A citation-based method for searching scientific literature

Qianqian Shi, Xinxing Li, Qirui Peng, Chuanchao Zhang, Luonan Chen. Comput Struct Biotechnol J 2021
Times Cited: 1







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



Times Cited
  Times     Co-cited
Similarity



Cell-specific network constructed by single-cell RNA sequencing data.
Hao Dai, Lin Li, Tao Zeng, Luonan Chen. Nucleic Acids Res 2019
31
100

PyClone: statistical inference of clonal population structure in cancer.
Andrew Roth, Jaswinder Khattra, Damian Yap, Adrian Wan, Emma Laks, Justina Biele, Gavin Ha, Samuel Aparicio, Alexandre Bouchard-Côté, Sohrab P Shah. Nat Methods 2014
470
100

Cancer as an evolutionary and ecological process.
Lauren M F Merlo, John W Pepper, Brian J Reid, Carlo C Maley. Nat Rev Cancer 2006
904
100

SCReadCounts: estimation of cell-level SNVs expression from scRNA-seq data.
N M Prashant, Nawaf Alomran, Yu Chen, Hongyu Liu, Pavlos Bousounis, Mercedeh Movassagh, Nathan Edwards, Anelia Horvath. BMC Genomics 2021
2
100

Single-cell exome sequencing and monoclonal evolution of a JAK2-negative myeloproliferative neoplasm.
Yong Hou, Luting Song, Ping Zhu, Bo Zhang, Ye Tao, Xun Xu, Fuqiang Li, Kui Wu, Jie Liang, Di Shao,[...]. Cell 2012
361
100

Divergent modes of clonal spread and intraperitoneal mixing in high-grade serous ovarian cancer.
Andrew McPherson, Andrew Roth, Emma Laks, Tehmina Masud, Ali Bashashati, Allen W Zhang, Gavin Ha, Justina Biele, Damian Yap, Adrian Wan,[...]. Nat Genet 2016
163
100

Recent Advances of Deep Learning in Bioinformatics and Computational Biology.
Binhua Tang, Zixiang Pan, Kang Yin, Asif Khateeb. Front Genet 2019
45
100

Deep learning in bioinformatics: Introduction, application, and perspective in the big data era.
Yu Li, Chao Huang, Lizhong Ding, Zhongxiao Li, Yijie Pan, Xin Gao. Methods 2019
66
100

Clonal evolution in breast cancer revealed by single nucleus genome sequencing.
Yong Wang, Jill Waters, Marco L Leung, Anna Unruh, Whijae Roh, Xiuqing Shi, Ken Chen, Paul Scheet, Selina Vattathil, Han Liang,[...]. Nature 2014
600
100

Data-Driven Phenotypic Dissection of AML Reveals Progenitor-like Cells that Correlate with Prognosis.
Jacob H Levine, Erin F Simonds, Sean C Bendall, Kara L Davis, El-ad D Amir, Michelle D Tadmor, Oren Litvin, Harris G Fienberg, Astraea Jager, Eli R Zunder,[...]. Cell 2015
712
100

Evolution of the cancer genome.
Lucy R Yates, Peter J Campbell. Nat Rev Genet 2012
370
100


A Survey of Data Mining and Deep Learning in Bioinformatics.
Kun Lan, Dan-Tong Wang, Simon Fong, Lian-Sheng Liu, Kelvin K L Wong, Nilanjan Dey. J Med Syst 2018
41
100

Dynamic edge-based biomarker non-invasively predicts hepatocellular carcinoma with hepatitis B virus infection for individual patients based on blood testing.
Yiyu Lu, Zhaoyuan Fang, Meiyi Li, Qian Chen, Tao Zeng, Lina Lu, Qilong Chen, Hui Zhang, Qianmei Zhou, Yan Sun,[...]. J Mol Cell Biol 2019
7
100

DeepCpG: accurate prediction of single-cell DNA methylation states using deep learning.
Christof Angermueller, Heather J Lee, Wolf Reik, Oliver Stegle. Genome Biol 2017
150
100

Tree inference for single-cell data.
Katharina Jahn, Jack Kuipers, Niko Beerenwinkel. Genome Biol 2016
108
100

Local network component analysis for quantifying transcription factor activities.
Qianqian Shi, Chuanchao Zhang, Weifeng Guo, Tao Zeng, Lina Lu, Zhonglin Jiang, Ziming Wang, Juan Liu, Luonan Chen. Methods 2017
3
100

The clonal and mutational evolution spectrum of primary triple-negative breast cancers.
Sohrab P Shah, Andrew Roth, Rodrigo Goya, Arusha Oloumi, Gavin Ha, Yongjun Zhao, Gulisa Turashvili, Jiarui Ding, Kane Tse, Gholamreza Haffari,[...]. Nature 2012
100

Computational enhancement of single-cell sequences for inferring tumor evolution.
Sayaka Miura, Louise A Huuki, Tiffany Buturla, Tracy Vu, Karen Gomez, Sudhir Kumar. Bioinformatics 2018
13
100

Pattern fusion analysis by adaptive alignment of multiple heterogeneous omics data.
Qianqian Shi, Chuanchao Zhang, Minrui Peng, Xiangtian Yu, Tao Zeng, Juan Liu, Luonan Chen. Bioinformatics 2017
27
100

Clonal genotype and population structure inference from single-cell tumor sequencing.
Andrew Roth, Andrew McPherson, Emma Laks, Justina Biele, Damian Yap, Adrian Wan, Maia A Smith, Cydney B Nielsen, Jessica N McAlpine, Samuel Aparicio,[...]. Nat Methods 2016
56
100

Dissecting the clonal origins of childhood acute lymphoblastic leukemia by single-cell genomics.
Charles Gawad, Winston Koh, Stephen R Quake. Proc Natl Acad Sci U S A 2014
160
100

Clonal evolution in cancer.
Mel Greaves, Carlo C Maley. Nature 2012
100

Cancer research meets evolutionary biology.
John W Pepper, C Scott Findlay, Rees Kassen, Sabrina L Spencer, Carlo C Maley. Evol Appl 2009
51
100


Tumour heterogeneity and metastasis at single-cell resolution.
Devon A Lawson, Kai Kessenbrock, Ryan T Davis, Nicholas Pervolarakis, Zena Werb. Nat Cell Biol 2018
168
100

Reliable detection of subclonal single-nucleotide variants in tumour cell populations.
Moritz Gerstung, Christian Beisel, Markus Rechsteiner, Peter Wild, Peter Schraml, Holger Moch, Niko Beerenwinkel. Nat Commun 2012
150
100

Cancer genomics: one cell at a time.
Nicholas E Navin. Genome Biol 2014
159
100

Generalized principal component analysis (GPCA).
René Vidal, Yi Ma, Shankar Sastry. IEEE Trans Pattern Anal Mach Intell 2005
67
100

Comprehensive Classification of Retinal Bipolar Neurons by Single-Cell Transcriptomics.
Karthik Shekhar, Sylvain W Lapan, Irene E Whitney, Nicholas M Tran, Evan Z Macosko, Monika Kowalczyk, Xian Adiconis, Joshua Z Levin, James Nemesh, Melissa Goldman,[...]. Cell 2016
491
100

Inferring clonal composition from multiple sections of a breast cancer.
Habil Zare, Junfeng Wang, Alex Hu, Kris Weber, Josh Smith, Debbie Nickerson, ChaoZhong Song, Daniela Witten, C Anthony Blau, William Stafford Noble. PLoS Comput Biol 2014
65
100

Genome-wide detection of single-nucleotide and copy-number variations of a single human cell.
Chenghang Zong, Sijia Lu, Alec R Chapman, X Sunney Xie. Science 2012
600
100

The evolution of tumour phylogenetics: principles and practice.
Russell Schwartz, Alejandro A Schäffer. Nat Rev Genet 2017
85
100

Single-cell RNA-seq denoising using a deep count autoencoder.
Gökcen Eraslan, Lukas M Simon, Maria Mircea, Nikola S Mueller, Fabian J Theis. Nat Commun 2019
189
100

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
256
100

Improved SNV Discovery in Barcode-Stratified scRNA-seq Alignments.
Prashant N M, Hongyu Liu, Christian Dillard, Helen Ibeawuchi, Turkey Alsaeedy, Hang Chan, Anelia Dafinova Horvath. Genes (Basel) 2021
1
100


TITAN: inference of copy number architectures in clonal cell populations from tumor whole-genome sequence data.
Gavin Ha, Andrew Roth, Jaswinder Khattra, Julie Ho, Damian Yap, Leah M Prentice, Nataliya Melnyk, Andrew McPherson, Ali Bashashati, Emma Laks,[...]. Genome Res 2014
166
100

Single-cell genome sequencing: current state of the science.
Charles Gawad, Winston Koh, Stephen R Quake. Nat Rev Genet 2016
581
100

Cell-level somatic mutation detection from single-cell RNA sequencing.
Trung Nghia Vu, Ha-Nam Nguyen, Stefano Calza, Krishna R Kalari, Liewei Wang, Yudi Pawitan. Bioinformatics 2019
15
100

OncoNEM: inferring tumor evolution from single-cell sequencing data.
Edith M Ross, Florian Markowetz. Genome Biol 2016
108
100

THetA: inferring intra-tumor heterogeneity from high-throughput DNA sequencing data.
Layla Oesper, Ahmad Mahmoody, Benjamin J Raphael. Genome Biol 2013
129
100

Deep generative modeling for single-cell transcriptomics.
Romain Lopez, Jeffrey Regier, Michael B Cole, Michael I Jordan, Nir Yosef. Nat Methods 2018
252
100

SiFit: inferring tumor trees from single-cell sequencing data under finite-sites models.
Hamim Zafar, Anthony Tzen, Nicholas Navin, Ken Chen, Luay Nakhleh. Genome Biol 2017
56
100

DENDRO: genetic heterogeneity profiling and subclone detection by single-cell RNA sequencing.
Zilu Zhou, Bihui Xu, Andy Minn, Nancy R Zhang. Genome Biol 2020
8
100

Deep learning in bioinformatics.
Seonwoo Min, Byunghan Lee, Sungroh Yoon. Brief Bioinform 2017
353
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.