Our work highlighted by the Oak Ridge Leadership Computing Facility
Our work was included in the OLCF’s 2025 year in review.
Tag: DNA repair
NEW INCITE POJECT AWARDED FOR 2026
Our INCITE Award was competitively renewed for 2026 by the DOE Office of Science. Open to researchers from academia, government laboratories, and industry, the Innovative and Novel Computational Impact on Theory and Experiment (INCITE) program is the major means by which the scientific community gains access to the world’s fastest supercomputers. The program aims to accelerate […]
NEW PAPER IN NATURE COMMUNICATIONS
Congratulations to Tanmoy Paul, Chunli Yan and Grant Derdeyn-Blackwell who are co-authors on a just published paper in the journal Nature Communications entitled “Translocation mechanism of xeroderma pigmentosum group D protein on single-stranded DNA and genetic disease etiology”. We investigated the molecular basis of translocation by the xeroderma pigmentosum group D (XPD) helicase on single-stranded […]
OAK RIDGE NATIONAL LAB HIGHLIGHTS OUR WORK ON GLOBAL GENOME REPAIR
Oak Ridge National Lab highlights our work on the mechanisms of global genome nucleotide excision repair: “Summit Supercomputer Draws Molecular Blueprint for Repairing Damaged DNA”. Related articles: Yu, J., Yan, C., Paul, T. et al. Molecular architecture and functional dynamics of the pre-incision complex in nucleotide excision repair. Nat Commun 15, 8511 (2024). Yu, J., Yan, C., Dodd, T. et […]
NEW PAPER IN NATURE COMMUNICATIONS
Congratulations to Tanmoy Paul, Chunli Yan and Jina Yu who are co-authors on a just published paper in the journal Nature Communications. The paper is entitled “Molecular model of TFIIH recruitment to the transcription-coupled repair machinery“. Transcription-coupled repair is a vital nucleotide excision repair sub-pathway that removes DNA lesions from actively transcribed DNA strands. Binding of the […]
NEW PAPER IN NATURE COMMUNICATIONS
Congratulations to Jina Yu, Chunli Yan, Tanmoy Paul and Lucas Brewer who are co-authors on a just published paper in the journal Nature Communications. The paper is entitled “Molecular architecture and functional dynamics of the pre-incision complex in nucleotide excision repair.” The nucleotide excision repair (NER) pathway is vital for genome integrity. By synthesizing cryo-EM and XL-MS […]
IVAYLO IVANOV RECEIVES NEW NIH GRANT
Ivaylo Ivanov receives a new R01 grant from the National Institute of Environmental Health Sciences.
OAK RIDGE NATIONAL LAB HIGHLIGHTS OUR WORK ON TRANSCRIPTION-COUPLED DNA REPAIR
Oak Ridge National Lab highlights our recent work on the mechanisms of transcription-coupled nucleotide excision repair: “Decoding the Role of CSB Protein in DNA Repair“. Below is a recent video recording on the same topic:
NEW PAPER IN NATURE COMMUNICATIONS
Congratulations to Chunli Yan, Tom Dodd and Jina Yu who are co-authors on a just accepted paper in the journal Nature Communications. The paper is entitled “Mechanism of Rad26-assisted rescue of stalled RNA polymerase II in transcription-coupled repair.” Our integrative modeling study elucidates the mechanism by which Cockayne Syndrome B protein (CSB) binds to lesion-arrested RNA Polymerase […]
Oak Ridge National Lab highlights our work on high fidelity DNA replication
Oak Ridge National Lab highlights our recent work on pathways for conformational switching in high fidelity DNA polymerases: “Simulations reveal Nature’s design for error correction during DNA replication“.
NEW PAPER IN NATURE STRUCTURAL & MOLECULAR BIOLOGY
Congratulation to Chunli Yan and Tom Dodd who published a new paper in the journal Nature Structural & Molecular Biology on the molecular architecture and functional dynamics of the transcription preinitiation complex (PIC). Yan, C.; Dodd, T.; Tainer, J.A.; He, Y.; Tsutakawa, S.E.; & Ivanov, I.* Transcription preinitiation complex structure and dynamics provide insight into genetic diseases Nature Structural […]
Our thymine DNA glycosylase story highlighted by SDSC
Our project on the base extrusion mechanism of thymine DNA glycosylase (TDG) was highlighted by the San Diego Supercomputer Center. How an Enzyme Repairs DNA via a “Pinch-Push-Pull” Mechanism
New Paper in Proceedings of the National Academy of Sciences USA
Congratulation to Tom Dodd, Chunli Yan, Kurt Martin and Brad Kossmann who published a new paper in the journal Proceedings of the National Academy of Sciences USA. Dodd, T.; Yan, C.; Kossmann, B.R.; Martin, K.; & Ivanov I. Uncovering universal rules governing the selectivity of the archetypal DNA glycosylase TDG Proceedings of the National Academy of Sciences USA (2018) doi:10.1073/pnas.1803323115 […]
Visit to Berkeley National Lab
Ivaylo visited Lawrence Berkeley National Lab in Feb. 2018 and gave a talk “DNA sculpting as a strategy for base extrusion and damage selection by the repair glycosylase TDG” at the Advanced Light Source synchrotron facility.
3rd DNA Replication/Repair Structures and Cancer Conference
Ivaylo gave a talk “DNA sculpting as a strategy for base extrusion and damage selection by the repair glycosylase TDG” at the 3rd DNA Replication/Repair Structures and Cancer Conference in Cancun Mexico.
New paper in PLOS Computational Biology
Our paper ‘Alkylpurine Glycosylase D Employs DNA Sculpting as a Strategy to Extrude and Excise Damaged Bases’ was published in PLOS Computational Biology. We employed chain-of-replicas path optimization strategy to determine a minimum energy path (MEP) for flipping out a 3-methyl adenine lesion by the DNA glycosylase AlkD. The path showed that AlkD acts by […]
Integrative Biomolecular Modeling 