pypi: PhenoGraph | Projects | Ecosyste.ms: Papers

10.15252/msb.20188746

Current best practices in single‐cell RNA‐seq analysis: a tutorial
Cited by: 1,173
Author(s): Malte D. Luecken, Fabian J. Theis
Software Mentions: 20
Published: over 5 years ago

CytoTree: an R/Bioconductor package for analysis and visualization of flow and mass cytometry data
Cited by: 13
Author(s): Yuting Dai, Aining Xu, Jianfeng Li, Liang Wu, Shanhe Yu, Jun Chen, Wei‐Li Zhao, Xiao Jian Sun, Jinyan Huang
Software Mentions: 17
Published: almost 4 years ago

10.1126/sciimmunol.abd6832

Natural killer cell immunotypes related to COVID-19 disease severity
Cited by: 315
Author(s): Christopher Maucourant, Iva Filipovic, Andrea Ponzetta, Soo Aleman, Martin Cornillet, Laura Hertwig, Benedikt Strunz, Antonio Lentini, Björn Reinius, Demi Brownlie, Angélica Cuapio, Eivind Heggernes Ask, Ryan M. Hull, Alvaro Haroun-Izquierdo, Marie Schaffer, Jonas Klingström, Elin Folkesson, Marcus Buggert, Johan K. Sandberg, Lars Eriksson, Olav Rooyackers, Hans‐Gustaf Ljunggren, Karl‐Johan Malmberg, Jakob Michaëlsson, Nicole Marquardt, Quirin Hammer, Kristoffer Strålin, Niklas K. Björkström
Software Mentions: 16
Published: over 4 years ago

10.12688/f1000research.11622.3

CyTOF workflow: differential discovery in high-throughput high-dimensional cytometry datasets
Cited by: 205
Author(s): Małgorzata Nowicka, Carsten Krieg, Helena L. Crowell, Lukas M. Weber, Felix J. Hartmann, Silvia Guglietta, Burkhard Becher, Mitchell P. Levesque, Mark D. Robinson
Software Mentions: 15
Published: over 5 years ago

10.7554/eLife.62915

ImmunoCluster provides a computational framework for the nonspecialist to profile high-dimensional cytometry data
Cited by: 9
Author(s): James W. Opzoomer, Jessica A Timms, Kevin Blighe, Thanos P. Mourikis, Nicolas Chapuis, Richard Bekoe, Sedigeh Kareemaghay, Paola Nocerino, Benedetta Apollonio, Alan G. Ramsay, Mahvash Tavassoli, Claire Harrison, Francesca D. Ciccarelli, Peter J. Parker, Michaéla Fontenay, Paul R. Barber, James N. Arnold, Shahram Kordasti
Software Mentions: 13
Published: over 3 years ago

10.4049/immunohorizons.1900097

Mass Cytometry Defines Virus-Specific CD4+ T Cells in Influenza Vaccination
Cited by: 3
Author(s): Priyanka B. Subrahmanyam, Tyson H. Holmes, Derek Lin, Laura F. Su, Gerlinde Obermoser, Jacques Banchereau, Virginia Pascual, Adolfo Garcı́a-Sastre, Randy A. Albrecht, Karolina Palucka, Mark M. Davis, Holden T. Maecker
Software Mentions: 13
Published: about 4 years ago

10.3389/fimmu.2020.01659

Conventional and Computational Flow Cytometry Analyses Reveal Sustained Human Intrathymic T Cell Development From Birth Until Puberty
Cited by: 2
Author(s): Marieke Lavaert, Brecht Valcke, Bart Vandekerckhove, Georges Leclercq, Kai Ling Liang, Tom Taghon
Software Mentions: 12
Published: over 4 years ago

10.1002/cam4.2983

Comprehensive insights on pivotal prognostic signature involved in clear cell renal cell carcinoma microenvironment using the ESTIMATE algorithm
Cited by: 30
Author(s): Jun Luo, Yi Xie, Yuxiao Zheng, Chenji Wang, Feng Qi, Jiateng Hu, Yixiang Xu
Software Mentions: 11
Published: over 4 years ago

10.1128/mSystems.00895-20

Computational Analysis of Microbial Flow Cytometry Data
Cited by: 16
Author(s): Peter Rubbens, Ruben Props
Software Mentions: 9
Published: almost 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

10.15252/msb.20209620

Probabilistic harmonization and annotation of single‐cell transcriptomics data with deep generative models
Cited by: 166
Author(s): Chenling Xu, Romain Lopez, Edouard Mehlman, Jeffrey Regier, Michael I. Jordan, Nir Yosef
Software Mentions: 9
Published: almost 4 years ago

10.3390/vaccines8010138

From Bivariate to Multivariate Analysis of Cytometric Data: Overview of Computational Methods and Their Application in Vaccination Studies
Cited by: 12
Author(s): Simone Lucchesi, Simone Furini, Donata Medaglini, Annalisa Ciabattini
Software Mentions: 9
Published: almost 5 years ago

10.3390/genes12020311

Clustering Single-Cell RNA-Seq Data with Regularized Gaussian Graphical Model
Cited by: 7
Author(s): Zhenqiu Liu
Software Mentions: 8
Published: almost 4 years ago

10.1186/s12859-021-04125-4

Censcyt: censored covariates in differential abundance analysis in cytometry
Cited by: 0
Author(s): Reto Gerber, Mark D. Robinson
Software Mentions: 8
Published: over 3 years ago

10.1093/bioinformatics/btz698

scds: computational annotation of doublets in single-cell RNA sequencing data
Cited by: 114
Author(s): Abha Bais, Dennis Kostka
Software Mentions: 7
Published: over 5 years ago

10.1016/j.gpb.2018.07.007

Deciphering Brain Complexity Using Single-cell Sequencing
Cited by: 50
Author(s): Quanhua Mu, Yiyun Chen, Jiguang Wang
Software Mentions: 7
Published: over 5 years ago

10.1016/j.isci.2020.101354

Network Approaches for Dissecting the Immune System
Cited by: 25
Author(s): Hao Shi, Koon-Kiu Yan, Liang Ding, Chenxi Qian, Hongbo Chi, Jiyang Yu
Software Mentions: 7
Published: over 4 years ago

10.1038/s42003-021-02595-z

Single-cell profiling defines the prognostic benefit of CD39high tissue resident memory CD8+ T cells in luminal-like breast cancer
Cited by: 9
Author(s): Agnese Losurdo, Caterina Scirgolea, Giorgia Alvisi, Jolanda Brummelman, Valentina Errico, Luca Di Tommaso, Karolina Pilipow, Federico Colombo, Bethania Fernandes, Clelia Peano, Alberto Testori, Corrado Tinterri, Massimo Roncalli, Armando Santoro, Emilia Maria Cristina Mazza, Enrico Lugli
Software Mentions: 6
Published: about 3 years ago

10.3389/fcell.2020.00234

Recent Advances in Computer-Assisted Algorithms for Cell Subtype Identification of Cytometry Data
Cited by: 17
Author(s): Peng Liu, Silvia Liu, Yusi Fang, Xiangning Xue, Jian Zou, George C. Tseng, Liza Konnikova
Software Mentions: 6
Published: over 4 years ago

10.1016/j.celrep.2020.03.063

A Targeted Multi-omic Analysis Approach Measures Protein Expression and Low-Abundance Transcripts on the Single-Cell Level
Cited by: 71
Author(s): Florian Mair, Jami R. Erickson, Valentin Voillet, Yannick Simoni, Timothy Bi, Aaron J. Tyznik, Jody Martin, Raphaël Gottardo, Evan W. Newell, Martin Prlic
Software Mentions: 6
Published: over 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

10.1186/s13059-019-1917-7

A comparison framework and guideline of clustering methods for mass cytometry data
Cited by: 71
Author(s): Xiao Liu, Weichen Song, Brandon Wong, Ting Zhang, Shunying Yu, Guan Ning Lin, Yiyang Li
Software Mentions: 5
Published: about 5 years ago

10.7554/eLife.53008

Functional heterogeneity of lymphocytic patterns in primary melanoma dissected through single-cell multiplexing
Cited by: 39
Author(s): Francesca Maria Bosisio, Asier Antoranz, Yannick Van Herck, Maddalena M. Bolognesi, Lukas Marcelis, Clizia Chinello, Jasper Wouters, Fulvio Magni, Leonidas G. Alexopoulos, Marguerite Stas, Veerle Boecxstaens, Oliver Bechter, Giorgio Cattoretti, Joost van den Oord
Software Mentions: 5
Published: almost 5 years ago

10.1186/s40779-021-00336-1

Advances in single-cell sequencing: insights from organ transplantation
Cited by: 7
Author(s): Ying Wang, Jian‐Ye Wang, Angelika Schnieke, Konrad Fischer
Software Mentions: 5
Published: over 3 years ago

10.1186/s40478-020-01010-8

Single-cell mass cytometry reveals complex myeloid cell composition in active lesions of progressive multiple sclerosis
Cited by: 34
Author(s): Chotima Böttcher, Marlijn van der Poel, Camila Fernández-Zapata, Stephan Schlickeiser, Julia Koehler Leman, Cheng-Chih Hsiao, Mark R. Mizee, Adelia, Maria C. J. Vincenten, Désirée Kunkel, Inge Huitinga, Jörg Hamann, Josef Priller
Software Mentions: 5
Published: over 4 years ago

10.7554/eLife.53839

Cancer systems immunology
Cited by: 12
Author(s): Nathan E. Reticker-Flynn, Edgar G. Engleman
Software Mentions: 5
Published: over 4 years ago

10.3389/fgene.2019.00958

Single-Cell Analysis of Circulating Tumor Cells: How Far Have We Come in the -Omics Era?
Cited by: 52
Author(s): Elisabetta Rossi, Rita Zamarchi
Software Mentions: 5
Published: about 5 years ago

10.1038/s41598-018-21444-4

QFMatch: multidimensional flow and mass cytometry samples alignment
Cited by: 12
Author(s): Darya Orlova, Stephen Meehan, David R. Parks, Wayne A. Moore, Connor Meehan, Qian Zhao, Eliver Ghosn, Leonore A. Herzenberg, Guenther Walther
Software Mentions: 5
Published: almost 7 years ago

10.3389/fimmu.2019.02657

Mass Cytometry Imaging for the Study of Human Diseases—Applications and Data Analysis Strategies
Cited by: 128
Author(s): Heeva Baharlou, Nicolas P Canete, Anthony L. Cunningham, Andrew N. Harman, Ellis Patrick
Software Mentions: 5
Published: about 5 years ago

10.7554/eLife.39800

Plasmodium-specific atypical memory B cells are short-lived activated B cells
Cited by: 42
Author(s): Damián Pérez‐Mazliah, Peter J. Gardner, Edina Schweighoffer, Sarah McLaughlin, Caroline Hosking, Irene Tumwine, Randall S. Davis, Alexandre J. Potocnik, Victor L. J. Tybulewicz, Jean Langhorne
Software Mentions: 5
Published: about 6 years ago

10.1186/s40478-021-01204-8

CSF1R inhibition rescues tau pathology and neurodegeneration in an A/T/N model with combined AD pathologies, while preserving plaque associated microglia
Cited by: 20
Author(s): Chritica Lodder, Isabelle Scheyltjens, Ilie-Cosmin Stancu, Pablo Botella Lucena, Manuel Gutiérrez de Ravé, Sarah Vanherle, Tim Vanmierlo, Niels Cremers, Hannah Vanrusselt, Bert Brône, Bernard Hanseeuw, Jean‐Noël Octave, Astrid Bottelbergs, Kiavash Movahedi, Ilse Dewachter
Software Mentions: 4
Published: over 3 years ago

10.1126/sciimmunol.abe1670

MAIT cell activation and dynamics associated with COVID-19 disease severity
Cited by: 138
Author(s): Tiphaine Parrot, Jean‐Baptiste Gorin, Andrea Ponzetta, Kimia T. Maleki, Tobias Kammann, Johanna Emgård, André Perez‐Potti, Takuya Sekine, Olga Rivera‐Ballesteros, Sara Gredmark‐Russ, Olav Rooyackers, Elin Folkesson, Lars Eriksson, Anna Norrby‐Teglund, Hans‐Gustaf Ljunggren, Niklas K. Björkström, Soo Aleman, Marcus Buggert, Jonas Klingström, Kristoffer Strålin, Johan K. Sandberg
Software Mentions: 4
Published: over 4 years ago

10.1172/jci.insight.146883

Highly multiplexed 2-dimensional imaging mass cytometry analysis of HBV-infected liver
Cited by: 14
Author(s): Daniel Traum, Yue J. Wang, Kathleen B. Schwarz, Jonathan Schug, David Wong, Harry L.A. Janssen, Norah A. Terrault, Mandana Khalili, Abdus S. Wahed, Karen F. Murray, Phillip Rosenthal, Simon C. Ling, Norberto Rodriguez‐Baez, Richard K. Sterling, Daryl Lau, Timothy M. Block, Michael D. Feldman, Elizabeth E. Furth, William M. Lee, David E. Kleiner, Anna S. Lok, Klaus H. Kaestner, Kyong Mi Chang
Software Mentions: 4
Published: over 3 years ago

10.3389/fonc.2021.620989

Characterization of the Tumor Immune Microenvironment in Lung Squamous Cell Carcinoma Using Imaging Mass Cytometry
Cited by: 17
Author(s): Ran Li, Ying Lin, Yu Wang, Shaoyuan Wang, Yang Yang, Xinlin Mu, Yu‐Sheng Chen, Zhancheng Gao
Software Mentions: 3
Published: over 3 years ago

10.3389/fgene.2019.00734

A Tool for Visualization and Analysis of Single-Cell RNA-Seq Data Based on Text Mining
Cited by: 13
Author(s): Gennaro Gambardella, Diego di Bernardo
Software Mentions: 3
Published: over 5 years ago

10.1038/s41598-020-72610-6

Ontogeny of different subsets of yellow fever virus-specific circulatory CXCR5+ CD4+ T cells after yellow fever vaccination
Cited by: 6
Author(s): Quinn DeGottardi, Theresa J. Gates, Junbao Yang, Eddie A. James, Uma Malhotra, I-Ting Chow, Yannick Simoni, Michael G. Fehlings, Evan W. Newell, Hannah A. DeBerg, William W. Kwok
Software Mentions: 3
Published: about 4 years ago

10.3389/fonc.2021.636057

A Multi-Omics Analysis of Metastatic Melanoma Identifies a Germinal Center-Like Tumor Microenvironment in HLA-DR-Positive Tumor Areas
Cited by: 6
Author(s): Laura Gadeyne, Yannick Van Herck, Giorgia Milli, Zeynep Kalender Atak, Maddalena M. Bolognesi, Jasper Wouters, Lukas Marcelis, Angeliki Minia, Vaia Pliaka, Jan Roznac, Leonidas G. Alexopoulos, Giorgio Cattoretti, Oliver Bechter, Joost van den Oord, Frederik De Smet, Asier Antoranz, Francesca Maria Bosisio
Software Mentions: 3
Published: over 3 years ago

10.3389/fmicb.2021.709728

Spatially Resolved Immunometabolism to Understand Infectious Disease Progression
Cited by: 6
Author(s): Roel Tans, Shoumit Dey, Nidhi Sharma Dey, Grant Calder, Peter O’Toole, Paul M. Kaye, Ron M. A. Heeren
Software Mentions: 3
Published: over 3 years ago

10.3389/fimmu.2018.01672

Mass Cytometry for the Assessment of Immune Reconstitution After Hematopoietic Stem Cell Transplantation
Cited by: 40
Author(s): Lauren Stern, Helen M. McGuire, Selmir Avdic, Simone Rizzetto, Barbara Fazekas de St Groth, Fabio Luciani, Barry Slobedman, Emily Blyth
Software Mentions: 3
Published: over 6 years ago

10.1016/j.isci.2021.103030

Single-cell transcriptome identifies FCGR3B upregulated subtype of alveolar macrophages in patients with critical COVID-19
Cited by: 11
Author(s): Nasna Nassir, Richa Tambi, Asma Bankapur, Saba Al Heialy, Noushad Karuvantevida, Hamda Khansaheb, Binte Zehra, Ghausia Begum, Reem Abdel Hameid, Awab Ahmed, Zulfa Deesi, Abdulmajeed Alkhajeh, K. M. Furkan Uddin, Hosneara Akter, Seyed Ali Safizadeh Shabestari, Omar Almidani, Abu Zafor Md. Touhidul Islam, Mellissa Gaudet, Richard K. Kandasamy, Tom Loney, Ahmad Abou Tayoun, Norbert Nowotny, Marc Woodbury‐Smith, Proton Rahman, Wolfgang M. Kuebler, Mahmood Yaseen Hachim, Jean‐Laurent Casanova, Bakhrom K. Berdiev, Alawi A. Alsheikh‐Ali, Mohammed Uddin
Software Mentions: 3
Published: over 3 years ago

10.26508/lsa.201900328

Tumor-intrinsic response to IFNγ shapes the tumor microenvironment and anti–PD-1 response in NSCLC
Cited by: 34
Author(s): Bonnie Bullock, Abigail K. Kimball, Joanna M. Poczobutt, Alexander J. Neuwelt, Howard Li, Amber M. Johnson, Jeff Kwak, Emily K. Kleczko, Rachael E. Kaspar, Emily Kay Wagner, Katharina Hopp, Erin L. Schenk, Mary C. Weiser-Evans, Eric T. Clambey, Raphael A. Nemenoff
Software Mentions: 3
Published: over 5 years ago

10.1016/j.immuni.2017.11.024

Cellular Differentiation of Human Monocytes Is Regulated by Time-Dependent Interleukin-4 Signaling and the Transcriptional Regulator NCOR2
Cited by: 118
Author(s): Jil Sander, Susanne V. Schmidt, Branko Cirovic, Naomi McGovern, Olympia Papantonopoulou, A. Hardt, Anna C. Aschenbrenner, Christoph Kreer, Thomas Quast, Alexander M. Xu, Lisa Schmidleithner, Heidi Theis, Lan Do Thi Huong, Hermi Sumatoh, Mario A. Lauterbach, Jonas Schulte-Schrepping, Patrick Günther, Jia Xue, Kevin Baßler, Thomas Ulas, Kathrin Klee, Natalie Katzmarski, Stefanie Herresthal, Wolfgang Krebs, Bianca Martin, Eicke Latz, Kristian Händler, Michael Kraut, Waldemar Kolanus, Marc Beyer, Christine S. Falk, Bettina Wiegmann, Sven Burgdorf, Nicholas A. Melosh, Evan W. Newell, Florent Ginhoux, Andreas Schlitzer, Joachim L. Schultze
Software Mentions: 3
Published: about 7 years ago

10.3389/fimmu.2019.01315

Development of a Comprehensive Antibody Staining Database Using a Standardized Analytics Pipeline
Cited by: 53
Author(s): El-ad David Amir, Brian Lee, Paul Badoual, Michael E. Gordon, Xinzheng V. Guo, Miriam Mérad, Adeeb Rahman
Software Mentions: 3
Published: over 5 years ago

10.1155/2021/9975423

Hyperion Image Analysis Depicts a Preliminary Landscape of Tumor Immune Microenvironment in OSCC with Lymph Node Metastasis
Cited by: 7
Author(s): Shang Xie, Mengjie Zhang, Xiaofeng Shan, Vicky Yau, Jianyun Zhang, Wei Wang, Yongpan Yan, Zhigang Cai
Software Mentions: 3
Published: over 3 years ago

10.1186/s12859-019-3294-3

Model-based cell clustering and population tracking for time-series flow cytometry data
Cited by: 9
Author(s): Kodai Minoura, Kayoko Abe, Yuka Maeda, Hiroyoshi Nishikawa, Teppei Shimamura
Software Mentions: 3
Published: about 5 years ago

10.1371/journal.pcbi.1009086

Mixture-of-Experts Variational Autoencoder for clustering and generating from similarity-based representations on single cell data
Cited by: 11
Author(s): Andreas Köpf, Vincent Fortuin, Vignesh Ram Somnath, Manfred Claassen
Software Mentions: 3
Published: over 3 years ago

10.7554/eLife.65412

Fate mapping analysis reveals a novel murine dermal migratory Langerhans-like cell population
Cited by: 13
Author(s): Jianpeng Sheng, Qi Chen, Xiaoting Wu, Yu Wen Dong, Johannes U Mayer, Junlei Zhang, Lin Wang, Xueli Bai, Yang Ho Sung, Wilson Wen Bin Goh, Franca Ronchese, Christiane Ruedl
Software Mentions: 3
Published: over 3 years ago

10.3390/genes10070531

SCINA: Semi-Supervised Analysis of Single Cells in Silico
Cited by: 127
Author(s): Ze Zhang, Danni Luo, Xue Zhong, Jin Huk Choi, Yuanqing Ma, Stacy Wang, Elena Mahrt, Wenfei Guo, Eric Stawiski, Zora Modrušan, Somasekar Seshagiri, Payal Kapur, Gary C. Hon, James Brugarolas, Tao Wang
Software Mentions: 3
Published: over 5 years ago

10.1172/jci.insight.146973

Single-cell profiling identifies impaired adaptive NK cells expanded after HCMV reactivation in haploidentical HSCT
Cited by: 15
Author(s): Elisa Zaghi, Michela Calvi, Simone Puccio, Gianmarco Spata, Sara Terzoli, Clelia Peano, Alessandra Roberto, Fédérica De Paoli, Jasper J. P. van Beek, Jacopo Mariotti, Chiara De Philippis, Barbara Sarina, Rossana Mineri, Stéfania Bramanti, Armando Santoro, Vu Thuy Khanh Le‐Trilling, Mirko Trilling, Emanuela Marcenaro, Luca Castagna, Clara Di Vito, Enrico Lugli, Domenico Mavilio
Software Mentions: 3
Published: over 3 years ago

10.1186/s40478-019-0779-2

The landscape of myeloid and astrocyte phenotypes in acute multiple sclerosis lesions
Cited by: 38
Author(s): Calvin Park, Gerald Ponath, Maya Levine-Ritterman, Edward Bull, Eric Swanson, Philip L. De Jager, Benjamin M. Segal, David Pitt
Software Mentions: 2
Published: over 5 years ago

10.1371/journal.pcbi.1005112

Cytofkit: A Bioconductor Package for an Integrated Mass Cytometry Data Analysis Pipeline
Cited by: 262
Author(s): Hao Chen, Mai Chan Lau, Michael Wong, Evan W. Newell, Michael Poidinger, Jinmiao Chen
Software Mentions: 2
Published: about 8 years ago

10.3390/cancers13040629

Unsupervised Flow Cytometry Analysis Allows for an Accurate Identification of Minimal Residual Disease Assessment in Acute Myeloid Leukemia
Cited by: 20
Author(s): Jean Vial, Nicolas Lechevalier, Francis Lacombe, Pierre‐Yves Dumas, Audrey Bidet, Thibaut Leguay, François Vergez, Arnaud Pigneux, Marie C. Béné
Software Mentions: 2
Published: almost 4 years ago

10.15252/emmm.201810092

Mutating chikungunya virus non‐structural protein produces potent live‐attenuated vaccine candidate
Cited by: 15
Author(s): Yi‐Hao Chan, Teck‐Hui Teo, Age Utt, Jeslin J. L. Tan, Siti Naqiah Amrun, Farhana Abu Bakar, Wearn‐Xin Yee, Étienne Becht, Cheryl Yi‐Pin Lee, Bernett Lee, Ravisankar Rajarethinam, Evan W. Newell, Andres Merits, Guillaume Carissimo, Fok‐Moon Lum, Lisa F. P. Ng
Software Mentions: 2
Published: over 5 years ago

10.3389/fbioe.2020.526814

Multiparametric Color Tendency Analysis (MCTA): A Method to Analyze Several Flow Cytometry Labelings Simultaneously
Cited by: 0
Author(s): Andréa Henriques-Pons, Carine Priscila Beatrici, Juan Camilo Sánchez‐Arcila, Fabrício Silva
Software Mentions: 2
Published: over 4 years ago

10.3389/fgene.2020.604790

Sc-GPE: A Graph Partitioning-Based Cluster Ensemble Method for Single-Cell
Cited by: 8
Author(s): Xiaoshu Zhu, Jian Li, Hongdong Li, Miao Xie, Jianxin Wang
Software Mentions: 2
Published: about 4 years ago

10.3389/fimmu.2020.607048

Bacterial and Fungal Toll-Like Receptor Activation Elicits Type I IFN Responses in Mast Cells
Cited by: 11
Author(s): Lisa Kornstädt, Sandra Pierre, Andreas Weigert, Stefanie Ebersberger, Tim J. Schäufele, Anja Kolbinger, Tobias Schmid, Jennifer Cohnen, Dominique Thomas, Nerea Ferreirós, Bernhard Brüne, Ingo Ebersberger, Klaus Scholich
Software Mentions: 2
Published: almost 4 years ago

10.3389/fimmu.2020.594658

Single-Cell RNA Sequencing Reveals the Expansion of Cytotoxic CD4+ T Lymphocytes and a Landscape of Immune Cells in Primary Sjögren’s Syndrome
Cited by: 40
Author(s): Xiaoping Hong, Shuhui Meng, Donge Tang, Tingting Wang, Liping Ding, Haiyan Yu, Heng Li, Dongzhou Liu, Yong Dai, Min Yang
Software Mentions: 2
Published: almost 4 years ago

10.3389/fimmu.2021.726428

CyTOF-Enabled Analysis Identifies Class-Switched B Cells as the Main Lymphocyte Subset Associated With Disease Relapse in Children With Idiopathic Nephrotic Syndrome
Cited by: 15
Author(s): Miguel Fribourg, Michela Cioni, G. M. Ghiggeri, Chiara Cantarelli, Jeremy S. Leventhal, Kelly L. Budge, Sofia Bin, Leonardo V. Riella, Manuela Colucci, Marina Vivarelli, Andrea Angeletti, Laura Perin, Paolo Cravedi
Software Mentions: 2
Published: over 3 years ago

10.3389/fimmu.2019.03039

Use of Mass Cytometry to Profile Human T Cell Exhaustion
Cited by: 36
Author(s): Frances Winkler, Bertram Bengsch
Software Mentions: 2
Published: almost 5 years ago

10.3389/fimmu.2021.679498

IFN-β Acts on Monocytes to Ameliorate CNS Autoimmunity by Inhibiting Proinflammatory Cross-Talk Between Monocytes and Th Cells
Cited by: 6
Author(s): Javad Rasouli, Giacomo Casella, Larissa Lumi Watanabe Ishikawa, Rodolfo Thomé, Alexandra Boehm, Adam Ertel, Carolina R. Melo‐Silva, Elisabeth R. Mari, Patrizia Porazzi, Weifeng Zhang, Dan Xiao, Luis J. Sigal, Paolo Fortina, Guang‐Xian Zhang, Abdolmohamad Rostami, Bogoljub Ćirić
Software Mentions: 2
Published: over 3 years ago

10.3389/fimmu.2020.579743

Unbiased Profiling Reveals Compartmentalization of Unconventional T-Cells Within the Intestinal Mucosa Irrespective of HIV Infection
Cited by: 6
Author(s): Magalli Magnoumba, Abhijeet Singh, Paul Ogongo, Julia Roider, Osaretin E. Asowata, Michael G. Fehlings, Farina Karim, Thumbi Ndung’u, Frank Anderson, Alasdair Leslie, Henrik N. Kløverpris
Software Mentions: 2
Published: about 4 years ago

10.3389/fmolb.2020.612801

Full Spectrum Flow Cytometry as a Powerful Technology for Cancer Immunotherapy Research
Cited by: 46
Author(s): Diana Bonilla, Gil Reinin, Edmond Chua
Software Mentions: 2
Published: almost 4 years ago

10.1117/1.JBO.25.5.056004

Oligonucleotide conjugated antibodies permit highly multiplexed immunofluorescence for future use in clinical histopathology
Cited by: 15
Author(s): Nathan P. McMahon, Jocelyn Jones, Sunjong Kwon, Koei Chin, Michel Nederlof, Joe W. Gray, Summer L. Gibbs
Software Mentions: 2
Published: over 4 years ago

10.1038/s41598-021-91816-w

Extended live-cell barcoding approach for multiplexed mass cytometry
Cited by: 7
Author(s): Muharrem Müftüoǧlu, Li Li, Shaoheng Liang, Duncan H. Mak, Angelique Lin, Junxiang Fang, Jared K. Burks, Ken Chen, Michael Andreeff
Software Mentions: 2
Published: over 3 years ago

10.7150/thno.52514

Mesenchymal stem cell-mediated immunomodulation of recruited mononuclear phagocytes during acute lung injury: a high-dimensional analysis study
Cited by: 14
Author(s): Jingqi Liu, Pan Li, Jiaqi Zhu, Feiyan Lin, Jiarong Zhou, Bing Feng, Xinyu Sheng, Xiaowei Shi, Qiaoling Pan, Jiong Yu, Gao J, Lanjuan Li, Hong Cao
Software Mentions: 2
Published: almost 4 years ago

10.1136/jitc-2020-002181

Deep immune profiling reveals targetable mechanisms of immune evasion in immune checkpoint inhibitor-refractory glioblastoma
Cited by: 39
Author(s): Erin F. Simonds, Edbert D Lu, O. Badillo, Shokoufeh Karimi, Eric V Liu, Whitney Tamaki, Chiara Rancan, Kira Downey, Jacob Stultz, Mala Sinha, Lauren McHenry, Nicole Nasholm, Pavlina Chuntova, Anders Sundström, Vassilis Genoud, Shilpa Shahani, Leo D. Wang, Christine E. Brown, Paul R Walker, Fredrik J. Swartling, Lawrence Fong, Hideho Okada, William A. Weiss, Mats Hellström
Software Mentions: 2
Published: over 3 years ago

10.7554/eLife.50325

Dullard-mediated Smad1/5/8 inhibition controls mouse cardiac neural crest cells condensation and outflow tract septation
Cited by: 14
Author(s): Jean-François Darrigrand, Mariana Valente, Glenda Comai, Pauline Martinez, Maxime Petit, Ryuichi Nishinakamura, Daniel S. Osório, Gilles Renault, Carmen Marchiol, Vanessa Ribes, Bruno Cadot
Software Mentions: 2
Published: almost 5 years ago

10.3389/fimmu.2020.00894

Longitudinal [18F]FB-IL-2 PET Imaging to Assess the Immunopathogenicity of O'nyong-nyong Virus Infection
Cited by: 5
Author(s): Yi‐Hao Chan, Teck‐Hui Teo, Anthony Torres‐Ruesta, Siddesh V. Hartimath, Rhonda Sin‐Ling Chee, Shivashankar Khanapur, Fui Fong Yong, Boominathan Ramasamy, Peter Cheng, Ravisankar Rajarethinam, Edward G. Robins, Julian Goggi, Fok‐Moon Lum, Guillaume Carissimo, Laurent Rénia, Lisa F. P. Ng
Software Mentions: 1
Published: over 4 years ago

10.3389/fimmu.2020.563044

The Expression Pattern and Clinical Significance of the Immune Checkpoint Regulator VISTA in Human Breast Cancer
Cited by: 25
Author(s): Xiaoxue Xie, Junying Zhang, Zhongyuan Shen, Wanmei Liu, Xiaofan Hu, Chenxin Qie, Wenting Chen, Yan Wang, Li Wang, Jingwei Jiang, Jun Li
Software Mentions: 1
Published: about 4 years ago

10.3389/fimmu.2018.01252

The Notch Signaling Pathway Is Balancing Type 1 Innate Lymphoid Cell Immune Functions
Cited by: 22
Author(s): Thibaut Perchet, Maxime Petit, Elena-Gaia Banchi, Sylvain Meunier, Ana Cumano, Rachel Golub
Software Mentions: 1
Published: over 6 years ago

10.3389/fimmu.2020.598727

Vitamin D/CD46 Crosstalk in Human T Cells in Multiple Sclerosis
Cited by: 8
Author(s): Justin Killick, Joanne Hay, Elena Morandi, Sonja Vermeren, Saniya Kari, Thibault Angles, Anna Williams, Jan Damoiseaux, Anne Astier
Software Mentions: 1
Published: about 4 years ago

10.3389/fimmu.2019.02692

29-Color Flow Cytometry: Unraveling Human Liver NK Cell Repertoire Diversity
Cited by: 20
Author(s): Iva Filipovic, Isabella Sönnerborg, Benedikt Strunz, Danielle Friberg, Martin Cornillet, Laura Hertwig, Martin A. Ivarsson, Niklas K. Björkström
Software Mentions: 1
Published: about 5 years ago

10.1371/journal.pone.0208187

Fingerprints of CD8+ T cells on human pre-plasma and memory B cells
Cited by: 4
Author(s): Ulrike Strittmatter-Keller, Caroline Walter, Céline Rauld, Nicole Egli, Camille Regairaz, Sabine Rabe, Gerhard Zenke, José M. Carballido, Tamás Schweighoffer
Software Mentions: 1
Published: about 6 years ago

10.1172/JCI142014

Tissue-resident-like CD4+ T cells secreting IL-17 control Mycobacterium tuberculosis in the human lung
Cited by: 40
Author(s): Paul Ogongo, Liku B. Tezera, Amanda Ardain, Shepherd Nhamoyebonde, Duran Ramsuran, Abhijeet Singh, Abigail Ngoepe, Farina Karim, Taryn Naidoo, Khadija Khan, Kaylesh J Dullabh, Michael G. Fehlings, Boon Heng Lee, Alessandra Nardin, Cecilia S. Lindestam Arlehamn, Alessandro Sette, Samuel M. Behar, Adrie J. C. Steyn, Rajhmun Madansein, Henrik N. Kløverpris, Paul Elkington, Alasdair Leslie
Software Mentions: 1
Published: over 3 years ago

10.1073/pnas.1913810117

<i> IGLV3-21 <i>*</i> 01 </i> is an inherited risk factor for CLL through the acquisition of a single-point mutation enabling autonomous BCR signaling
Cited by: 45
Author(s): Palash C. Maity, Mayas Bilal, Marvyn T. Koning, Marc Young, Cornelis A.M. van Bergen, Valerio Renna, Antonella Nicolò, Moumita Datta, Eva Gentner-Göbel, Rob S Barendse, Sebastiaan Somers, Ruben A.L. De Groen, Joost S.P. Vermaat, Daniela Steinbrecher, Christof Schneider, Eugen Tausch, Tamara Bittolo, Riccardo Bomben, Andrea Nicola Mazzarello, Giovanni Del Poeta, Wilma G. M. Kroes, Tom van Wezel, Katharina Imkeller, Christian E. Busse, Massimo Degano, Tamam Bakchoul, Axel Schulz, Henrik E. Mei, Paolo Ghia, Konstantia Kotta, Kostas Stamatopoulos, Hedda Wardemann, Antonella Zucchetto, Nicholas Chiorazzi, Valter Gattei, Stephan Stilgenbauer, Hendrik Veelken, Hassan Jumaa
Software Mentions: 1
Published: almost 5 years ago

10.3389/fimmu.2021.643692

Single-Cell Profiling to Explore Immunological Heterogeneity of Tumor Microenvironment in Breast Cancer
Cited by: 22
Author(s): Xiao Yuan, Jinxi Wang, Yixuan Huang, Dangang Shangguan, Peng Zhang
Software Mentions: 1
Published: almost 4 years ago

10.3389/fimmu.2021.632547

Combination of Immunotherapy and Radiotherapy for Recurrent Malignant Gliomas: Results From a Prospective Study
Cited by: 8
Author(s): Haihui Jiang, Kefu Yu, Yong Cui, Xiaohui Ren, Mingxiao Li, Cong Yang, Xuzhe Zhao, Qinghui Zhu, Song Lin
Software Mentions: 1
Published: over 3 years ago

10.3389/fimmu.2021.714461

Application of Genetic Studies to Flow Cytometry Data and Its Impact on Therapeutic Intervention for Autoimmune Disease
Cited by: 1
Author(s): Valeria Orrù, Maristella Steri, Francesco Cucca, Edoardo Fiorillo
Software Mentions: 1
Published: over 3 years ago

10.3389/fimmu.2019.01571

Immunocyte Profiling Using Single-Cell Mass Cytometry Reveals EpCAM+ CD4+ T Cells Abnormal in Colon Cancer
Cited by: 19
Author(s): Ting Zhang, Junwei Lv, Ziyang Tan, Boqian Wang, Antony R. Warden, Yiyang Li, Hui Jiang, Hao Li, Yiyang Li
Software Mentions: 1
Published: over 5 years ago

10.1038/s41598-020-80693-4

Alterations in B cell subsets correlate with body composition parameters in female adolescents with anorexia nervosa
Cited by: 5
Author(s): Jana Freff, Kathrin Schwarte, Lisa Bröker, Judith Bühlmeier, Isabelle Kraft, Dana Öztürk, Anke Hinney, Volker Arolt, Udo Dannlowski, Georg Romer, Bernhard T. Baune, Johannes Hebebrand, Manuel Föcker, Judith Alferink
Software Mentions: 1
Published: almost 4 years ago

10.3390/magnetochemistry7070092

Enrichment and Detection of Antigen-Binding B Cells for Mass Cytometry
Cited by: 6
Author(s): Zachary C. Stensland, Mia J. Smith
Software Mentions: 1
Published: over 3 years ago

10.1038/s41598-021-94163-y

Single-cell transcriptomic profile of human pulmonary artery endothelial cells in health and pulmonary arterial hypertension
Cited by: 10
Author(s): Kewal Asosingh, Suzy Comhair, Lori Mavrakis, Weiling Xu, Dean Horton, Ian Taylor, Svyatoslav Tkachenko, Bo Hu, Serpil C. Erzurum
Software Mentions: 1
Published: over 3 years ago

10.1186/s13058-019-1189-x

Targeting myeloid-derived suppressor cells in combination with primary mammary tumor resection reduces metastatic growth in the lungs
Cited by: 52
Author(s): Momir Bosiljcic, Rachel A. Cederberg, Melisa J. Hamilton, Nancy E. LePard, Bryant Harbourne, Jenna L. Collier, Elizabeth C. Halvorsen, Rocky Shi, S. Elizabeth Franks, Ada Y. Kim, Judit P. Banáth, Mark Hamer, Fábio Rossi, Kevin L. Bennewith
Software Mentions: 1
Published: over 5 years ago

10.1002/cti2.1296

Cord blood group 2 innate lymphoid cells are associated with lung function at 6 weeks of age
Cited by: 2
Author(s): Gabriela Martins Costa Gomes, Patricia de Gouveia Belinelo, Malcolm R. Starkey, Vanessa E. Murphy, Philip M. Hansbro, Peter D. Sly, Paul D. Robinson, Wilfried Karmaus, Péter G. Gibson, Joërg Mattes, Adam Collison
Software Mentions: 1
Published: almost 4 years ago

10.1186/s12938-021-00858-8

Computational flow cytometric analysis to detect epidermal subpopulations in human skin
Cited by: 1
Author(s): Lidan Zhang, Ying Cen, Qiaorong Huang, Huifang Li, Xianming Mo, Meng Wei, Junjie Chen
Software Mentions: 1
Published: almost 4 years ago

10.1136/jitc-2019-000441

Cancer cell-intrinsic expression of MHC II in lung cancer cell lines is actively restricted by MEK/ERK signaling and epigenetic mechanisms
Cited by: 26
Author(s): Alexander J. Neuwelt, Abigail K. Kimball, Amber M. Johnson, Benjamin W Arnold, Bonnie Bullock, Rachael E. Kaspar, Emily K. Kleczko, Jeff Kwak, Meng Wu, Lynn E. Heasley, Robert C. Doebele, Howard Li, Raphael A. Nemenoff, Eric T. Clambey
Software Mentions: 1
Published: over 4 years ago

10.1186/s40425-019-0700-3

PD-L1 blockade engages tumor-infiltrating lymphocytes to co-express targetable activating and inhibitory receptors
Cited by: 39
Author(s): Guillaume Beyrend, Esmé van der Gracht, Ayse N Yilmaz, Suzanne van Duikeren, Marcel Camps, Thomas Höllt, Anna Vilanova, Vincent van Unen, Frits Koning, Noel F.C.C. de Miranda, Ramon Arens, Ferry Ossendorp
Software Mentions: 1
Published: over 5 years ago

10.3390/cells9081751

Biological and Medical Importance of Cellular Heterogeneity Deciphered by Single-Cell RNA Sequencing
Cited by: 28
Author(s): Rishikesh Kumar Gupta, Jacek Kuźnicki
Software Mentions: 1
Published: over 4 years ago

10.1093/bioinformatics/btw227

densityCut: an efficient and versatile topological approach for automatic clustering of biological data
Cited by: 31
Author(s): Jiarui Ding, Sohrab P. Shah, Anne Condon
Software Mentions: 1
Published: over 8 years ago

10.1186/s13578-021-00544-1

Characteristic pancreatic and splenic immune cell infiltration patterns in mouse acute pancreatitis
Cited by: 5
Author(s): Bingyi Yang, Julia Davis, Thomas H. Gomez, Mamoun Younes, Xiurong Zhao, Qiang Shen, Run Wang, Tien C. Ko, Yanna Cao
Software Mentions: 1
Published: almost 4 years ago

10.3390/cancers13184579

3D Model of the Early Melanoma Microenvironment Captures Macrophage Transition into a Tumor-Promoting Phenotype
Cited by: 5
Author(s): Gabriela A. Pizzurro, Chang Liu, Kate Bridges, Amanda F. Alexander, Alice H. Huang, Janani P. Baskaran, Julie Y. Ramseier, Marcus W. Bosenberg, Michael Mak, Kathryn Miller‐Jensen
Software Mentions: 1
Published: over 3 years ago

10.3389/fped.2021.615724

Specific Immune Response and Cytokine Production in CD70 Deficiency
Cited by: 7
Author(s): Hassan Abolhassani
Software Mentions: 1
Published: over 3 years ago

10.3389/fmolb.2021.679797

Macrophage Plasticity and Atherosclerosis Therapy
Cited by: 71
Author(s): Ping Lin, Honghai Ji, Yanjie Li, Shoudong Guo
Software Mentions: 1
Published: over 3 years ago

10.1186/s13073-020-00773-y

FOXC1-mediated LINC00301 facilitates tumor progression and triggers an immune-suppressing microenvironment in non-small cell lung cancer by regulating the HIF1α pathway
Cited by: 90
Author(s): Chengcao Sun, Wei Zhu, Shujun Li, Wei Hu, Jian Zhang, Yue Zhuo, Han Zhang, Juan Wang, Yu Zhang, Shaoxin Huang, Qi-qiang He, Dejia Li
Software Mentions: 1
Published: over 4 years ago

10.1186/s13073-021-00834-w

Correction to: FOXC1-mediated LINC00301 facilitates tumor progression and triggers an immune-suppressing microenvironment in non-small cell lung cancer by regulating the HIF1α pathway
Cited by: 51
Author(s): Chengcao Sun, Wei Zhu, Shujun Li, Wei Hu, Jian Zhang, Yue Zhuo, Han Zhang, Juan Wang, Yu Zhang, Shaoxin Huang, Qi-qiang He, Dejia Li
Software Mentions: 1
Published: almost 4 years ago

10.3389/fmicb.2020.600989

Imaging Mass Cytometric Analysis of Postmortem Tissues Reveals Dysregulated Immune Cell and Cytokine Responses in Multiple Organs of COVID-19 Patients
Cited by: 24
Author(s): Chong Wang, Jiqian Xu, Shaoyuan Wang, Shangwen Pan, Jiancheng Zhang, Yu Han, Mingbin Huang, Di Wu, Qingyu Yang, Xiaobo Yang, Yang Yang, Ting Shu, Xiaojing Zou, Ruiting Li, Yousong Luo, Runqing Yao, Yaxin Wang, Yang Qiu, Yu Wang, Ding-Yu Zhang, Qun Yao, Yongpan Yan, Xi Zhou, You Shang
Software Mentions: 1
Published: almost 4 years ago

Projects: pypi: PhenoGraph

Papers Mentioning PhenoGraph 96