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 201–300 of 483
- Systematic identification of genotype-dependent enhancer variants in eosinophilic esophagitisMolly Shook, Xiaoming Lu, Xiaoting Chen, Sreeja Parameswaran, Lee Edsall, Michael P. Trimarchi, Kevin Ernst, Marissa Granitto, Carmy R. Forney, Omer A. Donmez et al. · 2024 · The American Journal of Human Genetics
- Machine-guided design of synthetic cell type-specific cis -regulatory elementsSager J. Gosai, Rodrigo I. Castro, N Fuentes, John C. Butts, Susan Kales, Ramil R. Noche, Kousuke Mouri, Pardis Christine Sabeti, Steven K. Reilly, Ryan Tewhey · 2023 · bioRxiv (Cold Spring Harbor Laboratory)
- Population-scale skeletal muscle single-nucleus multi-omic profiling reveals extensive context specific genetic regulationArushi Varshney, Nandini Manickam, Peter Orchard, Adelaide Tovar, Christa Ventresca, Zhenhao Zhang, Fan Feng, Joseph Mears, Michael R. Erdos, Narisu Narisu et al. · 2023 · bioRxiv (Cold Spring Harbor Laboratory)
- Leaving no patient behind! Expert recommendation in the use of innovative technologies for diagnosing rare diseasesClara van Karnebeek, Anne O’Donnell‐Luria, Gareth S Baynam, Anaı̈s Baudot, Tudor Groza, Judith J M Jans, Timo Lassmann, Mary Catherine V. Letinturier, Stephen B. Montgomery, Peter N. Robinson et al. · 2024 · Orphanet Journal of Rare Diseases
- Genetic coupling of enhancer activity and connectivity in gene expression controlHelen F. Ray-Jones, Chak Kei Sung, Lai Ting Chan, Alexander Haglund, Pavel Artemov, Monica Della Rosa, Luminiţa Ruje, Frances Burden, Roman Kreuzhuber, Anna Litovskikh et al. · 2025 · Nature Communications
- An in vivo systemic massively parallel platform for deciphering animal tissue-specific regulatory functionAshley R. Brown, Grant A Fox, Irene M. Kaplow, Alyssa J. Lawler, BaDoi N. Phan, Lahari Gadey, Morgan E. Wirthlin, Easwaran Ramamurthy, Gemma E. May, Ziheng Chen et al. · 2025 · Frontiers in Genetics
- Focus on Causality in ESC/iPSC-Based Modeling of Psychiatric DisordersAnke Hoffmann, Michael J. Ziller, Dietmar Spengler · 2020 · Cells
- Cis-regulatory variants affect gene expression dynamics in yeastChing-Hua Shih, Justin C. Fay · 2021 · eLife
- Identifying causal variants and genes using functional genomics in specialized cell types and contextsBo-Xiang Liu, S. Montgomery · 2019 · Human Genetics
- Whole-genome functional characterization of RE1 silencers using a modified massively parallel reporter assayKousuke Mouri, Hannah B. Dewey, Rodrigo Castro, Daniel Berenzy, Susan Kales, Ryan Tewhey · 2022 · Cell Genomics
- Optimized high-throughput screening of non-coding variants identified from genome-wide association studiesTunç Morova, Yi Ding, Chia-Chi Flora Huang, Funda Sar, Tommer Schwarz, Claudia Giambartolomei, Sylvan C. Baca, Dennis Grishin, Faraz Hach, Alexander Gusev et al. · 2022 · Nucleic Acids Research
- Modeling and designing enhancers by introducing and harnessing transcription factor binding unitsJiaqi Li, Pengcheng Zhang, Xi Xi, Liyang Liu, Lei Wei, Xiaowo Wang · 2025 · Nature Communications
- Accurate eQTL prioritization with an ensemble‐based frameworkHaoyang Zeng, Matthew D. Edwards, Yuchun Guo, David Kenneth Gifford · 2017 · Human Mutation
- (Epi)genomic heterogeneity of pancreatic islet function and failure in type 2 diabetesNathan T Lawlor, Michael L. Stitzel · 2019 · Molecular Metabolism
- In The Blood: Connecting Variant to Function In Human HematopoiesisSatish Kumar Nandakumar, Xiaotian Liao, Vijay G. Sankaran · 2020 · Trends in Genetics
- CoRE-ATAC: A deep learning model for the functional classification of regulatory elements from single cell and bulk ATAC-seq dataAsa Thibodeau, Shubham Khetan, Alper Eroğlu, Ryan Tewhey, Michael L. Stitzel, Duygu Ucar · 2021 · PLoS Computational Biology
- Buffering and non-monotonic behavior of gene dosage response curves for human complex traitsNikhil Milind, Courtney J. Smith, Huisheng Zhu, Tamara Gjorgjieva, Jeffrey P. Spence, Jonathan K. Pritchard · 2024 · medRxiv
- PROBER identifies proteins associated with programmable sequence-specific DNA in living cellsSmarajit Mondal, Muthukumar Ramanathan, Weili Miao, Robin M. Meyers, Deepti S. Rao, Vanessa Lopez-Pajares, Zurab Siprashvili, David L. Reynolds, Douglas F. Porter, Ian Ferguson et al. · 2022 · Nature Methods
- A brief guide to analyzing expression quantitative trait lociByung Su Ko, Sung Bae Lee, Tae-Kyung Kim · 2024 · Molecules and Cells
- A signature of Neanderthal introgression on molecular mechanisms of environmental responsesFindley, Anthony S., Zhang, Xinjun, Boye, Carly, Lin, Yen Lung, Kalita, Cynthia A., Barreiro, Luis, Lohmueller, Kirk E., Pique-Regi, Roger, Luca, Francesca · 2021 · PLoS Genetics
- Decoding polygenic diseases: advances in noncoding variant prioritization and validationIris M. Chin, Zachary A. Gardell, M. Ryan Corces · 2024 · Trends in Cell Biology
- Systematic prioritization of functional variants and effector genes underlying colorectal cancer riskPhilip Law, James B. Studd, James S. Smith, Jayaram Vijayakrishnan, Bradley T. Harris, Maria Mandelia, Charlie Mills, Malcolm G. Dunlop, Richard S. Houlston · 2024 · Nature Genetics
- Systematic characterization of regulatory variants of blood pressure genesWinona Oliveros, Kate Delfosse, Daniella F. Lato, Katerina Kiriakopulos, Milad Mokhtaridoost, Abdelrahman Said, Brandon J. McMurray, Jared W. L. Browning, Kaia Mattioli, Guoliang Meng et al. · 2023 · Cell Genomics
- Genome-wide census of ATF4 binding sites and functional profiling of trait-associated genetic variants overlapping ATF4 binding motifsTiit Örd, Daima Örd, Priit Adler, Tõnis Örd · 2023 · PLoS Genetics
- Archaic hominin genomics provides a window into gene expression evolutionStephanie M. Yan, Rajiv C. McCoy · 2020 · Current Opinion in Genetics & Development
- Genome editing to define the function of risk loci and variants in rheumatic diseaseYuriy Baglaenko, Dana Macfarlane, Alexander Marson, Peter Andrija Nigrovic, Soumya Raychaudhuri · 2021 · Nature Reviews Rheumatology
- A genome-wide interactome of DNA-associated proteins in the human liverRyne C. Ramaker, Daniel Savic, Andrew A. Hardigan, Kimberly M. Newberry, Gregory M. Cooper, R Myers, Sara J. Cooper · 2017 · Genome Research
- Functional characterization of enhancer activity during a long terminal repeat's evolutionAlan Y. Du, Xiaoyu Zhuo, Vasavi Sundaram, Nicholas O. Jensen, Hemangi G. Chaudhari, Nancy L. Saccone, Barak A. Cohen, Ting Wang · 2022 · Genome Research
- Stem Cell Models for Context-Specific Modeling in Psychiatric DisordersCarina Seah, Laura M. Huckins, Kristen Brennand · 2022 · Biological Psychiatry
- Widespread perturbation of ETS factor binding sites in cancerSebastian Carrasco Pro, H. Hook, D. Bray, D. Berenzy, Devlin C. Moyer, Meimei Yin, A. Labadorf, R. Tewhey, T. Siggers, J. F. Fuxman Bass · 2022 · bioRxiv
- Identification of 27 allele-specific regulatory variants in Parkinson’s disease using a massively parallel reporter assaySophie L. Farrow, Sreemol Gokuladhas, William S. Schierding, Michael Pudjihartono, Jo Kate Perry, Antony A. Cooper, Justin Martin O'Sullivan · 2024 · npj Parkinson s Disease
- Dynamic neuro-immune regulation of psychiatric risk loci in human neuronsKayla G. Townsley, S. H. Lee, Sarah Williams, Sam Cartwright, Sophie Cohen, Annabel Sen, Meng Jia, Hannah E. Young, Lee Dobbyn, Michael Deans et al. · 2026 · Nature Communications
- Long-adapter single-strand oligonucleotide probes for the massively multiplexed cloning of kilobase genome regionsLorenzo Tosi, Viswanadham Sridhara, Yunlong Yang, Dongli Guan, Polina Shpilker, Nicola Segata, H. Benjamin Larman, Biju Parekkadan · 2017 · Nature Biomedical Engineering
- cis-regulatory variation modulates susceptibility to enteric infection in the Drosophila genetic reference panelMichael Frochaux, Maroun S. Bou Sleiman, Vincent Gardeux, Riccardo Dainese, Brian Hollis, Maria Litovchenko, Virginie S. Braman, Tommaso Andreani, Dani Osman, Bart Deplancke · 2020 · Genome biology
- Fine-mapping within eQTL credible intervals by expression CROP-seqYidan Pan, Ruoyu Tian, Ciaran M. Lee, Gang Bao, Greg C. Gibson · 2020 · Biology Methods and Protocols
- Functional interrogation of autoimmune disease genetics using CRISPR/Cas9 technologies and massively parallel reporter assaysJames Ding, Antonios Frantzeskos, Gisela Orozco · 2021 · Seminars in Immunopathology
- Advances in profiling chromatin architecture shed light on the regulatory dynamics underlying brain disordersBrandon M. Pratt, Hyejung Won · 2021 · Seminars in Cell and Developmental Biology
- Gene regulatory activity associated with polycystic ovary syndrome revealed DENND1A-dependent testosterone productionLaavanya Sankaranarayanan, Kelly Brewer, Shauna Morrow, Graham D. Johnson, Alejandro Barrera, Revathy Venukuttan, Ryan K. Sisk, Andrea Elizabeth Dunaif, Timothy E. Reddy · 2025 · Nature Communications
- From variants to mechanisms: Neurogenomics in the post-GWAS eraMichael P. Margolis, Miao Tang, Miriam Gagliardi, Cindy H. Wen, Yeda Wu, Naomi R. Wray, Michael J. Ziller, Michael J. Gandal · 2025 · Neuron
- Proformer: a hybrid macaron transformer model predicts expression values from promoter sequencesIl‐Youp Kwak, Byeong-Chan Kim, Juhyun Lee, Taein Kang, Daniel J. Garry, Jianyi Jay Zhang, Wuming Gong · 2024 · BMC Bioinformatics
- A common regulatory haplotype doubles lactoferrin concentration in milkThomas Lopdell, Alexander J. Trevarton, Janelle Moody, Claire Prowse-Wilkins, Sarah Knowles, Kathryn Tiplady, Amanda Jane Chamberlain, Michael Edward Goddard, Richard J. Spelman, Klaus Lehnert et al. · 2024 · Genetics Selection Evolution
- Hidden secrets of the cancer genome: unlocking the impact of non-coding mutations in gene regulatory elementsSandra Íñiguez-Muñoz, Pere Llinàs‐Arias, Miquel Ensenyat-Méndez, Andrés F. Bedoya-López, Javier I. J. Orozco, Javier Cortés, Ananya Roy, Karin Forsberg‐Nilsson, Maggie Lee DiNome, Diego M. Marzese · 2024 · Cellular and Molecular Life Sciences
- Innovative Technologies for Advancement of WHO Risk Group 4 Pathogens ResearchJames Logue, Jeffrey M. Solomon, Brian F. Niemeyer, Kambez Hajipouran Benam, Aaron E. Lin, Zach B. Bjornson, Sizun Jiang, David R. McIlwain, Garry P. Nolan, Gustavo F. Palacios et al. · 2019 · Springer eBooks
- Tissue-Specific Alteration of Metabolic Pathways Influences Glycemic RegulationNatasha Hui Jin Ng, Sara M. Willems, Juan Fernandez, Rebecca S. Fine, Eleanor Wheeler, Jennifer Wessel, Hidetoshi Kitajima, Gaëlle Marenne, Jana K. Rundle, Xueling Sim et al. · 2019 · bioRxiv (Cold Spring Harbor Laboratory)
- Sex Significantly Impacts the Function of Major Depression–Linked Variants In VivoBernard Mulvey, Din Selmanovic, Joseph D. Dougherty · 2021 · Biological Psychiatry
- Neanderthal introgression reintroduced functional alleles lost in the human out of Africa bottleneckDavid C. Rinker, Corinne Simonti, Evonne McArthur, Douglas M. Shaw, Emily C. Hodges, John A. Capra · 2019 · bioRxiv (Cold Spring Harbor Laboratory)
- High-throughput identification of functional regulatory SNPs in systemic lupus erythematosusQiang Wang, Taehyeung Kim, M. Martínez-Bonet, V. Aguiar, Sangwan Sim, Jing Cui, J. Sparks, X. Chen, M. Todd, B. Wauford et al. · 2024 · Nature Communications
- Systematic representation and optimization enable the inverse design of cross-species regulatory sequences in bacteriaPeng-Cheng Zhang, Qi-Xiu Du, Ye Wang, Lei Wei, Xiao-Wo Wang · 2025 · Nature Communications
- Functional Neurogenomics to Dissect Disease Mechanisms Across ModelsXinhe Zheng, Jiwen Li, Xin Jin · 2025 · Annual Review of Genomics and Human Genetics
- Genetic and epigenetic screens in primary human T cells link candidate causal autoimmune variants to T cell networksChing‐Huang Ho, Maxwell A. Dippel, Meghan S. McQuade, LeAnn P. Nguyen, Arpit Mishra, Stephan Pribitzer, Samantha R. Hardy, Harshpreet Chandok, Florence M. Chardon, Troy A. McDiarmid et al. · 2025 · Nature Genetics
- Strategies for activity analysis of single nucleotide polymorphisms associated with human diseasesNaixia Ren, Shang‐Kun Dai, Shumin Ma, Fengtang Yang · 2022 · Clinical Genetics
- Genome-wide association study identifies human genetic variants associated with fatal outcome from Lassa feverDylan Kotliar, Siddharth S. Raju, Shervin Tabrizi, Ikponmwosa Odia, Augustine Goba, Mambu Momoh, John Demby Sandi, Parvathy Nair, Eric Phelan, Ridhi Tariyal et al. · 2024 · Nature Microbiology
- Functional genomics and assays of regulatory activity detect mechanisms at loci for lipid traits and coronary artery diseaseTamara S. Roman, Karen L. Mohlke · 2018 · Current Opinion in Genetics & Development
- High-efficiency genomic editing in Epstein-Barr virus-transformed lymphoblastoid B cells using a single-stranded donor oligonucleotide strategyAndrew D. Johnston, Claudia Avello Simões‐Pires, Masako Suzuki, John M. Greally · 2019 · Communications Biology
- USF3modulates osteoporosis risk by targetingWNT16,RANKL,RUNX2, and two GWAS lead SNPs rs2908007 and rs4531631Weiyuan Ye, Ya Wang, Sasa Hou, Bing Mei, Xinhong Liu, Han Huang, Qian Zhou, Yajing Niu, Yuanyuan Chen, Manling Zhang et al. · 2020 · Human Mutation
- Quality assessment and refinement of chromatin accessibility data using a sequence-based predictive modelSeong Kyu Han, Yoshiharu Muto, Parker C. Wilson, Benjamin D. Humphreys, Matthew Gordon Sampson, Aravinda Chakravarti, Dongwon Lee · 2022 · Proceedings of the National Academy of Sciences
- Blood cell traits’ GWAS loci colocalization with variation in PU.1 genomic occupancy prioritizes causal noncoding regulatory variantsRaehoon Jeong, Martha L. Bulyk · 2023 · Cell Genomics
- MPRAnalyze - A statistical framework for Massively Parallel Reporter AssaysTal Ashuach, David S. Fischer, Anat Kreimer, Nadav Ahituv, Fabian Joachim Theis, Nir Yosef · 2019 · bioRxiv (Cold Spring Harbor Laboratory)
- Multiplexed characterization of rationally designed promoter architectures deconstructs combinatorial logic for IPTG-inducible systemsTimothy C. Yu, Winnie L. Liu, Marcia S. Brinck, Jessica E. Davis, Jeremy Shek, Grace Bower, Tal Einav, Kimberly D. Insigne, Rob Phillips, Sriram Kosuri et al. · 2020 · bioRxiv (Cold Spring Harbor Laboratory)
- FUN-LDA: A LATENT DIRICHLET ALLOCATION MODEL FOR PREDICTING TISSUE-SPECIFIC FUNCTIONAL EFFECTS OF NONCODING VARIATIONDaniel Backenroth, Zihuai He, Krzysztof Kiryluk, Valentina Boeva, Lynn Pethukova, Ekta Khurana, Angela M. Christiano, Joseph D. Buxbaum, Iuliana Ionita‐Laza · 2016 · bioRxiv (Cold Spring Harbor Laboratory)
- Joint actions of diverse transcription factor families establish neuron-type identities and promote enhancer selectivityÁngela Jimeno-Martín, Erick Sousa, Rebeca Brocal-Ruiz, Noemi Daroqui, Miren Maicas, Nuria Flames · 2022 · Genome Research
- Identification of functional non-coding variants associated with orofacial cleftPriyanka Kumari, Ryan Z. Friedman, Sarah W. Curtis, Lira Pi, Kitt D. Paraiso, Axel Visel, Lindsey Rhea, Martine Dunnwald, Anjali P. Patni, Daniel Mar et al. · 2025 · Nature Communications
- Design tools for MPRA experimentsAndrew R. Ghazi, Edward S. Chen, David Morgan Henke, Namrata Madan, Leonard C. Edelstein, Chad A. Shaw · 2018 · Bioinformatics
- MPRAscore: robust and non-parametric analysis of massively parallel reporter assaysAbhishek Niroula, Ram Ajore, Björn Nilsson · 2019 · Bioinformatics
- Pitfalls in Single Clone CRISPR-Cas9 Mutagenesis to Fine-Map Regulatory IntervalsRuoyu Tian, Yidan Pan, Thomas H. A. Etheridge, Harshavardhan Deshmukh, Dalia Arafat Gulick, Greg C. Gibson, Gang Bao, Ciaran M. Lee · 2020 · Genes
- WEVar: a novel statistical learning framework for predicting noncoding regulatory variantsYe Wang, Yuchao Jiang, Bing Yao, Kun Huang, Yunlong Liu, Yue Wang, Xiao Qin, Andrew J. Saykin, Li Chen · 2021 · Briefings in Bioinformatics
- Multiplexed functional genomic assays to decipher the noncoding genomeYonatan A. Cooper, Qiuyu Guo, Daniel H. Geschwind · 2022 · Human Molecular Genetics
- Analysis of chromatin data supports a role for CD14+ monocytes/macrophages in mediating genetic risk for juvenile idiopathic arthritisElizabeth A. Crinzi, Emma K. Haley, Kerry E. Poppenberg, Kaiyu Jiang, Vincent M. Tutino, James N. Jarvis · 2022 · Frontiers in Immunology
- The role of transposon activity in shapingcis-regulatory element evolution after whole-genome duplicationØystein Monsen, Lars Grønvold, Alex K. Datsomor, Thomas Nelson Harvey, James Kijas, Alexander Suh, Torgeir Rhoden Hvidsten, Simen R. Sandve · 2025 · Genome Research
- Integrative multi-omics QTL colocalization maps regulatory architecture in aging human brainXuewei Cao, Haochen Sun, Ru Feng, Rahul Mazumder, Carlos F. Buen Abad Najar, Yang Li, Philip L. De Jager, David Alan Bennett, Kushal K. Dey, Gao Wang · 2025 · medRxiv
- Identification, Design, and Application of Noncoding Cis-Regulatory ElementsLingna Xu, Yuwen Liu · 2024 · Biomolecules
- Translation of genome-wide association study: from genomic signals to biological insightsWinter S. Bruner, Struan F.A. Grant · 2024 · Frontiers in Genetics
- Using individual barcodes to increase quantification power of massively parallel reporter assaysPia Keukeleire, Jonathan D. Rosen, Angelina Göbel-Knapp, Kilian Salomon, Max Schubach, Martin Kircher · 2025 · BMC Bioinformatics
- A polyclonal allelic expression assay for detecting regulatory effects of transcript variantsMargot K. Brandt, Alper Gokden, Marcello Ziosi, Tuuli Lappalainen · 2020 · Genome Medicine
- Functional assays for transcription mechanisms in high-throughputChenxi Qiu, Craig D. Kaplan · 2019 · Methods
- Candidate Causal Variants at the 8p12 Breast Cancer Risk Locus Regulate DUSP4Dylan M. Glubb, Wei Shi, Jonathan Beesley, Laura Fachal, Jayne-Louise Pritchard, Karen McCue, Daniel R. Barnes, Antonis C. Antoniou, Alison M. Dunning, Douglas F. Easton et al. · 2020 · Cancers
- Denisovan introgression has shaped the immune system of present-day PapuansDavide Maria Vespasiani, Guy S. Jacobs, Laura E. Cook, Nicolas Brucato, Matthew Leavesley, Christopher Kinipi, François‐Xavier Ricaut, Murray P. Cox, Irene Gallego Romero · 2020 · bioRxiv (Cold Spring Harbor Laboratory)
- Sequence-based correction of barcode bias in massively parallel reporter assaysDongwon Lee, Ashish Kapoor, Changhee Lee, Michael Mudgett, M Beer, Aravinda Chakravarti · 2021 · Genome Research
- Massively parallel approaches for characterizing noncoding functional variation in human evolutionStephen Rong, Elise Root, Steven K. Reilly · 2024 · Current Opinion in Genetics & Development
- MPRAVarDB: an online database and web server for exploring regulatory effects of genetic variantsWeijia Jin, Yi Xia, Javlon Nizomov, Yunlong Liu, Zhigang Li, Qing Lu, Li Chen · 2024 · Bioinformatics
- Comparative Analysis of Deep Learning Models for Predicting Causative Regulatory VariantsGaetano Manzo, Kathryn Borkowski, Ivan Ovcharenko · 2025 · Genes
- Translating non-coding genetic associations into a better understanding of immune-mediated diseaseChristina T. Stankey, James Christopher Lee · 2023 · Disease Models & Mechanisms
- Association of serum C1Q/TNF-related protein 4 levels with carotid atherosclerosis in subjects with type 2 diabetes mellitus: A cross-sectional studyZheng Liu, Junxia Han, Ye Wang, Minyi Yang, Lijuan Niu, Bimin Shi · 2022 · Clinica Chimica Acta
- RegVar: Tissue-Specific Prioritization of Non-Coding Regulatory VariantsHao Xin Lu, Luyu Ma, Cheng Quan, Lei Li, Yiming Lu, Gangqiao Zhou, Chenggang Zhang · 2021 · Genomics Proteomics & Bioinformatics
- A systematic strategy for identifying causal single nucleotide polymorphisms and their target genes on Juvenile arthritis risk haplotypesKaiyu Jiang, Tao Liu, Susan Kales, Ryan Tewhey, Dongkyeong Kim, Yungki Park, James N. Jarvis · 2024 · BMC Medical Genomics
- Methods for fine-mapping with chromatin and expression dataMegan Roytman, Gleb Kichaev, Alexander Gusev, Bogdan Paşaniuc · 2018 · PLoS Genetics
- Functional role of PLCE1 intronic insertion variant associated with susceptibility to esophageal squamous cell carcinomaLixuan Wei, Mingming Shao, Yanjie Zhao, Jian Zheng, Jiahui Chu, Jiang Chang, Xinxin Cheng, Qionghua Cui, Linna Peng, Yingying Luo et al. · 2017 · Carcinogenesis
- MPAthic: Quantitative Modeling of Sequence-Function Relationships for massively parallel assaysWilliam T. Ireland, Justin B. Kinney · 2016 · bioRxiv (Cold Spring Harbor Laboratory)
- funMotifs: Tissue-specific transcription factor motifsHusen Muhammad Umer, Karolina Smolinska Garbulowska, Nour‐Al‐Dain Marzouka, Zeeshan Khaliq, Claes Wadelius, Jan Komorowski · 2019 · bioRxiv (Cold Spring Harbor Laboratory)
- An atlas of cell type specific regulatory effects in cattleHoucheng Li, Huicong Zhang, Pengju Zhao, Qi Zhang, Senlin Zhu, Tao Shi, Yanan Wang, Jing-Sheng Lu, Yang Liu, John Francis O'Grady et al. · 2025 · bioRxiv (Cold Spring Harbor Laboratory)
- Deciphering Transcriptional Regulation of Human Core PromotersWeingarten-Gabbay, Shira, Nir, Ronit, Lubliner, Shai, Sharon, Eilon, Kalma, Yael, Weinberger, Adina, Segal, Eran · 2017
- Comprehensive mapping of genetic variation at Epromoters reveals pleiotropic association with multiple disease traitsJing Wan, Antoinette F. van Ouwerkerk, Jean-Christophe Mouren, Carla Heredia, Lydie C. Pradel, Benoît Ballester, Jean‐Christophe Andrau, Salvatore Spicuglia · 2024 · Nucleic Acids Research
- The contribution of silencer variants to human diseasesDi Huang, Ivan Ovcharenko · 2024 · Genome biology
- Progress towards precision functional genomics in cancerCory M. Johannessen, Jesse S. Boehm · 2017 · Current Opinion in Systems Biology
- Functional annotation of noncoding mutations in cancerHusen Muhammad Umer, Karolina Smolińska, Jan Komorowski, Claes Wadelius · 2021 · Life Science Alliance
- Coupling high-throughput mapping with proteomics analysis delineates cis-regulatory elements at high resolutionTing Wu, Danli Jiang, Meijuan Zou, Wei Sun, Di Wu, Jing Cui, Ian Huntress, Xinxia Peng, Gang Li · 2021 · Nucleic Acids Research
- A general framework for predicting the transcriptomic consequences of non-coding variation and small moleculesMoustafa Abdalla, Mohamed Abdalla, Mark I. McCarthy, Chris C. Holmes · 2022 · PLoS Computational Biology
- Massively parallel identification of functionally consequential noncoding genetic variants in undiagnosed rare disease patientsJasmine A. McQuerry, Merry Mclaird, Samantha N. Hartin, John C. Means, Jeffrey J. Johnston, Tomi Pastinen, Scott T. Younger · 2022 · Scientific Reports
- Deep learning-assisted genome-wide characterization of massively parallel reporter assaysFred Lu, Aaron Sossin, Nathan S. Abell, S. Montgomery, Zihuai He · 2022 · Nucleic Acids Research
- Report: NIA workshop on translating genetic variants associated with longevity into drug targetsOn behalf of Workshop Speakers and Participants, Nicholas J. Schork, Nalini Raghavachari · 2018 · GeroScience