RECENT PREPRINTS

rDNA copy number variation in yeast alters response to environmental conditions Kevin Thornton, Elizabeth X. Kwan, Kerry Bubb, Luana Paleologu, M. K. Raghuraman, Bonita J. Brewer, Josh T. Cuperus, Christine Queitsch bioRxiv 2024.09.30.615902; doi: https://doi.org/10.1101/2024.09.30.615902

Guidelines for releasing a variant effect predictor. Livesey BJ, Badonyi M, Dias M, Frazer J, Kumar S, Lindorff-Larsen K, McCandlish DM, Orenbuch R, Shearer CA, Muffley L, Foreman J, Glazer AM, Lehner B, Marks DS, Roth FP, Rubin AF, Starita LM, Marsh JA.ArXiv [Preprint]. 2024 Apr 16:arXiv:2404.10807v1.PMID: 3869916

The proteomic landscape and temporal dynamics of mammalian gastruloid development Riddhiman K. Garge, Valerie Lynch, Rose Fields, Silvia Casadei, Sabrina Best, Jeremy Stone, Matthew Snyder, Chris D. McGann, Jay Shendure, Lea M. Starita, Nobuhiko Hamazaki, Devin K. Schweppe bioRxiv 2024.09.05.609098; doi: https://doi.org/10.1101/2024.09.05.609098

Genetic variants affect diurnal glucose levels throughout the day Nasa Sinnott-Armstrong, Satu Strausz, Lea Urpa, Erik Abner, Jesse Valliere, Estonian Biobank Research Team, Priit Palta, Hassan S Dashti, Mark Daly, Jonathan K Pritchard, Richa Saxena, Samuel E Jones, Hanna M Ollila. bioRxiv 2024.07.22.604631; doi: https://doi.org/10.1101/2024.07.22.604631

Microdissected tumor cuboids: a microscale cancer model for large-scale testing that retains a complex tumor microenvironment Lisa F Horowitz, Ricard Rodriguez-Mias, Marina Chan, SongLi Zhu, Noah R Gottshall, Ivan Stepanov, Casey Stiles, Marcus Yeung, Tran NH Nguyen, Ethan J Lockhart, Raymond S Yeung, Judit Villen, Taranjit S Gujral, Albert Folch bioRxiv 2024.03.22.586189; doi: https://doi.org/10.1101/2024.03.22.586189

Image-based identification and isolation of micronucleated cells to dissect cellular consequences Lucian DiPeso, Sriram Pendyala, Heather Z Huang, Douglas M Fowler and Emily M Hatch. bioRxiv. posted 5 May 2023; doi: 10.1101/2023.05.04.539483

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

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

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

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

Genomics 2 Proteins portal: a resource and discovery tool for linking genetic screening outputs to protein sequences and structures. Kwon S, Safer J, Nguyen DT, Hoksza D, May P, Arbesfeld JA, Rubin AF, Campbell AJ, Burgin A, Iqbal S.Nat Methods. 2024 Oct;21(10):1947-1957. doi: 10.1038/s41592-024-02409-0. Epub 2024 Sep 18.PMID: 39294369

Benchmarking computational variant effect predictors by their ability to infer human traits. Tabet DR, Kuang D, Lancaster MC, Li R, Liu K, Weile J, Coté AG, Wu Y, Hegele RA, Roden DM, Roth FP. Genome Biol. 2024 Jul 1;25(1):172. doi: 10.1186/s13059-024-03314-7.PMID: 38951922

High-throughput functional mapping of variants in an arrhythmia gene, KCNE1, reveals novel biology. Muhammad A, Calandranis ME, Li B, Yang T, Blackwell DJ, Harvey ML, Smith JE, Chew AE, Capra JA, Matreyek KA, Fowler DM, Roden DM, Glazer AM. Genome Med 16, 73 (2024). https://doi.org/10.1186/s13073-024-01340-5

Workshop report: the clinical application of data from multiplex assays of variant effect (MAVEs), 12 July 2023. Allen S, Garrett A, Muffley L, Fayer S, Foreman J, Adams DJ, Hurles M, Rubin AF, Roth FP, Starita LM, Biesecker LG, Turnbull C. Eur J Hum Genet. 2024 May;32(5):593-600. doi: 10.1038/s41431-024-01566-2. Epub 2024 Mar 4. PMID: 38433264

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 Apr;17(2):e004377. doi: 10.1161/CIRCGEN.123.004377. Epub 2024 Feb 16.PMID: 38362799

Characterizing glucokinase variant mechanisms using a multiplexed abundance assay Gersing S, Schulze TK, Cagiada M, Stein A, Roth FP, Lindorff-Larsen K, Hartmann-Petersen R. Characterizing glucokinase variant mechanisms using a multiplexed abundance assay. Genome Biol. 2024 Apr 16;25(1):98. doi: 10.1186/s13059-024-03238-2. PMID: 38627865; PMCID: PMC11021015.

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

High-throughput identification of dominant negative polypeptides in yeast. Dorrity MW, Queitsch C, Fields S.Nat Methods. 2019 May;16(5):413-416. doi: 10.1038/s41592-019-0368-0. Epub 2019 Apr 8. PMID: 30962621