A citation-based method for searching scientific literature

Johan T den Dunnen, Raymond Dalgleish, Donna R Maglott, Reece K Hart, Marc S Greenblatt, Jean McGowan-Jordan, Anne-Francoise Roux, Timothy Smith, Stylianos E Antonarakis, Peter E M Taschner. Hum Mutat 2016
Times Cited: 724







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



Times Cited
  Times     Co-cited
Similarity


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
43

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

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
12

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
12

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
11

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
8

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
631
8

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
8

VarSome: the human genomic variant search engine.
Christos Kopanos, Vasilis Tsiolkas, Alexandros Kouris, Charles E Chapple, Monica Albarca Aguilera, Richard Meyer, Andreas Massouras. Bioinformatics 2019
516
8

ANNOVAR: functional annotation of genetic variants from high-throughput sequencing data.
Kai Wang, Mingyao Li, Hakon Hakonarson. Nucleic Acids Res 2010
7

MutationTaster2: mutation prediction for the deep-sequencing age.
Jana Marie Schwarz, David N Cooper, Markus Schuelke, Dominik Seelow. Nat Methods 2014
7

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
6

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
6

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
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
5

VariantValidator: Accurate validation, mapping, and formatting of sequence variation descriptions.
Peter J Freeman, Reece K Hart, Liam J Gretton, Anthony J Brookes, Raymond Dalgleish. Hum Mutat 2018
49
10


Sequence variant classification and reporting: recommendations for improving the interpretation of cancer susceptibility genetic test results.
Sharon E Plon, Diana M Eccles, Douglas Easton, William D Foulkes, Maurizio Genuardi, Marc S Greenblatt, Frans B L Hogervorst, Nicoline Hoogerbrugge, Amanda B Spurdle, Sean V Tavtigian. Hum Mutat 2008
576
5

Predicting Splicing from Primary Sequence with Deep Learning.
Kishore Jaganathan, Sofia Kyriazopoulou Panagiotopoulou, Jeremy F McRae, Siavash Fazel Darbandi, David Knowles, Yang I Li, Jack A Kosmicki, Juan Arbelaez, Wenwu Cui, Grace B Schwartz,[...]. Cell 2019
408
5


Combined genetic approaches yield a 48% diagnostic rate in a large cohort of French hearing-impaired patients.
D Baux, C Vaché, C Blanchet, M Willems, C Baudoin, M Moclyn, V Faugère, R Touraine, B Isidor, D Dupin-Deguine,[...]. Sci Rep 2017
37
10

Meta-analysis of the diagnostic and clinical utility of genome and exome sequencing and chromosomal microarray in children with suspected genetic diseases.
Michelle M Clark, Zornitza Stark, Lauge Farnaes, Tiong Y Tan, Susan M White, David Dimmock, Stephen F Kingsmore. NPJ Genom Med 2018
206
4

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

Standards and Guidelines for the Interpretation and Reporting of Sequence Variants in Cancer: A Joint Consensus Recommendation of the Association for Molecular Pathology, American Society of Clinical Oncology, and College of American Pathologists.
Marilyn M Li, Michael Datto, Eric J Duncavage, Shashikant Kulkarni, Neal I Lindeman, Somak Roy, Apostolia M Tsimberidou, Cindy L Vnencak-Jones, Daynna J Wolff, Anas Younes,[...]. J Mol Diagn 2017
669
4

Human Splicing Finder: an online bioinformatics tool to predict splicing signals.
François-Olivier Desmet, Dalil Hamroun, Marine Lalande, Gwenaëlle Collod-Béroud, Mireille Claustres, Christophe Béroud. Nucleic Acids Res 2009
4

The cBio cancer genomics portal: an open platform for exploring multidimensional cancer genomics data.
Ethan Cerami, Jianjiong Gao, Ugur Dogrusoz, Benjamin E Gross, Selcuk Onur Sumer, Bülent Arman Aksoy, Anders Jacobsen, Caitlin J Byrne, Michael L Heuer, Erik Larsson,[...]. Cancer Discov 2012
4


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
4

The Human Gene Mutation Database: towards a comprehensive repository of inherited mutation data for medical research, genetic diagnosis and next-generation sequencing studies.
Peter D Stenson, Matthew Mort, Edward V Ball, Katy Evans, Matthew Hayden, Sally Heywood, Michelle Hussain, Andrew D Phillips, David N Cooper. Hum Genet 2017
684
4

Mutational landscape of metastatic cancer revealed from prospective clinical sequencing of 10,000 patients.
Ahmet Zehir, Ryma Benayed, Ronak H Shah, Aijazuddin Syed, Sumit Middha, Hyunjae R Kim, Preethi Srinivasan, Jianjiong Gao, Debyani Chakravarty, Sean M Devlin,[...]. Nat Med 2017
4


OMIM.org: leveraging knowledge across phenotype-gene relationships.
Joanna S Amberger, Carol A Bocchini, Alan F Scott, Ada Hamosh. Nucleic Acids Res 2019
205
4

Technical standards for the interpretation and reporting of constitutional copy-number variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics (ACMG) and the Clinical Genome Resource (ClinGen).
Erin Rooney Riggs, Erica F Andersen, Athena M Cherry, Sibel Kantarci, Hutton Kearney, Ankita Patel, Gordana Raca, Deborah I Ritter, Sarah T South, Erik C Thorland,[...]. Genet Med 2020
250
4

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
4

Expert specification of the ACMG/AMP variant interpretation guidelines for genetic hearing loss.
Andrea M Oza, Marina T DiStefano, Sarah E Hemphill, Brandon J Cushman, Andrew R Grant, Rebecca K Siegert, Jun Shen, Alex Chapin, Nicole J Boczek, Lisa A Schimmenti,[...]. Hum Mutat 2018
155
4

The human genome browser at UCSC.
W James Kent, Charles W Sugnet, Terrence S Furey, Krishna M Roskin, Tom H Pringle, Alan M Zahler, David Haussler. Genome Res 2002
4

Accelerating Discovery of Functional Mutant Alleles in Cancer.
Matthew T Chang, Tripti Shrestha Bhattarai, Alison M Schram, Craig M Bielski, Mark T A Donoghue, Philip Jonsson, Debyani Chakravarty, Sarah Phillips, Cyriac Kandoth, Alexander Penson,[...]. Cancer Discov 2018
139
4

Relative quantification of 40 nucleic acid sequences by multiplex ligation-dependent probe amplification.
Jan P Schouten, Cathal J McElgunn, Raymond Waaijer, Danny Zwijnenburg, Filip Diepvens, Gerard Pals. Nucleic Acids Res 2002
3

Trimmomatic: a flexible trimmer for Illumina sequence data.
Anthony M Bolger, Marc Lohse, Bjoern Usadel. Bioinformatics 2014
3

Usher syndrome type 2 caused by activation of an USH2A pseudoexon: implications for diagnosis and therapy.
Christel Vaché, Thomas Besnard, Pauline le Berre, Gema García-García, David Baux, Lise Larrieu, Caroline Abadie, Catherine Blanchet, Hanno Jörn Bolz, Jose Millan,[...]. Hum Mutat 2012
78
3

LitVar: a semantic search engine for linking genomic variant data in PubMed and PMC.
Alexis Allot, Yifan Peng, Chih-Hsuan Wei, Kyubum Lee, Lon Phan, Zhiyong Lu. Nucleic Acids Res 2018
33
9

What's in a Name? A Coordinated Approach toward the Correct Use of a Uniform Nomenclature to Improve Patient Reports and Databases.
Véronique Tack, Zandra C Deans, Nicola Wolstenholme, Simon Patton, Elisabeth M C Dequeker. Hum Mutat 2016
20
15

LOVD v.2.0: the next generation in gene variant databases.
Ivo F A C Fokkema, Peter E M Taschner, Gerard C P Schaafsma, J Celli, Jeroen F J Laros, Johan T den Dunnen. Hum Mutat 2011
604
3

Whole Genome Sequencing Expands Diagnostic Utility and Improves Clinical Management in Pediatric Medicine.
Dimitri J Stavropoulos, Daniele Merico, Rebekah Jobling, Sarah Bowdin, Nasim Monfared, Bhooma Thiruvahindrapuram, Thomas Nalpathamkalam, Giovanna Pellecchia, Ryan K C Yuen, Michael J Szego,[...]. NPJ Genom Med 2016
188
3

Making new genetic diagnoses with old data: iterative reanalysis and reporting from genome-wide data in 1,133 families with developmental disorders.
Caroline F Wright, Jeremy F McRae, Stephen Clayton, Giuseppe Gallone, Stuart Aitken, Tomas W FitzGerald, Philip Jones, Elena Prigmore, Diana Rajan, Jenny Lord,[...]. Genet Med 2018
139
3

Clinical sequencing: is WGS the better WES?
Janine Meienberg, Rémy Bruggmann, Konrad Oexle, Gabor Matyas. Hum Genet 2016
138
3


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
3

The Protein Data Bank.
H M Berman, J Westbrook, Z Feng, G Gilliland, T N Bhat, H Weissig, I N Shindyalov, P E Bourne. Nucleic Acids Res 2000
3

The EMBL-EBI search and sequence analysis tools APIs in 2019.
Fábio Madeira, Young Mi Park, Joon Lee, Nicola Buso, Tamer Gur, Nandana Madhusoodanan, Prasad Basutkar, Adrian R N Tivey, Simon C Potter, Robert D Finn,[...]. Nucleic Acids Res 2019
3


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.