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 101–200 of 483

  1. A novel k -mer set memory (KSM) motif representation improves regulatory variant prediction
    Yuchun Guo, Kevin Tian, Haoyang Zeng, Xiaoyun Guo, David Kenneth Gifford · 2018 · Genome Research
  2. Multiplex profiling of developmental cis-regulatory elements with quantitative single-cell expression reporters
    Jean‐Benoît Lalanne, Samuel G. Regalado, Silvia Domcke, Diego Calderon, Beth Martin, Xiaoyi Li, Tony Li, Chase C. Suiter, Choli Lee, Cole Trapnell et al. · 2024 · Nature Methods
  3. Perfect and imperfect views of ultraconserved sequences
    Valentina Snetkova, Len A. Pennacchio, Axel Visel, Diane E. Dickel · 2021 · Nature Reviews Genetics
  4. Demystifying non-coding GWAS variants: an overview of computational tools and methods
    Marijn Schipper, Daniëlle Posthuma · 2022 · Human Molecular Genetics
  5. Systematic investigation of allelic regulatory activity of schizophrenia-associated common variants
    Jessica C. McAfee, Sool Lee, Jiseok Lee, Jessica Bell, Oleh Krupa, Jessica E. Davis, Kimberly D. Insigne, Marielle L. Bond, Nanxiang Zhao, Alan P. Boyle et al. · 2023 · Cell Genomics
  6. Identification of Functional Variant Enhancers Associated With Atrial Fibrillation
    Antoinette F. van Ouwerkerk, Fernanda M. Bosada, Jia Liu, Juan Zhang, Karel van Duijvenboden, Mark D. Chaffin, Nathan R. Tucker, Daniël A. Pijnappels, Patrick T. Ellinor, Phil Barnett et al. · 2020 · Circulation Research
  7. Denisovan introgression has shaped the immune system of present-day Papuans
    Vespasiani, Davide M., Jacobs, Guy S., Cook, Laura E., Brucato, Nicolas, Leavesley, Matthew, Kinipi, Christopher, Ricaut, François-Xavier, Cox, Murray P., Gallego Romero, Irene · 2022 · PLOS Genetics
  8. Neanderthal introgression reintroduced functional ancestral alleles lost in Eurasian populations
    Rinker, David C., Simonti, Corinne N., McArthur, Evonne, Shaw, Douglas, Hodges, Emily, Capra, John A. · 2020 · Nature Ecology & Evolution
  9. Resolving mechanisms of immune‐mediated disease in primary CD4 T cells
    Christophe Bourges, Abigail F. Groff, Oliver S. Burren, Chiara Gerhardinger, Kaia Mattioli, Anna Hutchinson, Theodore X. Hu, Tanmay Anand, Madeline W. Epping, Chris Wallace et al. · 2020 · EMBO Molecular Medicine
  10. Detection of Neanderthal Adaptively Introgressed Genetic Variants That Modulate Reporter Gene Expression in Human Immune Cells
    Jagoda, Evelyn, Xue, James R, Reilly, Steven K, Dannemann, Michael, Racimo, Fernando, Huerta-Sanchez, Emilia, Sankararaman, Sriram, Kelso, Janet, Pagani, Luca, Sabeti, Pardis C et al. · 2022 · Molecular Biology and Evolution
  11. Charting the cis-regulome of activated B cells by coupling structural and functional genomics
    Virendra K. Chaudhri, Krista Dienger-Stambaugh, Zhiguo Wu, M. Shrestha, Harinder Singh · 2019 · Nature Immunology
  12. Widespread variation in molecular interactions and regulatory properties among transcription factor isoforms
    Lambourne, Luke, Mattioli, Kaia, Santoso, Clarissa, Sheynkman, Gloria, Inukai, Sachi, Kaundal, Babita, Berenson, Anna, Spirohn-Fitzgerald, Kerstin, Bhattacharjee, Anukana, Rothman, Elisabeth et al. · 2025 · Molecular Cell
  13. Predicting enhancer activity and variant impact using gkm‐SVM
    M Beer · 2017 · Human Mutation
  14. Deep learning models predict regulatory variants in pancreatic islets and refine type 2 diabetes association signals
    Agata Wesolowska‐Andersen, Grace Zhuo Yu, Vibe Nylander, Fernando Abaitua, Matthias Thurner, Jason Torres, Anubha Mahajan, Anna L. Gloyn, Mark I. McCarthy · 2020 · eLife
  15. Massively parallel functional dissection of schizophrenia-associated noncoding genetic variants
    Christine K. Rummel, Miriam Gagliardi, Ruhel Ahmad, Alexander Herholt, Laura T. Jiménez-Barrón, Vanessa Murek, Liesa Weigert, Anna Hausruckinger, Susanne Maidl, Barbara Hauger et al. · 2023 · Cell
  16. Genetic regulation of cell type–specific chromatin accessibility shapes brain disease etiology
    Biao Zeng, Jaroslav M. Bendl, Chengyu Deng, Donghoon Lee, Ruth Misir, Sarah M. Reach, Steven P. Kleopoulos, Pavan Kumar Auluck, Stefano Marenco, David A. Lewis et al. · 2024 · Science
  17. Biological relevance of computationally predicted pathogenicity of noncoding variants
    Li Liu, Maxwell D. Sanderford, Ravi Patel, Pramod Bharadwaj Chandrashekar, Greg C. Gibson, Sudhir Kumar · 2019 · Nature Communications
  18. Local adaptation and archaic introgression shape global diversity at human structural variant loci
    Stephanie M. Yan, Rachel M. Sherman, Dylan J. Taylor, Divya R. Nair, Andrew N. Bortvin, Michael C. Schatz, Rajiv C. McCoy · 2021 · eLife
  19. echolocatoR : an automated end-to-end statistical and functional genomic fine-mapping pipeline
    Brian M. Schilder, Jack Humphrey, Towfique Raj · 2021 · Bioinformatics
  20. 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, Nora Franceschini, Mitchell J. Machiela et al. · 2024 · Genome biology
  21. Statistically and functionally fine-mapped blood eQTLs and pQTLs from 1,405 humans reveal distinct regulation patterns and disease relevance
    Wang, Qingbo S., Hasegawa, Takanori, Namkoong, Ho, Saiki, Ryunosuke, Edahiro, Ryuya, Sonehara, Kyuto, Tanaka, Hiromu, Azekawa, Shuhei, Chubachi, Shotaro, Takahashi, Yugo et al. · 2024 · Nature Genetics
  22. Decoding the role of regulatory element polymorphisms in complex disease
    Christopher M. Vockley, Alejandro Barrera, Timothy E. Reddy · 2016 · Current Opinion in Genetics & Development
  23. DNA variants affecting the expression of numerous genes in trans have diverse mechanisms of action and evolutionary histories
    Sheila Lutz, Christian Brion, Margaret Kliebhan, Frank Wolfgang Albert · 2019 · PLoS Genetics
  24. Multi-omic insights into Parkinson's Disease: From genetic associations to functional mechanisms
    Brian M. Schilder, Elisa Navarro, Towfique Raj · 2021 · Neurobiology of Disease
  25. Functional dissection of complex trait variants at single-nucleotide resolution
    Layla Siraj, Rodrigo I. Castro, Hannah B. Dewey, Susan Kales, John C. Butts, Thanh Thanh L. Nguyen, Masahiro Kanai, Daniel Berenzy, Kousuke Mouri, Qingbo S. Wang et al. · 2026 · Nature
  26. CRISPR Screens to Discover Functional Noncoding Elements
    Jason B. Wright, Neville E. Sanjana · 2016 · Trends in Genetics
  27. High‐Throughput Assays to Assess the Functional Impact of Genetic Variants: A Road Towards Genomic‐Driven Medicine
    Joseph Ipe, Marelize Swart, Kimberly Burgess, Todd C. Skaar · 2017 · Clinical and Translational Science
  28. Predicting gene expression in massively parallel reporter assays: A comparative study
    Anat Kreimer, Haoyang Zeng, Matthew D. Edwards, Yuchun Guo, Kevin Tian, Sunyoung Shin, Rene Welch, Michael Wainberg, Rahul Mohan, Nasa Sinnott-Armstrong et al. · 2017 · Human Mutation
  29. Prostaglandin receptor EP4 expression by Th17 cells is associated with high disease activity in ankylosing spondylitis
    Charlotte Klasen, Anja Meyer, Paula S. Wittekind, Iris Waqué, Schafiq Nabhani, David M. Kofler · 2019 · Arthritis Research & Therapy
  30. Cis-regulatory landscapes of four cell types of the retina
    Hartl, Dominik, Krebs, Arnaud R., Jüttner, Josephine, Roska, Botond, Schübeler, Dirk · 2017 · Nucleic Acids Research
  31. PGG.SNV: understanding the evolutionary and medical implications of human single nucleotide variations in diverse populations
    Chao Zhang, Yang Gao, Zhilin Ning, Yan Lü, Xiaoxi Zhang, Jiaojiao Liu, Bo Xie, Zhe Xue, Xiaoji Wang, Kai Yuan et al. · 2019 · Genome biology
  32. Massively Parallel Reporter Assays: Defining Functional Psychiatric Genetic Variants Across Biological Contexts
    Bernard Mulvey, Tomás Lagunas, Joseph D. Dougherty · 2020 · Biological Psychiatry
  33. Loss of CTRP4 alters adiposity and food intake behaviors in obese mice
    Dylan C. Sarver, Ashley N. Stewart, Susana Rodriguez, Hannah C. Little, Susan M. Aja, Guang William Wong · 2020 · American Journal of Physiology-Endocrinology and Metabolism
  34. cepip: context-dependent epigenomic weighting for prioritization of regulatory variants and disease-associated genes
    Mulin Jun Li, Zipeng Liu, Zipeng Liu, Bin Yan, Zhicheng Pan, Dandan Huang, Qian Liang, Dingge Ying, Feng Xu, Hongcheng Yao et al. · 2017 · Genome biology
  35. High-throughput identification of noncoding functional SNPs via type IIS enzyme restriction
    Gang Li, Marta Martínez‐Bonet, Di Wu, Yang Yu, Jing Cui, Hung N. Nguyen, Pierre Cunin, Anaïs Levescot, Ming Bai, Harm-Jan Westra et al. · 2018 · Nature Genetics
  36. Functional characterization of T2D-associated SNP effects on baseline and ER stress-responsive β cell transcriptional activation
    Shubham Khetan, Susan Kales, Romy Kursawe, Alexandria Jillette, Jacob C. Ulirsch, Steven K. Reilly, Duygu Ucar, Ryan Tewhey, Michael L. Stitzel · 2021 · Nature Communications
  37. High-throughput characterization of genetic effects on DNA–protein binding and gene transcription
    Cynthia A. Kalita, Christopher D. Brown, Andrew Freiman, Jenna Isherwood, Xiaoquan Wen, Roger Piqué-Regi, Francesca Luca · 2018 · Genome Research
  38. Optimized PCR conditions minimizing the formation of chimeric DNA molecules from MPRA plasmid libraries
    Omelina, Evgeniya S., Ivankin, Anton V., Letiagina, Anna E., Pindyurin, Alexey V. · 2019 · BMC Genomics
  39. Atlas of Transcription Factor Binding Sites from ENCODE DNase Hypersensitivity Data across 27 Tissue Types
    Cory C. Funk, Alex M. Casella, Segun C. Jung, Matthew A. Richards, Alex Rodriguez, Paul T. Shannon, Rory Donovan-Maiye, Ben Heavner, Kyle Chard, Yukai Xiao et al. · 2020 · Cell Reports
  40. Integrative analysis of liver-specific non-coding regulatory SNPs associated with the risk of coronary artery disease
    Ilakya Selvarajan, Anu Toropainen, Kristina M. Garske, Maykel López Rodríguez, Arthur Ko, Zong Miao, Dorota Kamińska, Kadri Õunap, Tiit Örd, Aarthi Ravindran et al. · 2021 · The American Journal of Human Genetics
  41. A semi-supervised approach for predicting cell-type specific functional consequences of non-coding variation using MPRAs
    Zihuai He, Lin-Xi Liu, Kai Wang, I. Ionita-Laza · 2018 · Nature Communications
  42. Beyond GWAS: from simple associations to functional insights
    Kazuyoshi Ishigaki · 2021 · Seminars in Immunopathology
  43. A survey of recently emerged genome-wide computational enhancer predictor tools
    Leonard Whye Kit Lim, Hung Hui Chung, Yee Ling Chong, Nung Kion Lee · 2018 · Computational Biology and Chemistry
  44. Redefining the hypotheses driving Parkinson’s diseases research
    Sophie L. Farrow, Antony A. Cooper, Justin Martin O'Sullivan · 2022 · npj Parkinson s Disease
  45. Hypergraph factorization for multi-tissue gene expression imputation
    Ramón Viñas, Chaitanya K. Joshi, Dobrik Georgiev, Phillip Lin, Bianca Dumitrascu, Eric R. Gamazon, Píetro Lió · 2023 · Nature Machine Intelligence
  46. PsychENCODE and beyond: transcriptomics and epigenomics of brain development and organoids
    Alexandre Jourdon, Soraya Scuderi, Davide Capauto, Alexej S. Abyzov, Flora Maria Vaccarino · 2020 · Neuropsychopharmacology
  47. Our Tangled Family Tree: New Genomic Methods Offer Insight into the Legacy of Archaic Admixture
    K. D. Ahlquist, Mayra M. Bañuelos, Alyssa Funk, Jiaying Lai, Stephen Rong, Fernando A. Villanea, Kelsey E. Witt · 2021 · Genome Biology and Evolution
  48. Methods for statistical fine-mapping and their applications to auto-immune diseases
    Qingbo S. Wang, Hailiang Huang · 2022 · Seminars in Immunopathology
  49. QuASAR-MPRA: Accurate allele-specific analysis for massively parallel reporter assays
    Cynthia A. Kalita, Gregory A. Moyerbrailean, Christopher D. Brown, X. Wen, Francesca Luca, R. Pique-Regi · 2017 · bioRxiv
  50. Functional effects of variation in transcription factor binding highlight long-range gene regulation by epromoters
    Mitchelmore, Joanna, Grinberg, Nastasiya F, Wallace, Chris, Spivakov, Mikhail · 2020 · Nucleic Acids Research
  51. Expediting rare disease diagnosis: a call to bridge the gap between clinical and functional genomics
    Samantha N. Hartin, John C. Means, Joseph T. Alaimo, Scott T. Younger · 2020 · Molecular Medicine
  52. Using CRISPR to understand and manipulate gene regulation
    Ersin Akıncı, Marisa C. Hamilton, Benyapa Khowpinitchai, Richard I. Sherwood · 2021 · Development
  53. Functional characterization of human genomic variation linked to polygenic diseases
    Tania Fabo, Paul A. Khavari · 2023 · Trends in Genetics
  54. Genetic insights into immune mechanisms of Alzheimer’s and Parkinson’s disease
    Alexi Nott, Inge R. Holtman · 2023 · Frontiers in Immunology
  55. Non-coding DNA in IBD: from sequence variation in DNA regulatory elements to novel therapeutic potential
    Claartje Meddens, Amy C. J. van der List, Edward E. S. Nieuwenhuis, Michal Mokrý · 2019 · Gut
  56. Beyond association: successes and challenges in linking non-coding genetic variation to functional consequences that modulate Alzheimer’s disease risk
    Gloriia Novikova, Shea J. Andrews, Alan Edward Renton, Edoardo M. Marcora · 2021 · Molecular Neurodegeneration
  57. A Cre-dependent massively parallel reporter assay allows for cell-type specific assessment of the functional effects of non-coding elements in vivo
    Tomas Lagunas, S. Plassmeyer, A. Fischer, Ryan Z. Friedman, M. Rieger, D. Selmanovic, S. Sarafinovska, Yvette K. Sol, Michael J. Kasper, Stuart B. Fass et al. · 2021 · bioRxiv
  58. Identifying Novel Enhancer Elements with CRISPR-Based Screens
    Jason C. Klein, Wei Chen, Molly J. Gasperini, Jay Shendure · 2018 · ACS Chemical Biology
  59. Multiple overlapping binding sites determine transcription factor occupancy
    Shubham Khetan, Brent S. Carroll, Martha L. Bulyk · 2025 · Nature
  60. Comprehensive Multiple eQTL Detection and Its Application to GWAS Interpretation
    Biao Zeng, Luke R. Lloyd‐Jones, Grant W. Montgomery, Andres Metspalu, Tõnu Esko, Lude Franke, Urmo Võsa, Annique Claringbould, Kenneth L. Brigham, Arshed Ali Quyyumi et al. · 2019 · Genetics
  61. Functional dissection of inherited non-coding variation influencing multiple myeloma risk
    Ram Ajore, Abhishek Niroula, Maroulio Pertesi, Caterina Cafaro, Malte Thodberg, Molly Went, Erik L. Bao, Laura Duran-Lozano, Aitzkoa Lopez de Lapuente Portilla, Thorunn Asta Olafsdottir et al. · 2022 · Nature Communications
  62. Comprehensive epigenomic profiling reveals the extent of disease-specific chromatin states and informs target discovery in ankylosing spondylitis
    Andrew Brown, C. Cohen, Olga Mielczarek, Gabriele Migliorini, Félicie Costantino, Alice Allcock, Connor Davidson, Katherine S. Elliott, Hai Fang, Alicia Lledó Lara et al. · 2023 · Cell Genomics
  63. Functional noncoding SNPs in human endothelial cells fine-map vascular trait associations
    Anu Toropainen, Lindsey K. Stolze, Tiit Örd, Michael Bernard Whalen, Paula Martí Torrell, Verena M. Link, Minna Unelma Kaikkonen, Casey E. Romanoski · 2022 · Genome Research
  64. Computational and experimental methods for classifying variants of unknown clinical significance.
    Malte Spielmann, Martin Kircher · 2022 · PubMed Central
  65. Update on the genetics of allergic diseases
    Lucinda P. Lawson, Sreeja Parameswaran, Ronald Allan M. Panganiban, Gregory M. Constantine, Matthew T. Weirauch, Leah Claire Kottyan · 2025 · Journal of Allergy and Clinical Immunology
  66. Regulatory dissection of the severe COVID-19 risk locus introgressed by Neanderthals
    Evelyn Jagoda, Davide Marnetto, Gayani Senevirathne, Victoria Gonzalez, Kaushal Baid, Francesco Montinaro, Daniel J. Richard, Darryl Falzarano, Emmanuelle V. LeBlanc, Che C. Colpitts et al. · 2023 · eLife
  67. Constraints on eQTL Fine Mapping in the Presence of Multisite Local Regulation of Gene Expression
    Biao Zeng, Luke R. Lloyd‐Jones, Alexander Holloway, Urko M. Marigorta, Andres Metspalu, Grant W. Montgomery, Tõnu Esko, Kenneth L. Brigham, Arshed Ali Quyyumi, Youssef Idaghdour et al. · 2017 · G3 Genes Genomes Genetics
  68. Proteogenomic network analysis reveals dysregulated mechanisms and potential mediators in Parkinson’s disease
    Abolfazl Doostparast Torshizi, Dongnhu T. Truong, Liping Hou, Bart Smets, Christopher D. Whelan, Shuwei Li · 2024 · Nature Communications
  69. Identification of Single Nucleotide Non-coding Driver Mutations in Cancer
    K. Gan, Sebastian Carrasco Pro, J. Sewell, J. F. Fuxman Bass · 2018 · Frontiers in Genetics
  70. A multi-dimensional integrative scoring framework for predicting functional variants in the human genome
    Xihao Li, Godwin Yung, Hufeng Zhou, Ryan Sun, Zilin Li, Kangcheng Hou, Martin Jinye Zhang, Yaowu Liu, Theodore Arapoglou, Chen Wang et al. · 2022 · The American Journal of Human Genetics
  71. Large-scale functional screen identifies genetic variants with splicing effects in modern and archaic humans
    Stephen Rong, Christopher R. Neil, Anastasia Welch, Chaorui Duan, Samantha Maguire, Ijeoma C. Meremikwu, Malcolm Meyerson, Ben J. Evans, William Guy Fairbrother · 2023 · Proceedings of the National Academy of Sciences
  72. Effects of Type 1 Diabetes Risk Alleles on Immune Cell Gene Expression
    Ramesh Ram, Grant Morahan · 2017 · Genes
  73. From Genotype to Phenotype
    Jennie J. Lin, Kiran Musunuru · 2018 · Circulation Genomic and Precision Medicine
  74. Systematic identification of cis-regulatory variants that cause gene expression differences in a yeast cross
    Kaushik Renganaath, Rockie Chong, Laura Day, Sriram Kosuri, Leonid Kruglyak, Frank Wolfgang Albert · 2020 · eLife
  75. Meta‐analysis of massively parallel reporter assays enables prediction of regulatory function across cell types
    Anat Kreimer, Zhongxia Yan, Nadav Ahituv, Nir Yosef · 2019 · Human Mutation
  76. Human-genome single nucleotide polymorphisms affecting transcription factor binding and their role in pathogenesis
    Elena V. Antontseva, Arina O. Degtyareva, Elena E. Korbolina, Igor S. Damarov, Tatiana I. Merkulova · 2023 · Vavilov Journal of Genetics and Breeding
  77. Liver eQTL meta-analysis illuminates potential molecular mechanisms of cardiometabolic traits.
    K. A. Broadaway, S. M. Brotman, Jonathan D. Rosen, Kevin W. Currin, Abdalla A. Alkhawaja, A. Etheridge, F. Wright, P. Gallins, Dereje D. Jima, Yi-Hui Zhou et al. · 2024 · American Journal of Human Genetics
  78. From sequence to function: Bridging single-molecule kinetics and molecular diversity
    Achillefs N. Kapanidis, L. Muras, Koushik Sreenivasa, Jagadish Prasad Hazra, John van Noort, Chirlmin Joo, Sebastian Deindl · 2026 · Science
  79. Functional genomic approaches to elucidate the role of enhancers during development
    Genevieve E. Ryan, Emma K. Farley · 2019 · WIREs Systems Biology and Medicine
  80. Transcriptional-regulatory convergence across functional MDD risk variants identified by massively parallel reporter assays
    Bernard Mulvey, Joseph D. Dougherty · 2021 · Translational Psychiatry
  81. Integrative analyses highlight functional regulatory variants associated with neuropsychiatric diseases
    M. Guo, D. Reynolds, C. Ang, Ying-Fei Liu, Yang Zhao, L. Donohue, Z. Siprashvili, Xue Yang, Yongjin Yoo, Smarajit Mondal et al. · 2023 · Nature Genetics
  82. Gene-centric functional dissection of human genetic variation uncovers regulators of hematopoiesis
    Satish Kumar Nandakumar, Sean McFarland, Laura Marlene Mateyka, Caleb A. Lareau, Jacob C. Ulirsch, Leif S. Ludwig, Gaurav Agarwal, J Engreitz, Bartlomiej P. Przychodzen, Marie Ellen McConkey et al. · 2019 · eLife
  83. Functional phenotyping of genomic variants using joint multiomic single-cell DNA–RNA sequencing
    Dominik Lindenhofer, Julia Bauman, John A. Hawkins, Donnacha Fitzgerald, Umut Yildiz, Haeyeon Jung, Anastasiia Korosteleva, Mikael Marttinen, Moritz Kueblbeck, Judith B. Zaugg et al. · 2025 · Nature Methods
  84. Identifying differential regulatory control of APOE ɛ4 on African versus European haplotypes as potential therapeutic targets
    Karen Nuytemans, Marina Lipkin Vasquez, Liyong Wang, Derek Van Booven, Antony J. Griswold, Farid Rajabli, Katrina Celis, Oded Oron, Natalia K. Hofmann, Sophie Rolati et al. · 2022 · Alzheimer s & Dementia
  85. Prediction of the cell-type-specific transcription of non-coding RNAs from genome sequences via machine learning
    Masaru Koido, Chung-Chau Hon, Satoshi Koyama, Hideya Kawaji, Yasuhiro Murakawa, Kazuyoshi Ishigaki, Kaoru Ito, Jun Sese, Nicholas F. Parrish, Yoichiro Kamatani et al. · 2022 · Nature Biomedical Engineering
  86. Single-cell multiomics of the human retina reveals hierarchical transcription factor collaboration in mediating cell type-specific effects of genetic variants on gene regulation
    Jun Wang, Xuesen Cheng, Qingnan Liang, Leah A. Owen, Jiaxiong Lu, Yiqiao Zheng, Meng Wang, Shiming Chen, Margaret M. DeAngelis, Yumei Li et al. · 2023 · Genome biology
  87. Somatic mosaicism in schizophrenia brains reveals prenatal mutational processes
    Eduardo A. Maury, Attila Jones, V. Seplyarskiy, T. T. Nguyen, C. Rosenbluh, Taejong Bae, Yifan Wang, A. Abyzov, S. Khoshkhoo, Y. Chahine et al. · 2024 · Science
  88. Functional genomics of autoimmune diseases
    Akari Suzuki, Matteo Maurizio Guerrini, Kazuhiko Yamamoto · 2021 · Annals of the Rheumatic Diseases
  89. De novopattern discovery enables robust assessment of functional consequences of non-coding variants
    Yang Hai, Rui Chen, Quan Wang, Qiang Wei, Ying Ji, Guangze Zheng, Xue Yun Zhong, Nancy Jean Cox, Bingshan Li · 2018 · Bioinformatics
  90. Exploiting deep transfer learning for the prediction of functional non-coding variants using genomic sequence
    Li Chen, Ye Wang, Fengdi Zhao · 2022 · Bioinformatics
  91. Characterization of enhancer activity in early human neurodevelopment using Massively Parallel Reporter Assay (MPRA) and forebrain organoids
    Davide Capauto, Yifan Wang, Feinan Wu, Scott Norton, Jessica Mariani, Fumitaka Inoue, Gregory E. Crawford, Nadav Ahituv, Alexej S. Abyzov, Flora Maria Vaccarino · 2024 · Scientific Reports
  92. Activity-by-Contact model of enhancer specificity from thousands of CRISPR perturbations
    Charles P. Fulco, Joseph Nasser, Thouis R. Jones, Glen Munson, Drew T. Bergman, Vidya Subramanian, Sharon R. Grossman, Rockwell Anyoha, Tejal A. Patwardhan, Tung H. Nguyen et al. · 2019 · bioRxiv (Cold Spring Harbor Laboratory)
  93. Chromatin Alterations in Neurological Disorders and Strategies of (Epi)Genome Rescue
    Marcin Janowski, Małgorzata Milewska, Payman Zare, Aleksandra Pękowska · 2021 · Pharmaceuticals
  94. Genetic insights into juvenile idiopathic arthritis derived from deep whole genome sequencing
    Lai-Ping Wong, Kaiyu Jiang, Yanmin Chen, James N. Jarvis · 2017 · Scientific Reports
  95. Emerging applications of genome-editing technology to examine functionality of GWAS-associated variants for complex traits
    Andrew J P Smith, Panos Deloukas, Patricia B. Munroe · 2018 · Physiological Genomics
  96. Prioritization of regulatory variants with tissue-specific function in the non-coding regions of human genome
    Sheng-Cheng Dong, A. Boyle · 2021 · bioRxiv
  97. PINES: phenotype-informed tissue weighting improves prediction of pathogenic noncoding variants
    Corneliu Alexandru Bodea, Adele A. Mitchell, Alex Bloemendal, Aaron Day-Williams, Heiko Runz, Shamil R. Sunyaev · 2018 · Genome biology
  98. Using QTL to Identify Genes and Pathways Underlying the Regulation and Production of Milk Components in Cattle
    Thomas Lopdell · 2023 · Animals
  99. Challenges and considerations for reproducibility of STARR-seq assays
    Maitreya Das, Ayaan Hossain, Deepro Banerjee, Craig A. Praul, Santhosh Girirajan · 2023 · Genome Research
  100. Epigenetics as a mediator of genetic risk in osteoarthritis: role during development, homeostasis, aging, and disease progression
    Daniel J. Richard, Terence Dante Capellini, Brian O. Diekman · 2023 · American Journal of Physiology-Cell Physiology