Xingcheng Lin

We extend our earlier version of the protein-DNA predictive tool (doi.org/10.7554/eLife.…) to predict position-specific methylation sensitivity and integrate WGBS data to improve genomic protein–DNA binding site predictions.

Glad to share our latest work on DNA methylation prediction, focusing on position-specific methylation sensitivity and genomic protein-DNA binding. biorxiv.org/content/10.110…

Excited to share our latest pre-print on predicting protein-RNA interactions! We present a biophysics-inspired machine learning framework that predicts sequence-specific binding and identifies strong-binding RNA motifs. biorxiv.org/content/10.110…

@DvirHarris @eLife Thank you!

@XingchengLin @eLife Very nice Xingcheng!

Glad to share that our protein-DNA binding prediction paper is now published in @eLife: Interpretable protein-DNA interactions captured by structure-sequence optimization doi.org/10.7554/eLife.… Check out Yafan's summary video for the upcoming ISMB/ECCB 2025 conference.

This work has been published in Biochemistry. Good job, Rina! pubs.acs.org/doi/full/10.10…

This work is led by Rina Li, a graduate student in Physics in our research group.

3. This modest reduction in inter-nucleosome interactions is amplified at the chromatin level, leading to nucleosome destacking and exposure of nucleosomal DNA. The destabilization of chromatin structure is driven by fluctuations in the entry-exit angles of linker DNA.

Excited to share our latest manuscript biorxiv.org/content/10.110… In this manuscript, we utilized an explicit-ion chromatin model to quantify the effects of histone 4 acetylation on the higher-order chromatin structure.

This work is led by Yafan Zhang, a first-year Bioinformatics graduate student at NCSU. We greatly appreciate fruitful discussions with Dr. Keith Weninger, Dr. Faruck Morcos (@faruckm), Dr. Qin Zhou, and Dr. Arun Kumar Ganesan (@genome_voyager).

3. The trained energy model allows for direct interpretation of physicochemical interactions between individual amino acids and nucleotides and is further incorporated into a coarse-grained simulation framework to accurately predict protein-DNA binding free energies.

Excited to share our latest manuscript biorxiv.org/content/10.110… In this manuscript, we introduce "IDEA", a predictive biophysical model for quantitative predictions of genome-wide binding sites and binding affinities of DNA-binding proteins.

@ChemistryMIT @gabriela_ssc Congratulations!

Congratulations to Professor Gabriela Schlau-Cohen (@gabriela_ssc), who has been promoted to Full Professor effective July 1, 2024! chemistry.mit.edu/chemistry-news…

Big news! Well deserved, and Congrats, @binzmit !