Selected Publications

Chaligne R, Gaiti F, Silverbush D, Schiffman JS, Weisman HR, Kluegel L, Gritsch S, Deochand SD, Gonzalez Castro LN, Richman AR, Klughammer J, Biancalani T, Muus C, Sheridan C, Alonso A, Izzo F, Park J, Rozenblatt-Rosen O, Regev A, Suvà ML, Landau DA: Epigenetic encoding, heritability and plasticity of glioma transcriptional cell states. Nature Genetics 53(10): 1469-1479, October 2021.

Shani O, Raz Y, Monteran L, Scharff Y, Levi-Galibov O, Megides O, Shacham H, Cohen N, Silverbush D, Avivi C, Sharan R, Madi A, Scherz-Shouval R, Barshack I, Tsarfaty I, Erez N: Evolution of fibroblasts in the lung metastatic microenvironment is driven by stage-specific transcriptional plasticity. Elife June 2021.

Ciccolella S, Ricketts C, Soto Gomez M, Patterson M, Silverbush D, Bonizzoni P, Hajirasouliha I, Della Vedova G: Inferring cancer progression from Single-Cell Sequencing while allowing mutation losses. Bioinformatics 37(3): 326-333, April 2021.

Venkatesh HS, Morishita W, Geraghty AC, Silverbush D, Gillespie SM, Arzt M, Tam LT, Espenel C, Ponnuswami A, Ni L, Woo PJ, Taylor KR, Agarwal A, Regev A, Brang D, Vogel H, Hervey-Jumper S, Bergles DE, Suvà ML, Malenka RC, Monje M: Electrical and synaptic integration of glioma into neural circuits. Nature 573(7775): 539-545, September 2019.

Neftel C, Laffy J, Filbin MG, Hara T, Shore ME, Rahme GJ, Richman AR, Silverbush D, Shaw ML, Hebert CM, Dewitt J, Gritsch S, Perez EM, Gonzalez Castro LN, Lan X, Druck N, Rodman C, Dionne D, Kaplan A, Bertalan MS, Small J, Pelton K, Becker S, Bonal D, Nguyen QD, Servis RL, Fung JM, Mylvaganam R, Mayr L, Gojo J, Haberler C, Geyeregger R, Czech T, Slavc I, Nahed BV, Curry WT, Carter BS, Wakimoto H, Brastianos PK, Batchelor TT, Stemmer-Rachamimov A, Martinez-Lage M, Frosch MP, Stamenkovic I, Riggi N, Rheinbay E, Monje M, Rozenblatt-Rosen O, Cahill DP, Patel AP, Hunter T, Verma IM, Ligon KL, Louis DN, Regev A, Bernstein BE, Tirosh I, Suvà ML: An Integrative Model of Cellular States, Plasticity, and Genetics for Glioblastoma. Cell 174(4): 835-849, August 2019.

Silverbush D, Sharan R: A systematic approach to orient the human protein-protein interaction network. Nature Communications 10(1), July 2019.

Silverbush D, Cristea S, Yanovich-Arad G, Geiger T, Beerenwinkel N, Sharan R: Simultaneous Integration of Multi-omics Data Improves the Identification of Cancer Driver Modules. Cell Systems 8(5): 456-466, May 2019.

Cho H, Berger B, Peng J, Galitzine C, Vitek O, Beltran PMJ, Cristea IM, Görtler F, Solbrig S, Wettig T, Oefner PJ, Spang R, Altenbuchinger M, Basso RS, Hochbaum D, Vandin F, Silverbush D, Cristea S, Yanovich G, Geiger T, Beerenwinkel N, Sharan R, Zhou Z, Luhmann N, Alikhan NF, Achtman M: Principles of Systems Biology, No. 31. Cell Systems 7(2): 133-135, August 2018.

Almozlino Y, Atias N, Silverbush D, Sharan R: ANAT 2.0: reconstructing functional protein subnetworks. BMC Bioinformatics 18(1): 495, November 2017.

Silverbush D, Grosskurth S, Wang D, Powell F, Gottgens B, Dry J, Fisher J: Cell-Specific Computational Modeling of the PIM Pathway in Acute Myeloid Leukemia. Cancer Research 77(4): 827-838, February 2017.