FlowCT for the analysis of large immunophenotypic data sets and biomarker discovery in cancer immunology

Mechanisms of Immune Evasion in Multiple Myeloma: Open Questions and Therapeutic Opportunities

(2021) Cirino Botta et al.   Cancers

PARC: ultrafast and accurate clustering of phenotypic data of millions of single cells

(2020) Shobana V Stassen et al.   BIOINFORMATICS

ShinySOM: graphical SOM-based analysis of single-cell cytometry data

(2020) Miroslav Kratochvíl et al.   BIOINFORMATICS

Immunogenomic identification and characterization of granulocytic myeloid derived suppressor cells in multiple myeloma

(2020) Cristina Perez et al.   BLOOD

Extensive Remodeling of the Immune Microenvironment in B Cell Acute Lymphoblastic Leukemia

(2020) Matthew T. Witkowski et al.   CANCER CELL

High-Dimensional Data Analysis Algorithms Yield Comparable Results for Mass Cytometry and Spectral Flow Cytometry Data

(2020) Laura Ferrer-Font et al.   CYTOMETRY PART A

Immunogenomic Landscape of Hematological Malignancies

(2020) Olli Dufva et al.   CANCER CELL

A Cancer Biologist's Primer on Machine Learning Applications in High‐Dimensional Cytometry

(2020) Timothy J. Keyes et al.   CYTOMETRY PART A

Isatuximab as monotherapy and combined with dexamethasone in patients with relapsed/refractory multiple myeloma

(2020) Meletios A Dimopoulos et al.   BLOOD

Model-based clustering for flow and mass cytometry data with clinical information

(2020) Ko Abe et al.   BMC BIOINFORMATICS

Cancer Biomarkers and Big Data: A Planetary Science Approach

(2020) Daniel J. Crichton et al.   CANCER CELL

A Multi-layer Molecular Fresco of the Immune Diversity across Hematologic Malignancies

(2020) Davide Bedognetti   CANCER CELL

International Myeloma Working Group risk stratification model for smoldering multiple myeloma (SMM)

(2020) María-Victoria Mateos et al.   Blood Cancer Journal

Effect of Integrating Machine Learning Mortality Estimates With Behavioral Nudges to Clinicians on Serious Illness Conversations Among Patients With Cancer

(2020) Christopher R. Manz et al.   JAMA Oncology

Multibatch Cytometry Data Integration for Optimal Immunophenotyping

(2020) Masato Ogishi et al.   JOURNAL OF IMMUNOLOGY

A comparison of machine learning methods for survival analysis of high-dimensional clinical data for dementia prediction

(2020) Annette Spooner et al.   Scientific Reports

CD8+ T cells expand stem and progenitor cells in favorable but not adverse risk acute myeloid leukemia

(2019) Ramin Radpour et al.   LEUKEMIA

Meeting the Challenges of High-Dimensional Single-Cell Data Analysis in Immunology

(2019) Subarna Palit et al.   Frontiers in Immunology

Bortezomib, lenalidomide, and dexamethasone as induction therapy prior to autologous transplantation in multiple myeloma

(2019) Laura Rosiñol et al.   BLOOD

Progression of Disease Within 24 Months in Follicular Lymphoma Is Associated With Reduced Intratumoral Immune Infiltration

(2019) Joshua W.D. Tobin et al.   JOURNAL OF CLINICAL ONCOLOGY

CytoNorm: A Normalization Algorithm for Cytometry Data

(2019) Sofie Van Gassen et al.   CYTOMETRY PART A

Measurable Residual Disease by Next-Generation Flow Cytometry in Multiple Myeloma

(2019) Bruno Paiva et al.   JOURNAL OF CLINICAL ONCOLOGY

The art of using t-SNE for single-cell transcriptomics

(2019) Dmitry Kobak et al.   Nature Communications

Advances in CD30- and PD-1-targeted therapies for classical Hodgkin lymphoma

(2018) Yucai Wang et al.   Journal of Hematology & Oncology

Immune cell contexture in the bone marrow tumor microenvironment impacts therapy response in CML

(2018) Oscar Brück et al.   LEUKEMIA

Integrating single-cell transcriptomic data across different conditions, technologies, and species

(2018) Andrew Butler et al.   NATURE BIOTECHNOLOGY

Single-cell developmental classification of B cell precursor acute lymphoblastic leukemia at diagnosis reveals predictors of relapse

(2018) Zinaida Good et al.   NATURE MEDICINE

Myeloma-escape after stem cell transplantation is a consequence of T cell exhaustion and is prevented by TIGIT blockade

(2018) Simone A. Minnie et al.   BLOOD

flowAI: automatic and interactive anomaly discerning tools for flow cytometry data

(2016) Gianni Monaco et al.   BIOINFORMATICS

MGUS to myeloma: a mysterious gammopathy of underexplored significance

(2016) M. V. Dhodapkar   BLOOD

Comparison of clustering methods for high-dimensional single-cell flow and mass cytometry data

(2016) Lukas M. Weber et al.   CYTOMETRY PART A

The route to solve the interplay between inflammation, angiogenesis and anti-cancer immune response

(2016) C Botta et al.   Cell Death & Disease

A gene expression inflammatory signature specifically predicts multiple myeloma evolution and patients survival

(2016) C Botta et al.   Blood Cancer Journal

Immune status of high-risk smoldering multiple myeloma patients and its therapeutic modulation under LenDex: a longitudinal analysis

(2015) Bruno Paiva et al.   BLOOD

FlowSOM: Using self-organizing maps for visualization and interpretation of cytometry data

(2015) Sofie Van Gassen et al.   CYTOMETRY PART A

Classification of current anticancer immunotherapies

(2015) Lorenzo Galluzzi et al.   Oncotarget

HTSeq--a Python framework to work with high-throughput sequencing data

(2014) S. Anders et al.   BIOINFORMATICS

OpenCyto: An Open Source Infrastructure for Scalable, Robust, Reproducible, and Automated, End-to-End Flow Cytometry Data Analysis

(2014) Greg Finak et al.   PLoS Computational Biology

Clinical, genomic, and imaging predictors of myeloma progression from asymptomatic monoclonal gammopathies (SWOG S0120)

(2013) M. V. Dhodapkar et al.   BLOOD

STAR: ultrafast universal RNA-seq aligner

(2012) Alexander Dobin et al.   BIOINFORMATICS

Analysis of the immune system of multiple myeloma patients achieving long-term disease control by multidimensional flow cytometry

(2012) R. J. Pessoa de Magalhaes et al.   HAEMATOLOGICA

EuroFlow standardization of flow cytometer instrument settings and immunophenotyping protocols

(2012) T Kalina et al.   LEUKEMIA