M. Gerstein

A Discard-and-Restart MD algorithm for the sampling of realistic protein transition states and enhance structure-based drug discovery

The paper introduces a Discard-and-Restart MD algorithm to efficiently sample protein transition states, enhancing structure-based drug discovery by reducing simulation times by up to 2000x.

Revisiting the bad luck hypothesis: Cancer risk and aging are linked to replication-driven changes to the epigenome

The paper shows that aging and cancer share an epigenetic replication signature linked to DNA methylation, which increases with age and correlates with cancer risk.

Minor intron splicing efficiency increases with the development of lethal prostate cancer

The paper shows that minor intron splicing efficiency increases in castration-resistant prostate cancer and that inhibiting the minor spliceosome reduces tumor burden.

Proteome-wide screening for mitogen-activated protein kinase docking motifs and interactors

The paper screens for MAPK docking motifs and interactors using a yeast-based genetic pipeline, identifying novel sequences and residues critical for binding to JNK1 and p38.

Differences in evolutionary accessibility determine which equally effective regulatory motif evolves to generate pulses

The paper shows that evolutionary accessibility, not just functionality, determines which regulatory motif evolves to generate protein pulses, with I1FFLs being more accessible under most conditions.

Latent Evolutionary Signatures: A General Framework for Analyzing Music and Cultural Evolution

This paper introduces a framework to identify evolutionary processes in music by extracting latent signatures, showing improved performance in period and genre prediction.

Cyclic and Multilevel Causation in Evolutionary Processes

This paper develops a theoretical framework for analyzing evolutionary processes with cyclic and multilevel causation, introducing causal models and information-theoretic tools to address complex trait analysis and cancer genetics.

Estimating growth patterns and driver effects in tumor evolution from individual samples

This paper develops a method to estimate tumor growth patterns and driver effects from individual whole genome sequencing data by analyzing variant allele frequencies.

microRNA-dependent regulation of biomechanical genes establishes tissue stiffness homeostasis

The paper identifies microRNA-dependent regulation of biomechanical genes that maintain tissue stiffness homeostasis through cytoskeletal and extracellular matrix control.