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: 14728







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



Times Cited
  Times     Co-cited
Similarity


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
10

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
9

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
9

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
8


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
767
7

Roles for retrotransposon insertions in human disease.
Dustin C Hancks, Haig H Kazazian. Mob DNA 2016
323
7

Regulatory activities of transposable elements: from conflicts to benefits.
Edward B Chuong, Nels C Elde, Cédric Feschotte. Nat Rev Genet 2017
604
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
128
7

LINE-1 activation after fertilization regulates global chromatin accessibility in the early mouse embryo.
Joanna W Jachowicz, Xinyang Bing, Julien Pontabry, Ana Bošković, Oliver J Rando, Maria-Elena Torres-Padilla. Nat Genet 2017
158
6

Restricting retrotransposons: a review.
John L Goodier. Mob DNA 2016
223
6

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
6

The mutational constraint spectrum quantified from variation in 141,456 humans.
Konrad J Karczewski, Laurent C Francioli, Grace Tiao, Beryl B Cummings, Jessica Alföldi, Qingbo Wang, Ryan L Collins, Kristen M Laricchia, Andrea Ganna, Daniel P Birnbaum,[...]. Nature 2020
6

Basic local alignment search tool.
S F Altschul, W Gish, W Miller, E W Myers, D J Lipman. J Mol Biol 1990
6

Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2.
Michael I Love, Wolfgang Huber, Simon Anders. Genome Biol 2014
6

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
557
6


Somatic retrotransposition alters the genetic landscape of the human brain.
J Kenneth Baillie, Mark W Barnett, Kyle R Upton, Daniel J Gerhardt, Todd A Richmond, Fioravante De Sapio, Paul M Brennan, Patrizia Rizzu, Sarah Smith, Mark Fell,[...]. Nature 2011
470
5

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
631
5

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
671
5

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
390
5

Transposable elements in human genetic disease.
Lindsay M Payer, Kathleen H Burns. Nat Rev Genet 2019
110
5

The complete sequence of a human genome.
Sergey Nurk, Sergey Koren, Arang Rhie, Mikko Rautiainen, Andrey V Bzikadze, Alla Mikheenko, Mitchell R Vollger, Nicolas Altemose, Lev Uralsky, Ariel Gershman,[...]. Science 2022
171
5

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
287
5

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
5



Pan-genomics in the human genome era.
Rachel M Sherman, Steven L Salzberg. Nat Rev Genet 2020
78
6

Alu elements: know the SINEs.
Prescott Deininger. Genome Biol 2011
330
5

Accurate circular consensus long-read sequencing improves variant detection and assembly of a human genome.
Aaron M Wenger, Paul Peluso, William J Rowell, Pi-Chuan Chang, Richard J Hall, Gregory T Concepcion, Jana Ebler, Arkarachai Fungtammasan, Alexey Kolesnikov, Nathan D Olson,[...]. Nat Biotechnol 2019
431
5

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
547
5

Syncytin is a captive retroviral envelope protein involved in human placental morphogenesis.
S Mi, X Lee, X Li, G M Veldman, H Finnerty, L Racie, E LaVallie, X Y Tang, P Edouard, S Howes,[...]. Nature 2000
5

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
337
5

The retrovirus HERVH is a long noncoding RNA required for human embryonic stem cell identity.
Xinyi Lu, Friedrich Sachs, LeeAnn Ramsay, Pierre-Étienne Jacques, Jonathan Göke, Guillaume Bourque, Huck-Hui Ng. Nat Struct Mol Biol 2014
229
5

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


A mouse model of human L1 retrotransposition.
Eric M Ostertag, Ralph J DeBerardinis, John L Goodier, Yue Zhang, Nuo Yang, George L Gerton, Haig H Kazazian. Nat Genet 2002
153
4

LINE-mediated retrotransposition of marked Alu sequences.
Marie Dewannieux, Cécile Esnault, Thierry Heidmann. Nat Genet 2003
708
4


The Role of Somatic L1 Retrotransposition in Human Cancers.
Emma C Scott, Scott E Devine. Viruses 2017
52
7


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
687
4


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
263
4

Haplotype-resolved de novo assembly using phased assembly graphs with hifiasm.
Haoyu Cheng, Gregory T Concepcion, Xiaowen Feng, Haowen Zhang, Heng Li. Nat Methods 2021
247
4

Fast gapped-read alignment with Bowtie 2.
Ben Langmead, Steven L Salzberg. Nat Methods 2012
4

Extensive sequencing of seven human genomes to characterize benchmark reference materials.
Justin M Zook, David Catoe, Jennifer McDaniel, Lindsay Vang, Noah Spies, Arend Sidow, Ziming Weng, Yuling Liu, Christopher E Mason, Noah Alexander,[...]. Sci Data 2016
299
4


Measuring and interpreting transposable element expression.
Sophie Lanciano, Gael Cristofari. Nat Rev Genet 2020
87
4

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
643
4


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.