A citation-based method for searching scientific literature

E S Lander, L M Linton, B Birren, C Nusbaum, M C Zody, J Baldwin, K Devon, K Dewar, M Doyle, W FitzHugh, R Funke, D Gage, K Harris, A Heaford, J Howland, L Kann, J Lehoczky, R LeVine, P McEwan, K McKernan, J Meldrim, J P Mesirov, C Miranda, W Morris, J Naylor, C Raymond, M Rosetti, R Santos, A Sheridan, C Sougnez, Y Stange-Thomann, N Stojanovic, A Subramanian, D Wyman, J Rogers, J Sulston, R Ainscough, S Beck, D Bentley, J Burton, C Clee, N Carter, A Coulson, R Deadman, P Deloukas, A Dunham, I Dunham, R Durbin, L French, D Grafham, S Gregory, T Hubbard, S Humphray, A Hunt, M Jones, C Lloyd, A McMurray, L Matthews, S Mercer, S Milne, J C Mullikin, A Mungall, R Plumb, M Ross, R Shownkeen, S Sims, R H Waterston, R K Wilson, L W Hillier, J D McPherson, M A Marra, E R Mardis, L A Fulton, A T Chinwalla, K H Pepin, W R Gish, S L Chissoe, M C Wendl, K D Delehaunty, T L Miner, A Delehaunty, J B Kramer, L L Cook, R S Fulton, D L Johnson, P J Minx, S W Clifton, T Hawkins, E Branscomb, P Predki, P Richardson, S Wenning, T Slezak, N Doggett, J F Cheng, A Olsen, S Lucas, C Elkin, E Uberbacher, M Frazier, R A Gibbs, D M Muzny, S E Scherer, J B Bouck, E J Sodergren, K C Worley, C M Rives, J H Gorrell, M L Metzker, S L Naylor, R S Kucherlapati, D L Nelson, G M Weinstock, Y Sakaki, A Fujiyama, M Hattori, T Yada, A Toyoda, T Itoh, C Kawagoe, H Watanabe, Y Totoki, T Taylor, J Weissenbach, R Heilig, W Saurin, F Artiguenave, P Brottier, T Bruls, E Pelletier, C Robert, P Wincker, D R Smith, L Doucette-Stamm, M Rubenfield, K Weinstock, H M Lee, J Dubois, A Rosenthal, M Platzer, G Nyakatura, S Taudien, A Rump, H Yang, J Yu, J Wang, G Huang, J Gu, L Hood, L Rowen, A Madan, S Qin, R W Davis, N A Federspiel, A P Abola, M J Proctor, R M Myers, J Schmutz, M Dickson, J Grimwood, D R Cox, M V Olson, R Kaul, C Raymond, N Shimizu, K Kawasaki, S Minoshima, G A Evans, M Athanasiou, R Schultz, B A Roe, F Chen, H Pan, J Ramser, H Lehrach, R Reinhardt, W R McCombie, M de la Bastide, N Dedhia, H Blöcker, K Hornischer, G Nordsiek, R Agarwala, L Aravind, J A Bailey, A Bateman, S Batzoglou, E Birney, P Bork, D G Brown, C B Burge, L Cerutti, H C Chen, D Church, M Clamp, R R Copley, T Doerks, S R Eddy, E E Eichler, T S Furey, J Galagan, J G Gilbert, C Harmon, Y Hayashizaki, D Haussler, H Hermjakob, K Hokamp, W Jang, L S Johnson, T A Jones, S Kasif, A Kaspryzk, S Kennedy, W J Kent, P Kitts, E V Koonin, I Korf, D Kulp, D Lancet, T M Lowe, A McLysaght, T Mikkelsen, J V Moran, N Mulder, V J Pollara, C P Ponting, G Schuler, J Schultz, G Slater, A F Smit, E Stupka, J Szustakowki, D Thierry-Mieg, J Thierry-Mieg, L Wagner, J Wallis, R Wheeler, A Williams, Y I Wolf, K H Wolfe, S P Yang, R F Yeh, F Collins, M S Guyer, J Peterson, A Felsenfeld, K A Wetterstrand, A Patrinos, M J Morgan, P de Jong, J J Catanese, K Osoegawa, H Shizuya, S Choi, Y J Chen, J Szustakowki. Nature 2001
Times Cited: 14030







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



Times Cited
  Times     Co-cited
Similarity


The sequence of the human genome.
J C Venter, M D Adams, E W Myers, P W Li, R J Mural, G G Sutton, H O Smith, M Yandell, C A Evans, R A Holt,[...]. Science 2001
14

Hot L1s account for the bulk of retrotransposition in the human population.
Brook Brouha, Joshua Schustak, Richard M Badge, Sheila Lutz-Prigge, Alexander H Farley, John V Moran, Haig H Kazazian. Proc Natl Acad Sci U S A 2003
633
13

A global reference for human genetic variation.
Adam Auton, Lisa D Brooks, Richard M Durbin, Erik P Garrison, Hyun Min Kang, Jan O Korbel, Jonathan L Marchini, Shane McCarthy, Gil A McVean, Gonçalo R Abecasis. Nature 2015
11


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
8

The Sequence Alignment/Map format and SAMtools.
Heng Li, Bob Handsaker, Alec Wysoker, Tim Fennell, Jue Ruan, Nils Homer, Gabor Marth, Goncalo Abecasis, Richard Durbin. Bioinformatics 2009
8

Roles for retrotransposon insertions in human disease.
Dustin C Hancks, Haig H Kazazian. Mob DNA 2016
248
8

Landscape of somatic retrotransposition in human cancers.
Eunjung Lee, Rebecca Iskow, Lixing Yang, Omer Gokcumen, Psalm Haseley, Lovelace J Luquette, Jens G Lohr, Christopher C Harris, Li Ding, Richard K Wilson,[...]. Science 2012
441
7

The human genome browser at UCSC.
W James Kent, Charles W Sugnet, Terrence S Furey, Krishna M Roskin, Tom H Pringle, Alan M Zahler, David Haussler. Genome Res 2002
7

High frequency retrotransposition in cultured mammalian cells.
J V Moran, S E Holmes, T P Naas, R J DeBerardinis, J D Boeke, H H Kazazian. Cell 1996
724
7

Regulatory evolution of innate immunity through co-option of endogenous retroviruses.
Edward B Chuong, Nels C Elde, Cédric Feschotte. Science 2016
341
7




Primate-specific ORF0 contributes to retrotransposon-mediated diversity.
Ahmet M Denli, Iñigo Narvaiza, Bilal E Kerman, Monique Pena, Christopher Benner, Maria C N Marchetto, Jolene K Diedrich, Aaron Aslanian, Jiao Ma, James J Moresco,[...]. Cell 2015
103
6

Somatic mosaicism in neuronal precursor cells mediated by L1 retrotransposition.
Alysson R Muotri, Vi T Chu, Maria C N Marchetto, Wei Deng, John V Moran, Fred H Gage. Nature 2005
587
6

Haemophilia A resulting from de novo insertion of L1 sequences represents a novel mechanism for mutation in man.
H H Kazazian, C Wong, H Youssoufian, A F Scott, D G Phillips, S E Antonarakis. Nature 1988
636
6

Restricting retrotransposons: a review.
John L Goodier. Mob DNA 2016
168
6

An evolutionary arms race between KRAB zinc-finger genes ZNF91/93 and SVA/L1 retrotransposons.
Frank M J Jacobs, David Greenberg, Ngan Nguyen, Maximilian Haeussler, Adam D Ewing, Sol Katzman, Benedict Paten, Sofie R Salama, David Haussler. Nature 2014
222
6

LINE-mediated retrotransposition of marked Alu sequences.
Marie Dewannieux, Cécile Esnault, Thierry Heidmann. Nat Genet 2003
667
6

Regulatory activities of transposable elements: from conflicts to benefits.
Edward B Chuong, Nels C Elde, Cédric Feschotte. Nat Rev Genet 2017
430
6

LINE-1 retrotransposition activity in human genomes.
Christine R Beck, Pamela Collier, Catriona Macfarlane, Maika Malig, Jeffrey M Kidd, Evan E Eichler, Richard M Badge, John V Moran. Cell 2010
353
6

Landscape of transcription in human cells.
Sarah Djebali, Carrie A Davis, Angelika Merkel, Alex Dobin, Timo Lassmann, Ali Mortazavi, Andrea Tanzer, Julien Lagarde, Wei Lin, Felix Schlesinger,[...]. Nature 2012
6

Trimmomatic: a flexible trimmer for Illumina sequence data.
Anthony M Bolger, Marc Lohse, Bjoern Usadel. Bioinformatics 2014
5



LINE-1 elements in structural variation and disease.
Christine R Beck, José Luis Garcia-Perez, Richard M Badge, John V Moran. Annu Rev Genomics Hum Genet 2011
308
5

Repetitive elements may comprise over two-thirds of the human genome.
A P Jason de Koning, Wanjun Gu, Todd A Castoe, Mark A Batzer, David D Pollock. PLoS Genet 2011
572
5

The impact of retrotransposons on human genome evolution.
Richard Cordaux, Mark A Batzer. Nat Rev Genet 2009
914
5

Widespread contribution of transposable elements to the innovation of gene regulatory networks.
Vasavi Sundaram, Yong Cheng, Zhihai Ma, Daofeng Li, Xiaoyun Xing, Peter Edge, Michael P Snyder, Ting Wang. Genome Res 2014
184
5

Ubiquitous L1 mosaicism in hippocampal neurons.
Kyle R Upton, Daniel J Gerhardt, J Samuel Jesuadian, Sandra R Richardson, Francisco J Sánchez-Luque, Gabriela O Bodea, Adam D Ewing, Carmen Salvador-Palomeque, Marjo S van der Knaap, Paul M Brennan,[...]. Cell 2015
175
5

L1 retrotransposition in human neural progenitor cells.
Nicole G Coufal, José L Garcia-Perez, Grace E Peng, Gene W Yeo, Yangling Mu, Michael T Lovci, Maria Morell, K Sue O'Shea, John V Moran, Fred H Gage. Nature 2009
517
5


The Landscape of L1 Retrotransposons in the Human Genome Is Shaped by Pre-insertion Sequence Biases and Post-insertion Selection.
Tania Sultana, Dominic van Essen, Oliver Siol, Marc Bailly-Bechet, Claude Philippe, Amal Zine El Aabidine, Léo Pioger, Pilvi Nigumann, Simona Saccani, Jean-Christophe Andrau,[...]. Mol Cell 2019
38
13

The UCSC Table Browser data retrieval tool.
Donna Karolchik, Angela S Hinrichs, Terrence S Furey, Krishna M Roskin, Charles W Sugnet, David Haussler, W James Kent. Nucleic Acids Res 2004
5

Initial sequencing and comparative analysis of the mouse genome.
Robert H Waterston, Kerstin Lindblad-Toh, Ewan Birney, Jane Rogers, Josep F Abril, Pankaj Agarwal, Richa Agarwala, Rachel Ainscough, Marina Alexandersson, Peter An,[...]. Nature 2002
5

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
63
7

A unified classification system for eukaryotic transposable elements.
Thomas Wicker, François Sabot, Aurélie Hua-Van, Jeffrey L Bennetzen, Pierre Capy, Boulos Chalhoub, Andrew Flavell, Philippe Leroy, Michele Morgante, Olivier Panaud,[...]. Nat Rev Genet 2007
5


Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2.
Michael I Love, Wolfgang Huber, Simon Anders. Genome Biol 2014
5

Multi-platform discovery of haplotype-resolved structural variation in human genomes.
Mark J P Chaisson, Ashley D Sanders, Xuefang Zhao, Ankit Malhotra, David Porubsky, Tobias Rausch, Eugene J Gardner, Oscar L Rodriguez, Li Guo, Ryan L Collins,[...]. Nat Commun 2019
205
5

CpG islands and the regulation of transcription.
Aimée M Deaton, Adrian Bird. Genes Dev 2011
4

A structural variation reference for medical and population genetics.
Ryan L Collins, Harrison Brand, Konrad J Karczewski, Xuefang Zhao, Jessica Alföldi, Laurent C Francioli, Amit V Khera, Chelsea Lowther, Laura D Gauthier, Harold Wang,[...]. Nature 2020
101
4

IQ-TREE: a fast and effective stochastic algorithm for estimating maximum-likelihood phylogenies.
Lam-Tung Nguyen, Heiko A Schmidt, Arndt von Haeseler, Bui Quang Minh. Mol Biol Evol 2015
4

Activation of neuronal genes via LINE-1 elements upon global DNA demethylation in human neural progenitors.
Marie E Jönsson, Per Ludvik Brattås, Charlotte Gustafsson, Rebecca Petri, David Yudovich, Karolina Pircs, Shana Verschuere, Sofia Madsen, Jenny Hansson, Jonas Larsson,[...]. Nat Commun 2019
23
17

Telomere-to-telomere assembly of a complete human X chromosome.
Karen H Miga, Sergey Koren, Arang Rhie, Mitchell R Vollger, Ariel Gershman, Andrey Bzikadze, Shelise Brooks, Edmund Howe, David Porubsky, Glennis A Logsdon,[...]. Nature 2020
100
4

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
138
4


LINE1 Derepression in Aged Wild-Type and SIRT6-Deficient Mice Drives Inflammation.
Matthew Simon, Michael Van Meter, Julia Ablaeva, Zhonghe Ke, Raul S Gonzalez, Taketo Taguchi, Marco De Cecco, Katerina I Leonova, Valeria Kogan, Stephen L Helfand,[...]. Cell Metab 2019
78
5



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.