A citation-based method for searching scientific literature

Mark Manzano, Thomas Günther, Hyunwoo Ju, John Nicholas, Elizabeth T Bartom, Adam Grundhoff, Eva Gottwein. mBio 2020
Times Cited: 8







List of co-cited articles
87 articles co-cited >1



Times Cited
  Times     Co-cited
Similarity


Primary effusion lymphoma enhancer connectome links super-enhancers to dependency factors.
Chong Wang, Luyao Zhang, Liangru Ke, Weiyue Ding, Sizun Jiang, Difei Li, Yohei Narita, Isabella Hou, Jun Liang, Shijun Li,[...]. Nat Commun 2020
9
62

Global epigenomic analysis of KSHV-infected primary effusion lymphoma identifies functional MYC superenhancers and enhancer RNAs.
Angela Park, Soohwan Oh, Kyle L Jung, Un Yung Choi, Hye-Ra Lee, Michael G Rosenfeld, Jae U Jung. Proc Natl Acad Sci U S A 2020
9
50

Detection of Enhancer-Associated Rearrangements Reveals Mechanisms of Oncogene Dysregulation in B-cell Lymphoma.
Russell J H Ryan, Yotam Drier, Holly Whitton, M Joel Cotton, Jasleen Kaur, Robbyn Issner, Shawn Gillespie, Charles B Epstein, Valentina Nardi, Aliyah R Sohani,[...]. Cancer Discov 2015
77
50

Discovery and characterization of super-enhancer-associated dependencies in diffuse large B cell lymphoma.
Bjoern Chapuy, Michael R McKeown, Charles Y Lin, Stefano Monti, Margaretha G M Roemer, Jun Qi, Peter B Rahl, Heather H Sun, Kelly T Yeda, John G Doench,[...]. Cancer Cell 2013
490
37

CDK7-dependent transcriptional addiction in triple-negative breast cancer.
Yubao Wang, Tinghu Zhang, Nicholas Kwiatkowski, Brian J Abraham, Tong Ihn Lee, Shaozhen Xie, Haluk Yuzugullu, Thanh Von, Heyuan Li, Ziao Lin,[...]. Cell 2015
263
37

The Epstein-Barr Virus Regulome in Lymphoblastoid Cells.
Sizun Jiang, Hufeng Zhou, Jun Liang, Catherine Gerdt, Chong Wang, Liangru Ke, Stefanie C S Schmidt, Yohei Narita, Yijie Ma, Shuangqi Wang,[...]. Cell Host Microbe 2017
59
37

Model-based analysis of ChIP-Seq (MACS).
Yong Zhang, Tao Liu, Clifford A Meyer, Jérôme Eeckhoute, David S Johnson, Bradley E Bernstein, Chad Nusbaum, Richard M Myers, Myles Brown, Wei Li,[...]. Genome Biol 2008
37

Targeting Myc in KSHV-associated primary effusion lymphoma with BET bromodomain inhibitors.
B Tolani, R Gopalakrishnan, V Punj, H Matta, P M Chaudhary. Oncogene 2014
74
37

Fast gapped-read alignment with Bowtie 2.
Ben Langmead, Steven L Salzberg. Nat Methods 2012
37

Epstein-Barr virus oncoprotein super-enhancers control B cell growth.
Hufeng Zhou, Stefanie C S Schmidt, Sizun Jiang, Bradford Willox, Katharina Bernhardt, Jun Liang, Eric C Johannsen, Peter Kharchenko, Benjamin E Gewurz, Elliott Kieff,[...]. Cell Host Microbe 2015
100
37

Oncogene regulation. An oncogenic super-enhancer formed through somatic mutation of a noncoding intergenic element.
Marc R Mansour, Brian J Abraham, Lars Anders, Alla Berezovskaya, Alejandro Gutierrez, Adam D Durbin, Julia Etchin, Lee Lawton, Stephen E Sallan, Lewis B Silverman,[...]. Science 2014
462
37

Coactivator condensation at super-enhancers links phase separation and gene control.
Benjamin R Sabari, Alessandra Dall'Agnese, Ann Boija, Isaac A Klein, Eliot L Coffey, Krishna Shrinivas, Brian J Abraham, Nancy M Hannett, Alicia V Zamudio, John C Manteiga,[...]. Science 2018
937
37

Master transcription factors and mediator establish super-enhancers at key cell identity genes.
Warren A Whyte, David A Orlando, Denes Hnisz, Brian J Abraham, Charles Y Lin, Michael H Kagey, Peter B Rahl, Tong Ihn Lee, Richard A Young. Cell 2013
37


Global changes in Kaposi's sarcoma-associated virus gene expression patterns following expression of a tetracycline-inducible Rta transactivator.
Hiroyuki Nakamura, Michael Lu, Yousang Gwack, John Souvlis, Steven L Zeichner, Jae U Jung. J Virol 2003
229
37

Identification of herpesvirus-like DNA sequences in AIDS-associated Kaposi's sarcoma.
Y Chang, E Cesarman, M S Pessin, F Lee, J Culpepper, D M Knowles, P S Moore. Science 1994
37

HiC-Pro: an optimized and flexible pipeline for Hi-C data processing.
Nicolas Servant, Nelle Varoquaux, Bryan R Lajoie, Eric Viara, Chong-Jian Chen, Jean-Philippe Vert, Edith Heard, Job Dekker, Emmanuel Barillot. Genome Biol 2015
797
25


Gene essentiality landscape and druggable oncogenic dependencies in herpesviral primary effusion lymphoma.
Mark Manzano, Ajinkya Patil, Alexander Waldrop, Sandeep S Dave, Amir Behdad, Eva Gottwein. Nat Commun 2018
29
25

CRISPR/Cas9 Screens Reveal Epstein-Barr Virus-Transformed B Cell Host Dependency Factors.
Yijie Ma, Michael J Walsh, Katharina Bernhardt, Camille W Ashbaugh, Stephen J Trudeau, Isabelle Y Ashbaugh, Sizun Jiang, Chang Jiang, Bo Zhao, David E Root,[...]. Cell Host Microbe 2017
72
25

Persistent KSHV Infection Increases EBV-Associated Tumor Formation In Vivo via Enhanced EBV Lytic Gene Expression.
Donal McHugh, Nicole Caduff, Mario Henrique M Barros, Patrick C Rämer, Ana Raykova, Anita Murer, Vanessa Landtwing, Isaak Quast, Christine T Styles, Michael Spohn,[...]. Cell Host Microbe 2017
78
25

Simple combinations of lineage-determining transcription factors prime cis-regulatory elements required for macrophage and B cell identities.
Sven Heinz, Christopher Benner, Nathanael Spann, Eric Bertolino, Yin C Lin, Peter Laslo, Jason X Cheng, Cornelis Murre, Harinder Singh, Christopher K Glass. Mol Cell 2010
25

NF-κB directs dynamic super enhancer formation in inflammation and atherogenesis.
Jonathan D Brown, Charles Y Lin, Qiong Duan, Gabriel Griffin, Alexander Federation, Ronald M Paranal, Steven Bair, Gail Newton, Andrew Lichtman, Andrew Kung,[...]. Mol Cell 2014
386
25

LANA binds to multiple active viral and cellular promoters and associates with the H3K4methyltransferase hSET1 complex.
Jianhong Hu, Yajie Yang, Peter C Turner, Vaibhav Jain, Lauren M McIntyre, Rolf Renne. PLoS Pathog 2014
48
25

Identification of host-chromosome binding sites and candidate gene targets for Kaposi's sarcoma-associated herpesvirus LANA.
Fang Lu, Kevin Tsai, Horng-Shen Chen, Priyankara Wikramasinghe, Ramana V Davuluri, Louise Showe, John Domsic, Ronen Marmorstein, Paul M Lieberman. J Virol 2012
52
25

Epstein-Barr virus exploits intrinsic B-lymphocyte transcription programs to achieve immortal cell growth.
Bo Zhao, James Zou, Hongfang Wang, Eric Johannsen, Chih-wen Peng, John Quackenbush, Jessica C Mar, Cynthia Casson Morton, Matthew L Freedman, Stephen C Blacklow,[...]. Proc Natl Acad Sci U S A 2011
137
25

TAF Family Proteins and MEF2C Are Essential for Epstein-Barr Virus Super-Enhancer Activity.
Chong Wang, Sizun Jiang, Luyao Zhang, Difei Li, Jun Liang, Yohei Narita, Isabella Hou, Qian Zhong, Benjamin E Gewurz, Mingxiang Teng,[...]. J Virol 2019
8
25

Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2.
Michael I Love, Wolfgang Huber, Simon Anders. Genome Biol 2014
25

Regulation of viral and cellular gene expression by Kaposi's sarcoma-associated herpesvirus polyadenylated nuclear RNA.
Cyprian C Rossetto, Margaret Tarrant-Elorza, Subhash Verma, Pravinkumar Purushothaman, Gregory S Pari. J Virol 2013
91
25

MYC activation and BCL2L11 silencing by a tumour virus through the large-scale reconfiguration of enhancer-promoter hubs.
C David Wood, Hildegonda Veenstra, Sarika Khasnis, Andrea Gunnell, Helen M Webb, Claire Shannon-Lowe, Simon Andrews, Cameron S Osborne, Michelle J West. Elife 2016
60
25



Kaposi's sarcoma-associated herpesvirus LANA-1 interacts with the short variant of BRD4 and releases cells from a BRD4- and BRD2/RING3-induced G1 cell cycle arrest.
Matthias Ottinger, Thomas Christalla, Kavita Nathan, Melanie M Brinkmann, Abel Viejo-Borbolla, Thomas F Schulz. J Virol 2006
117
25

Modulation of enhancer looping and differential gene targeting by Epstein-Barr virus transcription factors directs cellular reprogramming.
Michael J McClellan, C David Wood, Opeoluwa Ojeniyi, Tim J Cooper, Aditi Kanhere, Aaron Arvey, Helen M Webb, Richard D Palermo, Marie L Harth-Hertle, Bettina Kempkes,[...]. PLoS Pathog 2013
59
25

A structural basis for BRD2/4-mediated host chromatin interaction and oligomer assembly of Kaposi sarcoma-associated herpesvirus and murine gammaherpesvirus LANA proteins.
Jan Hellert, Magdalena Weidner-Glunde, Joern Krausze, Ulrike Richter, Heiko Adler, Roman Fedorov, Marcel Pietrek, Jessica Rückert, Christiane Ritter, Thomas F Schulz,[...]. PLoS Pathog 2013
65
25

BET inhibitors: a novel epigenetic approach.
D B Doroshow, J P Eder, P M LoRusso. Ann Oncol 2017
177
25

Oncogenic herpesvirus KSHV triggers hallmarks of alternative lengthening of telomeres.
Timothy P Lippert, Paulina Marzec, Aurora I Idilli, Grzegorz Sarek, Aleksandra Vancevska, Mark Bower, Paul J Farrell, Päivi M Ojala, Niklas Feldhahn, Simon J Boulton. Nat Commun 2021
7
28

Viral non-coding RNAs: Stealth strategies in the tug-of-war between humans and herpesviruses.
Takanobu Tagawa, Anna Serquiña, Insun Kook, Joseph Ziegelbauer. Semin Cell Dev Biol 2021
11
25

Epstein-Barr virus infection and nasopharyngeal carcinoma.
Sai Wah Tsao, Chi Man Tsang, Kwok Wai Lo. Philos Trans R Soc Lond B Biol Sci 2017
230
25

PDGFRA defines the mesenchymal stem cell Kaposi's sarcoma progenitors by enabling KSHV oncogenesis in an angiogenic environment.
Julian Naipauer, Santas Rosario, Sachin Gupta, Courtney Premer, Omayra Méndez-Solís, Mariana Schlesinger, Virginia Ponzinibbio, Vaibhav Jain, Lauren Gay, Rolf Renne,[...]. PLoS Pathog 2019
12
25


Construction and manipulation of a new Kaposi's sarcoma-associated herpesvirus bacterial artificial chromosome clone.
Kevin F Brulois, Heesoon Chang, Amy Si-Ying Lee, Armin Ensser, Lai-Yee Wong, Zsolt Toth, Sun Hwa Lee, Hye-Ra Lee, Jinjong Myoung, Don Ganem,[...]. J Virol 2012
223
25

Epstein-Barr virus super-enhancer eRNAs are essential for MYC oncogene expression and lymphoblast proliferation.
Jun Liang, Hufeng Zhou, Catherine Gerdt, Min Tan, Tyler Colson, Kenneth M Kaye, Elliott Kieff, Bo Zhao. Proc Natl Acad Sci U S A 2016
54
25

Non-coding recurrent mutations in chronic lymphocytic leukaemia.
Xose S Puente, Silvia Beà, Rafael Valdés-Mas, Neus Villamor, Jesús Gutiérrez-Abril, José I Martín-Subero, Marta Munar, Carlota Rubio-Pérez, Pedro Jares, Marta Aymerich,[...]. Nature 2015
550
25

Genetic Predisposition to Chronic Lymphocytic Leukemia Is Mediated by a BMF Super-Enhancer Polymorphism.
Radhika Kandaswamy, Georgina P Sava, Helen E Speedy, Sílvia Beà, José I Martín-Subero, James B Studd, Gabriele Migliorini, Philip J Law, Xose S Puente, David Martín-García,[...]. Cell Rep 2016
39
25

Myc is required for the maintenance of Kaposi's sarcoma-associated herpesvirus latency.
Xudong Li, Shijia Chen, Jun Feng, Hongyu Deng, Ren Sun. J Virol 2010
32
25

The role of enhancers in cancer.
Inderpreet Sur, Jussi Taipale. Nat Rev Cancer 2016
197
25

The Leukemogenic TCF3-HLF Complex Rewires Enhancers Driving Cellular Identity and Self-Renewal Conferring EP300 Vulnerability.
Yun Huang, Brice Mouttet, Hans-Jörg Warnatz, Thomas Risch, Fabian Rietmann, Fabian Frommelt, Quy A Ngo, Maria Pamela Dobay, Blerim Marovca, Silvia Jenni,[...]. Cancer Cell 2019
19
25

Expression of MUM1/IRF4 selectively clusters with primary effusion lymphoma among lymphomatous effusions: implications for disease histogenesis and pathogenesis.
A Carbone, A Gloghini, M R Cozzi, D Capello, A Steffan, P Monini, L De Marco, G Gaidano. Br J Haematol 2000
48
25

Intrinsic disorder in transcription factors.
Jiangang Liu, Narayanan B Perumal, Christopher J Oldfield, Eric W Su, Vladimir N Uversky, A Keith Dunker. Biochemistry 2006
486
25


Co-cited is the co-citation frequency, indicating how many articles cite the article together with the query article. Similarity is the co-citation as percentage of the times cited of the query article or the article in the search results, whichever is the lowest. These numbers are calculated for the last 100 citations when articles are cited more than 100 times.