A citation-based method for searching scientific literature

Robert H Waterston, Kerstin Lindblad-Toh, Ewan Birney, Jane Rogers, Josep F Abril, Pankaj Agarwal, Richa Agarwala, Rachel Ainscough, Marina Alexandersson, Peter An, Stylianos E Antonarakis, John Attwood, Robert Baertsch, Jonathon Bailey, Karen Barlow, Stephan Beck, Eric Berry, Bruce Birren, Toby Bloom, Peer Bork, Marc Botcherby, Nicolas Bray, Michael R Brent, Daniel G Brown, Stephen D Brown, Carol Bult, John Burton, Jonathan Butler, Robert D Campbell, Piero Carninci, Simon Cawley, Francesca Chiaromonte, Asif T Chinwalla, Deanna M Church, Michele Clamp, Christopher Clee, Francis S Collins, Lisa L Cook, Richard R Copley, Alan Coulson, Olivier Couronne, James Cuff, Val Curwen, Tim Cutts, Mark Daly, Robert David, Joy Davies, Kimberly D Delehaunty, Justin Deri, Emmanouil T Dermitzakis, Colin Dewey, Nicholas J Dickens, Mark Diekhans, Sheila Dodge, Inna Dubchak, Diane M Dunn, Sean R Eddy, Laura Elnitski, Richard D Emes, Pallavi Eswara, Eduardo Eyras, Adam Felsenfeld, Ginger A Fewell, Paul Flicek, Karen Foley, Wayne N Frankel, Lucinda A Fulton, Robert S Fulton, Terrence S Furey, Diane Gage, Richard A Gibbs, Gustavo Glusman, Sante Gnerre, Nick Goldman, Leo Goodstadt, Darren Grafham, Tina A Graves, Eric D Green, Simon Gregory, Roderic Guigó, Mark Guyer, Ross C Hardison, David Haussler, Yoshihide Hayashizaki, LaDeana W Hillier, Angela Hinrichs, Wratko Hlavina, Timothy Holzer, Fan Hsu, Axin Hua, Tim Hubbard, Adrienne Hunt, Ian Jackson, David B Jaffe, L Steven Johnson, Matthew Jones, Thomas A Jones, Ann Joy, Michael Kamal, Elinor K Karlsson, Donna Karolchik, Arkadiusz Kasprzyk, Jun Kawai, Evan Keibler, Cristyn Kells, W James Kent, Andrew Kirby, Diana L Kolbe, Ian Korf, Raju S Kucherlapati, Edward J Kulbokas, David Kulp, Tom Landers, J P Leger, Steven Leonard, Ivica Letunic, Rosie Levine, Jia Li, Ming Li, Christine Lloyd, Susan Lucas, Bin Ma, Donna R Maglott, Elaine R Mardis, Lucy Matthews, Evan Mauceli, John H Mayer, Megan McCarthy, W Richard McCombie, Stuart McLaren, Kirsten McLay, John D McPherson, Jim Meldrim, Beverley Meredith, Jill P Mesirov, Webb Miller, Tracie L Miner, Emmanuel Mongin, Kate T Montgomery, Michael Morgan, Richard Mott, James C Mullikin, Donna M Muzny, William E Nash, Joanne O Nelson, Michael N Nhan, Robert Nicol, Zemin Ning, Chad Nusbaum, Michael J O'Connor, Yasushi Okazaki, Karen Oliver, Emma Overton-Larty, Lior Pachter, Genís Parra, Kymberlie H Pepin, Jane Peterson, Pavel Pevzner, Robert Plumb, Craig S Pohl, Alex Poliakov, Tracy C Ponce, Chris P Ponting, Simon Potter, Michael Quail, Alexandre Reymond, Bruce A Roe, Krishna M Roskin, Edward M Rubin, Alistair G Rust, Ralph Santos, Victor Sapojnikov, Brian Schultz, Jörg Schultz, Matthias S Schwartz, Scott Schwartz, Carol Scott, Steven Seaman, Steve Searle, Ted Sharpe, Andrew Sheridan, Ratna Shownkeen, Sarah Sims, Jonathan B Singer, Guy Slater, Arian Smit, Douglas R Smith, Brian Spencer, Arne Stabenau, Nicole Stange-Thomann, Charles Sugnet, Mikita Suyama, Glenn Tesler, Johanna Thompson, David Torrents, Evanne Trevaskis, John Tromp, Catherine Ucla, Abel Ureta-Vidal, Jade P Vinson, Andrew C Von Niederhausern, Claire M Wade, Melanie Wall, Ryan J Weber, Robert B Weiss, Michael C Wendl, Anthony P West, Kris Wetterstrand, Raymond Wheeler, Simon Whelan, Jamey Wierzbowski, David Willey, Sophie Williams, Richard K Wilson, Eitan Winter, Kim C Worley, Dudley Wyman, Shan Yang, Shiaw-Pyng Yang, Evgeny M Zdobnov, Michael C Zody, Eric S Lander. Nature 2002
Times Cited: 4652







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



Times Cited
  Times     Co-cited
Similarity


Initial sequencing and analysis of the human genome.
E S Lander, L M Linton, B Birren, C Nusbaum, M C Zody, J Baldwin, K Devon, K Dewar, M Doyle, W FitzHugh,[...]. Nature 2001
31

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

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
9

Genome sequence of the Brown Norway rat yields insights into mammalian evolution.
Richard A Gibbs, George M Weinstock, Michael L Metzker, Donna M Muzny, Erica J Sodergren, Steven Scherer, Graham Scott, David Steffen, Kim C Worley, Paula E Burch,[...]. Nature 2004
9


Mouse genomic variation and its effect on phenotypes and gene regulation.
Thomas M Keane, Leo Goodstadt, Petr Danecek, Michael A White, Kim Wong, Binnaz Yalcin, Andreas Heger, Avigail Agam, Guy Slater, Martin Goodson,[...]. Nature 2011
963
6

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
116
6

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

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
5

Regulatory activities of transposable elements: from conflicts to benefits.
Edward B Chuong, Nels C Elde, Cédric Feschotte. Nat Rev Genet 2017
494
5


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
5

The Genome Analysis Toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data.
Aaron McKenna, Matthew Hanna, Eric Banks, Andrey Sivachenko, Kristian Cibulskis, Andrew Kernytsky, Kiran Garimella, David Altshuler, Stacey Gabriel, Mark Daly,[...]. Genome Res 2010
5


Of mice and not men: differences between mouse and human immunology.
Javier Mestas, Christopher C W Hughes. J Immunol 2004
5

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

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
5


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
5

Gene set enrichment analysis: a knowledge-based approach for interpreting genome-wide expression profiles.
Aravind Subramanian, Pablo Tamayo, Vamsi K Mootha, Sayan Mukherjee, Benjamin L Ebert, Michael A Gillette, Amanda Paulovich, Scott L Pomeroy, Todd R Golub, Eric S Lander,[...]. Proc Natl Acad Sci U S A 2005
4

The Genome of C57BL/6J "Eve", the Mother of the Laboratory Mouse Genome Reference Strain.
Vishal Kumar Sarsani, Narayanan Raghupathy, Ian T Fiddes, Joel Armstrong, Francoise Thibaud-Nissen, Oraya Zinder, Mohan Bolisetty, Kerstin Howe, Doug Hinerfeld, Xiaoan Ruan,[...]. G3 (Bethesda) 2019
18
22

A map of the cis-regulatory sequences in the mouse genome.
Yin Shen, Feng Yue, David F McCleary, Zhen Ye, Lee Edsall, Samantha Kuan, Ulrich Wagner, Jesse Dixon, Leonard Lee, Victor V Lobanenkov,[...]. Nature 2012
904
4

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
4

A 3D map of the human genome at kilobase resolution reveals principles of chromatin looping.
Suhas S P Rao, Miriam H Huntley, Neva C Durand, Elena K Stamenova, Ivan D Bochkov, James T Robinson, Adrian L Sanborn, Ido Machol, Arina D Omer, Eric S Lander,[...]. Cell 2014
4


TimeTree: A Resource for Timelines, Timetrees, and Divergence Times.
Sudhir Kumar, Glen Stecher, Michael Suleski, S Blair Hedges. Mol Biol Evol 2017
829
4

The hallmarks of aging.
Carlos López-Otín, Maria A Blasco, Linda Partridge, Manuel Serrano, Guido Kroemer. Cell 2013
4

Analysis of protein-coding genetic variation in 60,706 humans.
Monkol Lek, Konrad J Karczewski, Eric V Minikel, Kaitlin E Samocha, Eric Banks, Timothy Fennell, Anne H O'Donnell-Luria, James S Ware, Andrew J Hill, Beryl B Cummings,[...]. Nature 2016
4

A LINE1-Nucleolin Partnership Regulates Early Development and ESC Identity.
Michelle Percharde, Chih-Jen Lin, Yafei Yin, Juan Guan, Gabriel A Peixoto, Aydan Bulut-Karslioglu, Steffen Biechele, Bo Huang, Xiaohua Shen, Miguel Ramalho-Santos. Cell 2018
163
4

Chromatin signatures and retrotransposon profiling in mouse embryos reveal regulation of LINE-1 by RNA.
Anas Fadloun, Stéphanie Le Gras, Bernard Jost, Céline Ziegler-Birling, Hazuki Takahashi, Eduardo Gorab, Piero Carninci, Maria-Elena Torres-Padilla. Nat Struct Mol Biol 2013
137
4

The genome sequence of Drosophila melanogaster.
M D Adams, S E Celniker, R A Holt, C A Evans, J D Gocayne, P G Amanatides, S E Scherer, P W Li, R A Hoskins, R F Galle,[...]. Science 2000
4

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
4

Tandemly repeated DNA families in the mouse genome.
Aleksey S Komissarov, Ekaterina V Gavrilova, Sergey Ju Demin, Alexander M Ishov, Olga I Podgornaya. BMC Genomics 2011
34
8

Subspecific origin and haplotype diversity in the laboratory mouse.
Hyuna Yang, Jeremy R Wang, John P Didion, Ryan J Buus, Timothy A Bell, Catherine E Welsh, François Bonhomme, Alex Hon-Tsen Yu, Michael W Nachman, Jaroslav Pialek,[...]. Nat Genet 2011
291
3

Differences between germline and somatic mutation rates in humans and mice.
Brandon Milholland, Xiao Dong, Lei Zhang, Xiaoxiao Hao, Yousin Suh, Jan Vijg. Nat Commun 2017
149
3

Ultraconserved Enhancers Are Required for Normal Development.
Diane E Dickel, Athena R Ypsilanti, Ramón Pla, Yiwen Zhu, Iros Barozzi, Brandon J Mannion, Yupar S Khin, Yoko Fukuda-Yuzawa, Ingrid Plajzer-Frick, Catherine S Pickle,[...]. Cell 2018
94
3

Enhancer redundancy provides phenotypic robustness in mammalian development.
Marco Osterwalder, Iros Barozzi, Virginie Tissières, Yoko Fukuda-Yuzawa, Brandon J Mannion, Sarah Y Afzal, Elizabeth A Lee, Yiwen Zhu, Ingrid Plajzer-Frick, Catherine S Pickle,[...]. Nature 2018
225
3

Functional evaluation of transposable elements as enhancers in mouse embryonic and trophoblast stem cells.
Christopher D Todd, Özgen Deniz, Darren Taylor, Miguel R Branco. Elife 2019
43
6

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
202
3

Capturing chromosome conformation.
Job Dekker, Karsten Rippe, Martijn Dekker, Nancy Kleckner. Science 2002
3


Enhancer evolution across 20 mammalian species.
Diego Villar, Camille Berthelot, Sarah Aldridge, Tim F Rayner, Margus Lukk, Miguel Pignatelli, Thomas J Park, Robert Deaville, Jonathan T Erichsen, Anna J Jasinska,[...]. Cell 2015
324
3

The accessible chromatin landscape of the human genome.
Robert E Thurman, Eric Rynes, Richard Humbert, Jeff Vierstra, Matthew T Maurano, Eric Haugen, Nathan C Sheffield, Andrew B Stergachis, Hao Wang, Benjamin Vernot,[...]. Nature 2012
3

Ultrafast and memory-efficient alignment of short DNA sequences to the human genome.
Ben Langmead, Cole Trapnell, Mihai Pop, Steven L Salzberg. Genome Biol 2009
3

deepTools2: a next generation web server for deep-sequencing data analysis.
Fidel Ramírez, Devon P Ryan, Björn Grüning, Vivek Bhardwaj, Fabian Kilpert, Andreas S Richter, Steffen Heyne, Friederike Dündar, Thomas Manke. Nucleic Acids Res 2016
3

KEGG: kyoto encyclopedia of genes and genomes.
M Kanehisa, S Goto. Nucleic Acids Res 2000
3


Evolutionarily conserved elements in vertebrate, insect, worm, and yeast genomes.
Adam Siepel, Gill Bejerano, Jakob S Pedersen, Angie S Hinrichs, Minmei Hou, Kate Rosenbloom, Hiram Clawson, John Spieth, Ladeana W Hillier, Stephen Richards,[...]. Genome Res 2005
3

Salmon provides fast and bias-aware quantification of transcript expression.
Rob Patro, Geet Duggal, Michael I Love, Rafael A Irizarry, Carl Kingsford. Nat Methods 2017
3

Major satellite repeat RNA stabilize heterochromatin retention of Suv39h enzymes by RNA-nucleosome association and RNA:DNA hybrid formation.
Oscar Velazquez Camacho, Carmen Galan, Kalina Swist-Rosowska, Reagan Ching, Michael Gamalinda, Fethullah Karabiber, Inti De La Rosa-Velazquez, Bettina Engist, Birgit Koschorz, Nicholas Shukeir,[...]. Elife 2017
70
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.