A citation-based method for searching scientific literature

Anshul Kundaje, Wouter Meuleman, Jason Ernst, Misha Bilenky, Angela Yen, Alireza Heravi-Moussavi, Pouya Kheradpour, Zhizhuo Zhang, Jianrong Wang, Michael J Ziller, Viren Amin, John W Whitaker, Matthew D Schultz, Lucas D Ward, Abhishek Sarkar, Gerald Quon, Richard S Sandstrom, Matthew L Eaton, Yi-Chieh Wu, Andreas R Pfenning, Xinchen Wang, Melina Claussnitzer, Yaping Liu, Cristian Coarfa, R Alan Harris, Noam Shoresh, Charles B Epstein, Elizabeta Gjoneska, Danny Leung, Wei Xie, R David Hawkins, Ryan Lister, Chibo Hong, Philippe Gascard, Andrew J Mungall, Richard Moore, Eric Chuah, Angela Tam, Theresa K Canfield, R Scott Hansen, Rajinder Kaul, Peter J Sabo, Mukul S Bansal, Annaick Carles, Jesse R Dixon, Kai-How Farh, Soheil Feizi, Rosa Karlic, Ah-Ram Kim, Ashwinikumar Kulkarni, Daofeng Li, Rebecca Lowdon, GiNell Elliott, Tim R Mercer, Shane J Neph, Vitor Onuchic, Paz Polak, Nisha Rajagopal, Pradipta Ray, Richard C Sallari, Kyle T Siebenthall, Nicholas A Sinnott-Armstrong, Michael Stevens, Robert E Thurman, Jie Wu, Bo Zhang, Xin Zhou, Arthur E Beaudet, Laurie A Boyer, Philip L De Jager, Peggy J Farnham, Susan J Fisher, David Haussler, Steven J M Jones, Wei Li, Marco A Marra, Michael T McManus, Shamil Sunyaev, James A Thomson, Thea D Tlsty, Li-Huei Tsai, Wei Wang, Robert A Waterland, Michael Q Zhang, Lisa H Chadwick, Bradley E Bernstein, Joseph F Costello, Joseph R Ecker, Martin Hirst, Alexander Meissner, Aleksandar Milosavljevic, Bing Ren, John A Stamatoyannopoulos, Ting Wang, Manolis Kellis. Nature 2015
Times Cited: 2832







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



Times Cited
  Times     Co-cited
Similarity




Model-based analysis of ChIP-Seq (MACS).
Yong Zhang, Tao Liu, Clifford A Meyer, Jérôme Eeckhoute, David S Johnson, Bradley E Bernstein, Chad Nusbaum, Richard M Myers, Myles Brown, Wei Li,[...]. Genome Biol 2008
16

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
15

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
712
15

Genetic effects on gene expression across human tissues.
Alexis Battle, Christopher D Brown, Barbara E Engelhardt, Stephen B Montgomery. Nature 2017
14

Simple combinations of lineage-determining transcription factors prime cis-regulatory elements required for macrophage and B cell identities.
Sven Heinz, Christopher Benner, Nathanael Spann, Eric Bertolino, Yin C Lin, Peter Laslo, Jason X Cheng, Cornelis Murre, Harinder Singh, Christopher K Glass. Mol Cell 2010
14

Fast gapped-read alignment with Bowtie 2.
Ben Langmead, Steven L Salzberg. Nat Methods 2012
13

METAL: fast and efficient meta-analysis of genomewide association scans.
Cristen J Willer, Yun Li, Gonçalo R Abecasis. Bioinformatics 2010
13

A 3D map of the human genome at kilobase resolution reveals principles of chromatin looping.
Suhas S P Rao, Miriam H Huntley, Neva C Durand, Elena K Stamenova, Ivan D Bochkov, James T Robinson, Adrian L Sanborn, Ido Machol, Arina D Omer, Eric S Lander,[...]. Cell 2014
12


Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2.
Michael I Love, Wolfgang Huber, Simon Anders. Genome Biol 2014
12

Functional mapping and annotation of genetic associations with FUMA.
Kyoko Watanabe, Erdogan Taskesen, Arjen van Bochoven, Danielle Posthuma. Nat Commun 2017
635
11

Systematic localization of common disease-associated variation in regulatory DNA.
Matthew T Maurano, Richard Humbert, Eric Rynes, Robert E Thurman, Eric Haugen, Hao Wang, Alex P Reynolds, Richard Sandstrom, Hongzhu Qu, Jennifer Brody,[...]. Science 2012
11

Transposition of native chromatin for fast and sensitive epigenomic profiling of open chromatin, DNA-binding proteins and nucleosome position.
Jason D Buenrostro, Paul G Giresi, Lisa C Zaba, Howard Y Chang, William J Greenleaf. Nat Methods 2013
11

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
11

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
794
11

Genetic and epigenetic fine mapping of causal autoimmune disease variants.
Kyle Kai-How Farh, Alexander Marson, Jiang Zhu, Markus Kleinewietfeld, William J Housley, Samantha Beik, Noam Shoresh, Holly Whitton, Russell J H Ryan, Alexander A Shishkin,[...]. Nature 2015
926
10

Comprehensive functional genomic resource and integrative model for the human brain.
Daifeng Wang, Shuang Liu, Jonathan Warrell, Hyejung Won, Xu Shi, Fabio C P Navarro, Declan Clarke, Mengting Gu, Prashant Emani, Yucheng T Yang,[...]. Science 2018
214
10

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
581
10

LD Score regression distinguishes confounding from polygenicity in genome-wide association studies.
Brendan K Bulik-Sullivan, Po-Ru Loh, Hilary K Finucane, Stephan Ripke, Jian Yang, Nick Patterson, Mark J Daly, Alkes L Price, Benjamin M Neale. Nat Genet 2015
10


The Encyclopedia of DNA elements (ENCODE): data portal update.
Carrie A Davis, Benjamin C Hitz, Cricket A Sloan, Esther T Chan, Jean M Davidson, Idan Gabdank, Jason A Hilton, Kriti Jain, Ulugbek K Baymuradov, Aditi K Narayanan,[...]. Nucleic Acids Res 2018
483
9


Annotation of functional variation in personal genomes using RegulomeDB.
Alan P Boyle, Eurie L Hong, Manoj Hariharan, Yong Cheng, Marc A Schaub, Maya Kasowski, Konrad J Karczewski, Julie Park, Benjamin C Hitz, Shuai Weng,[...]. Genome Res 2012
8

An atlas of genetic correlations across human diseases and traits.
Brendan Bulik-Sullivan, Hilary K Finucane, Verneri Anttila, Alexander Gusev, Felix R Day, Po-Ru Loh, Laramie Duncan, John R B Perry, Nick Patterson, Elise B Robinson,[...]. Nat Genet 2015
8

GCTA: a tool for genome-wide complex trait analysis.
Jian Yang, S Hong Lee, Michael E Goddard, Peter M Visscher. Am J Hum Genet 2011
8

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
8

An atlas of active enhancers across human cell types and tissues.
Robin Andersson, Claudia Gebhard, Irene Miguel-Escalada, Ilka Hoof, Jette Bornholdt, Mette Boyd, Yun Chen, Xiaobei Zhao, Christian Schmidl, Takahiro Suzuki,[...]. Nature 2014
8

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
890
8

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
8

GREAT improves functional interpretation of cis-regulatory regions.
Cory Y McLean, Dave Bristor, Michael Hiller, Shoa L Clarke, Bruce T Schaar, Craig B Lowe, Aaron M Wenger, Gill Bejerano. Nat Biotechnol 2010
7

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
7


The Allelic Landscape of Human Blood Cell Trait Variation and Links to Common Complex Disease.
William J Astle, Heather Elding, Tao Jiang, Dave Allen, Dace Ruklisa, Alice L Mann, Daniel Mead, Heleen Bouman, Fernando Riveros-Mckay, Myrto A Kostadima,[...]. Cell 2016
429
7

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
7

A Compendium of Chromatin Contact Maps Reveals Spatially Active Regions in the Human Genome.
Anthony D Schmitt, Ming Hu, Inkyung Jung, Zheng Xu, Yunjiang Qiu, Catherine L Tan, Yun Li, Shin Lin, Yiing Lin, Cathy L Barr,[...]. Cell Rep 2016
311
7

MAGMA: generalized gene-set analysis of GWAS data.
Christiaan A de Leeuw, Joris M Mooij, Tom Heskes, Danielle Posthuma. PLoS Comput Biol 2015
735
7

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
544
7

The Dynamic Landscape of Open Chromatin during Human Cortical Neurogenesis.
Luis de la Torre-Ubieta, Jason L Stein, Hyejung Won, Carli K Opland, Dan Liang, Daning Lu, Daniel H Geschwind. Cell 2018
116
7

An improved ATAC-seq protocol reduces background and enables interrogation of frozen tissues.
M Ryan Corces, Alexandro E Trevino, Emily G Hamilton, Peyton G Greenside, Nicholas A Sinnott-Armstrong, Sam Vesuna, Ansuman T Satpathy, Adam J Rubin, Kathleen S Montine, Beijing Wu,[...]. Nat Methods 2017
423
7

Histone H3K27ac separates active from poised enhancers and predicts developmental state.
Menno P Creyghton, Albert W Cheng, G Grant Welstead, Tristan Kooistra, Bryce W Carey, Eveline J Steine, Jacob Hanna, Michael A Lodato, Garrett M Frampton, Phillip A Sharp,[...]. Proc Natl Acad Sci U S A 2010
7

The 3D Genome Browser: a web-based browser for visualizing 3D genome organization and long-range chromatin interactions.
Yanli Wang, Fan Song, Bo Zhang, Lijun Zhang, Jie Xu, Da Kuang, Daofeng Li, Mayank N K Choudhary, Yun Li, Ming Hu,[...]. Genome Biol 2018
169
7

Chromatin architecture reorganization during stem cell differentiation.
Jesse R Dixon, Inkyung Jung, Siddarth Selvaraj, Yin Shen, Jessica E Antosiewicz-Bourget, Ah Young Lee, Zhen Ye, Audrey Kim, Nisha Rajagopal, Wei Xie,[...]. Nature 2015
740
7


ATAC-seq: A Method for Assaying Chromatin Accessibility Genome-Wide.
Jason D Buenrostro, Beijing Wu, Howard Y Chang, William J Greenleaf. Curr Protoc Mol Biol 2015
961
7

Expanded encyclopaedias of DNA elements in the human and mouse genomes.
Jill E Moore, Michael J Purcaro, Henry E Pratt, Charles B Epstein, Noam Shoresh, Jessika Adrian, Trupti Kawli, Carrie A Davis, Alexander Dobin, Rajinder Kaul,[...]. Nature 2020
139
7

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
7

Mapping and analysis of chromatin state dynamics in nine human cell types.
Jason Ernst, Pouya Kheradpour, Tarjei S Mikkelsen, Noam Shoresh, Lucas D Ward, Charles B Epstein, Xiaolan Zhang, Li Wang, Robbyn Issner, Michael Coyne,[...]. Nature 2011
6

HiChIP: efficient and sensitive analysis of protein-directed genome architecture.
Maxwell R Mumbach, Adam J Rubin, Ryan A Flynn, Chao Dai, Paul A Khavari, William J Greenleaf, Howard Y Chang. Nat Methods 2016
348
6


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.