Recent Preprints
Multiplex, multimodal mapping of variant effects in secreted proteins Nicholas A Popp, Rachel L Powell, Melinda K Wheelock, Brendan D Zapp, Kristen J Holmes, Kathryn M Sheldon, Shelley N Fletcher, Xiaoping Wu, Shawn Fayer, Alan F Rubin, Kerry W Lannert, Alexis Taylor Chang, John P Sheehan, Jill M Johnsen and Douglas M Fowler bioRxiv; doi: 10.1101/2024.04.01.587474
A missense variant effect map for the human tumour suppressor protein CHK2 Marinella Gebbia, Daniel Zimmerman, Rosanna Jiang, Maria Nguyen, Jochen Weile, Roujia Li, Michelle Gavac, Nishka Kishore, Song Sun, Rick A Boonen, Jennifer N.Dines, Alexander Wahl, Jason Reuter, Britt Johnson, Douglas M Fowler, Haico van Attikum, Frederick P Roth bioRxiv 2024.02.13.579700; doi: https://doi.org/10.1101/2024.02.13.579700
Pseudotime analysis for time-series single-cell sequencing and imaging data Gang Li, Hyeon-Jin Kim, Sriram Pendyala, Ran Zhang, Christine M. Disteche, Jean-Philippe Vert, Xinxian Deng, Douglas M. Fowler, William Stafford Noble bioRxiv 2023.11.03.565575; doi: 10.1101/2023.11.03.565575
Deep mutational scanning of CYP2C19 reveals a substrate specificity-abundance tradeoff Gabriel E. Boyle, Katherine Sitko, Jared G. Galloway, Hugh K. Haddox, Aisha Haley Bianchi, Ajeya Dixon, Raine E. S. Thomson, Riddhiman K. Garge, Allan E. Rettie, Alan Rubin, Renee C. Geck, Elizabeth M. J. Gillam, William S. DeWitt, Frederick A. Matsen IV, Douglas M. Fowler bioRxiv 2023.10.06.561250; doi: https://doi.org/10.1101/2023.10.06.561250
Deep mutational scanning reveals a tight correlation between protein degradation and toxicity of thousands of non-native aspartoacylase protein variants Martin Grønbæk-Thygesen, Vasileios Voutsinos, Kristoffer E Johansson, Thea K Schulze, Matteo Cagiada, Line Pedersen, Lene Clausen, Snehal Nariya, Rachel L Powell, Amelie Stein, Douglas M Fowler, Kresten Lindorff-Larsen and Rasmus Hartmann-Petersen bioRxiv.posted 2 October 2023, 10.1101/2023.10.02.560410
Machine vision reveals micronucleus rupture as a potential driver of the transcriptomic response to aneuploidy Lucian DiPeso, Sriram Pendyala, Heather Z Huang, Douglas M Fowler, Emily M Hatch bioRxiv 2023.05.04.539483; doi: 10.1101/2023.05.04.539483
High-throughput functional mapping of variants in an arrhythmia gene, KCNE1, reveals novel biology Ayesha Muhammad, Maria E Calandranis, Bian Li, Tao Yang, Daniel J Blackwell, Margaret L Harvey, Jeremy E Smith, Ashli E Chew, John A Capra, Kenneth A Matreyek, Douglas M Fowler, Dan M Roden, Andrew M Glazer bioRxiv 2023.04.28.538612; doi: 10.1101/2023.04.28.538612
MaveDB v2: a curated community database with over three million variant effects from multiplexed functional assays Alan F Rubin, Joseph K Min, Nathan J Rollins, Estelle Y Da, Daniel Esposito, Matthew Harrington, Jeremy Stone, Aisha Haley Bianchi, Mafalda Dias, Jonathan Frazer, Yunfan Fu, Molly Gallaher, Iris Li, Olivia Moscatelli, Jesslyn YL Ong, Joshua E Rollins, Matthew J Wakefield, Shenyi “Sunny” Ye, Amy Tam, Abbye E McEwen, Lea M Starita, Vanessa L Bryant, Debora S Marks, Douglas M Fowler doi: 10.1101/2021.11.29.470445
PUBLICATIONS
2024
Pacybara: Accurate long-read sequencing for barcoded mutagenized allelic libraries. Weile J, Ferra G, Boyle G, Pendyala S, Amorosi C, Yeh CL, Cote AG, Kishore N, Tabet D, van Loggerenberg W, Rayhan A, Fowler DM, Dunham MJ, Roth FP. Bioinformatics. 2024 Apr 3:btae182. doi: 10.1093/bioinformatics/btae182. Online ahead of print. PMID: 38569896
Critical Assessment of Genome Interpretation Consortium. CAGI, the Critical Assessment of Genome Interpretation, establishes progress and prospects for computational genetic variant interpretation methods. Genome Biol. 2024 Feb 22;25(1):53. doi: 10.1186/s13059-023-03113-6. PMID: 38389099; PMCID: PMC10882881.
A mutational atlas for Parkin proteostasis. Clausen L, Voutsinos V, Cagiada M, Johansson KE, Grønbæk-Thygesen M, Nariya S, Powell RL, Have MKN, Oestergaard VH, Stein A, Fowler DM, Lindorff-Larsen K, Hartmann-Petersen R. Nat Commun. 2024 Feb 20;15(1):1541. doi: 10.1038/s41467-024-45829-4. PMID: 38378758.
Multiplexed Functional Assessments of MYH7 Variants in Human Cardiomyocytes. Friedman CE, Fayer S, Pendyala S, Chien WM, Loiben A, Tran L, Chao LS, McKinstry A, Ahmed D, Farris SD, Stempien-Otero A, Jonlin EC, Murry CE, Starita LM, Fowler DM, Yang KC.Circ Genom Precis Med. 2024 Feb 16:e004377. doi: 10.1161/CIRCGEN.123.004377. Online ahead of print.PMID: 38362799
Profiling of drug resistance in Src kinase at scale uncovers a regulatory network coupling autoinhibition and catalytic domain dynamics. Chakraborty S, Ahler E, Simon JJ, Fang L, Potter ZE, Sitko KA, Stephany JJ, Guttman M, Fowler DM, Maly DJ.Cell Chem Biol. 2024 Feb 15;31(2):207-220.e11. doi: 10.1016/j.chembiol.2023.08.005. Epub 2023 Sep 7.PMID: 37683649
Will variants of uncertain significance still exist in 2030? Fowler DM, Rehm HL. Am J Hum Genet. 2024 Jan 4;111(1):5-10. doi: 10.1016/j.ajhg.2023.11.005. Epub 2023 Dec 11. PMID: 38086381; PMCID: PMC10806733.
2023
Antigen perception in T cells by long-term Erk and NFAT signaling dynamics. Wither MJ, White WL, Pendyala S, Leanza PJ, Fowler DM, Kueh HY. Proc Natl Acad Sci U S A. 2023;120(52):e2308366120. doi:10.1073/pnas.2308366120 Epub 2023 Dec 19. PMID: 38113261
Optogenetic Microwell Array Screening System: A High-Throughput Engineering Platform for Genetically Encoded Fluorescent Indicators. Rappleye M, Wait SJ, Lee JD, Siebart JC, Torp L, Smith N, Muster J, Matreyek KA, Fowler DM, Berndt A. ACS Sens. 2023;8(11):4233-4244. doi:10.1021/acssensors.3c01573 PMID: 37956352
An Atlas of Variant Effects to understand the genome at nucleotide resolution. Fowler DM, Adams DJ, Gloyn AL, Hahn WC, Marks DS, Muffley LA, Neal JT, Roth FP, Rubin AF, Starita LM, Hurles ME. Genome Biol. 2023 Jul 3;24(1):147. doi: 10.1186/s13059-023-02986-x. PMID: 37394429
CRaTER enrichment for on-target gene-editing enables generation of variant libraries in hiPSCs Friedman CE, Fayer S, Pendyala S, Chien WM, Loiben A, Tran L, Chao LS, Mckinstry A, Ahmed D, Karbassi E, Fenix AM, Murry CE, Starita LM, Fowler DM, Yang KC. J Mol Cell Cardiol. 2023;179:60-71. doi:10.1016/j.yjmcc.2023.03.017. PMID: 37019277.
Molecular determinants of Hsp90 dependence of Src kinase revealed by deep mutational scanning. Nguyen V, Ahler E, Sitko KA, Stephany JJ, Maly DJ, Fowler DM. Epub 2023 May 11. Protein Sci. 2023;e4656. doi:10.1002/pro.4656
A chemically controlled Cas9 switch enables temporal modulation of diverse effectors. Wei CT, Popp NA, Peleg O, Powell RL, Borenstein E, Maly DJ, Fowler DM. Nat Chem Biol (2023). Epub 2022 Mar 06. doi: 10.1038/s41589-023-01278-6 PMID: 36879061
2022
Environmental selection and epistasis in an empirical phenotype-environment-fitness landscape JZ Chen, DM Fowler, N Tokuriki. Nat Ecol Evol 6, 427–438 (2022). Epub 2022 Feb 24. doi: 10.1038/s41559-022-01675-5 PMID: 35210579
2021
Probing ion channel functional architecture and domain recombination compatibility by massively parallel domain insertion profiling Coyote-Maestas W, Nedrud D, Suma A, He Y, Matreyek KA, Fowler DM, Carnevale V, Myers CL, Schmidt D. Nat Commun. 2021 Dec 8;12(1):7114. doi: 10.1038/s41467-021-27342-0. PMID: 34880224
Closing the gap: Systematic integration of multiplexed functional data resolves variants of uncertain significance in BRCA1, TP53, and PTEN Fayer S, Horton C, Dines JN, Rubin AF, Richardson ME, McGoldrick K, Hernandez F, Pesaran T, Karam R, Shirts BH, Fowler DM, Starita LM. Am J Hum Genet. 2021 Dec 2;108(12):2248-2258. doi: 10.1016/j.ajhg.2021.11.001. Epub 2021 Nov 17. PMID: 34793697
Integrating thousands of PTEN variant activity and abundance measurements reveals variant subgroups and new dominant negatives in cancers Matreyek KA, Stephany JJ, Ahler E, Fowler DM. Genome Med. 2021 Oct 14;13(1):165. doi: 10.1186/s13073-021-00984-x. PMID: 34649609
MaveRegistry: a collaboration platform for multiplexed assays of variant effect. Da Kuang, Weile J, Kishore N, Rubin AF, Fields S, Fowler DM, Roth FP. Bioinformatics. 2021 Oct 1; 37(19): 3382–3383. doi: 10.1093/bioinformatics/btab215. PMID: 33774657
Measuring Pharmacogene Variant Function at Scale Using Multiplexed Assays Renee C Geck, Gabriel Boyle, Clara J Amorosi, Douglas M Fowler, Maitreya J Dunham. Annu Rev Pharmacol Toxicol. 2022 Jan 6;62:531-550. doi: 10.1146/annurev-pharmtox-032221-085807. Epub 2021 Sep 13. PMID: 34516287
Massively parallel characterization of CYP2C9 variant enzyme activity and abundance Amorosi CJ, Chiasson MA, McDonald MG, Wong LH, Sitko KA, Boyle G, Kowalski JP, Rettie AE, Fowler DM, Dunham MJ. Am J Hum Genet. 2021 Sep 2;108(9):1735-1751. doi: 10.1016/j.ajhg.2021.07.001.Epub 2021 Jul 26.. PMID: 34314704
Understanding the origins of loss of protein function by analyzing the effects of thousands of variants on activity and abundance. Cagiada M, Johansson KE, Valanciute A, Nielsen SV, Hartmann-Petersen R, Yang JJ, Fowler DM, Stein A, Lindorff-Larsen K. Mol Biol Evol. 2021 Jul 29;38(8):3235-3246. doi: 10.1093/molbev/msab095. PMID: 33779753
2020
High-throughput discovery of trafficking-deficient variants in the cardiac potassium channel KV11.1. Kozek KA, Glazer AM, Ng CA, Blackwell D, Egly CL, Vanags LR, Blair M, Mitchell D, Matreyek KA, Fowler DM, Knollmann BC, Vandenberg JI, Roden DM, Kroncke BM. Heart Rhythm. 2020 Dec;17(12):2180-2189. doi: 10.1016/j.hrthm.2020.05.041. Epub 2020 Jun 6. PMID: 32522694
Multiplexed measurement of variant abundance and activity reveals VKOR topology, active site and human variant impact. Chiasson MA, Rollins NJ, Stephany JJ, Sitko KA, Matreyek KA, Verby M, Sun S, Roth FP, DeSloover D, Marks DS, Rettie AE, Fowler DM. Elife. 2020 Sep 1;9:e58026. doi: 10.7554/eLife.58026. PMID: 32870157
Parallel Chemoselective Profiling for Mapping Protein Structure. Potter ZE, Lau HT, Chakraborty S, Fang L, Guttman M, Ong SE, Fowler DM, Maly DJ. Cell Chem Biol. 2020 Aug 20;27(8):1084-1096.e4. Epub 2020 Jul 9. doi: 10.1016/j.chembiol.2020.06.014. PMID: 32649906
Comprehensive exploration of the translocation, stability and substrate recognition requirements in VIM-2 lactamase. Chen JZ, Fowler DM, Tokuriki N. Elife. 2020 Jun 8;9:e56707. doi: 10.7554/eLife.56707. PMID: 32510322
High-throughput, microscope-based sorting to dissect cellular heterogeneity. Hasle N, Cooke A, Srivatsan S, Huang H, Stephany JJ, Krieger Z, Jackson D, Tang W, Pendyala S, Monnat RJ Jr, Trapnell C, Hatch EM, Fowler DM. Mol Syst Biol. 2020 Jun;16(6):e9442. doi: 10.15252/msb.20209442. PMID: 32500953
Suppression of unwanted CRISPR-Cas9 editing by co-administration of catalytically inactivating truncated guide RNAs. Rose JC, Popp NA, Richardson CD, Stephany JJ, Mathieu J, Wei CT, Corn JE, Maly DJ, Fowler DM. Nat Commun. 2020 Jun 1;11(1):2697. doi: 10.1038/s41467-020-16542-9. PMID: 32483117
A Premalignant Cell-Based Model for Functionalization and Classification of PTEN Variants. Chao JT, Hollman R, Meyers WM, Meili F, Matreyek KA, Dean P, Fowler DM, Haas K, Roskelley CD, Loewen CJR. Cancer Res. 2020 Jul 1;80(13):2775-2789. doi: 10.1158/0008-5472.CAN-19-3278. Epub 2020 May 4. PMID: 32366478
Massively parallel variant characterization identifies NUDT15 alleles associated with thiopurine toxicity. Suiter CC, Moriyama T, Matreyek KA, Yang W, Scaletti ER, Nishii R, Yang W, Hoshitsuki K, Singh M, Trehan A, Parish C, Smith C, Li L, Bhojwani D, Yuen LYP, Li CK, Li CH, Yang YL, Walker GJ, Goodhand JR, Kennedy NA, Klussmann FA, Bhatia S, Relling MV, Kato M, Hori H, Bhatia P, Ahmad T, Yeoh AEJ, Stenmark P, Fowler DM, Yang JJ. Proc Natl Acad Sci U S A. 2020 Mar 10;117(10):5394-5401. doi: 10.1073/pnas.1915680117. Epub 2020 Feb 24. PMID: 32094176
Temporal and rheostatic control of genome editing with a chemically-inducible Cas9. Wei CT, Maly DJ, Fowler DM. Methods Enzymol. 2020;633:119-141. doi: 10.1016/bs.mie.2019.11.001. Epub 2019 Nov 22. PMID: 32046842
Deep Mutational Scan of an SCN5A Voltage Sensor. Glazer AM, Kroncke BM, Matreyek KA, Yang T, Wada Y, Shields T, Salem JE, Fowler DM, Roden DM. Circ Genom Precis Med. 2020 Feb;13(1):e002786. doi: 10.1161/CIRCGEN.119.002786. Epub 2020 Jan 12. PMID: 31928070
An improved platform for functional assessment of large protein libraries in mammalian cells. Matreyek KA, Stephany JJ, Chiasson MA, Hasle N, Fowler DM. Nucleic Acids Res. 2020 Jan 10;48(1):e1. doi: 10.1093/nar/gkz910. PMID: 31612958
Systematic misclassification of missense variants in BRCA1 and BRCA2 "coldspots". Dines JN, Shirts BH, Slavin TP, Walsh T, King MC, Fowler DM, Pritchard CC. Genet Med. 2020 May;22(5):825-83. doi: 10.1038/s41436-019-0740-6. Epub 2020 Jan 8. PMID: 31911673
2019
Keeping up with the genomes: scaling genomic variant interpretation. Rehm HL, Fowler DM. Genome Med. 2019 Dec 31;12(1):5. doi: 10.1186/s13073-019-0700-4. PMID: 31892366
Recommendations for the collection and use of multiplexed functional data for clinical variant interpretation. Gelman H, Dines JN, Berg J, Berger AH, Brnich S, Hisama FM, James RG, Rubin AF, Shendure J, Shirts B, Fowler DM, Starita LM; Brotman Baty Institute Mutational Scanning Working Group. Genome Med. 2019 Dec 20;11(1):85. doi: 10.1186/s13073-019-0698-7. PMID: 31862013
Elucidating the Molecular Determinants of Aβ Aggregation with Deep Mutational Scanning. Gray VE, Sitko K, Kameni FZN, Williamson M, Stephany JJ, Hasle N, Fowler DM. G3 (Bethesda). 2019 Nov 5;9(11):3683-3689. doi: 10.1534/g3.119.400535. PMID: 31558564
MaveDB: an open-source platform to distribute and interpret data from multiplexed assays of variant effect. Esposito D, Weile J, Shendure J, Starita LM, Papenfuss AT, Roth FP, Fowler DM, Rubin AF. Genome Biol. 2019 Nov 4;20(1):223. doi: 10.1186/s13059-019-1845-6. PMID: 31679514
The Impact of Genetic Variants on PTEN Molecular Functions and Cellular Phenotypes. Hasle N, Matreyek KA, Fowler DM. Cold Spring Harb Perspect Med. 2019 Nov 1;9(11):a036228. doi: 10.1101/cshperspect.a036228. PMID: 31451538
Interrogation of CYP2D6 Structural Variant Alleles Improves the Correlation Between CYP2D6 Genotype and CYP2D6-Mediated Metabolic Activity. Dalton R, Lee SB, Claw KG, Prasad B, Phillips BR, Shen DD, Wong LH, Fade M, McDonald MG, Dunham MJ, Fowler DM, Rettie AE, Schuetz E, Thornton TA, Nickerson DA, Gaedigk A, Thummel KE, Woodahl EL. Clin Transl Sci. 2020 Jan;13(1):147-156. doi: 10.1111/cts.12695. Epub 2019 Oct 25. PMID: 31536170
Mutagenesis-based protein structure determination. Chiasson M, Fowler DM. Nat Genet. 2019 Jul;51(7):1072-1073. doi: 10.1038/s41588-019-0461-4. PMID: 31253976
Applying Multiplex Assays to Understand Variation in Pharmacogenes. Chiasson M, Dunham MJ, Rettie AE, Fowler DM. Clin Pharmacol Ther. 2019 Aug;106(2):290-294. doi: 10.1002/cpt.1468. Epub 2019 May 30. PMID: 31145826
A Combined Approach Reveals a Regulatory Mechanism Coupling Src's Kinase Activity, Localization, and Phosphotransferase-Independent Functions. Ahler E, Register AC, Chakraborty S, Fang L, Dieter EM, Sitko KA, Vidadala RSR, Trevillian BM, Golkowski M, Gelman H, Stephany JJ, Rubin AF, Merritt EA, Fowler DM, Maly DJ. Mol Cell. 2019 Apr 18;74(2):393-408.e20. doi: 10.1016/j.molcel.2019.02.003. Epub 2019 Apr 4. PMID: 30956043
Biophysical and Mechanistic Models for Disease-Causing Protein Variants. Stein A, Fowler DM, Hartmann-Petersen R, Lindorff-Larsen K. Trends Biochem Sci. 2019 Jul;44(7):575-588. doi: 10.1016/j.tibs.2019.01.003. Epub 2019 Jan 31. PMID: 30712981
2018
Multiplex assessment of protein variant abundance by massively parallel sequencing. Matreyek KA, Starita LM, Stephany JJ, Martin B, Chiasson MA, Gray VE, Kircher M, Khechaduri A, Dines JN, Hause RJ, Bhatia S, Evans WE, Relling MV, Yang W, Shendure J, Fowler DM. Nat Genet. 2018 Jun;50(6):874-882. doi: 10.1038/s41588-018-0122-z. Epub 2018 May 21. PMID: 29785012
2017
Pharmacogenomics of CYP2C9: Functional and Clinical Considerations. Daly AK, Rettie AE, Fowler DM, Miners JO. J Pers Med. 2017 Dec 28;8(1):1. doi: 10.3390/jpm8010001. PMID: 29283396
A framework for exhaustively mapping functional missense variants. Weile J, Sun S, Cote AG, Knapp J, Verby M, Mellor JC, Wu Y, Pons C, Wong C, van Lieshout N, Yang F, Tasan M, Tan G, Yang S, Fowler DM, Nussbaum R, Bloom JD, Vidal M, Hill DE, Aloy P, Roth FP. Mol Syst Biol. 2017 Dec 21;13(12):957. doi: 10.15252/msb.20177908. PMID: 29269382
Quantitative Missense Variant Effect Prediction Using Large-Scale Mutagenesis Data. Gray VE, Hause RJ, Luebeck J, Shendure J, Fowler DM. Cell Syst. 2018 Jan 24;6(1):116-124.e3. doi: 10.1016/j.cels.2017.11.003. Epub 2017 Dec 6. PMID: 29226803
Expression and Functional Characterization of Breast Cancer-Associated Cytochrome P450 4Z1 in Saccharomyces cerevisiae. McDonald MG, Ray S, Amorosi CJ, Sitko KA, Kowalski JP, Paco L, Nath A, Gallis B, Totah RA, Dunham MJ, Fowler DM, Rettie AE. Drug Metab Dispos. 2017 Dec;45(12):1364-1371. doi: 10.1124/dmd.117.078188. Epub 2017 Oct 10. PMID: 29018033
Early emergence of negative regulation of the tyrosine kinase Src by the C-terminal Src kinase. Taskinen B, Ferrada E, Fowler DM. J Biol Chem. 2017 Nov 10;292(45):18518-18529. doi: 10.1074/jbc.M117.811174. Epub 2017 Sep 22. PMID: 28939764
Rheostatic Control of Cas9-Mediated DNA Double Strand Break (DSB) Generation and Genome Editing. Rose JC, Stephany JJ, Wei CT, Fowler DM, Maly DJ. ACS Chem Biol. 2018 Feb 16;13(2):438-442. doi: 10.1021/acschembio.7b00652. Epub 2017 Sep 15. PMID: 28895730
Variant Interpretation: Functional Assays to the Rescue. Starita LM, Ahituv N, Dunham MJ, Kitzman JO, Roth FP, Seelig G, Shendure J, Fowler DM. Am J Hum Genet. 2017 Sep 7;101(3):315-325. doi: 10.1016/j.ajhg.2017.07.014. PMID: 28886340
New Pharmacogenomics Research Network: An Open Community Catalyzing Research and Translation in Precision Medicine. Relling MV, Krauss RM, Roden DM, Klein TE, Fowler DM, Terada N, Lin L, Riel-Mehan M, Do TP, Kubo M, Yee SW, Johnson GT, Giacomini KM. Clin Pharmacol Ther. 2017 Dec;102(6):897-902. doi: 10.1002/cpt.755. Epub 2017 Aug 10. PMID: 28795399
A statistical framework for analyzing deep mutational scanning data. Rubin AF, Gelman H, Lucas N, Bajjalieh SM, Papenfuss AT, Speed TP, Fowler DM. Genome Biol. 2017 Aug 7;18(1):150. doi: 10.1186/s13059-017-1272-5. PMID: 28784151
Analysis of Large-Scale Mutagenesis Data To Assess the Impact of Single Amino Acid Substitutions. Gray VE, Hause RJ, Fowler DM. Genetics. 2017 Sep;207(1):53-61. doi: 10.1534/genetics.117.300064. Epub 2017 Jul 27. PMID: 28751422
Rapidly inducible Cas9 and DSB-ddPCR to probe editing kinetics. Rose JC, Stephany JJ, Valente WJ, Trevillian BM, Dang HV, Bielas JH, Maly DJ, Fowler DM. Nat Methods. 2017 Sep;14(9):891-896. doi: 10.1038/nmeth.4368. Epub 2017 Jul 24. PMID: 28737741
A platform for functional assessment of large variant libraries in mammalian cells. Matreyek KA, Stephany JJ, Fowler DM. Nucleic Acids Res. 2017 Jun 20;45(11):e102. doi: 10.1093/nar/gkx183. PMID: 28335006
Bedside Back to Bench: Building Bridges between Basic and Clinical Genomic Research. Manolio TA, Fowler DM, Starita LM, Haendel MA, MacArthur DG, Biesecker LG, Worthey E, Chisholm RL, Green ED, Jacob HJ, McLeod HL, Roden D, Rodriguez LL, Williams MS, Cooper GM, Cox NJ, Herman GE, Kingsmore S, Lo C, Lutz C, MacRae CA, Nussbaum RL, Ordovas JM, Ramos EM, Robinson PN, Rubinstein WS, Seidman C, Stranger BE, Wang H, Westerfield M, Bult C. Cell. 2017 Mar 23;169(1):6-12. doi: 10.1016/j.cell.2017.03.005. PMID: 28340351
2016
Novel Rhizosphere Soil Alleles for the Enzyme 1-Aminocyclopropane-1-Carboxylate Deaminase Queried for Function with an In Vivo Competition Assay. Jin Z, Di Rienzi SC, Janzon A, Werner JJ, Angenent LT, Dangl JL, Fowler DM, Ley RE. Appl Environ Microbiol. 2015 Dec 4;82(4):1050-9. doi: 10.1128/AEM.03074-15. Print 2016 Feb 15. PMID: 26637602
2015
Massively Parallel Functional Analysis of BRCA1 RING Domain Variants. Starita LM, Young DL, Islam M, Kitzman JO, Gullingsrud J, Hause RJ, Fowler DM, Parvin JD, Shendure J, Fields S. Genetics. 2015 Jun;200(2):413-22. doi: 10.1534/genetics.115.175802. Epub 2015 Mar 30. PMID: 25823446
2014
Measuring the activity of protein variants on a large scale using deep mutational scanning. Fowler DM, Stephany JJ, Fields S. Nat Protoc. 2014 Sep;9(9):2267-84. doi: 10.1038/nprot.2014.153. Epub 2014 Aug 28. PMID: 25167058
Deep mutational scanning: a new style of protein science. Fowler DM, Fields S. Nat Methods. 2014 Aug;11(8):801-7. doi: 10.1038/nmeth.3027. PMID: 25075907
2013
Contemporary, yeast-based approaches to understanding human genetic variation. Dunham MJ, Fowler DM. Curr Opin Genet Dev. 2013 Dec;23(6):658-64. doi: 10.1016/j.gde.2013.10.001. Epub 2013 Nov 16. PMID: 24252429
Engineering A-kinase anchoring protein (AKAP)-selective regulatory subunits of protein kinase A (PKA) through structure-based phage selection. Gold MG, Fowler DM, Means CK, Pawson CT, Stephany JJ, Langeberg LK, Fields S, Scott JD. J Biol Chem. 2013 Jun 14;288(24):17111-21. doi: 10.1074/jbc.M112.447326. Epub 2013 Apr 26. PMID: 23625929
Activity-enhancing mutations in an E3 ubiquitin ligase identified by high-throughput mutagenesis. Starita LM, Pruneda JN, Lo RS, Fowler DM, Kim HJ, Hiatt JB, Shendure J, Brzovic PS, Fields S, Klevit RE. Proc Natl Acad Sci U S A. 2013 Apr 2;110(14):E1263-72. doi: 10.1073/pnas.1303309110. Epub 2013 Mar 18. PMID: 23509263