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: 7889







List of co-cited articles
364 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
54

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
223
8

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
7


Hallmarks of cancer: the next generation.
Douglas Hanahan, Robert A Weinberg. Cell 2011
6


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
6

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
6

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
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


Long-read human genome sequencing and its applications.
Glennis A Logsdon, Mitchell R Vollger, Evan E Eichler. Nat Rev Genet 2020
129
5

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
116
5

Haplotype-resolved diverse human genomes and integrated analysis of structural variation.
Peter Ebert, Peter A Audano, Qihui Zhu, Bernardo Rodriguez-Martin, David Porubsky, Marc Jan Bonder, Arvis Sulovari, Jana Ebler, Weichen Zhou, Rebecca Serra Mari,[...]. Science 2021
81
6

The structure, function and evolution of a complete human chromosome 8.
Glennis A Logsdon, Mitchell R Vollger, PingHsun Hsieh, Yafei Mao, Mikhail A Liskovykh, Sergey Koren, Sergey Nurk, Ludovica Mercuri, Philip C Dishuck, Arang Rhie,[...]. Nature 2021
57
8


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
5

Expanded encyclopaedias of DNA elements in the human and mouse genomes.
Jill E Moore, Michael J Purcaro, Henry E Pratt, Charles B Epstein, Noam Shoresh, Jessika Adrian, Trupti Kawli, Carrie A Davis, Alexander Dobin, Rajinder Kaul,[...]. Nature 2020
299
5

The UK Biobank resource with deep phenotyping and genomic data.
Clare Bycroft, Colin Freeman, Desislava Petkova, Gavin Band, Lloyd T Elliott, Kevin Sharp, Allan Motyer, Damjan Vukcevic, Olivier Delaneau, Jared O'Connell,[...]. Nature 2018
5

A micropeptide encoded by a putative long noncoding RNA regulates muscle performance.
Douglas M Anderson, Kelly M Anderson, Chi-Lun Chang, Catherine A Makarewich, Benjamin R Nelson, John R McAnally, Prasad Kasaragod, John M Shelton, Jen Liou, Rhonda Bassel-Duby,[...]. Cell 2015
631
4

STRING v11: protein-protein association networks with increased coverage, supporting functional discovery in genome-wide experimental datasets.
Damian Szklarczyk, Annika L Gable, David Lyon, Alexander Junge, Stefan Wyder, Jaime Huerta-Cepas, Milan Simonovic, Nadezhda T Doncheva, John H Morris, Peer Bork,[...]. Nucleic Acids Res 2019
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

Reference sequence (RefSeq) database at NCBI: current status, taxonomic expansion, and functional annotation.
Nuala A O'Leary, Mathew W Wright, J Rodney Brister, Stacy Ciufo, Diana Haddad, Rich McVeigh, Bhanu Rajput, Barbara Robbertse, Brian Smith-White, Danso Ako-Adjei,[...]. Nucleic Acids Res 2016
4

Chromatin signature reveals over a thousand highly conserved large non-coding RNAs in mammals.
Mitchell Guttman, Ido Amit, Manuel Garber, Courtney French, Michael F Lin, David Feldser, Maite Huarte, Or Zuk, Bryce W Carey, John P Cassady,[...]. Nature 2009
4

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
118
4

Single-cell template strand sequencing by Strand-seq enables the characterization of individual homologs.
Ashley D Sanders, Ester Falconer, Mark Hills, Diana C J Spierings, Peter M Lansdorp. Nat Protoc 2017
42
9

The Simons Genome Diversity Project: 300 genomes from 142 diverse populations.
Swapan Mallick, Heng Li, Mark Lipson, Iain Mathieson, Melissa Gymrek, Fernando Racimo, Mengyao Zhao, Niru Chennagiri, Susanne Nordenfelt, Arti Tandon,[...]. Nature 2016
555
4

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
278
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
276
4

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
4

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

DNA sequencing with chain-terminating inhibitors.
F Sanger, S Nicklen, A R Coulson. Proc Natl Acad Sci U S A 1977
4


The druggable genome.
Andrew L Hopkins, Colin R Groom. Nat Rev Drug Discov 2002
4

Towards complete and error-free genome assemblies of all vertebrate species.
Arang Rhie, Shane A McCarthy, Olivier Fedrigo, Joana Damas, Giulio Formenti, Sergey Koren, Marcela Uliano-Silva, William Chow, Arkarachai Fungtammasan, Juwan Kim,[...]. Nature 2021
126
4

HiCanu: accurate assembly of segmental duplications, satellites, and allelic variants from high-fidelity long reads.
Sergey Nurk, Brian P Walenz, Arang Rhie, Mitchell R Vollger, Glennis A Logsdon, Robert Grothe, Karen H Miga, Evan E Eichler, Adam M Phillippy, Sergey Koren. Genome Res 2020
98
4

GENCODE reference annotation for the human and mouse genomes.
Adam Frankish, Mark Diekhans, Anne-Maud Ferreira, Rory Johnson, Irwin Jungreis, Jane Loveland, Jonathan M Mudge, Cristina Sisu, James Wright, Joel Armstrong,[...]. Nucleic Acids Res 2019
989
4

HISAT: a fast spliced aligner with low memory requirements.
Daehwan Kim, Ben Langmead, Steven L Salzberg. Nat Methods 2015
3

Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2.
Michael I Love, Wolfgang Huber, Simon Anders. Genome Biol 2014
3


Localization and abundance analysis of human lncRNAs at single-cell and single-molecule resolution.
Moran N Cabili, Margaret C Dunagin, Patrick D McClanahan, Andrew Biaesch, Olivia Padovan-Merhar, Aviv Regev, John L Rinn, Arjun Raj. Genome Biol 2015
369
3

The Translational Landscape of the Human Heart.
Sebastiaan van Heesch, Franziska Witte, Valentin Schneider-Lunitz, Jana F Schulz, Eleonora Adami, Allison B Faber, Marieluise Kirchner, Henrike Maatz, Susanne Blachut, Clara-Louisa Sandmann,[...]. Cell 2019
198
3

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
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
52
5

Liftoff: accurate mapping of gene annotations.
Alaina Shumate, Steven L Salzberg. Bioinformatics 2020
33
9

Weighted minimizer sampling improves long read mapping.
Chirag Jain, Arang Rhie, Haowen Zhang, Claudia Chu, Brian P Walenz, Sergey Koren, Adam M Phillippy. Bioinformatics 2020
28
10

Detecting DNA cytosine methylation using nanopore sequencing.
Jared T Simpson, Rachael E Workman, P C Zuzarte, Matei David, L J Dursi, Winston Timp. Nat Methods 2017
332
3

Characterizing polymorphic inversions in human genomes by single-cell sequencing.
Ashley D Sanders, Mark Hills, David Porubský, Victor Guryev, Ester Falconer, Peter M Lansdorp. Genome Res 2016
40
7

Merqury: reference-free quality, completeness, and phasing assessment for genome assemblies.
Arang Rhie, Brian P Walenz, Sergey Koren, Adam M Phillippy. Genome Biol 2020
76
3

Fully phased human genome assembly without parental data using single-cell strand sequencing and long reads.
David Porubsky, Peter Ebert, Peter A Audano, Mitchell R Vollger, William T Harvey, Pierre Marijon, Jana Ebler, Katherine M Munson, Melanie Sorensen, Arvis Sulovari,[...]. Nat Biotechnol 2021
30
10


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.