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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:

DeepC: predicting 3D genome folding using megabase-scale transfer learning
Ron Schweßinger, Matthew Gosden, Damien J. Downes, et al.
Nature Methods (2020) Vol. 17, Iss. 11, pp. 1118-1124
Open Access | Times Cited: 170

Showing 1-25 of 170 citing articles:

Effective gene expression prediction from sequence by integrating long-range interactions
Žiga Avsec, Vikram Agarwal, Daniel Visentin, et al.
Nature Methods (2021) Vol. 18, Iss. 10, pp. 1196-1203
Open Access | Times Cited: 717
Understanding 3D genome organization by multidisciplinary methods
Ivana Jerković, Giacomo Cavalli
Nature Reviews Molecular Cell Biology (2021) Vol. 22, Iss. 8, pp. 511-528
Open Access | Times Cited: 299
The relationship between genome structure and function
A. Marieke Oudelaar, Douglas R. Higgs
Nature Reviews Genetics (2020) Vol. 22, Iss. 3, pp. 154-168
Closed Access | Times Cited: 249
Topologically associating domain boundaries that are stable across diverse cell types are evolutionarily constrained and enriched for heritability
Evonne McArthur, John A. Capra
The American Journal of Human Genetics (2021) Vol. 108, Iss. 2, pp. 269-283
Open Access | Times Cited: 170
Identification of LZTFL1 as a candidate effector gene at a COVID-19 risk locus
Damien J. Downes, Amy Cross, Hua Peng, et al.
Nature Genetics (2021) Vol. 53, Iss. 11, pp. 1606-1615
Open Access | Times Cited: 150
Sequence-based modeling of three-dimensional genome architecture from kilobase to chromosome scale
Jian Zhou
Nature Genetics (2022) Vol. 54, Iss. 5, pp. 725-734
Open Access | Times Cited: 127
Machine learning meets omics: applications and perspectives
Rufeng Li, Lixin Li, Yungang Xu, et al.
Briefings in Bioinformatics (2021) Vol. 23, Iss. 1
Closed Access | Times Cited: 117
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-specific prediction of 3D chromatin organization enables high-throughput in silico genetic screening
Jimin Tan, Nina Shenker-Tauris, Javier Rodriguez-Hernaez, et al.
Nature Biotechnology (2023) Vol. 41, Iss. 8, pp. 1140-1150
Open Access | Times Cited: 65
Self-supervised learning on millions of primary RNA sequences from 72 vertebrates improves sequence-based RNA splicing prediction
Ken Chen, Yue Zhou, Maolin Ding, et al.
Briefings in Bioinformatics (2024) Vol. 25, Iss. 3
Open Access | Times Cited: 17
Multiscale modeling of genome organization with maximum entropy optimization
Xingcheng Lin, Yifeng Qi, Andrew P. Latham, et al.
The Journal of Chemical Physics (2021) Vol. 155, Iss. 1
Open Access | Times Cited: 83
AI applications in functional genomics
Claudia Caudai, Antonella Galizia, Filippo Geraci, et al.
Computational and Structural Biotechnology Journal (2021) Vol. 19, pp. 5762-5790
Open Access | Times Cited: 82
Loop-extrusion and polymer phase-separation can co-exist at the single-molecule level to shape chromatin folding
Mattia Conte, Ehsan Irani, Andrea M. Chiariello, et al.
Nature Communications (2022) Vol. 13, Iss. 1
Open Access | Times Cited: 68
Effective gene expression prediction from sequence by integrating long-range interactions
Žiga Avsec, Vikram Agarwal, Daniel Visentin, et al.
bioRxiv (Cold Spring Harbor Laboratory) (2021)
Open Access | Times Cited: 63
CLNN-loop: a deep learning model to predict CTCF-mediated chromatin loops in the different cell lines and CTCF-binding sites (CBS) pair types
Pengyu Zhang, Yingfu Wu, Haoru Zhou, et al.
Bioinformatics (2022) Vol. 38, Iss. 19, pp. 4497-4504
Closed Access | Times Cited: 48
Whole-genome sequencing of chronic lymphocytic leukemia identifies subgroups with distinct biological and clinical features
Pauline Robbe, Kate Ridout, Dimitrios V. Vavoulis, et al.
Nature Genetics (2022) Vol. 54, Iss. 11, pp. 1675-1689
Open Access | Times Cited: 47
Capture-C: a modular and flexible approach for high-resolution chromosome conformation capture
Damien J. Downes, Alastair Smith, Magdalena A. Karpińska, et al.
Nature Protocols (2022) Vol. 17, Iss. 2, pp. 445-475
Open Access | Times Cited: 45
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
Computational methods for analysing multiscale 3D genome organization
Yang Zhang, Lorenzo Boninsegna, Muyu Yang, et al.
Nature Reviews Genetics (2023) Vol. 25, Iss. 2, pp. 123-141
Open Access | Times Cited: 37
Epiphany: predicting Hi-C contact maps from 1D epigenomic signals
Rui Yang, Arnav Das, Vianne R. Gao, et al.
Genome biology (2023) Vol. 24, Iss. 1
Open Access | Times Cited: 36
Structural and non-coding variants increase the diagnostic yield of clinical whole genome sequencing for rare diseases
Alistair T. Pagnamenta, Carlos Camps, Edoardo Giacopuzzi, et al.
Genome Medicine (2023) Vol. 15, Iss. 1
Open Access | Times Cited: 32
Applying interpretable machine learning in computational biology—pitfalls, recommendations and opportunities for new developments
Valerie Chen, Muyu Yang, Wenbo Cui, et al.
Nature Methods (2024) Vol. 21, Iss. 8, pp. 1454-1461
Closed Access | Times Cited: 15
TrG2P: A transfer-learning-based tool integrating multi-trait data for accurate prediction of crop yield
Jinlong Li, Dongfeng Zhang, Feng Yang, et al.
Plant Communications (2024) Vol. 5, Iss. 7, pp. 100975-100975
Open Access | Times Cited: 13
DNALONGBENCH: A Benchmark Suite for Long-Range DNA Prediction Tasks
W. Cheng, Zhenqiao Song, Yang Zhang, et al.
bioRxiv (Cold Spring Harbor Laboratory) (2025)
Open Access | Times Cited: 1
Transfer learning reveals sequence determinants of the quantitative response to transcription factor dosage
Sahin Naqvi, Seungsoo Kim, Saman Tabatabaee, et al.
Cell Genomics (2025), pp. 100780-100780
Open Access | Times Cited: 1
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