3DGenBench: a web-server to benchmark computational models for 3D Genomics

Standard

3DGenBench: a web-server to benchmark computational models for 3D Genomics. / Belokopytova, Polina; Viesná, Emil; Chiliński, Mateusz et al.

In: Nucleic Acids Research, Vol. 50, No. W1, 05.07.2022, p. W4-W12.

Research output: Contribution to journal › Article › peer-review

Harvard

Belokopytova, P, Viesná, E, Chiliński, M, Qi, Y, Salari, H, Di Stefano, M, Esposito, A, Conte, M, Chiariello, AM, Teif, VB, Plewczynski, D, Zhang, B, Jost, D & Fishman, V 2022, '3DGenBench: a web-server to benchmark computational models for 3D Genomics', Nucleic Acids Research, vol. 50, no. W1, pp. W4-W12. https://doi.org/10.1093/nar/gkac396

APA

Belokopytova, P., Viesná, E., Chiliński, M., Qi, Y., Salari, H., Di Stefano, M., Esposito, A., Conte, M., Chiariello, A. M., Teif, V. B., Plewczynski, D., Zhang, B., Jost, D., & Fishman, V. (2022). 3DGenBench: a web-server to benchmark computational models for 3D Genomics. Nucleic Acids Research, 50(W1), W4-W12. https://doi.org/10.1093/nar/gkac396

Vancouver

Belokopytova P, Viesná E, Chiliński M, Qi Y, Salari H, Di Stefano M et al. 3DGenBench: a web-server to benchmark computational models for 3D Genomics. Nucleic Acids Research. 2022 Jul 5;50(W1):W4-W12. doi: 10.1093/nar/gkac396

Author

Belokopytova, Polina ; Viesná, Emil ; Chiliński, Mateusz et al. / 3DGenBench: a web-server to benchmark computational models for 3D Genomics. In: Nucleic Acids Research. 2022 ; Vol. 50, No. W1. pp. W4-W12.

BibTeX

@article{adfa2333f5634b30af6acd25330208e5,

title = "3DGenBench: a web-server to benchmark computational models for 3D Genomics",

abstract = "Modeling 3D genome organisation has been booming in the last years thanks to the availability of experimental datasets of genomic contacts. However, the field is currently missing the standardisation of methods and metrics to compare predictions and experiments. We present 3DGenBench, a web server available at https://inc-cost.eu/benchmarking/, that allows benchmarking computational models of 3D Genomics. The benchmark is performed using a manually curated dataset of 39 capture Hi-C profiles in wild type and genome-edited mouse cells, and five genome-wide Hi-C profiles in human, mouse, and Drosophila cells. 3DGenBench performs two kinds of analysis, each supplied with a specific scoring module that compares predictions of a computational method to experimental data using several metrics. With 3DGenBench, the user obtains model performance scores, allowing an unbiased comparison with other models. 3DGenBench aims to become a reference web server to test new 3D genomics models and is conceived as an evolving platform where new types of analysis will be implemented in the future.",

author = "Polina Belokopytova and Emil Viesn{\'a} and Mateusz Chili{\'n}ski and Yifeng Qi and Hossein Salari and {Di Stefano}, Marco and Andrea Esposito and Mattia Conte and Chiariello, {Andrea M.} and Teif, {Vladimir B.} and Dariusz Plewczynski and Bin Zhang and Daniel Jost and Veniamin Fishman",

note = "Publisher Copyright: {\textcopyright} 2022 The Author(s). Published by Oxford University Press on behalf of Nucleic Acids Research.",

year = "2022",

month = jul,

day = "5",

doi = "10.1093/nar/gkac396",

language = "English",

volume = "50",

pages = "W4--W12",

journal = "Nucleic Acids Research",

issn = "0305-1048",

publisher = "Oxford University Press",

number = "W1",

}

RIS

TY - JOUR

T1 - 3DGenBench: a web-server to benchmark computational models for 3D Genomics

AU - Belokopytova, Polina

AU - Viesná, Emil

AU - Chiliński, Mateusz

AU - Qi, Yifeng

AU - Salari, Hossein

AU - Di Stefano, Marco

AU - Esposito, Andrea

AU - Conte, Mattia

AU - Chiariello, Andrea M.

AU - Teif, Vladimir B.

AU - Plewczynski, Dariusz

AU - Zhang, Bin

AU - Jost, Daniel

AU - Fishman, Veniamin

PY - 2022/7/5

Y1 - 2022/7/5

N2 - Modeling 3D genome organisation has been booming in the last years thanks to the availability of experimental datasets of genomic contacts. However, the field is currently missing the standardisation of methods and metrics to compare predictions and experiments. We present 3DGenBench, a web server available at https://inc-cost.eu/benchmarking/, that allows benchmarking computational models of 3D Genomics. The benchmark is performed using a manually curated dataset of 39 capture Hi-C profiles in wild type and genome-edited mouse cells, and five genome-wide Hi-C profiles in human, mouse, and Drosophila cells. 3DGenBench performs two kinds of analysis, each supplied with a specific scoring module that compares predictions of a computational method to experimental data using several metrics. With 3DGenBench, the user obtains model performance scores, allowing an unbiased comparison with other models. 3DGenBench aims to become a reference web server to test new 3D genomics models and is conceived as an evolving platform where new types of analysis will be implemented in the future.

AB - Modeling 3D genome organisation has been booming in the last years thanks to the availability of experimental datasets of genomic contacts. However, the field is currently missing the standardisation of methods and metrics to compare predictions and experiments. We present 3DGenBench, a web server available at https://inc-cost.eu/benchmarking/, that allows benchmarking computational models of 3D Genomics. The benchmark is performed using a manually curated dataset of 39 capture Hi-C profiles in wild type and genome-edited mouse cells, and five genome-wide Hi-C profiles in human, mouse, and Drosophila cells. 3DGenBench performs two kinds of analysis, each supplied with a specific scoring module that compares predictions of a computational method to experimental data using several metrics. With 3DGenBench, the user obtains model performance scores, allowing an unbiased comparison with other models. 3DGenBench aims to become a reference web server to test new 3D genomics models and is conceived as an evolving platform where new types of analysis will be implemented in the future.

UR - http://www.scopus.com/inward/record.url?scp=85134752692&partnerID=8YFLogxK

U2 - 10.1093/nar/gkac396

DO - 10.1093/nar/gkac396

M3 - Article

C2 - 35639501

AN - SCOPUS:85134752692

VL - 50

SP - W4-W12

JO - Nucleic Acids Research

JF - Nucleic Acids Research

SN - 0305-1048

IS - W1

ER -

ID: 36730806