The power of multiplexed functional analysis of genetic variants

Cited by (161)

Items 101–161 of 161

1. Constructing and interpreting a large-scale variant effect map for an ultrarare disease gene: Comprehensive prediction of the functional impact of PSAT1 genotypes
   2023
2. AMaLa: Analysis of Directed Evolution Experiments via Annealed Mutational Approximated Landscape
   Luca Sesta, Guido Uguzzoni, Jorge Fernández-de-Cossio-Díaz, Andrea Pagnani · 2021 · International Journal of Molecular Sciences
3. Deconvolving mutation effects on protein stability and function with disentangled protein language models
   Kerr Ding, Ziang Li, Tony Tu, Jiaqi Luo, Yu-Nan Luo · 2026 · bioRxiv
4. Basket Trials: Past, Present, and Future
   Yonina R. Murciano‐Goroff, Manik Uppal, Monica F. Chen, Guilherme Harada, Alison M. Schram · 2023 · Annual Review of Cancer Biology
5. Mutagenesis-based protein structure determination
   Melissa A. Chiasson, Douglas M. Fowler · 2019 · Nature Genetics
6. Intragenic compensation through the lens of deep mutational scanning
   Nadezhda V. Azbukina, Anastasia A. Zharikova, Vasily E. Ramensky · 2022 · Biophysical Reviews
7. Many rare genetic variants have unrecognized large-effect disruptions to exon recognition
   Rocky Cheung, Kimberly D. Insigne, David Yao, Christina P. Burghard, Eric M. Jones, Daniel Bryan Goodman, Sriram Kosuri · 2017 · bioRxiv (Cold Spring Harbor Laboratory)
8. Synthetic genomic reconstitution reveals principles of mammalian Hox cluster regulation
   Sudarshan Pinglay, Milica Bulajić, Dylan P. Rahe, Emily Huang, Ran Brosh, Sergei V. German, John A. Cadley, Lila Rieber, Nicole Easo, Shaun Mahony et al. · 2021 · bioRxiv (Cold Spring Harbor Laboratory)
9. Saturation genome editing of BRCA1 across cell types accurately resolves cancer risk
   Phoebe Dace, N. Forrester, Maria Zanti, Laura Cubitt, Chloé Terwagne, Megan Buckley, Elke Maria van Veen, Thomas Stuart Wilson, Paola Scaffidi, Kyriaki Michailidou et al. · 2025 · medRxiv
10. Deep mutational scanning by FACS-sorting of encapsulated E. coli micro-colonies
    Lars Behrendt, Amelie Stein, Shiraz Ali Shah, Karsten Zengler, Søren Johannes Sørensen, Kresten Lindorff‐Larsen, Jakob Rahr Winther · 2018 · bioRxiv (Cold Spring Harbor Laboratory)
11. Enhancer Elements in Plants: Genomic Context and Biological Functions
    Hongwoo Lee, Dong Hyeon Kang, Pil Joon Seo · 2025 · Journal of Plant Biology
12. Reducing uncertainty in genetic testing with Saturation Genome Editing
    Phoebe Dace, Gregory M. Findlay · 2022 · Medizinische Genetik
13. Targeted sequencing for hereditary breast and ovarian cancer in BRCA1/2-negative families reveals complex genetic architecture and phenocopies
    Jocelyn N Plowman, Evanjalina J Matoy, Lavanya V. Uppala, Samantha B. Draves, Cynthia J. Watson, Bridget A. Sefranek, Mark L. Stacey, Samuel P. Anderson, Michael Belshan, Elizabeth Blue et al. · 2024 · Human Genetics and Genomics Advances
14. Variation to biology: optimizing functional analysis of cancer risk variants
    Stefanie A. Nelson, Danielle Mercatante Carrick, Danielle L. Daee, Ian M. Fingerman, Elizabeth M. Gillanders · 2024 · JNCI Journal of the National Cancer Institute
15. Imaging flow cytometry-based cellular screening elucidates pathophysiology in individuals with Variants of Uncertain Significance
    Irena Josephina Johanna Muffels, Hans R. Waterham, Giuseppina D’Alessandro, Guido Zagnoli-Vieira, Michael G. Sacher, Dirk J. Lefeber, Celine Van der Vinne, Chaim M. Roifman, Koen L.I. van Gassen, Holger Rehmann et al. · 2025 · Genome Medicine
16. Live‐cell PCR and one‐step purification streamline DNA engineering
    George T. Lyozin, Luca Brunelli · 2020 · The FASEB Journal
17. Genetic engineering: Lassoing genomic libraries
    Nathan B. Lubock, Sriram Kosuri · 2017 · Nature Biomedical Engineering
18. Mechanistic Mutational Scanning to Uncover the Secret Life of Proteins
    Matthew K. Howard, Willow Coyote‐Maestas · 2026 · Annual Review of Biomedical Data Science
19. Machine Learning-Driven Simulations of the SARS-CoV-2 Fitness Landscape from Deep Mutational Scanning Experiments
    Aleksander E. P. Durumeric, Sean McCarty, Jay Smith, Jonas Köhler, Katarina Elez, Lluı́s Raich, Patricia Suriana, Terra Sztain · 2026 · Journal of Chemical Information and Modeling
20. High-throughput navigation of the sequence space
    Alaksh Choudhury · 2022 · Elsevier eBooks
21. Massively parallel DNA target capture using long adapter single stranded oligonucleotide (LASSO) probes assembled through a novel DNA recombinase mediated methodology
    Lorenzo Tosi, Lamia Chkaiban, H. Benjamin Larman, Jeffrey Rosenfeld, Biju Parekkadan · 2021 · Biotechnology Journal
22. DITTO: An Explainable Machine-Learning Model for Transcript-Specific Variant Pathogenicity Prediction
    Tarun Karthik Kumar Mamidi, Brandon M. Wilk, Manavalan Gajapathy, Elizabeth A. Worthey · 2024 · Preprints.org
23. Functional assays in Drosophila facilitate classification of variants of uncertain significance associated with rare diseases
    Jung-Wan Mok, Shelley Gibson, Haley A Dostalik, Shinya Yamamoto · 2025 · Genome Research
24. Functional analysis of FH variants of uncertain significance using Caenorhabditis elegans model
    Suzanne Ferris, Ivette M. Menéndez‐Perdomo, Maja Tarailo‐Graovac · 2025 · Genetics in Medicine Open
25. SyMetrics: an integrated machine learning model for evaluating the pathogenicity of synonymous variants in the human genome
    Linnaeus Bundalian, Martina Strnadová, Felix Garten, Susanne Horn, Udo Stenzel, Denny Popp, Johannes R. Lemke, Saskia Biskup, Björn Schulte, Patrick May et al. · 2025 · NAR Genomics and Bioinformatics
26. Using Synthetic DNA Libraries to Investigate Chromatin and Gene Regulation
    Holly Kleinschmidt, Cheng Xu, Lu Bai · 2023 · Chromosoma
27. Precision mutational scanning: your multipass to the future of genetics
    Jonathan F. Roth, Francisco J. Sánchez Rivera · 2024 · Nature Methods
28. It’s prime time for multiplexed prime editing
    Ke Wu, Francisco J. Sánchez Rivera · 2025 · Cell Genomics
29. Functional divergence among hominins
    Stephanie M. Yan, Rajiv C. McCoy · 2019 · Nature Ecology & Evolution
30. The Evolution of Constitutional Sequence Variant Interpretation
    Jessica L. Mester, Tina F. Pesaran · 2020 · Clinics in Laboratory Medicine
31. The pathobiology of Mycobacterium abscessus revealed through phenogenomic analysis
    Lucas Boeck, Sophie Burbaud, Marcin J. Skwark, Will H. Pearson, Jasper Sangen, Aaron Weimann, Isobel Everall, Josephine M. Bryant, Sony Malhotra, Bridget P. Bannerman et al. · 2021 · bioRxiv (Cold Spring Harbor Laboratory)
32. Decoding molecular mechanisms for loss-of-function variants in the human proteome
    Matteo Cagiada, Nicolas Jonsson, Kresten Lindorff‐Larsen · 2025 · eLife
33. StructGuy: Data leakage free prediction of functional effects of genetic variants
    Alexander Greß, Carène Benasolo, Johanna Becher, Dominique Mias‐Lucquin, Roman Joeres, Sebastian Keller, Olga V. Kalinina · 2025 · bioRxiv (Cold Spring Harbor Laboratory)
34. ESMRank reveals a transferable axis of protein mutational constraint from overlapping variant effect assays
    Riccardo Arnese, Gennaro Gambardella · 2026 · bioRxiv (Cold Spring Harbor Laboratory)
35. A Multiplexed Assay for Exon Recognition Reveals That an Unappreciated Fraction of Rare Genetic Variants Cause Large-Effect Disruptions to Splicing
    Rocky Cheung, Kimberly D. Insigne, David Yao, Christina P. Burghard, Eric M. Jones, Daniel Bryan Goodman, Sriram Kosuri · 2018 · SSRN Electronic Journal
36. The Evolution of Constitutional Sequence Variant Interpretation
    Jessica L. Mester, Tina F. Pesaran · 2019 · Advances in Molecular Pathology
37. Engineering Escherichia coli for growth on methanol through dynamic regulation and protein engineering
    Julia Rohlhill · 2024 · Library, Museums and Press - UDSpace (University of Delaware)
38. Parallel genetics of regulatory sequences in vivo
    Jonathan J. Froehlich, Bora Uyar, Margareta Herzog, Kathrin Theil, Petar Glažar, Altuna Akalin, Nikolaus Rajewsky · 2020 · bioRxiv (Cold Spring Harbor Laboratory)
39. Practicing Prenatal Medicine in a Genomic Future: How the Practice of Pediatrics May (Or May Not) Change with the Introduction of Widespread Prenatal Sequencing
    Volkan Okur, Wendy K. Chung · 2021 · The International Library of Bioethics
40. Faculty Opinions recommendation of Accurate classification of BRCA1 variants with saturation genome editing.
    Michael Cole, Nadia Cumbal · 2018 · Faculty Opinions – Post-Publication Peer Review of the Biomedical Literature
41. Faculty Opinions recommendation of Inferring protein 3D structure from deep mutation scans.
    Patrice Koehl · 2019 · Faculty Opinions – Post-Publication Peer Review of the Biomedical Literature
42. Faculty Opinions recommendation of Accurate classification of BRCA1 variants with saturation genome editing.
    Junjie Chen · 2018 · Faculty Opinions – Post-Publication Peer Review of the Biomedical Literature
43. Faculty Opinions recommendation of Multiplexed gene synthesis in emulsions for exploring protein functional landscapes.
    Nobuhiko Tokuriki · 2019 · Faculty Opinions – Post-Publication Peer Review of the Biomedical Literature
44. Faculty Opinions recommendation of Overcoming the design, build, test bottleneck for synthesis of nonrepetitive protein-RNA cassettes.
    Janusz Marek Bujnicki · 2021 · Faculty Opinions – Post-Publication Peer Review of the Biomedical Literature
45. Interface-guided phenotyping of coding variants in the transcription factor RUNX1 with SEUSS
    Kıvılcım Öztürk, Rebecca Panwala, Jeanna Sheen, Kyle M. Ford, Nathan Payne, Dong‐Er Zhang, Stephan Hütter, Torsten Haferlach, Trey E. Ideker, Prashant Mali et al. · 2023 · bioRxiv (Cold Spring Harbor Laboratory)
46. Rapid classification of a novel ALS-causing I149S variant in superoxide dismutase-1
    Victoria K. Shephard, Mikayla L. Brown, Bryony A. Thompson, Alisha Harpur, Luke McAlary · 2024 · Amyotrophic Lateral Sclerosis and Frontotemporal Degeneration
47. Generative AI impact on protein stability prediction in breast cancer genes
    Rohan David Gnanaolivu, Steven N. Hart · 2024 · bioRxiv (Cold Spring Harbor Laboratory)
48. Using AI-predicted protein structures as a reference to predict loss-of-function activity in tumor suppressor breast cancer genes
    Rohan David Gnanaolivu, Steven N. Hart · 2024 · Computational and Structural Biotechnology Journal
49. After the Test
    Isabelle Thiffault, Carol Saunders · 2025 · Oxford University Press eBooks
50. Functional effect predictions for ion channel missense variants using a protein language model
    Seán Gies, Artoghrul Alishbayli, Paul H. E. Tiesinga, Marijn Bart Martens · 2026 · Journal of Human Genetics
51. Additional file 2 of Combining full-length gene assay and SpliceAI to interpret the splicing impact of all possible SPINK1 coding variants
    Wu, Hao, Jinhuan Lin, Tang, Xin-Ying, Gaëlle Marenne, Zou, Wen-Bin, Sacha Schutz, Emmanuelle Masson, Emmanuelle Génin, Yann Fichou, Gérald Le Gac et al. · 2024 · Figshare
52. Additional file 1 of Integrating thousands of PTEN variant activity and abundance measurements reveals variant subgroups and new dominant negatives in cancers
    Kenneth A. Matreyek, Jason J. Stephany, Ahler, Ethan, Douglas M. Fowler · 2021 · Figshare
53. Additional file 3 of Combining full-length gene assay and SpliceAI to interpret the splicing impact of all possible SPINK1 coding variants
    Wu, Hao, Jinhuan Lin, Xinying Tang, Gaëlle Marenne, Zou, Wen-Bin, Sacha Schutz, Emmanuelle Masson, Emmanuelle Génin, Yann Fichou, Gérald Le Gac et al. · 2024 · Figshare
54. Additional file 1 of Minimum information and guidelines for reporting a multiplexed assay of variant effect
    Melina Claussnitzer, Victoria Nicole Parikh, Wagner, Alex H., Arbesfeld, Jeremy A., Carol J. Bult, Firth, Helen V., Lara A. Muffley, Nguyen Ba, Alex N., Kevin P. Riehle, Frederick P. Roth et al. · 2024 · Figshare
55. Additional file 1 of Combining full-length gene assay and SpliceAI to interpret the splicing impact of all possible SPINK1 coding variants
    Wu, Hao, Jinhuan Lin, Xinying Tang, Gaëlle Marenne, Zou, Wen-Bin, Sacha Schutz, Emmanuelle Masson, Emmanuelle Génin, Yann Fichou, Gérald Le Gac et al. · 2024 · Figshare
56. DITTO: An explainable machine-learning model for transcript- specific variant pathogenicity prediction
    Tarun Karthik Kumar Mamidi, Brandon Michael Wilk, Manavalan Gajapathy, Elizabeth A. Worthey · 2026 · Research Square
57. Determining the intra-residue correlation of missense variant impact using MAVE scores: implications for the ACMG/AMP PM5 criterion for DNA variant classification
    Ziyi Dai, Bushra Haque, Sabrina Xi, Gregory Costain · 2026 · Genome Medicine
58. Développement de stratégies de criblage de mutations d'épissage dans des gènes de prédisposition au cancer.
    Hélène Tubeuf · 2019 · theses.fr (ABES)
59. Likelihood-based calibration improves the clinical utility of JAG1 functional data for variant classification
    Tristan J. Hayeck, Christopher J. Sottolano, Justin J. Blair, Markos N. Xenakis, Nancy Bettina Spinner, Melissa A. Gilbert · 2026 · The American Journal of Human Genetics
60. Missense3D: leveraging protein structures, including AlphaFold models, to understand the effect of missense variants
    Ifigenia Tsitsa, Gordon Hanna, Anja Conev, Suhail A. Islam, Michael J.E. Sternberg, Alessia David · 2026 · Journal of Molecular Biology
61. Protein destabilization underlies pathogenic missense mutations in ARID1B.
    Samuele Mercan · 2023 · Zenodo (CERN European Organization for Nuclear Research)