A citation-based method for searching scientific literature

Justin M Zook, David Catoe, Jennifer McDaniel, Lindsay Vang, Noah Spies, Arend Sidow, Ziming Weng, Yuling Liu, Christopher E Mason, Noah Alexander, Elizabeth Henaff, Alexa B R McIntyre, Dhruva Chandramohan, Feng Chen, Erich Jaeger, Ali Moshrefi, Khoa Pham, William Stedman, Tiffany Liang, Michael Saghbini, Zeljko Dzakula, Alex Hastie, Han Cao, Gintaras Deikus, Eric Schadt, Robert Sebra, Ali Bashir, Rebecca M Truty, Christopher C Chang, Natali Gulbahce, Keyan Zhao, Srinka Ghosh, Fiona Hyland, Yutao Fu, Mark Chaisson, Chunlin Xiao, Jonathan Trow, Stephen T Sherry, Alexander W Zaranek, Madeleine Ball, Jason Bobe, Preston Estep, George M Church, Patrick Marks, Sofia Kyriazopoulou-Panagiotopoulou, Grace X Y Zheng, Michael Schnall-Levin, Heather S Ordonez, Patrice A Mudivarti, Kristina Giorda, Ying Sheng, Karoline Bjarnesdatter Rypdal, Marc Salit. Sci Data 2016
Times Cited: 240







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



Times Cited
  Times     Co-cited
Similarity


Toward a More Precise Future for Oncology.
Yonina R Murciano-Goroff, Barry S Taylor, David M Hyman, Alison M Schram. Cancer Cell 2020
7
14

Diagnostic and clinical utility of whole genome sequencing in a cohort of undiagnosed Chinese families with rare diseases.
Hong-Yan Liu, Liyuan Zhou, Meng-Yue Zheng, Jia Huang, Shu Wan, Aiying Zhu, Mingjie Zhang, Anliang Dong, Ling Hou, Jia Li,[...]. Sci Rep 2019
8
12



NanoString, a novel digital color-coded barcode technology: current and future applications in molecular diagnostics.
Hin-Fung Tsang, Vivian Weiwen Xue, Su-Pin Koh, Ya-Ming Chiu, Lawrence Po-Wah Ng, Sze-Chuen Cesar Wong. Expert Rev Mol Diagn 2017
61
1

AnnotSV: an integrated tool for structural variations annotation.
Véronique Geoffroy, Yvan Herenger, Arnaud Kress, Corinne Stoetzel, Amélie Piton, Hélène Dollfus, Jean Muller. Bioinformatics 2018
54
1

Genome-wide analysis of SARS-CoV-2 virus strains circulating worldwide implicates heterogeneity.
M Rafiul Islam, M Nazmul Hoque, M Shaminur Rahman, A S M Rubayet Ul Alam, Masuda Akther, J Akter Puspo, Salma Akter, Munawar Sultana, Keith A Crandall, M Anwar Hossain. Sci Rep 2020
85
1

SVFX: a machine learning framework to quantify the pathogenicity of structural variants.
Sushant Kumar, Arif Harmanci, Jagath Vytheeswaran, Mark B Gerstein. Genome Biol 2020
3
33

Closing in on a complete human genome.
Michael Eisenstein. Nature 2021
2
50

SARS-CoV-2 genomic diversity and the implications for qRT-PCR diagnostics and transmission.
Nicolae Sapoval, Medhat Mahmoud, Michael D Jochum, Yunxi Liu, R A Leo Elworth, Qi Wang, Dreycey Albin, Huw A Ogilvie, Michael D Lee, Sonia Villapol,[...]. Genome Res 2021
13
7

A fast and agnostic method for bacterial genome-wide association studies: Bridging the gap between k-mers and genetic events.
Magali Jaillard, Leandro Lima, Maud Tournoud, Pierre Mahé, Alex van Belkum, Vincent Lacroix, Laurent Jacob. PLoS Genet 2018
45
2

Parliament2: Accurate structural variant calling at scale.
Samantha Zarate, Andrew Carroll, Medhat Mahmoud, Olga Krasheninina, Goo Jun, William J Salerno, Michael C Schatz, Eric Boerwinkle, Richard A Gibbs, Fritz J Sedlazeck. Gigascience 2020
7
14

PlasmidHawk improves lab of origin prediction of engineered plasmids using sequence alignment.
Qi Wang, Bryce Kille, Tian Rui Liu, R A Leo Elworth, Todd J Treangen. Nat Commun 2021
1
100

On the representation of de Bruijn graphs.
Rayan Chikhi, Antoine Limasset, Shaun Jackman, Jared T Simpson, Paul Medvedev. J Comput Biol 2015
13
7

A programmable dual-RNA-guided DNA endonuclease in adaptive bacterial immunity.
Martin Jinek, Krzysztof Chylinski, Ines Fonfara, Michael Hauer, Jennifer A Doudna, Emmanuelle Charpentier. Science 2012
1

Samplot: a platform for structural variant visual validation and automated filtering.
Jonathan R Belyeu, Murad Chowdhury, Joseph Brown, Brent S Pedersen, Michael J Cormier, Aaron R Quinlan, Ryan M Layer. Genome Biol 2021
1
100

Patterns of somatic structural variation in human cancer genomes.
Yilong Li, Nicola D Roberts, Jeremiah A Wala, Ofer Shapira, Steven E Schumacher, Kiran Kumar, Ekta Khurana, Sebastian Waszak, Jan O Korbel, James E Haber,[...]. Nature 2020
136
1

Germline copy number variations in BRCA1/2 negative families: Role in the molecular etiology of hereditary breast cancer in Tunisia.
Maroua Boujemaa, Yosr Hamdi, Nesrine Mejri, Lilia Romdhane, Kais Ghedira, Hanen Bouaziz, Houda El Benna, Soumaya Labidi, Hamza Dallali, Olfa Jaidane,[...]. PLoS One 2021
1
100

Detecting past and ongoing natural selection among ethnically Tibetan women at high altitude in Nepal.
Choongwon Jeong, David B Witonsky, Buddha Basnyat, Maniraj Neupane, Cynthia M Beall, Geoff Childs, Sienna R Craig, John Novembre, Anna Di Rienzo. PLoS Genet 2018
17
5


Systematic discovery of complex insertions and deletions in human cancers.
Kai Ye, Jiayin Wang, Reyka Jayasinghe, Eric-Wubbo Lameijer, Joshua F McMichael, Jie Ning, Michael D McLellan, Mingchao Xie, Song Cao, Venkata Yellapantula,[...]. Nat Med 2016
48
2

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
95
1

A genomic history of Aboriginal Australia.
Anna-Sapfo Malaspinas, Michael C Westaway, Craig Muller, Vitor C Sousa, Oscar Lao, Isabel Alves, Anders Bergström, Georgios Athanasiadis, Jade Y Cheng, Jacob E Crawford,[...]. Nature 2016
163
1

Heterogeneity in Palaeolithic Population Continuity and Neolithic Expansion in North Africa.
Gerard Serra-Vidal, Marcel Lucas-Sanchez, Karima Fadhlaoui-Zid, Asmahan Bekada, Pierre Zalloua, David Comas. Curr Biol 2019
6
16

Worldwide patterns of genomic variation and admixture in gray wolves.
Zhenxin Fan, Pedro Silva, Ilan Gronau, Shuoguo Wang, Aitor Serres Armero, Rena M Schweizer, Oscar Ramirez, John Pollinger, Marco Galaverni, Diego Ortega Del-Vecchyo,[...]. Genome Res 2016
78
1

Deep whole-genome sequencing reveals recent selection signatures linked to evolution and disease risk of Japanese.
Yukinori Okada, Yukihide Momozawa, Saori Sakaue, Masahiro Kanai, Kazuyoshi Ishigaki, Masato Akiyama, Toshihiro Kishikawa, Yasumichi Arai, Takashi Sasaki, Kenjiro Kosaki,[...]. Nat Commun 2018
62
1

Deep whole-genome sequencing of 100 southeast Asian Malays.
Lai-Ping Wong, Rick Twee-Hee Ong, Wan-Ting Poh, Xuanyao Liu, Peng Chen, Ruoying Li, Kevin Koi-Yau Lam, Nisha Esakimuthu Pillai, Kar-Seng Sim, Haiyan Xu,[...]. Am J Hum Genet 2013
104
1

Evolutionary genomic dynamics of Peruvians before, during, and after the Inca Empire.
Daniel N Harris, Wei Song, Amol C Shetty, Kelly S Levano, Omar Cáceres, Carlos Padilla, Víctor Borda, David Tarazona, Omar Trujillo, Cesar Sanchez,[...]. Proc Natl Acad Sci U S A 2018
54
1

Evaluation of artificial selection in Standard Poodles using whole-genome sequencing.
Steven G Friedenberg, Kathryn M Meurs, Trudy F C Mackay. Mamm Genome 2016
7
14

Optimal sequencing strategies for identifying disease-associated singletons.
Sara Rashkin, Goo Jun, Sai Chen, Goncalo R Abecasis. PLoS Genet 2017
10
10

Optimal sequencing depth design for whole genome re-sequencing in pigs.
Yifan Jiang, Yao Jiang, Sheng Wang, Qin Zhang, Xiangdong Ding. BMC Bioinformatics 2019
5
20

Whole-genome sequence analysis of a Pan African set of samples reveals archaic gene flow from an extinct basal population of modern humans into sub-Saharan populations.
Belen Lorente-Galdos, Oscar Lao, Gerard Serra-Vidal, Gabriel Santpere, Lukas F K Kuderna, Lara R Arauna, Karima Fadhlaoui-Zid, Ville N Pimenoff, Himla Soodyall, Pierre Zalloua,[...]. Genome Biol 2019
16
6

KoVariome: Korean National Standard Reference Variome database of whole genomes with comprehensive SNV, indel, CNV, and SV analyses.
Jungeun Kim, Jessica A Weber, Sungwoong Jho, Jinho Jang, JeHoon Jun, Yun Sung Cho, Hak-Min Kim, Hyunho Kim, Yumi Kim, OkSung Chung,[...]. Sci Rep 2018
18
5

Whole-genome sequencing of tibetan macaque (Macaca Thibetana) provides new insight into the macaque evolutionary history.
Zhenxin Fan, Guang Zhao, Peng Li, Naoki Osada, Jinchuan Xing, Yong Yi, Lianming Du, Pedro Silva, Hongxing Wang, Ryuichi Sakate,[...]. Mol Biol Evol 2014
27
3

Whole genome sequencing predicts novel human disease models in rhesus macaques.
Benjamin N Bimber, Ranjani Ramakrishnan, Rita Cervera-Juanes, Ravi Madhira, Samuel M Peterson, Robert B Norgren, Betsy Ferguson. Genomics 2017
17
5

Deep-coverage whole genome sequences and blood lipids among 16,324 individuals.
Pradeep Natarajan, Gina M Peloso, Seyedeh Maryam Zekavat, May Montasser, Andrea Ganna, Mark Chaffin, Amit V Khera, Wei Zhou, Jonathan M Bloom, Jesse M Engreitz,[...]. Nat Commun 2018
70
1

Khoisan hunter-gatherers have been the largest population throughout most of modern-human demographic history.
Hie Lim Kim, Aakrosh Ratan, George H Perry, Alvaro Montenegro, Webb Miller, Stephan C Schuster. Nat Commun 2014
34
2

Tracing the route of modern humans out of Africa by using 225 human genome sequences from Ethiopians and Egyptians.
Luca Pagani, Stephan Schiffels, Deepti Gurdasani, Petr Danecek, Aylwyn Scally, Yuan Chen, Yali Xue, Marc Haber, Rosemary Ekong, Tamiru Oljira,[...]. Am J Hum Genet 2015
71
1

Chad Genetic Diversity Reveals an African History Marked by Multiple Holocene Eurasian Migrations.
Marc Haber, Massimo Mezzavilla, Anders Bergström, Javier Prado-Martinez, Pille Hallast, Riyadh Saif-Ali, Molham Al-Habori, George Dedoussis, Eleftheria Zeggini, Jason Blue-Smith,[...]. Am J Hum Genet 2016
20
5

African evolutionary history inferred from whole genome sequence data of 44 indigenous African populations.
Shaohua Fan, Derek E Kelly, Marcia H Beltrame, Matthew E B Hansen, Swapan Mallick, Alessia Ranciaro, Jibril Hirbo, Simon Thompson, William Beggs, Thomas Nyambo,[...]. Genome Biol 2019
40
2

Khoe-San Genomes Reveal Unique Variation and Confirm the Deepest Population Divergence in Homo sapiens.
Carina M Schlebusch, Per Sjödin, Gwenna Breton, Torsten Günther, Thijessen Naidoo, Nina Hollfelder, Agnes E Sjöstrand, Jingzi Xu, Lucie M Gattepaille, Mário Vicente,[...]. Mol Biol Evol 2020
12
8

Genomic analyses inform on migration events during the peopling of Eurasia.
Luca Pagani, Daniel John Lawson, Evelyn Jagoda, Alexander Mörseburg, Anders Eriksson, Mario Mitt, Florian Clemente, Georgi Hudjashov, Michael DeGiorgio, Lauri Saag,[...]. Nature 2016
152
1

Novel variation and de novo mutation rates in population-wide de novo assembled Danish trios.
Søren Besenbacher, Siyang Liu, José M G Izarzugaza, Jakob Grove, Kirstine Belling, Jette Bork-Jensen, Shujia Huang, Thomas D Als, Shengting Li, Rachita Yadav,[...]. Nat Commun 2015
94
1


RIG: Recalibration and interrelation of genomic sequence data with the GATK.
Ryan F McCormick, Sandra K Truong, John E Mullet. G3 (Bethesda) 2015
33
3

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
386
1


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.