A citation-based method for searching scientific literature

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, J D Gocayne, P Amanatides, R M Ballew, D H Huson, J R Wortman, Q Zhang, C D Kodira, X H Zheng, L Chen, M Skupski, G Subramanian, P D Thomas, J Zhang, G L Gabor Miklos, C Nelson, S Broder, A G Clark, J Nadeau, V A McKusick, N Zinder, A J Levine, R J Roberts, M Simon, C Slayman, M Hunkapiller, R Bolanos, A Delcher, I Dew, D Fasulo, M Flanigan, L Florea, A Halpern, S Hannenhalli, S Kravitz, S Levy, C Mobarry, K Reinert, K Remington, J Abu-Threideh, E Beasley, K Biddick, V Bonazzi, R Brandon, M Cargill, I Chandramouliswaran, R Charlab, K Chaturvedi, Z Deng, V Di Francesco, P Dunn, K Eilbeck, C Evangelista, A E Gabrielian, W Gan, W Ge, F Gong, Z Gu, P Guan, T J Heiman, M E Higgins, R R Ji, Z Ke, K A Ketchum, Z Lai, Y Lei, Z Li, J Li, Y Liang, X Lin, F Lu, G V Merkulov, N Milshina, H M Moore, A K Naik, V A Narayan, B Neelam, D Nusskern, D B Rusch, S Salzberg, W Shao, B Shue, J Sun, Z Wang, A Wang, X Wang, J Wang, M Wei, R Wides, C Xiao, C Yan, A Yao, J Ye, M Zhan, W Zhang, H Zhang, Q Zhao, L Zheng, F Zhong, W Zhong, S Zhu, S Zhao, D Gilbert, S Baumhueter, G Spier, C Carter, A Cravchik, T Woodage, F Ali, H An, A Awe, D Baldwin, H Baden, M Barnstead, I Barrow, K Beeson, D Busam, A Carver, A Center, M L Cheng, L Curry, S Danaher, L Davenport, R Desilets, S Dietz, K Dodson, L Doup, S Ferriera, N Garg, A Gluecksmann, B Hart, J Haynes, C Haynes, C Heiner, S Hladun, D Hostin, J Houck, T Howland, C Ibegwam, J Johnson, F Kalush, L Kline, S Koduru, A Love, F Mann, D May, S McCawley, T McIntosh, I McMullen, M Moy, L Moy, B Murphy, K Nelson, C Pfannkoch, E Pratts, V Puri, H Qureshi, M Reardon, R Rodriguez, Y H Rogers, D Romblad, B Ruhfel, R Scott, C Sitter, M Smallwood, E Stewart, R Strong, E Suh, R Thomas, N N Tint, S Tse, C Vech, G Wang, J Wetter, S Williams, M Williams, S Windsor, E Winn-Deen, K Wolfe, J Zaveri, K Zaveri, J F Abril, R Guigó, M J Campbell, K V Sjolander, B Karlak, A Kejariwal, H Mi, B Lazareva, T Hatton, A Narechania, K Diemer, A Muruganujan, N Guo, S Sato, V Bafna, S Istrail, R Lippert, R Schwartz, B Walenz, S Yooseph, D Allen, A Basu, J Baxendale, L Blick, M Caminha, J Carnes-Stine, P Caulk, Y H Chiang, M Coyne, C Dahlke, A Mays, M Dombroski, M Donnelly, D Ely, S Esparham, C Fosler, H Gire, S Glanowski, K Glasser, A Glodek, M Gorokhov, K Graham, B Gropman, M Harris, J Heil, S Henderson, J Hoover, D Jennings, C Jordan, J Jordan, J Kasha, L Kagan, C Kraft, A Levitsky, M Lewis, X Liu, J Lopez, D Ma, W Majoros, J McDaniel, S Murphy, M Newman, T Nguyen, N Nguyen, M Nodell, S Pan, J Peck, M Peterson, W Rowe, R Sanders, J Scott, M Simpson, T Smith, A Sprague, T Stockwell, R Turner, E Venter, M Wang, M Wen, D Wu, M Wu, A Xia, A Zandieh, X Zhu. Science 2001
Times Cited: 7744







List of co-cited articles
300 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
42

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
5


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
5


Basic local alignment search tool.
S F Altschul, W Gish, W Miller, E W Myers, D J Lipman. J Mol Biol 1990
4

Pilon: an integrated tool for comprehensive microbial variant detection and genome assembly improvement.
Bruce J Walker, Thomas Abeel, Terrance Shea, Margaret Priest, Amr Abouelliel, Sharadha Sakthikumar, Christina A Cuomo, Qiandong Zeng, Jennifer Wortman, Sarah K Young,[...]. PLoS One 2014
4

Evaluation of GRCh38 and de novo haploid genome assemblies demonstrates the enduring quality of the reference assembly.
Valerie A Schneider, Tina Graves-Lindsay, Kerstin Howe, Nathan Bouk, Hsiu-Chuan Chen, Paul A Kitts, Terence D Murphy, Kim D Pruitt, Françoise Thibaud-Nissen, Derek Albracht,[...]. Genome Res 2017
218
4

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

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
4

Integrated Proteogenomic Characterization of Human High-Grade Serous Ovarian Cancer.
Hui Zhang, Tao Liu, Zhen Zhang, Samuel H Payne, Bai Zhang, Jason E McDermott, Jian-Ying Zhou, Vladislav A Petyuk, Li Chen, Debjit Ray,[...]. Cell 2016
419
4

Standards and guidelines for the interpretation of sequence variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology.
Sue Richards, Nazneen Aziz, Sherri Bale, David Bick, Soma Das, Julie Gastier-Foster, Wayne W Grody, Madhuri Hegde, Elaine Lyon, Elaine Spector,[...]. Genet Med 2015
4

Gapped BLAST and PSI-BLAST: a new generation of protein database search programs.
S F Altschul, T L Madden, A A Schäffer, J Zhang, Z Zhang, W Miller, D J Lipman. Nucleic Acids Res 1997
4

DNA sequencing with chain-terminating inhibitors.
F Sanger, S Nicklen, A R Coulson. Proc Natl Acad Sci U S A 1977
3

BLAT--the BLAST-like alignment tool.
W James Kent. Genome Res 2002
3

Genome-wide polygenic scores for common diseases identify individuals with risk equivalent to monogenic mutations.
Amit V Khera, Mark Chaffin, Krishna G Aragam, Mary E Haas, Carolina Roselli, Seung Hoan Choi, Pradeep Natarajan, Eric S Lander, Steven A Lubitz, Patrick T Ellinor,[...]. Nat Genet 2018
744
3

Global cancer statistics 2018: GLOBOCAN estimates of incidence and mortality worldwide for 36 cancers in 185 countries.
Freddie Bray, Jacques Ferlay, Isabelle Soerjomataram, Rebecca L Siegel, Lindsey A Torre, Ahmedin Jemal. CA Cancer J Clin 2018
3


Insights into human genetic variation and population history from 929 diverse genomes.
Anders Bergström, Shane A McCarthy, Ruoyun Hui, Mohamed A Almarri, Qasim Ayub, Petr Danecek, Yuan Chen, Sabine Felkel, Pille Hallast, Jack Kamm,[...]. Science 2020
78
3

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
3

Genome sequence, comparative analysis and haplotype structure of the domestic dog.
Kerstin Lindblad-Toh, Claire M Wade, Tarjei S Mikkelsen, Elinor K Karlsson, David B Jaffe, Michael Kamal, Michele Clamp, Jean L Chang, Edward J Kulbokas, Michael C Zody,[...]. Nature 2005
3

Proteogenomic Characterization Reveals Therapeutic Vulnerabilities in Lung Adenocarcinoma.
Michael A Gillette, Shankha Satpathy, Song Cao, Saravana M Dhanasekaran, Suhas V Vasaikar, Karsten Krug, Francesca Petralia, Yize Li, Wen-Wei Liang, Boris Reva,[...]. Cell 2020
57
5

The Cancer Genome Atlas: Creating Lasting Value beyond Its Data.
Carolyn Hutter, Jean Claude Zenklusen. Cell 2018
169
3

Proteogenomics connects somatic mutations to signalling in breast cancer.
Philipp Mertins, D R Mani, Kelly V Ruggles, Michael A Gillette, Karl R Clauser, Pei Wang, Xianlong Wang, Jana W Qiao, Song Cao, Francesca Petralia,[...]. Nature 2016
719
3

Linear assembly of a human centromere on the Y chromosome.
Miten Jain, Hugh E Olsen, Daniel J Turner, David Stoddart, Kira V Bulazel, Benedict Paten, David Haussler, Huntington F Willard, Mark Akeson, Karen H Miga. Nat Biotechnol 2018
101
3

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
116
3


A whole-genome assembly of Drosophila.
E W Myers, G G Sutton, A L Delcher, I M Dew, D P Fasulo, M J Flanigan, S A Kravitz, C M Mobarry, K H Reinert, K A Remington,[...]. Science 2000
930
3

A new initiative on precision medicine.
Francis S Collins, Harold Varmus. N Engl J Med 2015
3

The Cancer Genome Atlas Pan-Cancer analysis project.
John N Weinstein, Eric A Collisson, Gordon B Mills, Kenna R Mills Shaw, Brad A Ozenberger, Kyle Ellrott, Ilya Shmulevich, Chris Sander, Joshua M Stuart. Nat Genet 2013
3

Cancer statistics, 2020.
Rebecca L Siegel, Kimberly D Miller, Ahmedin Jemal. CA Cancer J Clin 2020
3

Genome-wide association studies for common diseases and complex traits.
Joel N Hirschhorn, Mark J Daly. Nat Rev Genet 2005
3

Hallmarks of cancer: the next generation.
Douglas Hanahan, Robert A Weinberg. Cell 2011
3

The sequence of sequencers: The history of sequencing DNA.
James M Heather, Benjamin Chain. Genomics 2016
249
3

Coming of age: ten years of next-generation sequencing technologies.
Sara Goodwin, John D McPherson, W Richard McCombie. Nat Rev Genet 2016
3

Human Artificial Chromosomes that Bypass Centromeric DNA.
Glennis A Logsdon, Craig W Gambogi, Mikhail A Liskovykh, Evelyne J Barrey, Vladimir Larionov, Karen H Miga, Patrick Heun, Ben E Black. Cell 2019
42
7


Critical assessment of methods of protein structure prediction (CASP)-Round XIII.
Andriy Kryshtafovych, Torsten Schwede, Maya Topf, Krzysztof Fidelis, John Moult. Proteins 2019
117
3

Improved protein structure prediction using predicted interresidue orientations.
Jianyi Yang, Ivan Anishchenko, Hahnbeom Park, Zhenling Peng, Sergey Ovchinnikov, David Baker. Proc Natl Acad Sci U S A 2020
171
3

Trends in GPCR drug discovery: new agents, targets and indications.
Alexander S Hauser, Misty M Attwood, Mathias Rask-Andersen, Helgi B Schiöth, David E Gloriam. Nat Rev Drug Discov 2017
757
3

The G-protein-coupled receptors in the human genome form five main families. Phylogenetic analysis, paralogon groups, and fingerprints.
Robert Fredriksson, Malin C Lagerström, Lars-Gustav Lundin, Helgi B Schiöth. Mol Pharmacol 2003
3

The Protein Data Bank.
H M Berman, J Westbrook, Z Feng, G Gilliland, T N Bhat, H Weissig, I N Shindyalov, P E Bourne. Nucleic Acids Res 2000
3

FastQ Screen: A tool for multi-genome mapping and quality control.
Steven W Wingett, Simon Andrews. F1000Res 2018
257
2

Whole-genome random sequencing and assembly of Haemophilus influenzae Rd.
R D Fleischmann, M D Adams, O White, R A Clayton, E F Kirkness, A R Kerlavage, C J Bult, J F Tomb, B A Dougherty, J M Merrick. Science 1995
2



Using RepeatMasker to identify repetitive elements in genomic sequences.
Maja Tarailo-Graovac, Nansheng Chen. Curr Protoc Bioinformatics 2009
620
2

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
577
2


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.