A citation-based method for searching scientific literature

Jason C Klein, Vikram Agarwal, Fumitaka Inoue, Aidan Keith, Beth Martin, Martin Kircher, Nadav Ahituv, Jay Shendure. Nat Methods 2020
Times Cited: 26







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



Times Cited
  Times     Co-cited
Similarity


Genome-wide quantitative enhancer activity maps identified by STARR-seq.
Cosmas D Arnold, Daniel Gerlach, Christoph Stelzer, Łukasz M Boryń, Martina Rath, Alexander Stark. Science 2013
530
53


A systematic comparison reveals substantial differences in chromosomal versus episomal encoding of enhancer activity.
Fumitaka Inoue, Martin Kircher, Beth Martin, Gregory M Cooper, Daniela M Witten, Michael T McManus, Nadav Ahituv, Jay Shendure. Genome Res 2017
128
38

Towards a comprehensive catalogue of validated and target-linked human enhancers.
Molly Gasperini, Jacob M Tome, Jay Shendure. Nat Rev Genet 2020
99
34

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
200
30

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
193
30

Resolving systematic errors in widely used enhancer activity assays in human cells.
Felix Muerdter, Łukasz M Boryń, Ashley R Woodfin, Christoph Neumayr, Martina Rath, Muhammad A Zabidi, Michaela Pagani, Vanja Haberle, Tomáš Kazmar, Rui R Catarino,[...]. Nat Methods 2018
70
30

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
26

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
176
26

Activity-by-contact model of enhancer-promoter regulation from thousands of CRISPR perturbations.
Charles P Fulco, Joseph Nasser, Thouis R Jones, Glen Munson, Drew T Bergman, Vidya Subramanian, Sharon R Grossman, Rockwell Anyoha, Benjamin R Doughty, Tejal A Patwardhan,[...]. Nat Genet 2019
214
26

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
72
26

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
82
26

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
62
26

lentiMPRA and MPRAflow for high-throughput functional characterization of gene regulatory elements.
M Grace Gordon, Fumitaka Inoue, Beth Martin, Max Schubach, Vikram Agarwal, Sean Whalen, Shiyun Feng, Jingjing Zhao, Tal Ashuach, Ryan Ziffra,[...]. Nat Protoc 2020
17
41

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
385
26

Decoding enhancers using massively parallel reporter assays.
Fumitaka Inoue, Nadav Ahituv. Genomics 2015
112
26

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
33
23

Synthetic and genomic regulatory elements reveal aspects of cis-regulatory grammar in mouse embryonic stem cells.
Dana M King, Clarice Kit Yee Hong, James L Shepherdson, David M Granas, Brett B Maricque, Barak A Cohen. Elife 2020
22
27

Systematic dissection of regulatory motifs in 2000 predicted human enhancers using a massively parallel reporter assay.
Pouya Kheradpour, Jason Ernst, Alexandre Melnikov, Peter Rogov, Li Wang, Xiaolan Zhang, Jessica Alston, Tarjei S Mikkelsen, Manolis Kellis. Genome Res 2013
177
23

Fast gapped-read alignment with Bowtie 2.
Ben Langmead, Steven L Salzberg. Nat Methods 2012
23

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
403
23

MPRAnalyze: statistical framework for massively parallel reporter assays.
Tal Ashuach, David S Fischer, Anat Kreimer, Nadav Ahituv, Fabian J Theis, Nir Yosef. Genome Biol 2019
23
26

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
19

High-resolution genome-wide functional dissection of transcriptional regulatory regions and nucleotides in human.
Xinchen Wang, Liang He, Sarah M Goggin, Alham Saadat, Li Wang, Nasa Sinnott-Armstrong, Melina Claussnitzer, Manolis Kellis. Nat Commun 2018
47
19


Functional assessment of human enhancer activities using whole-genome STARR-sequencing.
Yuwen Liu, Shan Yu, Vineet K Dhiman, Tonya Brunetti, Heather Eckart, Kevin P White. Genome Biol 2017
43
19

STARRPeaker: uniform processing and accurate identification of STARR-seq active regions.
Donghoon Lee, Manman Shi, Jennifer Moran, Martha Wall, Jing Zhang, Jason Liu, Dominic Fitzgerald, Yasuhiro Kyono, Lijia Ma, Kevin P White,[...]. Genome Biol 2020
16
31

High-throughput functional testing of ENCODE segmentation predictions.
Jamie C Kwasnieski, Christopher Fiore, Hemangi G Chaudhari, Barak A Cohen. Genome Res 2014
137
19

Deciphering eukaryotic gene-regulatory logic with 100 million random promoters.
Carl G de Boer, Eeshit Dhaval Vaishnav, Ronen Sadeh, Esteban Luis Abeyta, Nir Friedman, Aviv Regev. Nat Biotechnol 2020
65
19

The role of regulatory variation in complex traits and disease.
Frank W Albert, Leonid Kruglyak. Nat Rev Genet 2015
517
19

A Genome-wide Framework for Mapping Gene Regulation via Cellular Genetic Screens.
Molly Gasperini, Andrew J Hill, José L McFaline-Figueroa, Beth Martin, Seungsoo Kim, Melissa D Zhang, Dana Jackson, Anh Leith, Jacob Schreiber, William S Noble,[...]. Cell 2019
168
19

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
318
19


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
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
19

Genome-wide mapping of autonomous promoter activity in human cells.
Joris van Arensbergen, Vincent D FitzPatrick, Marcel de Haas, Ludo Pagie, Jasper Sluimer, Harmen J Bussemaker, Bas van Steensel. Nat Biotechnol 2017
44
19

High-throughput functional comparison of promoter and enhancer activities.
Thomas A Nguyen, Richard D Jones, Andrew R Snavely, Andreas R Pfenning, Rory Kirchner, Martin Hemberg, Jesse M Gray. Genome Res 2016
65
15

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
126
15

Integration of multiple epigenomic marks improves prediction of variant impact in saturation mutagenesis reporter assay.
Dustin Shigaki, Orit Adato, Aashish N Adhikari, Shengcheng Dong, Alex Hawkins-Hooker, Fumitaka Inoue, Tamar Juven-Gershon, Henry Kenlay, Beth Martin, Ayoti Patra,[...]. Hum Mutat 2019
17
23

Perturb-Seq: Dissecting Molecular Circuits with Scalable Single-Cell RNA Profiling of Pooled Genetic Screens.
Atray Dixit, Oren Parnas, Biyu Li, Jenny Chen, Charles P Fulco, Livnat Jerby-Arnon, Nemanja D Marjanovic, Danielle Dionne, Tyler Burks, Raktima Raychowdhury,[...]. Cell 2016
564
15

A massively parallel reporter assay dissects the influence of chromatin structure on cis-regulatory activity.
Brett B Maricque, Hemangi G Chaudhari, Barak A Cohen. Nat Biotechnol 2018
32
15

Massively parallel reporter assays of melanoma risk variants identify MX2 as a gene promoting melanoma.
Jiyeon Choi, Tongwu Zhang, Andrew Vu, Julien Ablain, Matthew M Makowski, Leandro M Colli, Mai Xu, Rebecca C Hennessey, Jinhu Yin, Harriet Rothschild,[...]. Nat Commun 2020
25
16

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
15

STARR-seq - principles and applications.
Felix Muerdter, Łukasz M Boryń, Cosmas D Arnold. Genomics 2015
47
15

FIMO: scanning for occurrences of a given motif.
Charles E Grant, Timothy L Bailey, William Stafford Noble. Bioinformatics 2011
15

Enhanced regulatory sequence prediction using gapped k-mer features.
Mahmoud Ghandi, Dongwon Lee, Morteza Mohammad-Noori, Michael A Beer. PLoS Comput Biol 2014
225
15

Enhancer evolution across 20 mammalian species.
Diego Villar, Camille Berthelot, Sarah Aldridge, Tim F Rayner, Margus Lukk, Miguel Pignatelli, Thomas J Park, Robert Deaville, Jonathan T Erichsen, Anna J Jasinska,[...]. Cell 2015
363
15

Systematic interrogation of human promoters.
Shira Weingarten-Gabbay, Ronit Nir, Shai Lubliner, Eilon Sharon, Yael Kalma, Adina Weinberger, Eran Segal. Genome Res 2019
42
15

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
15

Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2.
Michael I Love, Wolfgang Huber, Simon Anders. Genome Biol 2014
15


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.