Publications — Johnstone Lab

Rewiring cancer: 3D genome determinants of cancer hallmarks

Amodeo ME, Eyler CE, Johnstone SE

Curr Opin Genet Dev, 2025

DOI: 10.1016/j.gde.2024.102307

High-resolution CTCF footprinting reveals impact of chromatin state on cohesin extrusion dynamics

Sept CE, Tak YE, Cerda-Smith CG, Hutchinson HM, Goel V, Blanchette M, Bhakta MS, Hansen AS, Joung JK, Johnstone SE, Eyler CE, Aryee MJ

bioRxiv, 2023

DOI: 10.1101/2023.10.20.563340

Integrative PTEN Enhancer Discovery Reveals a New Model of Enhancer Organization

Cerda-Smith CG, Hutchinson HM, Liu A, Goel VY, Sept C, Kim H, Casaní-Galdón S, Burkman KG, Bassil CF, Hansen AS, Aryee MJ, Johnstone SE, Eyler CE, Wood KC

bioRxiv, 2023

DOI: 10.1101/2023.09.20.558459

Modeling epigenetic lesions that cause gliomas

Rahme GJ, Javed NM, Puorro KL, Xin S, Hovestadt V, Johnstone SE, Bernstein BE

Cell, 2023

DOI: 10.1016/j.cell.2023.06.022

Impact of supraphysiologic MDM2 expression on chromatin networks and therapeutic responses in sarcoma

Bevill SM, Casaní-Galdón S, El Farran CA, Cytrynbaum EG, Macias KA, Oldeman SE, Oliveira KJ, Moore MM, Hegazi E, Adriaens C, Najm FJ, Demetri GD, Cohen S, Mullen JT, Riggi N, Johnstone SE, Bernstein BE

Cell Genom, 2023

DOI: 10.1016/j.xgen.2023.100321

Epigenetic clocks, aging, and cancer

Johnstone SE, Gladyshev VN, Aryee MJ, Bernstein BE

Science, 2022

DOI: 10.1126/science.ade4009

Polycomb-lamina antagonism partitions heterochromatin at the nuclear periphery

Siegenfeld AP, Roseman SA, Roh H, Lue NZ, Wagen CC, Zhou E, Johnstone SE, Aryee MJ, Liau BB

Nat Commun, 2022

DOI: 10.1038/s41467-022-31857-5

Data-Driven Polymer Model for Mechanistic Exploration of Diploid Genome Organization

Qi Y, Reyes A, Johnstone SE, Aryee MJ, Bernstein BE, Zhang B

Biophys J, 2020

DOI: 10.1016/j.bpj.2020.09.009

Large-Scale Topological Changes Restrain Malignant Progression in Colorectal Cancer

Johnstone SE, Reyes A, Qi Y, Adriaens C, Hegazi E, Pelka K, Chen JH, Zou LS, Drier Y, Hecht V, Shoresh N, Selig MK, Lareau CA, Iyer S, Nguyen SC, Joyce EF, Hacohen N, Irizarry RA, Zhang B, Aryee MJ, Bernstein BE

Cell, 2020

DOI: 10.1016/j.cell.2020.07.030

Prognostic Value of Myogenic Differentiation in Dedifferentiated Liposarcoma

Kurzawa P, Mullen JT, Chen YL, Johnstone SE, Deshpande V, Chebib I, Nielsen GP

Am J Surg Pathol, 2020

DOI: 10.1097/PAS.0000000000001436

Altered chromosomal topology drives oncogenic programs in SDH-deficient GIST

Flavahan WA, Drier Y, Johnstone SE, Hemming ML, Tarjan DR, Hegazi E, Shareef SJ, Javed NM, Raut CP, Eschle BK, Gokhale PC, Hornick JL, Sicinska ET, Demetri GD, Bernstein BE

Nature, 2019

DOI: 10.1038/s41586-019-1668-3

Genomic Analysis of Posterior Fossa Meningioma Demonstrates Frequent AKT1 E17K Mutations in Foramen Magnum Meningiomas

Williams SR, Juratli TA, Castro BA, Lazaro TT, Gill CM, Nayyar N, Strickland MR, Babinski M, Johnstone SE, Frosch MP, Silverman IM, Ely HA, Kaplan AB, D'Andrea MR, Bihun IV, Hoang K, Batchelor E, Christiansen J, Cahill DP, Barker FG, Brastianos PK

J Neurol Surg B Skull Base, 2019

DOI: 10.1055/s-0038-1676821

Cohesin Loss Eliminates All Loop Domains

Rao SSP, Huang SC, Glenn St Hilaire B, Engreitz JM, Perez EM, Kieffer-Kwon KR, Sanborn AL, Johnstone SE, Bascom GD, Bochkov ID, Huang X, Shamim MS, Shin J, Turner D, Ye Z, Omer AD, Robinson JT, Schlick T, Bernstein BE, Casellas R, Lander ES, Aiden EL

Cell, 2017

DOI: 10.1016/j.cell.2017.09.026

A DNA hypermethylation module for the stem/progenitor cell signature of cancer

Easwaran H, Johnstone SE, Van Neste L, Ohm J, Mosbruger T, Wang Q, Aryee MJ, Joyce P, Ahuja N, Weisenberger D, Collisson E, Zhu J, Yegnasubramanian S, Matsui W, Baylin SB

Genome Res, 2012

DOI: 10.1101/gr.131169.111

Stress and the epigenetic landscape: a link to the pathobiology of human diseases?

Johnstone SE, Baylin SB

Nat Rev Genet, 2010

DOI: 10.1038/nrg2881

Connecting microRNA genes to the core transcriptional regulatory circuitry of embryonic stem cells

Marson A, Levine SS, Cole MF, Frampton GM, Brambrink T, Johnstone S, Guenther MG, Johnston WK, Wernig M, Newman J, Calabrese JM, Dennis LM, Volkert TL, Gupta S, Love J, Hannett N, Sharp PA, Bartel DP, Jaenisch R, Young RA

Cell, 2008

DOI: 10.1016/j.cell.2008.07.020

Tcf3 is an integral component of the core regulatory circuitry of embryonic stem cells

Cole MF, Johnstone SE, Newman JJ, Kagey MH, Young RA

Genes Dev, 2008

DOI: 10.1101/gad.1642408

Control of developmental regulators by Polycomb in human embryonic stem cells

Lee TI, Jenner RG, Boyer LA, Guenther MG, Levine SS, Kumar RM, Chevalier B, Johnstone SE, Cole MF, Isono K, Koseki H, Fuchikami T, Abe K, Murray HL, Zucker JP, Yuan B, Bell GW, Herbolsheimer E, Hannett NM, Sun K, Odom DT, Otte AP, Volkert TL, Bartel DP, Melton DA, Gifford DK, Jaenisch R, Young RA

Cell, 2006

DOI: 10.1016/j.cell.2006.02.043

Chromatin immunoprecipitation and microarray-based analysis of protein location

Lee TI, Johnstone SE, Young RA

Nat Protoc, 2006

DOI: 10.1038/nprot.2006.98

Strong solute-solute dispersive interactions in a protein-ligand complex

Malham R, Johnstone S, Bingham RJ, Barratt E, Phillips SE, Laughton CA, Homans SW

J Am Chem Soc, 2005

DOI: 10.1021/ja055454g

Core transcriptional regulatory circuitry in human embryonic stem cells

Boyer LA, Lee TI, Cole MF, Johnstone SE, Levine SS, Zucker JP, Guenther MG, Kumar RM, Murray HL, Jenner RG, Gifford DK, Melton DA, Jaenisch R, Young RA

Cell, 2005

DOI: 10.1016/j.cell.2005.08.020

Gene families from the Arabidopsis thaliana pollen coat proteome

Mayfield JA, Fiebig A, Johnstone SE, Preuss D

Science, 2001

DOI: 10.1126/science.1060972

Johnstone Lab

Lab Publications