Macrogenomic engineering via modulation of the scaling of chromatin packing density

Review of interferometric spectroscopy of scattered light for the quantification of subdiffractional structure of biomaterials

(2017) Lusik Cherkezyan et al.   JOURNAL OF BIOMEDICAL OPTICS

Rare cell variability and drug-induced reprogramming as a mode of cancer drug resistance

(2017) Sydney M. Shaffer et al.   NATURE

The Global Relationship between Chromatin Physical Topology, Fractal Structure and Gene Expression

(2017) L. M. Almassalha et al.   Scientific Reports

Higher Order Chromatin Modulator Cohesin SA1 Is an Early Biomarker for Colon Carcinogenesis: Race-Specific Implications

(2016) Ramesh K. Wali et al.   Cancer Prevention Research

The Greater Genomic Landscape: The Heterogeneous Evolution of Cancer

(2016) Luay M. Almassalha et al.   CANCER RESEARCH

Commentary on Almassalha et al., “The Greater Genomic Landscape: The Heterogeneous Evolution of Cancer”

(2016) Henry T. Lynch et al.   CANCER RESEARCH

Cell-to-Cell Variation in p53 Dynamics Leads to Fractional Killing

(2016) Andrew L. Paek et al.   CELL

Formation of new chromatin domains determines pathogenicity of genomic duplications

(2016) Martin Franke et al.   NATURE

Super-resolution imaging reveals distinct chromatin folding for different epigenetic states

(2016) Alistair N. Boettiger et al.   NATURE

Transcript-level expression analysis of RNA-seq experiments with HISAT, StringTie and Ballgown

(2016) Mihaela Pertea et al.   Nature Protocols

Label-free imaging of the native, living cellular nanoarchitecture using partial-wave spectroscopic microscopy

(2016) Luay M. Almassalha et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Superresolution intrinsic fluorescence imaging of chromatin utilizing native, unmodified nucleic acids for contrast

(2016) Biqin Dong et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Using electron microscopy to calculate optical properties of biological samples

(2016) Wenli Wu et al.   Biomedical Optics Express

Disruptions of Topological Chromatin Domains Cause Pathogenic Rewiring of Gene-Enhancer Interactions

(2015) Darío G. Lupiáñez et al.   CELL

Macromolecular crowding creates heterogeneous environments of gene expression in picolitre droplets

(2015) Maike M. K. Hansen et al.   Nature Nanotechnology

Macromolecular Crowding as a Regulator of Gene Transcription

(2014) Hiroaki Matsuda et al.   BIOPHYSICAL JOURNAL

Nanoscale changes in chromatin organization represent the initial steps of tumorigenesis: a transmission electron microscopy study

(2014) Lusik Cherkezyan et al.   BMC CANCER

A 3D Map of the Human Genome at Kilobase Resolution Reveals Principles of Chromatin Looping

(2014) Suhas S.P. Rao et al.   CELL

Pioneer transcription factors in cell reprogramming

(2014) Makiko Iwafuchi-Doi et al.   GENES & DEVELOPMENT

COSMIC: exploring the world's knowledge of somatic mutations in human cancer

(2014) Simon A. Forbes et al.   NUCLEIC ACIDS RESEARCH

What structural length scales can be detected by the spectral variance of a microscope image?

(2014) Lusik Cherkezyan et al.   OPTICS LETTERS

Single-cell analyses of transcriptional heterogeneity during drug tolerance transition in cancer cells by RNA sequencing

(2014) M.-C. W. Lee et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The Impact of the Human Genome Project on Complex Disease

(2014) Jessica Bailey et al.   Genes

Nano-Architectural Alterations in Mucus Layer Fecal Colonocytes in Field Carcinogenesis: Potential for Screening

(2013) H. K. Roy et al.   Cancer Prevention Research

Nanoscale markers of esophageal field carcinogenesis: potential implications for esophageal cancer screening

(2013) Vani Konda et al.   ENDOSCOPY

Fractal dimension of chromatin: potential molecular diagnostic applications for cancer prognosis

(2013) Konradin Metze   EXPERT REVIEW OF MOLECULAR DIAGNOSTICS

Pan-cancer patterns of somatic copy number alteration

(2013) Travis I Zack et al.   NATURE GENETICS

Interferometric Spectroscopy of Scattered Light Can Quantify the Statistics of Subdiffractional Refractive-Index Fluctuations

(2013) L. Cherkezyan et al.   PHYSICAL REVIEW LETTERS

HDAC Up-Regulation in Early Colon Field Carcinogenesis Is Involved in Cell Tumorigenicity through Regulation of Chromatin Structure

(2013) Yolanda Stypula-Cyrus et al.   PLoS One

Nanocytology of Rectal Colonocytes to Assess Risk of Colon Cancer Based on Field Cancerization

(2012) D. Damania et al.   CANCER RESEARCH

A fractal model for nuclear organization: current evidence and biological implications

(2012) A. Bancaud et al.   NUCLEIC ACIDS RESEARCH

Versatile pathway-centric approach based on high-throughput sequencing to anticancer drug discovery

(2012) H. Li et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Effects of Macromolecular Crowding on Genetic Networks

(2011) Marco J. Morelli et al.   BIOPHYSICAL JOURNAL

High-Resolution Genome-wide Mapping of the Primary Structure of Chromatin

(2011) Zhenhai Zhang et al.   CELL

The fractal globule as a model of chromatin architecture in the cell

(2011) Leonid A. Mirny   CHROMOSOME RESEARCH

High order chromatin architecture shapes the landscape of chromosomal alterations in cancer

(2011) Geoff Fudenberg et al.   NATURE BIOTECHNOLOGY

Role of Cytoskeleton in Controlling the Disorder Strength of Cellular Nanoscale Architecture

(2010) Dhwanil Damania et al.   BIOPHYSICAL JOURNAL

Optical Detection of Buccal Epithelial Nanoarchitectural Alterations in Patients Harboring Lung Cancer: Implications for Screening

(2010) H. K. Roy et al.   CANCER RESEARCH

Nanocytology for field carcinogenesis detection: novel paradigm for lung cancer risk stratification

(2010) Hemant K Roy et al.   Future Oncology

Depletion Effect on Polymers Induced by Small Depleting Spheres

(2010) Jun Soo Kim et al.   Journal of Physical Chemistry C

Nanoscale Cellular Changes in Field Carcinogenesis Detected by Partial Wave Spectroscopy

(2009) Hariharan Subramanian et al.   CANCER RESEARCH

Molecular crowding affects diffusion and binding of nuclear proteins in heterochromatin and reveals the fractal organization of chromatin

(2009) Aurélien Bancaud et al.   EMBO JOURNAL

Preferential associations between co-regulated genes reveal a transcriptional interactome in erythroid cells

(2009) Stefan Schoenfelder et al.   NATURE GENETICS

Nonscalar elastic light scattering from continuous random media in the Born approximation

(2009) Jeremy D. Rogers et al.   OPTICS LETTERS

Comprehensive Mapping of Long-Range Interactions Reveals Folding Principles of the Human Genome

(2009) E. Lieberman-Aiden et al.   SCIENCE

Macromolecular crowding and its potential impact on nuclear function

(2008) Karsten Richter et al.   BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH

lumi: a pipeline for processing Illumina microarray

(2008) P. Du et al.   BIOINFORMATICS

Optical methodology for detecting histologically unapparent nanoscale consequences of genetic alterations in biological cells

(2008) H. Subramanian et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA