A citation-based method for searching scientific literature

Jamie K Teer, Eric D Green, James C Mullikin, Leslie G Biesecker. Bioinformatics 2012
Times Cited: 109







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



Times Cited
  Times     Co-cited
Similarity


ANNOVAR: functional annotation of genetic variants from high-throughput sequencing data.
Kai Wang, Mingyao Li, Hakon Hakonarson. Nucleic Acids Res 2010
31


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
25

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
24

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
23

Systematic comparison of three genomic enrichment methods for massively parallel DNA sequencing.
Jamie K Teer, Lori L Bonnycastle, Peter S Chines, Nancy F Hansen, Natsuyo Aoyama, Amy J Swift, Hatice Ozel Abaan, Thomas J Albert, Elliott H Margulies, Eric D Green,[...]. Genome Res 2010
158
23

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
16

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
16

Accurate whole human genome sequencing using reversible terminator chemistry.
David R Bentley, Shankar Balasubramanian, Harold P Swerdlow, Geoffrey P Smith, John Milton, Clive G Brown, Kevin P Hall, Dirk J Evers, Colin L Barnes, Helen R Bignell,[...]. Nature 2008
15

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
15

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
13

Integrative genomics viewer.
James T Robinson, Helga Thorvaldsdóttir, Wendy Winckler, Mitchell Guttman, Eric S Lander, Gad Getz, Jill P Mesirov. Nat Biotechnol 2011
10

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
10

Solution hybrid selection with ultra-long oligonucleotides for massively parallel targeted sequencing.
Andreas Gnirke, Alexandre Melnikov, Jared Maguire, Peter Rogov, Emily M LeProust, William Brockman, Timothy Fennell, Georgia Giannoukos, Sheila Fisher, Carsten Russ,[...]. Nat Biotechnol 2009
900
9

The ClinSeq Project: piloting large-scale genome sequencing for research in genomic medicine.
Leslie G Biesecker, James C Mullikin, Flavia M Facio, Clesson Turner, Praveen F Cherukuri, Robert W Blakesley, Gerard G Bouffard, Peter S Chines, Pedro Cruz, Nancy F Hansen,[...]. Genome Res 2009
201
9


Exome sequencing: the sweet spot before whole genomes.
Jamie K Teer, James C Mullikin. Hum Mol Genet 2010
190
9


Sensitive detection of somatic point mutations in impure and heterogeneous cancer samples.
Kristian Cibulskis, Michael S Lawrence, Scott L Carter, Andrey Sivachenko, David Jaffe, Carrie Sougnez, Stacey Gabriel, Matthew Meyerson, Eric S Lander, Gad Getz. Nat Biotechnol 2013
8

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
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

The variant call format and VCFtools.
Petr Danecek, Adam Auton, Goncalo Abecasis, Cornelis A Albers, Eric Banks, Mark A DePristo, Robert E Handsaker, Gerton Lunter, Gabor T Marth, Stephen T Sherry,[...]. Bioinformatics 2011
7

A comprehensive framework for prioritizing variants in exome sequencing studies of Mendelian diseases.
Miao-Xin Li, Hong-Sheng Gui, Johnny S H Kwan, Su-Ying Bao, Pak C Sham. Nucleic Acids Res 2012
162
7

MutationTaster evaluates disease-causing potential of sequence alterations.
Jana Marie Schwarz, Christian Rödelsperger, Markus Schuelke, Dominik Seelow. Nat Methods 2010
7

The National Institutes of Health Undiagnosed Diseases Program: insights into rare diseases.
William A Gahl, Thomas C Markello, Camilo Toro, Karin Fuentes Fajardo, Murat Sincan, Fred Gill, Hannah Carlson-Donohoe, Andrea Gropman, Tyler Mark Pierson, Gretchen Golas,[...]. Genet Med 2012
180
7

Strelka: accurate somatic small-variant calling from sequenced tumor-normal sample pairs.
Christopher T Saunders, Wendy S W Wong, Sajani Swamy, Jennifer Becq, Lisa J Murray, R Keira Cheetham. Bioinformatics 2012
829
6

Secondary variants in individuals undergoing exome sequencing: screening of 572 individuals identifies high-penetrance mutations in cancer-susceptibility genes.
Jennifer J Johnston, Wendy S Rubinstein, Flavia M Facio, David Ng, Larry N Singh, Jamie K Teer, James C Mullikin, Leslie G Biesecker. Am J Hum Genet 2012
159
6


A map of human genome variation from population-scale sequencing.
Gonçalo R Abecasis, David Altshuler, Adam Auton, Lisa D Brooks, Richard M Durbin, Richard A Gibbs, Matt E Hurles, Gil A McVean. Nature 2010
6

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
6

Joubert syndrome: congenital cerebellar ataxia with the molar tooth.
Marta Romani, Alessia Micalizzi, Enza Maria Valente. Lancet Neurol 2013
184
6

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
848
5

SVA: software for annotating and visualizing sequenced human genomes.
Dongliang Ge, Elizabeth K Ruzzo, Kevin V Shianna, Min He, Kimberly Pelak, Erin L Heinzen, Anna C Need, Elizabeth T Cirulli, Jessica M Maia, Samuel P Dickson,[...]. Bioinformatics 2011
51
9

A probabilistic disease-gene finder for personal genomes.
Mark Yandell, Chad Huff, Hao Hu, Marc Singleton, Barry Moore, Jinchuan Xing, Lynn B Jorde, Martin G Reese. Genome Res 2011
138
5

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
5

Exome sequencing identifies MLL2 mutations as a cause of Kabuki syndrome.
Sarah B Ng, Abigail W Bigham, Kati J Buckingham, Mark C Hannibal, Margaret J McMillin, Heidi I Gildersleeve, Anita E Beck, Holly K Tabor, Gregory M Cooper, Heather C Mefford,[...]. Nat Genet 2010
832
5

Massively parallel sequencing of exons on the X chromosome identifies RBM10 as the gene that causes a syndromic form of cleft palate.
Jennifer J Johnston, Jamie K Teer, Praveen F Cherukuri, Nancy F Hansen, Stacie K Loftus, Karen Chong, James C Mullikin, Leslie G Biesecker. Am J Hum Genet 2010
100
5

GEMINI: integrative exploration of genetic variation and genome annotations.
Umadevi Paila, Brad A Chapman, Rory Kirchner, Aaron R Quinlan. PLoS Comput Biol 2013
236
5

Exome sequencing identifies the cause of a mendelian disorder.
Sarah B Ng, Kati J Buckingham, Choli Lee, Abigail W Bigham, Holly K Tabor, Karin M Dent, Chad D Huff, Paul T Shannon, Ethylin Wang Jabs, Deborah A Nickerson,[...]. Nat Genet 2010
4

SomaticSniper: identification of somatic point mutations in whole genome sequencing data.
David E Larson, Christopher C Harris, Ken Chen, Daniel C Koboldt, Travis E Abbott, David J Dooling, Timothy J Ley, Elaine R Mardis, Richard K Wilson, Li Ding. Bioinformatics 2012
328
4

Exome sequencing as a tool for Mendelian disease gene discovery.
Michael J Bamshad, Sarah B Ng, Abigail W Bigham, Holly K Tabor, Mary J Emond, Deborah A Nickerson, Jay Shendure. Nat Rev Genet 2011
4

Integrative Genomics Viewer (IGV): high-performance genomics data visualization and exploration.
Helga Thorvaldsdóttir, James T Robinson, Jill P Mesirov. Brief Bioinform 2013
4

Targeted capture and massively parallel sequencing of 12 human exomes.
Sarah B Ng, Emily H Turner, Peggy D Robertson, Steven D Flygare, Abigail W Bigham, Choli Lee, Tristan Shaffer, Michelle Wong, Arindam Bhattacharjee, Evan E Eichler,[...]. Nature 2009
4

ACMG recommendations for reporting of incidental findings in clinical exome and genome sequencing.
Robert C Green, Jonathan S Berg, Wayne W Grody, Sarah S Kalia, Bruce R Korf, Christa L Martin, Amy L McGuire, Robert L Nussbaum, Julianne M O'Daniel, Kelly E Ormond,[...]. Genet Med 2013
4

Human Gene Mutation Database (HGMD): 2003 update.
Peter D Stenson, Edward V Ball, Matthew Mort, Andrew D Phillips, Jacqueline A Shiel, Nick S T Thomas, Shaun Abeysinghe, Michael Krawczak, David N Cooper. Hum Mutat 2003
4

Analysis of DNA sequence variants detected by high-throughput sequencing.
David R Adams, Murat Sincan, Karin Fuentes Fajardo, James C Mullikin, Tyler M Pierson, Camilo Toro, Cornelius F Boerkoel, Cynthia J Tifft, William A Gahl, Tom C Markello. Hum Mutat 2012
32
12

Detection of nonneutral substitution rates on mammalian phylogenies.
Katherine S Pollard, Melissa J Hubisz, Kate R Rosenbloom, Adam Siepel. Genome Res 2010
4

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
472
4

The NIH Undiagnosed Diseases Program: lessons learned.
William A Gahl, Cynthia J Tifft. JAMA 2011
77
5

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


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.