A citation-based method for searching scientific literature

Guangsheng Pei, Ruifeng Hu, Yulin Dai, Astrid Marilyn Manuel, Zhongming Zhao, Peilin Jia. Nucleic Acids Res 2021
Times Cited: 3







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



Times Cited
  Times     Co-cited
Similarity


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
234
66

Decoding whole-genome mutational signatures in 37 human pan-cancers by denoising sparse autoencoder neural network.
Guangsheng Pei, Ruifeng Hu, Yulin Dai, Zhongming Zhao, Peilin Jia. Oncogene 2020
5
66

FunSeq2: a framework for prioritizing noncoding regulatory variants in cancer.
Yao Fu, Zhu Liu, Shaoke Lou, Jason Bedford, Xinmeng Jasmine Mu, Kevin Y Yip, Ekta Khurana, Mark Gerstein. Genome Biol 2014
172
33

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
33

Beyond GWASs: illuminating the dark road from association to function.
Stacey L Edwards, Jonathan Beesley, Juliet D French, Alison M Dunning. Am J Hum Genet 2013
424
33

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
33

ANNOVAR: functional annotation of genetic variants from high-throughput sequencing data.
Kai Wang, Mingyao Li, Hakon Hakonarson. Nucleic Acids Res 2010
33


The UCSC Genome Browser Database: update 2006.
A S Hinrichs, D Karolchik, R Baertsch, G P Barber, G Bejerano, H Clawson, M Diekhans, T S Furey, R A Harte, F Hsu,[...]. Nucleic Acids Res 2006
643
33


The Post-GWAS Era: From Association to Function.
Michael D Gallagher, Alice S Chen-Plotkin. Am J Hum Genet 2018
232
33

Pathway-based analysis of GWAS datasets: effective but caution required.
Peilin Jia, Lily Wang, Herbert Y Meltzer, Zhongming Zhao. Int J Neuropsychopharmacol 2011
51
33


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
33

Gene expression imputation and cell-type deconvolution in human brain with spatiotemporal precision and its implications for brain-related disorders.
Guangsheng Pei, Yin-Ying Wang, Lukas M Simon, Yulin Dai, Zhongming Zhao, Peilin Jia. Genome Res 2021
3
33


Completing the ENCODE3 compendium yields accurate imputations across a variety of assays and human biosamples.
Jacob Schreiber, Jeffrey Bilmes, William Stafford Noble. Genome Biol 2020
8
33

TSEA-DB: a trait-tissue association map for human complex traits and diseases.
Peilin Jia, Yulin Dai, Ruifeng Hu, Guangsheng Pei, Astrid Marilyn Manuel, Zhongming Zhao. Nucleic Acids Res 2020
11
33

Similarity regression predicts evolution of transcription factor sequence specificity.
Samuel A Lambert, Ally W H Yang, Alexander Sasse, Gwendolyn Cowley, Mihai Albu, Mark X Caddick, Quaid D Morris, Matthew T Weirauch, Timothy R Hughes. Nat Genet 2019
35
33

Sequential regulatory activity prediction across chromosomes with convolutional neural networks.
David R Kelley, Yakir A Reshef, Maxwell Bileschi, David Belanger, Cory Y McLean, Jasper Snoek. Genome Res 2018
79
33


A single-cell atlas of entorhinal cortex from individuals with Alzheimer's disease reveals cell-type-specific gene expression regulation.
Alexandra Grubman, Gabriel Chew, John F Ouyang, Guizhi Sun, Xin Yi Choo, Catriona McLean, Rebecca K Simmons, Sam Buckberry, Dulce B Vargas-Landin, Daniel Poppe,[...]. Nat Neurosci 2019
161
33

Predicting the sequence specificities of DNA- and RNA-binding proteins by deep learning.
Babak Alipanahi, Andrew Delong, Matthew T Weirauch, Brendan J Frey. Nat Biotechnol 2015
789
33

Whole-genome deep-learning analysis identifies contribution of noncoding mutations to autism risk.
Jian Zhou, Christopher Y Park, Chandra L Theesfeld, Aaron K Wong, Yuan Yuan, Claudia Scheckel, John J Fak, Julien Funk, Kevin Yao, Yoko Tajima,[...]. Nat Genet 2019
83
33


Ulcerative colitis-risk loci on chromosomes 1p36 and 12q15 found by genome-wide association study.
Mark S Silverberg, Judy H Cho, John D Rioux, Dermot P B McGovern, Jing Wu, Vito Annese, Jean-Paul Achkar, Philippe Goyette, Regan Scott, Wei Xu,[...]. Nat Genet 2009
301
33

FTO Obesity Variant Circuitry and Adipocyte Browning in Humans.
Melina Claussnitzer, Simon N Dankel, Kyoung-Han Kim, Gerald Quon, Wouter Meuleman, Christine Haugen, Viktoria Glunk, Isabel S Sousa, Jacqueline L Beaudry, Vijitha Puviindran,[...]. N Engl J Med 2015
672
33

Microglia in Alzheimer's Disease: Risk Factors and Inflammation.
Atsuko Katsumoto, Hideyuki Takeuchi, Keita Takahashi, Fumiaki Tanaka. Front Neurol 2018
53
33

Deep learning sequence-based ab initio prediction of variant effects on expression and disease risk.
Jian Zhou, Chandra L Theesfeld, Kevin Yao, Kathleen M Chen, Aaron K Wong, Olga G Troyanskaya. Nat Genet 2018
115
33

Functional annotation of noncoding sequence variants.
Graham R S Ritchie, Ian Dunham, Eleftheria Zeggini, Paul Flicek. Nat Methods 2014
299
33

ClinVar: public archive of interpretations of clinically relevant variants.
Melissa J Landrum, Jennifer M Lee, Mark Benson, Garth Brown, Chen Chao, Shanmuga Chitipiralla, Baoshan Gu, Jennifer Hart, Douglas Hoffman, Jeffrey Hoover,[...]. Nucleic Acids Res 2016
33


Weak sharing of genetic association signals in three lung cancer subtypes: evidence at the SNP, gene, regulation, and pathway levels.
Timothy D O'Brien, Peilin Jia, Neil E Caporaso, Maria Teresa Landi, Zhongming Zhao. Genome Med 2018
15
33


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
219
33

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
186
33

Comprehensive functional annotation of 77 prostate cancer risk loci.
Dennis J Hazelett, Suhn Kyong Rhie, Malaina Gaddis, Chunli Yan, Daniel L Lakeland, Simon G Coetzee, Brian E Henderson, Houtan Noushmehr, Wendy Cozen, Zsofia Kote-Jarai,[...]. PLoS Genet 2014
120
33

Diversity and complexity in DNA recognition by transcription factors.
Gwenael Badis, Michael F Berger, Anthony A Philippakis, Shaheynoor Talukder, Andrew R Gehrke, Savina A Jaeger, Esther T Chan, Genita Metzler, Anastasia Vedenko, Xiaoyu Chen,[...]. Science 2009
650
33

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
33

Predicting transcription factor binding sites using DNA shape features based on shared hybrid deep learning architecture.
Siguo Wang, Qinhu Zhang, Zhen Shen, Ying He, Zhen-Heng Chen, Jianqiang Li, De-Shuang Huang. Mol Ther Nucleic Acids 2021
1
100

GBA Variants are associated with a distinct pattern of cognitive deficits in Parkinson's disease.
Ignacio F Mata, James B Leverenz, Daniel Weintraub, John Q Trojanowski, Alice Chen-Plotkin, Vivianna M Van Deerlin, Beate Ritz, Rebecca Rausch, Stewart A Factor, Cathy Wood-Siverio,[...]. Mov Disord 2016
110
33

JASPAR 2020: update of the open-access database of transcription factor binding profiles.
Oriol Fornes, Jaime A Castro-Mondragon, Aziz Khan, Robin van der Lee, Xi Zhang, Phillip A Richmond, Bhavi P Modi, Solenne Correard, Marius Gheorghe, Damir Baranašić,[...]. Nucleic Acids Res 2020
424
33

Co-expression networks reveal the tissue-specific regulation of transcription and splicing.
Ashis Saha, Yungil Kim, Ariel D H Gewirtz, Brian Jo, Chuan Gao, Ian C McDowell, Barbara E Engelhardt, Alexis Battle. Genome Res 2017
76
33

Proteome-wide analysis of disease-associated SNPs that show allele-specific transcription factor binding.
Falk Butter, Lucy Davison, Tar Viturawong, Marion Scheibe, Michiel Vermeulen, John A Todd, Matthias Mann. PLoS Genet 2012
67
33

Identification of a mutation in a GATA binding site of the platelet glycoprotein Ibbeta promoter resulting in the Bernard-Soulier syndrome.
L B Ludlow, B P Schick, M L Budarf, D A Driscoll, E H Zackai, A Cohen, B A Konkle. J Biol Chem 1996
110
33

Pseudoexfoliation and Alzheimer's associated CLU risk variant, rs2279590, lies within an enhancer element and regulates CLU, EPHX2 and PTK2B gene expression.
Biswajit Padhy, Bushra Hayat, Gargi Gouranga Nanda, Pranjya Paramita Mohanty, Debasmita Pankaj Alone. Hum Mol Genet 2017
17
33

Single Nucleotide Polymorphisms (SNPs) Distant from Xenobiotic Response Elements Can Modulate Aryl Hydrocarbon Receptor Function: SNP-Dependent CYP1A1 Induction.
Duan Liu, Sisi Qin, Balmiki Ray, Krishna R Kalari, Liewei Wang, Richard M Weinshilboum. Drug Metab Dispos 2018
5
33

SNP rs17079281 decreases lung cancer risk through creating an YY1-binding site to suppress DCBLD1 expression.
Yu Wang, Rongna Ma, Ben Liu, Jinyu Kong, Hongyan Lin, Xiao Yu, Ruoyang Wang, Lei Li, Ming Gao, Baosen Zhou,[...]. Oncogene 2020
8
33

Comprehensive Multiple eQTL Detection and Its Application to GWAS Interpretation.
Biao Zeng, Luke R Lloyd-Jones, Grant W Montgomery, Andres Metspalu, Tonu Esko, Lude Franke, Urmo Vosa, Annique Claringbould, Kenneth L Brigham, Arshed A Quyyumi,[...]. Genetics 2019
11
33



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.