Publications

Phage Resistance in Multidrug-Resistant Klebsiella pneumoniae ST258 Evolves via Diverse Mutations That Culminate in Impaired Adsorption

Shayla Hesse, Manoj Rajaure, Erin Wall, Joy Johnson, Valery Bliskovsky, Susan Gottesman, Sankar Adhya.

2019

Single-Cell Transcriptome Analysis Reveals Gene Signatures Associated with T-Cell Persistence.

Lu YC, Jia L, Zheng Z, Tran E, Robbins P and Rosenberg SA.

The transcription factor MZF1 differentially regulates murine Mtor promoter variants linked to tumor susceptibility.

Zhang S, Shi W, Ramsay ES, Bliskovsky V, Eiden AM, Connors D, Steinsaltz M, DuBois W, Mock BA.

Human macrophages survive and adopt activated genotypes in living zebrafish.

Paul CD, Devine A, Bishop K, Xu Q, Wulftange WJ, Burr H, Daly KM, Lewis C, Green DS, Staunton JR, Choksi S, Liu ZG, Sood R, Tanner K.

Histone hyperacetylation disrupts core gene regulatory architecture in rhabdomyosarcoma

Gryder, Berkley & Pomella, Silvia & Sayers, Carly & Wu, Xiaoli & Song, Young & Chiarella, Anna & Bagchi, Sukriti & Chou, Hsien-chao & Sinniah, Ranu & Walton, Ashley & Wen, Xinyu & Rota, Rossella & Hathaway, Nathaniel & Zhao, Keji & Chen, Jiji & Vakoc, Christopher & Shern, Jack & Stanton, Benjamin & Khan, Javed.

Spatial control of oxygen delivery to three‐dimensional cultures alters cancer cell growth and gene expression.

Wulftange WJ, Rose MA, Garmendia‐Cedillos M, et al.

Topoisomerase II-Induced Chromosome Breakage and Translocation Is Determined by Chromosome Architecture and Transcriptional Activity

Andres Canela, Yaakov Maman, Shar-yin N. Huang, Gordana Wutz, Wen Tang, Guido Zagnoli-Vieira, Elsa Callen, Nancy Wong, Amanda Day, Jan-Michael Peters, Keith W. Caldecott, Yves Pommier, André Nussenzweig.

Intra-Vκ Cluster Recombination Shapes the Ig Kappa Locus Repertoire

Kenta Shinoda, Yaakov Maman, Andres Canela, David G. Schatz, Ferenc Livak, André Nussenzweig.

Low Abundance of Circulating Tumor DNA in Localized Prostate Cancer.

S. Thomas Hennigan, Shana Y. Trostel, Nicholas T. Terrigino, Olga S. Voznesensky, M, Rachel J. Schaefer, MS, Nichelle C. Whitlock, PhD, Scott Wilkinson, PhD, Nicole V. Carrabba, Rayann Atway, Steven Shema, Ross Lake, Amalia R. Sweet, David J. Einstein, M, Fatima Karzai, MD, James L. Gulley, MD, PhD, Peter Chang, MD, MPH, Glenn J. Bubley, MD, Steven P. Balk, MD, Huihui Ye, MD, Adam G. Sowalsky, PhD.

2018

Interaction between the microbiome and TP53 in human lung cancer.

K. Leigh Greathouse, James R. White, Ashely J. Vargas, Valery V. Bliskovsky, Jessica A. Beck, Natalia von Muhlinen, Eric C. Polley, Elise D. Bowman, Mohammed A. Khan, Ana I. Robles, Tomer Cooks, Bríd M. Ryan, Noah Padgett, Amiran H. Dzutsev, Giorgio Trinchieri, Marbin A. Pineda, Sven Bilke, Paul S. Meltzer, Alexis N. Hokenstad, Tricia M. Stickrod, Marina R. Walther-Antonio, Joshua P. Earl, Joshua C. Mell, Jaroslaw E. Krol, Sergey V. Balashov, Archana S. Bhat, Garth D. Ehrlich, Alex Valm, Clayton Deming, Sean Conlan, Julia Oh, Julie A. Segre & Curtis C. Harris.

Targeting loss of the Hippo signaling pathway in NF2-deficient papillary kidney cancers. (Acknowledgement).

Sourbier, C., Liao, P.-J., Ricketts, C. J., Wei, D., Yang, Y., Baranes, S. M., … Marston Linehan, W.

Characterization of BK Polyomaviruses from Kidney Transplant Recipients Suggests a Role for APOBEC3 in Driving In-Host Virus Evolution.

Peretti A, Geoghegan EM, Pastrana DV, Smola S, Feld P, Sauter M, Lohse S, Ramesh M, Lim ES, Wang D, Borgogna C, FitzGerald PC, Bliskovsky V, Starrett GJ, Law EK, Harris RS, Killian JK, Zhu J, Pineda M, Meltzer PS, Boldorini R, Gariglio M, Buck CB.

An Efficient Single-Cell RNA-Seq Approach to Identify Neoantigen-Specific T Cell Receptors.

Yong-Chen Lu, Zhili Zheng, Paul F. Robbins, Eric Tran, Todd D. Prickett, Jared J. Gartner, Yong F. Li, Satyajit Ray, Zulmarie Franco, Valery Bliskovsky, Peter C. Fitzgerald, Steven A. Rosenberg.

HOXA9 methylation and blood vessel invasion in FFPE tissues for prognostic stratification of stage I lung adenocarcinoma patients.

Lissa D, Ishigame T, Noro R, Tucker MJ, Bliskovsky V, Shema S, Beck JA, Bowman ED, Harris CC, Robles AI.

Dual Roles of Poly(dA:dT) Tracts in Replication Initiation and Fork Collapse.

Tubbs A, Sridharan S, van Wietmarschen N, Maman Y, Callen E, Stanlie A, Wu W, Wu X, Day A, Wong N, Yin M, Canela A, Fu H, Redon C, Pruitt SC, Jaszczyszyn Y, Aladjem MI, Aplan PD, Hyrien O, Nussenzweig A.

Four-dimensional, dynamic mosaicism is a hallmark of normal human skin that permits mapping of the organization and patterning of human epidermis during terminal differentiation.

Wang Y, Masaki T, Khan SG, Tamura D, Kuschal C, Rogers M, DiGiovanna JJ, Kraemer KH.

Genomic perturbations reveal distinct regulatory networks in intrahepatic cholangiocarcinoma.

Nepal C, O’Rourke CJ, Oliveira DVNP, Taranta A, Shema S, Gautam P, Calderaro J, Barbour A, Raggi C, Wennerberg K, Wang XW, Lautem A, Roberts LR, Andersen JB.

CDC73 Germline Mutation in a family with mixed epithelial and stromal tumors.

Vocke CD, Ricketts CJ, Ball MW, Schmidt LS, Metwalli AR, Middelton LA, Killian JK, Khan J, Meltzer PS, Simmonds WF, Merino MJ, Linehan WM.

2017

Novel “superspreader” bacteriophages promote horizontal gene transfer by transformation.

Keen EC, Bliskovsky VV, Malagon F, Baker JD, Prince JS, Klaus JS, Adhya SL.

Δ133p53 represses p53-inducible senescence genes and enhances the generation of human induced pluripotent stem cells .  (Acknowledgement)

Izumi Horikawa, Kye-yoon Park, Kazunobu Isogaya, Yukiharu Hiyoshi, Han Li, Katsuhiro Anami, Ana I Robles, Abdul M Mondal, Kaori Fujita, Manuel Serrano and Curtis C Harris.

2016

MET signaling in keratinocytes activates EGFR and initiates squamous carcinogenesis, (Acknowledgement).

Stuart H. Yuspa Dubois, Fan Liu, Anne Zhuang, Kameron B. Rodrigues, Shelley Hoover, Jennifer Dwyer, Mark R. Simpson, Glenn Merlino and Christophe Cataisson, Aleksandra M. Michalowski, Kelly Shibuya, Andrew Ryscavage, Mary Klosterman, Lisa Wright, Wendy.

2015

Isolation of neoantigen-specific T cells from tumor and peripheral lymphocytes.

Cohen CJ, Gartner JJ, Horovitz-Fried M, Shamalov K, Trebska-McGowan K, Bliskovsky VV, Parkhurst MR, Ankri C, Prickett TD, Crystal JS, Li YF, El-Gamil M, Rosenberg SA, Robbins PF.

Hamburger polyomaviruses.

Peretti A, FitzGerald PC, Bliskovsky V, Buck CB, Pastrana DV.

A Quality-Control Mechanism Removes Unfit Cells from a Population of Sporulating Bacteria.

Tan IS, Weiss CA, Popham DL, Ramamurth KS.

2013

Transcription signatures encoded by ultraconserved genomic regions in human prostate cancer. (Methods). Hudson RS, Yi M, Volfovsky N, et al.