# Research — Yossi Eliaz

Canonical page: https://yossieliaz.netlify.app/research/

COMPUTATIONAL SCIENCE / GENOMICS / PHYSICAL BIOLOGY / ML / AI SYSTEMS

A curated, source-linked research record with peer-reviewed work, preprints, thesis material, stable identifiers, and primary publication links.

## Genome architecture & large-scale genomics

### Chromatin alternates between A and B compartments at kilobase scale for subgenic organization (PEER REVIEWED)

Nature Communications · 2023

Ultra-deep Hi-C and fine-scale chromatin compartment organization.

[Nature](https://www.nature.com/articles/s41467-023-38429-1) [PubMed](https://pubmed.ncbi.nlm.nih.gov/37280210/)

### The ENCODE uniform analysis pipelines (PREPRINT)

bioRxiv / Research Square · 2023

Uniform, reproducible analysis infrastructure for major functional-genomics assays.

[bioRxiv](https://doi.org/10.1101/2023.04.04.535623) [PubMed](https://pubmed.ncbi.nlm.nih.gov/37503119/) [PMC](https://pmc.ncbi.nlm.nih.gov/articles/PMC10371165/)

### CTCF loss has limited effects on global genome architecture in Drosophila despite critical regulatory functions (PEER REVIEWED)

Nature Communications · 2021

3D genome architecture, chromatin organization, and regulatory function.

[Nature](https://www.nature.com/articles/s41467-021-21366-2) [PubMed](https://pubmed.ncbi.nlm.nih.gov/33579945/)

## 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)

PNAS · 2020

Simulation and theory of branched actomyosin organization and dynamics.

[PNAS](https://www.pnas.org/doi/10.1073/pnas.1922494117) [PubMed](https://pubmed.ncbi.nlm.nih.gov/32354995/)

### Insights from graph theory on the morphologies of actomyosin networks with multilinkers (PEER REVIEWED)

Physical Review E · 2020

Graph-theoretic descriptors for complex cytoskeletal network morphology.

[PubMed](https://pubmed.ncbi.nlm.nih.gov/33466104/)

### Forecasting Avalanches in Branched Actomyosin Networks with Network Science and Machine Learning (PEER REVIEWED)

Journal of Physical Chemistry B · 2021

Network-science and ML methods for predicting collective rearrangements in active matter.

[ACS](https://pubs.acs.org/doi/10.1021/acs.jpcb.1c04792)

### Impact of hydrodynamic interactions on protein folding rates depends on temperature (PEER REVIEWED)

Physical Review E · 2018

Computational protein physics and hydrodynamic effects on folding kinetics.

[PubMed](https://pubmed.ncbi.nlm.nih.gov/29776093/) [PMC](https://pmc.ncbi.nlm.nih.gov/articles/PMC6080349/)

## Cancer, CRISPR & computational biology

### A unique malignant cell type per patient tumor encoded in each cancer cell transcriptome (PEER REVIEWED)

iScience · 2026

Patient-specific malignant-cell identity in cancer transcriptomes; computational-biology work from the Harvard Medical School appointment (2024–2026), published with HIT and Harvard Medical School affiliations.

[PubMed](https://pubmed.ncbi.nlm.nih.gov/41884004/)

### CaXML: Chemistry-informed machine learning explains mutual changes between protein conformations and calcium ions (PEER REVIEWED)

Protein Science · 2025

Chemistry-informed ML for structural/topological relationships in calcium-binding proteins.

[Wiley](https://onlinelibrary.wiley.com/doi/10.1002/pro.70023) [PubMed](https://pubmed.ncbi.nlm.nih.gov/39865355/)

### OffRisk: a Docker image for annotating CRISPR off-target sites in the human genome (PEER REVIEWED)

Bioinformatics Advances · 2023

Reproducible software for CRISPR off-target annotation, bridging genomics and deployable tooling.

[Oxford Academic](https://academic.oup.com/bioinformaticsadvances/article/3/1/vbad138/7295524) [PubMed](https://pubmed.ncbi.nlm.nih.gov/37840905/)

### A genome-scale CRISPR Cas9 dropout screen identifies synthetically lethal targets in SRC-3 inhibited cancer cells (PEER REVIEWED)

Communications Biology · 2021

Genome-scale CRISPR screening and cancer vulnerabilities.

[Nature](https://www.nature.com/articles/s42003-021-01929-1) [PubMed](https://pubmed.ncbi.nlm.nih.gov/33767353/)

### Drug-induced PD-L1 expression and cell stress response in breast cancer cells can be balanced by drug combination (PEER REVIEWED)

Scientific Reports · 2019

Cancer-cell stress response and drug-combination effects.

[Nature](https://www.nature.com/articles/s41598-019-51537-7) [PubMed](https://pubmed.ncbi.nlm.nih.gov/31641154/)

## AI systems & new directions

### Evidence-Aware MapReduce for Forkable Compute (PREPRINT)

arXiv · 2026

An evidence-aware reduction contract for forked AI branches: inverse-information pooling with evidence IDs and fork lineage, so repeated errors are not counted as independent agreement.

[arXiv](https://arxiv.org/abs/2607.09689)

### Physics of Self-assembly in Complex Matter (PHD THESIS)

University of Houston · 2020

The physical-computation foundation behind later network-science, biological, and systems work.

[ProQuest](https://search.proquest.com/openview/04865b477093cbcba3aecd4d02eb4dab/1?pq-origsite=gscholar&cbl=18750&diss=y)

**Canonical bibliography:** publication databases count papers, corrections, preprints, theses, and consortium outputs differently. Google Scholar provides the broad index; this page presents a verified representative set.