RECENT PREPRINTS
Guidelines for releasing a variant effect predictor Benjamin J. Livesey, Mihaly Badonyi, Mafalda Dias, Jonathan Frazer, Sushant Kumar, Kresten Lindorff-Larsen, David M. McCandlish, Rose Orenbuch, Courtney A. Shearer, Lara Muffley, Julia Foreman, Andrew M. Glazer, Ben Lehner, Debora S. Marks, Frederick P. Roth, Alan F. Rubin, Lea M. Starita, Joseph A. Marsh. arXiv 2404.10807; doi: https://doi.org/10.48550/arXiv.2404.10807
Defining and Reducing Variant Classification Disparities Moez Dawood, Shawn Fayer, Sriram Pendyala, Mason Post, Divya Kalra, Karynne Patterson, Eric Venner, Lara A. Muffley, Douglas M. Fowler, Alan F. Rubin, Jennifer E. Posey, Sharon E. Plon, James R. Lupski, Richard A. Gibbs, Lea M. Starita, Carla Daniela Robles-Espinoza, Willow Coyote-Maestas, Irene Gallego Romero. medRxiv 2024.04.11.24305690; doi: https://doi.org/10.1101/2024.04.11.24305690
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
Genomics 2 Proteins portal: A resource and discovery tool for linking genetic screening outputs to protein sequences and structures Seulki Kwon, Jordan Safer, Duyen T. Nguyen, David Hoksza, Patrick May, Jeremy A. Arbesfeld, Alan F. Rubin, Arthur J Campbell, Alex Burgin, Sumaiya Iqbal. bioRxiv 2024.01.02.573913; doi: https://doi.org/10.1101/2024.01.02.573913
A multiplex, prime editing framework for identifying drug resistance variants at scale Florence M. Chardon, Chase C. Suiter, Riza M. Daza, Nahum T. Smith, Phoebe Parrish, Troy McDiarmid, Jean-Benoît Lalanne, Beth Martin, Diego Calderon, Amira Ellison, Alice H. Berger, Jay Shendure, Lea M. Starita bioRxiv 2023.07.27.550902; doi: https://doi.org/10.1101/2023.07.27.550902
Multiplexed functional assessments of MYH7 variants in human cardiomyocytes at scale Clayton E. Friedman, Shawn Fayer, Sriram Pendyala, Wei-Ming Chien, Linda Tran, Leslie S. Chao, Ashley McKinstry, Dania Ahmed, Alexander Loiben, Stephen D. Farris, April Stempien-Otero, Erica Jonlin, Charles E Murry, Lea M Starita, Douglas M. Fowler, Kai-Chun Yang bioRxiv 2023.07.28.551073; doi: https://doi.org/10.1101/2023.07.28.551073
Mapping MAVE data for use in human genomics applications Jeremy A Arbesfeld, Estelle Y Da, Kori Kuzma, Anika Paul, Tierra Farris, Kevin Riehle, Nuno Daniel Saraiva Agostinho, Jordan F Safer, Aleksandar Milosavljevic, Julia Foreman, Helen V Firth, Sarah E Hunt, Sumaiya Iqbal, Melissa Cline, Alan F Rubin, Alex H Wagner bioRxiv 2023.06.20.545702; doi: https://doi.org/10.1101/2023.06.20.545702
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: https://doi.org/10.1101/2023.05.04.539483
Characterizing glucokinase variant mechanisms using a multiplexed abundance assay Sarah Gersing, Thea K. Schulze, Matteo Cagiada, Amelie Stein, Frederick P. Roth, Kresten Lindorff-Larsen, Rasmus Hartmann-Petersen bioRxiv 2023.05.24.542036; doi: https://doi.org/10.1101/2023.05.24.542036
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: https://doi.org/10.1101/2023.04.28.538612
Integrating deep mutational scanning and low-throughput mutagenesis data to predict the impact of amino acid variants Yunfan Fu, Justin Bedo, Anthony T Papenfuss, Alan F Rubin. bioRxiv 2022.12.14.520494; doi: 10.1101/2022.12.14.520494
Empowering rare variant burden-based gene-trait association studies via optimized computational predictor choice Da Kuang, Roujia Li, Yingzhou Wu, Jochen Weile, Robert A. Hegele, Frederick P. Roth bioRxiv 2021.09.20.459182; doi: 10.1101/2021.09.20.459182
Proteostasis governs differential temperature sensitivity across embryonic cell types Michael W. Dorrity, Lauren M. Saunders, Madeleine Duran, Sanjay R. Srivatsan, Brent Ewing, Christine Queitsch, Jay Shendure, David W. Raible, David Kimelman, Cole Trapnell bioRxiv 2022.08.04.502669; doi: 10.1101/2022.08.04.502669
Proteome-wide identification of amino acid substitutions deleterious for protein function Ricard A. Rodriguez-Mias, Kyle N. Hess, Bianca Y. Ruiz, Ian R. Smith, Anthony S. Barente, Stephanie M. Zimmerman, Yang Y. Lu, William S. Noble, Stanley Fields, Judit Villen bioRxiv 2022.04.06.487405; doi: 10.1101/2022.04.06.487405
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 bioRxiv 2021.11.29.470445; doi: 10.1101/2021.11.29.470445
A systematic genotype-phenotype map for missense variants in the human intellectual disability-associated gene GDI1 Rachel A. Silverstein, Song Sun, Marta Verby, Jochen Weile, Yingzhou Wu, Frederick P. Roth bioRxiv 2021.10.06.463360; doi: 10.1101/2021.10.06.463360
Transcriptional re-wiring by mutation of the yeast Hsf1 oligomerization domain Elizabeth A. Morton, Michael W. Dorrity, Wei Zhou, Stanley Fields, Christine Queitsch bioRxiv 2020.05.23.112250; doi: 10.1101/2020.05.23.112250
PUBLICATIONS
2024
Minimum information and guidelines for reporting a Multiplexed Assay of Variant Effect. Claussnitzer M, Parikh VN, Wagner AH, Arbesfeld JA, Bult CJ, Firth HV, Muffley LA, Ba ANN, Riehle K, Roth FP, Tabet D, Bolognesi B, Glazer AM, Rubin AF. Genome Biol 25, 100 (2024). https://doi.org/10.1186/s13059-024-03223-9
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.
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 Review.
LTP2 hypomorphs show genotype-by-environment interaction in early seedling traits in Arabidopsis thaliana. Alexandre CM, Bubb KL, Schultz KM, Lempe J, Cuperus JT, Queitsch C.New Phytol. 2024 Jan;241(1):253-266. doi: 10.1111/nph.19334. Epub 2023 Oct 22.PMID: 37865885
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
Impact on splicing in Saccharomyces cerevisiae of random 50-base sequences inserted into an intron. Perchlik M, Sasse A, Mostafavi S, Fields S, Cuperus JT.RNA. 2023 Dec 18;30(1):52-67. doi: 10.1261/rna.079752.123. PMID: 37879864
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 Nov 24;8(11):4233-4244. doi: 10.1021/acssensors.3c01573. Epub 2023 Nov 13.PMID: 37956352
Anticodon sequence determines the impact of mistranslating tRNAAla variants. Cozma E, Rao M, Dusick M, Genereaux J, Rodriguez-Mias RA, Villén J, Brandl CJ, Berg MD.RNA Biol. 2023 Jan;20(1):791-804. doi: 10.1080/15476286.2023.2257471. Epub 2023 Sep 30.PMID: 37776539
Systematically testing human HMBS missense variants to reveal mechanism and pathogenic variation. van Loggerenberg W, Sowlati-Hashjin S, Weile J, Hamilton R, Chawla A, Sheykhkarimli D, Gebbia M, Kishore N, Frésard L, Mustajoki S, Pischik E, Di Pierro E, Barbaro M, Floderus Y, Schmitt C, Gouya L, Colavin A, Nussbaum R, Friesema ECH, Kauppinen R, To-Figueras J, Aarsand AK, Desnick RJ, Garton M, Roth FP.Am J Hum Genet. 2023 Oct 5;110(10):1769-1786. doi: 10.1016/j.ajhg.2023.08.012. Epub 2023 Sep 19.PMID: 37729906
Proteostasis governs differential temperature sensitivity across embryonic cell types. Dorrity MW, Saunders LM, Duran M, Srivatsan SR, Barkan E, Jackson DL, Sattler SM, Ewing B, Queitsch C, Shendure J, Raible DW, Kimelman D, Trapnell C.Cell. 2023 Nov 9;186(23):5015-5027.e12. doi: 10.1016/j.cell.2023.10.013.PMID: 37949057
Genome-scale mapping of DNA damage suppressors through phenotypic CRISPR-Cas9 screens Zhao Y, Tabet D, Rubio Contreras D, Lao L, Kousholt AN, Weile J, Melo H, Hoeg L, Feng S, Coté AG, Lin ZY, Setiaputra D, Jonkers J, Gingras AC, Gómez Herreros F, Roth FP, Durocher D.Mol Cell. 2023 Aug 3;83(15):2792-2809.e9. doi: 10.1016/j.molcel.2023.06.025. Epub 2023 Jul 20.PMID: 37478847
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 Aug;19(8):981-991. doi: 10.1038/s41589-023-01278-6.
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.
Substantial rDNA copy number reductions alter timing of development and produce variable tissue-specific phenotypes in C. elegans. Morton EA, Hall AN, Cuperus JT, Queitsch C. Genetics. 2023 May 4;224(1):iyad039. doi: 10.1093/genetics/iyad039. PMID: 36919976.
A comprehensive map of human glucokinase variant activity. Gersing S, Cagiada M, Gebbia M, Gjesing AP, Coté AG, Seesankar G, Li R, Tabet D, Weile J, Stein A, Gloyn AL, Hansen T, Roth FP, Lindorff-Larsen K, Hartmann-Petersen R. Genome Biol. 2023 Apr 26;24(1):97. doi: 10.1186/s13059-023-02935-8. PMID: 37101203; PMCID: PMC10131484.
Ribosomal DNA replication time coordinates completion of genome replication and anaphase in yeast Kwan EX, Alvino GM, Lynch KL, Levan PF, Amemiya HM, Wang XS, Johnson SA, Sanchez JC, Miller MA, Croy M, Lee SB, Naushab M, Bedalov A, Cuperus JT, Brewer BJ, Queitsch C, Raghuraman MK. Cell Reports, 2023 Mar 28, Volume 42, Issue 3, 112161, Epub 24 Feb 2023, doi: 10.1016/j.celrep.2023.112161 PMID: 36842087
Cardiomyocyte Apoptosis Is Associated with Contractile Dysfunction in Stem Cell Model of MYH7 E848G Hypertrophic Cardiomyopathy. Loiben AM, Chien WM, Friedman CE, Chao LS, Weber G, Goldstein A, Sniadecki NJ, Murry CE, Yang KC. Int J Mol Sci. 2023 Mar 3;24(5):4909. doi: 10.3390/ijms24054909. PMID: 36902340
Proactive Variant Effect Mapping Aids Diagnosis in Pediatric Cardiac Arrest Brendan J. Floyd, Jochen Weile, Prince J. Kannankeril, Andrew M. Glazer, Chloe M. Reuter, Calum A. MacRae, Euan A. Ashley, Dan M. Roden, Frederick P. Roth and Victoria N. Parikh Originally published 30 Jan 2023 Circulation: Genomic and Precision Medicine. 2023;16, doi: 10.1161/CIRCGEN.122.003792 PMID: 36716194
2022
Mapping functional regions of essential bacterial proteins with dominant-negative protein fragments Andrew Savinov, Andres Fernandez, Stanley Fields. Proc Natl Acad Sci U S A. 2022 Jun 28; 119(26):e2200124119. doi: 10.1073/pnas.2200124119. Epub 2022 Jun 24. PMID: 3574936
Scalable Functional Assays for the Interpretation of Human Genetic Variation. Tabet D, Parikh V, Mali P, Roth FP, Claussnitzer M, Annu Rev Genet. 2022 Nov 30;56:441-465. doi: 10.1146/annurev-genet-072920-032107. Epub 2022 Sep 2. PMID: 36055970
Coisolation of Peptide Pairs for Peptide Identification and MS/MS-Based Quantification. Smith IR, Eng JK, Barente AS, Hogrebe A, Llovet A, Rodriguez-Mias RA, Villén J. Anal Chem. 2022 Nov 8;94(44):15198-15206. doi: 10.1021/acs.analchem.2c01711. Epub 2022 Oct 28.PMID: 36306373
IsobaricQuant enables cross-platform quantification, visualization, and filtering of isobarically-labeled peptides Alexander Hogrebe, Kyle N. Hess, Ariadna Llovet, Y. Julian Ramos, Anthony S. Barente, Daniel Hernandez-Portugues, Ian R. Smith, Ricard A. Rodríguez-Mias, Judit Villén Proteomics. 2022 Jul 1:e2100253. doi: 10.1002/pmic.202100253. Epub ahead of print. PMID: 35776068.
2021
SwabExpress: An End-to-End Protocol for Extraction-Free COVID-19 Testing. Srivatsan S, Heidl S, Pfau B, Martin BK, Han PD, Zhong W, van Raay K, McDermot E, Opsahl J, Gamboa L, Smith N, Truong M, Cho S, Barrow KA, Rich LM, Stone J, Wolf CR, McCulloch DJ, Kim AE, Brandstetter E, Sohlberg SL, Ilcisin M, Geyer RE, Chen W, Gehring J; Seattle Flu Study Investigators; Kosuri S, Bedford T, Rieder MJ, Nickerson DA, Chu HY, Konnick EQ, Debley JS, Shendure J, Lockwood CM, Starita LM. Clin Chem. 2021 Dec 30;68(1):143-152. doi: 10.1093/clinchem/hvab132. PMID: 34286830
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, and 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
GA4GH: International policies and standards for data sharing across genomic research and healthcare. Heidi L Rehm, et al. Cell Genom. 2021 Nov 10;1(2):100029. doi:10.1016/j.xgen.2021.100029. PMID: 35072136
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 Kuang D, Weile J, Kishore N, Nguyen M, Rubin AF, Fields S, Fowler DM, Roth FP. Bioinformatics. 2021 Oct 11;37(19):3382-3383. doi: 10.1093/bioinformatics/btab215. PMID: 33774657
Improved pathogenicity prediction for rare human missense variants. Wu Y, Li R, Sun S, Weile J, Roth FP. Am J Hum Genet. 2021 Oct 7;108(10):1891-1906. doi: 10.1016/j.ajhg.2021.08.012. Epub 2021 Sep 21. PMID: 34551312
Balance between promiscuity and specificity in phage λ host range. Andrews B, Fields S. ISME J. 2021 Aug; 15(8):2195-2205. doi: 10.1038/s41396-021-00912-2. Epub 2021 Feb 15. PMID: 33589767
Shifting landscapes of human MTHFR missense-variant effects. Weile J, Kishore N, Sun S, Maaieh R, Verby M, Li R, Fotiadou I, Kitaygorodsky J, Wu Y, Holenstein A, Bürer C, Blomgren L, Yang S, Nussbaum R, Rozen R, Watkins D, Gebbia M, Kozich V, Garton M, Froese DS, Roth FP.Am J Hum Genet. 2021 Jul 1;108(7):1283-1300. doi: 10.1016/j.ajhg.2021.05.009. PMID: 34214447
Identification of phosphosites that alter protein thermal stability. Smith IR, Hess KN, Bakhtina AA, Valente AS, Rodríguez-Mias RA, Villén J. Nat Methods 18, 760–762 (2021). doi: https://doi.org/10.1038/s41592-021-01178-4. Epub 2021 Jun 17. PMID: 34140699
The regulatory landscape of Arabidopsis thaliana roots at single-cell resolution. Dorrity MW, Alexandre CM, Hamm MO, Vigil AL, Fields S, Queitsch C, Cuperus JT. Nat Commun. 2021 Jun 7;12(1):3334. doi: 10.1038/s41467-021-23675-y. PMID: 34099698
Comparable Specimen Collection from Both Ends of At-Home Midturbinate Swabs. Truong M, Pfau B, McDermot E, Han PD, Brandstetter E, Richardson M, Kim AE, Rieder MJ, Chu HY, Englund JA, Nickerson DA, Shendure J, Lockwood CM, Konnick EQ, Starita LM. J Clin Microbiol. 2021 Apr 20; 59(5):e03073-20. doi: 10.1128/JCM.03073-20. Print 2021 Apr 20. PMID: 33597259
Prioritizing genes for systematic variant effect mapping. Kuang D, Truty R, Weile J, Johnson B, Nykamp K, Araya C, Nussbaum RL, Roth FP. Bioinformatics. 2021 Apr 1; 36(22-23):5448-5455. doi: 10.1093/bioinformatics/btaa1008. PMID: 33300982
Thousands of high-quality sequencing samples fail to show meaningful correlation between 5S and 45S ribosomal DNA arrays in humans. Hall AN, Turner TN, Queitsch C. Sci Rep. 2021 Jan 11;11(1):449. doi: 10.1038/s41598-020-80049-y. PMID: 33432083; PMCID: PMC7801704.
Decoding Post-Translational Modification Crosstalk With Proteomics. Leutert M, Entwisle SW, Villén J. Mol Cell Proteomics. 2021;20:100129. doi: 10.1016/j.mcpro.2021.100129. Epub 2021 Jul 30. PMID: 34339852
2020
Multiplexed Functional Assessment of Genetic Variants in CARD11. Meitlis I, Allenspach EJ, Bauman BM, Phan IQ, Dabbah G, Schmitt EG, Camp ND, Torgerson TR, Nickerson DA, Bamshad MJ, Hagin D, Luthers CR, Stinson JR, Gray J, Lundgren I, Church JA, Butte MJ, Jordan MB, Aceves SS, Schwartz DM, Milner JD, Schuval S, Skoda-Smith S, Cooper MA, Starita LM, Rawlings DJ, Snow AL, James RG. Am J Hum Genet. 2020 Dec 3; 107(6):1029-1043. doi: 10.1016/j.ajhg.2020.10.015. Epub 2020 Nov 16. PMID: 33202260
Cryptic transmission of SARS-CoV-2 in Washington state. Bedford T, Greninger AL, Roychoudhury P, Starita LM, Famulare M, Huang ML, Nalla A, Pepper G, Reinhardt A, Xie H, Shrestha L, Nguyen TN, Adler A, Brandstetter E, Cho S, Giroux D, Han PD, Fay K, Frazar CD, Ilcisin M, Lacombe K, Lee J, Kiavand A, Richardson M, Sibley TR, Truong M, Wolf CR, Nickerson DA, Rieder MJ, Englund JA; Seattle Flu Study Investigators, Hadfield J, Hodcroft EB, Huddleston J, Moncla LH, Müller NF, Neher RA, Deng X, Gu W, Federman S, Chiu C, Duchin JS, Gautom R, Melly G, Hiatt B, Dykema P, Lindquist S, Queen K, Tao Y, Uehara A, Tong S, MacCannell D, Armstrong GL, Baird GS, Chu HY, Shendure J, Jerome KR. Science. 2020 Oct 30;370(6516):571-575. doi: 10.1126/science.abc0523. Epub 2020 Sep 10. PMID: 32913002
Multiplexed measurement of variant abundance and activity reveals VKOR topology, active site and human variant impact Melissa A. Chiasson, Nathan J. Rollins, Jason J. Stephany, Katherine A. Sitko, Kenneth A. Matreyek, Marta Verby, Song Sun, Frederick P. Roth, Daniel DeSloover, Debora Marks, Allan E. Rettie, Douglas M. Fowler; eLife 2020;9:e58026 doi: 10.7554/eLife.58026 PMID: 32870157
Identification of Plant Enhancers and Their Constituent Elements by STARR-seq in Tobacco Leaves. Jores T, Tonnies J, Dorrity MW, Cuperus JT, Fields S, Queitsch C.Plant Cell. 2020 Jul;32(7):2120-2131. doi: 10.1105/tpc.20.00155. Epub 2020 May 14. PMID: 32409318
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
MaveQuest: a web resource for planning experimental tests of human variant effects. Kuang D, Weile J, Li R, Ouellette TW, Barber JA, Roth FP. Bioinformatics. 2020 Jun 1;36(12):3938-3940. doi: 10.1093/bioinformatics/btaa228. PMID: 32251504
Dimensionality reduction by UMAP to visualize physical and genetic interactions. Dorrity MW, Saunders LM, Queitsch C, Fields S, Trapnell C. Nat Commun. 2020 Mar 24;11(1):1537. doi: 10.1038/s41467-020-15351-4. PMID: 32210240
A proactive genotype-to-patient-phenotype map for cystathionine beta-synthase. Sun S, Weile J, Verby M, Wu Y, Wang Y, Cote AG, Fotiadou I, Kitaygorodsky J, Vidal M, Rine J, Ješina P, Kožich V, Roth FP. Genome Med. 2020 Jan 30;12(1):13. doi: 10.1186/s13073-020-0711-1. PMID: 32000841
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
Challenges and Approaches to Genotyping Repetitive DNA. Morton EA, Hall AN, Kwan E, Mok C, Queitsch K, Nandakumar V, Stamatoyannopoulos J, Brewer BJ, Waterston R, Queitsch C. G3 (Bethesda). 2020 Jan 7;10(1):417-430. doi: 10.1534/g3.119.400771. PMID: 31757929
fqfa: A pure Python package for genomic sequence files Rubin AF, The Journal of Open Source Software, 5(47), 2076. 2020 Mar 01, doi: 10.21105/joss.02076 PMID: 33855258
Chapter 5 - Classifying disease-associated variants using measures of protein activity and stability, Michael Maglegaard Jepsen, Douglas M. Fowler, Rasmus Hartmann-Petersen, Amelie Stein, Kresten Lindorff-Larsen, Editor(s): Angel L. Pey, Protein Homeostasis Diseases, Academic Press, 2020, Pages 91-107, ISBN 9780128191323, doi: 10.1016/B978-0-12-819132-3.00005-1.
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: 3186201
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 Review.
Thesaurus: quantifying phosphopeptide positional isomers. Searle BC, Lawrence RT, MacCoss MJ, Villén J. Nat Methods. 2019 Aug;16(8):703-706. doi: 10.1038/s41592-019-0498-4. Epub 2019 Jul 29. PMID: 31363206
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
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