bioconductor: FlowSOM | Projects | Ecosyste.ms: Papers

10.1186/s12859-021-04054-2

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

10.12688/f1000research.15666.3

A systematic performance evaluation of clustering methods for single-cell RNA-seq data
Cited by: 33
Author(s): Angelo Duò, Mark D. Robinson, Charlotte Soneson
Software Mentions: 17
Published: about 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

10.1038/s42003-019-0415-5

diffcyt: Differential discovery in high-dimensional cytometry via high-resolution clustering
Cited by: 137
Author(s): Lukas M. Weber, Małgorzata Nowicka, Charlotte Soneson, Mark D. Robinson
Software Mentions: 12
Published: over 5 years ago

10.1186/s40425-019-0764-0

34th Annual Meeting & Pre-Conference Programs of the Society for Immunotherapy of Cancer (SITC 2019): part 2
Cited by: 28
Author(s):
Software Mentions: 12
Published: about 5 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

10.1186/s13059-021-02368-1

treeclimbR pinpoints the data-dependent resolution of hierarchical hypotheses
Cited by: 4
Author(s): Ronald Huang, Charlotte Soneson, Pierre‐Luc Germain, Thomas Schmidt, Christian von Mering, Mark D. Robinson
Software Mentions: 10
Published: over 3 years ago

10.1038/s42003-020-0842-3

Loss of the branched-chain amino acid transporter CD98hc alters the development of colonic macrophages in mice
Cited by: 17
Author(s): Philipp Wuggenig, Berna Kaya, Hassan Melhem, C. Korcan Ayata, Swiss Ibd Cohort Investigators, Petr Hrúz, Emre Sayan, Hideki Tsumura, Morihiro Ito, Julien Roux, Jan Hendrik Niess
Software Mentions: 10
Published: almost 5 years ago

10.1186/s13059-021-02363-6

Multi-omic profiling of lung and liver tumor microenvironments of metastatic pancreatic cancer reveals site-specific immune regulatory pathways
Cited by: 24
Author(s): Won Jin Ho, Rossin Erbe, Ludmila Danilova, Zaw Phyo, Emma Bigelow, Genevieve Stein-O’Brien, Dwayne L. Thomas, Soren Charmsaz, Nicole Groß, Skylar Woolman, Kayla Cruz, Rebecca M Munday, Neeha Zaidi, Todd D. Armstrong, Marcelo B. Sztein, Mark Yarchoan, Elizabeth D. Thompson, Elizabeth M. Jaffee, Elana J. Fertig
Software Mentions: 9
Published: over 3 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

10.1186/s40425-019-0763-1

34th Annual Meeting & Pre-Conference Programs of the Society for Immunotherapy of Cancer (SITC 2019): part 1
Cited by: 31
Author(s):
Software Mentions: 9
Published: about 5 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

10.1038/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

10.12688/f1000research.21642.2

Generalized EmbedSOM on quadtree-structured self-organizing maps
Cited by: 3
Author(s): Miroslav Kratochvíl, Abhishek Koladiya, Jiřı́ Vondrášek
Software Mentions: 8
Published: over 4 years ago

10.3389/fonc.2020.01254

Unraveling the Complexity of the Cancer Microenvironment With Multidimensional Genomic and Cytometric Technologies
Cited by: 39
Author(s): Natasja L. de Vries, Ahmed Mahfouz, Frits Koning, Noel F.C.C. de Miranda
Software Mentions: 8
Published: over 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

10.3389/fimmu.2021.634127

Immunophenotyping of Peripheral Blood Mononuclear Cells in Septic Shock Patients With High-Dimensional Flow Cytometry Analysis Reveals Two Subgroups With Differential Responses to Immunostimulant Drugs
Cited by: 4
Author(s): Ya Wang, Brian Gloss, Benjamin Tang, Suat Dervish, Brigitte Santner-Nanan, Christina Whitehead, Kristy Masters, Kristen K. Skarratt, Sally Teoh, Stephen D. Schibeci, Nicole Fewings, Chrystelle Brignone, Frédéric Triebel, David R. Booth, Anthony S. McLean, Marek Nalos
Software Mentions: 7
Published: almost 4 years ago

10.3389/fimmu.2020.01166

Non-sterilizing, Infection-Permissive Vaccination With Inactivated Influenza Virus Vaccine Reshapes Subsequent Virus Infection-Induced Protective Heterosubtypic Immunity From Cellular to Humoral Cross-Reactive Immune Responses
Cited by: 6
Author(s): Angela Choi, Lorena Itatí Ibáñez, Shirin Strohmeier, Florian Krammer, Adolfo Garcı́a-Sastre, Michael Schotsaert
Software Mentions: 7
Published: over 4 years ago

10.3390/vaccines7030113

TIV Vaccination Modulates Host Responses to Influenza Virus Infection that Correlate with Protection against Bacterial Superinfection
Cited by: 5
Author(s): Angela Choi, Ioanna Christopoulou, Xavier Saelens, Adolfo Garcı́a-Sastre, Michael Schotsaert
Software Mentions: 7
Published: over 5 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

10.1101/2021.07.06.21259528

Pre-vaccination and early B cell signatures predict antibody response to SARS-CoV-2 mRNA vaccine
Cited by: 2
Author(s): Lela Kardava, Nicholas Rachmaninoff, Lau Ww, Buckner Cm, Krittin Trihemasava, de Assis Fl, W Wang, X Zhang, Y Wang, Cheng Feng Chiang, Sandeep Narpala, Robert Reger, McCormack Ge, Seamon Ca, Childs Rw, A. F. Suffredini, Strich, Chertow Ds, Davey Rt, Sneller Mc, Sarah O’Connell, Li Y, Adrian B. McDermott, Tae‐Wook Chun, Fauci As, Tsang Js, Susan Moir
Software Mentions: 6
Published: over 3 years ago

10.1371/journal.pcbi.1009071

CytoPy: An autonomous cytometry analysis framework
Cited by: 8
Author(s): Ross J. Burton, Raya Ahmed, Simone Cuff, Sarah Baker, Andreas Artemiou, Matthias Eberl
Software Mentions: 6
Published: over 3 years ago

10.1038/s41598-020-64516-0

Cyto-Feature Engineering: A Pipeline for Flow Cytometry Analysis to Uncover Immune Populations and Associations with Disease
Cited by: 7
Author(s): Amy Fox, Taru Dutt, Burton Karger, Mauricio Rojas, Andrés Obregón-Henao, G. Brooke Anderson, Marcela Henao-Tamayo
Software Mentions: 6
Published: over 4 years ago

10.3390/ijms21010079

Current Projection Methods-Induced Biases at Subgroup Detection for Machine-Learning Based Data-Analysis of Biomedical Data
Cited by: 10
Author(s): Jörn Lötsch, Alfred Ultsch
Software Mentions: 6
Published: about 5 years ago

10.1016/j.cell.2020.05.039

Multimodal Analysis of Composition and Spatial Architecture in Human Squamous Cell Carcinoma
Cited by: 438
Author(s): Andrew L. Ji, Adam J. Rubin, Kim Thrane, Sizun Jiang, David L. Reynolds, Robin M. Meyers, Margaret Guo, Benson M. George, Annelie Mollbrink, Joseph Bergenstråhle, Ludvig Larsson, Yunhao Bai, Bokai Zhu, Aparna Bhaduri, Jordan M. Meyers, Xavier Rovira-Clavé, S. Tyler Hollmig, Sumaira Z. Aasi, Garry P. Nolan, Joakim Lundeberg, Paul A. Khavari
Software Mentions: 6
Published: over 4 years ago

10.3389/fimmu.2020.00714

Characterization of the Impact of Daclizumab Beta on Circulating Natural Killer Cells by Mass Cytometry
Cited by: 7
Author(s): Thanmayi Ranganath, Laura J. Simpson, Anne-Maud Ferreira, Christof Seiler, Elena Vendrame, Nancy Q. Zhao, Jason D. Fontenot, Susan Holmes, Catherine A. Blish
Software Mentions: 6
Published: over 4 years ago

10.1002/cyto.a.23775

Automating the Shared Resource Laboratory Using Computer Scripts: A Case Report
Cited by: 0
Author(s): Christopher Hall, Laura Brown, Jennifer Graham, Sam Thompson, Bee Ling Ng
Software Mentions: 6
Published: over 5 years ago

10.1007/s00401-021-02299-y

Single-cell profiling of myasthenia gravis identifies a pathogenic T cell signature
Cited by: 21
Author(s): Florian Ingelfinger, Sinduya Krishnarajah, Michael H. Kramer, Sebastian G. Utz, Edoardo Galli, Mirjam Lutz, Pascale Zwicky, Ayse U. Akarca, Nicole Puertas Jurado, Can Ulutekin, David Bamert, Corinne C. Widmer, Luca Piccoli, Federica Sallusto, Nicolás Gonzalo Núñez, Teresa Marafioti, Didier Schneiter, Isabelle Opitz, Antonio Lanzavecchia, Hans H. Jung, Donatella De Feo, Sarah Mundt, Bettina Schreiner, Burkhard Becher
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

10.3389/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

10.3389/fimmu.2021.626098

GMP-Compliant Universal Antigen Presenting Cells (uAPC) Promote the Metabolic Fitness and Antitumor Activity of Armored Cord Blood CAR-NK Cells
Cited by: 18
Author(s): Enli Liu, Sonny Ang, Lucila Nassif Kerbauy, Rafet Basar, Indreshpal Kaur, Mecit Kaplan, Li Li, Yijiu Tong, May Daher, Emily L. Ensley, Nadima Uprety, Ana Karen Nunez Cortes, Ryan Z Yang, Ye Li, Hila Shaim, Francia Reyes Silva, Paul Lin, Vakul Mohanty, Sunil Acharya, Mayra Shanley, Luis Muniz-Feliciano, Pinaki P. Banerjee, Ken Chen, Richard E. Champlin, Elizabeth J. Shpall, Katayoun Rezvani
Software Mentions: 5
Published: almost 4 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.53839

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

10.1038/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

10.1172/jci.insight.148435

A specific low-density neutrophil population correlates with hypercoagulation and disease severity in hospitalized COVID-19 patients
Cited by: 70
Author(s): Samantha M. Morrissey, Anne E Geller, Xiaoling Hu, David Tieri, Chuan‐Fan Ding, Christopher K Klaes, Elizabeth A. Cooke, Matthew R Woeste, Zachary C Martin, Oscar Chen, Sarah A. Bush, Huang‐Ge Zhang, Rodrigo Cavallazzi, Sean P. Clifford, James Chen, Smita Ghare, Shirish Barve, Lu Cai, Maiying Kong, Eric C. Rouchka, Kenneth R. McLeish, Silvia M. Uriarte, Corey T. Watson, Jiapeng Huang, Jun Yan
Software Mentions: 5
Published: over 3 years ago

10.1002/cyto.a.23663

<i>CytoML</i> for cross‐platform cytometry data sharing
Cited by: 23
Author(s): Greg Finak, Wenxin Jiang, Raphaël Gottardo
Software Mentions: 5
Published: about 6 years ago

10.3389/fimmu.2021.590742

High Throughput Multi-Omics Approaches for Clinical Trial Evaluation and Drug Discovery
Cited by: 30
Author(s): Jessica Zielinski, Jason J. Luke, Silvia Guglietta, Carsten Krieg
Software Mentions: 5
Published: over 3 years ago

10.1093/gigascience/giaa127

GigaSOM.jl: High-performance clustering and visualization of huge cytometry datasets
Cited by: 6
Author(s): Miroslav Kratochvíl, Oliver Hunewald, Laurent Heirendt, Vasco Verissimo, Jiřı́ Vondrášek, Venkata Satagopam, Reinhard Schneider, Christophe Trefois, Markus Ollert
Software Mentions: 4
Published: about 4 years ago

10.1016/j.immuni.2020.06.013

An Integrated Multi-omic Single-Cell Atlas of Human B Cell Identity
Cited by: 129
Author(s): David R. Glass, Albert Tsai, John Paul Oliveria, Felix J. Hartmann, Samuel C. Kimmey, Ariel A. Calderon, Luciene Borges, Marla C. Glass, Lisa E. Wagar, Mark M. Davis, Sean C. Bendall
Software Mentions: 4
Published: over 4 years ago

10.1038/s41598-019-55852-x

Multi-parameter immune profiling of peripheral blood mononuclear cells by multiplexed single-cell mass cytometry in patients with early multiple sclerosis
Cited by: 34
Author(s): Chotima Böttcher, Camila Fernández-Zapata, Stephan Schlickeiser, Désirée Kunkel, Axel Schulz, Henrik E. Mei, Carl Weidinger, René M. Gieß, Susanna Asseyer, Britta Siegmund, Friedemann Paul, Klemens Ruprecht, Josef Priller
Software Mentions: 4
Published: about 5 years ago

10.7554/eLife.64653

Unsupervised machine learning reveals key immune cell subsets in COVID-19, rhinovirus infection, and cancer therapy
Cited by: 13
Author(s): Sierra Barone, Alberta Paul, Lyndsey M. Muehling, Joanne Lannigan, William W. Kwok, Ronald B. Turner, Judith A. Woodfolk, Jonathan M. Irish
Software Mentions: 4
Published: over 3 years ago

10.1016/j.celrep.2019.06.049

Comprehensive Immune Monitoring of Clinical Trials to Advance Human Immunotherapy
Cited by: 81
Author(s): Felix J. Hartmann, Joël Babdor, Pier Federico Gherardini, El-ad David Amir, Kyle Jones, Bita Sahaf, Diana M. Márquez, Peter O. Krutzik, Erika O’Donnell, Natalia Sigal, Holden T. Maecker, Everett Meyer, Matthew H. Spitzer, Sean C. Bendall
Software Mentions: 4
Published: over 5 years ago

10.1084/jem.20201793

A positive feedback loop reinforces the allergic immune response in human peanut allergy
Cited by: 10
Author(s): Xiaoying Zhou, Wei Yu, Shu‐Chen Lyu, Claudia Macaubas, Bryan Bunning, Ziyuan He, Elizabeth Mellins, Kari Nadeau
Software Mentions: 4
Published: over 3 years ago

10.3389/fimmu.2021.652631

Adjacent Cell Marker Lateral Spillover Compensation and Reinforcement for Multiplexed Images
Cited by: 19
Author(s): Yunhao Bai, Bokai Zhu, Xavier Rovira-Clavé, Han Chen, Maxim Markovic, Chi N. Chan, Tung–Hung Su, David R. McIlwain, Jacob D. Estes, Leeat Keren, Garry P. Nolan, Sizun Jiang
Software Mentions: 4
Published: over 3 years ago

10.3389/fimmu.2021.691725

Severe COVID-19 Recovery Is Associated with Timely Acquisition of a Myeloid Cell Immune-Regulatory Phenotype
Cited by: 29
Author(s): A.C. Trombetta, Guilherme B. Farias, André M. C. Gomes, Ana Godinho‐Santos, Pedro Rosmaninho, Carolina M. Conceição, Joel Laia, Diana Santos, Afonso R. M. Almeida, Catarina Mota, Andréia Gomes, María Luisa Madueño Serrano, Marc Veldhoen, Ana E. Sousa, S. Fernandes
Software Mentions: 4
Published: over 3 years ago

10.3389/fimmu.2021.740708

Evidence of SARS-CoV-2-Specific Memory B Cells Six Months After Vaccination With the BNT162b2 mRNA Vaccine
Cited by: 78
Author(s): Annalisa Ciabattini, Gabiria Pastore, Fabio Fiorino, Jacopo Polvere, Simone Lucchesi, Elena Pettini, Stefano Auddino, Ilaria Rancan, Miriam Durante, Michele Miscia, Barbara Rossetti, Massimiliano Fabbiani, Francesca Montagnani, Donata Medaglini
Software Mentions: 4
Published: about 3 years ago

10.3389/fimmu.2020.00829

Treated HIV Infection Alters Phenotype but Not HIV-Specific Function of Peripheral Blood Natural Killer Cells
Cited by: 8
Author(s): Nancy Q. Zhao, Anne-Maud Ferreira, Philip Grant, Susan Holmes, Catherine A. Blish
Software Mentions: 4
Published: over 4 years ago

10.3389/fimmu.2021.620386

CMV Status Drives Distinct Trajectories of CD4+ T Cell Differentiation
Cited by: 11
Author(s): Weiwen Zhang, Anna B. Morris, Erica V. Peek, Geeta Karadkhele, Jennifer Rosenstein, Haydn Kissick, Christian Larsen
Software Mentions: 4
Published: over 3 years ago

10.3389/fimmu.2019.01194

Quantitative Comparison of Conventional and t-SNE-guided Gating Analyses
Cited by: 39
Author(s): Shadi Toghi Eshghi, Amelia Au-Yeung, Chikara Takahashi, Christopher R. Bolen, Maclean N. Nyachienga, Sean Lear, Cherie Green, W. Rodney Mathews, William O’Gorman
Software Mentions: 3
Published: over 5 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

10.1093/bioinformatics/btaa946

Agile workflow for interactive analysis of mass cytometry data
Cited by: 6
Author(s): Julia Casado, Oskari Lehtonen, Ville Rantanen, Katja Kaipio, Luca Pasquini, Antti Häkkinen, Eleonora Petrucci, Johanna Hynninen, Sakari Hietanen, Olli Carpén, Mauro Biffoni, Anniina Färkkilä, Sampsa Hautaniemi
Software Mentions: 3
Published: about 4 years ago

10.1038/s41408-021-00440-4

Relapsed multiple myeloma demonstrates distinct patterns of immune microenvironment and malignant cell-mediated immunosuppression
Cited by: 22
Author(s): Alissa Visram, Surendra Dasari, Emilie Anderson, Shaji Kumar, Taxiarchis Kourelis
Software Mentions: 3
Published: almost 4 years ago

10.3390/vaccines9060579

Predictive Markers of Immunogenicity and Efficacy for Human Vaccines
Cited by: 23
Author(s): Matthieu Van Tilbeurgh, Katia Lemdani, Anne-Sophie Beignon, Catherine Chapon, Nicolas Tchitchek, Lina Cheraitia, Ernesto Marcos López, Quentin Pascal, Roger Le Grand, Pauline Maisonnasse, Caroline Manet
Software Mentions: 3
Published: over 3 years ago

10.3390/v13091805

Acute HIV-1 and SARS-CoV-2 Infections Share Slan+ Monocyte Depletion—Evidence from an Hyperacute HIV-1 Case Report
Cited by: 1
Author(s): Guilherme B. Farias, Robert Badura, Carolina M. Conceição, André M. C. Gomes, Ana Godinho‐Santos, Joel Laia, Pedro Rosmaninho, Diana Santos, Catarina Mota, Afonso R. M. Almeida, S. Fernandes, A.C. Trombetta, Ana E. Sousa
Software Mentions: 3
Published: over 3 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

10.3390/cancers13081776

Activated Regulatory T-Cells, Dysfunctional and Senescent T-Cells Hinder the Immunity in Pancreatic Cancer
Cited by: 22
Author(s): Shivan Sivakumar, Enas Abu-Shah, David Ahern, Edward H. Arbe-Barnes, Ashwin Kumar Jainarayanan, Nagina Mangal, Srikanth Reddy, Anikó Rendek, Alistair Easton, Elke Kurz, Michael Silva, Zahir Soonawalla, Lara Heij, Rachael Bashford-Rogers, Mark R. Middleton, Michael L. Dustin
Software Mentions: 3
Published: over 3 years ago

10.1038/s41419-021-03408-1

SCA-1 micro-heterogeneity in the fate decision of dystrophic fibro/adipogenic progenitors
Cited by: 13
Author(s): Giulio Giuliani, Simone Vumbaca, Claudia Fuoco, Cesare Gargioli, Ezio Giorda, Giorgia Massacci, Alessandro Palma, Alessio Reggio, Federica Riccio, Marco Rosina, Maria Vinci, Luisa Castagnoli, Gianni Cesareni
Software Mentions: 3
Published: almost 4 years ago

10.1038/s41419-020-03333-9

SARS-CoV-2 infection is associated with a pro-thrombotic platelet phenotype
Cited by: 74
Author(s): Dario Bongiovanni, Melissa Klug, Olga Lazareva, Simon Weidlich, Marina Pietro Biasi, Simona Ursu, Sarah Warth, Christian Buske, Marina Lukas, Christoph D. Spinner, Moritz von Scheidt, Gianluigi Condorelli, Jan Baumbach, Karl‐Ludwig Laugwitz, Markus List, Isabell Bernlochner
Software Mentions: 3
Published: almost 4 years ago

10.15252/emmm.202013001

Altered bioenergetics and mitochondrial dysfunction of monocytes in patients with COVID‐19 pneumonia
Cited by: 113
Author(s): Lara Gibellini, Sara De Biasi, Annamaria Paolini, Rebecca Borella, Federica Boraldi, Marco Mattioli, Domenico Lo Tartaro, Lucia Fidanza, Alfredo Caro‐Maldonado, Marianna Meschiari, Vittorio Iadisernia, Erica Bacca, Giovanni Riva, Luca Cicchetti, Daniela Quaglino, Giovanni Guaraldi, Stefano Busani, Massimo Girardis, Cristina Mussini, Andrea Cossarizza
Software Mentions: 3
Published: about 4 years ago

10.3389/fimmu.2020.01481

Pediatric Burn Survivors Have Long-Term Immune Dysfunction With Diminished Vaccine Response
Cited by: 8
Author(s): Blair Z. Johnson, Sonia McAlister, Helen M. McGuire, Vetrichevvel Thirthar Palanivelu, Andrew Stevenson, Peter Richmond, Debra J. Palmer, Jessica Metcalfe, Susan L. Prescott, Fiona Wood, Barbara Fazekas de St Groth, Matthew D. Linden, Mark W. Fear, Vanessa S. Fear
Software Mentions: 3
Published: over 4 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

10.3389/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

10.3389/fimmu.2019.02009

A Computational Pipeline for the Diagnosis of CVID Patients
Cited by: 11
Author(s): Annelies Emmaneel, Debby Bogaert, Sofie Van Gassen, Simon Tavernier, Mélissa Dullaers, Filomeen Haerynck, Yvan Saeys
Software Mentions: 3
Published: over 5 years ago

10.3389/fimmu.2021.728669

CD49a Identifies Polyfunctional Memory CD8 T Cell Subsets that Persist in the Lungs After Influenza Infection
Cited by: 11
Author(s): Emma Reilly, Mike Sportiello, Kris Lambert Emo, Andrea M. Amitrano, Rakshanda Jha, Ashwin B. R. Kumar, Nathan Laniewski, Hongmei Yang, Min‐Soo Kim, David J. Topham
Software Mentions: 3
Published: over 3 years ago

10.3389/fimmu.2019.01515

Meeting the Challenges of High-Dimensional Single-Cell Data Analysis in Immunology
Cited by: 57
Author(s): Subarna Palit, Claudia Heuser, Gustavo Pereira de Almeida, Fabian J. Theis, Christina E. Zielinski
Software Mentions: 3
Published: over 5 years ago

10.3389/fimmu.2021.656846

Expression of Senescence Marker TIGIT Identifies Polyfunctional Donor-Reactive CD4+ T Cells Preferentially Lost After Kidney Transplantation
Cited by: 12
Author(s): Amy C. J. van der List, Nicolle H.R. Litjens, Mariska Klepper, M. Betjes
Software Mentions: 3
Published: over 3 years ago

10.3389/fimmu.2021.659018

Immunological Biomarkers of Fatal COVID-19: A Study of 868 Patients
Cited by: 13
Author(s): Esperanza Martín-Sánchez, Juan-José Garcés, Catarina Maia, Susana Inogés, Ascensión López‐Díaz de Cerio, Francisco Carmona-Torre, Marta Marín-Oto, Félix Alegre, Eduardo Molano, Mirian Fernández-Alonso, Cristina Fernández Pérez, Cirino Botta, Aintzane Zabaleta, Ana B. Alcaide, Manuel F. Landecho, Marta Covela Rúa, Teresa Pérez-Warnisher, Laura Blanco, Sarai Sarvide, Amaia Vilas-Zornoza, Diego Alignani, Cristina Moreno, Iñigo Pineda, Miguel Sogbe, Josepmaría Argemi, Bruno Paiva, José Ramón Yuste
Software Mentions: 3
Published: over 3 years ago

10.3389/fphar.2019.01695

Ex Vivo Human Adipose Tissue Derived Mesenchymal Stromal Cells (ASC) Are a Heterogeneous Population That Demonstrate Rapid Culture-Induced Changes
Cited by: 21
Author(s): Anna Brooks, Megan Iminitoff, Eloise Williams, Tanvi Damani, Victoria Jackson-Patel, Vicky Fan, Joanna L. James, P. Rod Dunbar, Vaughan Feisst, Hilary Sheppard
Software Mentions: 3
Published: almost 5 years ago

10.1016/j.immuni.2020.06.002

Transcriptional and Functional Analysis of CD1c+ Human Dendritic Cells Identifies a CD163+ Subset Priming CD8+CD103+ T Cells
Cited by: 174
Author(s): Pierre Bourdely, Giorgio Anselmi, Kristine Vaivode, Rodrigo Nalio Ramos, Yoann Missolo-Koussou, Sofía Hidalgo, Jimena Tosselo, Nicolás Gonzalo Núñez, Wilfrid Richer, Anne Vincent‐Salomon, Alka Saxena, Kristie Wood, Álvaro Lladser, Eliane Piaggio, Julie Helft, Pierre Guermonprez
Software Mentions: 3
Published: over 4 years ago

10.1172/jci.insight.144913

MMP2 and TLRs modulate immune responses in the tumor microenvironment
Cited by: 21
Author(s): Luciana Rebiero Muniz-Bongers, Christopher B. McClain, Mansi Saxena, Gerold Bongers, Miriam Mérad, Nina Bhardwaj
Software Mentions: 3
Published: over 3 years ago

10.1172/jci.insight.148086

High-dimensional mass cytometry identifies T cell and B cell signatures predicting reduced risk of Plasmodium vivax malaria
Cited by: 6
Author(s): Lisa J Ioannidis, Halina M. Pietrzak, Ann Ly, Retno A. S. Utami, Emily M. Eriksson, Stephanie I Studniberg, Waruni Abeysekera, Connie S. N. Li Wai Suen, Dylan Sheerin, Julie Healer, Agatha M. Puspitasari, Dwi Apriyanti, Farah N. Coutrier, Jeanne Rini Poespoprodjo, Enny Kenangalem, Benediktus Andries, Pak Prayoga, Novita Sariyanti, Gordon K. Smyth, Leily Trianty, Alan F. Cowman, Ric N. Price, Rintis Noviyanti, Diana S. Hansen
Software Mentions: 3
Published: over 3 years ago

10.1371/journal.ppat.1008870

Eomes cannot replace its paralog T-bet during expansion and differentiation of CD8 effector T cells
Cited by: 7
Author(s): Jonas Fixemer, Jonas Hummel, Frederic Arnold, Christoph S. N. Klose, Alexis Hofherr, Kristoffer Weißert, Tamara Kögl, Michael Köttgen, Sebastian J. Arnold, Peter Aichele, Yakup Tanriver
Software Mentions: 3
Published: about 4 years ago

10.1371/journal.ppat.1009843

Hantavirus infection-induced B cell activation elevates free light chains levels in circulation
Cited by: 5
Author(s): Jussi Hepojoki, Luz E. Cabrera, Satu Hepojoki, Carla Bellomo, Lauri Kareinen, Leif C. Andersson, Antti Vaheri, Satu Mäkelä, Jukka Mustonen, Olli Vapalahti, Valeria P. Martínez, Tomas Strandin
Software Mentions: 3
Published: over 3 years ago

10.21203/rs.3.rs-802084/v1

Immune responses in COVID-19 respiratory tract and blood reveal mechanisms of disease severity
Cited by: 0
Author(s): Wuji Zhang, Brendon Y Chua, Kevin J. Selva, Łukasz Kędzierski, Thomas Myles Ashhurst, Ebene R Haycroft, Suzanne K. Shoffner, Luca Hensen, David F. Boyd, Fiona James, Effie Mouhtouris, Jason C Kwong, Kyra Chua, George Drewett, Ana Copaescu, Julie E. Dobson, Louise C. Rowntree, Jennifer R Habel, Lilith F Allen, Hui‐Fern Koay, Jessica A. Neil, Matthew J. Gartner, Christina Y. Lee, Patiyan Andersson, Torsten Seemann, Norelle L Sherry, Fatima Amanat, Florian Krammer, Sarah L. Londrigan, Linda M. Wakim, Nöel King, Dale I. Godfrey, Laura K. Mackay, Paul G. Thomas, Suellen Nicholson, Kelly B. Arnold, Amy W. Chung, Natasha E Holmes, Olivia C Smibert, Jason A Trubiano, Claire L. Gordon, Thi H. O. Nguyen, Katherine Kedzierska
Software Mentions: 3
Published: over 3 years ago

10.1038/sdata.2018.15

ImmPort, toward repurposing of open access immunological assay data for translational and clinical research
Cited by: 439
Author(s): Sanchita Bhattacharya, Patrick Dunn, Cristel G. Thomas, Barry Smith, Henry Schaefer, Jieming Chen, Zicheng Hu, Kelly A. Zalocusky, Ravi Shankar, Shai S. Shen-Orr, Elizabeth Thomson, Jeffrey Wiser, Atul J. Butte
Software Mentions: 3
Published: almost 7 years ago

10.1101/2020.08.03.235242

Robotic High-Throughput Biomanufacturing and Functional Differentiation of Human Pluripotent Stem Cells
Cited by: 3
Author(s): Carlos A. Tristan, Pinar Ormanoglu, Jaroslav Slamecka, Claire Malley, Pei-Hsuan Chu, Vukasin M. Jovanovic, Yeliz Gedik, Charles Bonney, Elena Barnaeva, John C. Braisted, Sunil K. Mallanna, Dorjbal Dorjsuren, Michael J. Iannotti, Ty C. Voss, Sam Michael, Anton Simeonov, Ilyas Singeç
Software Mentions: 3
Published: over 4 years ago

10.4049/jimmunol.2100063

Defining T Cell Subsets in Human Tonsils Using ChipCytometry
Cited by: 3
Author(s): Joachim Hagel, Kyle Bennett, Francesca M. Buffa, Paul Klenerman, Christian Willberg, Kate Powell
Software Mentions: 3
Published: over 3 years ago

10.3390/ijms22052424

Dysregulated CD38 Expression on Peripheral Blood Immune Cell Subsets in SLE
Cited by: 17
Author(s): Marie Burns, Lennard Ostendorf, Robert Biesen, Andreas Grützkau, Falk Hiepe, Henrik E. Mei, Tobias Alexander
Software Mentions: 3
Published: almost 4 years ago

10.1093/bioinformatics/btaa091

ShinySOM: graphical SOM-based analysis of single-cell cytometry data
Cited by: 5
Author(s): Miroslav Kratochvíl, David Bednárek, Tomáš Sieger, Karel Fišer, Jiřı́ Vondrášek
Software Mentions: 2
Published: almost 5 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

10.1080/2162402X.2020.1730538

Tumor endothelial cell up-regulation of IDO1 is an immunosuppressive feed-back mechanism that reduces the response to CD40-stimulating immunotherapy
Cited by: 21
Author(s): Maria Georganaki, Mohanraj Ramachandran, Sander Tuit, Nicolás Gonzalo Núñez, Alexandros Karampatzakis, Grammatiki Fotaki, Luuk van Hooren, Hua Huang, Roberta Lugano, Thomas Ulas, Aura Kaunisto, Eric C. Holland, Peter Ellmark, Sara M. Mangsbo, Joachim L. Schultze, Magnus Essand, Sònia Tugues, Anna Dimberg
Software Mentions: 2
Published: almost 5 years ago

10.3389/fimmu.2021.674279

A Virus-Specific Immune Rheostat in the Immunome of Patients Recovering From Mild COVID-19
Cited by: 4
Author(s): Joo Guan Yeo, Jing Yao Leong, Tay Sh, Karen Donceras Nadua, Danielle E. Anderson, Amanda Jin Mei Lim, Xiang Wen Ng, Su Li Poh, D. Guo, Katherine Nay Yaung, Pavanish Kumar, Martin Wasser, Sharifah Nur Hazirah, Nursyuhadah Sutamam, Camillus Chua, Martin Qui, Randy Foo, Akshamal M Gamage, Kee Thai Yeo, Lakshmi Ramakrishna, Thaschawee Arkachaisri, Barnaby Edward Young, David C. Lye, Lin‐Fa Wang, Chia Yin Chong, Natalie Woon Hui Tan, Jiahui Li, Kai Qian Kam, Florent Ginhoux, Koh Cheng Thoon, Jerry Kok Yen Chan, Chee Fu Yung, Salvatore Albani
Software Mentions: 2
Published: over 3 years ago

10.3389/fimmu.2021.700755

Circulating Plasmacytoid and Conventional Dendritic Cells Are Numerically and Functionally Deficient in Patients With Scrub Typhus
Cited by: 3
Author(s): Seung-Ji Kang, Ki-Jeong Park, Hye-Mi Jin, Young-Nan Cho, Tae Hoon Oh, Seong Eun Kim, Uh Jin Kim, Kyung‐Hwa Park, Sook-In Jung, Tae-Ok Kim, Hyo Shin Kim, Younggoun Jo, Jae Kyun Ju, Seung‐Jung Kee, Yong-Wook Park
Software Mentions: 2
Published: over 3 years ago

10.3389/fimmu.2020.574057

Vi-Vaccinations Induce Heterogeneous Plasma Cell Responses That Associate With Protection From Typhoid Fever
Cited by: 9
Author(s): Deborah L Cross, Marije K. Verheul, Holden Maecker, Gerlinde Obermoser, Chunlin Jin, Elizabeth Jones, Joshua S Starr, Irina Mohorianu, Christoph J. Blohmke, Holden T. Maecker, Giorgio Napolitani, Jennifer Hill, Andrew J. Pollard
Software Mentions: 2
Published: about 4 years ago

10.7554/eLife.60933

Phenotypic analysis of the unstimulated in vivo HIV CD4 T cell reservoir
Cited by: 55
Author(s): Jason Neidleman, Xiaoyu Luo, Julie Frouard, Guorui Xie, Feng Hsiao, Tongcui Ma, Vincent Morcilla, Ashley Lee, Sushama Telwatte, Reuben Thomas, Whitney Tamaki, Benjamin J Wheeler, Rebecca Hoh, Ma Somsouk, Poonam Vohra, Jeffrey M. Milush, Katherine S James, Nancie M. Archin, Peter W. Hunt, Steven G. Deeks, Steven A. Yukl, Sarah Palmer, Warner C. Greene, Nadia R. Roan
Software Mentions: 2
Published: about 4 years ago

10.3389/fimmu.2021.661551

Association of Premature Immune Aging and Cytomegalovirus After Solid Organ Transplant
Cited by: 12
Author(s): Lauren E. Higdon, Claire E. Gustafson, Xuhuai Ji, Malaya K. Sahoo, Benjamin A. Pinsky, Kenneth B. Margulies, Holden T. Maecker, Jörg J. Goronzy, Jonathan S. Maltzman
Software Mentions: 2
Published: over 3 years ago

10.3389/fimmu.2021.655934

T Cell Activation, Highly Armed Cytotoxic Cells and a Shift in Monocytes CD300 Receptors Expression Is Characteristic of Patients With Severe COVID-19
Cited by: 46
Author(s): Olatz Zenarruzabeitia, Gabirel Astarloa-Pando, Íñigo Terrén, Ane Orrantia, Raquel Pérez-Garay, Iratxe Seijas-Betolaza, Javier Nieto-Arana, Natale Imaz-Ayo, Silvia Pérez‐Fernández, Eunate Arana-Arri, Francisco Borrego
Software Mentions: 2
Published: almost 4 years ago

10.1186/s12918-019-0690-2

Ultrafast clustering of single-cell flow cytometry data using FlowGrid
Cited by: 24
Author(s): Xiaoxin Ye, Joshua W. K. Ho
Software Mentions: 2
Published: over 5 years ago

10.3389/fimmu.2021.645478

Restoration of NK Cell Cytotoxic Function With Elotuzumab and Daratumumab Promotes Elimination of Circulating Plasma Cells in Patients With SLE
Cited by: 13
Author(s): Morgane Humbel, Florence Bellanger, Natalia Fluder, Alice Horisberger, Madeleine Suffiotti, Craig Fenwick, Camillo Ribi, Denis Comte
Software Mentions: 2
Published: almost 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

10.7554/eLife.55487

HIV efficiently infects T cells from the endometrium and remodels them to promote systemic viral spread
Cited by: 31
Author(s): Tongcui Ma, Xiaoyu Luo, Ashley F George, Gourab Mukherjee, Nandini Sen, Trimble Spitzer, Linda C. Giudice, Warner C. Greene, Nadia R. Roan
Software Mentions: 2
Published: over 4 years ago

10.1016/j.stem.2017.02.014

Comprehensive Cell Surface Protein Profiling Identifies Specific Markers of Human Naive and Primed Pluripotent States
Cited by: 134
Author(s): Amanda J. Collier, Sarita Panula, John P. Schell, Peter Chovanec, Álvaro Plaza Reyes, Sophie Petropoulos, Anne E. Corcoran, Rachael Walker, Iyadh Douagi, Fredrik Lanner, Peter J. Rugg‐Gunn
Software Mentions: 2
Published: over 7 years ago

10.1016/j.celrep.2021.109038

Characterization of HIV-induced remodeling reveals differences in infection susceptibility of memory CD4+ T cell subsets in vivo
Cited by: 13
Author(s): Guorui Xie, Xiaoyu Luo, Tongcui Ma, Julie Frouard, Jason Neidleman, Rebecca Hoh, Steven G. Deeks, Warner C. Greene, Nadia R. Roan
Software Mentions: 2
Published: over 3 years ago

10.3390/cancers12071860

Tumor-Associated Neutrophils Dampen Adaptive Immunity and Promote Cutaneous Squamous Cell Carcinoma Development
Cited by: 24
Author(s): Sokchea Khou, Alexandra Popa, Carmelo Luci, Franck Bihl, Aïda Meghraoui-Kheddar, Pierre Bourdely, Emie Salavagione, Estelle Cosson, Alain Rubod, Julie Cazareth, Pascal Barbry, Bernard Mari, Roger Rezzonico, Fabienne Anjuère, Véronique M. Braud
Software Mentions: 2
Published: over 4 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

10.7554/eLife.59630

Removing unwanted variation with CytofRUV to integrate multiple CyTOF datasets
Cited by: 25
Author(s): Marie Trussart, Charis E. Teh, Tania Tan, Lawrence Leong, Daniel H.D. Gray, Terence P. Speed
Software Mentions: 2
Published: over 4 years ago

10.1172/jci.insight.145389

Systemic inflammation is a determinant of outcomes of CD40 agonist–based therapy in pancreatic cancer patients
Cited by: 12
Author(s): Max M. Wattenberg, Veronica M. Herrera, Michael A. Giannone, Whitney L. Gladney, Erica L. Carpenter, Gregory L. Beatty
Software Mentions: 2
Published: almost 4 years ago

10.1172/jci.insight.143283

A global live cell barcoding approach for multiplexed mass cytometry profiling of mouse tumors
Cited by: 8
Author(s): Soren Charmsaz, Nicole Groß, Elizabeth M. Jaffee, Won Jin Ho
Software Mentions: 2
Published: over 3 years ago

10.7554/eLife.51678

High-dimensional analysis of intestinal immune cells during helminth infection
Cited by: 21
Author(s): Laura Ferrer‐Font, Palak Mehta, Phoebe Harmos, Alfonso Schmidt, Sally Claire Chappell, Kylie M. Price, Ian F. Hermans, Franca Ronchese, Graham Le Gros, Johannes U Mayer
Software Mentions: 2
Published: almost 5 years ago

Projects: bioconductor: FlowSOM

Papers Mentioning FlowSOM 177