A citation-based method for searching scientific literature

Andrea Guarracino, Simon Heumos, Sven Nahnsen, Pjotr Prins, Erik Garrison. Bioinformatics 2022
Times Cited: 4







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



Times Cited
  Times     Co-cited
Similarity


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
120
50

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
85
50

Variation graph toolkit improves read mapping by representing genetic variation in the reference.
Erik Garrison, Jouni Sirén, Adam M Novak, Glenn Hickey, Jordan M Eizenga, Eric T Dawson, William Jones, Shilpa Garg, Charles Markello, Michael F Lin,[...]. Nat Biotechnol 2018
154
50

Pangenome Graphs.
Jordan M Eizenga, Adam M Novak, Jonas A Sibbesen, Simon Heumos, Ali Ghaffaari, Glenn Hickey, Xian Chang, Josiah D Seaman, Robin Rounthwaite, Jana Ebler,[...]. Annu Rev Genomics Hum Genet 2020
27
50

Pan-genomics in the human genome era.
Rachel M Sherman, Steven L Salzberg. Nat Rev Genet 2020
74
50

Ribbon: intuitive visualization for complex genomic variation.
Maria Nattestad, Robert Aboukhalil, Chen-Shan Chin, Michael C Schatz. Bioinformatics 2021
18
25

Two Reference-Quality Sea Snake Genomes Reveal Their Divergent Evolution of Adaptive Traits and Venom Systems.
An Li, Junjie Wang, Kuo Sun, Shuocun Wang, Xin Zhao, Tingfang Wang, Liyan Xiong, Weiheng Xu, Lei Qiu, Yan Shang,[...]. Mol Biol Evol 2021
5
25




SyRI: finding genomic rearrangements and local sequence differences from whole-genome assemblies.
Manish Goel, Hequan Sun, Wen-Biao Jiao, Korbinian Schneeberger. Genome Biol 2019
62
25

De novo assembly of haplotype-resolved genomes with trio binning.
Sergey Koren, Arang Rhie, Brian P Walenz, Alexander T Dilthey, Derek M Bickhart, Sarah B Kingan, Stefan Hiendleder, John L Williams, Timothy P L Smith, Adam M Phillippy. Nat Biotechnol 2018
149
25

Versatile and open software for comparing large genomes.
Stefan Kurtz, Adam Phillippy, Arthur L Delcher, Michael Smoot, Martin Shumway, Corina Antonescu, Steven L Salzberg. Genome Biol 2004
25

Gamete binning: chromosome-level and haplotype-resolved genome assembly enabled by high-throughput single-cell sequencing of gamete genomes.
José A Campoy, Hequan Sun, Manish Goel, Wen-Biao Jiao, Kat Folz-Donahue, Nan Wang, Manuel Rubio, Chang Liu, Christian Kukat, David Ruiz,[...]. Genome Biol 2020
17
25

genozip: a fast and efficient compression tool for VCF files.
Divon Lan, Raymond Tobler, Yassine Souilmi, Bastien Llamas. Bioinformatics 2020
5
25

Bioconda: sustainable and comprehensive software distribution for the life sciences.
Björn Grüning, Ryan Dale, Andreas Sjödin, Brad A Chapman, Jillian Rowe, Christopher H Tomkins-Tinch, Renan Valieris, Johannes Köster. Nat Methods 2018
340
25

Scalable Workflows and Reproducible Data Analysis for Genomics.
Francesco Strozzi, Roel Janssen, Ricardo Wurmus, Michael R Crusoe, George Githinji, Paolo Di Tommaso, Dominique Belhachemi, Steffen Möller, Geert Smant, Joep de Ligt,[...]. Methods Mol Biol 2019
12
25


The Bioperl toolkit: Perl modules for the life sciences.
Jason E Stajich, David Block, Kris Boulez, Steven E Brenner, Stephen A Chervitz, Chris Dagdigian, Georg Fuellen, James G R Gilbert, Ian Korf, Hilmar Lapp,[...]. Genome Res 2002
25

A Bayesian approach to inferring population structure from dominant markers.
Kent E Holsinger, Paul O Lewis, Dipak K Dey. Mol Ecol 2002
200
25

Superbubbles, Ultrabubbles, and Cacti.
Benedict Paten, Jordan M Eizenga, Yohei M Rosen, Adam M Novak, Erik Garrison, Glenn Hickey. J Comput Biol 2018
22
25

BioRuby: bioinformatics software for the Ruby programming language.
Naohisa Goto, Pjotr Prins, Mitsuteru Nakao, Raoul Bonnal, Jan Aerts, Toshiaki Katayama. Bioinformatics 2010
109
25

Biopython: freely available Python tools for computational molecular biology and bioinformatics.
Peter J A Cock, Tiago Antao, Jeffrey T Chang, Brad A Chapman, Cymon J Cox, Andrew Dalke, Iddo Friedberg, Thomas Hamelryck, Frank Kauff, Bartek Wilczynski,[...]. Bioinformatics 2009
25

vcfr: a package to manipulate and visualize variant call format data in R.
Brian J Knaus, Niklaus J Grünwald. Mol Ecol Resour 2017
251
25


ESTIMATION OF GENE FLOW FROM F-STATISTICS.
C Clark Cockerham, B S Weir. Evolution 1993
152
25

Genome graphs and the evolution of genome inference.
Benedict Paten, Adam M Novak, Jordan M Eizenga, Erik Garrison. Genome Res 2017
126
25

cyvcf2: fast, flexible variant analysis with Python.
Brent S Pedersen, Aaron R Quinlan. Bioinformatics 2017
24
25

Vcfanno: fast, flexible annotation of genetic variants.
Brent S Pedersen, Ryan M Layer, Aaron R Quinlan. Genome Biol 2016
84
25

BioJava: an open-source framework for bioinformatics.
R C G Holland, T A Down, M Pocock, A Prlić, D Huen, K James, S Foisy, A Dräger, A Yates, M Heuer,[...]. Bioinformatics 2008
123
25

Twelve years of SAMtools and BCFtools.
Petr Danecek, James K Bonfield, Jennifer Liddle, John Marshall, Valeriu Ohan, Martin O Pollard, Andrew Whitwham, Thomas Keane, Shane A McCarthy, Robert M Davies,[...]. Gigascience 2021
611
25

The variant call format and VCFtools.
Petr Danecek, Adam Auton, Goncalo Abecasis, Cornelis A Albers, Eric Banks, Mark A DePristo, Robert E Handsaker, Gerton Lunter, Gabor T Marth, Stephen T Sherry,[...]. Bioinformatics 2011
25

Effective variant filtering and expected candidate variant yield in studies of rare human disease.
Brent S Pedersen, Joe M Brown, Harriet Dashnow, Amelia D Wallace, Matt Velinder, Martin Tristani-Firouzi, Joshua D Schiffman, Tatiana Tvrdik, Rong Mao, D Hunter Best,[...]. NPJ Genom Med 2021
12
25

Genome-wide detection and characterization of positive selection in human populations.
Pardis C Sabeti, Patrick Varilly, Ben Fry, Jason Lohmueller, Elizabeth Hostetter, Chris Cotsapas, Xiaohui Xie, Elizabeth H Byrne, Steven A McCarroll, Rachelle Gaudet,[...]. Nature 2007
25

HTSlib: C library for reading/writing high-throughput sequencing data.
James K Bonfield, John Marshall, Petr Danecek, Heng Li, Valeriu Ohan, Andrew Whitwham, Thomas Keane, Robert M Davies. Gigascience 2021
38
25


Unified representation of genetic variants.
Adrian Tan, Gonçalo R Abecasis, Hyun Min Kang. Bioinformatics 2015
198
25

The FAIR Guiding Principles for scientific data management and stewardship.
Mark D Wilkinson, Michel Dumontier, I Jsbrand Jan Aalbersberg, Gabrielle Appleton, Myles Axton, Arie Baak, Niklas Blomberg, Jan-Willem Boiten, Luiz Bonino da Silva Santos, Philip E Bourne,[...]. Sci Data 2016
25

Sparse Project VCF: efficient encoding of population genotype matrices.
Michael F Lin, Xiaodong Bai, William J Salerno, Jeffrey G Reid. Bioinformatics 2021
3
33

hts-nim: scripting high-performance genomic analyses.
Brent S Pedersen, Aaron R Quinlan. Bioinformatics 2018
9
25

Toward effective software solutions for big biology.
Pjotr Prins, Joep de Ligt, Artem Tarasov, Ritsert C Jansen, Edwin Cuppen, Philip E Bourne. Nat Biotechnol 2015
19
25

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
25

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
25

Methods and Developments in Graphical Pangenomics.
Joseph Outten, Andrew Warren. J Indian Inst Sci 2021
1
100

svviz: a read viewer for validating structural variants.
Noah Spies, Justin M Zook, Marc Salit, Arend Sidow. Bioinformatics 2015
26
25

Searching thousands of genomes to classify somatic and novel structural variants using STIX.
Murad Chowdhury, Brent S Pedersen, Fritz J Sedlazeck, Aaron R Quinlan, Ryan M Layer. Nat Methods 2022
1
100

Graphtyper enables population-scale genotyping using pangenome graphs.
Hannes P Eggertsson, Hakon Jonsson, Snaedis Kristmundsdottir, Eirikur Hjartarson, Birte Kehr, Gisli Masson, Florian Zink, Kristjan E Hjorleifsson, Aslaug Jonasdottir, Adalbjorg Jonasdottir,[...]. Nat Genet 2017
94
25

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
177
25

DELLY: structural variant discovery by integrated paired-end and split-read analysis.
Tobias Rausch, Thomas Zichner, Andreas Schlattl, Adrian M Stütz, Vladimir Benes, Jan O Korbel. Bioinformatics 2012
989
25



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.