Pier Federico Gherardini

178 Leveraging a novel, multi-modal platform to identify drug resistant clones with distinct mechanisms of resistance to EGFR inhibitors Open

Yunmin Li, Shan Sabri, Teresa L. Ai, Pier Federico Gherardini, Annarita Scaramozza , et al. · 2025

417 Enhancing immunotherapy efficacy in glycolytic tumors <i>via</i> antiangiogenic modulation Open

Giorgia Colombo, Inna Serganova, Francesco Ballesio, Jee Hye Kang, Triantafyllia Karakousi , et al. · 2025

The Integrated Cellular and Molecular Landscape of Autoimmunity Open

Romina Appierdo, Gerardo Pepe, Manuela Helmer‐Citterich, Marina Sirota, Francesco Vallania , et al. · 2025

Summary We performed a large-scale immunogenomic analysis of ∼13,000 transcriptomic profiles from 10 autoimmune diseases, integrating publicly available datasets from both blood and tissue. Using meta-analysis, we identified core immune me…

Integrating gene expression, genomic, and phosphoproteomic data to infer transcription factor activity in lung cancer Open

Chiara Carrino, Gerardo Pepe, Luca Parca, Manuela Helmer‐Citterich, Pier Federico Gherardini · 2025

Transcription factors (TFs) are key regulators of cellular gene expression programs in health and disease. Here we set out to integrate genomic, transcriptomic, and phosphoproteomic data to characterize TF activity in lung adenocarcinoma p…

Multi-omic landscape of human gliomas from diagnosis to treatment and recurrence Open

Hadeesha Piyadasa, Benjamin Oberlton, Mikaela Ribi, Jolene S. Ranek, Inna Averbukh , et al. · 2025

Gliomas are among the most lethal cancers, with limited treatment options. To uncover hallmarks of therapeutic escape and tumor microenvironment (TME) evolution, we applied spatial proteomics, transcriptomics, and glycomics to 670 lesions …

1359 A tumor metabolism-angiogenesis-immune axis impacts the response to cancer immunotherapy Open

Inna Serganova, Giorgia Colombo, Jee Hye Kang, Francesco Ballesio, Pier Federico Gherardini , et al. · 2024

Circulating KRAS G12D but not G12V is associated with survival in metastatic pancreatic ductal adenocarcinoma Open

Jacob E. Till, Lee McDaniel, Changgee Chang, Qi Long, Shannon M. Pfeiffer , et al. · 2024

While high circulating tumor DNA (ctDNA) levels are associated with poor survival for multiple cancers, variant-specific differences in the association of ctDNA levels and survival have not been examined. Here we investigate KRAS ctDNA (ct…

Human lncRNAs harbor conserved modules embedded in different sequence contexts Open

Francesco Ballesio, Gerardo Pepe, Gabriele Ausiello, Andrea Novelletto, Manuela Helmer‐Citterich , et al. · 2024

We analyzed the structure of human long non-coding RNA (lncRNAs) genes to investigate whether the non-coding transcriptome is organized in modular domains, as is the case for protein-coding genes. To this aim, we compared all known human l…

A Meta-Analysis Approach to Gene Regulatory Network Inference Identifies Key Regulators of Cardiovascular Diseases Open

Gerardo Pepe, Romina Appierdo, Gabriele Ausiello, Manuela Helmer‐Citterich, Pier Federico Gherardini · 2024

Cardiovascular diseases (CVDs) represent a major concern for global health, whose mechanistic understanding is complicated by a complex interplay between genetic predisposition and environmental factors. Specifically, heart failure (HF), e…

Beagle 2.0: A Web Server for Rna Secondary Structure Similarity Detection Leveraging Shape-Directed Rna Structure Determination Open

Francesco Ballesio, Adelaide Teofani, Chiara Carrino, María Inés Catalano, Mihail Lorentz Nicolaeasa , et al. · 2024

Human lncRNAs harbor conserved modules embedded in different sequence contexts Open

Francesco Ballesio, Gerardo Pepe, Gabriele Ausiello, Andrea Novelletto, Manuela Helmer‐Citterich , et al. · 2023

We analyzed the structure of human long non-coding RNA (lncRNAs) genes to investigate whether the non-coding transcriptome is organized in modular domains, as is the case for protein-coding genes. To this aim, we compared all known human l…

Sotigalimab and/or nivolumab with chemotherapy in first-line metastatic pancreatic cancer: clinical and immunologic analyses from the randomized phase 2 PRINCE trial Open

Lacey Padrón, Deena M. Maurer, Mark H. O’Hara, Eileen M. O’Reilly, Robert A. Wolff , et al. · 2022

Ipilimumab alone or in combination with nivolumab in patients with advanced melanoma who have progressed or relapsed on PD-1 blockade: clinical outcomes and translational biomarker analyses Open

Claire F. Friedman, Christine N. Spencer, Christopher R. Cabanski, Katherine S. Panageas, Daniel K. Wells , et al. · 2022

Background There are no validated biomarkers that can aid clinicians in selecting who would best benefit from anticytotoxic T lymphocyte-associated antigen 4 monotherapy versus combination checkpoint blockade in patients with advanced mela…

343 Multiomic biomarker signatures identify subsets of patients who may benefit from either nivolumab or sotigalimab in combination with chemotherapy in metastatic pancreatic cancer Open

Deena M. Maurer, Jia Xin Yu, Kamil Skłodowski, Marco Tognetti, Lukas Reiter , et al. · 2021

Background Gemcitabine/nab-Paclitaxel (GnP) is a standard of care regimen for first-line metastatic pancreatic ductal adenocarcinoma (PDAC) and has a 1-year overall survival (OS) rate of approximately 35%. There is an urgent need for novel…

A vision of immuno-oncology: the Siena think tank of the Italian network for tumor biotherapy (NIBIT) foundation Open

Michele Maio, Michael Lahn, Anna Maria Di Giacomo, Alessia Covre, Luana Calabrò , et al. · 2021

A “data sharing trust” model for rapid, collaborative science Open

Vincent T. Chan, Pier Federico Gherardini, Matthew F. Krummel, Gabriela K. Fragiadakis · 2021

Landscape of coordinated immune responses to H1N1 challenge in humans Open

Zainab Rahil, Rebecca Leylek, Christian M. Schürch, Han Chen, Zach Bjornson-Hooper , et al. · 2020

Influenza is a significant cause of morbidity and mortality worldwide. Here we show changes in the abundance and activation states of more than 50 immune cell subsets in 35 individuals over 11 time points during human A/California/2009 (H1…

Comprehensive Immune Monitoring of Clinical Trials to Advance Human Immunotherapy Open

Felix J. Hartmann, Joël Babdor, Pier Federico Gherardini, El-ad David Amir, Kyle B. Jones , et al. · 2019

The success of immunotherapy has led to a myriad of clinical trials accompanied by efforts to gain mechanistic insight and identify predictive signatures for personalization. However, many immune monitoring technologies face investigator b…

Comprehensive Immune Monitoring of Clinical Trials to Advance Human Immunotherapy Open

Felix J. Hartmann, Joël Babdor, Pier Federico Gherardini, El-ad David Amir, Kyle B. Jones , et al. · 2018

Summary The success of immunotherapy has led to a myriad of new clinical trials. Connected to these trials are efforts to discover biomarkers providing mechanistic insight and predictive signatures for personalization. Still, the plethora …

MetaCyto: A Tool for Automated Meta-analysis of Mass and Flow Cytometry Data Open

Zicheng Hu, Chethan Jujjavarapu, Jacob Hughey, Sandra Andorf, Hao-Chih Lee , et al. · 2018

While meta-analysis has demonstrated increased statistical power and more robust estimations in studies, the application of this commonly accepted methodology to cytometry data has been challenging. Different cytometry studies often involv…

GateFinder: projection-based gating strategy optimization for flow and mass cytometry Open

Nima Aghaeepour, Erin F. Simonds, David J. H. F. Knapp, Robert V. Bruggner, Karen Sachs , et al. · 2018

Motivation High-parameter single-cell technologies can reveal novel cell populations of interest, but studying or validating these populations using lower-parameter methods remains challenging. Results Here, we present GateFinder, an algor…

Epigenomic-Guided Mass Cytometry Profiling Reveals Disease-Specific Features of Exhausted CD8 T Cells Open

Bertram Bengsch, Takuya Ohtani, Omar Khan, Manu Setty, Sasikanth Manne , et al. · 2018

Comprehensive Immune Monitoring of Clinical Trials to Advance Human Immunotherapy Open

Felix J. Hartmann, Joël Babdor, Pier Federico Gherardini, El-ad David Amir, Kyle B. Jones , et al. · 2018

High response rate to PD-1 blockade in desmoplastic melanomas Open

Zeynep Eroglu, Jesse M. Zaretsky, Siwen Hu‐Lieskovan, Dae Won Kim, Alain P. Algazi , et al. · 2018

Meta-analysis of Cytometry Data Reveals Racial Differences in Immune Cells Open

Zicheng Hu, Chethan Jujjavarapu, Jacob Hughey, Sandra Andorf, Hao-Chih Lee , et al. · 2017

While meta-analysis has demonstrated increased statistical power and more robust estimations in studies, the application of this commonly accepted methodology to cytometry data has been challenging. Different cytometry studies often involv…

High‐throughput precision measurement of subcellular localization in single cells Open

Tyler J. Burns, Andreas P. Frei, Pier Federico Gherardini, Felice-Alessio Bava, Jake E. Batchelder , et al. · 2017

To quantify visual and spatial information in single cells with a throughput of thousands of cells per second, we developed Subcellular Localization Assay (SLA). This adaptation of Proximity Ligation Assay expands the capabilities of flow …

Systemic Immunity Is Required for Effective Cancer Immunotherapy Open

Matthew H. Spitzer, Yaron Carmi, Nathan E. Reticker-Flynn, Serena S. Kwek, Deepthi Madhireddy , et al. · 2017

Mapping the Fetomaternal Peripheral Immune System at Term Pregnancy Open

Gabriela K. Fragiadakis, Quentin Baca, Pier Federico Gherardini, Edward A. Ganio, Dyani Gaudillière , et al. · 2016

Preterm labor and infections are the leading causes of neonatal deaths worldwide. During pregnancy, immunological cross talk between the mother and her fetus is critical for the maintenance of pregnancy and the delivery of an immunocompete…

Deep Proteomics of Breast Cancer Cells Reveals that Metformin Rewires Signaling Networks Away from a Pro-growth State Open

Francesca Sacco, Alessandra Silvestri, Daniela Posca, S Pirro, Pier Federico Gherardini , et al. · 2016

An interactive reference framework for modeling a dynamic immune system Open

Matthew H. Spitzer, Pier Federico Gherardini, Gabriela K. Fragiadakis, Nupur Bhattacharya, Robert Yuan , et al. · 2015

Single-cell measurements map immunity Multiple characteristics of individual cells define cell types and their physiological states. Spitzer et al. quantitated the abundance of 39 different cell surface proteins or transcription factors on…

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