A citation-based method for searching scientific literature

Xiaoping Liu, Yuetong Wang, Hongbin Ji, Kazuyuki Aihara, Luonan Chen. Nucleic Acids Res 2016
Times Cited: 109







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



Times Cited
  Times     Co-cited
Similarity


Detecting early-warning signals for sudden deterioration of complex diseases by dynamical network biomarkers.
Luonan Chen, Rui Liu, Zhi-Ping Liu, Meiyi Li, Kazuyuki Aihara. Sci Rep 2012
273
29

Diagnosing phenotypes of single-sample individuals by edge biomarkers.
Wanwei Zhang, Tao Zeng, Xiaoping Liu, Luonan Chen. J Mol Cell Biol 2015
44
50

Individual-specific edge-network analysis for disease prediction.
Xiangtian Yu, Jingsong Zhang, Shaoyan Sun, Xin Zhou, Tao Zeng, Luonan Chen. Nucleic Acids Res 2017
35
57

Quantifying critical states of complex diseases using single-sample dynamic network biomarkers.
Xiaoping Liu, Xiao Chang, Rui Liu, Xiangtian Yu, Luonan Chen, Kazuyuki Aihara. PLoS Comput Biol 2017
40
45

Dynamic network biomarker indicates pulmonary metastasis at the tipping point of hepatocellular carcinoma.
Biwei Yang, Meiyi Li, Wenqing Tang, Weixin Liu, Si Zhang, Luonan Chen, Jinglin Xia. Nat Commun 2018
74
22


Part mutual information for quantifying direct associations in networks.
Juan Zhao, Yiwei Zhou, Xiujun Zhang, Luonan Chen. Proc Natl Acad Sci U S A 2016
78
17

Dysfunction of PLA2G6 and CYP2C44-associated network signals imminent carcinogenesis from chronic inflammation to hepatocellular carcinoma.
Meiyi Li, Chen Li, Wei-Xin Liu, Conghui Liu, Jingru Cui, Qingrun Li, Hong Ni, Yingcheng Yang, Chaochao Wu, Chunlei Chen,[...]. J Mol Cell Biol 2017
36
38

Network medicine: a network-based approach to human disease.
Albert-László Barabási, Natali Gulbahce, Joseph Loscalzo. Nat Rev Genet 2011
14

Hunt for the tipping point during endocrine resistance process in breast cancer by dynamic network biomarkers.
Rui Liu, Jinzeng Wang, Masao Ukai, Ki Sewon, Pei Chen, Yutaka Suzuki, Haiyun Wang, Kazuyuki Aihara, Mariko Okada-Hatakeyama, Luonan Chen. J Mol Cell Biol 2019
32
43

Estimating Sample-Specific Regulatory Networks.
Marieke Lydia Kuijjer, Matthew George Tung, GuoCheng Yuan, John Quackenbush, Kimberly Glass. iScience 2019
38
36

WGCNA: an R package for weighted correlation network analysis.
Peter Langfelder, Steve Horvath. BMC Bioinformatics 2008
13

Discovering personalized driver mutation profiles of single samples in cancer by network control strategy.
Wei-Feng Guo, Shao-Wu Zhang, Li-Li Liu, Fei Liu, Qian-Qian Shi, Lei Zhang, Ying Tang, Tao Zeng, Luonan Chen. Bioinformatics 2018
33
36

Pan-cancer network analysis identifies combinations of rare somatic mutations across pathways and protein complexes.
Mark D M Leiserson, Fabio Vandin, Hsin-Ta Wu, Jason R Dobson, Jonathan V Eldridge, Jacob L Thomas, Alexandra Papoutsaki, Younhun Kim, Beifang Niu, Michael McLellan,[...]. Nat Genet 2015
451
11

A census of human cancer genes.
P Andrew Futreal, Lachlan Coin, Mhairi Marshall, Thomas Down, Timothy Hubbard, Richard Wooster, Nazneen Rahman, Michael R Stratton. Nat Rev Cancer 2004
11


Gene set enrichment analysis: a knowledge-based approach for interpreting genome-wide expression profiles.
Aravind Subramanian, Pablo Tamayo, Vamsi K Mootha, Sayan Mukherjee, Benjamin L Ebert, Michael A Gillette, Amanda Paulovich, Scott L Pomeroy, Todd R Golub, Eric S Lander,[...]. Proc Natl Acad Sci U S A 2005
11


Cell-specific network constructed by single-cell RNA sequencing data.
Hao Dai, Lin Li, Tao Zeng, Luonan Chen. Nucleic Acids Res 2019
38
26

Big-data-based edge biomarkers: study on dynamical drug sensitivity and resistance in individuals.
Tao Zeng, Wanwei Zhang, Xiangtian Yu, Xiaoping Liu, Meiyi Li, Luonan Chen. Brief Bioinform 2016
28
32

Mutual exclusivity analysis identifies oncogenic network modules.
Giovanni Ciriello, Ethan Cerami, Chris Sander, Nikolaus Schultz. Genome Res 2012
402
9

DriverNet: uncovering the impact of somatic driver mutations on transcriptional networks in cancer.
Ali Bashashati, Gholamreza Haffari, Jiarui Ding, Gavin Ha, Kenneth Lui, Jamie Rosner, David G Huntsman, Carlos Caldas, Samuel A Aparicio, Sohrab P Shah. Genome Biol 2012
140
9

The Cancer Genome Atlas Pan-Cancer analysis project.
John N Weinstein, Eric A Collisson, Gordon B Mills, Kenna R Mills Shaw, Brad A Ozenberger, Kyle Ellrott, Ilya Shmulevich, Chris Sander, Joshua M Stuart. Nat Genet 2013
9

Identifying critical transitions and their leading biomolecular networks in complex diseases.
Rui Liu, Meiyi Li, Zhi-Ping Liu, Jiarui Wu, Luonan Chen, Kazuyuki Aihara. Sci Rep 2012
90
10

Cancer genome landscapes.
Bert Vogelstein, Nickolas Papadopoulos, Victor E Velculescu, Shibin Zhou, Luis A Diaz, Kenneth W Kinzler. Science 2013
8

Cytoscape: a software environment for integrated models of biomolecular interaction networks.
Paul Shannon, Andrew Markiel, Owen Ozier, Nitin S Baliga, Jonathan T Wang, Daniel Ramage, Nada Amin, Benno Schwikowski, Trey Ideker. Genome Res 2003
8

Controllability of complex networks.
Yang-Yu Liu, Jean-Jacques Slotine, Albert-László Barabási. Nature 2011
663
8


Reactome: a database of reactions, pathways and biological processes.
David Croft, Gavin O'Kelly, Guanming Wu, Robin Haw, Marc Gillespie, Lisa Matthews, Michael Caudy, Phani Garapati, Gopal Gopinath, Bijay Jassal,[...]. Nucleic Acids Res 2011
964
8

Detection for disease tipping points by landscape dynamic network biomarkers.
Xiaoping Liu, Xiao Chang, Siyang Leng, Hui Tang, Kazuyuki Aihara, Luonan Chen. Natl Sci Rev 2019
17
47

KEGG: kyoto encyclopedia of genes and genomes.
M Kanehisa, S Goto. Nucleic Acids Res 2000
7

Controllability analysis of the directed human protein interaction network identifies disease genes and drug targets.
Arunachalam Vinayagam, Travis E Gibson, Ho-Joon Lee, Bahar Yilmazel, Charles Roesel, Yanhui Hu, Young Kwon, Amitabh Sharma, Yang-Yu Liu, Norbert Perrimon,[...]. Proc Natl Acad Sci U S A 2016
107
7

Enrichment or depletion of a GO category within a class of genes: which test?
Isabelle Rivals, Léon Personnaz, Lieng Taing, Marie-Claude Potier. Bioinformatics 2007
424
7

PID: the Pathway Interaction Database.
Carl F Schaefer, Kira Anthony, Shiva Krupa, Jeffrey Buchoff, Matthew Day, Timo Hannay, Kenneth H Buetow. Nucleic Acids Res 2009
919
7

Identifying disease genes and module biomarkers by differential interactions.
Xiaoping Liu, Zhi-Ping Liu, Xing-Ming Zhao, Luonan Chen. J Am Med Inform Assoc 2012
73
9

Identifying critical transitions of complex diseases based on a single sample.
Rui Liu, Xiangtian Yu, Xiaoping Liu, Dong Xu, Kazuyuki Aihara, Luonan Chen. Bioinformatics 2014
50
14

Dynamic versus static biomarkers in cancer immune checkpoint blockade: unravelling complexity.
W Joost Lesterhuis, Anthony Bosco, Michael J Millward, Michael Small, Anna K Nowak, Richard A Lake. Nat Rev Drug Discov 2017
114
7

Conditional mutual inclusive information enables accurate quantification of associations in gene regulatory networks.
Xiujun Zhang, Juan Zhao, Jin-Kao Hao, Xing-Ming Zhao, Luonan Chen. Nucleic Acids Res 2015
63
9


Patient-specific driver gene prediction and risk assessment through integrated network analysis of cancer omics profiles.
Denis Bertrand, Kern Rei Chng, Faranak Ghazi Sherbaf, Anja Kiesel, Burton K H Chia, Yee Yen Sia, Sharon K Huang, Dave S B Hoon, Edison T Liu, Axel Hillmer,[...]. Nucleic Acids Res 2015
62
9

Edge biomarkers for classification and prediction of phenotypes.
Tao Zeng, WanWei Zhang, XiangTian Yu, XiaoPing Liu, MeiYi Li, Rui Liu, LuoNan Chen. Sci China Life Sci 2014
21
28

Similarity network fusion for aggregating data types on a genomic scale.
Bo Wang, Aziz M Mezlini, Feyyaz Demir, Marc Fiume, Zhuowen Tu, Michael Brudno, Benjamin Haibe-Kains, Anna Goldenberg. Nat Methods 2014
579
6

KEGG for integration and interpretation of large-scale molecular data sets.
Minoru Kanehisa, Susumu Goto, Yoko Sato, Miho Furumichi, Mao Tanabe. Nucleic Acids Res 2012
6


Functional impact bias reveals cancer drivers.
Abel Gonzalez-Perez, Nuria Lopez-Bigas. Nucleic Acids Res 2012
207
6

OncodriveCLUST: exploiting the positional clustering of somatic mutations to identify cancer genes.
David Tamborero, Abel Gonzalez-Perez, Nuria Lopez-Bigas. Bioinformatics 2013
241
6

Mutational heterogeneity in cancer and the search for new cancer-associated genes.
Michael S Lawrence, Petar Stojanov, Paz Polak, Gregory V Kryukov, Kristian Cibulskis, Andrey Sivachenko, Scott L Carter, Chip Stewart, Craig H Mermel, Steven A Roberts,[...]. Nature 2013
6

Network biology: understanding the cell's functional organization.
Albert-László Barabási, Zoltán N Oltvai. Nat Rev Genet 2004
6

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