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中国科学院数学与系统科学研究院机构知识库
KMS Of Academy of mathematics and systems sciences, CAS
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A New Context Tree Inference Algorithm for Variable Length Markov Chain Model with Applications to Biological Sequence Analyses
期刊论文
JOURNAL OF COMPUTATIONAL BIOLOGY, 2022, 页码: 18
Authors:
An, Shaokun
;
Ren, Jie
;
Sun, Fengzhu
;
Wan, Lin
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  |  
View/Download:86/0
  |  
Submit date:2022/06/21
biological sequence analyses
consistent context algorithm
variable length Markov chains
word count statistics
BiTSC2: Bayesian inference of tumor clonal tree by joint analysis of single-cell SNV and CNA data
期刊论文
BRIEFINGS IN BIOINFORMATICS, 2022, 页码: 12
Authors:
Chen, Ziwei
;
Gong, Fuzhou
;
Wan, Lin
;
Ma, Liang
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View/Download:96/0
  |  
Submit date:2022/06/21
single-cell DNA sequencing
intra-tumor heterogeneity
single nucleotide variation
copy number alteration
Bayesian modeling
cancer evolution
Database Resources of the National Genomics Data Center, China National Center for Bioinformation in 2022
期刊论文
NUCLEIC ACIDS RESEARCH, 2022, 卷号: 50, 期号: D1, 页码: D27-D38
Authors:
Xue, Yongbiao
;
Bao, Yiming
;
Zhang Zhang
;
Zhao, Wenming
;
Xiao, Jingfa
;
He, Shun-min
;
Zhang, Guoqing
;
Li, Yixue
;
Guoping, Zhao
;
Chen, Runsheng
;
Zeng, Jingyao
;
Zhang, Yadong
;
Shang, Yun-fei
;
Mai, Jialin
;
Shi, Shuo
;
Lu, Mingming
;
Bu, Congfan
;
Zhang, Zhewen
;
Du, Zhenglin
;
Wang, Yinying
;
Kang, Hongen
;
Xu, Tianyi
;
Hao, Lili
;
Jia, Peilin
;
Jiang, Shuai
;
Qian, Qiheng
;
Zhu, Tong-tong
;
Shang, Yunfei
;
Zong, Wenting
;
Jin, Tong
;
Zhang, Yuansheng
;
Zou, Dong
;
Zhang, Zhang
;
Du, Qiang
;
Feng, Changrui
;
Ma, Lina
;
Zhang, Sisi
;
Wang, Anke
;
Dong, Lili
;
Wang, Yan-qing
;
Liu, Wan
;
Yan, Xing
;
Ling, Yunchao
;
Zhao, Guoping
;
Zhou, Zhihua
;
Kang, Wang
;
Zhang, Tao
;
Ma, Shuai
;
Yan, Haoteng
;
Liu, Zunpeng
;
Ji, Zejun
;
Cai, Yusheng
;
Wang, Si
;
Song, Moshi
;
Ren, Jie
;
Zhou, Qi
;
Qu, Jing
;
Zhang, Weiqi
;
Liu, Guanghui
;
Chen, Xu
;
Chen, Tingting
;
Sisi, Zhang
;
Sun, Yanling
;
Yu, Caixia
;
Tang, Bixia
;
Zhu, Junwei
;
Zhai, Shuang
;
Sun, Yubin
;
Chen, Qiancheng
;
Yang, Xiaoyu
;
Zhang, Xin
;
Sang, Zhengqi
;
Wang, Yonggang
;
Zhao, Yilin
;
Chen, Huanxin
;
Lan, Li
;
Wang, Yanqing
;
Ma, Yingke
;
Jia, Yaokai
;
Zheng, Xin-chang
;
Chen, Meili
;
Dong, Zou
;
Zhu, Tongtong
;
Ming, Chen
;
Niu, Guangyi
;
Pan, Rong
;
Jing, Wei
;
Sang, Jian
;
Liu, Chang
;
Xiong, Yujia
;
Lili, Hao
;
Zhang, Mochen
;
Wang, Guoliang
;
Yi, Lizhi
;
Wei, Zhao
;
Zong, Wenting
;
Wu, Song
;
Xiong, Zhuang
;
Rujiao, Li
;
Zheng, Gong
;
Li, Rujiao
;
Liu, Lin
;
Li, Zhao
;
Li, Qianpeng
;
Wei, Jing
;
Luo, Sicheng
;
Wang, Jiajia
;
Shi, Yirong
;
Zhou, Honghong
;
Zhang, Peng
;
Song, Tingrui
;
Li, Yanyan
;
Yang, Fei
;
Li, Mengwei
;
Li, Zhao-hua
;
Kang, Hongen
;
Zheng, Xinchang
;
Li, Ru-jiao
;
Tian, Dongmei
;
Liu, Xiaonan
;
Li, Cuiping
;
Teng, Xufei
;
Song, Shuhui
;
Zhang, Yang
;
Niu, Guangyi
;
Zhu, Tongtong
;
Zhang, Yuansheng
;
Chen, Ruru
;
Zhang, Rongqin
;
Xu, Feng
;
Wang, Yifan
;
Ling, Yunchao
;
Zhou, Chenfen
;
Wang, Haizhou
;
Teschendorff, Andrew E.
;
He, Yungang
;
Zhen, Yang
;
Li, Cuiping
;
Zhu, Junwei
;
Li, Lun
;
Li, Na
;
Gong, Zheng
;
Chen, Meili
;
Ying Cui
;
Duan, Guangya
;
Tong, Jin
;
Wu, Gangao
;
Huang, Tianhao
;
Jin, Enhui
;
Zhao, Wei
;
Kang, Hailong
;
Wang, Zhonghuang
;
Zeng, Jingyao
;
Chen, Hua
;
Li, Mingkun
;
Zhao, Wenming
;
Ning, Wanshan
;
Xue, Yu
;
Liu, Yanhu
;
Cui, Ying
;
Zhou, Qijun
;
Liu, Xingyan
;
Zhang, Longlong
;
Mao, Bingyu
;
Zhang, Shihua
;
Zhang, Yaping
;
Wang, Guodong
;
Zhu, Qianghui
;
Li, Xin
;
Li, Menghua
;
Liu, Yuanming
;
Luo, Hong
;
Wu, Xiaoyuan
;
Jing, Haichun
;
Pan, Yitong
;
Chen, Ming
;
Ma, Lina
;
Shi, Leisheng
;
Li, Mingkun
;
Lan, Li
;
Bao, Yiming
;
Zhao, Wen-ming
;
Zuo, Zhixiang
;
Ren, Jian
;
Zhang, Xinxin
;
Xiao, Yun
;
Li, Xia
;
Liu, Dan
;
Zhang, Chi
;
Xue, Yu
;
Zhao, Zheng
;
Jiang, Tao
;
Wu, Wanying
;
Zhao, Fangqing
;
Meng, Xianwen
;
Peng, Di
;
Luo, Hao
;
Gao, Feng
;
Lin, Shaofeng
;
Liu, Chuijie
;
Guo, Anyuan
;
Yuan, Hao
;
Su, Tianhan
;
Zhang, Yong E.
;
Zhou, Yincong
;
Zhang, Weizhi
;
Fu, Shanshan
;
Tan, Xiaodan
;
Xie, Yubin
;
Guo, Guoji
;
Wang, Chenwei
;
Liao, Xingyu
;
Gao, Xin
;
Wang, Jianxin
;
Xie, Guiyan
;
Yuan, Chunhui
;
Tian, Feng
;
Yang, Dechang
;
Tang, Dachao
;
Wu, Wenyi
;
Gou, Yujie
;
Han, Cheng
;
Cui, Qinghua
;
Li, Xiang Shang
;
Li, Chuan-Yun
;
Luo, XiaoTong
;
Ren, Jia
;
Li, Xia
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  |  
View/Download:227/0
  |  
Submit date:2022/04/02
Manifold alignment for heterogeneous single-cell multi-omics data integration using Pamona
期刊论文
BIOINFORMATICS, 2022, 卷号: 38, 期号: 1, 页码: 211-219
Authors:
Cao, Kai
;
Hong, Yiguang
;
Wan, Lin
Favorite
  |  
View/Download:108/0
  |  
Submit date:2022/04/02
NeuralEE: A GPU-Accelerated Elastic Embedding Dimensionality Reduction Method for Visualizing Large-Scale scRNA-Seq Data
期刊论文
FRONTIERS IN GENETICS, 2020, 卷号: 11, 页码: 8
Authors:
Xiong, Jiankang
;
Gong, Fuzhou
;
Wan, Lin
;
Ma, Liang
Favorite
  |  
View/Download:125/0
  |  
Submit date:2021/01/14
single-cell RNA sequencing
elastic embedding
neural networks
large-scale
stochastic optimization
parametric models
generalizable models
Unsupervised topological alignment for single-cell multi-omics integration
期刊论文
BIOINFORMATICS, 2020, 卷号: 36, 页码: 48-56
Authors:
Cao, Kai
;
Bai, Xiangqi
;
Hong, Yiguang
;
Wan, Lin
Favorite
  |  
View/Download:96/0
  |  
Submit date:2021/01/14
RobustClone: a robust PCA method for tumor clone and evolution inference from single-cell sequencing data
期刊论文
BIOINFORMATICS, 2020, 卷号: 36, 期号: 11, 页码: 3299-3306
Authors:
Chen, Ziwei
;
Gong, Fuzhou
;
Wan, Lin
;
Ma, Liang
Favorite
  |  
View/Download:147/0
  |  
Submit date:2020/09/23
A Branch Point on Differentiation Trajectory is the Bifurcating Event Revealed by Dynamical Network Biomarker Analysis of Single-Cell Data
期刊论文
IEEE-ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS, 2020, 卷号: 17, 期号: 2, 页码: 366-375
Authors:
Chen, Ziwei
;
Bai, Xiangqi
;
Ma, Liang
;
Wang, Xiawei
;
Liu, Xiuqin
;
Liu, Yuting
;
Chen, Luonan
;
Wan, Lin
Favorite
  |  
View/Download:142/0
  |  
Submit date:2020/05/24
Trajectory
Heuristic algorithms
Mice
Correlation
Reactive power
Pseudo temporal trajectory
branch point
DNB theory
reconstruction
single-cell data
bifurcation
dynamical system
Confidence intervals for Markov chain transition probabilities based on next generation sequencing reads data
期刊论文
QUANTITATIVE BIOLOGY, 2020, 卷号: 8, 期号: 2, 页码: 143-154
Authors:
Wan, Lin
;
Kang, Xin
;
Ren, Jie
;
Sun, Fengzhu
Favorite
  |  
View/Download:157/0
  |  
Submit date:2021/01/14
DNA
FREQUENCIES
PREDICTION
Markov chains
next generation sequencing
transition probabilities
confidence intervals
Statistical test of structured continuous trees based on discordance matrix
期刊论文
BIOINFORMATICS, 2019, 卷号: 35, 期号: 23, 页码: 4962-4970
Authors:
Bai, Xiangqi
;
Ma, Liang
;
Wan, Lin
Favorite
  |  
View/Download:104/0
  |  
Submit date:2020/05/24