A citation-based method for searching scientific literature

Vincent Plagnol, James Curtis, Michael Epstein, Kin Y Mok, Emma Stebbings, Sofia Grigoriadou, Nicholas W Wood, Sophie Hambleton, Siobhan O Burns, Adrian J Thrasher, Dinakantha Kumararatne, Rainer Doffinger, Sergey Nejentsev. Bioinformatics 2012
Times Cited: 288







List of co-cited articles
402 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
33


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
22

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
20


Copy number variation detection and genotyping from exome sequence data.
Niklas Krumm, Peter H Sudmant, Arthur Ko, Brian J O'Roak, Maika Malig, Bradley P Coe, Aaron R Quinlan, Deborah A Nickerson, Evan E Eichler. Genome Res 2012
356
13

Computational tools for copy number variation (CNV) detection using next-generation sequencing data: features and perspectives.
Min Zhao, Qingguo Wang, Quan Wang, Peilin Jia, Zhongming Zhao. BMC Bioinformatics 2013
250
13

Discovery and statistical genotyping of copy-number variation from whole-exome sequencing depth.
Menachem Fromer, Jennifer L Moran, Kimberly Chambert, Eric Banks, Sarah E Bergen, Douglas M Ruderfer, Robert E Handsaker, Steven A McCarroll, Michael C O'Donovan, Michael J Owen,[...]. Am J Hum Genet 2012
329
13

An evaluation of copy number variation detection tools from whole-exome sequencing data.
Renjie Tan, Yadong Wang, Sarah E Kleinstein, Yongzhuang Liu, Xiaolin Zhu, Hongzhe Guo, Qinghua Jiang, Andrew S Allen, Mingfu Zhu. Hum Mutat 2014
122
13

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
12

ANNOVAR: functional annotation of genetic variants from high-throughput sequencing data.
Kai Wang, Mingyao Li, Hakon Hakonarson. Nucleic Acids Res 2010
11

CODEX: a normalization and copy number variation detection method for whole exome sequencing.
Yuchao Jiang, Derek A Oldridge, Sharon J Diskin, Nancy R Zhang. Nucleic Acids Res 2015
73
13

Validation of copy number variation analysis for next-generation sequencing diagnostics.
Jamie M Ellingford, Christopher Campbell, Stephanie Barton, Sanjeev Bhaskar, Saurabh Gupta, Rachel L Taylor, Panagiotis I Sergouniotis, Bradley Horn, Janine A Lamb, Michel Michaelides,[...]. Eur J Hum Genet 2017
49
20

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
9

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
9

Exome sequencing-based copy-number variation and loss of heterozygosity detection: ExomeCNV.
Jarupon Fah Sathirapongsasuti, Hane Lee, Basil A J Horst, Georg Brunner, Alistair J Cochran, Scott Binder, John Quackenbush, Stanley F Nelson. Bioinformatics 2011
266
9

Genome structural variation discovery and genotyping.
Can Alkan, Bradley P Coe, Evan E Eichler. Nat Rev Genet 2011
729
9

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
464
9

Integrative genomics viewer.
James T Robinson, Helga Thorvaldsdóttir, Wendy Winckler, Mitchell Guttman, Eric S Lander, Gad Getz, Jill P Mesirov. Nat Biotechnol 2011
9

The Database of Genomic Variants: a curated collection of structural variation in the human genome.
Jeffrey R MacDonald, Robert Ziman, Ryan K C Yuen, Lars Feuk, Stephen W Scherer. Nucleic Acids Res 2014
625
9

VarScan 2: somatic mutation and copy number alteration discovery in cancer by exome sequencing.
Daniel C Koboldt, Qunyuan Zhang, David E Larson, Dong Shen, Michael D McLellan, Ling Lin, Christopher A Miller, Elaine R Mardis, Li Ding, Richard K Wilson. Genome Res 2012
8

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
125
8

panelcn.MOPS: Copy-number detection in targeted NGS panel data for clinical diagnostics.
Gundula Povysil, Antigoni Tzika, Julia Vogt, Verena Haunschmid, Ludwine Messiaen, Johannes Zschocke, Günter Klambauer, Sepp Hochreiter, Katharina Wimmer. Hum Mutat 2017
31
22


DECIPHER: Database of Chromosomal Imbalance and Phenotype in Humans Using Ensembl Resources.
Helen V Firth, Shola M Richards, A Paul Bevan, Stephen Clayton, Manuel Corpas, Diana Rajan, Steven Van Vooren, Yves Moreau, Roger M Pettett, Nigel P Carter. Am J Hum Genet 2009
909
7

Exome sequence read depth methods for identifying copy number changes.
Latha Kadalayil, Sajjad Rafiq, Matthew J J Rose-Zerilli, Reuben J Pengelly, Helen Parker, David Oscier, Jonathan C Strefford, William J Tapper, Jane Gibson, Sarah Ennis,[...]. Brief Bioinform 2015
46
15

American College of Medical Genetics standards and guidelines for interpretation and reporting of postnatal constitutional copy number variants.
Hutton M Kearney, Erik C Thorland, Kerry K Brown, Fabiola Quintero-Rivera, Sarah T South. Genet Med 2011
511
7

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
7

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
7

CONTRA: copy number analysis for targeted resequencing.
Jason Li, Richard Lupat, Kaushalya C Amarasinghe, Ella R Thompson, Maria A Doyle, Georgina L Ryland, Richard W Tothill, Saman K Halgamuge, Ian G Campbell, Kylie L Gorringe. Bioinformatics 2012
197
6



Detection of clinically relevant copy-number variants by exome sequencing in a large cohort of genetic disorders.
Rolph Pfundt, Marisol Del Rosario, Lisenka E L M Vissers, Michael P Kwint, Irene M Janssen, Nicole de Leeuw, Helger G Yntema, Marcel R Nelen, Dorien Lugtenberg, Erik-Jan Kamsteeg,[...]. Genet Med 2017
71
8

Clinical Validation of Copy Number Variant Detection from Targeted Next-Generation Sequencing Panels.
Jennifer Kerkhof, Laila C Schenkel, Jack Reilly, Sheri McRobbie, Erfan Aref-Eshghi, Alan Stuart, C Anthony Rupar, Paul Adams, Robert A Hegele, Hanxin Lin,[...]. J Mol Diagn 2017
62
9

Assessing the reproducibility of exome copy number variations predictions.
Celine S Hong, Larry N Singh, James C Mullikin, Leslie G Biesecker. Genome Med 2016
21
28

Detection of clinically relevant copy number variants with whole-exome sequencing.
Joep de Ligt, Philip M Boone, Rolph Pfundt, Lisenka E L M Vissers, Todd Richmond, Joel Geoghegan, Kathleen O'Moore, Nicole de Leeuw, Christine Shaw, Han G Brunner,[...]. Hum Mutat 2013
78
7

Evaluation of three read-depth based CNV detection tools using whole-exome sequencing data.
Ruen Yao, Cheng Zhang, Tingting Yu, Niu Li, Xuyun Hu, Xiumin Wang, Jian Wang, Yiping Shen. Mol Cytogenet 2017
42
14

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
6

Increasing the diagnostic yield of exome sequencing by copy number variant analysis.
Daniel S Marchuk, Kristy Crooks, Natasha Strande, Kathleen Kaiser-Rogers, Laura V Milko, Alicia Brandt, Alexandra Arreola, Christian R Tilley, Chris Bizon, Neeta L Vora,[...]. PLoS One 2018
23
26

AnnotSV: an integrated tool for structural variations annotation.
Véronique Geoffroy, Yvan Herenger, Arnaud Kress, Corinne Stoetzel, Amélie Piton, Hélène Dollfus, Jean Muller. Bioinformatics 2018
45
13

Consensus statement: chromosomal microarray is a first-tier clinical diagnostic test for individuals with developmental disabilities or congenital anomalies.
David T Miller, Margaret P Adam, Swaroop Aradhya, Leslie G Biesecker, Arthur R Brothman, Nigel P Carter, Deanna M Church, John A Crolla, Evan E Eichler, Charles J Epstein,[...]. Am J Hum Genet 2010
5

Modeling read counts for CNV detection in exome sequencing data.
Michael I Love, Alena Myšičková, Ruping Sun, Vera Kalscheuer, Martin Vingron, Stefan A Haas. Stat Appl Genet Mol Biol 2011
39
12

Integrative Genomics Viewer (IGV): high-performance genomics data visualization and exploration.
Helga Thorvaldsdóttir, James T Robinson, Jill P Mesirov. Brief Bioinform 2013
5

Fast gapped-read alignment with Bowtie 2.
Ben Langmead, Steven L Salzberg. Nat Methods 2012
5

Origins and functional impact of copy number variation in the human genome.
Donald F Conrad, Dalila Pinto, Richard Redon, Lars Feuk, Omer Gokcumen, Yujun Zhang, Jan Aerts, T Daniel Andrews, Chris Barnes, Peter Campbell,[...]. Nature 2010
5

Assessment of the incorporation of CNV surveillance into gene panel next-generation sequencing testing for inherited retinal diseases.
Jamie M Ellingford, Bradley Horn, Christopher Campbell, Gavin Arno, Stephanie Barton, Catriona Tate, Sanjeev Bhaskar, Panagiotis I Sergouniotis, Rachel L Taylor, Keren J Carss,[...]. J Med Genet 2018
27
18

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
789
5

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
574
5

PennCNV: an integrated hidden Markov model designed for high-resolution copy number variation detection in whole-genome SNP genotyping data.
Kai Wang, Mingyao Li, Dexter Hadley, Rui Liu, Joseph Glessner, Struan F A Grant, Hakon Hakonarson, Maja Bucan. Genome Res 2007
5

Genetic diagnosis of Mendelian disorders via RNA sequencing.
Laura S Kremer, Daniel M Bader, Christian Mertes, Robert Kopajtich, Garwin Pichler, Arcangela Iuso, Tobias B Haack, Elisabeth Graf, Thomas Schwarzmayr, Caterina Terrile,[...]. Nat Commun 2017
191
5


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.