A citation-based method for searching scientific literature

Sai Chen, Peter Krusche, Egor Dolzhenko, Rachel M Sherman, Roman Petrovski, Felix Schlesinger, Melanie Kirsche, David R Bentley, Michael C Schatz, Fritz J Sedlazeck, Michael A Eberle. Genome Biol 2019
Times Cited: 34







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



Times Cited
  Times     Co-cited
Similarity


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
247
52


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
153
50

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
37
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
120
44

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
999
44

Accurate detection of complex structural variations using single-molecule sequencing.
Fritz J Sedlazeck, Philipp Rescheneder, Moritz Smolka, Han Fang, Maria Nattestad, Arndt von Haeseler, Michael C Schatz. Nat Methods 2018
390
41

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
67
35

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
73
32

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
861
32

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
24
45

A robust benchmark for detection of germline large deletions and insertions.
Justin M Zook, Nancy F Hansen, Nathan D Olson, Lesley Chapman, James C Mullikin, Chunlin Xiao, Stephen Sherry, Sergey Koren, Adam M Phillippy, Paul C Boutros,[...]. Nat Biotechnol 2020
55
32

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
29

Genome graphs and the evolution of genome inference.
Benedict Paten, Adam M Novak, Jordan M Eizenga, Erik Garrison. Genome Res 2017
110
29

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
528
26

Transient structural variations have strong effects on quantitative traits and reproductive isolation in fission yeast.
Daniel C Jeffares, Clemency Jolly, Mimoza Hoti, Doug Speed, Liam Shaw, Charalampos Rallis, Francois Balloux, Christophe Dessimoz, Jürg Bähler, Fritz J Sedlazeck. Nat Commun 2017
134
26

LUMPY: a probabilistic framework for structural variant discovery.
Ryan M Layer, Colby Chiang, Aaron R Quinlan, Ira M Hall. Genome Biol 2014
582
26

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
26

Discovery and genotyping of structural variation from long-read haploid genome sequence data.
John Huddleston, Mark J P Chaisson, Karyn Meltz Steinberg, Wes Warren, Kendra Hoekzema, David Gordon, Tina A Graves-Lindsay, Katherine M Munson, Zev N Kronenberg, Laura Vives,[...]. Genome Res 2017
159
26

Accurate genotyping across variant classes and lengths using variant graphs.
Jonas Andreas Sibbesen, Lasse Maretty, Anders Krogh. Nat Genet 2018
19
47


Accurate circular consensus long-read sequencing improves variant detection and assembly of a human genome.
Aaron M Wenger, Paul Peluso, William J Rowell, Pi-Chuan Chang, Richard J Hall, Gregory T Concepcion, Jana Ebler, Arkarachai Fungtammasan, Alexey Kolesnikov, Nathan D Olson,[...]. Nat Biotechnol 2019
269
26

Structural variant calling: the long and the short of it.
Medhat Mahmoud, Nastassia Gobet, Diana Ivette Cruz-Dávalos, Ninon Mounier, Christophe Dessimoz, Fritz J Sedlazeck. Genome Biol 2019
78
26

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
125
23

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
393
23

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
242
20


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
657
20

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
252
20

Pan-genomics in the human genome era.
Rachel M Sherman, Steven L Salzberg. Nat Rev Genet 2020
44
20

Assembly of a pan-genome from deep sequencing of 910 humans of African descent.
Rachel M Sherman, Juliet Forman, Valentin Antonescu, Daniela Puiu, Michelle Daya, Nicholas Rafaels, Meher Preethi Boorgula, Sameer Chavan, Candelaria Vergara, Victor E Ortega,[...]. Nat Genet 2019
115
20

De novo assembly and phasing of a Korean human genome.
Jeong-Sun Seo, Arang Rhie, Junsoo Kim, Sangjin Lee, Min-Hwan Sohn, Chang-Uk Kim, Alex Hastie, Han Cao, Ji-Young Yun, Jihye Kim,[...]. Nature 2016
176
17

SpeedSeq: ultra-fast personal genome analysis and interpretation.
Colby Chiang, Ryan M Layer, Gregory G Faust, Michael R Lindberg, David B Rose, Erik P Garrison, Gabor T Marth, Aaron R Quinlan, Ira M Hall. Nat Methods 2015
218
17

A synthetic-diploid benchmark for accurate variant-calling evaluation.
Heng Li, Jonathan M Bloom, Yossi Farjoun, Mark Fleharty, Laura Gauthier, Benjamin Neale, Daniel MacArthur. Nat Methods 2018
44
17

Mapping and phasing of structural variation in patient genomes using nanopore sequencing.
Mircea Cretu Stancu, Markus J van Roosmalen, Ivo Renkens, Marleen M Nieboer, Sjors Middelkamp, Joep de Ligt, Giulia Pregno, Daniela Giachino, Giorgia Mandrile, Jose Espejo Valle-Inclan,[...]. Nat Commun 2017
140
17

FORGe: prioritizing variants for graph genomes.
Jacob Pritt, Nae-Chyun Chen, Ben Langmead. Genome Biol 2018
24
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
17

Bit-parallel sequence-to-graph alignment.
Mikko Rautiainen, Veli Mäkinen, Tobias Marschall. Bioinformatics 2019
21
28

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
95
17

Piercing the dark matter: bioinformatics of long-range sequencing and mapping.
Fritz J Sedlazeck, Hayan Lee, Charlotte A Darby, Michael C Schatz. Nat Rev Genet 2018
172
17

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
517
17

Major Impacts of Widespread Structural Variation on Gene Expression and Crop Improvement in Tomato.
Michael Alonge, Xingang Wang, Matthias Benoit, Sebastian Soyk, Lara Pereira, Lei Zhang, Hamsini Suresh, Srividya Ramakrishnan, Florian Maumus, Danielle Ciren,[...]. Cell 2020
108
17

Structural variation in the sequencing era.
Steve S Ho, Alexander E Urban, Ryan E Mills. Nat Rev Genet 2020
81
17

Long-read sequencing and de novo assembly of a Chinese genome.
Lingling Shi, Yunfei Guo, Chengliang Dong, John Huddleston, Hui Yang, Xiaolu Han, Aisi Fu, Quan Li, Na Li, Siyi Gong,[...]. Nat Commun 2016
133
14

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
14

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
14

Phased diploid genome assembly with single-molecule real-time sequencing.
Chen-Shan Chin, Paul Peluso, Fritz J Sedlazeck, Maria Nattestad, Gregory T Concepcion, Alicia Clum, Christopher Dunn, Ronan O'Malley, Rosa Figueroa-Balderas, Abraham Morales-Cruz,[...]. Nat Methods 2016
706
14

Haplotype-aware graph indexes.
Jouni Sirén, Erik Garrison, Adam M Novak, Benedict Paten, Richard Durbin. Bioinformatics 2020
20
25

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
166
14

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
293
14


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.