Chromatin alternates between A and B compartments at kilobase scale for subgenic organization PEER REVIEWED
Ultra-deep Hi-C and fine-scale chromatin compartment organization.
Research
A curated, source-linked research record with peer-reviewed work, preprints, thesis material, stable identifiers, and primary publication links.
Genome architecture & large-scale genomics
The ENCODE uniform analysis pipelines PEER REVIEWED
Uniform, reproducible analysis infrastructure for major functional-genomics assays.
CTCF loss has limited effects on global genome architecture in Drosophila despite critical regulatory functions PEER REVIEWED
3D genome architecture, chromatin organization, and regulatory function.
Physical biology, network science & machine learning
The role of the Arp2/3 complex in shaping the dynamics and structures of branched actomyosin networks PEER REVIEWED
Simulation and theory of branched actomyosin organization and dynamics.
Insights from graph theory on the morphologies of actomyosin networks with multilinkers PEER REVIEWED
Graph-theoretic descriptors for complex cytoskeletal network morphology.
Forecasting Avalanches in Branched Actomyosin Networks with Network Science and Machine Learning PEER REVIEWED
Network-science and ML methods for predicting collective rearrangements in active matter.
Impact of hydrodynamic interactions on protein folding rates depends on temperature PEER REVIEWED
Computational protein physics and hydrodynamic effects on folding kinetics.
Cancer, CRISPR & computational biology
A unique malignant cell type per patient tumor encoded in each cancer cell transcriptome PEER REVIEWED
Patient-specific malignant-cell identity in cancer transcriptomes; current computational-biology work spanning HIT and Harvard Medical School affiliations.
CaXML: Chemistry-informed machine learning explains mutual changes between protein conformations and calcium ions PEER REVIEWED
Chemistry-informed ML for structural/topological relationships in calcium-binding proteins.
OffRisk: a Docker image for annotating CRISPR off-target sites in the human genome PEER REVIEWED
Reproducible software for CRISPR off-target annotation, bridging genomics and deployable tooling.
A genome-scale CRISPR Cas9 dropout screen identifies synthetically lethal targets in SRC-3 inhibited cancer cells PEER REVIEWED
Genome-scale CRISPR screening and cancer vulnerabilities.
Drug-induced PD-L1 expression and cell stress response in breast cancer cells can be balanced by drug combination PEER REVIEWED
Cancer-cell stress response and drug-combination effects.
AI systems & new directions
Boltzmann MapReduce: A Partition-Function Reduce for Forkable Sandboxes PREPRINT
Connects statistical-mechanics style aggregation with forkable compute and agent execution.
Physics of Self-assembly in Complex Matter PHD THESIS
The physical-computation foundation behind later network-science, biological, and systems work.
Canonical bibliography: publication databases count papers, corrections, preprints, theses, and consortium outputs differently. Google Scholar and ORCID provide the broad indexes; this page presents a verified representative set.