Direct Identification of Hundreds of Expression-Modulating Variants using a Multiplexed Reporter Assay

Tewhey, Ryan, Kotliar, Dylan, Park, Daniel S., Liu, Brandon, Winnicki, Sarah, Reilly, Steven K., Andersen, Kristian G., Mikkelsen, Tarjei S. +3 more·2016·Cell

Cited by (483)

Items 401–483 of 483

  1. Expanding the DNA Motif Lexicon of the Transcriptional Regulatory Code
    Jing‐Yu Fan, Virendra K. Chaudhri, Deepa Bisht, Nicholas A. Pease, Swapnil Keshari, Peter Gerges, David Reed Hall, Vivian Fang Yi, Susan Kales, Ching‐Huang Ho et al. · 2025 · bioRxiv (Cold Spring Harbor Laboratory)
  2. Global cis-regulatory landscape of double-stranded DNA viruses
    Tommy Henry Taslim, Joseph Alexander Finkelberg, Susan Kales, Luis F. Soto-Ugaldi, Benedetta D’Elia, Berkay Engin, George D. Muñoz-Esquivel, Elvis Morara, Jacob Purinton, Harshpreet Chandok et al. · 2025 · bioRxiv (Cold Spring Harbor Laboratory)
  3. Massively parallel reporter assay reveals promoter-, position-, and strand-specific effects in transcription start sites
    Maya L. Bose, Adelaide Tovar, Yasuhiro Kyono, Arushi Varshney, J. Kitzman, Stephen C. J. Parker · 2025 · bioRxiv
  4. Massively parallel functional screen identifies thousands of regulatory differences in human versus chimpanzee postcranial skeletal development
    Alexander S. Okamoto, Clarissa R. Coveney, Danalaxshmi Shanen Ganapathee, Terence Dante Capellini · 2025 · bioRxiv (Cold Spring Harbor Laboratory)
  5. Systematic functional dissection of germline noncoding risk variants impacting clonal hematopoiesis
    Trieu Nguyen, Jessica Jeejan, Takeshi Iwasaki, Susan Kales, Joyeeta Chakraborty, Chie Yanase, Aruna N. C. Shekhar, Dominika Kwasniak, Aditi Hegde, Richard A. Voit et al. · 2026 · bioRxiv (Cold Spring Harbor Laboratory)
  6. Multi-scale dissection, compaction and derivatization of mammalian developmental enhancers
    Jean‐Benoît Lalanne, Tony Li, Emma A.N. Kajiwara, Chau Huynh, Tiffany V. Do, Beth K. Martin, Samuel G. Regalado, Jay Shendure · 2026 · bioRxiv (Cold Spring Harbor Laboratory)
  7. Influence of cis -regulatory elements on expression divergence in human segmental duplications
    Colin J. Shew, Gulhan Kaya, Sean P. McGinty, Megan Y. Dennis · 2026 · Genome Research
  8. Putting a finer point on it—Resolving QT loci using multiethnic studies
    Patrick T. Ellinor · 2017 · Heart Rhythm
  9. Quantifying Eukaryotic Gene Regulation in Hormone Response and Disease.
    Christopher M. Vockley · 2016 · DukeSpace (Duke University)
  10. Leveraging CRISPR/Cas Genome Editing Technology to Identify and Characterize Causal GWAS Variants for Blood Lipids
    Avanthi Raghavan · 2017 · Digital Access to Scholarship at Harvard (DASH) (Harvard University)
  11. Sensing foul AIRE: Investigating possible reporter genes for AIRE mutations
    Amund Holte Berger · 2018 · NORA - Norwegian Open Research Archives
  12. Unbiased genome-scale identification of cis -regulatory modules in the human genome by GRAMc
    Catherine L. Guay, Jongmin Nam · 2018 · bioRxiv (Cold Spring Harbor Laboratory)
  13. Functional Genomics
    Michael Mannstadt, Marc Nathan Wein · 2017 · Elsevier eBooks
  14. Organizational Properties of a Functional Mammalian Cis-Regulome
    Virendra K. Chaudhri, Krista Dienger-Stambaugh, Zhiguo Wu, Mahesh Shreshtha, Harinder Singh · 2018 · SSRN Electronic Journal
  15. Integrative Modeling and Novel Technologies in Human Genomics
    Paulina Carmona-Mora, Juan I. Young · 2019 · Elsevier eBooks
  16. Analysis of regulatory element evolution between human and mouse reveals a lack of cis-trans compensation
    Kaia Mattioli, Winona Oliveros, C. Gerhardinger, Daniel Andergassen, P. Maass, J. Rinn, Marta Melé · 2019 · bioRxiv
  17. Characterizing human regulatory genetic variation using CRISPR/Cas9 genome editing
    Margot K. Brandt · 2020
  18. Assaying 3-Prime Untranslated Region Variants in a Massively Parallel Fashion
    Dustin S. Griesemer · 2017 · Digital Access to Scholarship at Harvard (DASH) (Harvard University)
  19. Massively parallel identification of causal variants underlying gene expression differences in a yeast cross
    Kaushik Renganaath, Rocky Cheung, Laura Day, Sriam Kosuri, L. Kruglyak, F. Albert · 2020 · bioRxiv
  20. Faculty Opinions recommendation of Allele-specific open chromatin in human iPSC neurons elucidates functional disease variants.
    Leah Claire Kottyan · 2020 · Faculty Opinions – Post-Publication Peer Review of the Biomedical Literature
  21. Faculty Opinions recommendation of Deep learning sequence-based ab initio prediction of variant effects on expression and disease risk.
    Chao Cheng · 2019 · Faculty Opinions – Post-Publication Peer Review of the Biomedical Literature
  22. Scaled-up functional tests of genetic variants
    2016 · Nature Methods
  23. Widespread perturbation of ETS factor binding sites in cancer
    Sebastian Carrasco Pro, Heather Hook, D Bray, Daniel Berenzy, Devlin C. Moyer, M Yin, Adam Thomas Labadorf, Ryan Tewhey, Trevor Siggers, Juan I. Fuxman Bass · 2022 · bioRxiv (Cold Spring Harbor Laboratory)
  24. Mapping Alzheimer's Disease Variants to Their Target Genes Using Computational Analysis of Chromatin Configuration
    Nana Matoba, Ivana Yoseli Quiroga, Douglas H. Phanstiel, Hyejung Won · 2020 · Journal of Visualized Experiments
  25. Three linked opposing regulatory variants under selection associate with IVD
    Elizabeth A. Brown, Susan Kales, Michael J. Boyle, Joseph J. Vitti, Dylan Kotliar, Stephen F. Schaffner, Ryan Tewhey, Pardis Christine Sabeti · 2022 · bioRxiv (Cold Spring Harbor Laboratory)
  26. Utilizing Large Functional and Population Genomics Resources for CRISPR/Cas Perturbation Experiment Design
    Qingbo S. Wang, Kumiko Ui‐Tei · 2023 · Methods in molecular biology
  27. Bibliography
    2023 · The MIT Press eBooks
  28. MPRAVarDB: an online database and web server for exploring regulatory effects of genetic variants
    Javlon Nizomov, Weijia Jin, Yi Xia, Yunlong Liu, Zhigang Li, Li Chen · 2024 · bioRxiv (Cold Spring Harbor Laboratory)
  29. Uncovering methylation-dependent genetic effects on regulatory element function in diverse genomes
    Rachel M. Petersen, Christopher M. Vockley, Amanda J. Lea · 2024 · bioRxiv (Cold Spring Harbor Laboratory)
  30. The OMICS and PD models: Hopes or hypes
    Kholoud Elsamman · 2024 · Elsevier eBooks
  31. Methods for Functional Characterization of Genetic Polymorphisms of Non-Coding Regulatory Regions of the Human Genome (Review)
    Aksinya Nicolaevna Uvarova, E. A. Tkachenko, Ekaterina M. Stasevich, Elina A. Zheremyan, Kirill V. Korneev, Dmitry V. Kuprash · 2024 · Biochemistry (Moscow)
  32. MIRACN: a residual convolutional neural network for predicting cell line specific functional regulatory variants
    Zeyin Li, Min Wang, Songge Li, Fangyuan Shi · 2025 · Briefings in Bioinformatics
  33. esMPRA: an easy-to-use systematic pipeline for MPRA experiment quality control and data analysis
    Jiaqi Li, Pengcheng Zhang, Xi Xi, Xiaowo Wang · 2025 · Bioinformatics
  34. Genome-wide discovery of multiple sclerosis genetic risk variant allelic regulatory activity
    Marissa Granitto, Lois G. Parks, Molly Shook, Carmy R. Forney, Xiaoting Chen, Lee Edsall, Omer A Donmez, Sreeja Parameswaran, Kristen S. Fisher, Aram Zabeti et al. · 2025 · G3 Genes Genomes Genetics
  35. Interactions Between Dietary Metabolites and Regulatory Risk Variants for Human Colon Cancer
    Tania Fabo, Robin M. Meyers, Evin M. Padhi, Laura N. Kellman, Yang Zhao, Soumya Kundu, David L. Reynolds, Ziwei Chen, Xue Yang, Lisa A. Ko et al. · 2025 · bioRxiv (Cold Spring Harbor Laboratory)
  36. Mapping causal non-coding variants in coronary artery disease
    Stephen B. Montgomery · 2025 · Nature Cardiovascular Research
  37. Quantifying the impact of genetic mutations on enhancer dynamics
    Maitreya Das, Deepro Banerjee, Ayaan Hossain, Matthew Jensen, Saie Mogre, Jiawan Sun, Joseph Mao, Adam B. Glick, Howard M. Salis, Santhosh Girirajan · 2025 · bioRxiv (Cold Spring Harbor Laboratory)
  38. Genomic basis of human-specific brain features
    Federica Mosti, Debra L. Silver · 2025 · Elsevier eBooks
  39. PETRA: Prime editing of transcribed regulatory elements to assay expression
    Magdalena Armas, Michael Herger, Laura Cubitt, Gregory M. Findlay · 2025 · bioRxiv (Cold Spring Harbor Laboratory)
  40. Global Evaluation of Congenital Heart Disease-Associated Non-Coding Variants
    Edwin G. Peña-Martínez, Edwin Peña-Martínez, Shreya Sharma, Joshua Medina-Feliciano, Elise Root, Lois Parks, Marissa Granitto, Diego Pomales-Matos, Jean Messon- Bird, Adriana Barreiro-Rosario et al. · 2025 · Research Square
  41. Additional file 2 of FORGEdb: a tool for identifying candidate functional variants and uncovering target genes and mechanisms for complex diseases
    Charles E. Breeze, Eric Haugen, María Gutiérrez‐Arcelus, Xiaozheng Yao, Andrew Erich Teschendorff, Stephan Beck, Ian Dunham, John A. Stamatoyannopoulos, Franceschini, Nora, Mitchell J. Machiela et al. · 2024 · Figshare
  42. Additional file 1 of The contribution of silencer variants to human diseases
    Di Huang, Ivan Ovcharenko · 2024 · Figshare
  43. Additional file 1 of FORGEdb: a tool for identifying candidate functional variants and uncovering target genes and mechanisms for complex diseases
    Charles E. Breeze, Eric Haugen, María Gutiérrez‐Arcelus, Xiaozheng Yao, Andrew Erich Teschendorff, Stephan Beck, Ian Dunham, John A. Stamatoyannopoulos, Franceschini, Nora, Mitchell J. Machiela et al. · 2024 · Figshare
  44. Additional file 4 of A common regulatory haplotype doubles lactoferrin concentration in milk
    Thomas Lopdell, Trevarton, Alexander J., Janelle Moody, Claire Prowse-Wilkins, Knowles, Sarah, Kathryn Tiplady, Amanda Jane Chamberlain, Michael Edward Goddard, Richard J. Spelman, Klaus Lehnert et al. · 2024 · Figshare
  45. Additional file 2 of Single-cell multiomics of the human retina reveals hierarchical transcription factor collaboration in mediating cell type-specific effects of genetic variants on gene regulation
    Wang, Jun, Cheng, Xuesen, Liang, Qingnan, Leah A. Owen, Lu, Jiaxiong, Yiqiao Zheng, Meng Wang, Shiming Chen, Margaret M. DeAngelis, Li, Yumei et al. · 2024 · Figshare
  46. Additional file 3 of FORGEdb: a tool for identifying candidate functional variants and uncovering target genes and mechanisms for complex diseases
    Charles E. Breeze, Eric Haugen, María Gutiérrez‐Arcelus, Xiaozheng Yao, Andrew Erich Teschendorff, Stephan Beck, Ian Dunham, John A. Stamatoyannopoulos, Franceschini, Nora, Mitchell J. Machiela et al. · 2024 · Figshare
  47. Additional file 1 of Single-cell multiomics of the human retina reveals hierarchical transcription factor collaboration in mediating cell type-specific effects of genetic variants on gene regulation
    Wang, Jun, Xuesen Cheng, Liang, Qingnan, Leah A. Owen, Lu, Jiaxiong, Yiqiao Zheng, Meng Wang, Shiming Chen, Margaret M. DeAngelis, Li, Yumei et al. · 2023 · Figshare
  48. Additional file 1 of A common regulatory haplotype doubles lactoferrin concentration in milk
    Thomas Lopdell, Alexander J. Trevarton, Janelle Moody, Claire Prowse-Wilkins, Knowles, Sarah, Kathryn Tiplady, Amanda Jane Chamberlain, Michael Edward Goddard, Richard J. Spelman, Klaus Lehnert et al. · 2024 · Figshare
  49. Additional file 3 of Single-cell multiomics of the human retina reveals hierarchical transcription factor collaboration in mediating cell type-specific effects of genetic variants on gene regulation
    Wang, Jun, Xuesen Cheng, Liang, Qingnan, Leah A. Owen, Lu, Jiaxiong, Yiqiao Zheng, Meng Wang, Shiming Chen, Margaret M. DeAngelis, Li, Yumei et al. · 2024 · Figshare
  50. Additional file 2 of A common regulatory haplotype doubles lactoferrin concentration in milk
    Thomas Lopdell, Trevarton, Alexander J., Janelle Moody, Claire Prowse-Wilkins, Knowles, Sarah, Kathryn Tiplady, Amanda Jane Chamberlain, Michael Edward Goddard, Richard J. Spelman, Klaus Lehnert et al. · 2024 · Figshare
  51. Additional file 2 of The contribution of silencer variants to human diseases
    Di Huang, Ivan Ovcharenko · 2024 · Figshare
  52. Additional file 3 of The contribution of silencer variants to human diseases
    Di Huang, Ivan Ovcharenko · 2024 · Figshare
  53. Additional file 1 of A systematic strategy for identifying causal single nucleotide polymorphisms and their target genes on Juvenile arthritis risk haplotypes
    Kaiyu Jiang, Liu, Tao, Susan Kales, Ryan Tewhey, Dongkyeong Kim, Yungki Park, James N. Jarvis · 2024 · Figshare
  54. Additional file 3 of A common regulatory haplotype doubles lactoferrin concentration in milk
    Thomas Lopdell, Trevarton, Alexander J., Janelle Moody, Claire Prowse-Wilkins, Knowles, Sarah, Kathryn Tiplady, Amanda Jane Chamberlain, Michael Edward Goddard, Richard J. Spelman, Klaus Lehnert et al. · 2024 · Figshare
  55. Regulatory QTLs affecting miRNA-mRNA interactions in cancer: mechanisms, methods, and clinical implications
    Vivek Kumar, Rohit Shukla, Amit Chaudhary, Mansi Gautam · 2026 · Frontiers in Molecular Biosciences
  56. CEBPB binding at rs2643219 modulates insulin sensitivity via RASGRP1–GLUT4 axis
    Yongqiang Ning, Linbu Liao, Lijun Zhang, Xiao Yang, Jie Wang, Qianwen Xie, Yihui Zhang, Rui Li, Qian Liu, Xiling Zhao et al. · 2026 · Genes & Diseases
  57. Multi‐Tissue Omics Analysis Uncovers Translational Regulation Underlying Complex Traits in Pigs
    Chao Wang, Yuanyuan Zhang, Choulin Chen, Xiaoxian Xu, Shenghua Qin, Junyan Qi, Yongzhou Bao, Huiming Li, Ruipu Chen, Weigang Zheng et al. · 2026 · Advanced Science
  58. keju: powerful and accurate inference in Massively Parallel Reporter Assays
    Albert Xue, Adam M. Zahm, Justin G. English, Sriram Sankararaman, Harold Pimentel · 2026 · bioRxiv (Cold Spring Harbor Laboratory)
  59. Characterization of variants associated with Cerebral Small Vessel Disease identifies a functional SNV in Versican
    Jae‐Ryeon Ryu, Ankita Narang, Quentin Le Grand, David‐Alexandre Trégouët, Stéphanie Debette, Sarah J. Childs · 2026 · bioRxiv (Cold Spring Harbor Laboratory)
  60. Genome-wide association studies (GWAS) in 2026: From gene hunting to biological discovery in endocrine and cardiometabolic diseases
    Takiy-Eddine Berrandou · 2026 · Annales d Endocrinologie
  61. Genetic influences on haematopoiesis
    Michael Poeschla, Vijay G. Sankaran · 2026 · Nature Reviews Genetics
  62. Functional genomics
    Michael Mannstadt, Marc Nathan Wein · 2026 · Elsevier eBooks
  63. La dérive génétique : un outil pour identifier de nouveaux facteurs impliqués dans la pathogénie des maladies complexes tel le diabète auto-immune de la souris non obèse diabétique
    Anne‐Perrine Foray · 2019
  64. Etude des polymorphismes altérant la régulation de l'expression des gènes chez le bovin
    Gabriel Guillocheau · 2018
  65. High-throughput study of silencer elements in T cells
    Saadat Hussain · 2019
  66. Caractérisation des enhancers dérégulés dans la leucémie aiguë lymphoblastique de type T
    Alexandre P. España · 2019
  67. Au-delà des études d'association à l'échelle du génome : étude transcriptomique et identification des variants régulateurs impliqués dans le développement du sepsis
    Florian Rosier · 2019 · theses.fr (ABES)
  68. Atlas of HIV cis-regulatory elements reveals extensive transcriptional variation across clades, isolates, and within individuals
    Berkay ENGİN, Mohamed Yousry ElSadec, Joseph Alexander Finkelberg, Tommy Henry Taslim, Daniel L. Bryant, Luis F. Soto-Ugaldi, Susan Kales, Ching‐Huang Ho, Maryam Dashtiahangar, George D. Muñoz-Esquivel et al. · 2026 · bioRxiv (Cold Spring Harbor Laboratory)
  69. Comprehensive mapping of human genetic variation at Epromoters
    Jing Wan · 2024 · theses.fr (ABES)
  70. Mapping functional non-coding variation in individual human genomes through haplotyping, multiomics, and deep learning
    Mikhail D. Magnitov, Robin H. van der Weide, Aster F. Witvliet, Miguel Hernández-Quiles, Moreno Martinovic, Hans Teunissen, Luca Braccioli, Michiel Vermeulen, Elzo de Wit · 2026 · Nature Communications
  71. Evolving computational paradigms for noncoding variant pathogenicity prediction
    Beibei Wang, Siyuan Song, Cheng SONG, Yihang Lin, Liang Yu, Yan Li, Xin Chen · 2026 · Frontiers in Molecular Biosciences
  72. Integrative Mapping of Regulatory Variation in African American Hepatocytes Using Colocalization and MPRA: Toward Precision Drug Response
    C. Clark, Guang Yang, C. Alarcon, Mrinal Mishra, M. Perera · 2026 · Research Square
  73. Immune context unmasks regulatory effects of Neanderthal and Denisovan introgression
    Zhi Li, Gaspard Kerner, Javier Mendoza‐Revilla, Fumitaka Inoue, Simon Fishilevich, Étienne Patin, David Gokhman, Lluís Quintana‐Murci, Maxime Rotival · 2026 · bioRxiv (Cold Spring Harbor Laboratory)
  74. Expression-linked promoter selection (ELiPS) engineers short, strong ubiquitous promoters for gene therapy applications
    Sydney V. Oraskovich, Kazuomori K. Lewis, Joost van Haasteren, Hyun‐Cheol Lee, Esther Chu, David V. Schaffer · 2026 · bioRxiv (Cold Spring Harbor Laboratory)
  75. GenBench: A Comprehensive Benchmark Dataset for Sequence-Based Genomic Models
    Yue Liu, Yanlei Kang, Junfeng Zhang, Shulin Wang, Zhong Li · 2026 · Lecture notes in computer science
  76. Cross-Model Uncertainty-Aware Minimal Editing of Cis-Regulatory Elements for Cell-Type-Selective Design
    Angran Xia, Changwei Wang, Yemao Xia · 2026 · Genes
  77. Non-Coding Negative Regulatory Features in Livestock Genomes: Functional Annotation and Causal Validation
    Lingzehui Zhang, Bingjie Ma, Yiming Zhang, Xin Wang, Le Wang, Ruijun Wang, Yanjun Zhang, Fangzheng Shang · 2026 · Animals
  78. Designing gene expression with MPRA and AI: A new paradigm for synthetic and therapeutic regulation
    Xue Zhang, Xiao-Yan Huang, Hui-Yu Wang, Feng‐Wu Bai, Kai Li, Shen S. Hu · 2026 · Biotechnology Advances
  79. Dissecting functional regulatory convergence over 160 million years of therian evolution
    Navya Shukla, Laura E. Cook, Davide Maria Vespasiani, Andrew J. Pask, Irene Gallego Romero · 2026 · Genome Research
  80. Genome-wide association studies of osteoarthritis: from genetic discovery to precision medicine
    Yuezhou Wu, Yang Hong, Xukun Lyu, Peng Wang, Houfeng Zheng, Jiacan Su · 2026 · Journal of genetics and genomics/Journal of Genetics and Genomics
  81. Quantifying the impact of genetic mutations on enhancer dynamics
    Maitreya Das, Deepro Banerjee, Ayaan Hossain, Matthew Jensen, Saie Mogre, Jiawan Sun, Joseph Mao, Adam B. Glick, Howard M. Salis, Santhosh Girirajan · 2026 · Cell Reports
  82. Identifying non-coding variant effects at scale via machine learning models of cis-regulatory reporter assays
    John C. Butts, Stephen Rong, Sager J. Gosai, Rodrigo I. Castro, Mackenzie Noon, Tian Xia, Isabel Nadine Goronzy, Kehinde Adeniran, Rohit Ghosh, Pardis Sabeti et al. · 2025 · Zenodo (CERN European Organization for Nuclear Research)
  83. VarNexus: an integrative database for interpreting disease-associated regulatory variants through multimodal predictions and functional evidence
    Gong, Lihai, Tan, Cheng, Zhang, Jinhui, Shu, Rigan, Guo, Shutong, Xiao, Tingting, Shi, Jialin, Wang, Jing, Ni, Ting, Ding, Ruofan · 2026 · Nucleic Acids Research