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Congratulations to the following authors for their recent publications featuring data derived from the CCR Genomics Core.

2020

53BP1 Enforces Distinct Pre- and Post-resection Blocks on Homologous Recombination

Elsa Callen, Dali Zong, Wei Wu, Nancy Wong, Andre Stanlie, Momoko Ishikawa, Raphael Pavani, Lavinia C. Dumitrache, Andrea K. Byrum, Carlos Mendez-Dorantes, Paula Martinez, Andres Canela, Yaakov Maman, Amanda Day, Michael J.Kruhlak, Maria A. Blasco, Jeremy M. Stark, Nima Mosammaparast, Peter J. McKinnon, André Nussenzweig.

PubMed Link
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.

PubMed Link

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.

PubMed Link
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.

PubMed Link
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.

PubMed Link
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.

PubMed Link
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.

PubMed Link
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.

ScienceDirect Link
Intra-Vκ Cluster Recombination Shapes the Ig Kappa Locus Repertoire

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

ScienceDirect Link
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.

PubMed Link

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.

PubMed Link
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. 

PubMed Link
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. 

PubMed Link
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.

PubMed Link
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. 

PubMed Link
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. 

PubMed Link
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. 

PubMed Link
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. 

PubMed Link
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. 

PubMed Link

2017

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

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

PubMed Link
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.  

PubMed Link

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.

PubMed Link

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. 

PubMed Link
Hamburger polyomaviruses.

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

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

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

PubMed Link

2013

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

PubMed Link

2013-2015

A divergent variant of the eleventh human polyomavirus species, saint louis polyomavirus.  Pastrana DV, Fitzgerald PC, Phan GQ, Raiji MT, Murphy PM, McDermott DH, Velez D, Bliskovsky V, McBride AA, Buck CB.

PubMed Link

Genome Sequence of a Fish-Associated Polyomavirus, Black Sea Bass (Centropristis striata) Polyomavirus 1.  Peretti A, FitzGerald PC, Bliskovsky V, Pastrana DV, Buck CB. 

PubMed Link