A citation-based method for searching scientific literature

Pauline C Ng, Steven Henikoff. Nucleic Acids Res 2003
Times Cited: 3218







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



Times Cited
  Times     Co-cited
Similarity


A method and server for predicting damaging missense mutations.
Ivan A Adzhubei, Steffen Schmidt, Leonid Peshkin, Vasily E Ramensky, Anna Gerasimova, Peer Bork, Alexey S Kondrashov, Shamil R Sunyaev. Nat Methods 2010
48

Standards and guidelines for the interpretation of sequence variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology.
Sue Richards, Nazneen Aziz, Sherri Bale, David Bick, Soma Das, Julie Gastier-Foster, Wayne W Grody, Madhuri Hegde, Elaine Lyon, Elaine Spector,[...]. Genet Med 2015
27

Predicting functional effect of human missense mutations using PolyPhen-2.
Ivan Adzhubei, Daniel M Jordan, Shamil R Sunyaev. Curr Protoc Hum Genet 2013
24

ANNOVAR: functional annotation of genetic variants from high-throughput sequencing data.
Kai Wang, Mingyao Li, Hakon Hakonarson. Nucleic Acids Res 2010
24

Analysis of protein-coding genetic variation in 60,706 humans.
Monkol Lek, Konrad J Karczewski, Eric V Minikel, Kaitlin E Samocha, Eric Banks, Timothy Fennell, Anne H O'Donnell-Luria, James S Ware, Andrew J Hill, Beryl B Cummings,[...]. Nature 2016
19

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
19

MutationTaster2: mutation prediction for the deep-sequencing age.
Jana Marie Schwarz, David N Cooper, Markus Schuelke, Dominik Seelow. Nat Methods 2014
18

A general framework for estimating the relative pathogenicity of human genetic variants.
Martin Kircher, Daniela M Witten, Preti Jain, Brian J O'Roak, Gregory M Cooper, Jay Shendure. Nat Genet 2014
18


CADD: predicting the deleteriousness of variants throughout the human genome.
Philipp Rentzsch, Daniela Witten, Gregory M Cooper, Jay Shendure, Martin Kircher. Nucleic Acids Res 2019
844
16

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
16

The mutational constraint spectrum quantified from variation in 141,456 humans.
Konrad J Karczewski, Laurent C Francioli, Grace Tiao, Beryl B Cummings, Jessica Alföldi, Qingbo Wang, Ryan L Collins, Kristen M Laricchia, Andrea Ganna, Daniel P Birnbaum,[...]. Nature 2020
15

MutationTaster evaluates disease-causing potential of sequence alterations.
Jana Marie Schwarz, Christian Rödelsperger, Markus Schuelke, Dominik Seelow. Nat Methods 2010
14


The Ensembl Variant Effect Predictor.
William McLaren, Laurent Gil, Sarah E Hunt, Harpreet Singh Riat, Graham R S Ritchie, Anja Thormann, Paul Flicek, Fiona Cunningham. Genome Biol 2016
11

Predicting the functional impact of protein mutations: application to cancer genomics.
Boris Reva, Yevgeniy Antipin, Chris Sander. Nucleic Acids Res 2011
11

dbSNP: the NCBI database of genetic variation.
S T Sherry, M H Ward, M Kholodov, J Baker, L Phan, E M Smigielski, K Sirotkin. Nucleic Acids Res 2001
10

Identifying a high fraction of the human genome to be under selective constraint using GERP++.
Eugene V Davydov, David L Goode, Marina Sirota, Gregory M Cooper, Arend Sidow, Serafim Batzoglou. PLoS Comput Biol 2010
869
10

Predicting the functional effect of amino acid substitutions and indels.
Yongwook Choi, Gregory E Sims, Sean Murphy, Jason R Miller, Agnes P Chan. PLoS One 2012
10

REVEL: An Ensemble Method for Predicting the Pathogenicity of Rare Missense Variants.
Nilah M Ioannidis, Joseph H Rothstein, Vikas Pejaver, Sumit Middha, Shannon K McDonnell, Saurabh Baheti, Anthony Musolf, Qing Li, Emily Holzinger, Danielle Karyadi,[...]. Am J Hum Genet 2016
518
8

Predicting the functional, molecular, and phenotypic consequences of amino acid substitutions using hidden Markov models.
Hashem A Shihab, Julian Gough, David N Cooper, Peter D Stenson, Gary L A Barker, Keith J Edwards, Ian N M Day, Tom R Gaunt. Hum Mutat 2013
599
8

M-CAP eliminates a majority of variants of uncertain significance in clinical exomes at high sensitivity.
Karthik A Jagadeesh, Aaron M Wenger, Mark J Berger, Harendra Guturu, Peter D Stenson, David N Cooper, Jonathan A Bernstein, Gill Bejerano. Nat Genet 2016
339
8

ClinVar: public archive of relationships among sequence variation and human phenotype.
Melissa J Landrum, Jennifer M Lee, George R Riley, Wonhee Jang, Wendy S Rubinstein, Deanna M Church, Donna R Maglott. Nucleic Acids Res 2014
7

Integrative genomics viewer.
James T Robinson, Helga Thorvaldsdóttir, Wendy Winckler, Mitchell Guttman, Eric S Lander, Gad Getz, Jill P Mesirov. Nat Biotechnol 2011
7


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
7

ClinVar: public archive of interpretations of clinically relevant variants.
Melissa J Landrum, Jennifer M Lee, Mark Benson, Garth Brown, Chen Chao, Shanmuga Chitipiralla, Baoshan Gu, Jennifer Hart, Douglas Hoffman, Jeffrey Hoover,[...]. Nucleic Acids Res 2016
7


CNVkit: Genome-Wide Copy Number Detection and Visualization from Targeted DNA Sequencing.
Eric Talevich, A Hunter Shain, Thomas Botton, Boris C Bastian. PLoS Comput Biol 2016
513
6


Detection of nonneutral substitution rates on mammalian phylogenies.
Katherine S Pollard, Melissa J Hubisz, Kate R Rosenbloom, Adam Siepel. Genome Res 2010
6

Comparison and integration of deleteriousness prediction methods for nonsynonymous SNVs in whole exome sequencing studies.
Chengliang Dong, Peng Wei, Xueqiu Jian, Richard Gibbs, Eric Boerwinkle, Kai Wang, Xiaoming Liu. Hum Mol Genet 2015
497
6

Human non-synonymous SNPs: server and survey.
Vasily Ramensky, Peer Bork, Shamil Sunyaev. Nucleic Acids Res 2002
6

I-Mutant2.0: predicting stability changes upon mutation from the protein sequence or structure.
Emidio Capriotti, Piero Fariselli, Rita Casadio. Nucleic Acids Res 2005
810
5


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
5

Second-generation PLINK: rising to the challenge of larger and richer datasets.
Christopher C Chang, Carson C Chow, Laurent Cam Tellier, Shashaank Vattikuti, Shaun M Purcell, James J Lee. Gigascience 2015
5

From FastQ data to high confidence variant calls: the Genome Analysis Toolkit best practices pipeline.
Geraldine A Van der Auwera, Mauricio O Carneiro, Christopher Hartl, Ryan Poplin, Guillermo Del Angel, Ami Levy-Moonshine, Tadeusz Jordan, Khalid Shakir, David Roazen, Joel Thibault,[...]. Curr Protoc Bioinformatics 2013
5

An integrative approach to predicting the functional effects of non-coding and coding sequence variation.
Hashem A Shihab, Mark F Rogers, Julian Gough, Matthew Mort, David N Cooper, Ian N M Day, Tom R Gaunt, Colin Campbell. Bioinformatics 2015
271
5

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
5

COSMIC: the Catalogue Of Somatic Mutations In Cancer.
John G Tate, Sally Bamford, Harry C Jubb, Zbyslaw Sondka, David M Beare, Nidhi Bindal, Harry Boutselakis, Charlotte G Cole, Celestino Creatore, Elisabeth Dawson,[...]. Nucleic Acids Res 2019
5

ClinVar: improving access to variant interpretations and supporting evidence.
Melissa J Landrum, Jennifer M Lee, Mark Benson, Garth R Brown, Chen Chao, Shanmuga Chitipiralla, Baoshan Gu, Jennifer Hart, Douglas Hoffman, Wonhee Jang,[...]. Nucleic Acids Res 2018
887
5

SNAP: predict effect of non-synonymous polymorphisms on function.
Yana Bromberg, Burkhard Rost. Nucleic Acids Res 2007
515
5

ConSurf 2016: an improved methodology to estimate and visualize evolutionary conservation in macromolecules.
Haim Ashkenazy, Shiran Abadi, Eric Martz, Ofer Chay, Itay Mayrose, Tal Pupko, Nir Ben-Tal. Nucleic Acids Res 2016
928
5

SIFT web server: predicting effects of amino acid substitutions on proteins.
Ngak-Leng Sim, Prateek Kumar, Jing Hu, Steven Henikoff, Georg Schneider, Pauline C Ng. Nucleic Acids Res 2012
988
5


A program for annotating and predicting the effects of single nucleotide polymorphisms, SnpEff: SNPs in the genome of Drosophila melanogaster strain w1118; iso-2; iso-3.
Pablo Cingolani, Adrian Platts, Le Lily Wang, Melissa Coon, Tung Nguyen, Luan Wang, Susan J Land, Xiangyi Lu, Douglas M Ruden. Fly (Austin) 2012
4

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
4

The ExAC browser: displaying reference data information from over 60 000 exomes.
Konrad J Karczewski, Ben Weisburd, Brett Thomas, Matthew Solomonson, Douglas M Ruderfer, David Kavanagh, Tymor Hamamsy, Monkol Lek, Kaitlin E Samocha, Beryl B Cummings,[...]. Nucleic Acids Res 2017
278
4

DANN: a deep learning approach for annotating the pathogenicity of genetic variants.
Daniel Quang, Yifei Chen, Xiaohui Xie. Bioinformatics 2015
389
4


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.