User profiles for Ivan N. Zheludev

Ivan Nikolay Zheludev

Biochemistry PhD Candidate, Stanford University
Verified email at stanford.edu
Cited by 659

RNA genome conservation and secondary structure in SARS-CoV-2 and SARS-related viruses: a first look

R Rangan, IN Zheludev, RJ Hagey, EA Pham… - Rna, 2020 - rnajournal.cshlp.org
As the COVID-19 outbreak spreads, there is a growing need for a compilation of conserved
RNA genome regions in the SARS-CoV-2 virus along with their structural propensities to …

[HTML][HTML] Cryo-EM and antisense targeting of the 28-kDa frameshift stimulation element from the SARS-CoV-2 RNA genome

K Zhang, IN Zheludev, RJ Hagey, R Haslecker… - Nature Structural & …, 2021 - nature.com
Drug discovery campaigns against COVID-19 are beginning to target the SARS-CoV-2 RNA
genome. The highly conserved frameshift stimulation element (FSE), required for balanced …

[HTML][HTML] Hybrids of RNA viruses and viroid-like elements replicate in fungi

…, MF Akinyuwa, E Gobbi, IN Zheludev… - Nature …, 2023 - nature.com
Earth’s life may have originated as self-replicating RNA, and it has been argued that RNA
viruses and viroid-like elements are remnants of such pre-cellular RNA world. RNA viruses are …

Accelerated cryo-EM-guided determination of three-dimensional RNA-only structures

…, S Li, G Pintilie, VV Topkar, R Rangan, IN Zheludev… - Nature …, 2020 - nature.com
The discovery and design of biologically important RNA molecules is outpacing three-dimensional
structural characterization. Here, we demonstrate that cryo-electron microscopy can …

Promotion of protocell self-assembly from mixed amphiphiles at the origin of life

…, IN Zheludev, AM Hartley, A Maréchal, N Lane - Nature ecology & …, 2019 - nature.com
Vesicles formed from single-chain amphiphiles (SCAs) such as fatty acids probably played
an important role in the origin of life. A major criticism of the hypothesis that life arose in an …

De novo 3D models of SARS-CoV-2 RNA elements from consensus experimental secondary structures

…, R Kretsch, W Kladwang, IN Zheludev… - Nucleic acids …, 2021 - academic.oup.com
The rapid spread of COVID-19 is motivating development of antivirals targeting conserved
SARS-CoV-2 molecular machinery. The SARS-CoV-2 genome includes conserved RNA …

RNA target highlights in CASP15: Evaluation of predicted models by structure providers

…, L Xu, K Zhang, IN Zheludev… - Proteins: Structure …, 2023 - Wiley Online Library
The first RNA category of the Critical Assessment of Techniques for Structure Prediction
competition was only made possible because of the scientists who provided experimental …

Cryo-electron microscopy and exploratory antisense targeting of the 28-kDa frameshift stimulation element from the SARS-CoV-2 RNA genome

K Zhang, IN Zheludev, RJ Hagey, MTP Wu… - Biorxiv, 2020 - biorxiv.org
Drug discovery campaigns against Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2)
are beginning to target the viral RNA genome 1 , 2 . The frameshift stimulation …

Tertiary folds of the SL5 RNA from the 5′ proximal region of SARS-CoV-2 and related coronaviruses

RC Kretsch, L Xu, IN Zheludev… - Proceedings of the …, 2024 - National Acad Sciences
Coronavirus genomes sequester their start codons within stem-loop 5 (SL5), a structured, 5′
genomic RNA element. In most alpha- and betacoronaviruses, the secondary structure of …

[PDF][PDF] SPLASH: a statistical, reference-free genomic algorithm unifies biological discovery

K Chaung, TZ Baharav, G Henderson, IN Zheludev… - Cell, 2023 - cell.com
Today's genomics workflows typically require alignment to a reference sequence, which
limits discovery. We introduce a unifying paradigm, SPLASH (Statistically Primary aLignment …