated enhancer, interferon-B enhancer	Human cell culture (HEK239T)	Transcription	in silico design and synthesis	Illumina	GSE31982	XLS
22609971	10.1038/nbt.2205	Sharon	2012	MPRA	designed promoters	Yeast	Fluorescence, Transcription	microarray synthesis	Illumina	No	No
22634563	10.1038/nbt.2214	Whitehead	2012	DMS	Designed influenza binder	Yeast	FACS	synthesized	Illumina	No	No
22665811	10.1073/pnas.1202107109	Schlinkmann	2012	DMS	Neurotensin receptor 1 GPCR	E.coli	FACS	NNN PCR	Roche 454	No	No
22846908	10.1016/j.jmb.2012.07.017	Traxlmayr	2012	DMS	IgG	Yeast	FACS	error-prone PCR	Roche 454	No	No
23017428	10.1016/j.jmb.2012.09.014	Deng	2012	DMS	TEM1 Beta-lactamase	E.coli	Amp resistance	NNS Kunkel	Roche 454	No	XLS
23035249	10.1073/pnas.1209751109	Araya	2012	DMS	WW domain	Phage	Binding	doped oligo synthesis	Illumina	Yes	No
23041932	10.1038/nature11500	McLaughlin	2012	DMS	PSD95 PDZ	Bacteria	Special	NNS PCR	Illumina	No	No
23103372	10.1016/j.bbrc.2012.10.066	Fujino	2012	DMS	Fab antibody fragment	in vitro	Ribodisplay	PCR with fragments	Roche 454	No	No
23152521	10.1128/JVI.01658-12	Wu	2012	DMS	Neuraminidase	Human/H1N1	Oseltamivir resistance	error prone pcr	Roche 454	No	No
23241746	10.1101/gr.144659.112	Liachko	2012	MPRA	Autonomously replicating sequences	Yeast	Growth	doped oligo synthesis	Illumina	SRA051406	No
23287719	10.1126/science.1230161	Ernst	2013	DMS	Ubiquitin	Phage	Binding	site-directed mutagenesis with doped oligos	ELISA	No	No
23376099	10.1016/j.jmb.2013.01.032	Roscoe	2013	DMS	Ubiquitin	Yeast	Growth	NNN PCR	Illumina	No	XLS
23509263	10.1073/pnas.1303309110	Starita	2013	DMS	E4B	Phage	Auto-ubiquitination	doped oligo synthesis	Illumina (barcoded and subassembly)	No	XLS
23512712	10.1101/gr.144899.112	Kheradpour	2013	MPRA	Regulatory motifs for HNF1, HNF4, FOXA, GATA, NFE2L2, GFI1, ZFP161	Human cell culture (K562 and HepG2)	Transcription	microarray synthesis	Illumina	GSE33367	TXT
23625929	10.1074/jbc.M112.447326	Gold	2013	DMS	PKA RII	Phage	Binding	doped oligo synthesis	Illumina	No	No
23765106	10.4161/mabs.24979	Forsyth	2013	DMS	IgG	Human cells	FACS	NNK PCR	Roche 454	No	PDF
23818646	10.1073/pnas.1307449110	White	2013	MPRA	Crx target sequences	Mouse retina	Transcription	microarray synthesis	Illumina	No	TXT
23825969	10.1371/journal.pgen.1003600	Jiang	2013	DMS	Hsp90	Yeast	Growth	NNN PCR	Illumina	No	XLS
23827138	10.1016/j.jmb.2013.06.035	Procko	2013	DMS	Designed protein binder	Yeast	FACS	site-directed mutagenesis and error-prone PCR	Illumina	No	No
23878237	10.1073/pnas.1215206110	Jacquier	2013	DMS	TEM1 Beta-lactamase	E.coli	Amoxicillin resistance	single nucleotide random	Sanger!	No	XLS
23892608	10.1038/ng.2713	Smith	2013	MPRA	Synthetic liver enhancers	mouse primary liver, human HepG2 cell line	Transcription	designed combinations of binding sites	Illumina	SRP018414	XLS
23897579	10.1074/mcp.O113.031708	Kim	2013	DMS	Yeast degron	Yeast	Growth	doped oligo synthesis	Illumina	No	No
23921661	10.1101/gr.157891.113	Mogno	2013	MPRA	Synthetic promoters	Yeast	Transcription	Combinatorial	Illumina	No	TXT
23924614	10.1073/pnas.1301301110	Kosuri	2013	MPRA	Synthetic promoters and ribosome binding sites	E.coli	Transcription and translation	designed combinations of binding sites	Illumina	No	XLS
24005320	10.1038/nature12443	Tinberg	2013	DMS	Designed digoxigenin binder	Yeast	FACS	doped oligo synthesis	Illumina	No	PDF (Counts)
24064791	10.1261/rna.040709.113	Melamed	2013	DMS	Pab1	Yeast	Growth	doped oligo synthesis	Illumina	No	XLS
24112705	10.1111/pcmr.12171	Wagenaar	2013	DMS	BRAF V600E	Human	vemurafenib resistance	NNN PCR	Illumina	No	No
24204297	10.1371/journal.pgen.1003882	Rockah-Shmuel	2012	DMS	M.HaeIII	E.coli	Indel read-through, activity	error-prone PCR	Illumina	No	No
24299404	10.1111/evo.12207	Hietpas	2013	DMS	Hsp90	Yeast	Growth	NNN PCR	Illumina	No	XLS
24381156	10.1073/pnas.1313605111	Strauch	2014	DMS	Designed IgG	Yeast	FACS	error-prone PCR	Illumina	No	No
24567513	10.1093/molbev/msu081	Firnberg	2014	DMS	TEM-1 BL	Bacteria	Growth	PFunkel	Roche 454	No	XLS
24603708	10.1371/journal.pgen.1004169	Liachko	2014	MPRA	Autonomously replicating sequences	Yeast	Growth	doped oligo synthesis	Illumina	SRP031760	No
24633241	10.1038/nbt.2851	Zhao	2014	MPRA	3' UTR	Human cell culture (BEAS-2B, Jurkat or WiDr cells)	mRNA stability and protein level	microarray synthesis	Illumina	SRX463338	XLS
24656821	10.1016/j.celrep.2014.03.001	Oikonomou	2014	MPRA	3' UTR	Human cells (FlpIn293)	FACS	microarray synthesis	Illumina	GSE55396	XLS
24722365	10.1371/journal.ppat.1004064	Qi	2014	DMS	NS4B	Human cell culture (Huh-7.5.1)	Growth	NNK PCR	Illumina	No	XLS
24859245	10.1093/molbev/msu173	Bloom	2014	DMS	influenza nucleoprotein	Human/H1N1	viral replication	NNN PCR	Illumina	SRP036064	XLS
24862281	10.1016/j.jmb.2014.05.019	Roscoe	2014	DMS	Ubiquitin	Yeast	Binding	NNN PCR	Illumina	No	XLS
24887409	10.1371/journal.pone.0097817	Shin	2014	DMS	flavin mononucleotide binding fluorescent protein	E.coli	Fluorescence	error-prone PCR	Illumina (barcoded)	PRJNA242983	XLS
24914046	10.1093/nar/gku511	Melnikov	2014	DMS	APH(3')II	Bacteria	Growth	microarray synthesis	Illumina	SRP042113	TXT
25006036	10.7554/eLife.03300	Thyagarajan	2014	DMS	Hemagglutinin	Influenza	Growth	NNN PCR	Illumina	SRP040983	TXT
25030889	10.1101/gr.168773.113	Sharon	2014	MPRA	designed promoters	Yeast	Fluorescence, Transcription	?	Illumina	GSE55346	TXT
25064858	10.1093/nar/gku689	Gajula	2014	DMS	AID	E.coli	Growth	NNS PCR	Illumina	No	PDF (Counts)
25085423	10.1101/gad.245936.114	Guy	2014	DMS	tRNA	Yeast	FACS	doped oligo synthesis	Illumina	No	XLS
25141179	10.1038/nature13695	Findlay	2014	DMS	DBR1	Hap1	Growth	CRISPR	Illumina	SRP044126	XLS
25170020	10.15252/msb.20145136	Noderer	2014	DMS	Start codon efficiency	Mammalian cell culture	FACS	degenrate PCR	Illumina (barcoded)	No	TXT
25311858	10.1016/j.jmb.2014.09.025	Reich	2015	DMS	BH3	Yeast	FACS	?	Illumina	No	No
25371431	10.1093/molbev/msu301	Bank	2015	DMS	Hsp90	Yeast	Growth	NNN PCR	Illumina	No	No
25451031	10.1016/j.jmb.2014.10.024	Doolan	2015	DMS	PrP	Yeast	FACS	site-directed mutagenesis	PacBio	No	No
25455030	10.1016/j.cub.2014.09.072	Olson	2014	DMS	GB1	mRNA display	Binding	NNK PCR	Illumina	No	XLS
25522661	10.1186/s12977-014-0124-6	Al-Mawsawi	2014	DMS	HIV genome	HIV	Growth	error-prone PCR	Illumina	PRJNA259391	XLS
25559584	10.1038/nmeth.3223	Kitzman	2014	DMS	Gal4	Yeast	Growth	PALS (array+PCR)	Illumina (barcoded and subassembly)	PRJNA268398	No
25657251	10.1126/science.1257360	Podgornaia	2015	DMS	PhoQ	Bacteria	FACS	NNS PCR	Illumina	No	No
25723163	10.1016/j.cell.2015.01.035	Stiffler	2015	DMS	TEM1 B-lactamase	E.coli	Growth	NNS PCR	Illumina	No	XLS
25823446	10.1534/genetics.115.175802	Starita	2015	DMS	BRCA1	Yeast, Phage	Growth, Binding	microarray synthesis	Illumina (barcoded and subassembly)	No	XLS
25875337	10.1371/journal.pgen.1005147	Shalem	2015	MPRA	3' UTR	Yeast	Fluorescence, Transcription	microarray synthesis	Illumina	No	XLS
26040002	10.1073/pnas.1422285112	Romero	2015	DMS	Bgl2	Bacteria/microfluidic droplets	Activity	error-prone PCR	Illumina	No	No
26088137	10.1074/jbc.M115.662783	Koenig	2015	DMS	IgG CDR	Phage	Binding	NNK PCR	Illumina	No	No
26132554	10.1371/journal.pgen.1005310	Wu	2015	DMS	Polymerase PA	Influenza	Growth	error-prone PCR	Illumina	PRJNA254185	XLS
26170332	10.1073/pnas.1511328112	Kretz	2015	DMS	VWF	Phage	Binding/cleavage	doped oligo synthesis	Illumina	No	XLS
26226986	10.1093/molbev/msv167	Doud	2015	DMS	Nucleoproteins	Influenza	Growth	NNN PCR	Illumina	SRP056028	TXT
26274323	10.1371/journal.pcbi.1004421	Rockah-Shmuel	2015	DMS	M.HaeIII	Bacteria	Activity	error-prone PCR	Illumina	No	XLS
26296891	10.1074/jbc.M115.676635	Kowalsky	2015	DMS	IgG	Yeast	FACS	PFunkel	Illumina	No	TXT
26369947	10.1021/acssynbio.5b00131	Klesmith	2015	DMS	LGK	E.coli	Growth	PFunkel	Illumina	No	No
26478181	10.1016/j.cell.2015.09.055	Aakre	2015	DMS	ParD	Bacteria	Growth	ProxiMax	Illumina	No	No
26496609	10.1016/j.cell.2015.09.054	Rosenberg	2015	MPRA	Splice sites	HEK293	Isoform occurrence	degenrate PCR	Illumina	GSE74070	No
26576614	10.1101/gr.193789.115	Shen	2016	MPRA	Promoters and enhancers	Mouse retina, mouse cortex	Transcription	capture of existing elements	Illumina	GSM1463994	XLS
26626484	10.1016/j.molcel.2015.10.029	Vvedenskaya	2015	MPRA	TSS	Bacteria	Transcription	MASTER	Illumina	SRP057850	XLS
26637602	10.1128/AEM.03074-15	Jin	2015	DMS	ACD-1	Bacteria	Growth	doped oligo synthesis	Roche 454	PRJEB11657	No
26656922	10.1016/j.jmb.2015.11.027	Jiang	2016	DMS	Neuraminidase	Influenza	Growth	NNN PCR	Illumina	PRJNA272490	XLS
26689263	10.1038/nmeth.3696	Taylor	2016	DMS	lac repressor	Bacteria	Growth	microarray synthesis	Illumina	GSE75009	No
26716404	10.7554/eLife.09532	Sahoo	2015	DMS	CcdB, DgkA	Bacteria	Growth	NNN PCR	Roche 454	No	No
26754751	10.1186/s12864-015-2358-7	Wu	2016	DMS	M segment	Influenza	Growth	error-prone PCR	Illumina	PRJNA285135	XLS
26779844	10.1002/pro.2881	Foight	2016	DMS	CD40, TANK	Bacteria	FACS	NNK PCR	Illumina	No	No
26824389	10.7554/eLife.12125	Elazar	2016	DMS	Transmembrane segment	Bacteria	Growth	NNS PCR	Illumina	No	XLS (Counts)
26865697	10.1534/g3.116.027904	Hoggard	2016	MPRA	Autonomously replicating sequences	Yeast	Growth	doped oligo synthesis	Illumina	SRP065331	No
26936925	10.1534/genetics.116.188037	Rich	2016	MPRA	SUL1 promoter	Yeast	Growth	error-prone PCR	Illumina (barcoded and subassembly)	PRJNA273419	XLS
26941320	10.1126/science.aad6881	Winkelman	2016	MPRA	TSS	Bacteria	Transcription	MASTER	Illumina	No	No
27013733	10.1126/science.aad9195	Jardine	2016	DMS	IgG	Yeast	FACS	NNK PCR	Illumina	No	No
27068472	10.1016/j.celrep.2016.03.046	Mishra	2016	DMS	Hsp90	Yeast	Growth	NNN PCR	Illumina	No	XLS
27080103	10.1126/science.aaf0965	Puchta	2016	DMS	snoRNA U3	yeast	inducible covering allele	doped oligo synthesis	Illumina (barcoded)	GSE77709	TXT (Counts)
27080104	10.1126/science.aae0568	Li	2016	DMS	tRNA(Arg-CCU)	yeast	tRNA folding stability	random single nucleotide	Illumina	PRJNA311172	No
27111525	10.7554/eLife.15802	Mavor	2016	DMS	Ubiquitin	Yeast	Growth	NNN PCR	Illumina (barcoded)	SRR3194828	No
27161764	10.1038/ncomms11558	Julien	2016	MPRA	FAS/CD95	Human	splicing	commercial library cassete ligation	collapsing read pairs	PRJEB13140	XLS
27162333	10.1073/pnas.1603271113	Vvedenskaya	2016	MPRA	TSS	in vitro, E.coli	Transcription	MASTER	Illumina	SRP071742	No
27173379	10.1016/j.jmb.2016.04.033	Steinberg	2016	DMS	TEM1 Beta-lactamase	E.coli	Amp resistance	PFunkel	Roche 454	No	XLS
27193686	10.1038/nature17995	Sarkisyan	2016	DMS	GFP	Bacteria	Activity	error-prone PCR	Illumina	PRJNA282342.	TXT
27259153	10.1016/j.cell.2016.04.027	Tewhey	2016	MPRA	eQTL peaks	Human cell lines (NA12878, NA19239, HepG22)	Transcription	microarray synthesis	Illumina	GSE75661	XLS
27259154	10.1016/j.cell.2016.04.048	Ulirsch	2016	MPRA	GWAS peaks	Human cell lines (K562)	Transcription	microarray synthesis	Illumina	No	No
27271655	10.3390/v8060155	Doud	2016	DMS	Hemagglutinin	Influenza	Growth	NNN PCR	Illumina	PRJNA309339	TXT
27374328	10.1016/j.cell.2016.05.070	Gamble	2016	DMS	GFP	Yeast	FACS	NNN/VNN PCR	Illumina	No	No
27391790	10.7554/eLife.16965	Wu	2016	DMS	GB1	mRNA display	Binding	random single nucleotide	Illumina	PRJNA278685	XLS
27563054	10.1093/molbev/msw182	Tripathi	2016	DMS	CcdB	E.coli	Growth	NNK PCR	Illumina	No	No
27681597	10.1074/jbc.M116.748681	Harris	2016	DMS	TCR	Yeast	FACS	site-directed mutagenesis	?	No	No
27699856	10.1002/prot.25175	Kowalsky	2016	DMS	cohesin	Yeast	FACS	NNN PCR	Illumina	No	TXT
27701403	10.1038/nbt.3678	Ernst	2016	MPRA	H3K27ac sites	Human cell lines (K562, HepG2)	Transcription	microarray synthesis	Illumina	GSE71279	TXT
27741319	10.1371/journal.pone.0164296	Gaiotto	2016	DMS	HA	Yeast	Antibody binding	error-prone PCR	Illumina (barcoded)	PRJEB15301	DOC
27749844	10.1038/ng.3700	Majithia	2016	DMS	PPARG	Human cells	FACS	microarray synthesis	Illumina	No	No
27760319	10.1016/j.celrep.2016.09.061	Brenan	2016	DMS	Mapk1/Erk2	Human	inhibitor resistance	microarray synthesis	Illumina	No	XLS
27898685	10.1371/journal.pgen.1006321	Qiu	2016	DMS	RNAPII trigger loop	Yeast	Growth	site-directed mutagenesis	Illumina	PRJNA340979	No
27959955	10.1371/journal.ppat.1006114	Haddox	2016	DMS	Env	HIV	Growth	NNN PCR	Illumina	PRJNA320270	TXT
27974464	10.1074/jbc.M116.764225	van Rosmalen	2017	DMS	Cyclic peptide	Yeast	FACS	site-directed mutagenesis	Illumina	No	No
27984726	10.1016/j.cell.2016.11.031	Fernandes	2016	DMS	Tat, Rev	HIV	Growth	NNN PCR	Illumina	E-MTAB-5154	XLS
28007883	10.1534/genetics.116.196428	Keskin	2017	DMS	Fis1p	Yeast	Growth	site-directed mutagenesis	Illumina	10.5061/dryad.j14r5	XLS (Counts)
28009265	10.1016/j.cels.2016.11.004	Kelsic	2016	DMS	infA	Bacteria	Growth	MAGE	amplicon	E-MTAB-4020	TXT
28024160	10.1038/nmeth.4121	Yartseva	2017	MPRA	mRNA stability	Zebrafish	Transcription	selected RNA sequences	Illumina	SRP090954	No
28035901	10.7554/eLife.23156	Adams	2016	DMS	scFV antibody	Yeast	Yeast display	Cassette Ligation	Illumina	PRJNA344711	CSV
28057863	10.1073/pnas.1613231114	Koenig	2017	DMS	IgG	Phage	Binding	NNK PCR	Illumina	No	No
28137873	10.1073/pnas.1621150114	Grossman	2017	MPRA	natural and synthetic enhancers	mouse	Transcription	microarray synthesis	Illumina (barcoded)	GSE84888	No
28196882	10.1073/pnas.1614437114	Klesmith	2017	DMS	TEM-1 BL, LGK	Yeast, Bacteria	FACS, Growth	NNN PCR	Illumina	No	No
28204611	10.1093/nar/gkw942	Maricque	2017	MPRA	genomic regions	Human cells	Transcription	microarray synthesis	Illumina	No	No
28212748	10.1016/j.molcel.2017.01.007	Levo	2017	MPRA	yeast promoters	Yeast	Transcription	microarray synthesis	Illumina	GSE92300	XLS
28262665	10.1038/ncomms14614	Chan	2017	DMS	IGPS	Yeast	Growth	NNN PCR	Illumina	No	No
28288189	10.1371/journal.ppat.1006271	Doud	2017	DMS	HA	Influenza	Antibody binding	NNN PCR	Illumina	SAMN05789126	TXT
28335006	10.1093/nar/gkx183	Matreyek	2017	DMS	GFP N-terminal codon	Human cell lines (HEK293T)	FACS	oligo synthesis	Illumina (barcoded)	SRP095490	TXT
28346537	10.1371/journal.ppat.1006288	Ashenberg	2017	DMS	NP	Virus	Growth	NNN PCR	Illumina	SRP082554	TXT
28579254	10.1016/j.chom.2017.05.003	Dingens	2017	DMS	Env	HIV	Antibody binding	NNN PCR	Illumina (barcoded)	SRA: SRX2548567-SRX2548579	TXT
28585537	10.1038/ncomms15695	Wrenbeck	2017	DMS	amiE	E.coli	Growth	Pfunkel	Illumina	PRJNA360623	TXT
28585908	10.1080/19420862.2017.1337618	Koenig	2017	DMS	IgG heavy chain	Phage	Binding	NNK PCR	Illumina (barcoded)	No	PDF
28618270	10.1016/j.chom.2017.05.011	Wu	2017	DMS	HA RBS	Human cells	Growth	NNK PCR	amplicon	PRJNA353496	XLS
28652265	10.1158/1541-7786.MCR-17-0245	Bhagavatula	2017	DMS	TP53 synonymous	HEK293T	FACS	doped oligo synthesis	Illumina	PRJNA384242	No
28686159	10.7554/eLife.27810	Bandaru	2017	DMS	Ras	Bacteria	activity	NNS PCR	Illumina	No	XLS
28902834	10.1038/nature23902	Starr	2017	DMS	ancestral RH	Yeast	FACS	NNK PCR	Illumina	PRJNA362734	No
29039417	10.1038/nmeth.4464	Woodsmith	2017	DMS	BBSome	yeast	Y2H	PALS (array+PCR)	simple deep sequencing	PRJNA407860	XLS
29078326	10.1073/pnas.1708268114	Ma	2017	DMS	BCR-ABL	Ba/F3 cells	Growth	CRISPR	Illumina	No	No
29097404	10.1101/gr.224964.117	Cuperus	2017	MPRA	5' UTR	yeast	Growth	random oligos	Illumina	GSE104252	XLS
29203891	10.1038/s41598-017-17081-y	Spencer	2017	DMS	Cas9	Bacteria	Growth	error-prone PCR	Illumina	SRP107783	XLS
29225039	10.1016/j.molcel.2017.11.014	Rabani	2017	MPRA	3' UTR	Zebrafish	Transcript abundance	known UTRs	Illumina	GSE106677	XLS
29242188	10.1101/gr.219683.116	Ke	2017	MPRA	DHFR exon 1-5	human	splicing	microarray synthesis	Illumina	GSE105785	XLS
29269382	10.15252/msb.20177908	Weile	2017	DMS	UBE2I, SUMO1, TPK1, CALM1-3	yeast	complementation	popcode	Barseq+TileSeq (Illumina)	PRJNA390305	TXT
29301959	10.1126/science.aao5167	Plesa	2018	DMS	PPAT	E.coli	Growth	ortholog synthesis	Illumina	SRP126669	XLS
29410437	10.1038/s41467-018-02980-z	Vainberg Slutskin	2018	MPRA	microRNA	K562	FACS	microarray synthesis	Illumina	SRP128656	No
29466705	10.1016/j.jmb.2018.02.009	Canale	2018	DMS	HA	Human/infulenza	viral replication	?	Illumina	No	XLS (Counts)
29525204	10.1016/j.cels.2018.01.015	Staller	2018	DMS	Gcn4	Yeast	FACS	microarray synthesis	Illumina	10.17632/rbfr6m4733.1	TXT
29590010	10.7554/eLife.34420	Haddox	2018	DMS	Env	Human/HIV	viral replication	NNN PCR	Illumina (barcoded)	PRJNA371844, PRJNA412552	CSV (Counts)
29638215	10.7554/eLife.32472	Diss	2018	DMS	AP-1	Yeast	Growth	doped oligo synthesis	Illumina	GSE102901	XLS
29643335	10.1038/s41467-018-03783-y	Hartman	2018	DMS	MS2 phage capsid	MS2	SyMAPS	NNN PCR	Illumina	No	XLS
29643370	10.1038/s41467-018-03665-3	Doud	2018	DMS	H1 hemaglutinin	Influenza	Growth	NNN PCR	Illumina	SAMN05789126	TXT
29663315	10.1002/bit.26706	Medina-Cucurella	2018	DMS	canine nerve growth factor	Yeast	Antibody binding by FACS	Pfunkel	Illumina	SRA (SAMN07693504-SAMN07693526)	TSV
29678950	10.4049/jimmunol.1800343	Heredia	2018	DMS	CXCR4, CCR5	Expi293F	FACS, Binding	?	Illumina	GSE100368	XLS
29706350	10.1016/j.ajhg.2018.03.018	Mighell	2018	DMS	PTEN	Yeast	lipid phosphatase activity	MITE	Illumina	SRP134135	XLS
29728462	10.1073/pnas.1722055115	Belliveau	2018	MPRA	lacZYA, relBE, marRAB, yebG, purT, xylE, dgoRKADT promoters	E.coli	FACS	Cassette Ligation	Illumina	SRP121362	CSV
29785012	10.1038/s41588-018-0122-z	Matreyek	2018	DMS	PTEN + TPMT	human	Protein stability	inverse PCR	Illumina (barcoded and subassembly)	PRJNA428380	XLS
29813059	10.1371/journal.pgen.1007419	Dandage	2018	DMS	GmR	E.coli	Gentamicin resistance	NNK PCR	Illumina (barcoded)	PRJNA384918	XLS
29912470	10.1093/nar/gky255	Atkinson	2018	DMS	adenylate kinase	E.coli	activity	Transposon mutagenesis (not substitution)	Illumina	SRR6327683, SRR6327684	No
29931269	10.1093/nar/gky550	Mason	2018	DMS	CDR	PnP hybridoma cells	FACS	CRISPR	Illumina	No	No
29979580	10.1021/acssynbio.8b00121	Scott	2018	DMS	tetracycline inactivating enzyme	Yeast	Tetracycline resistance	error-prone PCR	Illumina	No	No
29979965	10.1016/j.molcel.2018.06.012	Kotler	2018	DMS	TP53	HEK293T	Growth	microarray synthesis	Illumina	GSE115072	XLS
30012625	10.1073/pnas.1803598115	Cantor	2018	DMS	EGFR	E.coli	FACS	NNS PCR	Illumina	No	No
30024376	10.7554/eLife.34300	Salinas	2018	DMS	PDZ	Bacteria	activity	NNS PCR	Illumina	No	No
30037883	10.1242/bio.036103	Mavor	2018	DMS	Ubiquitin	Yeast	Growth	NNN PCR	Illumina (barcoded)	SRP070953	No
30068600	10.1073/pnas.1805882115	Dorrity	2018	DMS	Ste12	Yeast	Mating/Invasion	doped oligo synthesis	Illumina	PRJNA379449	XLS
30079747	10.1164/rccm.201802-0337OC	Castaldi	2019	MPRA	FAM13A locus	human	Transcription	microarray synthesis	Illumina	No	No
30104379	10.1073/pnas.1806133115	Lee	2018	DMS	HA	Virus	Growth	NNN PCR	Illumina	SAMN08102609, SAMN08102610	TXT
30174293	10.1016/j.molcel.2018.07.033	Wong	2018	MPRA	Splice sites	HeLa	Transcription	?	Illumina	SRP135892	No
30188321	10.7554/eLife.38795	Phillips	2018	DMS	HA	Influenza	Growth	NNN PCR	Illumina	SRP149672	TXT
30209399	10.1038/s41586-018-0461-z	Findlay	2018	DMS	BRCA1	HAP1	Growth	microarray synthesis + CRISPR	Illumina	No	XLS
30219179	10.1016/j.ajhg.2018.07.016	Starita	2018	DMS	BRCA1	human	DNA-repair assay	NNK PCR	Illumina	GSE116427	XLS
30224458	10.1073/pnas.1811993115	Blaesi	2018	DMS	RNR	Bacteria	Growth	NNS PCR	Illumina	No	No
30224644	10.1038/s41588-018-0204-y	Giacomelli	2018	DMS	TP53	human	Growth	microarray synthesis	Illumina	No	XLS
30258049	10.1038/s41467-018-06403-x	Naftaly	2018	DMS	APPI	Yeast	FACS	NNS PCR	Illumina	No	No
30478237	10.15252/msb.20188371	Bassalo	2018	DMS	Lysine metabolic pathway	Bacteria	Growth	microarray synthesis	Illumina	No	XLS
30503770	10.1016/j.molcel.2018.10.037	Cheung	2019	MPRA	Splice sites	human cells	FACS	microarray synthesis	Illumina	GSE120695	No
30709739	10.1016/j.immuni.2018.12.017	Dingens	2019	DMS	Env	HIV	Antibody binding	NNN PCR	Illumina (barcoded)	SRP15794, PRJNA486029	CSV
30716072	10.1371/journal.pcbi.1006226	Barnes	2019	MPRA	LacI binding site	E.coli	FACS	Cassette Ligation	Illumina	SRP146291	CSV
30721031	10.1021/acssynbio.8b00486	Wrenbeck	2019	DMS	pyrrolidine ketide synthase, levoglucosan kinase	E.coli	VAMP-seq	NNN, NNK PCR	Illumina	SUB4818031	CSV
30723160	10.1074/jbc.RA118.006173	Park	2020	DMS	T1R2	Expi293F	FACS, surface expression	error-prone PCR	Illumina	GSE115751	XLS
30761651	10.1002/jmr.2778	Wollacott	2019	DMS	Proliferation-inducing ligand	Yeast	Binding by FACS	NNK PCR	Illumina	No	No
30778069	10.1038/s41467-019-08777-y	Michaels	2019	MPRA	microRNA	HEK293T	polysome profiling	degenerate oligos	Illumina	PRJNA516224	No
30886357	10.1038/s41564-019-0399-4	Setoh	2019	DMS	Zika envelope	Zika	viral replication	NNN PCR	Illumina (barcoded)	PRJNA449413	CSV
30894475	10.1128/JVI.00219-19	Heredia	2019	DMS	Env	Expi293F	Binding by FACS	overlap extension PCR	Illumina (barcoded)	GSE102276, GSE117328, GSE126136	XLS
30936490	10.1038/s41564-019-0412-y	Noda-Garcia	2019	DMS	GDH	Bacteria	Growth	NNS PCR	Illumina	No	XLS
30956043	10.1016/j.molcel.2019.02.003	Ahler	2019	DMS	Src	Yeast	Growth	NNK PCR	Illumina (barcoded and subassembly)	GSE114098	XLS
30969963	10.1371/journal.pgen.1008079	Pokusaeva	2019	DMS	IGPD	Yeast	Growth	?	Illumina	GSE99990	TXT
30977563	10.1002/humu.23762	Wan	2019	DMS	rhodopsin	HEK293T	FACS, surface expression	site-directed mutagenesis	Illumina	No	XLS
31019050	10.1128/JVI.00161-19	Hom	2019	DMS	matrix protein	Human/influenza A	viral replication	NNN PCR	Illumina (barcoded)	SRP144482	CSV
31038123	10.7554/eLife.45079	Soh	2019	DMS	PB2	Influenza	viral replication	NNN PCR	Illumina (barcoded)	PRJNA511556	CSV
31081325	10.1021/acssynbio.9b00104	Nikoomanzar	2019	DMS	Kod DNA polymerase	E.coli	activity by DrOPS	site-directed mutagenesis	Illumina	No	No
31242389	10.1021/acs.molpharmaceut.9b00418	Klesmith	2019	DMS	CD19	Yeast	Binding by FACS	NNK PCR	Illumina	No	No
31267113	10.1038/s41587-019-0164-5	Sample	2019	MPRA	5' UTR	human cells	polysome profiling	random bases	Illumina	GSE114002	No
31325330	10.1002/prot.25786	Warszawski	2020	DMS	basigin	Yeast	Binding, expression	NNS PCR	Illumina (barcoded)	No	XLS
31395865	10.1038/s41467-019-11526-w	Kircher	2019	MPRA	Multiple mammalian promoters and enhancers	multiple cell lines	Transcription	error-prone PCR	Illumina	GSE126550	TXT
31400199	10.1093/molbev/msz184	Faber	2019	DMS	AmiE	E.coli	Growth	Pfunkel	Illumina (barcoded)	SRA SAMN11258744-SAMN11258771	XLS
31442220	10.1371/journal.pcbi.1007207	Warszawski	2019	DMS	IgG	Yeast	Binding, expression	NNS PCR	Illumina (barcoded)	https://www.addgene.org/110212/	XLS
31511387	10.1128/JVI.01291-19	Sourisseau	2019	DMS	Zika envelope	Human/Zika	viral replication	NNN PCR	Illumina (barcoded)	PRJNA530795	XLS
31558564	10.1534/g3.119.400535	Gray	2019	DMS	amyloid beta 42	Yeast	Growth	NNK PCR	Illumina	GSE139122	TSV
31697803	10.1182/blood.2019002561	Bridgford	2020	DMS	MPL	Ba/F3 cells	Growth	NNN PCR	Illumina	SRR10193506	TXT
31808666	10.1021/acschembio.9b00669	Zinkus-Boltz	2019	DMS	RAF	E.coli	Binding	error-prone PCR	Illumina	No	XLS
31925410	10.1038/s41594-019-0358-z	Persky	2020	DMS	CDK4, CDK6	Human cells	Growth	MITE	?	PRJNA559517	XLS
32004414	10.1111/cts.12758	Zhang	2020	DMS	CYP2C9, CYP2C19	HEK293T	VAMP-seq	Nicking mutagenesis	Illumina	No	DOC
32094176	10.1073/pnas.1915680117	Suiter	2020	DMS	NUDT15	HEK293T	VAMP-seq, drug sensitivity	Synthesized	Illumina	No	XLS
32144244	10.1038/s41467-020-15102-5	Wu	2020	DMS	HA	Influenza	Growth	?	Illumina	PRJNA563320	XLS
32152544	10.1038/s41589-020-0480-6	Newberry	2020	DMS	alpha-synuclein	Yeast	Growth	Provided	Illumina (barcoded)	PRJNA564806	XLS
32175691	10.15252/msb.20199265	Choudhury	2020	DMS	rpoB	E.coli	Rifampicin resistance	CRISPR	Miseq	GSE143629	CSV
32181350	10.1126/sciadv.aay7505	Penn	2020	DMS	rhodopsin	HEK293T	FACS, surface expression	NNN PCR	Illumina	No	PDF (Counts)
32238226	10.1099/mgen.0.000364	Andrews	2020	DMS	LamB	E.coli	Growth	error prone pcr	Illumina	PRJNA604031	XLS
32385156	10.1073/pnas.1918680117	Mehlhoff	2020	DMS	TEM-1 BL	E.coli	Growth	NNN PCR	Illumina	PRJNA565437	XLS
32510322	10.7554/eLife.56707	Chen	2020	DMS	VIM-2 lactamase	E.coli	Antibiotics resistance	NNN PCR	Illumina	PRJNA606894	XLS
32511321	10.1101/2020.03.16.994236	Procko	2020	DMS	ACE2	Expi293F	FACS, Binding	NNK PCR	Illumina	GSE147194	XLS
32554590	10.1126/science.aaz5143	Wu	2020	DMS	HA	Influenza	Growth	NNS/NNK PCR	Illumina	PRJNA510654, PRJNA493101, PRJNA510700	TXT
32587970	10.1101/2020.06.17.157982	Starr	2020	DMS	SARS-CoV-2 spike	yeast	Yeast display	NNS PCR	Illumina	PRJNA639956	TXT
32701056	10.7554/eLife.53476	Thompson	2020	DMS	DHFR	E.coli	Growth	NNS PCR	Illumina	?	CSV
32703877	10.1101/2020.04.01.020487	Russ	2020	DMS	Chorismate mutase	E.coli	Growth	oligo synthesis	Illumina	No	No
32744131	10.1080/19420862.2020.1803646	Simons	2020	DMS	IgG	Yeast	Binding by FACS	error-prone PCR, NNK PCR	Sequel System	No	TIF
32747536	10.1073/pnas.1909634117	Walker	2020	DMS	23S rRNA	E.coli	Growth	?	Illumina (barcoded)	Bioproject 511591	No
32786289	10.1101/2020.05.01.072884	Newberry	2020	DMS	alpha-synuclein	Yeast	Compound resistance	Provided	Illumina (barcoded)	PRJNA56480	XLS
32870157	10.1101/2020.05.10.087312	Chiasson	2020	DMS	VKOR	HEK293T	VAMP-seq	Mutagenesis primer	Illumina (barcoded)	GSE149922	CSV
-	10.1101/2020.06.26.174375	Nedrud	2020	DMS	PSD95 PDZ	E.coli	Binding	oligo synthesis	Illumina	No (private)	No (private)
-	10.1101/623108	Jones	2020	DMS	ADRB2	HEK293T	Receptor activity	oligo synthesis	Illumina (barcoded)	No (preprint)	TSV
31467279	10.1038/s41467-019-11735-3	Li	2019	DMS	Phage lambda repressor	E.coli	Transcription	doped oligonucleotide synthesis	Illumina	GSE122806	XLS
31527666	10.1038/s41467-019-12130-8	Poelwijk	2019	DMS	Entacmaea quadricolor fluorescent protein	E.coli	Fluorescence	?	Illumina (barcoded)	PRJNA560590	XLS
29849145	10.1038/s41586-018-0170-7	Domingo	2018	DMS	Yeast tRNA	Yeast	Growth	oligo synthesise	Illumina	GSE99418	XLS
31745561	10.1093/nar/gkz1110	Coyote-Maestas	2020	DMS	HEK293FT	Kir2.1	Surface expression	saturated programmable insertion engineering	Illumina	PRJNA506141, PRJNA554355	No
32500953	10.15252/msb.20209442	Hasle	2020	DMS	U-2 OS H3-Dendra2	simian virus 40 NLS	Visual cell sorting	NNK PCR	Illumina	GSE141030	XLS
27545349	10.1016/j.cell.2016.07.024	Keren	2016	MPRA	Designed and native promoters	Yeast	Growth, fluorescence transcription	microarray synthesis	Illumina	GSE83936	No
31519910	10.1038/s41467-019-12101-z	Bolognesi	2019	DMS	TDP-43 prion-like domain	Yeast	Protein hydrophobicity	error-prone PCR	Illumina	GSE128165	XLS
31727844	10.1073/pnas.1916916116	Tang	2019	DMS	PD-1	Yeast	Binding, FACS	NNN PCR	?	No	No
32313011	10.1038/s41467-020-15796-7	Despres	2020	DMS	Yeast essential genes	Yeast	Growth	CRISPR	Illumina	PRJNA552472	No
32098152	10.3390/v12020241	Roop	2020	DMS	HIV env	HIV/Human and macaque 293T	Growth	NNN PCR	Illumina (barcoded)	SRX5199658–SRX5199665	CSV
32019920	10.1038/s41467-020-14495-7	Yoo	2020	DMS	human adenosine A2a receptor	Yeast	Binding, FACS	NNS PCR	Illumina	PRJNA545342	No
32000841	10.1186/s13073-020-0711-1	Sun	2020	DMS	cystathionine beta-synthase (CBS)	Yeast	Growth	popcode	Illumina	No	XLS
32559251	10.1371/journal.ppat.1008647	Park	2020	DMS	Platelet-derived growth factor receptor alpha	Expi293F	Binding, FACS	NNK PCR	Illumina	GSE138169	XLS
31928070	10.1161/CIRCGEN.119.002786	Glazer	2020	DMS	SCN5A	HEK293	Drug resistance	NNN PCR	Illumina (barcoded)	No	XLS
31825605	10.1021/acssynbio.9b00411	Faber	2020	DMS	F capsid and G spike protein	Phi X 174/E.coli	Growth	Nicking mutagenesis	Illumina	SAMN12660301-SAMN12660308	No
31796585	10.1073/pnas.1915562116	McShan	2019	DMS	MHCI	Expi293F	Surface expression, binding affinity	site-directed mutagenesis	Illumina	GSE128957	XLS
30301798	10.1073/pnas.1809901115	Rogers	2018	DMS	PUMA and CP2	in vivo	Binding	NNK PCR	Illumina	No	No
31452511	10.7554/eLife.49324	Lee	2019	DMS	HA	Influenza/human sera	Antibody binding	NNN PCR	Illumina	SAMN10183083, SAMN11310465, SAMN10183146, SAMN11341221, SAMN11310371-SAMN11310373	CSV
30908907	10.1021/acssynbio.8b00529	McGeachy	2019	DMS	RPL28	Yeast	Cycloheximide resistance	error-prone PCR	Illumina (barcoded)	No	No