cran: DDRTree | Projects | Ecosyste.ms: Papers

10.3389/fgene.2021.655536

Machine Intelligence in Single-Cell Data Analysis: Advances and New Challenges
Cited 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 gravis
Cited 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: about 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 learning
Cited 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 subjects
Cited 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: about 3 years ago

10.7554/eLife.38519

Insulin mutations impair beta-cell development in a patient-derived iPSC model of neonatal diabetes
Cited 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 Herniation
Cited 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 transcriptomics
Cited 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 formation
Cited 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 Cancer
Cited by: 7
Author(s): Hongyu Zhao, Zhefeng Li, Yan Gao, Jie Li, Xiaoting Zhao, Wentao Yue
Software Mentions: 8
Published: about 3 years ago

10.1371/journal.pgen.1008506

Latent transcriptional variations of individual Plasmodium falciparum uncovered by single-cell RNA-seq and fluorescence imaging
Cited by: 21
Author(s): Katelyn A. Walzer, Hélène Fradin, Liane Y. Emerson, David L. Corcoran, Jen‐Tsan Chi
Software Mentions: 7
Published: almost 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 chemotherapy
Cited 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: about 3 years ago

10.3389/fimmu.2021.709986

Dissecting Tumor Antigens and Immune Subtypes of Glioma to Develop mRNA Vaccine
Cited 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: about 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-19
Cited 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 model
Cited 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 environment
Cited 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 flow
Cited 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 profiling
Cited 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 airway
Cited 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: over 3 years ago

10.3389/fgene.2021.681206

LISA2: Learning Complex Single-Cell Trajectory and Expression Trends
Cited 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 aging
Cited 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 sepsis
Cited 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 lymphoma
Cited 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 rhabdomyosarcoma
Cited 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 sequencing
Cited 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 rejection
Cited 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 glioblastoma
Cited 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 cells
Cited 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 Development
Cited 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 Mice
Cited 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 Sequencing
Cited 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 development
Cited 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 Subtypes
Cited 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‐seq
Cited 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 cerebellum
Cited 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 Analysis
Cited 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 inactivation
Cited 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: about 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 Failure
Cited 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: over 3 years ago

10.3389/fbioe.2020.564057

Cell Development Deficiency and Gene Expression Dysregulation of Trisomy 21 Retina Revealed by Single-Nucleus RNA Sequencing
Cited by: 2
Author(s): Fangyuan Hu, Feng‐Juan Gao, Ping Xu, Shenghai Zhang
Software Mentions: 2
Published: about 4 years ago

10.3389/fimmu.2018.01435

Immune Cell Dynamics Unfolded by Single-Cell Technologies
Cited 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 process
Cited 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 ElPiGraph
Cited 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: over 4 years ago

Projects: cran: DDRTree

Papers Mentioning DDRTree 42