Genome-scale high-resolution mapping of activating and repressive nucleotides in regulatory regions

Ernst, Jason, Melnikov, Alexandre, Zhang, Xiaolan, Wang, Li, Rogov, Peter, Mikkelsen, Tarjei S, Kellis, Manolis·2016·Nature Biotechnology

DOI 10.1038/nbt.3678

Cited by (169)

Items 101–169 of 169

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Rozita Razavi, Ali Fathi, Isaac Yellan, Alexander V. Brechalov, Kaitlin U. Laverty, Arttu Jolma, Aldo Hernández-Corchado, Hong Zheng, Ally W. H. Yang, Mihai Albu et al. · 2026 · Nature Communications
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Function and constraint in enhancers with multiple evolutionary origins
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Genome-wide regulatory model from MPRA data predicts functional regions, eQTLs, and GWAS hits
Yue Li, Alvin Shi, Ryan Tewhey, Pardis C. Sabeti, Jason Ernst, M Kellis · 2017 · bioRxiv (Cold Spring Harbor Laboratory)
Multinomial Convolutions for Joint Modeling of Sequence Motifs and Enhancer Activities
Minjun Park, Salvi Singh, Francisco Jose Grisanti Canozo, Md. Abul Hassan Samee · 2020 · bioRxiv (Cold Spring Harbor Laboratory)
Using Synthetic DNA Libraries to Investigate Chromatin and Gene Regulation
Holly Kleinschmidt, Cheng Xu, Lu Bai · 2023 · Chromosoma
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Mckenzie Tu, Sarah Saputo · 2022 · Bioinformatics and Biology Insights
Functional Interpretation of Genetic Variants Using Deep Learning Predicts Impact on Epigenome
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GRAM: A generalized model to predict the molecular effect of a non-coding variant in a cell-type specific manner
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Customizable high-throughput platform for profiling cofactor recruitment to DNA to characterize cis-regulatory elements and screen non-coding single-nucleotide polymorphisms
David Bray, Heather Hook, Rose W. Zhao, Jessica L. Keenan, Ashley R. Penvose, Yemi Osayame, Nima Mohaghegh, Trevor Siggers · 2020 · bioRxiv (Cold Spring Harbor Laboratory)
A transcription start site map in human pancreatic islets reveals functional regulatory signatures
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Evolution of transposable element-derived enhancer activity
Alan Y. Du, Xiaoyu Zhuo, Vasavi Sundaram, Nicholas O. Jensen, Hemangi G. Chaudhari, Nancy L. Saccone, Barak A. Cohen, Ting Wang · 2022 · bioRxiv (Cold Spring Harbor Laboratory)
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)
Retracing and rewriting the evolutionary trajectories of mammalian developmental enhancers
Tony Li, Jean‐Benoît Lalanne, Emma A.N. Kajiwara, Shruti Jain, Xiaoyi Li, Tiffany V. Do, Beth K. Martin, Samuel G. Regalado, Riza M. Daza, Jay Shendure · 2026 · bioRxiv (Cold Spring Harbor Laboratory)
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
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Cis-acting Super-Enhancer lncRNAs as Biomarkers of Early-Stage Breast Cancer
Ali S. Ropri, Rebecca DeVaux, Jonah Eng, Sridar V. Chittur, Jason I. Herschkowitz · 2021 · Research Square
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Konstantinn Bonnet, Nicolas Hulo, Raphaël Mourad, Adam D. Ewing, Olivier Croce, Magali Naville, Nikita S. Vassetzky, Éric Gilson, Didier Picard, Geneviève Fourel · 2023 · bioRxiv (Cold Spring Harbor Laboratory)
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)
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Meng Wang, Xiaoxu Yang, Qixi Wu · 2025 · Genomics
Additional file 6 of Global properties of regulatory sequences are predicted by transcription factor recognition mechanisms
Zain M. Patel, Hughes, Timothy R. · 2021 · Figshare
Additional file 1 of Functional mapping of androgen receptor enhancer activity
Huang, Chia-Chi Flora, Shreyas Lingadahalli, Tunç Morova, Doğancan Özturan, Eugene Hu, Ivan Pak Lok Yu, Linder, Simon, Marlous Hoogstraat, Suzan Stelloo, Funda Sar et al. · 2021 · Figshare
Additional file 2 of Functional mapping of androgen receptor enhancer activity
Huang, Chia-Chi Flora, Shreyas Lingadahalli, Tunç Morova, Doğancan Özturan, Eugene Hu, Ivan Pak Lok Yu, Linder, Simon, Marlous Hoogstraat, Suzan Stelloo, Funda Sar et al. · 2021 · Figshare
Additional file 1 of The contribution of silencer variants to human diseases
Di Huang, Ivan Ovcharenko · 2024 · Figshare
Additional file 2 of Cis-acting super-enhancer lncRNAs as biomarkers to early-stage breast cancer
Ali S. Ropri, DeVaux, Rebecca S., Jonah Eng, Sridar V. Chittur, Jason I. Herschkowitz · 2021 · Figshare
Additional file 4 of Functional mapping of androgen receptor enhancer activity
Huang, Chia-Chi Flora, Shreyas Lingadahalli, Tunç Morova, Doğancan Özturan, Eugene Hu, Ivan Pak Lok Yu, Linder, Simon, Marlous Hoogstraat, Suzan Stelloo, Funda Sar et al. · 2021 · Figshare
Additional file 1 of Cis-acting super-enhancer lncRNAs as biomarkers to early-stage breast cancer
Ali S. Ropri, DeVaux, Rebecca S., Jonah Eng, Sridar V. Chittur, Jason I. Herschkowitz · 2021 · Figshare
Additional file 2 of Global properties of regulatory sequences are predicted by transcription factor recognition mechanisms
Zain M. Patel, Hughes, Timothy R. · 2021 · Figshare
Additional file 3 of Cis-acting super-enhancer lncRNAs as biomarkers to early-stage breast cancer
Ali S. Ropri, DeVaux, Rebecca S., Jonah Eng, Sridar V. Chittur, Jason I. Herschkowitz · 2021 · Figshare
Additional file 1 of Fast activation maximization for molecular sequence design
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Additional file 2 of The contribution of silencer variants to human diseases
Di Huang, Ivan Ovcharenko · 2024 · Figshare
Additional file 3 of The contribution of silencer variants to human diseases
Di Huang, Ivan Ovcharenko · 2024 · Figshare
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Alexandre P. España · 2019 · theses.fr (ABES)
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Hjörleifur Einarsson, Natsuda Navamajiti, Christian Vaagensø, Stefano Pellegrini, Lykke Jirström, Nicolás Alcaraz, Malte Thodberg, Daniel Solvie, Wei‐Lin Qiu, Maya U. Sheth et al. · 2026 · bioRxiv (Cold Spring Harbor Laboratory)
Directed evolution of compact synthetic promoters via AlphaGenome and genetic algorithms
聂麟枭 · 2026 · bioRxiv (Cold Spring Harbor Laboratory)
Enhancer Tuning by Sequence-Specific Repressors
Lucia Ichino, Kaelan Brennan, Benjamin J. Mallory, Tomek Swigut, Stephanie C. Bohaczuk, Jaaved Mohammed, Devaraja Gouda Mudeppa, Saman Tabatabaee, Chunyang Ni, Andrew B. Stergachis et al. · 2026 · bioRxiv (Cold Spring Harbor Laboratory)
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Xue Zhang, Xiao-Yan Huang, Hui-Yu Wang, Feng‐Wu Bai, Kai Li, Shen S. Hu · 2026 · Biotechnology Advances
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