A citation-based method for searching scientific literature

Li Sun, Xiuling Fu, Gang Ma, Andrew P Hutchins. Front Cell Dev Biol 2021
Times Cited: 2







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



Times Cited
  Times     Co-cited
Similarity


The Branched Nature of the Nonsense-Mediated mRNA Decay Pathway.
Zhongxia Yi, Manu Sanjeev, Guramrit Singh. Trends Genet 2021
10
50

Models of global gene expression define major domains of cell type and tissue identity.
Andrew P Hutchins, Zhongzhou Yang, Yuhao Li, Fangfang He, Xiuling Fu, Xiaoshan Wang, Dongwei Li, Kairong Liu, Jiangping He, Yong Wang,[...]. Nucleic Acids Res 2017
25
50

Unique properties of a subset of human pluripotent stem cells with high capacity for self-renewal.
Kevin X Lau, Elizabeth A Mason, Joshua Kie, David P De Souza, Joachim Kloehn, Dedreia Tull, Malcolm J McConville, Andrew Keniry, Tamara Beck, Marnie E Blewitt,[...]. Nat Commun 2020
11
50

Identifying transposable element expression dynamics and heterogeneity during development at the single-cell level with a processing pipeline scTE.
Jiangping He, Isaac A Babarinde, Li Sun, Shuyang Xu, Ruhai Chen, Junjie Shi, Yuanjie Wei, Yuhao Li, Gang Ma, Qiang Zhuang,[...]. Nat Commun 2021
8
50

glbase: a framework for combining, analyzing and displaying heterogeneous genomic and high-throughput sequencing data.
Andrew Paul Hutchins, Ralf Jauch, Mateusz Dyla, Diego Miranda-Saavedra. Cell Regen 2014
46
50

Transposable elements are major contributors to the origin, diversification, and regulation of vertebrate long noncoding RNAs.
Aurélie Kapusta, Zev Kronenberg, Vincent J Lynch, Xiaoyu Zhuo, LeeAnn Ramsay, Guillaume Bourque, Mark Yandell, Cédric Feschotte. PLoS Genet 2013
358
50

Identification of an infectious progenitor for the multiple-copy HERV-K human endogenous retroelements.
Marie Dewannieux, Francis Harper, Aurélien Richaud, Claire Letzelter, David Ribet, Gérard Pierron, Thierry Heidmann. Genome Res 2006
202
50

Primate-specific endogenous retrovirus-driven transcription defines naive-like stem cells.
Jichang Wang, Gangcai Xie, Manvendra Singh, Avazeh T Ghanbarian, Tamás Raskó, Attila Szvetnik, Huiqiang Cai, Daniel Besser, Alessandro Prigione, Nina V Fuchs,[...]. Nature 2014
228
50

Retroelement distributions in the human genome: variations associated with age and proximity to genes.
Patrik Medstrand, Louie N van de Lagemaat, Dixie L Mager. Genome Res 2002
227
50

Distinct Processing of lncRNAs Contributes to Non-conserved Functions in Stem Cells.
Chun-Jie Guo, Xu-Kai Ma, Yu-Hang Xing, Chuan-Chuan Zheng, Yi-Feng Xu, Lin Shan, Jun Zhang, Shaohua Wang, Yangming Wang, Gordon G Carmichael,[...]. Cell 2020
47
50

Transposable elements have rewired the core regulatory network of human embryonic stem cells.
Galih Kunarso, Na-Yu Chia, Justin Jeyakani, Catalina Hwang, Xinyi Lu, Yun-Shen Chan, Huck-Hui Ng, Guillaume Bourque. Nat Genet 2010
470
50

RNAsamba: neural network-based assessment of the protein-coding potential of RNA sequences.
Antonio P Camargo, Vsevolod Sourkov, Gonçalo A G Pereira, Marcelo F Carazzolle. NAR Genom Bioinform 2020
10
50

The Dfam database of repetitive DNA families.
Robert Hubley, Robert D Finn, Jody Clements, Sean R Eddy, Thomas A Jones, Weidong Bao, Arian F A Smit, Travis J Wheeler. Nucleic Acids Res 2016
236
50

Population-scale proteome variation in human induced pluripotent stem cells.
Bogdan Andrei Mirauta, Daniel D Seaton, Dalila Bensaddek, Alejandro Brenes, Marc Jan Bonder, Helena Kilpinen, Oliver Stegle, Angus I Lamond. Elife 2020
11
50

The RNA Helicase DDX6 Controls Cellular Plasticity by Modulating P-Body Homeostasis.
Bruno Di Stefano, En-Ching Luo, Chuck Haggerty, Stefan Aigner, Jocelyn Charlton, Justin Brumbaugh, Fei Ji, Inés Rabano Jiménez, Katie J Clowers, Aaron J Huebner,[...]. Cell Stem Cell 2019
22
50


Long noncoding RNAs and human disease.
Orly Wapinski, Howard Y Chang. Trends Cell Biol 2011
50

Not so bad after all: retroviruses and long terminal repeat retrotransposons as a source of new genes in vertebrates.
M Naville, I A Warren, Z Haftek-Terreau, D Chalopin, F Brunet, P Levin, D Galiana, J-N Volff. Clin Microbiol Infect 2016
26
50

The Transcriptionally Permissive Chromatin State of Embryonic Stem Cells Is Acutely Tuned to Translational Output.
Aydan Bulut-Karslioglu, Trisha A Macrae, Juan A Oses-Prieto, Sergio Covarrubias, Michelle Percharde, Gregory Ku, Aaron Diaz, Michael T McManus, Alma L Burlingame, Miguel Ramalho-Santos. Cell Stem Cell 2018
31
50

Linking RNA biology to lncRNAs.
Loyal A Goff, John L Rinn. Genome Res 2015
119
50

Transposable elements in cancer.
Kathleen H Burns. Nat Rev Cancer 2017
175
50

Detection of nonneutral substitution rates on mammalian phylogenies.
Katherine S Pollard, Melissa J Hubisz, Kate R Rosenbloom, Adam Siepel. Genome Res 2010
50

Intrinsic retroviral reactivation in human preimplantation embryos and pluripotent cells.
Edward J Grow, Ryan A Flynn, Shawn L Chavez, Nicholas L Bayless, Mark Wossidlo, Daniel J Wesche, Lance Martin, Carol B Ware, Catherine A Blish, Howard Y Chang,[...]. Nature 2015
286
50

EuRBPDB: a comprehensive resource for annotation, functional and oncological investigation of eukaryotic RNA binding proteins (RBPs).
Jian-You Liao, Bing Yang, Yu-Chan Zhang, Xiao-Juan Wang, Yushan Ye, Jing-Wen Peng, Zhi-Zhi Yang, Jie-Hua He, Yin Zhang, KaiShun Hu,[...]. Nucleic Acids Res 2020
19
50

Induced pluripotent stem cell lines derived from human somatic cells.
Junying Yu, Maxim A Vodyanik, Kim Smuga-Otto, Jessica Antosiewicz-Bourget, Jennifer L Frane, Shulan Tian, Jeff Nie, Gudrun A Jonsdottir, Victor Ruotti, Ron Stewart,[...]. Science 2007
50


deepTools: a flexible platform for exploring deep-sequencing data.
Fidel Ramírez, Friederike Dündar, Sarah Diehl, Björn A Grüning, Thomas Manke. Nucleic Acids Res 2014
961
50


STAR: ultrafast universal RNA-seq aligner.
Alexander Dobin, Carrie A Davis, Felix Schlesinger, Jorg Drenkow, Chris Zaleski, Sonali Jha, Philippe Batut, Mark Chaisson, Thomas R Gingeras. Bioinformatics 2013
50

SCANPY: large-scale single-cell gene expression data analysis.
F Alexander Wolf, Philipp Angerer, Fabian J Theis. Genome Biol 2018
812
50

A promoter-level mammalian expression atlas.
Alistair R R Forrest, Hideya Kawaji, Michael Rehli, J Kenneth Baillie, Michiel J L de Hoon, Vanja Haberle, Timo Lassmann, Ivan V Kulakovskiy, Marina Lizio, Masayoshi Itoh,[...]. Nature 2014
50

Loose ends: almost one in five human genes still have unresolved coding status.
Federico Abascal, David Juan, Irwin Jungreis, Manolis Kellis, Laura Martinez, Maria Rigau, Jose Manuel Rodriguez, Jesus Vazquez, Michael L Tress. Nucleic Acids Res 2018
26
50

Regulatory activities of transposable elements: from conflicts to benefits.
Edward B Chuong, Nels C Elde, Cédric Feschotte. Nat Rev Genet 2017
494
50

Molecular Criteria for Defining the Naive Human Pluripotent State.
Thorold W Theunissen, Marc Friedli, Yupeng He, Evarist Planet, Ryan C O'Neil, Styliani Markoulaki, Julien Pontis, Haoyi Wang, Alexandra Iouranova, Michaël Imbeault,[...]. Cell Stem Cell 2016
245
50

Ten things you should know about transposable elements.
Guillaume Bourque, Kathleen H Burns, Mary Gehring, Vera Gorbunova, Andrei Seluanov, Molly Hammell, Michaël Imbeault, Zsuzsanna Izsvák, Henry L Levin, Todd S Macfarlan,[...]. Genome Biol 2018
246
50

Human Primordial Germ Cells Are Specified from Lineage-Primed Progenitors.
Di Chen, Na Sun, Lei Hou, Rachel Kim, Jared Faith, Marianna Aslanyan, Yu Tao, Yi Zheng, Jianping Fu, Wanlu Liu,[...]. Cell Rep 2019
34
50

Dynamic transcription of distinct classes of endogenous retroviral elements marks specific populations of early human embryonic cells.
Jonathan Göke, Xinyi Lu, Yun-Shen Chan, Huck-Hui Ng, Lam-Ha Ly, Friedrich Sachs, Iwona Szczerbinska. Cell Stem Cell 2015
151
50

Widespread transcript shortening through alternative polyadenylation in secretory cell differentiation.
Larry C Cheng, Dinghai Zheng, Erdene Baljinnyam, Fangzheng Sun, Koichi Ogami, Percy Luk Yeung, Mainul Hoque, Chi-Wei Lu, James L Manley, Bin Tian. Nat Commun 2020
8
50


Transposable elements modulate human RNA abundance and splicing via specific RNA-protein interactions.
David R Kelley, David G Hendrickson, Danielle Tenen, John L Rinn. Genome Biol 2014
56
50

Mammalian-wide interspersed repeat (MIR)-derived enhancers and the regulation of human gene expression.
Daudi Jjingo, Andrew B Conley, Jianrong Wang, Leonardo Mariño-Ramírez, Victoria V Lunyak, I King Jordan. Mob DNA 2014
39
50

Widespread Polycistronic Transcripts in Fungi Revealed by Single-Molecule mRNA Sequencing.
Sean P Gordon, Elizabeth Tseng, Asaf Salamov, Jiwei Zhang, Xiandong Meng, Zhiying Zhao, Dongwan Kang, Jason Underwood, Igor V Grigoriev, Melania Figueroa,[...]. PLoS One 2015
156
50

Human endogenous retrovirus K (HML-2) RNA and protein expression is a marker for human embryonic and induced pluripotent stem cells.
Nina V Fuchs, Sabine Loewer, George Q Daley, Zsuzsanna Izsvák, Johannes Löwer, Roswitha Löwer. Retrovirology 2013
57
50

LncBook: a curated knowledgebase of human long non-coding RNAs.
Lina Ma, Jiabao Cao, Lin Liu, Qiang Du, Zhao Li, Dong Zou, Vladimir B Bajic, Zhang Zhang. Nucleic Acids Res 2019
79
50

The regulated retrotransposon transcriptome of mammalian cells.
Geoffrey J Faulkner, Yasumasa Kimura, Carsten O Daub, Shivangi Wani, Charles Plessy, Katharine M Irvine, Kate Schroder, Nicole Cloonan, Anita L Steptoe, Timo Lassmann,[...]. Nat Genet 2009
520
50

ILF2 Is a Regulator of RNA Splicing and DNA Damage Response in 1q21-Amplified Multiple Myeloma.
Matteo Marchesini, Yamini Ogoti, Elena Fiorini, Anil Aktas Samur, Luigi Nezi, Marianna D'Anca, Paola Storti, Mehmet Kemal Samur, Irene Ganan-Gomez, Maria Teresa Fulciniti,[...]. Cancer Cell 2017
64
50


Transposable elements drive widespread expression of oncogenes in human cancers.
Hyo Sik Jang, Nakul M Shah, Alan Y Du, Zea Z Dailey, Erica C Pehrsson, Paula M Godoy, David Zhang, Daofeng Li, Xiaoyun Xing, Sungsu Kim,[...]. Nat Genet 2019
84
50

The GENCODE v7 catalog of human long noncoding RNAs: analysis of their gene structure, evolution, and expression.
Thomas Derrien, Rory Johnson, Giovanni Bussotti, Andrea Tanzer, Sarah Djebali, Hagen Tilgner, Gregory Guernec, David Martin, Angelika Merkel, David G Knowles,[...]. Genome Res 2012
50

Graph-based genome alignment and genotyping with HISAT2 and HISAT-genotype.
Daehwan Kim, Joseph M Paggi, Chanhee Park, Christopher Bennett, Steven L Salzberg. Nat Biotechnol 2019
50


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.