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: 31







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



Times Cited
  Times     Co-cited
Similarity


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
9

Long-range enhancer-promoter contacts in gene expression control.
Stefan Schoenfelder, Peter Fraser. Nat Rev Genet 2019
366
9


Functional Dissection of the Enhancer Repertoire in Human Embryonic Stem Cells.
Tahsin Stefan Barakat, Florian Halbritter, Man Zhang, André F Rendeiro, Elena Perenthaler, Christoph Bock, Ian Chambers. Cell Stem Cell 2018
80
9

GENCODE reference annotation for the human and mouse genomes.
Adam Frankish, Mark Diekhans, Anne-Maud Ferreira, Rory Johnson, Irwin Jungreis, Jane Loveland, Jonathan M Mudge, Cristina Sisu, James Wright, Joel Armstrong,[...]. Nucleic Acids Res 2019
9

Massively parallel decoding of mammalian regulatory sequences supports a flexible organizational model.
Robin P Smith, Leila Taher, Rupali P Patwardhan, Mee J Kim, Fumitaka Inoue, Jay Shendure, Ivan Ovcharenko, Nadav Ahituv. Nat Genet 2013
141
9

Determinants of enhancer and promoter activities of regulatory elements.
Robin Andersson, Albin Sandelin. Nat Rev Genet 2020
194
9

Genome-wide assessment of sequence-intrinsic enhancer responsiveness at single-base-pair resolution.
Cosmas D Arnold, Muhammad A Zabidi, Michaela Pagani, Martina Rath, Katharina Schernhuber, Tomáš Kazmar, Alexander Stark. Nat Biotechnol 2017
49
9

A method to predict the impact of regulatory variants from DNA sequence.
Dongwon Lee, David U Gorkin, Maggie Baker, Benjamin J Strober, Alessandro L Asoni, Andrew S McCallion, Michael A Beer. Nat Genet 2015
248
9

Genomic Patterns of De Novo Mutation in Simplex Autism.
Tychele N Turner, Bradley P Coe, Diane E Dickel, Kendra Hoekzema, Bradley J Nelson, Michael C Zody, Zev N Kronenberg, Fereydoun Hormozdiari, Archana Raja, Len A Pennacchio,[...]. Cell 2017
175
9

STARR-seq and UMI-STARR-seq: Assessing Enhancer Activities for Genome-Wide-, High-, and Low-Complexity Candidate Libraries.
Christoph Neumayr, Michaela Pagani, Alexander Stark, Cosmas D Arnold. Curr Protoc Mol Biol 2019
15
20

The Kipoi repository accelerates community exchange and reuse of predictive models for genomics.
Žiga Avsec, Roman Kreuzhuber, Johnny Israeli, Nancy Xu, Jun Cheng, Avanti Shrikumar, Abhimanyu Banerjee, Daniel S Kim, Thorsten Beier, Lara Urban,[...]. Nat Biotechnol 2019
59
9



Base-resolution models of transcription-factor binding reveal soft motif syntax.
Žiga Avsec, Melanie Weilert, Avanti Shrikumar, Sabrina Krueger, Amr Alexandari, Khyati Dalal, Robin Fropf, Charles McAnany, Julien Gagneur, Anshul Kundaje,[...]. Nat Genet 2021
87
9

Low-Affinity Binding Sites and the Transcription Factor Specificity Paradox in Eukaryotes.
Judith F Kribelbauer, Chaitanya Rastogi, Harmen J Bussemaker, Richard S Mann. Annu Rev Cell Dev Biol 2019
58
9

Transcriptional enhancers: from properties to genome-wide predictions.
Daria Shlyueva, Gerald Stampfel, Alexander Stark. Nat Rev Genet 2014
763
9

The accessible chromatin landscape of the human genome.
Robert E Thurman, Eric Rynes, Richard Humbert, Jeff Vierstra, Matthew T Maurano, Eric Haugen, Nathan C Sheffield, Andrew B Stergachis, Hao Wang, Benjamin Vernot,[...]. Nature 2012
9

Ever-Changing Landscapes: Transcriptional Enhancers in Development and Evolution.
Hannah K Long, Sara L Prescott, Joanna Wysocka. Cell 2016
421
9

A unique chromatin signature uncovers early developmental enhancers in humans.
Alvaro Rada-Iglesias, Ruchi Bajpai, Tomek Swigut, Samantha A Brugmann, Ryan A Flynn, Joanna Wysocka. Nature 2011
9

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
32
9

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
9

Genome-wide functional screen of 3'UTR variants uncovers causal variants for human disease and evolution.
Dustin Griesemer, James R Xue, Steven K Reilly, Jacob C Ulirsch, Kalki Kukreja, Joe R Davis, Masahiro Kanai, David K Yang, John C Butts, Mehmet H Guney,[...]. Cell 2021
13
23

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
9



Genome-wide enhancer maps link risk variants to disease genes.
Joseph Nasser, Drew T Bergman, Charles P Fulco, Philine Guckelberger, Benjamin R Doughty, Tejal A Patwardhan, Thouis R Jones, Tung H Nguyen, Jacob C Ulirsch, Fritz Lekschas,[...]. Nature 2021
75
9

Distinct and predictive chromatin signatures of transcriptional promoters and enhancers in the human genome.
Nathaniel D Heintzman, Rhona K Stuart, Gary Hon, Yutao Fu, Christina W Ching, R David Hawkins, Leah O Barrera, Sara Van Calcar, Chunxu Qu, Keith A Ching,[...]. Nat Genet 2007
9

High-resolution mapping and characterization of open chromatin across the genome.
Alan P Boyle, Sean Davis, Hennady P Shulha, Paul Meltzer, Elliott H Margulies, Zhiping Weng, Terrence S Furey, Gregory E Crawford. Cell 2008
899
9

A scalable platform for the development of cell-type-specific viral drivers.
Sinisa Hrvatin, Christopher P Tzeng, M Aurel Nagy, Hume Stroud, Charalampia Koutsioumpa, Oren F Wilcox, Elena G Assad, Jonathan Green, Christopher D Harvey, Eric C Griffith,[...]. Elife 2019
37
6

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
335
6


A viral strategy for targeting and manipulating interneurons across vertebrate species.
Jordane Dimidschstein, Qian Chen, Robin Tremblay, Stephanie L Rogers, Giuseppe-Antonio Saldi, Lihua Guo, Qing Xu, Runpeng Liu, Congyi Lu, Jianhua Chu,[...]. Nat Neurosci 2016
214
6

Genome-wide de novo risk score implicates promoter variation in autism spectrum disorder.
Joon-Yong An, Kevin Lin, Lingxue Zhu, Donna M Werling, Shan Dong, Harrison Brand, Harold Z Wang, Xuefang Zhao, Grace B Schwartz, Ryan L Collins,[...]. Science 2018
118
6


Large-Scale Exome Sequencing Study Implicates Both Developmental and Functional Changes in the Neurobiology of Autism.
F Kyle Satterstrom, Jack A Kosmicki, Jiebiao Wang, Michael S Breen, Silvia De Rubeis, Joon-Yong An, Minshi Peng, Ryan Collins, Jakob Grove, Lambertus Klei,[...]. Cell 2020
683
6

Enhancer redundancy provides phenotypic robustness in mammalian development.
Marco Osterwalder, Iros Barozzi, Virginie Tissières, Yoko Fukuda-Yuzawa, Brandon J Mannion, Sarah Y Afzal, Elizabeth A Lee, Yiwen Zhu, Ingrid Plajzer-Frick, Catherine S Pickle,[...]. Nature 2018
275
6

A curated benchmark of enhancer-gene interactions for evaluating enhancer-target gene prediction methods.
Jill E Moore, Henry E Pratt, Michael J Purcaro, Zhiping Weng. Genome Biol 2020
37
6

Integrative functional genomic analysis of human brain development and neuropsychiatric risks.
Mingfeng Li, Gabriel Santpere, Yuka Imamura Kawasawa, Oleg V Evgrafov, Forrest O Gulden, Sirisha Pochareddy, Susan M Sunkin, Zhen Li, Yurae Shin, Ying Zhu,[...]. Science 2018
300
6

Transcriptome-wide isoform-level dysregulation in ASD, schizophrenia, and bipolar disorder.
Michael J Gandal, Pan Zhang, Evi Hadjimichael, Rebecca L Walker, Chao Chen, Shuang Liu, Hyejung Won, Harm van Bakel, Merina Varghese, Yongjun Wang,[...]. Science 2018
478
6

Mutations in Human Accelerated Regions Disrupt Cognition and Social Behavior.
Ryan N Doan, Byoung-Il Bae, Beatriz Cubelos, Cindy Chang, Amer A Hossain, Samira Al-Saad, Nahit M Mukaddes, Ozgur Oner, Muna Al-Saffar, Soher Balkhy,[...]. Cell 2016
130
6

Multiplex assessment of protein variant abundance by massively parallel sequencing.
Kenneth A Matreyek, Lea M Starita, Jason J Stephany, Beth Martin, Melissa A Chiasson, Vanessa E Gray, Martin Kircher, Arineh Khechaduri, Jennifer N Dines, Ronald J Hause,[...]. Nat Genet 2018
152
6

Cell type-specific genetic regulation of gene expression across human tissues.
Sarah Kim-Hellmuth, François Aguet, Meritxell Oliva, Manuel Muñoz-Aguirre, Silva Kasela, Valentin Wucher, Stephane E Castel, Andrew R Hamel, Ana Viñuela, Amy L Roberts,[...]. Science 2020
87
6


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
810
6

Synergistic effects of common schizophrenia risk variants.
Nadine Schrode, Seok-Man Ho, Kazuhiko Yamamuro, Amanda Dobbyn, Laura Huckins, Marliette R Matos, Esther Cheng, P J Michael Deans, Erin Flaherty, Natalie Barretto,[...]. Nat Genet 2019
91
6


A massively parallel 3' UTR reporter assay reveals relationships between nucleotide content, sequence conservation, and mRNA destabilization.
Adam J Litterman, Robin Kageyama, Olivier Le Tonqueze, Wenxue Zhao, John D Gagnon, Hani Goodarzi, David J Erle, K Mark Ansel. Genome Res 2019
13
15

High-throughput mapping of regulatory DNA.
Nisha Rajagopal, Sharanya Srinivasan, Kameron Kooshesh, Yuchun Guo, Matthew D Edwards, Budhaditya Banerjee, Tahin Syed, Bart J M Emons, David K Gifford, Richard I Sherwood. Nat Biotechnol 2016
153
6

A new class of temporarily phenotypic enhancers identified by CRISPR/Cas9-mediated genetic screening.
Yarui Diao, Bin Li, Zhipeng Meng, Inkyung Jung, Ah Young Lee, Jesse Dixon, Lenka Maliskova, Kun-Liang Guan, Yin Shen, Bing Ren. Genome Res 2016
77
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.