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
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- Characterizing human regulatory genetic variation using CRISPR/Cas9 genome editingMargot K. Brandt · 2020
- Assaying 3-Prime Untranslated Region Variants in a Massively Parallel FashionDustin S. Griesemer · 2017 · Digital Access to Scholarship at Harvard (DASH) (Harvard University)
- Massively parallel identification of causal variants underlying gene expression differences in a yeast crossKaushik Renganaath, Rocky Cheung, Laura Day, Sriam Kosuri, L. Kruglyak, F. Albert · 2020 · bioRxiv
- 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
- 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
- Scaled-up functional tests of genetic variants2016 · Nature Methods
- Widespread perturbation of ETS factor binding sites in cancerSebastian 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)
- Mapping Alzheimer's Disease Variants to Their Target Genes Using Computational Analysis of Chromatin ConfigurationNana Matoba, Ivana Yoseli Quiroga, Douglas H. Phanstiel, Hyejung Won · 2020 · Journal of Visualized Experiments
- Three linked opposing regulatory variants under selection associate with IVDElizabeth 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)
- Utilizing Large Functional and Population Genomics Resources for CRISPR/Cas Perturbation Experiment DesignQingbo S. Wang, Kumiko Ui‐Tei · 2023 · Methods in molecular biology
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- MPRAVarDB: an online database and web server for exploring regulatory effects of genetic variantsJavlon Nizomov, Weijia Jin, Yi Xia, Yunlong Liu, Zhigang Li, Li Chen · 2024 · bioRxiv (Cold Spring Harbor Laboratory)
- Uncovering methylation-dependent genetic effects on regulatory element function in diverse genomesRachel M. Petersen, Christopher M. Vockley, Amanda J. Lea · 2024 · bioRxiv (Cold Spring Harbor Laboratory)
- The OMICS and PD models: Hopes or hypesKholoud Elsamman · 2024 · Elsevier eBooks
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- MIRACN: a residual convolutional neural network for predicting cell line specific functional regulatory variantsZeyin Li, Min Wang, Songge Li, Fangyuan Shi · 2025 · Briefings in Bioinformatics
- esMPRA: an easy-to-use systematic pipeline for MPRA experiment quality control and data analysisJiaqi Li, Pengcheng Zhang, Xi Xi, Xiaowo Wang · 2025 · Bioinformatics
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- Mapping causal non-coding variants in coronary artery diseaseStephen B. Montgomery · 2025 · Nature Cardiovascular Research
- Quantifying the impact of genetic mutations on enhancer dynamicsMaitreya 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)
- Genomic basis of human-specific brain featuresFederica Mosti, Debra L. Silver · 2025 · Elsevier eBooks
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- Additional file 2 of FORGEdb: a tool for identifying candidate functional variants and uncovering target genes and mechanisms for complex diseasesCharles 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
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- Additional file 4 of A common regulatory haplotype doubles lactoferrin concentration in milkThomas 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
- 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 regulationWang, 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
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- 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 regulationWang, 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
- Additional file 1 of A common regulatory haplotype doubles lactoferrin concentration in milkThomas 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
- 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 regulationWang, 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
- Additional file 2 of A common regulatory haplotype doubles lactoferrin concentration in milkThomas 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
- Additional file 2 of The contribution of silencer variants to human diseasesDi Huang, Ivan Ovcharenko · 2024 · Figshare
- Additional file 3 of The contribution of silencer variants to human diseasesDi Huang, Ivan Ovcharenko · 2024 · Figshare
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- Evolving computational paradigms for noncoding variant pathogenicity predictionBeibei Wang, Siyuan Song, Cheng SONG, Yihang Lin, Liang Yu, Yan Li, Xin Chen · 2026 · Frontiers in Molecular Biosciences
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