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OpenAlex Citation Counts

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OpenAlex is a bibliographic catalogue of scientific papers, authors and institutions accessible in open access mode, named after the Library of Alexandria. It's citation coverage is excellent and I hope you will find utility in this listing of citing articles!

If you click the article title, you'll navigate to the article, as listed in CrossRef. If you click the Open Access links, you'll navigate to the "best Open Access location". Clicking the citation count will open this listing for that article. Lastly at the bottom of the page, you'll find basic pagination options.

Requested Article:

DeepSTARR predicts enhancer activity from DNA sequence and enables the de novo design of synthetic enhancers
Bernardo P. de Almeida, Franziska Reiter, Michaela Pagani, et al.
Nature Genetics (2022) Vol. 54, Iss. 5, pp. 613-624
Open Access | Times Cited: 188

Showing 1-25 of 188 citing articles:

Ensembl 2022
Fiona Cunningham, James E. Allen, Jamie Allen, et al.
Nucleic Acids Research (2021) Vol. 50, Iss. D1, pp. D988-D995
Open Access | Times Cited: 1644
Obtaining genetics insights from deep learning via explainable artificial intelligence
Gherman Novakovsky, Nick Dexter, Maxwell W. Libbrecht, et al.
Nature Reviews Genetics (2022) Vol. 24, Iss. 2, pp. 125-137
Closed Access | Times Cited: 223
Deciphering the multi-scale, quantitative cis-regulatory code
Seungsoo Kim, Joanna Wysocka
Molecular Cell (2023) Vol. 83, Iss. 3, pp. 373-392
Open Access | Times Cited: 166
The Nucleotide Transformer: Building and Evaluating Robust Foundation Models for Human Genomics
Hugo Dalla-Torre, Liam Gonzalez, Javier Mendoza‐Revilla, et al.
bioRxiv (Cold Spring Harbor Laboratory) (2023)
Open Access | Times Cited: 105
Human-specific genetics: new tools to explore the molecular and cellular basis of human evolution
Alex A. Pollen, Umut Kilik, Craig B. Lowe, et al.
Nature Reviews Genetics (2023) Vol. 24, Iss. 10, pp. 687-711
Open Access | Times Cited: 96
Current sequence-based models capture gene expression determinants in promoters but mostly ignore distal enhancers
Alexander Karollus, Thomas Mauermeier, Julien Gagneur
Genome biology (2023) Vol. 24, Iss. 1
Open Access | Times Cited: 74
Cell-type-directed design of synthetic enhancers
Ibrahim Ihsan Taskiran, Katina I. Spanier, Hannah Dickmänken, et al.
Nature (2023) Vol. 626, Iss. 7997, pp. 212-220
Open Access | Times Cited: 68
Transient loss of Polycomb components induces an epigenetic cancer fate
Victoria Parreno, Vincent Loubière, Bernd Schuettengruber, et al.
Nature (2024) Vol. 629, Iss. 8012, pp. 688-696
Open Access | Times Cited: 65
Hold out the genome: a roadmap to solving the cis-regulatory code
Carl G. de Boer, Jussi Taipale
Nature (2023) Vol. 625, Iss. 7993, pp. 41-50
Open Access | Times Cited: 43
Nucleotide Transformer: building and evaluating robust foundation models for human genomics
Hugo Dalla-Torre, Liam Gonzalez, Javier Mendoza‐Revilla, et al.
Nature Methods (2024)
Open Access | Times Cited: 37
Selective gene expression maintains human tRNA anticodon pools during differentiation
Lexi Gao, Andrew Behrens, Geraldine Rodschinka, et al.
Nature Cell Biology (2024) Vol. 26, Iss. 1, pp. 100-112
Open Access | Times Cited: 27
Single-cell spatial multi-omics and deep learning dissect enhancer-driven gene regulatory networks in liver zonation
Carmen Bravo González‐Blas, Irina Matetovici, Hanne Hillen, et al.
Nature Cell Biology (2024) Vol. 26, Iss. 1, pp. 153-167
Open Access | Times Cited: 23
Massively parallel characterization of regulatory elements in the developing human cortex
Chengyu Deng, Sean Whalen, Marilyn Steyert, et al.
Science (2024) Vol. 384, Iss. 6698
Closed Access | Times Cited: 23
Machine-guided design of cell-type-targeting cis-regulatory elements
Sager J. Gosai, Rodrigo Castro, Natalia Fuentes, et al.
Nature (2024) Vol. 634, Iss. 8036, pp. 1211-1220
Open Access | Times Cited: 19
Multiplex profiling of developmental cis-regulatory elements with quantitative single-cell expression reporters
Jean‐Benoît Lalanne, Samuel G. Regalado, Silvia Domcke, et al.
Nature Methods (2024) Vol. 21, Iss. 6, pp. 983-993
Open Access | Times Cited: 18
Genomic language models: opportunities and challenges
Gonzalo Benegas, Chengzhong Ye, Carlos Albors, et al.
Trends in Genetics (2025)
Open Access | Times Cited: 5
GENA-LM: a family of open-source foundational DNA language models for long sequences
Veniamin Fishman, Yuri Kuratov, Aleksei Shmelev, et al.
Nucleic Acids Research (2025) Vol. 53, Iss. 2
Open Access | Times Cited: 3
Scalable Functional Assays for the Interpretation of Human Genetic Variation
Daniel Tabet, Victoria N. Parikh, Prashant Mali, et al.
Annual Review of Genetics (2022) Vol. 56, Iss. 1, pp. 441-465
Closed Access | Times Cited: 48
Current challenges in understanding the role of enhancers in disease
Judith B. Zaugg, Pelin Sahlén, Robin Andersson, et al.
Nature Structural & Molecular Biology (2022) Vol. 29, Iss. 12, pp. 1148-1158
Open Access | Times Cited: 48
Evaluating deep learning for predicting epigenomic profiles
Shushan Toneyan, Ziqi Tang, Peter K. Koo
Nature Machine Intelligence (2022) Vol. 4, Iss. 12, pp. 1088-1100
Open Access | Times Cited: 43
Targeted design of synthetic enhancers for selected tissues in the Drosophila embryo
Bernardo P. de Almeida, Christoph Schaub, Michaela Pagani, et al.
Nature (2023) Vol. 626, Iss. 7997, pp. 207-211
Open Access | Times Cited: 40
Interpreting non-coding disease-associated human variants using single-cell epigenomics
Kyle J. Gaulton, Sebastian Preißl, Bing Ren
Nature Reviews Genetics (2023) Vol. 24, Iss. 8, pp. 516-534
Open Access | Times Cited: 39
Transposable elements as tissue-specific enhancers in cancers of endodermal lineage
Konsta Karttunen, Divyesh Patel, Ji‐Han Xia, et al.
Nature Communications (2023) Vol. 14, Iss. 1
Open Access | Times Cited: 35
Enhancer architecture and chromatin accessibility constrain phenotypic space during Drosophila development
Rafael Galupa, Gilberto Álvarez-Canales, Noa Ottilie Borst, et al.
Developmental Cell (2023) Vol. 58, Iss. 1, pp. 51-62.e4
Open Access | Times Cited: 34
Deep flanking sequence engineering for efficient promoter design using DeepSEED
Pengcheng Zhang, Haochen Wang, Hanwen Xu, et al.
Nature Communications (2023) Vol. 14, Iss. 1
Open Access | Times Cited: 34
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