A citation-based method for searching scientific literature

Andrey A Shabalin. Bioinformatics 2012
Times Cited: 692







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



Times Cited
  Times     Co-cited
Similarity


Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2.
Michael I Love, Wolfgang Huber, Simon Anders. Genome Biol 2014
21

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
21

Genetic effects on gene expression across human tissues.
Alexis Battle, Christopher D Brown, Barbara E Engelhardt, Stephen B Montgomery. Nature 2017
19

STAR: ultrafast universal RNA-seq aligner.
Alexander Dobin, Carrie A Davis, Felix Schlesinger, Jorg Drenkow, Chris Zaleski, Sonali Jha, Philippe Batut, Mark Chaisson, Thomas R Gingeras. Bioinformatics 2013
19

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
18

Integration of summary data from GWAS and eQTL studies predicts complex trait gene targets.
Zhihong Zhu, Futao Zhang, Han Hu, Andrew Bakshi, Matthew R Robinson, Joseph E Powell, Grant W Montgomery, Michael E Goddard, Naomi R Wray, Peter M Visscher,[...]. Nat Genet 2016
661
17







Principal components analysis corrects for stratification in genome-wide association studies.
Alkes L Price, Nick J Patterson, Robert M Plenge, Michael E Weinblatt, Nancy A Shadick, David Reich. Nat Genet 2006
9

METAL: fast and efficient meta-analysis of genomewide association scans.
Cristen J Willer, Yun Li, Gonçalo R Abecasis. Bioinformatics 2010
9

limma powers differential expression analyses for RNA-sequencing and microarray studies.
Matthew E Ritchie, Belinda Phipson, Di Wu, Yifang Hu, Charity W Law, Wei Shi, Gordon K Smyth. Nucleic Acids Res 2015
9


WGCNA: an R package for weighted correlation network analysis.
Peter Langfelder, Steve Horvath. BMC Bioinformatics 2008
9

ANNOVAR: functional annotation of genetic variants from high-throughput sequencing data.
Kai Wang, Mingyao Li, Hakon Hakonarson. Nucleic Acids Res 2010
8

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
8

A gene-based association method for mapping traits using reference transcriptome data.
Eric R Gamazon, Heather E Wheeler, Kaanan P Shah, Sahar V Mozaffari, Keston Aquino-Michaels, Robert J Carroll, Anne E Eyler, Joshua C Denny, Dan L Nicolae, Nancy J Cox,[...]. Nat Genet 2015
605
8

Integrative approaches for large-scale transcriptome-wide association studies.
Alexander Gusev, Arthur Ko, Huwenbo Shi, Gaurav Bhatia, Wonil Chung, Brenda W J H Penninx, Rick Jansen, Eco J C de Geus, Dorret I Boomsma, Fred A Wright,[...]. Nat Genet 2016
575
8

clusterProfiler: an R package for comparing biological themes among gene clusters.
Guangchuang Yu, Li-Gen Wang, Yanyan Han, Qing-Yu He. OMICS 2012
8

edgeR: a Bioconductor package for differential expression analysis of digital gene expression data.
Mark D Robinson, Davis J McCarthy, Gordon K Smyth. Bioinformatics 2010
8

Partitioning heritability by functional annotation using genome-wide association summary statistics.
Hilary K Finucane, Brendan Bulik-Sullivan, Alexander Gusev, Gosia Trynka, Yakir Reshef, Po-Ru Loh, Verneri Anttila, Han Xu, Chongzhi Zang, Kyle Farh,[...]. Nat Genet 2015
741
8

Developmental and genetic regulation of the human cortex transcriptome illuminate schizophrenia pathogenesis.
Andrew E Jaffe, Richard E Straub, Joo Heon Shin, Ran Tao, Yuan Gao, Leonardo Collado-Torres, Tony Kam-Thong, Hualin S Xi, Jie Quan, Qiang Chen,[...]. Nat Neurosci 2018
130
7

Transcriptome and genome sequencing uncovers functional variation in humans.
Tuuli Lappalainen, Michael Sammeth, Marc R Friedländer, Peter A C 't Hoen, Jean Monlong, Manuel A Rivas, Mar Gonzàlez-Porta, Natalja Kurbatova, Thasso Griebel, Pedro G Ferreira,[...]. Nature 2013
7

Integrative analysis of 111 reference human epigenomes.
Anshul Kundaje, Wouter Meuleman, Jason Ernst, Misha Bilenky, Angela Yen, Alireza Heravi-Moussavi, Pouya Kheradpour, Zhizhuo Zhang, Jianrong Wang, Michael J Ziller,[...]. Nature 2015
7

A linear complexity phasing method for thousands of genomes.
Olivier Delaneau, Jonathan Marchini, Jean-François Zagury. Nat Methods 2011
7

The sva package for removing batch effects and other unwanted variation in high-throughput experiments.
Jeffrey T Leek, W Evan Johnson, Hilary S Parker, Andrew E Jaffe, John D Storey. Bioinformatics 2012
7

Statistical significance for genomewide studies.
John D Storey, Robert Tibshirani. Proc Natl Acad Sci U S A 2003
7

The NHGRI-EBI GWAS Catalog of published genome-wide association studies, targeted arrays and summary statistics 2019.
Annalisa Buniello, Jacqueline A L MacArthur, Maria Cerezo, Laura W Harris, James Hayhurst, Cinzia Malangone, Aoife McMahon, Joannella Morales, Edward Mountjoy, Elliot Sollis,[...]. Nucleic Acids Res 2019
885
7

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
7

Opportunities and challenges for transcriptome-wide association studies.
Michael Wainberg, Nasa Sinnott-Armstrong, Nicholas Mancuso, Alvaro N Barbeira, David A Knowles, David Golan, Raili Ermel, Arno Ruusalepp, Thomas Quertermous, Ke Hao,[...]. Nat Genet 2019
175
7


Bayesian test for colocalisation between pairs of genetic association studies using summary statistics.
Claudia Giambartolomei, Damjan Vukcevic, Eric E Schadt, Lude Franke, Aroon D Hingorani, Chris Wallace, Vincent Plagnol. PLoS Genet 2014
565
6

Potential etiologic and functional implications of genome-wide association loci for human diseases and traits.
Lucia A Hindorff, Praveen Sethupathy, Heather A Junkins, Erin M Ramos, Jayashri P Mehta, Francis S Collins, Teri A Manolio. Proc Natl Acad Sci U S A 2009
6

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
6

10 Years of GWAS Discovery: Biology, Function, and Translation.
Peter M Visscher, Naomi R Wray, Qian Zhang, Pamela Sklar, Mark I McCarthy, Matthew A Brown, Jian Yang. Am J Hum Genet 2017
6

The role of regulatory variation in complex traits and disease.
Frank W Albert, Leonid Kruglyak. Nat Rev Genet 2015
462
6

Gene expression elucidates functional impact of polygenic risk for schizophrenia.
Menachem Fromer, Panos Roussos, Solveig K Sieberts, Jessica S Johnson, David H Kavanagh, Thanneer M Perumal, Douglas M Ruderfer, Edwin C Oh, Aaron Topol, Hardik R Shah,[...]. Nat Neurosci 2016
462
6

A reference panel of 64,976 haplotypes for genotype imputation.
Shane McCarthy, Sayantan Das, Warren Kretzschmar, Olivier Delaneau, Andrew R Wood, Alexander Teumer, Hyun Min Kang, Christian Fuchsberger, Petr Danecek, Kevin Sharp,[...]. Nat Genet 2016
6

Next-generation genotype imputation service and methods.
Sayantan Das, Lukas Forer, Sebastian Schönherr, Carlo Sidore, Adam E Locke, Alan Kwong, Scott I Vrieze, Emily Y Chew, Shawn Levy, Matt McGue,[...]. Nat Genet 2016
962
6


Fast gapped-read alignment with Bowtie 2.
Ben Langmead, Steven L Salzberg. Nat Methods 2012
6


Common schizophrenia alleles are enriched in mutation-intolerant genes and in regions under strong background selection.
Antonio F Pardiñas, Peter Holmans, Andrew J Pocklington, Valentina Escott-Price, Stephan Ripke, Noa Carrera, Sophie E Legge, Sophie Bishop, Darren Cameron, Marian L Hamshere,[...]. Nat Genet 2018
543
5


Association analysis identifies 65 new breast cancer risk loci.
Kyriaki Michailidou, Sara Lindström, Joe Dennis, Jonathan Beesley, Shirley Hui, Siddhartha Kar, Audrey Lemaçon, Penny Soucy, Dylan Glubb, Asha Rostamianfar,[...]. Nature 2017
484
5

Robust enumeration of cell subsets from tissue expression profiles.
Aaron M Newman, Chih Long Liu, Michael R Green, Andrew J Gentles, Weiguo Feng, Yue Xu, Chuong D Hoang, Maximilian Diehn, Ash A Alizadeh. Nat Methods 2015
5

Fast and efficient QTL mapper for thousands of molecular phenotypes.
Halit Ongen, Alfonso Buil, Andrew Anand Brown, Emmanouil T Dermitzakis, Olivier Delaneau. Bioinformatics 2016
161
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.