A citation-based method for searching scientific literature

Chen-Shan Chin, Justin Wagner, Qiandong Zeng, Erik Garrison, Shilpa Garg, Arkarachai Fungtammasan, Mikko Rautiainen, Sergey Aganezov, Melanie Kirsche, Samantha Zarate, Michael C Schatz, Chunlin Xiao, William J Rowell, Charles Markello, Jesse Farek, Fritz J Sedlazeck, Vikas Bansal, Byunggil Yoo, Neil Miller, Xin Zhou, Andrew Carroll, Alvaro Martinez Barrio, Marc Salit, Tobias Marschall, Alexander T Dilthey, Justin M Zook. Nat Commun 2020
Times Cited: 14







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



Times Cited
  Times     Co-cited
Similarity


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
108
64

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
64


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
50

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
50

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
42

Nanopore sequencing and the Shasta toolkit enable efficient de novo assembly of eleven human genomes.
Kishwar Shafin, Trevor Pesout, Ryan Lorig-Roach, Marina Haukness, Hugh E Olsen, Colleen Bosworth, Joel Armstrong, Kristof Tigyi, Nicholas Maurer, Sergey Koren,[...]. Nat Biotechnol 2020
79
42

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
42

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
61
42

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
42

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
35

Assembly of long, error-prone reads using repeat graphs.
Mikhail Kolmogorov, Jeffrey Yuan, Yu Lin, Pavel A Pevzner. Nat Biotechnol 2019
564
35

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
35

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
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
35

The HLA genomic loci map: expression, interaction, diversity and disease.
Takashi Shiina, Kazuyoshi Hosomichi, Hidetoshi Inoko, Jerzy K Kulski. J Hum Genet 2009
356
35

An open resource for accurately benchmarking small variant and reference calls.
Justin M Zook, Jennifer McDaniel, Nathan D Olson, Justin Wagner, Hemang Parikh, Haynes Heaton, Sean A Irvine, Len Trigg, Rebecca Truty, Cory Y McLean,[...]. Nat Biotechnol 2019
80
28

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
28

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
34
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
28

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
28

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
28

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
28

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
28

Merqury: reference-free quality, completeness, and phasing assessment for genome assemblies.
Arang Rhie, Brian P Walenz, Sergey Koren, Adam M Phillippy. Genome Biol 2020
46
21

HLA*LA-HLA typing from linearly projected graph alignments.
Alexander T Dilthey, Alexander J Mentzer, Raphael Carapito, Clare Cutland, Nezih Cereb, Shabir A Madhi, Arang Rhie, Sergey Koren, Seiamak Bahram, Gil McVean,[...]. Bioinformatics 2019
24
21

An integrated map of genetic variation from 1,092 human genomes.
Goncalo R Abecasis, Adam Auton, Lisa D Brooks, Mark A DePristo, Richard M Durbin, Robert E Handsaker, Hyun Min Kang, Gabor T Marth, Gil A McVean. Nature 2012
21

Fast and accurate long-read assembly with wtdbg2.
Jue Ruan, Heng Li. Nat Methods 2020
266
21

QUAST: quality assessment tool for genome assemblies.
Alexey Gurevich, Vladislav Saveliev, Nikolay Vyahhi, Glenn Tesler. Bioinformatics 2013
21

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
21

GenomeScope: fast reference-free genome profiling from short reads.
Gregory W Vurture, Fritz J Sedlazeck, Maria Nattestad, Charles J Underwood, Han Fang, James Gurtowski, Michael C Schatz. Bioinformatics 2017
405
21

Integrative genomics viewer.
James T Robinson, Helga Thorvaldsdóttir, Wendy Winckler, Mitchell Guttman, Eric S Lander, Gad Getz, Jill P Mesirov. Nat Biotechnol 2011
21

Gene map of the extended human MHC.
Roger Horton, Laurens Wilming, Vikki Rand, Ruth C Lovering, Elspeth A Bruford, Varsha K Khodiyar, Michael J Lush, Sue Povey, C Conover Talbot, Mathew W Wright,[...]. Nat Rev Genet 2004
683
21

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
21

The design and construction of reference pangenome graphs with minigraph.
Heng Li, Xiaowen Feng, Chong Chu. Genome Biol 2020
35
21

Schizophrenia risk from complex variation of complement component 4.
Aswin Sekar, Allison R Bialas, Heather de Rivera, Avery Davis, Timothy R Hammond, Nolan Kamitaki, Katherine Tooley, Jessy Presumey, Matthew Baum, Vanessa Van Doren,[...]. Nature 2016
21

From genome-wide associations to candidate causal variants by statistical fine-mapping.
Daniel J Schaid, Wenan Chen, Nicholas B Larson. Nat Rev Genet 2018
193
21

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
20
21

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
21

Chromosome-scale, haplotype-resolved assembly of human genomes.
Shilpa Garg, Arkarachai Fungtammasan, Andrew Carroll, Mike Chou, Anthony Schmitt, Xiang Zhou, Stephen Mac, Paul Peluso, Emily Hatas, Jay Ghurye,[...]. Nat Biotechnol 2021
18
21

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
111
21


Mapping Bias Overestimates Reference Allele Frequencies at the HLA Genes in the 1000 Genomes Project Phase I Data.
Débora Y C Brandt, Vitor R C Aguiar, Bárbara D Bitarello, Kelly Nunes, Jérôme Goudet, Diogo Meyer. G3 (Bethesda) 2015
73
21

State-of-the-art genome inference in the human MHC.
Alexander T Dilthey. Int J Biochem Cell Biol 2021
3
100

WhatsHap: Weighted Haplotype Assembly for Future-Generation Sequencing Reads.
Murray Patterson, Tobias Marschall, Nadia Pisanti, Leo van Iersel, Leen Stougie, Gunnar W Klau, Alexander Schönhuth. J Comput Biol 2015
88
21

A Novel Framework for Characterizing Genomic Haplotype Diversity in the Human Immunoglobulin Heavy Chain Locus.
Oscar L Rodriguez, William S Gibson, Tom Parks, Matthew Emery, James Powell, Maya Strahl, Gintaras Deikus, Kathryn Auckland, Evan E Eichler, Wayne A Marasco,[...]. Front Immunol 2020
13
23

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
34
21


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
21

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
21


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.