Genome biologyBioinformaticsPeer-reviewed journal article
MalariaSED: a deep learning framework to decipher the regulatory contributions of noncoding variants in malaria parasites
Chengqi C. Q. WangiD, Yibo DongiD, Chang LiiD, Jenna OberstalleriD, Min ZhangiD, Justin GibbonsiD, Camilla Valente PiresiD, Mianli Xiao, Lei ZhuiD, Rays H. Y. JiangiD, Kami KimiD, Jun MiaoiD, Thomas D. OttoiD, Liwang CuiiD, John H. AdamsiD, Xiaoming LiuiD
Abstract
Malaria remains one of the deadliest infectious diseases. Transcriptional regulation effects of noncoding variants in this unusual genome of malaria parasites remain elusive. We developed a sequence-based, ab initio deep learning framework, MalariaSED, for predicting chromatin profiles in malaria parasites. The MalariaSED performance was validated by published ChIP-qPCR and TF motifs results. Applying MalariaSED to [~]1.3 million variants shows that geographically differentiated noncoding variants are associated with parasite invasion and drug resistance. Further analysis reveals chromatin accessibility changes at Plasmodium falciparum rings are partly associated with artemisinin resistance. MalariaSED illuminates the potential functional roles of noncoding variants in malaria parasites.
- Citations
- 6
- FWCI
- 1.53
- Field percentile
- top 18%
Reproducibility ledger
Nobody has reported trying to reproduce this paper yet. Did you replicate an experiment or run the code? Your report saves the next lab a week.
Sign in to file a reproducibility report.
Related papers
- Genome variation and meiotic recombination in Plasmodium falciparum: insights from deep sequencing of genetic crosses
Alistair Miles, Zamin Iqbal, … Dominic Kwiatkowski·bioRxiv·Dec 23, 2015
- Chromatin structure and var2csa - a tango in regulation of var gene expression in the human malaria parasite Plasmodium falciparum?
Todd Lenz, Xu Zhang, … Karine G. Le Roch·bioRxiv·Feb 13, 2024
- A coordinated transcriptional switching network mediates antigenic variation of human malaria parasites
X. Zhang, F. Florini, … K. W. Deitsch·bioRxiv·Sep 29, 2022
- PfMORC protein regulates chromatin accessibility and transcriptional repression in the human malaria parasite, Plasmodium falciparum
Z. M. Chahine, M. Gupta, … K. G. Le Roch·bioRxiv·Sep 11, 2023
- The mechanism of artemisinin resistance of Plasmodium falciparum malaria parasites originates in their initial transcriptional response.
Lei Zhu, Rob W. van der Pluijm, … Zbynek Bozdech·bioRxiv·May 17, 2021
- Antigenic diversity in malaria parasites is maintained on extrachromosomal DNA
Emily R. Ebel, Bernard Y. Kim, … Dmitri A. Petrov·bioRxiv·Feb 2, 2023