A citation-based method for searching scientific literature

Xi Chen, Jian Zhou, Ran Zhang, Aaron K Wong, Christopher Y Park, Chandra L Theesfeld, Olga G Troyanskaya. Cell Syst 2021
Times Cited: 1







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



Times Cited
  Times     Co-cited
Similarity


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
100

MYC and Breast Cancer.
Jinhua Xu, Yinghua Chen, Olufunmilayo I Olopade. Genes Cancer 2010
163
100

ChIP-Seq identification of weakly conserved heart enhancers.
Matthew J Blow, David J McCulley, Zirong Li, Tao Zhang, Jennifer A Akiyama, Amy Holt, Ingrid Plajzer-Frick, Malak Shoukry, Crystal Wright, Feng Chen,[...]. Nat Genet 2010
321
100

Optimizing ChIP-seq peak detectors using visual labels and supervised machine learning.
Toby Dylan Hocking, Patricia Goerner-Potvin, Andreanne Morin, Xiaojian Shao, Tomi Pastinen, Guillaume Bourque. Bioinformatics 2017
10
100

Low-affinity transcription factor binding sites shape morphogen responses and enhancer evolution.
Andrea I Ramos, Scott Barolo. Philos Trans R Soc Lond B Biol Sci 2013
63
100


IRF2 is a master regulator of human keratinocyte stem cell fate.
Nicolas Mercado, Gabi Schutzius, Christian Kolter, David Estoppey, Sebastian Bergling, Guglielmo Roma, Caroline Gubser Keller, Florian Nigsch, Adrian Salathe, Remi Terranova,[...]. Nat Commun 2019
9
100

Inactivation of Arid1a in the endometrium is associated with endometrioid tumorigenesis through transcriptional reprogramming.
Yohan Suryo Rahmanto, Wenjing Shen, Xu Shi, Xi Chen, Yu Yu, Zheng-Cheng Yu, Tsutomu Miyamoto, Meng-Horng Lee, Vivek Singh, Ryoichi Asaka,[...]. Nat Commun 2020
5
100

Estrogen receptors: role in breast cancer.
M J Duffy. Crit Rev Clin Lab Sci 2006
68
100

CNN-Peaks: ChIP-Seq peak detection pipeline using convolutional neural networks that imitate human visual inspection.
Dongpin Oh, J Seth Strattan, Junho K Hur, José Bento, Alexander Eckehart Urban, Giltae Song, J Michael Cherry. Sci Rep 2020
1
100

ChIP-BIT: Bayesian inference of target genes using a novel joint probabilistic model of ChIP-seq profiles.
Xi Chen, Jin-Gyoung Jung, Ayesha N Shajahan-Haq, Robert Clarke, Ie-Ming Shih, Yue Wang, Luca Magnani, Tian-Li Wang, Jianhua Xuan. Nucleic Acids Res 2016
5
100


BICORN: An R package for integrative inference of de novo cis-regulatory modules.
Xi Chen, Jinghua Gu, Andrew F Neuwald, Leena Hilakivi-Clarke, Robert Clarke, Jianhua Xuan. Sci Rep 2020
1
100

ChIP-seq guidelines and practices of the ENCODE and modENCODE consortia.
Stephen G Landt, Georgi K Marinov, Anshul Kundaje, Pouya Kheradpour, Florencia Pauli, Serafim Batzoglou, Bradley E Bernstein, Peter Bickel, James B Brown, Philip Cayting,[...]. Genome Res 2012
970
100

ChIP-Seq of transcription factors predicts absolute and differential gene expression in embryonic stem cells.
Zhengqing Ouyang, Qing Zhou, Wing Hung Wong. Proc Natl Acad Sci U S A 2009
209
100

What is a Master Regulator?
Sunny Sun-Kin Chan, Michael Kyba. J Stem Cell Res Ther 2013
61
100

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
100

48
100

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
100

ChIP-seq accurately predicts tissue-specific activity of enhancers.
Axel Visel, Matthew J Blow, Zirong Li, Tao Zhang, Jennifer A Akiyama, Amy Holt, Ingrid Plajzer-Frick, Malak Shoukry, Crystal Wright, Feng Chen,[...]. Nature 2009
100

Epigenomic analysis reveals DNA motifs regulating histone modifications in human and mouse.
Vu Ngo, Zhao Chen, Kai Zhang, John W Whitaker, Mengchi Wang, Wei Wang. Proc Natl Acad Sci U S A 2019
7
100

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
100

Transcriptional enhancers: from properties to genome-wide predictions.
Daria Shlyueva, Gerald Stampfel, Alexander Stark. Nat Rev Genet 2014
668
100

Tudor Domain Containing Protein 3 Promotes Tumorigenesis and Invasive Capacity of Breast Cancer Cells.
Alan Morettin, Geneviève Paris, Younes Bouzid, R Mitchell Baldwin, Theresa J Falls, John C Bell, Jocelyn Côté. Sci Rep 2017
7
100

Chromatin extrusion explains key features of loop and domain formation in wild-type and engineered genomes.
Adrian L Sanborn, Suhas S P Rao, Su-Chen Huang, Neva C Durand, Miriam H Huntley, Andrew I Jewett, Ivan D Bochkov, Dharmaraj Chinnappan, Ashok Cutkosky, Jian Li,[...]. Proc Natl Acad Sci U S A 2015
726
100

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
100

The chromatin insulator CTCF and the emergence of metazoan diversity.
Peter Heger, Birger Marin, Marek Bartkuhn, Einhard Schierenberg, Thomas Wiehe. Proc Natl Acad Sci U S A 2012
95
100

CRNET: an efficient sampling approach to infer functional regulatory networks by integrating large-scale ChIP-seq and time-course RNA-seq data.
Xi Chen, Jinghua Gu, Xiao Wang, Jin-Gyoung Jung, Tian-Li Wang, Leena Hilakivi-Clarke, Robert Clarke, Jianhua Xuan. Bioinformatics 2018
7
100


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.