A citation-based method for searching scientific literature

Chun-Xiao Song, Senlin Yin, Li Ma, Amanda Wheeler, Yu Chen, Yan Zhang, Bin Liu, Junjie Xiong, Weihan Zhang, Jiankun Hu, Zongguang Zhou, Biao Dong, Zhiqi Tian, Stefanie S Jeffrey, Mei-Sze Chua, Samuel So, Weimin Li, Yuquan Wei, Jiajie Diao, Dan Xie, Stephen R Quake. Cell Res 2017
Times Cited: 130







List of co-cited articles
1062 articles co-cited >1



Times Cited
  Times     Co-cited
Similarity


5-Hydroxymethylcytosine signatures in circulating cell-free DNA as diagnostic biomarkers for human cancers.
Wenshuai Li, Xu Zhang, Xingyu Lu, Lei You, Yanqun Song, Zhongguang Luo, Jun Zhang, Ji Nie, Wanwei Zheng, Diannan Xu,[...]. Cell Res 2017
160
57

Conversion of 5-methylcytosine to 5-hydroxymethylcytosine in mammalian DNA by MLL partner TET1.
Mamta Tahiliani, Kian Peng Koh, Yinghua Shen, William A Pastor, Hozefa Bandukwala, Yevgeny Brudno, Suneet Agarwal, Lakshminarayan M Iyer, David R Liu, L Aravind,[...]. Science 2009
35

Selective chemical labeling reveals the genome-wide distribution of 5-hydroxymethylcytosine.
Chun-Xiao Song, Keith E Szulwach, Ye Fu, Qing Dai, Chengqi Yi, Xuekun Li, Yujing Li, Chih-Hsin Chen, Wen Zhang, Xing Jian,[...]. Nat Biotechnol 2011
724
31

Sensitive tumour detection and classification using plasma cell-free DNA methylomes.
Shu Yi Shen, Rajat Singhania, Gordon Fehringer, Ankur Chakravarthy, Michael H A Roehrl, Dianne Chadwick, Philip C Zuzarte, Ayelet Borgida, Ting Ting Wang, Tiantian Li,[...]. Nature 2018
389
30

Comprehensive human cell-type methylation atlas reveals origins of circulating cell-free DNA in health and disease.
Joshua Moss, Judith Magenheim, Daniel Neiman, Hai Zemmour, Netanel Loyfer, Amit Korach, Yaacov Samet, Myriam Maoz, Henrik Druid, Peter Arner,[...]. Nat Commun 2018
314
25

Cell-free DNA Comprises an In Vivo Nucleosome Footprint that Informs Its Tissues-Of-Origin.
Matthew W Snyder, Martin Kircher, Andrew J Hill, Riza M Daza, Jay Shendure. Cell 2016
689
23

Tet proteins can convert 5-methylcytosine to 5-formylcytosine and 5-carboxylcytosine.
Shinsuke Ito, Li Shen, Qing Dai, Susan C Wu, Leonard B Collins, James A Swenberg, Chuan He, Yi Zhang. Science 2011
22

Tet-mediated formation of 5-carboxylcytosine and its excision by TDG in mammalian DNA.
Yu-Fei He, Bin-Zhong Li, Zheng Li, Peng Liu, Yang Wang, Qingyu Tang, Jianping Ding, Yingying Jia, Zhangcheng Chen, Lin Li,[...]. Science 2011
22

Liquid biopsies come of age: towards implementation of circulating tumour DNA.
Jonathan C M Wan, Charles Massie, Javier Garcia-Corbacho, Florent Mouliere, James D Brenton, Carlos Caldas, Simon Pacey, Richard Baird, Nitzan Rosenfeld. Nat Rev Cancer 2017
21

Enhanced detection of circulating tumor DNA by fragment size analysis.
Florent Mouliere, Dineika Chandrananda, Anna M Piskorz, Elizabeth K Moore, James Morris, Lise Barlebo Ahlborn, Richard Mair, Teodora Goranova, Francesco Marass, Katrin Heider,[...]. Sci Transl Med 2018
408
21

5-Hydroxymethylcytosine is a predominantly stable DNA modification.
Martin Bachman, Santiago Uribe-Lewis, Xiaoping Yang, Michael Williams, Adele Murrell, Shankar Balasubramanian. Nat Chem 2014
324
21


Base-resolution analysis of 5-hydroxymethylcytosine in the mammalian genome.
Miao Yu, Gary C Hon, Keith E Szulwach, Chun-Xiao Song, Liang Zhang, Audrey Kim, Xuekun Li, Qing Dai, Yin Shen, Beomseok Park,[...]. Cell 2012
709
20

Circulating tumor DNA 5-hydroxymethylcytosine as a novel diagnostic biomarker for esophageal cancer.
Xin Tian, Baofa Sun, Chuanyuan Chen, Chunchun Gao, Ji Zhang, Xingyu Lu, Linchen Wang, Xiangnan Li, Yurong Xing, Ruijuan Liu,[...]. Cell Res 2018
44
45

Quantitative sequencing of 5-methylcytosine and 5-hydroxymethylcytosine at single-base resolution.
Michael J Booth, Miguel R Branco, Gabriella Ficz, David Oxley, Felix Krueger, Wolf Reik, Shankar Balasubramanian. Science 2012
605
19

5-Hydroxymethylome in Circulating Cell-free DNA as A Potential Biomarker for Non-small-cell Lung Cancer.
Ji Zhang, Xiao Han, Chunchun Gao, Yurong Xing, Zheng Qi, Ruijuan Liu, Yueqin Wang, Xiaojian Zhang, Yun-Gui Yang, Xiangnan Li,[...]. Genomics Proteomics Bioinformatics 2018
37
51

Genome-wide mapping of 5-hydroxymethylcytosines in circulating cell-free DNA as a non-invasive approach for early detection of hepatocellular carcinoma.
Jiabin Cai, Lei Chen, Zhou Zhang, Xinyu Zhang, Xingyu Lu, Weiwei Liu, Guoming Shi, Yang Ge, Pingting Gao, Yuan Yang,[...]. Gut 2019
116
19

Genome-wide cell-free DNA fragmentation in patients with cancer.
Stephen Cristiano, Alessandro Leal, Jillian Phallen, Jacob Fiksel, Vilmos Adleff, Daniel C Bruhm, Sarah Østrup Jensen, Jamie E Medina, Carolyn Hruban, James R White,[...]. Nature 2019
413
19

Plasma DNA tissue mapping by genome-wide methylation sequencing for noninvasive prenatal, cancer, and transplantation assessments.
Kun Sun, Peiyong Jiang, K C Allen Chan, John Wong, Yvonne K Y Cheng, Raymond H S Liang, Wai-kong Chan, Edmond S K Ma, Stephen L Chan, Suk Hang Cheng,[...]. Proc Natl Acad Sci U S A 2015
390
18

Circulating tumour DNA methylation markers for diagnosis and prognosis of hepatocellular carcinoma.
Rui-Hua Xu, Wei Wei, Michal Krawczyk, Wenqiu Wang, Huiyan Luo, Ken Flagg, Shaohua Yi, William Shi, Qingli Quan, Kang Li,[...]. Nat Mater 2017
424
18

Detection of circulating tumor DNA in early- and late-stage human malignancies.
Chetan Bettegowda, Mark Sausen, Rebecca J Leary, Isaac Kinde, Yuxuan Wang, Nishant Agrawal, Bjarne R Bartlett, Hao Wang, Brandon Luber, Rhoda M Alani,[...]. Sci Transl Med 2014
18


Detection and localization of surgically resectable cancers with a multi-analyte blood test.
Joshua D Cohen, Lu Li, Yuxuan Wang, Christopher Thoburn, Bahman Afsari, Ludmila Danilova, Christopher Douville, Ammar A Javed, Fay Wong, Austin Mattox,[...]. Science 2018
17

Detection of early stage pancreatic cancer using 5-hydroxymethylcytosine signatures in circulating cell free DNA.
Gulfem D Guler, Yuhong Ning, Chin-Jen Ku, Tierney Phillips, Erin McCarthy, Christopher K Ellison, Anna Bergamaschi, Francois Collin, Paul Lloyd, Aaron Scott,[...]. Nat Commun 2020
48
35


A Highly Sensitive and Robust Method for Genome-wide 5hmC Profiling of Rare Cell Populations.
Dali Han, Xingyu Lu, Alan H Shih, Ji Nie, Qiancheng You, Meng Michelle Xu, Ari M Melnick, Ross L Levine, Chuan He. Mol Cell 2016
79
20

Current and future perspectives of liquid biopsies in genomics-driven oncology.
Ellen Heitzer, Imran S Haque, Charles E S Roberts, Michael R Speicher. Nat Rev Genet 2019
565
16

CancerLocator: non-invasive cancer diagnosis and tissue-of-origin prediction using methylation profiles of cell-free DNA.
Shuli Kang, Qingjiao Li, Quan Chen, Yonggang Zhou, Stacy Park, Gina Lee, Brandon Grimes, Kostyantyn Krysan, Min Yu, Wei Wang,[...]. Genome Biol 2017
140
15

Identification of tissue-specific cell death using methylation patterns of circulating DNA.
Roni Lehmann-Werman, Daniel Neiman, Hai Zemmour, Joshua Moss, Judith Magenheim, Adi Vaknin-Dembinsky, Sten Rubertsson, Bengt Nellgård, Kaj Blennow, Henrik Zetterberg,[...]. Proc Natl Acad Sci U S A 2016
355
15

Inferring expressed genes by whole-genome sequencing of plasma DNA.
Peter Ulz, Gerhard G Thallinger, Martina Auer, Ricarda Graf, Karl Kashofer, Stephan W Jahn, Luca Abete, Gunda Pristauz, Edgar Petru, Jochen B Geigl,[...]. Nat Genet 2016
193
15

Loss of 5-hydroxymethylcytosine is an epigenetic hallmark of melanoma.
Christine Guo Lian, Yufei Xu, Craig Ceol, Feizhen Wu, Allison Larson, Karen Dresser, Wenqi Xu, Li Tan, Yeguang Hu, Qian Zhan,[...]. Cell 2012
558
15

Noninvasive detection of cancer-associated genome-wide hypomethylation and copy number aberrations by plasma DNA bisulfite sequencing.
K C Allen Chan, Peiyong Jiang, Carol W M Chan, Kun Sun, John Wong, Edwin P Hui, Stephen L Chan, Wing Cheong Chan, David S C Hui, Simon S M Ng,[...]. Proc Natl Acad Sci U S A 2013
258
14

DNA fragments in the blood plasma of cancer patients: quantitations and evidence for their origin from apoptotic and necrotic cells.
S Jahr, H Hentze, S Englisch, D Hardt, F O Fackelmayer, R D Hesch, R Knippers. Cancer Res 2001
14

Role of Tet proteins in 5mC to 5hmC conversion, ES-cell self-renewal and inner cell mass specification.
Shinsuke Ito, Ana C D'Alessio, Olena V Taranova, Kwonho Hong, Lawrence C Sowers, Yi Zhang. Nature 2010
14


5-hydroxymethylcytosine in cancer: significance in diagnosis and therapy.
Aparna Vasanthakumar, Lucy A Godley. Cancer Genet 2015
62
20

Tissue type is a major modifier of the 5-hydroxymethylcytosine content of human genes.
Colm E Nestor, Raffaele Ottaviano, James Reddington, Duncan Sproul, Diana Reinhardt, Donncha Dunican, Elad Katz, J Michael Dixon, David J Harrison, Richard R Meehan. Genome Res 2012
286
13

5-Hydroxymethylcytosine is associated with enhancers and gene bodies in human embryonic stem cells.
Hume Stroud, Suhua Feng, Shannon Morey Kinney, Sriharsa Pradhan, Steven E Jacobsen. Genome Biol 2011
329
13

Detection and discrimination of intracranial tumors using plasma cell-free DNA methylomes.
Farshad Nassiri, Ankur Chakravarthy, Shengrui Feng, Shu Yi Shen, Romina Nejad, Jeffrey A Zuccato, Mathew R Voisin, Vikas Patil, Craig Horbinski, Kenneth Aldape,[...]. Nat Med 2020
110
13

Model-based analysis of ChIP-Seq (MACS).
Yong Zhang, Tao Liu, Clifford A Meyer, Jérôme Eeckhoute, David S Johnson, Bradley E Bernstein, Chad Nusbaum, Richard M Myers, Myles Brown, Wei Li,[...]. Genome Biol 2008
12

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

Bisulfite-free direct detection of 5-methylcytosine and 5-hydroxymethylcytosine at base resolution.
Yibin Liu, Paulina Siejka-Zielińska, Gergana Velikova, Ying Bi, Fang Yuan, Marketa Tomkova, Chunsen Bai, Lei Chen, Benjamin Schuster-Böckler, Chun-Xiao Song. Nat Biotechnol 2019
146
12

An ultrasensitive method for quantitating circulating tumor DNA with broad patient coverage.
Aaron M Newman, Scott V Bratman, Jacqueline To, Jacob F Wynne, Neville C W Eclov, Leslie A Modlin, Chih Long Liu, Joel W Neal, Heather A Wakelee, Robert E Merritt,[...]. Nat Med 2014
12

Circulating mutant DNA to assess tumor dynamics.
Frank Diehl, Kerstin Schmidt, Michael A Choti, Katharine Romans, Steven Goodman, Meng Li, Katherine Thornton, Nishant Agrawal, Lori Sokoll, Steve A Szabo,[...]. Nat Med 2008
11

Fragment Length of Circulating Tumor DNA.
Hunter R Underhill, Jacob O Kitzman, Sabine Hellwig, Noah C Welker, Riza Daza, Daniel N Baker, Keith M Gligorich, Robert C Rostomily, Mary P Bronner, Jay Shendure. PLoS Genet 2016
366
11

Phylogenetic ctDNA analysis depicts early-stage lung cancer evolution.
Christopher Abbosh, Nicolai J Birkbak, Gareth A Wilson, Mariam Jamal-Hanjani, Tudor Constantin, Raheleh Salari, John Le Quesne, David A Moore, Selvaraju Veeriah, Rachel Rosenthal,[...]. Nature 2017
897
11

Preferred end coordinates and somatic variants as signatures of circulating tumor DNA associated with hepatocellular carcinoma.
Peiyong Jiang, Kun Sun, Yu K Tong, Suk Hang Cheng, Timothy H T Cheng, Macy M S Heung, John Wong, Vincent W S Wong, Henry L Y Chan, K C Allen Chan,[...]. Proc Natl Acad Sci U S A 2018
92
11

Dynamic regulation of 5-hydroxymethylcytosine in mouse ES cells and during differentiation.
Gabriella Ficz, Miguel R Branco, Stefanie Seisenberger, Fátima Santos, Felix Krueger, Timothy A Hore, C Joana Marques, Simon Andrews, Wolf Reik. Nature 2011
824
11

Integrated digital error suppression for improved detection of circulating tumor DNA.
Aaron M Newman, Alexander F Lovejoy, Daniel M Klass, David M Kurtz, Jacob J Chabon, Florian Scherer, Henning Stehr, Chih Long Liu, Scott V Bratman, Carmen Say,[...]. Nat Biotechnol 2016
603
11

Direct detection of early-stage cancers using circulating tumor DNA.
Jillian Phallen, Mark Sausen, Vilmos Adleff, Alessandro Leal, Carolyn Hruban, James White, Valsamo Anagnostou, Jacob Fiksel, Stephen Cristiano, Eniko Papp,[...]. Sci Transl Med 2017
586
11


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.