A citation-based method for searching scientific literature

Hannes P Eggertsson, Hakon Jonsson, Snaedis Kristmundsdottir, Eirikur Hjartarson, Birte Kehr, Gisli Masson, Florian Zink, Kristjan E Hjorleifsson, Aslaug Jonasdottir, Adalbjorg Jonasdottir, Ingileif Jonsdottir, Daniel F Gudbjartsson, Pall Melsted, Kari Stefansson, Bjarni V Halldorsson. Nat Genet 2017
Times Cited: 98







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



Times Cited
  Times     Co-cited
Similarity


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
162
38

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
35

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
28

Large-scale whole-genome sequencing of the Icelandic population.
Daniel F Gudbjartsson, Hannes Helgason, Sigurjon A Gudjonsson, Florian Zink, Asmundur Oddson, Arnaldur Gylfason, Soren Besenbacher, Gisli Magnusson, Bjarni V Halldorsson, Eirikur Hjartarson,[...]. Nat Genet 2015
444
24

Detection of sharing by descent, long-range phasing and haplotype imputation.
Augustine Kong, Gisli Masson, Michael L Frigge, Arnaldur Gylfason, Pasha Zusmanovich, Gudmar Thorleifsson, Pall I Olason, Andres Ingason, Stacy Steinberg, Thorunn Rafnar,[...]. Nat Genet 2008
301
23

Whole genome characterization of sequence diversity of 15,220 Icelanders.
Hákon Jónsson, Patrick Sulem, Birte Kehr, Snaedis Kristmundsdottir, Florian Zink, Eirikur Hjartarson, Marteinn T Hardarson, Kristjan E Hjorleifsson, Hannes P Eggertsson, Sigurjon Axel Gudjonsson,[...]. Sci Data 2017
69
33

Genome graphs and the evolution of genome inference.
Benedict Paten, Adam M Novak, Jordan M Eizenga, Erik Garrison. Genome Res 2017
129
21

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
21

Improved genome inference in the MHC using a population reference graph.
Alexander Dilthey, Charles Cox, Zamin Iqbal, Matthew R Nelson, Gil McVean. Nat Genet 2015
101
19


Fast and accurate genomic analyses using genome graphs.
Goran Rakocevic, Vladimir Semenyuk, Wan-Ping Lee, James Spencer, John Browning, Ivan J Johnson, Vladan Arsenijevic, Jelena Nadj, Kaushik Ghose, Maria C Suciu,[...]. Nat Genet 2019
82
23

Graph-based genome alignment and genotyping with HISAT2 and HISAT-genotype.
Daehwan Kim, Joseph M Paggi, Chanhee Park, Christopher Bennett, Steven L Salzberg. Nat Biotechnol 2019
18

GraphTyper2 enables population-scale genotyping of structural variation using pangenome graphs.
Hannes P Eggertsson, Snaedis Kristmundsdottir, Doruk Beyter, Hakon Jonsson, Astros Skuladottir, Marteinn T Hardarson, Daniel F Gudbjartsson, Kari Stefansson, Bjarni V Halldorsson, Pall Melsted. Nat Commun 2019
40
45

Paragraph: a graph-based structural variant genotyper for short-read sequence data.
Sai Chen, Peter Krusche, Egor Dolzhenko, Rachel M Sherman, Roman Petrovski, Felix Schlesinger, Melanie Kirsche, David R Bentley, Michael C Schatz, Fritz J Sedlazeck,[...]. Genome Biol 2019
52
32

A framework for variation discovery and genotyping using next-generation DNA sequencing data.
Mark A DePristo, Eric Banks, Ryan Poplin, Kiran V Garimella, Jared R Maguire, Christopher Hartl, Anthony A Philippakis, Guillermo del Angel, Manuel A Rivas, Matt Hanna,[...]. Nat Genet 2011
16

Weighting sequence variants based on their annotation increases power of whole-genome association studies.
Gardar Sveinbjornsson, Anders Albrechtsen, Florian Zink, Sigurjón A Gudjonsson, Asmundur Oddson, Gísli Másson, Hilma Holm, Augustine Kong, Unnur Thorsteinsdottir, Patrick Sulem,[...]. Nat Genet 2016
106
16

LD Score regression distinguishes confounding from polygenicity in genome-wide association studies.
Brendan K Bulik-Sullivan, Po-Ru Loh, Hilary K Finucane, Stephan Ripke, Jian Yang, Nick Patterson, Mark J Daly, Alkes L Price, Benjamin M Neale. Nat Genet 2015
16



FORGe: prioritizing variants for graph genomes.
Jacob Pritt, Nae-Chyun Chen, Ben Langmead. Genome Biol 2018
31
48

Genotyping structural variants in pangenome graphs using the vg toolkit.
Glenn Hickey, David Heller, Jean Monlong, Jonas A Sibbesen, Jouni Sirén, Jordan Eizenga, Eric T Dawson, Erik Garrison, Adam M Novak, Benedict Paten. Genome Biol 2020
65
23

Accurate genotyping across variant classes and lengths using variant graphs.
Jonas Andreas Sibbesen, Lasse Maretty, Anders Krogh. Nat Genet 2018
29
48

An integrated map of structural variation in 2,504 human genomes.
Peter H Sudmant, Tobias Rausch, Eugene J Gardner, Robert E Handsaker, Alexej Abyzov, John Huddleston, Yan Zhang, Kai Ye, Goo Jun, Markus Hsi-Yang Fritz,[...]. Nature 2015
13

Simultaneous alignment of short reads against multiple genomes.
Korbinian Schneeberger, Jörg Hagmann, Stephan Ossowski, Norman Warthmann, Sandra Gesing, Oliver Kohlbacher, Detlef Weigel. Genome Biol 2009
126
12

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
12

Fast gapped-read alignment with Bowtie 2.
Ben Langmead, Steven L Salzberg. Nat Methods 2012
12

Genome analysis of multiple pathogenic isolates of Streptococcus agalactiae: implications for the microbial "pan-genome".
Hervé Tettelin, Vega Masignani, Michael J Cieslewicz, Claudio Donati, Duccio Medini, Naomi L Ward, Samuel V Angiuoli, Jonathan Crabtree, Amanda L Jones, A Scott Durkin,[...]. Proc Natl Acad Sci U S A 2005
12

The design and construction of reference pangenome graphs with minigraph.
Heng Li, Xiaowen Feng, Chong Chu. Genome Biol 2020
71
16

De novo assembly and genotyping of variants using colored de Bruijn graphs.
Zamin Iqbal, Mario Caccamo, Isaac Turner, Paul Flicek, Gil McVean. Nat Genet 2012
312
11

Sequence variants from whole genome sequencing a large group of Icelanders.
Daniel F Gudbjartsson, Patrick Sulem, Hannes Helgason, Arnaldur Gylfason, Sigurjon A Gudjonsson, Florian Zink, Asmundur Oddson, Gisli Magnusson, Bjarni V Halldorsson, Eirikur Hjartarson,[...]. Sci Data 2015
47
23

Near-optimal probabilistic RNA-seq quantification.
Nicolas L Bray, Harold Pimentel, Páll Melsted, Lior Pachter. Nat Biotechnol 2016
11

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
11

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
11

Sequencing and de novo assembly of 150 genomes from Denmark as a population reference.
Lasse Maretty, Jacob Malte Jensen, Bent Petersen, Jonas Andreas Sibbesen, Siyang Liu, Palle Villesen, Laurits Skov, Kirstine Belling, Christian Theil Have, Jose M G Izarzugaza,[...]. Nature 2017
71
14


Indexing Graphs for Path Queries with Applications in Genome Research.
Jouni Sirén, Niko Välimäki, Veli Mäkinen. IEEE/ACM Trans Comput Biol Bioinform 2014
106
10

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
339
10

Nanopore sequencing and assembly of a human genome with ultra-long reads.
Miten Jain, Sergey Koren, Karen H Miga, Josh Quick, Arthur C Rand, Thomas A Sasani, John R Tyson, Andrew D Beggs, Alexander T Dilthey, Ian T Fiddes,[...]. Nat Biotechnol 2018
780
10

Characterizing the Major Structural Variant Alleles of the Human Genome.
Peter A Audano, Arvis Sulovari, Tina A Graves-Lindsay, Stuart Cantsilieris, Melanie Sorensen, AnneMarie E Welch, Max L Dougherty, Bradley J Nelson, Ankeeta Shah, Susan K Dutcher,[...]. Cell 2019
194
10

Haplotype-aware graph indexes.
Jouni Sirén, Erik Garrison, Adam M Novak, Benedict Paten, Richard Durbin. Bioinformatics 2020
29
34

Manta: rapid detection of structural variants and indels for germline and cancer sequencing applications.
Xiaoyu Chen, Ole Schulz-Trieglaff, Richard Shaw, Bret Barnes, Felix Schlesinger, Morten Källberg, Anthony J Cox, Semyon Kruglyak, Christopher T Saunders. Bioinformatics 2016
715
9

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
9

PLINK: a tool set for whole-genome association and population-based linkage analyses.
Shaun Purcell, Benjamin Neale, Kathe Todd-Brown, Lori Thomas, Manuel A R Ferreira, David Bender, Julian Maller, Pamela Sklar, Paul I W de Bakker, Mark J Daly,[...]. Am J Hum Genet 2007
9

Resolving the complexity of the human genome using single-molecule sequencing.
Mark J P Chaisson, John Huddleston, Megan Y Dennis, Peter H Sudmant, Maika Malig, Fereydoun Hormozdiari, Francesca Antonacci, Urvashi Surti, Richard Sandstrom, Matthew Boitano,[...]. Nature 2015
433
9

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
9

A structural variation reference for medical and population genetics.
Ryan L Collins, Harrison Brand, Konrad J Karczewski, Xuefang Zhao, Jessica Alföldi, Laurent C Francioli, Amit V Khera, Chelsea Lowther, Laura D Gauthier, Harold Wang,[...]. Nature 2020
251
9

The impact of structural variation on human gene expression.
Colby Chiang, Alexandra J Scott, Joe R Davis, Emily K Tsang, Xin Li, Yungil Kim, Tarik Hadzic, Farhan N Damani, Liron Ganel, Stephen B Montgomery,[...]. Nat Genet 2017
162
8

Short read alignment with populations of genomes.
Lin Huang, Victoria Popic, Serafim Batzoglou. Bioinformatics 2013
45
17

Canu: scalable and accurate long-read assembly via adaptive k-mer weighting and repeat separation.
Sergey Koren, Brian P Walenz, Konstantin Berlin, Jason R Miller, Nicholas H Bergman, Adam M Phillippy. Genome Res 2017
8

The pangenome of an agronomically important crop plant Brassica oleracea.
Agnieszka A Golicz, Philipp E Bayer, Guy C Barker, Patrick P Edger, HyeRan Kim, Paula A Martinez, Chon Kit Kenneth Chan, Anita Severn-Ellis, W Richard McCombie, Isobel A P Parkin,[...]. Nat Commun 2016
185
8


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.