A citation-based method for searching scientific literature

Jiyeon Choi, Tongwu Zhang, Andrew Vu, Julien Ablain, Matthew M Makowski, Leandro M Colli, Mai Xu, Rebecca C Hennessey, Jinhu Yin, Harriet Rothschild, Cathrin Gräwe, Michael A Kovacs, Karen M Funderburk, Myriam Brossard, John Taylor, Bogdan Pasaniuc, Raj Chari, Stephen J Chanock, Clive J Hoggart, Florence Demenais, Jennifer H Barrett, Matthew H Law, Mark M Iles, Kai Yu, Michiel Vermeulen, Leonard I Zon, Kevin M Brown. Nat Commun 2020
Times Cited: 24







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



Times Cited
  Times     Co-cited
Similarity


Systematic Functional Dissection of Common Genetic Variation Affecting Red Blood Cell Traits.
Jacob C Ulirsch, Satish K Nandakumar, Li Wang, Felix C Giani, Xiaolan Zhang, Peter Rogov, Alexandre Melnikov, Patrick McDonel, Ron Do, Tarjei S Mikkelsen,[...]. Cell 2016
173
37

Direct Identification of Hundreds of Expression-Modulating Variants using a Multiplexed Reporter Assay.
Ryan Tewhey, Dylan Kotliar, Daniel S Park, Brandon Liu, Sarah Winnicki, Steven K Reilly, Kristian G Andersen, Tarjei S Mikkelsen, Eric S Lander, Stephen F Schaffner,[...]. Cell 2016
191
37

High-resolution analysis of DNA regulatory elements by synthetic saturation mutagenesis.
Rupali P Patwardhan, Choli Lee, Oren Litvin, David L Young, Dana Pe'er, Jay Shendure. Nat Biotechnol 2009
198
33

Genetic effects on gene expression across human tissues.
Alexis Battle, Christopher D Brown, Barbara E Engelhardt, Stephen B Montgomery. Nature 2017
29

Functional testing of thousands of osteoarthritis-associated variants for regulatory activity.
Jason C Klein, Aidan Keith, Sarah J Rice, Colin Shepherd, Vikram Agarwal, John Loughlin, Jay Shendure. Nat Commun 2019
35
29

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
29


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
25



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
20

Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2.
Michael I Love, Wolfgang Huber, Simon Anders. Genome Biol 2014
20

Cell-type-specific eQTL of primary melanocytes facilitates identification of melanoma susceptibility genes.
Tongwu Zhang, Jiyeon Choi, Michael A Kovacs, Jianxin Shi, Mai Xu, Alisa M Goldstein, Adam J Trower, D Timothy Bishop, Mark M Iles, David L Duffy,[...]. Genome Res 2018
37
20

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
20

motifbreakR: an R/Bioconductor package for predicting variant effects at transcription factor binding sites.
Simon G Coetzee, Gerhard A Coetzee, Dennis J Hazelett. Bioinformatics 2015
101
20

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
16

Complex effects of nucleotide variants in a mammalian cis-regulatory element.
Jamie C Kwasnieski, Ilaria Mogno, Connie A Myers, Joseph C Corbo, Barak A Cohen. Proc Natl Acad Sci U S A 2012
151
16

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
726
16

Genome-scale high-resolution mapping of activating and repressive nucleotides in regulatory regions.
Jason Ernst, Alexandre Melnikov, Xiaolan Zhang, Li Wang, Peter Rogov, Tarjei S Mikkelsen, Manolis Kellis. Nat Biotechnol 2016
71
16

High-throughput identification of human SNPs affecting regulatory element activity.
Joris van Arensbergen, Ludo Pagie, Vincent D FitzPatrick, Marcel de Haas, Marijke P Baltissen, Federico Comoglio, Robin H van der Weide, Hans Teunissen, Urmo Võsa, Lude Franke,[...]. Nat Genet 2019
76
16

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
16

Massively parallel functional dissection of mammalian enhancers in vivo.
Rupali P Patwardhan, Joseph B Hiatt, Daniela M Witten, Mee J Kim, Robin P Smith, Dalit May, Choli Lee, Jennifer M Andrie, Su-In Lee, Gregory M Cooper,[...]. Nat Biotechnol 2012
314
16

Genome-wide association study identifies three new melanoma susceptibility loci.
Jennifer H Barrett, Mark M Iles, Mark Harland, John C Taylor, Joanne F Aitken, Per Arne Andresen, Lars A Akslen, Bruce K Armstrong, Marie-Francoise Avril, Esther Azizi,[...]. Nat Genet 2011
187
16

Systematic dissection and optimization of inducible enhancers in human cells using a massively parallel reporter assay.
Alexandre Melnikov, Anand Murugan, Xiaolan Zhang, Tiberiu Tesileanu, Li Wang, Peter Rogov, Soheil Feizi, Andreas Gnirke, Curtis G Callan, Justin B Kinney,[...]. Nat Biotechnol 2012
380
16

Saturation mutagenesis of twenty disease-associated regulatory elements at single base-pair resolution.
Martin Kircher, Chenling Xiong, Beth Martin, Max Schubach, Fumitaka Inoue, Robert J A Bell, Joseph F Costello, Jay Shendure, Nadav Ahituv. Nat Commun 2019
59
16

Biology and Clinical Implications of the 19q13 Aggressive Prostate Cancer Susceptibility Locus.
Ping Gao, Ji-Han Xia, Csilla Sipeky, Xiao-Ming Dong, Qin Zhang, Yuehong Yang, Peng Zhang, Sara Pereira Cruz, Kai Zhang, Jing Zhu,[...]. Cell 2018
73
16

Linking disease associations with regulatory information in the human genome.
Marc A Schaub, Alan P Boyle, Anshul Kundaje, Serafim Batzoglou, Michael Snyder. Genome Res 2012
488
12

Massively parallel in vivo enhancer assay reveals that highly local features determine the cis-regulatory function of ChIP-seq peaks.
Michael A White, Connie A Myers, Joseph C Corbo, Barak A Cohen. Proc Natl Acad Sci U S A 2013
125
12

Human 5' UTR design and variant effect prediction from a massively parallel translation assay.
Paul J Sample, Ban Wang, David W Reid, Vlad Presnyak, Iain J McFadyen, David R Morris, Georg Seelig. Nat Biotechnol 2019
63
12

Identification of Functional Variants in the FAM13A Chronic Obstructive Pulmonary Disease Genome-Wide Association Study Locus by Massively Parallel Reporter Assays.
Peter J Castaldi, Feng Guo, Dandi Qiao, Fei Du, Zun Zar Chi Naing, Yan Li, Betty Pham, Tarjei S Mikkelsen, Michael H Cho, Edwin K Silverman,[...]. Am J Respir Crit Care Med 2019
21
14

Genome-wide association analyses identify 44 risk variants and refine the genetic architecture of major depression.
Naomi R Wray, Stephan Ripke, Manuel Mattheisen, Maciej Trzaskowski, Enda M Byrne, Abdel Abdellaoui, Mark J Adams, Esben Agerbo, Tracy M Air, Till M F Andlauer,[...]. Nat Genet 2018
12

A systematic evaluation of the design and context dependencies of massively parallel reporter assays.
Jason C Klein, Vikram Agarwal, Fumitaka Inoue, Aidan Keith, Beth Martin, Martin Kircher, Nadav Ahituv, Jay Shendure. Nat Methods 2020
24
12

Partitioning heritability of regulatory and cell-type-specific variants across 11 common diseases.
Alexander Gusev, S Hong Lee, Gosia Trynka, Hilary Finucane, Bjarni J Vilhjálmsson, Han Xu, Chongzhi Zang, Stephan Ripke, Brendan Bulik-Sullivan, Eli Stahl,[...]. Am J Hum Genet 2014
339
12

Identification and Massively Parallel Characterization of Regulatory Elements Driving Neural Induction.
Fumitaka Inoue, Anat Kreimer, Tal Ashuach, Nadav Ahituv, Nir Yosef. Cell Stem Cell 2019
31
12

Resolving mechanisms of immune-mediated disease in primary CD4 T cells.
Christophe Bourges, Abigail F Groff, Oliver S Burren, Chiara Gerhardinger, Kaia Mattioli, Anna Hutchinson, Theodore Hu, Tanmay Anand, Madeline W Epping, Chris Wallace,[...]. EMBO Mol Med 2020
13
23

Massively parallel quantification of the regulatory effects of noncoding genetic variation in a human cohort.
Christopher M Vockley, Cong Guo, William H Majoros, Michael Nodzenski, Denise M Scholtens, M Geoffrey Hayes, William L Lowe, Timothy E Reddy. Genome Res 2015
56
12

Learning the sequence determinants of alternative splicing from millions of random sequences.
Alexander B Rosenberg, Rupali P Patwardhan, Jay Shendure, Georg Seelig. Cell 2015
117
12

Massively parallel cis-regulatory analysis in the mammalian central nervous system.
Susan Q Shen, Connie A Myers, Andrew E O Hughes, Leah C Byrne, John G Flannery, Joseph C Corbo. Genome Res 2016
62
12

Trimmomatic: a flexible trimmer for Illumina sequence data.
Anthony M Bolger, Marc Lohse, Bjoern Usadel. Bioinformatics 2014
12

CHiCAGO: robust detection of DNA looping interactions in Capture Hi-C data.
Jonathan Cairns, Paula Freire-Pritchett, Steven W Wingett, Csilla Várnai, Andrew Dimond, Vincent Plagnol, Daniel Zerbino, Stefan Schoenfelder, Biola-Maria Javierre, Cameron Osborne,[...]. Genome Biol 2016
187
12

Fast gapped-read alignment with Bowtie 2.
Ben Langmead, Steven L Salzberg. Nat Methods 2012
12

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
12

Genome-wide association study identifies three loci associated with melanoma risk.
D Timothy Bishop, Florence Demenais, Mark M Iles, Mark Harland, John C Taylor, Eve Corda, Juliette Randerson-Moor, Joanne F Aitken, Marie-Francoise Avril, Esther Azizi,[...]. Nat Genet 2009
335
12

MX 2 is a novel regulator of cell cycle in melanoma cells.
Marina Juraleviciute, Joanna Pozniak, Jérémie Nsengimana, Mark Harland, Juliette Randerson-Moor, Patrik Wernhoff, Assia Bassarova, Geir Frode Øy, Gunhild Trøen, Vivi Ann Flørenes,[...]. Pigment Cell Melanoma Res 2020
8
37


Genome engineering using the CRISPR-Cas9 system.
F Ann Ran, Patrick D Hsu, Jason Wright, Vineeta Agarwala, David A Scott, Feng Zhang. Nat Protoc 2013
12

Systematic analysis of binding of transcription factors to noncoding variants.
Jian Yan, Yunjiang Qiu, André M Ribeiro Dos Santos, Yimeng Yin, Yang E Li, Nick Vinckier, Naoki Nariai, Paola Benaglio, Anugraha Raman, Xiaoyu Li,[...]. Nature 2021
25
12

Functional characterization of a multi-cancer risk locus on chr5p15.33 reveals regulation of TERT by ZNF148.
Jun Fang, Jinping Jia, Matthew Makowski, Mai Xu, Zhaoming Wang, Tongwu Zhang, Jason W Hoskins, Jiyeon Choi, Younghun Han, Mingfeng Zhang,[...]. Nat Commun 2017
27
12

A functional variant on 20q13.33 related to glioma risk alters enhancer activity and modulates expression of multiple genes.
Mourad Wagdy Ali, C Pawan K Patro, Jacqueline Jufen Zhu, Christopher H Dampier, Sarah J Plummer, Cem Kuscu, Mazhar Adli, Ching Lau, Rose K Lai, Graham Casey. Hum Mutat 2021
5
60

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
357
12


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.