A citation-based method for searching scientific literature

Celestia Fang, Zhenjia Wang, Cuijuan Han, Stephanie L Safgren, Kathryn A Helmin, Emmalee R Adelman, Valentina Serafin, Giuseppe Basso, Kyle P Eagen, Alexandre Gaspar-Maia, Maria E Figueroa, Benjamin D Singer, Aakrosh Ratan, Panagiotis Ntziachristos, Chongzhi Zang. Genome Biol 2020
Times Cited: 14







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



Times Cited
  Times     Co-cited
Similarity


Topological domains in mammalian genomes identified by analysis of chromatin interactions.
Jesse R Dixon, Siddarth Selvaraj, Feng Yue, Audrey Kim, Yan Li, Yin Shen, Ming Hu, Jun S Liu, Bing Ren. Nature 2012
50

Comprehensive mapping of long-range interactions reveals folding principles of the human genome.
Erez Lieberman-Aiden, Nynke L van Berkum, Louise Williams, Maxim Imakaev, Tobias Ragoczy, Agnes Telling, Ido Amit, Bryan R Lajoie, Peter J Sabo, Michael O Dorschner,[...]. Science 2009
28

Spatial partitioning of the regulatory landscape of the X-inactivation centre.
Elphège P Nora, Bryan R Lajoie, Edda G Schulz, Luca Giorgetti, Ikuhiro Okamoto, Nicolas Servant, Tristan Piolot, Nynke L van Berkum, Johannes Meisig, John Sedat,[...]. Nature 2012
21

DNA-Demethylating Agents Target Colorectal Cancer Cells by Inducing Viral Mimicry by Endogenous Transcripts.
David Roulois, Helen Loo Yau, Rajat Singhania, Yadong Wang, Arnavaz Danesh, Shu Yi Shen, Han Han, Gangning Liang, Peter A Jones, Trevor J Pugh,[...]. Cell 2015
650
21

Epigenetic Determinants of Cancer.
Stephen B Baylin, Peter A Jones. Cold Spring Harb Perspect Biol 2016
425
21

Transcription factors orchestrate dynamic interplay between genome topology and gene regulation during cell reprogramming.
Ralph Stadhouders, Enrique Vidal, François Serra, Bruno Di Stefano, François Le Dily, Javier Quilez, Antonio Gomez, Samuel Collombet, Clara Berenguer, Yasmina Cuartero,[...]. Nat Genet 2018
153
14

Chromatin architecture reorganization during stem cell differentiation.
Jesse R Dixon, Inkyung Jung, Siddarth Selvaraj, Yin Shen, Jessica E Antosiewicz-Bourget, Ah Young Lee, Zhen Ye, Audrey Kim, Nisha Rajagopal, Wei Xie,[...]. Nature 2015
818
14

Formation of Chromosomal Domains by Loop Extrusion.
Geoffrey Fudenberg, Maxim Imakaev, Carolyn Lu, Anton Goloborodko, Nezar Abdennur, Leonid A Mirny. Cell Rep 2016
766
14

An oestrogen-receptor-alpha-bound human chromatin interactome.
Melissa J Fullwood, Mei Hui Liu, You Fu Pan, Jun Liu, Han Xu, Yusoff Bin Mohamed, Yuriy L Orlov, Stoyan Velkov, Andrea Ho, Poh Huay Mei,[...]. Nature 2009
14

Two independent modes of chromatin organization revealed by cohesin removal.
Wibke Schwarzer, Nezar Abdennur, Anton Goloborodko, Aleksandra Pekowska, Geoffrey Fudenberg, Yann Loe-Mie, Nuno A Fonseca, Wolfgang Huber, Christian H Haering, Leonid Mirny,[...]. Nature 2017
468
14

H3.3/H2A.Z double variant-containing nucleosomes mark 'nucleosome-free regions' of active promoters and other regulatory regions.
Chunyuan Jin, Chongzhi Zang, Gang Wei, Kairong Cui, Weiqun Peng, Keji Zhao, Gary Felsenfeld. Nat Genet 2009
540
14

Disruption of chromatin folding domains by somatic genomic rearrangements in human cancer.
Kadir C Akdemir, Victoria T Le, Sahaana Chandran, Yilong Li, Roel G Verhaak, Rameen Beroukhim, Peter J Campbell, Lynda Chin, Jesse R Dixon, P Andrew Futreal. Nat Genet 2020
73
14

Mediator and cohesin connect gene expression and chromatin architecture.
Michael H Kagey, Jamie J Newman, Steve Bilodeau, Ye Zhan, David A Orlando, Nynke L van Berkum, Christopher C Ebmeier, Jesse Goossens, Peter B Rahl, Stuart S Levine,[...]. Nature 2010
14

Control of inducible gene expression links cohesin to hematopoietic progenitor self-renewal and differentiation.
Sergi Cuartero, Felix D Weiss, Gopuraja Dharmalingam, Ya Guo, Elizabeth Ing-Simmons, Silvia Masella, Irene Robles-Rebollo, Xiaolin Xiao, Yi-Fang Wang, Iros Barozzi,[...]. Nat Immunol 2018
92
14

Cohesin-Dependent and -Independent Mechanisms Mediate Chromosomal Contacts between Promoters and Enhancers.
Michiel J Thiecke, Gordana Wutz, Matthias Muhar, Wen Tang, Stephen Bevan, Valeriya Malysheva, Roman Stocsits, Tobias Neumann, Johannes Zuber, Peter Fraser,[...]. Cell Rep 2020
45
14

Multi-level remodelling of chromatin underlying activation of human T cells.
Naiara G Bediaga, Hannah D Coughlan, Timothy M Johanson, Alexandra L Garnham, Gaetano Naselli, Jan Schröder, Liam G Fearnley, Esther Bandala-Sanchez, Rhys S Allan, Gordon K Smyth,[...]. Sci Rep 2021
7
28

Cohesins form chromosomal cis-interactions at the developmentally regulated IFNG locus.
Suzana Hadjur, Luke M Williams, Natalie K Ryan, Bradley S Cobb, Tom Sexton, Peter Fraser, Amanda G Fisher, Matthias Merkenschlager. Nature 2009
393
14

The Cohesin Release Factor WAPL Restricts Chromatin Loop Extension.
Judith H I Haarhuis, Robin H van der Weide, Vincent A Blomen, J Omar Yáñez-Cuna, Mario Amendola, Marjon S van Ruiten, Peter H L Krijger, Hans Teunissen, René H Medema, Bas van Steensel,[...]. Cell 2017
333
14

Domain organization of human chromosomes revealed by mapping of nuclear lamina interactions.
Lars Guelen, Ludo Pagie, Emilie Brasset, Wouter Meuleman, Marius B Faza, Wendy Talhout, Bert H Eussen, Annelies de Klein, Lodewyk Wessels, Wouter de Laat,[...]. Nature 2008
14

CTCF-Mediated Enhancer-Promoter Interaction Is a Critical Regulator of Cell-to-Cell Variation of Gene Expression.
Gang Ren, Wenfei Jin, Kairong Cui, Joseph Rodrigez, Gangqing Hu, Zhiying Zhang, Daniel R Larson, Keji Zhao. Mol Cell 2017
111
14

INO80 exchanges H2A.Z for H2A by translocating on DNA proximal to histone dimers.
Sandipan Brahma, Maheshi I Udugama, Jongseong Kim, Arjan Hada, Saurabh K Bhardwaj, Solomon G Hailu, Tae-Hee Lee, Blaine Bartholomew. Nat Commun 2017
68
14

Non-coding Transcription Instructs Chromatin Folding and Compartmentalization to Dictate Enhancer-Promoter Communication and T Cell Fate.
Takeshi Isoda, Amanda J Moore, Zhaoren He, Vivek Chandra, Masatoshi Aida, Matthew Denholtz, Jan Piet van Hamburg, Kathleen M Fisch, Aaron N Chang, Shawn P Fahl,[...]. Cell 2017
129
14

The role of enhancers in cancer.
Inderpreet Sur, Jussi Taipale. Nat Rev Cancer 2016
184
14

Three-dimensional chromatin landscapes in T cell acute lymphoblastic leukemia.
Andreas Kloetgen, Palaniraja Thandapani, Panagiotis Ntziachristos, Yohana Ghebrechristos, Sofia Nomikou, Charalampos Lazaris, Xufeng Chen, Hai Hu, Sofia Bakogianni, Jingjing Wang,[...]. Nat Genet 2020
33
14

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
14
14

Developmental gene networks: a triathlon on the course to T cell identity.
Mary A Yui, Ellen V Rothenberg. Nat Rev Immunol 2014
190
14

A NOTCH1-driven MYC enhancer promotes T cell development, transformation and acute lymphoblastic leukemia.
Daniel Herranz, Alberto Ambesi-Impiombato, Teresa Palomero, Stephanie A Schnell, Laura Belver, Agnieszka A Wendorff, Luyao Xu, Mireia Castillo-Martin, David Llobet-Navás, Carlos Cordon-Cardo,[...]. Nat Med 2014
252
14

Activation of proto-oncogenes by disruption of chromosome neighborhoods.
Denes Hnisz, Abraham S Weintraub, Daniel S Day, Anne-Laure Valton, Rasmus O Bak, Charles H Li, Johanna Goldmann, Bryan R Lajoie, Zi Peng Fan, Alla A Sigova,[...]. Science 2016
493
14

3D Chromosome Regulatory Landscape of Human Pluripotent Cells.
Xiong Ji, Daniel B Dadon, Benjamin E Powell, Zi Peng Fan, Diego Borges-Rivera, Sigal Shachar, Abraham S Weintraub, Denes Hnisz, Gianluca Pegoraro, Tong Ihn Lee,[...]. Cell Stem Cell 2016
228
14

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
14

Lineage-Specific Genome Architecture Links Enhancers and Non-coding Disease Variants to Target Gene Promoters.
Biola M Javierre, Oliver S Burren, Steven P Wilder, Roman Kreuzhuber, Steven M Hill, Sven Sewitz, Jonathan Cairns, Steven W Wingett, Csilla Várnai, Michiel J Thiecke,[...]. Cell 2016
449
14

The transcription factor Bcl11b is specifically expressed in group 2 innate lymphoid cells and is essential for their development.
Yong Yu, Cui Wang, Simon Clare, Juexuan Wang, Song-Choon Lee, Cordelia Brandt, Shannon Burke, Liming Lu, Daqian He, Nancy A Jenkins,[...]. J Exp Med 2015
109
14

Transformation of Accessible Chromatin and 3D Nucleome Underlies Lineage Commitment of Early T Cells.
Gangqing Hu, Kairong Cui, Difeng Fang, Satoshi Hirose, Xun Wang, Darawalee Wangsa, Wenfei Jin, Thomas Ried, Pentao Liu, Jinfang Zhu,[...]. Immunity 2018
80
14

Lineage-Determining Transcription Factor TCF-1 Initiates the Epigenetic Identity of T Cells.
John L Johnson, Georgios Georgakilas, Jelena Petrovic, Makoto Kurachi, Stanley Cai, Christelle Harly, Warren S Pear, Avinash Bhandoola, E John Wherry, Golnaz Vahedi. Immunity 2018
94
14


Whole-genome fingerprint of the DNA methylome during human B cell differentiation.
Marta Kulis, Angelika Merkel, Simon Heath, Ana C Queirós, Ronald P Schuyler, Giancarlo Castellano, Renée Beekman, Emanuele Raineri, Anna Esteve, Guillem Clot,[...]. Nat Genet 2015
193
14

Pioneering Activity of the C-Terminal Domain of EBF1 Shapes the Chromatin Landscape for B Cell Programming.
Sören Boller, Senthilkumar Ramamoorthy, Duygu Akbas, Robert Nechanitzky, Lukas Burger, Rabih Murr, Dirk Schübeler, Rudolf Grosschedl. Immunity 2016
61
14

Control of cell identity genes occurs in insulated neighborhoods in mammalian chromosomes.
Jill M Dowen, Zi Peng Fan, Denes Hnisz, Gang Ren, Brian J Abraham, Lyndon N Zhang, Abraham S Weintraub, Jurian Schujiers, Tong Ihn Lee, Keji Zhao,[...]. Cell 2014
528
14

Super-enhancers in the control of cell identity and disease.
Denes Hnisz, Brian J Abraham, Tong Ihn Lee, Ashley Lau, Violaine Saint-André, Alla A Sigova, Heather A Hoke, Richard A Young. Cell 2013
14

Implications of Genetic and Epigenetic Alterations of CDKN2A (p16(INK4a)) in Cancer.
Ran Zhao, Bu Young Choi, Mee-Hyun Lee, Ann M Bode, Zigang Dong. EBioMedicine 2016
139
14

DNMT3A and TET2 compete and cooperate to repress lineage-specific transcription factors in hematopoietic stem cells.
Xiaotian Zhang, Jianzhong Su, Mira Jeong, Myunggon Ko, Yun Huang, Hyun Jung Park, Anna Guzman, Yong Lei, Yung-Hsin Huang, Anjana Rao,[...]. Nat Genet 2016
128
14

DNA Hypomethylation Contributes to Genomic Instability and Intestinal Cancer Initiation.
Karyn L Sheaffer, Ellen N Elliott, Klaus H Kaestner. Cancer Prev Res (Phila) 2016
55
14

CTCF loss mediates unique DNA hypermethylation landscapes in human cancers.
Nathan A Damaschke, Joseph Gawdzik, Mele Avilla, Bing Yang, John Svaren, Avtar Roopra, Jian-Hua Luo, Yan P Yu, Sunduz Keles, David F Jarrard. Clin Epigenetics 2020
9
22

DNA (de)methylation in embryonic stem cells controls CTCF-dependent chromatin boundaries.
Laura Wiehle, Graeme J Thorn, Günter Raddatz, Christopher T Clarkson, Karsten Rippe, Frank Lyko, Achim Breiling, Vladimir B Teif. Genome Res 2019
33
14

Paradoxical association of TET loss of function with genome-wide DNA hypomethylation.
Isaac F López-Moyado, Ageliki Tsagaratou, Hiroshi Yuita, Hyungseok Seo, Benjamin Delatte, Sven Heinz, Christopher Benner, Anjana Rao. Proc Natl Acad Sci U S A 2019
37
14

Regulatory evolution of innate immunity through co-option of endogenous retroviruses.
Edward B Chuong, Nels C Elde, Cédric Feschotte. Science 2016
391
14

IDH mutation impairs histone demethylation and results in a block to cell differentiation.
Chao Lu, Patrick S Ward, Gurpreet S Kapoor, Dan Rohle, Sevin Turcan, Omar Abdel-Wahab, Christopher R Edwards, Raya Khanin, Maria E Figueroa, Ari Melnick,[...]. Nature 2012
14

Genomic and epigenomic landscapes of adult de novo acute myeloid leukemia.
Timothy J Ley, Christopher Miller, Li Ding, Benjamin J Raphael, Andrew J Mungall, A Gordon Robertson, Katherine Hoadley, Timothy J Triche, Peter W Laird, Jack D Baty,[...]. N Engl J Med 2013
14

Inhibiting DNA Methylation Causes an Interferon Response in Cancer via dsRNA Including Endogenous Retroviruses.
Katherine B Chiappinelli, Pamela L Strissel, Alexis Desrichard, Huili Li, Christine Henke, Benjamin Akman, Alexander Hein, Neal S Rote, Leslie M Cope, Alexandra Snyder,[...]. Cell 2015
806
14

TET2 inactivation results in pleiotropic hematopoietic abnormalities in mouse and is a recurrent event during human lymphomagenesis.
Cyril Quivoron, Lucile Couronné, Véronique Della Valle, Cécile K Lopez, Isabelle Plo, Orianne Wagner-Ballon, Marcio Do Cruzeiro, Francois Delhommeau, Bertrand Arnulf, Marc-Henri Stern,[...]. Cancer Cell 2011
631
14


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.