A citation-based method for searching scientific literature

Xiaoyi Gao, Jianpeng Xu, Joshua Starmer. BMC Res Notes 2015
Times Cited: 8







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



Times Cited
  Times     Co-cited
Similarity


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
100



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
62

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
62

ANNOVAR: functional annotation of genetic variants from high-throughput sequencing data.
Kai Wang, Mingyao Li, Hakon Hakonarson. Nucleic Acids Res 2010
50

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
50

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
50

WEP: a high-performance analysis pipeline for whole-exome data.
Mattia D'Antonio, Paolo D'Onorio De Meo, Daniele Paoletti, Berardino Elmi, Matteo Pallocca, Nico Sanna, Ernesto Picardi, Graziano Pesole, Tiziana Castrignanò. BMC Bioinformatics 2013
34
50

SeqMule: automated pipeline for analysis of human exome/genome sequencing data.
Yunfei Guo, Xiaolei Ding, Yufeng Shen, Gholson J Lyon, Kai Wang. Sci Rep 2015
37
50

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
50

A survey of tools for variant analysis of next-generation genome sequencing data.
Stephan Pabinger, Andreas Dander, Maria Fischer, Rene Snajder, Michael Sperk, Mirjana Efremova, Birgit Krabichler, Michael R Speicher, Johannes Zschocke, Zlatko Trajanoski. Brief Bioinform 2014
304
37

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
682
37

SIMPLEX: cloud-enabled pipeline for the comprehensive analysis of exome sequencing data.
Maria Fischer, Rene Snajder, Stephan Pabinger, Andreas Dander, Anna Schossig, Johannes Zschocke, Zlatko Trajanoski, Gernot Stocker. PLoS One 2012
25
37

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
37

STORMSeq: an open-source, user-friendly pipeline for processing personal genomics data in the cloud.
Konrad J Karczewski, Guy Haskin Fernald, Alicia R Martin, Michael Snyder, Nicholas P Tatonetti, Joel T Dudley. PLoS One 2014
15
37

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
37

Integrating mapping-, assembly- and haplotype-based approaches for calling variants in clinical sequencing applications.
Andy Rimmer, Hang Phan, Iain Mathieson, Zamin Iqbal, Stephen R F Twigg, Andrew O M Wilkie, Gil McVean, Gerton Lunter. Nat Genet 2014
560
37

SNVer: a statistical tool for variant calling in analysis of pooled or individual next-generation sequencing data.
Zhi Wei, Wei Wang, Pingzhao Hu, Gholson J Lyon, Hakon Hakonarson. Nucleic Acids Res 2011
167
37

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
37

Sequencing technologies - the next generation.
Michael L Metzker. Nat Rev Genet 2010
37

Atlas2 Cloud: a framework for personal genome analysis in the cloud.
Uday S Evani, Danny Challis, Jin Yu, Andrew R Jackson, Sameer Paithankar, Matthew N Bainbridge, Adinarayana Jakkamsetti, Peter Pham, Cristian Coarfa, Aleksandar Milosavljevic,[...]. BMC Genomics 2012
29
37

DSigDB: drug signatures database for gene set analysis.
Minjae Yoo, Jimin Shin, Jihye Kim, Karen A Ryall, Kyubum Lee, Sunwon Lee, Minji Jeon, Jaewoo Kang, Aik Choon Tan. Bioinformatics 2015
103
25

Evaluation of somatic copy number estimation tools for whole-exome sequencing data.
Jae-Yong Nam, Nayoung K D Kim, Sang Cheol Kim, Je-Gun Joung, Ruibin Xi, Semin Lee, Peter J Park, Woong-Yang Park. Brief Bioinform 2016
30
25

An integrative variant analysis suite for whole exome next-generation sequencing data.
Danny Challis, Jin Yu, Uday S Evani, Andrew R Jackson, Sameer Paithankar, Cristian Coarfa, Aleksandar Milosavljevic, Richard A Gibbs, Fuli Yu. BMC Bioinformatics 2012
203
25


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
25


Trimmomatic: a flexible trimmer for Illumina sequence data.
Anthony M Bolger, Marc Lohse, Bjoern Usadel. Bioinformatics 2014
25



Validation and assessment of variant calling pipelines for next-generation sequencing.
Mehdi Pirooznia, Melissa Kramer, Jennifer Parla, Fernando S Goes, James B Potash, W Richard McCombie, Peter P Zandi. Hum Genomics 2014
74
25

Ultrafast and memory-efficient alignment of short DNA sequences to the human genome.
Ben Langmead, Cole Trapnell, Mihai Pop, Steven L Salzberg. Genome Biol 2009
25

Variant callers for next-generation sequencing data: a comparison study.
Xiangtao Liu, Shizhong Han, Zuoheng Wang, Joel Gelernter, Bao-Zhu Yang. PLoS One 2013
92
25

Quality control and preprocessing of metagenomic datasets.
Robert Schmieder, Robert Edwards. Bioinformatics 2011
25

SOAP2: an improved ultrafast tool for short read alignment.
Ruiqiang Li, Chang Yu, Yingrui Li, Tak-Wah Lam, Siu-Ming Yiu, Karsten Kristiansen, Jun Wang. Bioinformatics 2009
25


Searching for SNPs with cloud computing.
Ben Langmead, Michael C Schatz, Jimmy Lin, Mihai Pop, Steven L Salzberg. Genome Biol 2009
25


Fast gapped-read alignment with Bowtie 2.
Ben Langmead, Steven L Salzberg. Nat Methods 2012
25


Personalized copy number and segmental duplication maps using next-generation sequencing.
Can Alkan, Jeffrey M Kidd, Tomas Marques-Bonet, Gozde Aksay, Francesca Antonacci, Fereydoun Hormozdiari, Jacob O Kitzman, Carl Baker, Maika Malig, Onur Mutlu,[...]. Nat Genet 2009
448
25

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
356
25

Using Drosophila melanogaster as a Model for Genotoxic Chemical Mutational Studies with a New Program, SnpSift.
Pablo Cingolani, Viral M Patel, Melissa Coon, Tung Nguyen, Susan J Land, Douglas M Ruden, Xiangyi Lu. Front Genet 2012
449
25

Next-generation DNA sequencing.
Jay Shendure, Hanlee Ji. Nat Biotechnol 2008
25


Mutational heterogeneity in cancer and the search for new cancer-associated genes.
Michael S Lawrence, Petar Stojanov, Paz Polak, Gregory V Kryukov, Kristian Cibulskis, Andrey Sivachenko, Scott L Carter, Chip Stewart, Craig H Mermel, Steven A Roberts,[...]. Nature 2013
25

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
25

VarScan: variant detection in massively parallel sequencing of individual and pooled samples.
Daniel C Koboldt, Ken Chen, Todd Wylie, David E Larson, Michael D McLellan, Elaine R Mardis, George M Weinstock, Richard K Wilson, Li Ding. Bioinformatics 2009
791
25



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.