Ecosyste.ms: Papers
An open API service providing mapping between scientific papers and software projects that are mentioned in them.
All mentions data is based on the CZI Software Mentions dataset.
Projects: cran: DDRTree
https://packages.ecosyste.ms/registries/cran.r-project.org/packages/DDRTree
Learning Principal Graphs with DDRTree
3 versions
Latest release: over 7 years ago
1,960 downloads last month
Papers Mentioning DDRTree 42
10.3389/fgene.2021.655536
Machine Intelligence in Single-Cell Data Analysis: Advances and New ChallengesCited by: 30
Author(s): Jiajia Li, Zusen Fan, Weiling Zhao, Xiaobo Zhou
Software Mentions: 12
Published: over 3 years ago
10.1038/s41421-021-00314-w
Single-cell RNA-Seq reveals transcriptional heterogeneity and immune subtypes associated with disease activity in human myasthenia gravisCited by: 12
Author(s): Jin Wu, Qi Yang, Yuyao Peng, Chengkai Yan, Yi Li, Zhaohui Luo, Bo Xiao, Liqun Xu, Huan Yang
Software Mentions: 11
Published: over 3 years ago
10.1186/s13059-020-02083-3
DISC: a highly scalable and accurate inference of gene expression and structure for single-cell transcriptomes using semi-supervised deep learningCited by: 23
Author(s): Yong He, Hao Yuan, Changbao Wu, Zhi Xie
Software Mentions: 9
Published: over 4 years ago
10.1038/s41422-021-00562-1
Distinct immune signatures discriminate between asymptomatic and presymptomatic SARS-CoV-2pos subjectsCited by: 8
Author(s): Shanhe Yu, Caixia Di, Shijun Chen, Mingquan Guo, Jiayang Yan, Zhaoqin Zhu, Li Liu, Rilu Feng, Yinyin Xie, Ruihong Zhang, Juan Chen, Mengxi Wang, Dong Wei, Hai Fang, Tong Yin, Jinyan Huang, Sai‐Juan Chen, Hongzhou Lu, Jiang Zhu, Jieming Qu
Software Mentions: 9
Published: over 3 years ago
10.7554/eLife.38519
Insulin mutations impair beta-cell development in a patient-derived iPSC model of neonatal diabetesCited by: 106
Author(s): Diego Balboa, Jonna Saarimäki-Vire, Daniel Borshagovski, Mantas Survila, Päivi Lindholm, Emilia Galli, Solja Eurola, Jarkko Ustinov, Heli Grym, Hanna Huopio, Juha Partanen, Kirmo Wartiovaara, Timo Otonkoski
Software Mentions: 8
Published: about 6 years ago
10.3389/fimmu.2021.666355
Revealing the Immune Infiltration Landscape and Identifying Diagnostic Biomarkers for Lumbar Disc HerniationCited by: 32
Author(s): Linbang Wang, Tao He, Jingkun Liu, Jiaojiao Tai, Bing Wang, Lanyue Zhang, Zhengxue Quan
Software Mentions: 8
Published: over 3 years ago
10.1186/s12864-018-4772-0
Slingshot: cell lineage and pseudotime inference for single-cell transcriptomicsCited by: 1,344
Author(s): Kelly Street, Davide Risso, Russell B. Fletcher, Diya Das, John Ngai, Nir Yosef, Elizabeth Purdom, Sandrine Dudoit
Software Mentions: 8
Published: over 6 years ago
10.1016/j.celrep.2021.109118
Resident memory T cells in tumor-distant tissues fortify against metastasis formationCited by: 14
Author(s): Laura S. Christian, Liuyang Wang, Bryan Jian Wei Lim, Dachuan Deng, Haiyang Wu, Xiaofan Wang, Qi-Jing Li
Software Mentions: 8
Published: over 3 years ago
10.3389/fcell.2021.677697
Single-Cell RNA-Sequencing Portraying Functional Diversity and Clinical Implications of IFI6 in Ovarian CancerCited by: 7
Author(s): Hongyu Zhao, Zhefeng Li, Yan Gao, Jie Li, Xiaoting Zhao, Wentao Yue
Software Mentions: 8
Published: over 3 years ago
10.1371/journal.pgen.1008506
Latent transcriptional variations of individual Plasmodium falciparum uncovered by single-cell RNA-seq and fluorescence imagingCited by: 21
Author(s): Katelyn A. Walzer, Hélène Fradin, Liane Y. Emerson, David L. Corcoran, Jen‐Tsan Chi
Software Mentions: 7
Published: about 5 years ago
10.1038/s41421-021-00312-y
A single-cell atlas of liver metastases of colorectal cancer reveals reprogramming of the tumor microenvironment in response to preoperative chemotherapyCited by: 42
Author(s): Li-Heng Che, Jingwen Li, Jian-Ping Huo, Rong Luo, Rui-Ming Xu, He Cai, Yuqing Li, Anni Zhou, Pinbo Huang, Yongyu Chen, Weijian Ni, Yunxia Zhou, Yuan-Yuan Liu, Huiyan Li, Rong Zhou, Ming Hui, Jianming Li
Software Mentions: 7
Published: over 3 years ago
10.3389/fimmu.2021.709986
Dissecting Tumor Antigens and Immune Subtypes of Glioma to Develop mRNA VaccineCited by: 30
Author(s): Hua Zhong, Shuai Liu, Fang Cao, Yi Zhao, Jianguo Zhou, Feng Tang, Zhaohua Peng, Yangsheng Li, Shen Xu, Chunlin Wang, Guohua Yang, Zhiqiang Li
Software Mentions: 7
Published: over 3 years ago
10.1126/sciimmunol.abd1554
Immunophenotyping of COVID-19 and influenza highlights the role of type I interferons in development of severe COVID-19Cited by: 627
Author(s): Jeong Seok Lee, Seong-Wan Park, Hye Won Jeong, Jin Young Ahn, Seong Jin Choi, Hoyoung Lee, Baekgyu Choi, Su Kyung Nam, Moa Sa, Ji Soo Kwon, Su Jin Jeong, Kyung-Mi Lee, Sung Ho Park, Su–Hyung Park, Jun Yong Choi, Sung-Han Kim, Inkyung Jung, Eui Cheol Shin
Software Mentions: 7
Published: over 4 years ago
10.1093/dnares/dsz015
Uncovering the mouse olfactory long non-coding transcriptome with a novel machine-learning modelCited by: 8
Author(s): Antônio Pedro Camargo, Thiago S. Nakahara, Luiz E R Firmino, Paulo H.M. Netto, João Batista Plácido do Nascimento, Elisa Donnard, Pedro A. F. Galante, Marcelo Falsarella Carazzolle, Bettina Malnic, Fábio Papes
Software Mentions: 6
Published: over 5 years ago
10.7554/eLife.54695
Single cell transcriptomics identifies a unique adipose lineage cell population that regulates bone marrow environmentCited by: 168
Author(s): Leilei Zhong, Lutian Yao, Robert J. Tower, Yulong Wei, Zhen Miao, Jihwan Park, Rojesh Shrestha, Luqiang Wang, Wei Yu, Nicholas Holdreith, Xiaobin Huang, Yejia Zhang, Wei Tong, Yanqing Gong, Jaimo Ahn, Katalin Suszták, Nathaniel A. Dyment, Mingyao Li, Fanxin Long, Chider Chen, Patrick Seale, Ling Qin
Software Mentions: 6
Published: over 4 years ago
10.1038/s41420-021-00567-0
Single-cell RNA-seq reveals cellular heterogeneity of mouse carotid artery under disturbed flowCited by: 22
Author(s): Fengchan Li, Kunmin Yan, Lili Wu, Zhong Zheng, Yinan Du, Ziting Liu, Luyao Zhao, Wei Li, Yulan Sheng, Luping Ren, Chaojun Tang, Li Zhu
Software Mentions: 6
Published: over 3 years ago
10.1002/1878-0261.12707
Classification of diffuse lower‐grade glioma based on immunological profilingCited by: 40
Author(s): Fan Wu, Zhiliang Wang, Kuan‐Yu Wang, Guanzhang Li, Rui‐Chao Chai, Yuqing Liu, Haiyan Jiang, You Zhai, Yuemei Feng, Zheng Zhao, Wei Zhang
Software Mentions: 6
Published: over 4 years ago
10.1038/s41598-021-86002-x
Comprehensive transcriptomic analysis of COVID-19 blood, lung, and airwayCited by: 102
Author(s): Andrea R. Daamen, Prathyusha Bachali, Katherine A. Owen, Kathryn M. Kingsmore, Erika L. Hubbard, Adam C. Labonte, Robert Robl, Sneha Shrotri, Amrie C. Grammer, Peter E. Lipsky
Software Mentions: 5
Published: almost 4 years ago
10.3389/fgene.2021.681206
LISA2: Learning Complex Single-Cell Trajectory and Expression TrendsCited by: 1
Author(s): Yang Chen, Yuping Zhang, Kairong Li, Zhengqing Ouyang
Software Mentions: 5
Published: over 3 years ago
10.1007/s13238-021-00852-9
Single-nucleus transcriptomic landscape of primate hippocampal agingCited by: 41
Author(s): Hui Zhang, Jiaming Li, Jie Ren, Shuhui Sun, Shuai Ma, Weiqi Zhang, Yang Yu, Yusheng Cai, Yan Ke, Wei Li, Baoyang Hu, Piu Chan, Guoguang Zhao, Juan Carlos Izpisúa Belmonte, Qi Zhou, Jing Qu, Si Wang, Guanghui Liu
Software Mentions: 5
Published: over 3 years ago
10.1186/s12967-020-02561-z
Gene correlation network analysis to identify regulatory factors in sepsisCited by: 25
Author(s): Zhongheng Zhang, Lin Chen, Ping Xu, Lifeng Xing, Yucai Hong, Pengpeng Chen
Software Mentions: 5
Published: about 4 years ago
10.1186/s13027-021-00365-4
Immunophenotypic characterization of TCR γδ T cells and MAIT cells in HIV-infected individuals developing Hodgkin’s lymphomaCited by: 2
Author(s): Christina K. S. Muller, Julian Spagnuolo, Annette Audigé, Andrew Chancellor, Doris Russenberger, Alexandra U. Scherrer, Matthias Hoffmann, Roger D. Kouyos, Manuel Battegay, Gennaro De Libero, Roberto F. Speck
Software Mentions: 5
Published: over 3 years ago
10.1097/MD.0000000000026775
Single-cell transcriptional profiling reveals the heterogeneity in embryonal rhabdomyosarcomaCited by: 1
Author(s): Bo Hong, Tian Xia, Chun-Jing Ye, Yong Zhan, Ran Yang, Jia Liu, Yang Li, Zhi-Xue Chen, Wei Yao, Kai Li, Jia Wang, Rui Dong
Software Mentions: 4
Published: over 3 years ago
10.18632/aging.202857
Two reactive behaviors of chondrocytes in an IL-1β-induced inflammatory environment revealed by the single-cell RNA sequencingCited by: 4
Author(s): Chenghao Gao, Hongxu Pu, Qian Zhou, Tenghui Tao, Hui Liu, Xuying Sun, Ximiao He, Jun Xiao
Software Mentions: 4
Published: over 3 years ago
10.1172/jci.insight.141321
Single cell transcriptomics of mouse kidney transplants reveals a myeloid cell pathway for transplant rejectionCited by: 26
Author(s): Anil Dangi, Naveen Natesh, Irma Husain, Zhicheng Ji, Laura Barisoni, Jean Kwun, Xiling Shen, Edward B. Thorp, Xunrong Luo
Software Mentions: 4
Published: about 4 years ago
10.1038/s41598-020-76657-3
Distinct regional ontogeny and activation of tumor associated macrophages in human glioblastomaCited by: 64
Author(s): Alexander Landry, Michael Balas, Saira Alli, Julian Spears, Zsolt Zádor
Software Mentions: 4
Published: about 4 years ago
10.1186/s13059-017-1384-y
Epidermal Wnt signalling regulates transcriptome heterogeneity and proliferative fate in neighbouring cellsCited by: 16
Author(s): Arsham Ghahramani, Giacomo Donati, Nicholas M. Luscombe, Fiona M. Watt
Software Mentions: 3
Published: almost 7 years ago
10.3389/fgene.2021.679616
Integrative Single-Cell Transcriptomic Analysis of Human Fetal Thymocyte DevelopmentCited by: 5
Author(s): Yuchen Li, Weihong Zeng, Tong Li, Yi Guo, Guangyong Zheng, Xiaoyun He, Lilian Bai, Guolian Ding, Li Jin, Xinmei Liu
Software Mentions: 3
Published: over 3 years ago
10.3390/ijms22147696
Identification of Intercellular Crosstalk between Decidual Cells and Niche Cells in MiceCited by: 6
Author(s): Jia-Peng He, Qing Tian, Qiu-Yang Zhu, Ji‐Long Liu
Software Mentions: 3
Published: over 3 years ago
10.1161/ATVBAHA.119.312399
Adventitial Cell Atlas of wt (Wild Type) and ApoE (Apolipoprotein E)-Deficient Mice Defined by Single-Cell RNA SequencingCited by: 73
Author(s): Wenduo Gu, Zhichao Ni, Yuan Qing Tan, Jiacheng Deng, Si Jin Zhang, Zi Lv, Xiao Jian Wang, Ting Chen, Zhongyi Zhang, Yanhua Hu, Zhi‐Cheng Jing, Qingbo Xu
Software Mentions: 3
Published: over 5 years ago
10.1371/journal.pbio.3000152
Single-cell transcriptomics reveals gene expression dynamics of human fetal kidney developmentCited by: 113
Author(s): Mazène Hochane, Patrick R. van den Berg, Xueying Fan, Noémie M. L. P. Bérenger-Currias, Esmée Adegeest, Monika Bialecka, Maaike Nieveen, Maarten Menschaart, Susana M. Chuva de Sousa Lopes, Stefan Semrau
Software Mentions: 3
Published: almost 6 years ago
10.1002/advs.201801531
Ex vivo Dynamics of Human Glioblastoma Cells in a Microvasculature‐on‐a‐Chip System Correlates with Tumor Heterogeneity and SubtypesCited by: 67
Author(s): Yang Xiao, Dongjoo Kim, Burak Dura, Kerou Zhang, Runchen Yan, Huamin Li, Edward Han, Joshua Ip, Pan Zou, Jun Li, Ann Tai Chen, Alexander O. Vortmeyer, Jiangbing Zhou, Rong Fan
Software Mentions: 3
Published: almost 6 years ago
10.1002/cam4.2113
Dissecting intratumoral myeloid cell plasticity by single cell RNA‐seqCited by: 89
Author(s): Qisheng Song, Gregory A. Hawkins, L. James Wudel, Ping-Chieh Chou, M. Elizabeth Forbes, Ashok Pullikuth, Liang Liu, Guangxu Jin, Lou Craddock, Ümit Topaloğlu, Gregory L. Kucera, Stacey S. O’Neill, Edward A. Levine, Peiqing Sun, Kounosuke Watabe, Yong Lu, Martha A. Alexander-Miller, Boris Pasche, Lance D. Miller, Wei Zhang
Software Mentions: 3
Published: over 5 years ago
10.7554/eLife.42388
Specification of diverse cell types during early neurogenesis of the mouse cerebellumCited by: 57
Author(s): John Wizeman, Qiu Guo, Elliott M Wilion, Kairong Li
Software Mentions: 2
Published: almost 6 years ago
10.3390/ijms22105177
Cell–Cell Communication at the Embryo Implantation Site of Mouse Uterus Revealed by Single-Cell AnalysisCited by: 10
Author(s): Yi Yang, Jia-Peng He, Ji‐Long Liu
Software Mentions: 2
Published: over 3 years ago
10.1186/s13059-021-02432-w
Single-cell landscape of nuclear configuration and gene expression during stem cell differentiation and X inactivationCited by: 10
Author(s): Giancarlo Bonora, Vijay Ramani, Ritambhara Singh, Fang He, Dana L. Jackson, Sanjay Srivatsan, Ruolan Qiu, Choli Lee, Cole Trapnell, Jay Shendure, Zhijun Duan, Xinxian Deng, William Stafford Noble, Christine M. Distèche
Software Mentions: 2
Published: over 3 years ago
10.3389/fcell.2021.617853
Single-Cell RNA Sequencing and Quantitative Proteomics Analysis Elucidate Marker Genes and Molecular Mechanisms in Hypoplastic Left Heart Patients With Heart FailureCited by: 2
Author(s): Li Ma, Na Zhou, Rongjun Zou, Wu Shi, Yuanyuan Luo, Na Du, Jing Zhong, Xiaodong Zhao, Xinxin Chen, Huimin Xia, Xianyu Qin
Software Mentions: 2
Published: almost 4 years ago
10.3389/fbioe.2020.564057
Cell Development Deficiency and Gene Expression Dysregulation of Trisomy 21 Retina Revealed by Single-Nucleus RNA SequencingCited by: 2
Author(s): Fangyuan Hu, Feng‐Juan Gao, Ping Xu, Shenghai Zhang
Software Mentions: 2
Published: over 4 years ago
10.3389/fimmu.2018.01435
Immune Cell Dynamics Unfolded by Single-Cell TechnologiesCited by: 34
Author(s): Daniel J. Kunz, Tomás Gomes, Kylie R. James
Software Mentions: 1
Published: over 6 years ago
10.1186/s13059-018-1440-2
BGP: identifying gene-specific branching dynamics from single-cell data with a branching Gaussian processCited by: 23
Author(s): Alexis Boukouvalas, James Hensman, Magnus Rattray
Software Mentions: 1
Published: over 6 years ago
10.3390/e22030296
Robust and Scalable Learning of Complex Intrinsic Dataset Geometry via ElPiGraphCited by: 41
Author(s): Luca Albergante, Evgeny M. Mirkes, Jonathan Bac, Huidong Chen, Alexis Martin, Louis Faure, Emmanuel Barillot, Luca Pinello, Alexander N. Gorban, Andreï Zinovyev
Software Mentions: 1
Published: almost 5 years ago