Marchionni Lab Surfing the Genome

Research

Below is the complete list of our work through the years. We know that one team won’t find all solutions, so we strive to develop tools that other scientist can use too. Our research philosophy prioritizes reproducibility, rigor, and transparency.

Highlighted (never boring …)

The cytokine Meteorin-like inhibits anti-tumor CD8
The cytokine Meteorin-like inhibits anti-tumor CD8
Christopher M Jackson, Ayush Pant, Wikum Dinalankara, John Choi, Aanchal Jain, …, Crystal L Mackall, Drew M Pardoll, Charles G Drake, Luigi Marchionni, Michael Lim
Immunity  ·  06 Aug 2024  ·  pubmed:39111315
genomics transcriptomics cancer immunity tme

All

The search box below allows to find the manuscripts of interest from the list below.

biology medicine breast-cancer prognosis gene-expression cancer class-prediction epigenomics bioconductor bioinformatics data-analysis omics tumor-heterogenity tumor-modeling acute-myeloid-leukemia transplantation clonal-hematopoiesis tumor-evolution gene-signature notch-signaling triple-negative-breast-cancer neoadjuvant-chemotherapy structural-variants metabolism immunotherapy

2025

YAP1 induces bladder cancer progression and promotes immune evasion through IL-6 STAT3 pathway and CXCL deregulation.
YAP1 induces bladder cancer progression and promotes immune evasion through IL-6/STAT3 pathway and CXCL deregulation.
Pritam Sadhukhan, Mingxiao Feng, Emily Illingworth, Ido Sloma, Akira Ooki, …, Luigi Marchionni, Fenna C.M. Sillé, Woonyoung Choi, David McConkey, Mohammad Hoque
Journal of Clinical Investigation  ·  16 Jan 2025  ·  doi:10.1172/JCI171164
bladder-cancer immunotherapy signaling-dysregulation

2024

YAP1 induces bladder cancer progression and promotes immune evasion through IL-6 STAT3 pathway and CXCL deregulation.
YAP1 induces bladder cancer progression and promotes immune evasion through IL-6/STAT3 pathway and CXCL deregulation.
Pritam Sadhukhan, Mingxiao Feng, Emily Illingworth, Ido Sloma, Akira Ooki, …, Luigi Marchionni, Fenna Cm Sillé, Woonyoung Choi, David McConkey, Mohammad Hoque
The Journal of clinical investigation  ·  04 Dec 2024  ·  pubmed:39630608
Validation of an artificial intelligence-based prognostic biomarker in patients with oligometastatic Castration-Sensitive prostate cancer.
Validation of an artificial intelligence-based prognostic biomarker in patients with oligometastatic Castration-Sensitive prostate cancer.
Jarey H Wang, Matthew P Deek, Adrianna A Mendes, Yang Song, Amol Shetty, …, Andre Esteva, Felix Y Feng, Phuoc T Tran, Philip Sutera, Piet Ost
Radiotherapy and oncology : journal of the European Society for Therapeutic Radiology and Oncology  ·  06 Nov 2024  ·  pubmed:39510141
prostate-cancer cancer radiotherapy robin
Emergence of transmissible SARS-CoV-2 variants with decreased sensitivity to antivirals in immunocompromised patients with persistent infections.
Emergence of transmissible SARS-CoV-2 variants with decreased sensitivity to antivirals in immunocompromised patients with persistent infections.
Mohammed Nooruzzaman, Katherine E E Johnson, Ruchi Rani, Eli J Finkelsztein, Leonardo C Caserta, …, Luigi Marchionni, Rosemary Soave, Elodie Ghedin, Diego G Diel, Mirella Salvatore
Nature communications  ·  18 Sep 2024  ·  pubmed:39294134
covid19 sars sars-cov-2 rna-sequencing
A triple hormone receptor ER, AR, and VDR signature is a robust prognosis predictor in breast cancer.
A triple hormone receptor ER, AR, and VDR signature is a robust prognosis predictor in breast cancer.
Mohamed Omar, J Chuck Harrell, Rulla Tamimi, Luigi Marchionni, Cihat Erdogan, Harikrishna Nakshatri, Tan A Ince
Breast cancer research : BCR  ·  13 Sep 2024  ·  pubmed:39272208
breast-cancer hormone-signaling gene-expression-signature
Gene Signature for Predicting Metastasis in Prostate Cancer Using Primary Tumor Expression Profiles.
Gene Signature for Predicting Metastasis in Prostate Cancer Using Primary Tumor Expression Profiles.
Itzel Valencia, Pier Vitale Nuzzo, Edoardo Francini, Francesco Ravera, Giuseppe Nicolò Fanelli, Sara Bleve, Cristian Scatena, Luigi Marchionni, Mohamed Omar
medRxiv : the preprint server for health sciences  ·  31 Aug 2024  ·  pubmed:39252915
prostate-cancer progression metastasis gene-expression
Gene Signature for Predicting Metastasis in Prostate Cancer Using Primary Tumor Expression Profiles.
Gene Signature for Predicting Metastasis in Prostate Cancer Using Primary Tumor Expression Profiles.
Itzel Valencia, Pier Vitale Nuzzo, Edoardo Francini, Francesco Ravera, Giuseppe Nicolò Fanelli, Sara Bleve, Cristian Scatena, Luigi Marchionni, Mohamed Omar
Cold Spring Harbor Laboratory  ·  31 Aug 2024  ·  doi:10.1101/2024.08.30.24312735
prostate-cancer progression metastasis gene-expression
The cytokine Meteorin-like inhibits anti-tumor CD8
The cytokine Meteorin-like inhibits anti-tumor CD8
Christopher M Jackson, Ayush Pant, Wikum Dinalankara, John Choi, Aanchal Jain, …, Crystal L Mackall, Drew M Pardoll, Charles G Drake, Luigi Marchionni, Michael Lim
Immunity  ·  06 Aug 2024  ·  pubmed:39111315
genomics transcriptomics cancer immunity tme
Machine learning predicts conventional imaging metastasis-free survival MFS for oligometastatic castration-sensitive prostate cancer omCSPC using prostate-specific membrane antigen PSMA PET radiomics.
Machine learning predicts conventional imaging metastasis-free survival (MFS) for oligometastatic castration-sensitive prostate cancer (omCSPC) using prostate-specific membrane antigen (PSMA) PET radiomics.
Yufeng Cao, Philip Sutera, William Silva Mendes, Bardia Yousefi, Tom Hrinivich, …, Luigi Marchionni, Nicole L Simone, Phuoc Tran, Cem Onal, Lei Ren
Radiotherapy and oncology : journal of the European Society for Therapeutic Radiology and Oncology  ·  31 Jul 2024  ·  pubmed:39094629
post-trancriptional-regulation cancer prostate-cancer radioterapy metastasis robin
ChatGPT for digital pathology research.
ChatGPT for digital pathology research.
Mohamed Omar, Varun Ullanat, Massimo Loda, Luigi Marchionni, Renato Umeton
The Lancet. Digital health  ·  09 Jul 2024  ·  pubmed:38987117
review digital-pathology artificial-intelligence machine-learning algorithm
Emergence of transmissible SARS-CoV-2 variants with decreased sensitivity to antivirals in immunocompromised patients with persistent infections.
Emergence of transmissible SARS-CoV-2 variants with decreased sensitivity to antivirals in immunocompromised patients with persistent infections.
Mohammed Nooruzzaman, Katherine E E Johnson, Ruchi Rani, Eli J Finkelsztein, Leonardo C Caserta, …, Luigi Marchionni, Rosemary Soave, Elodie Ghedin, Diego G Diel, Mirella Salvatore
medRxiv : the preprint server for health sciences  ·  18 Jun 2024  ·  pubmed:38946967
covid19 sars sars-cov-2 rna-sequencing
Genomic Determinants Associated with Modes of Progression and Patterns of Failure in Metachronous Oligometastatic Castration-sensitive Prostate Cancer.
Genomic Determinants Associated with Modes of Progression and Patterns of Failure in Metachronous Oligometastatic Castration-sensitive Prostate Cancer.
Philip Sutera, Yang Song, Amol C Shetty, Keara English, Kim Van der Eecken, …, Alejandro Berlin, Cem Onal, Phuoc T Tran, Piet Ost, Matthew P Deek
European urology oncology  ·  10 Jun 2024  ·  pubmed:38862340
Obesogenic High-Fat Diet and MYC Cooperate to Promote Lactate Accumulation and Tumor Microenvironment Remodeling in Prostate Cancer.
Obesogenic High-Fat Diet and MYC Cooperate to Promote Lactate Accumulation and Tumor Microenvironment Remodeling in Prostate Cancer.
Nadia Boufaied, Paolo Chetta, Tarek Hallal, Stefano Cacciatore, Daniela Lalli, …, François Bordeleau, Massimo Loda, Valentina Vaira, David P Labbé, Giorgia Zadra
Cancer research  ·  04 Jun 2024  ·  pubmed:38831751
Comparison of three machine learning algorithms for classification of B-cell neoplasms using clinical flow cytometry data.
Comparison of three machine learning algorithms for classification of B-cell neoplasms using clinical flow cytometry data.
Wikum Dinalankara, David P Ng, Luigi Marchionni, Paul D Simonson
Cytometry. Part B, Clinical cytometry  ·  09 May 2024  ·  pubmed:38721890
Semi-Supervised, Attention-Based Deep Learning for Predicting TMPRSS2:ERG Fusion Status in Prostate Cancer Using Whole Slide Images.
Semi-Supervised, Attention-Based Deep Learning for Predicting TMPRSS2:ERG Fusion Status in Prostate Cancer Using Whole Slide Images.
Mohamed Omar, Zhuoran Xu, Sophie B Rand, Mohammad K Alexanderani, Daniela C Salles, …, Edward M Schaeffer, Brian D Robinson, Tamara L Lotan, Massimo Loda, Luigi Marchionni
Molecular cancer research : MCR  ·  02 Apr 2024  ·  pubmed:38284821
Gene Signature for Predicting Metastasis in Prostate Cancer Using Primary Tumor Expression Profiles.
Gene Signature for Predicting Metastasis in Prostate Cancer Using Primary Tumor Expression Profiles.
Cagla Deniz Bahadir, Mohamed Omar, Jacob Rosenthal, Luigi Marchionni, Benjamin Liechty, David J. Pisapia, Mert R. Sabuncu
Nature Reviews Electrical Engineering  ·  09 Feb 2024  ·  doi:10.1038/s44287-023-00012-7
review digital-pathology artificial-intelligence machine-learning algorithm
Divergent immune microenvironments in two tumor nodules from a patient with mismatch repair-deficient prostate cancer.
Divergent immune microenvironments in two tumor nodules from a patient with mismatch repair-deficient prostate cancer.
Hannah E Bergom, Laura A Sena, Abderrahman Day, Benjamin Miller, Carly D Miller, …, Charles G Drake, Tamara Lotan, Angelo M De Marzo, Justin Hwang, Emmanuel S Antonarakis
NPJ genomic medicine  ·  22 Jan 2024  ·  pubmed:38253539
Distinct mesenchymal cell states mediate prostate cancer progression.
Distinct mesenchymal cell states mediate prostate cancer progression.
Hubert Pakula, Mohamed Omar, Ryan Carelli, Filippo Pederzoli, Giuseppe Nicolò Fanelli, …, David S Rickman, Christopher E Barbieri, Brian D Robinson, Luigi Marchionni, Massimo Loda
Nature communications  ·  08 Jan 2024  ·  pubmed:38191471
prostate-cancer tme single-cell spatial-transcriptomics

2023

Concomitant assessment of PD-1 and CD56 expression identifies subsets of resting cord blood Vδ2 T cells with disparate cytotoxic potential.
Concomitant assessment of PD-1 and CD56 expression identifies subsets of resting cord blood Vδ2 T cells with disparate cytotoxic potential.
Haoting Hsu, Claudio Zanettini, Modupe Coker, Sarah Boudova, David Rach, …, Riccardo Manganelli, Miriam K Laufer, Yuji Zhang, Luigi Marchionni, Cristiana Cairo
Cellular immunology  ·  23 Dec 2023  ·  pubmed:38157646
PhenoSV: interpretable phenotype-aware model for the prioritization of genes affected by structural variants.
PhenoSV: interpretable phenotype-aware model for the prioritization of genes affected by structural variants.
Zhuoran Xu, Quan Li, Luigi Marchionni, Kai Wang
Nature communications  ·  28 Nov 2023  ·  pubmed:38016949
method cancer
Notch-based gene signature for predicting the response to neoadjuvant chemotherapy in triple-negative breast cancer.
Notch-based gene signature for predicting the response to neoadjuvant chemotherapy in triple-negative breast cancer.
Mohamed Omar, Pier Vitale Nuzzo, Francesco Ravera, Sara Bleve, Giuseppe Nicolò Fanelli, Claudio Zanettini, Itzel Valencia, Luigi Marchionni
Journal of translational medicine  ·  15 Nov 2023  ·  pubmed:37964363
method structural-variants
TP53 structure-function relationships in metastatic castrate-sensitive prostate cancer and the impact of APR-246 treatment.
TP53 structure-function relationships in metastatic castrate-sensitive prostate cancer and the impact of APR-246 treatment.
Tung Hoang, Philip Sutera, Triet Nguyen, Jinhee Chang, Shreya Jagtap, …, Kim Van Der Eecken, Fred Bunz, Piet Ost, Phuoc T Tran, Matthew P Deek
The Prostate  ·  09 Oct 2023  ·  pubmed:37812042
Tumor-Specific CD8
Tumor-Specific CD8
Elizabeth M Zawidzka, Luca Biavati, Amy Thomas, Claudio Zanettini, Luigi Marchionni, Robert Leone, Ivan Borrello
bioRxiv : the preprint server for biology  ·  29 Aug 2023  ·  pubmed:37693379
Tumor-Specific CD8 sup sup T Cells from the Bone Marrow Resist Exhaustion and Exhibit Increased Persistence in Tumor-Bearing Hosts as Compared to Tumor Infiltrating Lymphocytes
Tumor-Specific CD8+T Cells from the Bone Marrow Resist Exhaustion and Exhibit Increased Persistence in Tumor-Bearing Hosts as Compared to Tumor Infiltrating Lymphocytes
Elizabeth M. Zawidzka, Luca Biavati, Amy Thomas, Claudio Zanettini, Luigi Marchionni, Robert Leone, Ivan Borrello
Cold Spring Harbor Laboratory  ·  29 Aug 2023  ·  doi:10.1101/2023.08.28.555119
Federated benchmarking of medical artificial intelligence with MedPerf.
Federated benchmarking of medical artificial intelligence with MedPerf.
Alexandros Karargyris, Renato Umeton, Micah J Sheller, Alejandro Aristizabal, Johnu George, …, Luigi Marchionni, Massimo Loda, Jason M Johnson, Spyridon Bakas, Peter Mattson
Nature machine intelligence  ·  17 Jul 2023  ·  pubmed:38706981
Optimal fluid volume for detecting malignancy in serous effusions: a single institution experience.
Optimal fluid volume for detecting malignancy in serous effusions: a single institution experience.
Shaham Beg, Claudio Zanettini, Lucio Queiroz, Luigi Marchionni, Susan A Alperstein, Momin T Siddiqui
Journal of the American Society of Cytopathology  ·  13 Jun 2023  ·  pubmed:37419704
MultiNEP: a multi-omics network enhancement framework for prioritizing disease genes and metabolites simultaneously.
MultiNEP: a multi-omics network enhancement framework for prioritizing disease genes and metabolites simultaneously.
Zhuoran Xu, Luigi Marchionni, Shuang Wang
Bioinformatics (Oxford, England)  ·  01 Jun 2023  ·  pubmed:37216914
CALANGO: A phylogeny-aware comparative genomics tool for discovering quantitative genotype-phenotype associations across species.
CALANGO: A phylogeny-aware comparative genomics tool for discovering quantitative genotype-phenotype associations across species.
Jorge Augusto Hongo, Giovanni Marques de Castro, Alison Pelri Albuquerque Menezes, Agnello César Rios Picorelli, Thieres Tayroni Martins da Silva, …, Luiz-Eduardo Del-Bem, Anderson Vieira Chaves, Gabriel Magno de Freitas Almeida, Felipe Campelo, Francisco Pereira Lobo
Patterns (New York, N.Y.)  ·  14 Apr 2023  ·  pubmed:37409050
method genetics
Distinct mesenchymal cell states mediate prostate cancer progression.
Distinct mesenchymal cell states mediate prostate cancer progression.
Hubert Pakula, Mohamed Omar, Ryan Carelli, Filippo Pederzoli, Giuseppe Nicolò Fanelli, …, David S Rickman, Christopher E Barbieri, Brian D Robinson, Luigi Marchionni, Massimo Loda
bioRxiv : the preprint server for biology  ·  01 Apr 2023  ·  pubmed:37034687
Using biological constraints to improve prediction in precision oncology.
Using biological constraints to improve prediction in precision oncology.
Mohamed Omar, Wikum Dinalankara, Lotte Mulder, Tendai Coady, Claudio Zanettini, Eddie Luidy Imada, Laurent Younes, Donald Geman, Luigi Marchionni
iScience  ·  01 Mar 2023  ·  doi:10.1016/j.isci.2023.106108
method machine-learning overfitting
REPAC: analysis of alternative polyadenylation from RNA-sequencing data.
REPAC: analysis of alternative polyadenylation from RNA-sequencing data.
Eddie L Imada, Christopher Wilks, Ben Langmead, Luigi Marchionni
Genome biology  ·  09 Feb 2023  ·  pubmed:36759904
post-trancriptional-regulation splicing cancer genomics transcriptomics method
Association of self-identified race and genetic ancestry with the immunogenomic landscape of primary prostate cancer.
Association of self-identified race and genetic ancestry with the immunogenomic landscape of primary prostate cancer.
Thiago Vidotto, Eddie L Imada, Farzana Faisal, Sanjana Murali, Adrianna A Mendes, …, Edward M Schaeffer, William B Isaacs, Karen S Sfanos, Luigi Marchionni, Tamara L Lotan
JCI insight  ·  08 Feb 2023  ·  pubmed:36752203
Using biological constraints to improve prediction in precision oncology.
Using biological constraints to improve prediction in precision oncology.
Mohamed Omar, Wikum Dinalankara, Lotte Mulder, Tendai Coady, Claudio Zanettini, Eddie Luidy Imada, Laurent Younes, Donald Geman, Luigi Marchionni
iScience  ·  02 Feb 2023  ·  pubmed:36852282
cancer tumor-heterogeneity statistical-method
A Phase 1 Trial of Durvalumab in Combination with Bacillus Calmette-Guerin BCG or External Beam Radiation Therapy in Patients with BCG-unresponsive Non-muscle-Invasive Bladder Cancer: The Hoosier Cancer Research Network GU16-243 ADAPT-BLADDER Study.
A Phase 1 Trial of Durvalumab in Combination with Bacillus Calmette-Guerin (BCG) or External Beam Radiation Therapy in Patients with BCG-unresponsive Non-muscle-Invasive Bladder Cancer: The Hoosier Cancer Research Network GU16-243 ADAPT-BLADDER Study.
Noah M Hahn, Michael A O’Donnell, Jason A Efstathiou, Marianna Zahurak, Gary L Rosner, …, Alexander Kutikov, Gordon Guo, Timothy A Masterson, Nabil Adra, Hristos Z Kaimakliotis
European urology  ·  28 Jan 2023  ·  pubmed:36717286

2022

Recurrent germline variant in ATM associated with familial myeloproliferative neoplasms.
Recurrent germline variant in ATM associated with familial myeloproliferative neoplasms.
Evan M Braunstein, Eddie Imada, Sergiu Pasca, Shiyu Wang, Hang Chen, …, Yujia Liu, Luigi Marchionni, Alison Moliterno, Christopher S Hourigan, Lukasz P Gondek
Leukemia  ·  21 Dec 2022  ·  pubmed:36543879
A FOXO1-dependent transcription network is a targetable vulnerability of mantle cell lymphomas.
A FOXO1-dependent transcription network is a targetable vulnerability of mantle cell lymphomas.
Ja-Young Jang, Inah Hwang, Heng Pan, Jun Yao, Lapo Alinari, …, Robert A Baiocchi, Selina Chen-Kiang, Sandro Belvedere, Hongwu Zheng, Jihye Paik
The Journal of clinical investigation  ·  15 Dec 2022  ·  pubmed:36282572
cancer lymphoma
Hyaluronan driven by epithelial aPKC deficiency remodels the microenvironment and creates a vulnerability in mesenchymal colorectal cancer.
Hyaluronan driven by epithelial aPKC deficiency remodels the microenvironment and creates a vulnerability in mesenchymal colorectal cancer.
Anxo Martinez-Ordoñez, Angeles Duran, Marc Ruiz-Martinez, Tania Cid-Diaz, Xiao Zhang, …, Giorgio Inghirami, Luigi Marchionni, Darren Sigal, Maria T Diaz-Meco, Jorge Moscat
Cancer cell  ·  15 Dec 2022  ·  pubmed:36525970
cancer tme colorectal-cancer
Donor-derived acute myeloid leukemia in solid organ transplantation.
Donor-derived acute myeloid leukemia in solid organ transplantation.
Luigi Marchionni, Francisco Pereira Lobo, Rumen Kostadinov, Anna Serra, Federico Genzano Besso, …, Mohamed N. Omar, Gianluca Gaidano, Benedetto Bruno, Giuseppe Saglio, Antonio Amoroso
American Journal of Transplantation  ·  01 Dec 2022  ·  doi:10.1111/ajt.17174
transplantation acute-myeloid-leukemia cancer clonal-hematopoiesis
Using Attention-based Deep Learning to Predict ERG:TMPRSS2 Fusion Status in Prostate Cancer from Whole Slide Images
Using Attention-based Deep Learning to Predict ERG:TMPRSS2 Fusion Status in Prostate Cancer from Whole Slide Images
Mohamed Omar, Zhuoran Xu, Sophie B Rand, Mohammad Mohammad, Daniela C. Salles, Edward M. Schaeffer, Brian D. Robinson, Tamara L. Lotan, Massimo Loda, Luigi Marchionni
Cold Spring Harbor Laboratory  ·  20 Nov 2022  ·  doi:10.1101/2022.11.18.517111
Multi-omics biomarkers aid prostate cancer prognostication
Multi-omics biomarkers aid prostate cancer prognostication
Zhuoran Xu, Mohamed Omar, Elisa Benedetti, Jacob Rosenthal, Renato Umeton, Jan Krumsiek, Mark Pomerantz, Eddie Imada, Massimo Loda, Luigi Marchionni
Cold Spring Harbor Laboratory  ·  22 Sep 2022  ·  doi:10.1101/2022.09.20.508244
prostate-cancer coverings tumor-heterogeneity multiomics prediction
Donor-derived acute myeloid leukemia in solid organ transplantation.
Donor-derived acute myeloid leukemia in solid organ transplantation.
Luigi Marchionni, Francisco Pereira Lobo, Rumen Kostadinov, Anna Serra, Federico Genzano Besso, …, Mohamed N Omar, Gianluca Gaidano, Benedetto Bruno, Giuseppe Saglio, Antonio Amoroso
American journal of transplantation : official journal of the American Society of Transplantation and the American Society of Transplant Surgeons  ·  08 Sep 2022  ·  pubmed:35979657
acute-myeloid-leukemia transplantation genomics cancer clonal-hematopoiesis
ZNF92, an unexplored transcription factor with remarkably distinct breast cancer over-expression associated with prognosis and cell-of-origin.
ZNF92, an unexplored transcription factor with remarkably distinct breast cancer over-expression associated with prognosis and cell-of-origin.
Mohammad Kamran, Udayan Bhattacharya, Mohamed Omar, Luigi Marchionni, Tan A Ince
NPJ breast cancer  ·  29 Aug 2022  ·  pubmed:36038558
ZNF92, an unexplored transcription factor with remarkably distinct breast cancer over-expression associated with prognosis and cell-of-origin
ZNF92, an unexplored transcription factor with remarkably distinct breast cancer over-expression associated with prognosis and cell-of-origin
Mohammad Kamran, Udayan Bhattacharya, Mohamed Omar, Luigi Marchionni, Tan A. Ince
npj Breast Cancer  ·  29 Aug 2022  ·  doi:10.1038/s41523-022-00474-2
cancer cell-of-origin breast-cancer
Rapid detection of SARS-CoV-2 variants of concern by single nucleotide polymorphism genotyping using TaqMan assays.
Rapid detection of SARS-CoV-2 variants of concern by single nucleotide polymorphism genotyping using TaqMan assays.
Priya Velu, Lin Cong, Sophie Rand, Yuqing Qiu, Zhengmao Zhang, …, David Brundage, Lars Westblade, Luigi Marchionni, Melissa M Cushing, Hanna Rennert
Diagnostic microbiology and infectious disease  ·  21 Aug 2022  ·  pubmed:36122486
sars-cov-2 rna-sequencing
Precision health diagnostic and surveillance network uses S gene target failure SGTF combined with sequencing technologies to track emerging SARS-CoV-2 variants.
Precision health diagnostic and surveillance network uses S gene target failure (SGTF) combined with sequencing technologies to track emerging SARS-CoV-2 variants.
Rafael Guerrero-Preston, Vanessa Rivera-Amill, Karem Caraballo, Sebastian Rodríguez-Torres, Ana Purcell-Wiltz, …, Luigi Marchionni, José F Rodríguez-Orengo, Adriana Baez, Christopher E Mason, David Sidransky
Immunity, inflammation and disease  ·  01 Jun 2022  ·  pubmed:35634961
genomics surveillance precision-medicine sars‐cov‐2
Unleashing alternative polyadenylation analyses with REPAC
Unleashing alternative polyadenylation analyses with REPAC
Eddie L Imada, Christopher Wilks, Ben Langmead, Luigi Marchionni
Cold Spring Harbor Laboratory  ·  16 Mar 2022  ·  doi:10.1101/2022.03.14.484280
gene-expression polyadenylation method resource

2021

Building Tools for Machine Learning and Artificial Intelligence in Cancer Research: Best Practices and a Case Study with the PathML Toolkit for Computational Pathology.
Building Tools for Machine Learning and Artificial Intelligence in Cancer Research: Best Practices and a Case Study with the PathML Toolkit for Computational Pathology.
Jacob Rosenthal, Ryan Carelli, Mohamed Omar, David Brundage, Ella Halbert, …, Surya N Hari, Eliezer M Van Allen, Luigi Marchionni, Renato Umeton, Massimo Loda
Molecular cancer research : MCR  ·  08 Dec 2021  ·  pubmed:34880124
digital-pathology pathml resource
Hobotnica: exploring molecular signature quality.
Hobotnica: exploring molecular signature quality.
Alexey Stupnikov, Alexey Sizykh, Anna Budkina, Alexander Favorov, Bahman Afsari, Sarah Wheelan, Luigi Marchionni, Yulia Medvedeva
F1000Research  ·  08 Dec 2021  ·  pubmed:36204675
Building Tools for Machine Learning and Artificial Intelligence in Cancer Research: Best Practices and a Case Study with the PathML Toolkit for Computational Pathology
Building Tools for Machine Learning and Artificial Intelligence in Cancer Research: Best Practices and a Case Study with the PathML Toolkit for Computational Pathology
Jacob Rosenthal, Ryan Carelli, Mohamed Omar, David Brundage, Ella Halbert, …, Surya N. Hari, Eliezer M. Van Allen, Luigi Marchionni, Renato Umeton, Massimo Loda
Molecular Cancer Research  ·  08 Dec 2021  ·  doi:10.1158/1541-7786.MCR-21-0665
digital-pathology pathml resource
Building tools for machine learning and artificial intelligence in cancer research: best practices and a case study with the PathML toolkit for computational pathology
Building tools for machine learning and artificial intelligence in cancer research: best practices and a case study with the PathML toolkit for computational pathology
Jacob Rosenthal, Ryan Carelli, Mohamed Omar, David Brundage, Ella Halbert, …, Surya Narayanan Hari, Eliezer Mendel Van Allen, Luigi Marchionni, Renato Umeton, Massimo Loda
Cold Spring Harbor Laboratory  ·  24 Oct 2021  ·  doi:10.1101/2021.10.21.465212
digital-pathology pathml resource
Host Blood Gene Signatures Can Detect the Progression to Severe and Cerebral Malaria.
Host Blood Gene Signatures Can Detect the Progression to Severe and Cerebral Malaria.
Mohamed Omar, Luigi Marchionni, Georg Häcker, Mohamed Tarek Badr
Frontiers in cellular and infection microbiology  ·  22 Oct 2021  ·  pubmed:34746025
prediction malaria gene-expression
A robust and interpretable gene signature for predicting the lymph node status of primary T1 T2 oral cavity squamous cell carcinoma.
A robust and interpretable gene signature for predicting the lymph node status of primary T1/T2 oral cavity squamous cell carcinoma.
Yasmin Ghantous, Mohamed Omar, Esther Channah Broner, Nishant Agrawal, Alexander T Pearson, …, Imad Abu El-Naaj, Peter A Savage, David Sidransky, Luigi Marchionni, Evgeny Izumchenko
International journal of cancer  ·  14 Oct 2021  ·  pubmed:34569064
head-and-neck-cancer gene-expression prediction metastasis
A field guide to cultivating computational biology.
A field guide to cultivating computational biology.
Gregory P Way, Casey S Greene, Piero Carninci, Benilton S Carvalho, Michiel de Hoon, …, Suzanne S Sindi, Fabian J Theis, Jean Y H Yang, Anne E Carpenter, Elana J Fertig
PLoS biology  ·  07 Oct 2021  ·  pubmed:34618807
review computational-biology collaboration
Hobotnica: exploring molecular signature quality
Hobotnica: exploring molecular signature quality
Alexey Stupnikov, Alexey Sizykh, Alexander Favorov, Bahman Afsari, Sarah Wheelan, Luigi Marchionni, Yulia A. Medvedeva
Cold Spring Harbor Laboratory  ·  15 Sep 2021  ·  doi:10.1101/2021.09.12.459931
method gene-signatures resource
CALANGO: a phylogeny-aware comparative genomics tool for discovering quantitative genotype-phenotype associations across species
CALANGO: a phylogeny-aware comparative genomics tool for discovering quantitative genotype-phenotype associations across species
Jorge Augusto Hongo, Giovanni Marques de Castro, Alison Pelri Albuquerque Menezes, Agnello César Rios Picorelli, Thieres Tayroni Martins da Silva, …, Luiz-Eduardo Del-Bem, Anderson Vieira Chaves, Gabriel Magno de Freitas Almeida, Felipe Campelo, Francisco Pereira Lobo
Cold Spring Harbor Laboratory  ·  27 Aug 2021  ·  doi:10.1101/2021.08.25.457574
method genetics
Transcriptional landscape of PTEN loss in primary prostate cancer.
Transcriptional landscape of PTEN loss in primary prostate cancer.
Eddie Luidy Imada, Diego Fernando Sanchez, Wikum Dinalankara, Thiago Vidotto, Ericka M Ebot, …, Lorelei Ann Mucci, Massimo Loda, Edward Matthew Schaeffer, Tamara Lotan, Luigi Marchionni
BMC cancer  ·  26 Jul 2021  ·  pubmed:34311724
prostate-cancer pten gene-expression
RNA-sequencing highlights differential regulated pathways involved in cell cycle and inflammation in orbitofacial neurofibromas.
RNA-sequencing highlights differential regulated pathways involved in cell cycle and inflammation in orbitofacial neurofibromas.
Eddie Luidy Imada, Diego Strianese, Deepak P Edward, Rawan alThaqib, Antionette Price, Antje Arnold, Hailah Al-Hussain, Luigi Marchionni, Fausto J Rodriguez
Brain pathology (Zurich, Switzerland)  ·  23 Jul 2021  ·  pubmed:34297428
Efficient representations of tumor diversity with paired DNA-RNA aberrations.
Efficient representations of tumor diversity with paired DNA-RNA aberrations.
Qian Ke, Wikum Dinalankara, Laurent Younes, Donald Geman, Luigi Marchionni
PLoS computational biology  ·  11 Jun 2021  ·  pubmed:34115745
cancer tumor-heterogeneity statistical-method resource
Efficient representations of tumor diversity with paired DNA-RNA aberrations
Efficient representations of tumor diversity with paired DNA-RNA aberrations
Qian Ke, Wikum Dinalankara, Laurent Younes, Donald Geman, Luigi Marchionni
PLOS Computational Biology  ·  11 Jun 2021  ·  doi:10.1371/journal.pcbi.1008944
cancer tumor-heterogeneity statistical-method resource
Using Biological Constraints to Improve Prediction in Precision Oncology
Using Biological Constraints to Improve Prediction in Precision Oncology
Mohamed Omar, Wikum Dinalankara, Lotte Mulder, Tendai Coady, Claudio Zanettini, Eddie Luidy Imada, Laurent Younes, Donald Geman, Luigi Marchionni
Cold Spring Harbor Laboratory  ·  27 May 2021  ·  doi:10.1101/2021.05.25.445604
cancer tumor-heterogeneity statistical-method prediction mechanistic-classifier
covid19census: U.S. and Italy COVID-19 metrics and other epidemiological data.
covid19census: U.S. and Italy COVID-19 metrics and other epidemiological data.
Claudio Zanettini, Mohamed Omar, Wikum Dinalankara, Eddie Luidy Imada, Elizabeth Colantuoni, Giovanni Parmigiani, Luigi Marchionni
Database : the journal of biological databases and curation  ·  15 May 2021  ·  pubmed:33991092
resource covid19 sars-cov-2
Influenza Vaccination and COVID-19 Mortality in the USA: An Ecological Study.
Influenza Vaccination and COVID-19 Mortality in the USA: An Ecological Study.
Claudio Zanettini, Mohamed Omar, Wikum Dinalankara, Eddie Luidy Imada, Elizabeth Colantuoni, Giovanni Parmigiani, Luigi Marchionni
Vaccines  ·  24 Apr 2021  ·  pubmed:33923159
covid-19 influenza propensity-score
Influenza Vaccination and COVID-19 Mortality in the USA: An Ecological Study
Influenza Vaccination and COVID-19 Mortality in the USA: An Ecological Study
Claudio Zanettini, Mohamed Omar, Wikum Dinalankara, Eddie Luidy Imada, Elizabeth Colantuoni, Giovanni Parmigiani, Luigi Marchionni
Vaccines  ·  24 Apr 2021  ·  doi:10.3390/vaccines9050427
covid-19 influenza propensity-score
An R package for divergence analysis of omics data.
An R package for divergence analysis of omics data.
Wikum Dinalankara, Qian Ke, Donald Geman, Luigi Marchionni
PloS one  ·  05 Apr 2021  ·  pubmed:33819273
method genomics transcriptomics heterogeneity
An R package for divergence analysis of omics data
An R package for divergence analysis of omics data
Wikum Dinalankara, Qian Ke, Donald Geman, Luigi Marchionni
PLOS ONE  ·  05 Apr 2021  ·  doi:10.1371/journal.pone.0249002
method genomics transcriptomics heterogeneity
Newly Identified Members of FGFR1 Splice Variants Engage in Cross-talk with AXL AKT Axis in Salivary Adenoid Cystic Carcinoma
Newly Identified Members of FGFR1 Splice Variants Engage in Cross-talk with AXL/AKT Axis in Salivary Adenoid Cystic Carcinoma
Joseph O. Humtsoe, Hyun-Su Kim, Brandon Leonard, Shizhang Ling, Bhumsuk Keam, …, Michael Considine, Alexander V. Favorov, Elana J. Fertig, Hyunseok Kang, Patrick K. Ha
Cancer Research  ·  15 Feb 2021  ·  doi:10.1158/0008-5472.CAN-20-1780
Plasma cells are enriched in localized prostate cancer in Black men and are associated with improved outcomes.
Plasma cells are enriched in localized prostate cancer in Black men and are associated with improved outcomes.
Adam B Weiner, Thiago Vidotto, Yang Liu, Adrianna A Mendes, Daniela C Salles, …, Stephen J Freedland, Daniel E Spratt, Jennifer D Wu, Tamara L Lotan, Edward M Schaeffer
Nature communications  ·  10 Feb 2021  ·  pubmed:33568675
prostate-cancer health-disparities gene-expression tcga
Newly Identified Members of FGFR1 Splice Variants Engage in Cross-talk with AXL AKT Axis in Salivary Adenoid Cystic Carcinoma.
Newly Identified Members of FGFR1 Splice Variants Engage in Cross-talk with AXL/AKT Axis in Salivary Adenoid Cystic Carcinoma.
Joseph O Humtsoe, Hyun-Su Kim, Brandon Leonard, Shizhang Ling, Bhumsuk Keam, …, Michael Considine, Alexander V Favorov, Elana J Fertig, Hyunseok Kang, Patrick K Ha
Cancer research  ·  06 Jan 2021  ·  pubmed:33408119

2020

Identifying Personalized Metabolic Signatures in Breast Cancer.
Identifying Personalized Metabolic Signatures in Breast Cancer.
Priyanka Baloni, Wikum Dinalankara, John C Earls, Theo A Knijnenburg, Donald Geman, Luigi Marchionni, Nathan D Price
Metabolites  ·  30 Dec 2020  ·  pubmed:33396819
cancer metabolism
GULP1 regulates the NRF2-KEAP1 signaling axis in urothelial carcinoma.
GULP1 regulates the NRF2-KEAP1 signaling axis in urothelial carcinoma.
Masamichi Hayashi, Elisa Guida, Yoshikuni Inokawa, Rachel Goldberg, Leonardo O Reis, …, Alexander Baras, George J Netto, Wayne Koch, Anju Singh, Mohammad O Hoque
Science signaling  ·  18 Aug 2020  ·  pubmed:32817372
bladder-cancer dna-methylation
Comparative transcriptomics of primary cells in vertebrates.
Comparative transcriptomics of primary cells in vertebrates.
Tanvir Alam, Saumya Agrawal, Jessica Severin, Robert S Young, Robin Andersson, …, Alistair R R Forrest, Levon M Khachigian, Yoshihide Hayashizaki, Piero Carninci, Michiel J L de Hoon
Genome research  ·  27 Jul 2020  ·  pubmed:32718981
fantom gene-expression genome evolution
Functional annotation of human long noncoding RNAs via molecular phenotyping.
Functional annotation of human long noncoding RNAs via molecular phenotyping.
Jordan A Ramilowski, Chi Wai Yip, Saumya Agrawal, Jen-Chien Chang, Yari Ciani, …, Harukazu Suzuki, Ken Yagi, Michiel J L de Hoon, Jay W Shin, Piero Carninci
Genome research  ·  27 Jul 2020  ·  pubmed:32718982
genome-architecture long-non-coding-rna antisense fantom
Influenza Vaccination and COVID19 Mortality in the USA.
Influenza Vaccination and COVID19 Mortality in the USA.
Claudio Zanettini, Mohamed Omar, Wikum Dinalankara, Eddie Luidy Imada, Elizabeth Colantuoni, Giovanni Parmigiani, Luigi Marchionni
medRxiv : the preprint server for health sciences  ·  26 Jun 2020  ·  pubmed:32607525
Influenza Vaccination and COVID19 Mortality in the USA
Influenza Vaccination and COVID19 Mortality in the USA
Claudio Zanettini, Mohamed Omar, Wikum Dinalankara, Eddie Luidy Imada, Elizabeth Colantuoni, Giovanni Parmigiani, Luigi Marchionni
Cold Spring Harbor Laboratory  ·  26 Jun 2020  ·  doi:10.1101/2020.06.24.20129817
Correction to: Differential gene methylation and expression of HOX transcription factor family in orbitofacial neurofibroma.
Correction to: Differential gene methylation and expression of HOX transcription factor family in orbitofacial neurofibroma.
Antje Arnold, Eddie Luidy Imada, M Lisa Zhang, Deepak P Edward, Luigi Marchionni, Fausto J Rodriguez
Acta neuropathologica communications  ·  14 May 2020  ·  pubmed:32410671
Differential gene methylation and expression of HOX transcription factor family in orbitofacial neurofibroma.
Differential gene methylation and expression of HOX transcription factor family in orbitofacial neurofibroma.
Antje Arnold, Eddie Luidy Imada, M Lisa Zhang, Deepak P Edward, Luigi Marchionni, Fausto J Rodriguez
Acta neuropathologica communications  ·  04 May 2020  ·  pubmed:32366326
Efficient Representations of Tumor Diversity with Paired DNA-RNA Aberrations
Efficient Representations of Tumor Diversity with Paired DNA-RNA Aberrations
Qian Ke, Wikum Dinalankara, Laurent Younes, Donald Geman, Luigi Marchionni
Cold Spring Harbor Laboratory  ·  25 Apr 2020  ·  doi:10.1101/2020.04.24.060129
cancer tumor-heterogeneity statistical-method resource
Genetic Analysis of Small Well-differentiated Pancreatic Neuroendocrine Tumors Identifies Subgroups With Differing Risks of Liver Metastases.
Genetic Analysis of Small Well-differentiated Pancreatic Neuroendocrine Tumors Identifies Subgroups With Differing Risks of Liver Metastases.
Antonio Pea, Jun Yu, Luigi Marchionni, Michael Noe, Claudio Luchini, …, Rita T Lawlor, Aldo Scarpa, Christopher M Heaphy, Laura D Wood, Christopher L Wolfgang
Annals of surgery  ·  01 Mar 2020  ·  pubmed:30339629
Recounting the FANTOM CAGE-Associated Transcriptome.
Recounting the FANTOM CAGE-Associated Transcriptome.
Eddie Luidy Imada, Diego Fernando Sanchez, Leonardo Collado-Torres, Christopher Wilks, Tejasvi Matam, …, Jeffrey T Leek, Alexander Favorov, Gloria R Franco, Ben Langmead, Luigi Marchionni
Genome research  ·  20 Feb 2020  ·  pubmed:32079618
genomics transcriptomics long-non-coding-rna fantom gene-expression

2019

Look for methods, not conclusions.
Look for methods, not conclusions.
Roberto Bassi, Enrico M Bucci, Raffaele A Calogero, Piero Carninci, Gennaro Ciliberto, …, Antonio Giordano, Luigi Marchionni, Giacomina Massaro Giordano, Angelo Parini, Gianluca Sbardella
Cell death & disease  ·  05 Dec 2019  ·  pubmed:31804462
review computational-biology collaborative-science
Combined extracts of Echinacea angustifolia DC. and Zingiber officinale Roscoe in softgel capsules: Pharmacokinetics and immunomodulatory effects assessed by gene expression profiling.
Combined extracts of Echinacea angustifolia DC. and Zingiber officinale Roscoe in softgel capsules: Pharmacokinetics and immunomodulatory effects assessed by gene expression profiling.
Stefano Dall’Acqua, Iztok Grabnar, Roberto Verardo, Enio Klaric, Luigi Marchionni, …, Stefania Sut, Chiara Agostinis, Roberta Bulla, Beatrice Perissutti, Dario Voinovich
Phytomedicine : international journal of phytotherapy and phytopharmacology  ·  16 Sep 2019  ·  pubmed:31557666
citation image
[no title info]
Nora M Haney, Farzana A Faisal, Jiayun Lu, Liana B Guedes, Victor E Reuter, …, James A Eastham, Luigi Marchionni, Corinne Joshu, Anuradha Gopalan, Tamara L Lotan
The Journal of urology  ·  10 Sep 2019  ·  pubmed:31502941
An R package for divergence analysis of omics data
An R package for divergence analysis of omics data
Wikum Dinalankara, Qian Ke, Donald Geman, Luigi Marchionni
Cold Spring Harbor Laboratory  ·  13 Aug 2019  ·  doi:10.1101/720391
CDK12 inactivation across solid tumors: an actionable genetic subtype.
CDK12 inactivation across solid tumors: an actionable genetic subtype.
Catherine H Marshall, Eddie L Imada, Zhuojun Tang, Luigi Marchionni, Emmanuel S Antonarakis
Oncoscience  ·  10 May 2019  ·  pubmed:31360735
Ezrin Promotes Stem Cell Properties in Pancreatic Ductal Adenocarcinoma
Ezrin Promotes Stem Cell Properties in Pancreatic Ductal Adenocarcinoma
Vesselin R. Penchev, Yu-Tai Chang, Asma Begum, Theodore Ewachiw, Christian Gocke, …, Luigi Marchionni, Anirban Maitra, Aykut Uren, Zeshaan Rasheed, William Matsui
Molecular Cancer Research  ·  01 Apr 2019  ·  doi:10.1158/1541-7786.MCR-18-0367
citation image
[no title info]
Rafael Guerrero-Preston, Fahcina Lawson, Sebastian Rodriguez-Torres, Maartje G Noordhuis, Francesca Pirini, …, Wayne M Koch, William H Westra, Young J Kim, James R Eshleman, David Sidransky
Cancer prevention research (Philadelphia, Pa.)  ·  18 Feb 2019  ·  pubmed:30777857
PDCD4 Is an Androgen-Repressed Tumor Suppressor that Regulates Prostate Cancer Growth and Castration Resistance
PDCD4 Is an Androgen-Repressed Tumor Suppressor that Regulates Prostate Cancer Growth and Castration Resistance
Kenji Zennami, Su Mi Choi, Ross Liao, Ying Li, Wikum Dinalankara, Luigi Marchionni, Fatema H. Rafiqi, Akira Kurozumi, Koji Hatano, Shawn E. Lupold
Molecular Cancer Research  ·  01 Feb 2019  ·  doi:10.1158/1541-7786.MCR-18-0837
Ezrin Promotes Stem Cell Properties in Pancreatic Ductal Adenocarcinoma.
Ezrin Promotes Stem Cell Properties in Pancreatic Ductal Adenocarcinoma.
Vesselin R Penchev, Yu-Tai Chang, Asma Begum, Theodore Ewachiw, Christian Gocke, …, Luigi Marchionni, Anirban Maitra, Aykut Uren, Zeshaan Rasheed, William Matsui
Molecular cancer research : MCR  ·  17 Jan 2019  ·  pubmed:30655325

2018

PDCD4 Is an Androgen-Repressed Tumor Suppressor that Regulates Prostate Cancer Growth and Castration Resistance.
PDCD4 Is an Androgen-Repressed Tumor Suppressor that Regulates Prostate Cancer Growth and Castration Resistance.
Kenji Zennami, Su Mi Choi, Ross Liao, Ying Li, Wikum Dinalankara, Luigi Marchionni, Fatema H Rafiqi, Akira Kurozumi, Koji Hatano, Shawn E Lupold
Molecular cancer research : MCR  ·  05 Dec 2018  ·  pubmed:30518628
Hypomethylation, endogenous retrovirus expression, and interferon signaling in testicular germ cell tumors.
Hypomethylation, endogenous retrovirus expression, and interferon signaling in testicular germ cell tumors.
Michael C Haffner, Diana Taheri, Eddie Luidy-Imada, Doreen N Palsgrove, Marie-Lisa Eich, …, William G Nelson, Angelo M De Marzo, Luigi Marchionni, Charles G Drake, Srinivasan Yegnasubramanian
Proceedings of the National Academy of Sciences of the United States of America  ·  04 Sep 2018  ·  pubmed:30181298
Hedgehog GLI1 activation leads to leukemic transformation of myelodysplastic syndrome in vivo and GLI1 inhibition results in antitumor activity.
Hedgehog/GLI1 activation leads to leukemic transformation of myelodysplastic syndrome in vivo and GLI1 inhibition results in antitumor activity.
Bonnie W Lau, Kyounghee Huh, Rafael Madero-Marroquin, Federico De Marchi, Yiting Lim, …, Amy DeZern, Mark J Levis, Peter D Aplan, William Matsui, Lukasz P Gondek
Oncogene  ·  31 Aug 2018  ·  pubmed:30171262
Epigenetically regulated PAX6 drives cancer cells toward a stem-like state via GLI-SOX2 signaling axis in lung adenocarcinoma.
Epigenetically regulated PAX6 drives cancer cells toward a stem-like state via GLI-SOX2 signaling axis in lung adenocarcinoma.
Akira Ooki, Wikum Dinalankara, Luigi Marchionni, Jun-Chieh J Tsay, Chandra Goparaju, Zahra Maleki, William N Rom, Harvey I Pass, Mohammad O Hoque
Oncogene  ·  06 Jul 2018  ·  pubmed:29980786
Cell-type specific expression of oncogenic and tumor suppressive microRNAs in the human prostate and prostate cancer.
Cell-type specific expression of oncogenic and tumor suppressive microRNAs in the human prostate and prostate cancer.
Binod Kumar, Avi Z Rosenberg, Su Mi Choi, Karen Fox-Talbot, Angelo M De Marzo, Larisa Nonn, W Nathaniel Brennen, Luigi Marchionni, Marc K Halushka, Shawn E Lupold
Scientific reports  ·  08 May 2018  ·  pubmed:29739972
PD-L1 Expression Heterogeneity in Non-Small Cell Lung Cancer: Defining Criteria for Harmonization between Biopsy Specimens and Whole Sections.
PD-L1 Expression Heterogeneity in Non-Small Cell Lung Cancer: Defining Criteria for Harmonization between Biopsy Specimens and Whole Sections.
Enrico Munari, Giuseppe Zamboni, Gianluigi Lunardi, Luigi Marchionni, Marcella Marconi, …, Giulio Rossi, Francesca Romana Mariotti, Paola Vacca, Lorenzo Moretta, Giuseppe Bogina
Journal of thoracic oncology : official publication of the International Association for the Study of Lung Cancer  ·  25 Apr 2018  ·  pubmed:29704674
Genome-Wide Somatic Copy Number Alterations and Mutations in High-Grade Pancreatic Intraepithelial Neoplasia.
Genome-Wide Somatic Copy Number Alterations and Mutations in High-Grade Pancreatic Intraepithelial Neoplasia.
Tatsuo Hata, Masaya Suenaga, Luigi Marchionni, Anne Macgregor-Das, Jun Yu, Koji Shindo, Koji Tamura, Ralph H Hruban, Michael Goggins
The American journal of pathology  ·  22 Apr 2018  ·  pubmed:29684357
Digitizing omics profiles by divergence from a baseline.
Digitizing omics profiles by divergence from a baseline.
Wikum Dinalankara, Qian Ke, Yiran Xu, Lanlan Ji, Nicole Pagane, …, Elana J Fertig, Nathan D Price, Laurent Younes, Luigi Marchionni, Donald Geman
Proceedings of the National Academy of Sciences of the United States of America  ·  16 Apr 2018  ·  pubmed:29666255
cancer tumor-heterogeneity statistical-method
Cell-autonomous and cell non-autonomous downregulation of tumor suppressor DAB2IP by microRNA-149-3p promotes aggressiveness of cancer cells.
Cell-autonomous and cell non-autonomous downregulation of tumor suppressor DAB2IP by microRNA-149-3p promotes aggressiveness of cancer cells.
Arianna Bellazzo, Giulio Di Minin, Elena Valentino, Daria Sicari, Denis Torre, …, Chiara Agostinis, Roberta Bulla, Miguel Mano, Giannino Del Sal, Licio Collavin
Cell death and differentiation  ·  22 Mar 2018  ·  pubmed:29568059
Bifunctional immune checkpoint-targeted antibody-ligand traps that simultaneously disable TGFβ enhance the efficacy of cancer immunotherapy.
Bifunctional immune checkpoint-targeted antibody-ligand traps that simultaneously disable TGFβ enhance the efficacy of cancer immunotherapy.
Rajani Ravi, Kimberly A Noonan, Vui Pham, Rishi Bedi, Alex Zhavoronkov, …, Luigi Marchionni, David Sidransky, Ivan M Borrello, Evgeny Izumchenko, Atul Bedi
Nature communications  ·  21 Feb 2018  ·  pubmed:29467463
Bifunctional immune checkpoint-targeted antibody-ligand traps that simultaneously disable TGFβ enhance the efficacy of cancer immunotherapy
Bifunctional immune checkpoint-targeted antibody-ligand traps that simultaneously disable TGFβ enhance the efficacy of cancer immunotherapy
Rajani Ravi, Kimberly A. Noonan, Vui Pham, Rishi Bedi, Alex Zhavoronkov, …, Luigi Marchionni, David Sidransky, Ivan M. Borrello, Evgeny Izumchenko, Atul Bedi
Nature Communications  ·  21 Feb 2018  ·  doi:10.1038/s41467-017-02696-6
Arsenic promotes the COX2 PGE2-SOX2 axis to increase the malignant stemness properties of urothelial cells.
Arsenic promotes the COX2/PGE2-SOX2 axis to increase the malignant stemness properties of urothelial cells.
Akira Ooki, Asma Begum, Luigi Marchionni, Christopher J VandenBussche, Shifeng Mao, Max Kates, Mohammad Obaidul Hoque
International journal of cancer  ·  14 Feb 2018  ·  pubmed:29396848
Arsenic promotes the scp COX2 PGE2 SOX2 scp axis to increase the malignant stemness properties of urothelial cells
Arsenic promotes the COX2/PGE2–SOX2 axis to increase the malignant stemness properties of urothelial cells
Akira Ooki, Asma Begum, Luigi Marchionni, Christopher J. VandenBussche, Shifeng Mao, Max Kates, Mohammad Obaidul Hoque
International Journal of Cancer  ·  14 Feb 2018  ·  doi:10.1002/ijc.31290
YAP1 and COX2 Coordinately Regulate Urothelial Cancer Stem-like Cells
YAP1 and COX2 Coordinately Regulate Urothelial Cancer Stem-like Cells
Akira Ooki, Maria Del Carmen Rodriguez Pena, Luigi Marchionni, Wikum Dinalankara, Asma Begum, …, Zeshaan A. Rasheed, Shifeng Mao, George J. Netto, David Sidransky, Mohammad O. Hoque
Cancer Research  ·  01 Jan 2018  ·  doi:10.1158/0008-5472.CAN-17-0836

2017

YAP1 and COX2 Coordinately Regulate Urothelial Cancer Stem-like Cells.
YAP1 and COX2 Coordinately Regulate Urothelial Cancer Stem-like Cells.
Akira Ooki, Maria Del Carmen Rodriguez Pena, Luigi Marchionni, Wikum Dinalankara, Asma Begum, …, Zeshaan A Rasheed, Shifeng Mao, George J Netto, David Sidransky, Mohammad O Hoque
Cancer research  ·  27 Nov 2017  ·  pubmed:29180467
Pharmacodynamic and pharmacokinetic neoadjuvant study of hedgehog pathway inhibitor Sonidegib LDE-225 in men with high-risk localized prostate cancer undergoing prostatectomy.
Pharmacodynamic and pharmacokinetic neoadjuvant study of hedgehog pathway inhibitor Sonidegib (LDE-225) in men with high-risk localized prostate cancer undergoing prostatectomy.
Ashley E Ross, Robert M Hughes, Stephanie Glavaris, Kamyar Ghabili, Ping He, …, Tanya O’Neal, Angelo M DeMarzo, Paula J Hurley, Michelle A Rudek, Emmanuel S Antonarakis
Oncotarget  ·  26 Oct 2017  ·  pubmed:29262631
Pharmacodynamic and pharmacokinetic neoadjuvant study of hedgehog pathway inhibitor Sonidegib LDE-225 in men with high-risk localized prostate cancer undergoing prostatectomy
Pharmacodynamic and pharmacokinetic neoadjuvant study of hedgehog pathway inhibitor Sonidegib (LDE-225) in men with high-risk localized prostate cancer undergoing prostatectomy
Ashley E. Ross, Robert M. Hughes, Stephanie Glavaris, Kamyar Ghabili, Ping He, …, Tanya O’Neal, Angelo M. DeMarzo, Paula J. Hurley, Michelle A. Rudek, Emmanuel S. Antonarakis
Oncotarget  ·  26 Oct 2017  ·  doi:10.18632/oncotarget.22115
MicroRNAs, promising biomarkers in the diagnosis of Xp11 translocation RCC reply
MicroRNAs, promising biomarkers in the diagnosis of Xp11 translocation RCC—reply
Luigi Marchionni, George J Netto, Mohammad O. Hoque, Pedram Argani
Human Pathology  ·  01 Oct 2017  ·  doi:10.1016/j.humpath.2017.06.021
High-resolution microbiome profiling uncovers
High-resolution microbiome profiling uncovers
Rafael Guerrero-Preston, James Robert White, Filipa Godoy-Vitorino, Arnold Rodríguez-Hilario, Kelvin Navarro, …, Wayne Koch, Hyunseok Kang, Luigi Marchionni, Young Kim, David Sidransky
Oncotarget  ·  07 Sep 2017  ·  pubmed:29340028
High-resolution microbiome profiling uncovers i Fusobacterium nucleatum i , i Lactobacillus gasseri johnsonii i , and i Lactobacillus vaginalis i associated to oral and oropharyngeal cancer in saliva from HPV positive and HPV negative patients treated with surgery and chemo-radiation
High-resolution microbiome profiling uncoversFusobacterium nucleatum,Lactobacillus gasseri/johnsonii, andLactobacillus vaginalisassociated to oral and oropharyngeal cancer in saliva from HPV positive and HPV negative patients treated with surgery and chemo-radiation
Rafael Guerrero-Preston, James Robert White, Filipa Godoy-Vitorino, Arnold Rodríguez-Hilario, Kelvin Navarro, …, Wayne Koch, Hyunseok Kang, Luigi Marchionni, Young Kim, David Sidransky
Oncotarget  ·  07 Sep 2017  ·  doi:10.18632/oncotarget.20677
MicroRNA expression profiling of Xp11 renal cell carcinoma
MicroRNA expression profiling of Xp11 renal cell carcinoma
Luigi Marchionni, Masamichi Hayashi, Elisa Guida, Akira Ooki, Enrico Munari, …, Wikum Dinalankara, Ali Raza, George J. Netto, Mohammad O. Hoque, Pedram Argani
Human Pathology  ·  01 Sep 2017  ·  doi:10.1016/j.humpath.2017.03.011
MicroRNAs, promising biomarkers in the diagnosis of Xp11 translocation RCC-reply.
MicroRNAs, promising biomarkers in the diagnosis of Xp11 translocation RCC-reply.
Luigi Marchionni, George J Netto, Mohammad O Hoque, Pedram Argani
Human pathology  ·  12 Aug 2017  ·  pubmed:28811253
The extracellular matrix and focal adhesion kinase signaling regulate cancer stem cell function in pancreatic ductal adenocarcinoma.
The extracellular matrix and focal adhesion kinase signaling regulate cancer stem cell function in pancreatic ductal adenocarcinoma.
Asma Begum, Theodore Ewachiw, Clinton Jung, Ally Huang, K Jessica Norberg, …, Mahesh Padval, Jonathan A Pachter, David T Weaver, Zeshaan A Rasheed, William Matsui
PloS one  ·  10 Jul 2017  ·  pubmed:28692661
The extracellular matrix and focal adhesion kinase signaling regulate cancer stem cell function in pancreatic ductal adenocarcinoma
The extracellular matrix and focal adhesion kinase signaling regulate cancer stem cell function in pancreatic ductal adenocarcinoma
Asma Begum, Theodore Ewachiw, Clinton Jung, Ally Huang, K. Jessica Norberg, …, Mahesh Padval, Jonathan A. Pachter, David T. Weaver, Zeshaan A. Rasheed, William Matsui
PLOS ONE  ·  10 Jul 2017  ·  doi:10.1371/journal.pone.0180181
Analysis of differential gene expression mediated by clozapine in human postmortem brains
Analysis of differential gene expression mediated by clozapine in human postmortem brains
Brian J. Lee, Luigi Marchionni, Carrie E. Andrews, Alexis L. Norris, Leslie G. Nucifora, …, Jonathan Pevsner, Christopher A. Ross, Russell L. Margolis, Akira Sawa, Frederick C. Nucifora
Schizophrenia Research  ·  01 Jul 2017  ·  doi:10.1016/j.schres.2016.12.017
PatternMarkers GWCoGAPS for novel data-driven biomarkers via whole transcriptome NMF.
PatternMarkers & GWCoGAPS for novel data-driven biomarkers via whole transcriptome NMF.
Genevieve L Stein-O’Brien, Jacob L Carey, Wai Shing Lee, Michael Considine, Alexander V Favorov, …, Daria A Gaykalova, Ronald D McKay, Michael F Ochs, Carlo Colantuoni, Elana J Fertig
Bioinformatics (Oxford, England)  ·  15 Jun 2017  ·  pubmed:28174896
Selective analysis of cancer-cell intrinsic transcriptional traits defines novel clinically relevant subtypes of colorectal cancer.
Selective analysis of cancer-cell intrinsic transcriptional traits defines novel clinically relevant subtypes of colorectal cancer.
Claudio Isella, Francesco Brundu, Sara E Bellomo, Francesco Galimi, Eugenia Zanella, …, Elisa Ficarra, Luigi Marchionni, Livio Trusolino, Enzo Medico, Andrea Bertotti
Nature communications  ·  31 May 2017  ·  pubmed:28561063
Selective analysis of cancer-cell intrinsic transcriptional traits defines novel clinically relevant subtypes of colorectal cancer
Selective analysis of cancer-cell intrinsic transcriptional traits defines novel clinically relevant subtypes of colorectal cancer
Claudio Isella, Francesco Brundu, Sara E. Bellomo, Francesco Galimi, Eugenia Zanella, …, Elisa Ficarra, Luigi Marchionni, Livio Trusolino, Enzo Medico, Andrea Bertotti
Nature Communications  ·  31 May 2017  ·  doi:10.1038/ncomms15107
Synthesizer: Expediting synthesis studies from context-free data with information retrieval techniques.
Synthesizer: Expediting synthesis studies from context-free data with information retrieval techniques.
Lisa M Gandy, Jordan Gumm, Benjamin Fertig, Anne Thessen, Michael J Kennish, Sameer Chavan, Luigi Marchionni, Xiaoxin Xia, Shambhavi Shankrit, Elana J Fertig
PloS one  ·  24 Apr 2017  ·  pubmed:28437440
Synthesizer: Expediting synthesis studies from context-free data with information retrieval techniques
Synthesizer: Expediting synthesis studies from context-free data with information retrieval techniques
Lisa M. Gandy, Jordan Gumm, Benjamin Fertig, Anne Thessen, Michael J. Kennish, Sameer Chavan, Luigi Marchionni, Xiaoxin Xia, Shambhavi Shankrit, Elana J. Fertig
PLOS ONE  ·  24 Apr 2017  ·  doi:10.1371/journal.pone.0175860
MicroRNA expression profiling of Xp11 renal cell carcinoma.
MicroRNA expression profiling of Xp11 renal cell carcinoma.
Luigi Marchionni, Masamichi Hayashi, Elisa Guida, Akira Ooki, Enrico Munari, …, Wikum Dinalankara, Ali Raza, George J Netto, Mohammad O Hoque, Pedram Argani
Human pathology  ·  12 Apr 2017  ·  pubmed:28411178
cancer renal-cell-carcinoma microrna gene-expression gene-fusion
PatternMarkers amp; GWCoGAPS for novel data-driven biomarkers via whole transcriptome NMF
PatternMarkers & GWCoGAPS for novel data-driven biomarkers via whole transcriptome NMF
Genevieve L Stein-O’Brien, Jacob L Carey, Wai Shing Lee, Michael Considine, Alexander V Favorov, …, Daria A Gaykalova, Ronald D McKay, Michael F Ochs, Carlo Colantuoni, Elana J Fertig
Bioinformatics  ·  08 Feb 2017  ·  doi:10.1093/bioinformatics/btx058
Dysregulation of EGFR Pathway in EphA2 Cell Subpopulation Significantly Associates with Poor Prognosis in Colorectal Cancer
Dysregulation of EGFR Pathway in EphA2 Cell Subpopulation Significantly Associates with Poor Prognosis in Colorectal Cancer
Mariangela De Robertis, Luisa Loiacono, Caterina Fusilli, Maria Luana Poeta, Tommaso Mazza, …, Emanuela Signori, Giuseppe Lamorte, Angelo Luigi Vescovi, Jesus Garcia-Foncillas, Vito Michele Fazio
Clinical Cancer Research  ·  01 Jan 2017  ·  doi:10.1158/1078-0432.CCR-16-0709

2016

Analysis of differential gene expression mediated by clozapine in human postmortem brains.
Analysis of differential gene expression mediated by clozapine in human postmortem brains.
Brian J Lee, Luigi Marchionni, Carrie E Andrews, Alexis L Norris, Leslie G Nucifora, …, Jonathan Pevsner, Christopher A Ross, Russell L Margolis, Akira Sawa, Frederick C Nucifora
Schizophrenia research  ·  27 Dec 2016  ·  pubmed:28038920
Identification of miR-30b-3p and miR-30d-5p as direct regulators of androgen receptor signaling in prostate cancer by complementary functional microRNA library screening.
Identification of miR-30b-3p and miR-30d-5p as direct regulators of androgen receptor signaling in prostate cancer by complementary functional microRNA library screening.
Binod Kumar, Salar Khaleghzadegan, Brian Mears, Koji Hatano, Tarana A Kudrolli, …, Charles M Ewing, Jun Luo, William B Isaacs, Luigi Marchionni, Shawn E Lupold
Oncotarget  ·  08 Nov 2016  ·  pubmed:27683042
Expression of HIV-1 matrix protein p17 and association with B-cell lymphoma in HIV-1 transgenic mice.
Expression of HIV-1 matrix protein p17 and association with B-cell lymphoma in HIV-1 transgenic mice.
Virginia A Carroll, Mark K Lafferty, Luigi Marchionni, Joseph L Bryant, Robert C Gallo, Alfredo Garzino-Demo
Proceedings of the National Academy of Sciences of the United States of America  ·  31 Oct 2016  ·  pubmed:27799525
Expression of HIV-1 matrix protein p17 and association with B-cell lymphoma in HIV-1 transgenic mice
Expression of HIV-1 matrix protein p17 and association with B-cell lymphoma in HIV-1 transgenic mice
Virginia A. Carroll, Mark K. Lafferty, Luigi Marchionni, Joseph L. Bryant, Robert C. Gallo, Alfredo Garzino-Demo
Proceedings of the National Academy of Sciences  ·  31 Oct 2016  ·  doi:10.1073/pnas.1615258113
Identification of miR-30b-3p and miR-30d-5p as direct regulators of androgen receptor signaling in prostate cancer by complementary functional microRNA library screening
Identification of miR-30b-3p and miR-30d-5p as direct regulators of androgen receptor signaling in prostate cancer by complementary functional microRNA library screening
Binod Kumar, Salar Khaleghzadegan, Brian Mears, Koji Hatano, Tarana A. Kudrolli, …, Charles M. Ewing, Jun Luo, William B. Isaacs, Luigi Marchionni, Shawn E. Lupold
Oncotarget  ·  24 Sep 2016  ·  doi:10.18632/oncotarget.12241
Human T sub h sub 17 Cells Lack HIV-Inhibitory RNases and Are Highly Permissive to Productive HIV Infection
Human T h 17 Cells Lack HIV-Inhibitory RNases and Are Highly Permissive to Productive HIV Infection
Aaron Christensen-Quick, Mark Lafferty, Lingling Sun, Luigi Marchionni, Anthony DeVico, Alfredo Garzino-Demo
Journal of Virology  ·  01 Sep 2016  ·  doi:10.1128/JVI.02869-15
Human Th17 Cells Lack HIV-Inhibitory RNases and Are Highly Permissive to Productive HIV Infection.
Human Th17 Cells Lack HIV-Inhibitory RNases and Are Highly Permissive to Productive HIV Infection.
Aaron Christensen-Quick, Mark Lafferty, Lingling Sun, Luigi Marchionni, Anthony DeVico, Alfredo Garzino-Demo
Journal of virology  ·  12 Aug 2016  ·  pubmed:27334595
Dysregulation of EGFR Pathway in EphA2 Cell Subpopulation Significantly Associates with Poor Prognosis in Colorectal Cancer.
Dysregulation of EGFR Pathway in EphA2 Cell Subpopulation Significantly Associates with Poor Prognosis in Colorectal Cancer.
Mariangela De Robertis, Luisa Loiacono, Caterina Fusilli, Maria Luana Poeta, Tommaso Mazza, …, Emanuela Signori, Giuseppe Lamorte, Angelo Luigi Vescovi, Jesus Garcia-Foncillas, Vito Michele Fazio
Clinical cancer research : an official journal of the American Association for Cancer Research  ·  11 Jul 2016  ·  pubmed:27401248
Summary and Recommendations from the National Cancer Institute s Clinical Trials Planning Meeting on Novel Therapeutics for Non-Muscle Invasive Bladder Cancer.
Summary and Recommendations from the National Cancer Institute's Clinical Trials Planning Meeting on Novel Therapeutics for Non-Muscle Invasive Bladder Cancer.
Seth P Lerner, Dean F Bajorin, Colin P Dinney, Jason A Efstathiou, Susan Groshen, …, Abdul Tawab Amiri, Eliezer Van Allen, Pamela J West, J A Witjes, Diane Zipursky Quale
Bladder cancer (Amsterdam, Netherlands)  ·  27 Apr 2016  ·  pubmed:27376138
Whole-Genome Sequencing of Salivary Gland Adenoid Cystic Carcinoma
Whole-Genome Sequencing of Salivary Gland Adenoid Cystic Carcinoma
Eleni M. Rettig, C. Conover Talbot, Mark Sausen, Sian Jones, Justin A. Bishop, …, Nickolas Papadopoulos, Kenneth W. Kinzler, Bert Vogelstein, Patrick K. Ha, Nishant Agrawal
Cancer Prevention Research  ·  31 Mar 2016  ·  doi:10.1158/1940-6207.CAPR-15-0316
Whole-Genome Sequencing of Salivary Gland Adenoid Cystic Carcinoma.
Whole-Genome Sequencing of Salivary Gland Adenoid Cystic Carcinoma.
Eleni M Rettig, C Conover Talbot, Mark Sausen, Sian Jones, Justin A Bishop, …, Nickolas Papadopoulos, Kenneth W Kinzler, Bert Vogelstein, Patrick K Ha, Nishant Agrawal
Cancer prevention research (Philadelphia, Pa.)  ·  09 Feb 2016  ·  pubmed:26862087
cancer
Germline Variants in Asporin Vary by Race, Modulate the Tumor Microenvironment, and Are Differentially Associated with Metastatic Prostate Cancer
Germline Variants in Asporin Vary by Race, Modulate the Tumor Microenvironment, and Are Differentially Associated with Metastatic Prostate Cancer
Paula J. Hurley, Debasish Sundi, Brian Shinder, Brian W. Simons, Robert M. Hughes, …, Ben H. Park, William B. Isaacs, Luigi Marchionni, Ashley E. Ross, Edward M. Schaeffer
Clinical Cancer Research  ·  14 Jan 2016  ·  doi:10.1158/1078-0432.CCR-15-0256
Tissue-based Genomics Augments Post-prostatectomy Risk Stratification in a Natural History Cohort of Intermediate- and High-Risk Men
Tissue-based Genomics Augments Post-prostatectomy Risk Stratification in a Natural History Cohort of Intermediate- and High-Risk Men
Ashley E. Ross, Michael H. Johnson, Kasra Yousefi, Elai Davicioni, George J. Netto, …, Stephania M. Bezerra, Misop Han, Alan W. Partin, Bruce J. Trock, Edward M. Schaeffer
European Urology  ·  01 Jan 2016  ·  doi:10.1016/j.eururo.2015.05.042

2015

Correction: Identification and Validation of Protein Biomarkers of Response to Neoadjuvant Platinum Chemotherapy in Muscle Invasive Urothelial Carcinoma.
Correction: Identification and Validation of Protein Biomarkers of Response to Neoadjuvant Platinum Chemotherapy in Muscle Invasive Urothelial Carcinoma.
Alexander S Baras, Nilay Gandhi, Enrico Munari, Sheila Faraj, Luciana Shultz, …, Noah Hahn, Mohammad Obaidul Hoque, David Berman, Trinity J Bivalacqua, George Netto
PloS one  ·  24 Nov 2015  ·  pubmed:26599435
Correction: Identification and Validation of Protein Biomarkers of Response to Neoadjuvant Platinum Chemotherapy in Muscle Invasive Urothelial Carcinoma
Correction: Identification and Validation of Protein Biomarkers of Response to Neoadjuvant Platinum Chemotherapy in Muscle Invasive Urothelial Carcinoma
Alexander S. Baras, Nilay Gandhi, Enrico Munari, Sheila Faraj, Luciana Shultz, …, Noah Hahn, Mohammad Obaidul Hoque, David Berman, Trinity J. Bivalacqua, George Netto
PLOS ONE  ·  24 Nov 2015  ·  doi:10.1371/journal.pone.0143990
A multi-omic analysis of human naïve CD4 T cells.
A multi-omic analysis of human naïve CD4+ T cells.
Christopher J Mitchell, Derese Getnet, Min-Sik Kim, Srikanth S Manda, Praveen Kumar, …, Leslie Cope, Yasushi Ishihama, Charles Wang, Harsha Gowda, Akhilesh Pandey
BMC systems biology  ·  06 Nov 2015  ·  pubmed:26542228
A multi-omic analysis of human naïve CD4 T cells
A multi-omic analysis of human naïve CD4+ T cells
Christopher J. Mitchell, Derese Getnet, Min-Sik Kim, Srikanth S. Manda, Praveen Kumar, …, Leslie Cope, Yasushi Ishihama, Charles Wang, Harsha Gowda, Akhilesh Pandey
BMC Systems Biology  ·  06 Nov 2015  ·  doi:10.1186/s12918-015-0225-4
Alterations in cellular metabolome after pharmacological inhibition of Notch in glioblastoma cells.
Alterations in cellular metabolome after pharmacological inhibition of Notch in glioblastoma cells.
Ulf D Kahlert, Menglin Cheng, Katharina Koch, Luigi Marchionni, Xing Fan, Eric H Raabe, Jarek Maciaczyk, Kristine Glunde, Charles G Eberhart
International journal of cancer  ·  13 Oct 2015  ·  pubmed:26422827
Alterations in cellular metabolome after pharmacological inhibition of scp N scp otch in glioblastoma cells
Alterations in cellular metabolome after pharmacological inhibition of Notch in glioblastoma cells
Ulf D. Kahlert, Menglin Cheng, Katharina Koch, Luigi Marchionni, Xing Fan, Eric H. Raabe, Jarek Maciaczyk, Kristine Glunde, Charles G. Eberhart
International Journal of Cancer  ·  13 Oct 2015  ·  doi:10.1002/ijc.29873
Germline Variants in Asporin Vary by Race, Modulate the Tumor Microenvironment, and Are Differentially Associated with Metastatic Prostate Cancer.
Germline Variants in Asporin Vary by Race, Modulate the Tumor Microenvironment, and Are Differentially Associated with Metastatic Prostate Cancer.
Paula J Hurley, Debasish Sundi, Brian Shinder, Brian W Simons, Robert M Hughes, …, Ben H Park, William B Isaacs, Luigi Marchionni, Ashley E Ross, Edward M Schaeffer
Clinical cancer research : an official journal of the American Association for Cancer Research  ·  07 Oct 2015  ·  pubmed:26446945
Targeted sequencing reveals clonal genetic changes in the progression of early lung neoplasms and paired circulating DNA.
Targeted sequencing reveals clonal genetic changes in the progression of early lung neoplasms and paired circulating DNA.
Evgeny Izumchenko, Xiaofei Chang, Mariana Brait, Elana Fertig, Luciane T Kagohara, …, Rajani Ravi, Sian Jones, Mohammad O Hoque, William H Westra, David Sidransky
Nature communications  ·  16 Sep 2015  ·  pubmed:26374070
Targeted sequencing reveals clonal genetic changes in the progression of early lung neoplasms and paired circulating DNA
Targeted sequencing reveals clonal genetic changes in the progression of early lung neoplasms and paired circulating DNA
Evgeny Izumchenko, Xiaofei Chang, Mariana Brait, Elana Fertig, Luciane T. Kagohara, …, Rajani Ravi, Sian Jones, Mohammad O. Hoque, William H. Westra, David Sidransky
Nature Communications  ·  16 Sep 2015  ·  doi:10.1038/ncomms9258
Identification and Validation of Protein Biomarkers of Response to Neoadjuvant Platinum Chemotherapy in Muscle Invasive Urothelial Carcinoma.
Identification and Validation of Protein Biomarkers of Response to Neoadjuvant Platinum Chemotherapy in Muscle Invasive Urothelial Carcinoma.
Alexander S Baras, Nilay Gandhi, Enrico Munari, Sheila Faraj, Luciana Shultz, …, Noah Hahn, Mohammad Obaidul Hoque, David Berman, Trinity J Bivalacqua, George Netto
PloS one  ·  31 Jul 2015  ·  pubmed:26230923
Neutrophil to lymphocyte ratio NLR improves the risk assessment of ISS staging in newly diagnosed MM patients treated upfront with novel agents
Neutrophil to lymphocyte ratio (NLR) improves the risk assessment of ISS staging in newly diagnosed MM patients treated upfront with novel agents
A. Romano, N. L. Parrinello, M. L. Consoli, L. Marchionni, S. Forte, …, A. Pompa, A. Corso, G. Milone, F. Di Raimondo, I. Borrello
Annals of Hematology  ·  31 Jul 2015  ·  doi:10.1007/s00277-015-2462-4
Identification and Validation of Protein Biomarkers of Response to Neoadjuvant Platinum Chemotherapy in Muscle Invasive Urothelial Carcinoma
Identification and Validation of Protein Biomarkers of Response to Neoadjuvant Platinum Chemotherapy in Muscle Invasive Urothelial Carcinoma
Alexander S. Baras, Nilay Gandhi, Enrico Munari, Sheila Faraj, Luciana Shultz, …, Noah Hahn, Mohammad Hoque, David Berman, Trinity J. Bivalacqua, George Netto
PLOS ONE  ·  31 Jul 2015  ·  doi:10.1371/journal.pone.0131245
Erratum for the Research Article: Integration of Hedgehog and mutant FLT3 signaling in myeloid leukemia by Y. Lim, L. Gondek, L. Li, Q. Wang, H. Ma, E. Chang, D. L. Huso, S. Foerster, L. Marchionni, K. McGovern, D. N. Watkins, C. D. Peacock, M. Levis, B. D. Smith, A. A. Merchant, D. Small, W. Matsui
Erratum for the Research Article: “Integration of Hedgehog and mutant FLT3 signaling in myeloid leukemia” by Y. Lim, L. Gondek, L. Li, Q. Wang, H. Ma, E. Chang, D. L. Huso, S. Foerster, L. Marchionni, K. McGovern, D. N. Watkins, C. D. Peacock, M. Levis, B. D. Smith, A. A. Merchant, D. Small, W. Matsui
Science Translational Medicine  ·  08 Jul 2015  ·  doi:10.1126/scitranslmed.aac9303
Removal of Abnormal Myofilament O-GlcNAcylation Restores Ca2 Sensitivity in Diabetic Cardiac Muscle.
Removal of Abnormal Myofilament O-GlcNAcylation Restores Ca2+ Sensitivity in Diabetic Cardiac Muscle.
Genaro A Ramirez-Correa, Junfeng Ma, Chad Slawson, Quira Zeidan, Nahyr S Lugo-Fagundo, …, Robert N Cole, Luigi Marchionni, Nazareno Paolocci, Gerald W Hart, Anne M Murphy
Diabetes  ·  24 Jun 2015  ·  pubmed:26109417
Removal of Abnormal Myofilament i O i -GlcNAcylation Restores Ca2 Sensitivity in Diabetic Cardiac Muscle
Removal of Abnormal Myofilament O-GlcNAcylation Restores Ca2+ Sensitivity in Diabetic Cardiac Muscle
Genaro A. Ramirez-Correa, Junfeng Ma, Chad Slawson, Quira Zeidan, Nahyr S. Lugo-Fagundo, …, Robert N. Cole, Luigi Marchionni, Nazareno Paolocci, Gerald W. Hart, Anne M. Murphy
Diabetes  ·  24 Jun 2015  ·  doi:10.2337/db14-1107
Integration of Hedgehog and mutant FLT3 signaling in myeloid leukemia.
Integration of Hedgehog and mutant FLT3 signaling in myeloid leukemia.
Yiting Lim, Lukasz Gondek, Li Li, Qiuju Wang, Hayley Ma, …, Mark Levis, Bruce Douglas Smith, Akil A Merchant, Donald Small, William Matsui
Science translational medicine  ·  10 Jun 2015  ·  pubmed:26062848
Integration of Hedgehog and mutant FLT3 signaling in myeloid leukemia
Integration of Hedgehog and mutant FLT3 signaling in myeloid leukemia
Yiting Lim, Lukasz Gondek, Li Li, Qiuju Wang, Hayley Ma, …, Mark Levis, Bruce Douglas Smith, Akil A. Merchant, Donald Small, William Matsui
Science Translational Medicine  ·  10 Jun 2015  ·  doi:10.1126/scitranslmed.aaa5731
Tissue-based Genomics Augments Post-prostatectomy Risk Stratification in a Natural History Cohort of Intermediate- and High-Risk Men.
Tissue-based Genomics Augments Post-prostatectomy Risk Stratification in a Natural History Cohort of Intermediate- and High-Risk Men.
Ashley E Ross, Michael H Johnson, Kasra Yousefi, Elai Davicioni, George J Netto, …, Stephania M Bezerra, Misop Han, Alan W Partin, Bruce J Trock, Edward M Schaeffer
European urology  ·  06 Jun 2015  ·  pubmed:26058959
HES6 promotes prostate cancer aggressiveness independently of Notch signalling.
HES6 promotes prostate cancer aggressiveness independently of Notch signalling.
Filipe L F Carvalho, Luigi Marchionni, Anuj Gupta, Basheer A Kummangal, Edward M Schaeffer, Ashley E Ross, David M Berman
Journal of cellular and molecular medicine  ·  12 Apr 2015  ·  pubmed:25864518
HES6 promotes prostate cancer aggressiveness independently of Notch signalling
HES6 promotes prostate cancer aggressiveness independently of Notch signalling
Filipe L. F. Carvalho, Luigi Marchionni, Anuj Gupta, Basheer A. Kummangal, Edward M. Schaeffer, Ashley E. Ross, David M. Berman
Journal of Cellular and Molecular Medicine  ·  12 Apr 2015  ·  doi:10.1111/jcmm.12537
Notch signaling activation in pediatric low-grade astrocytoma.
Notch signaling activation in pediatric low-grade astrocytoma.
William D Brandt, Karisa C Schreck, Eli E Bar, Isabella Taylor, Luigi Marchionni, Eric Raabe, Charles G Eberhart, Fausto J Rodriguez
Journal of neuropathology and experimental neurology  ·  01 Feb 2015  ·  pubmed:25575134
notch cancer
Notch Signaling Activation in Pediatric Low-Grade Astrocytoma
Notch Signaling Activation in Pediatric Low-Grade Astrocytoma
William D. Brandt, Karisa C. Schreck, Eli E. Bar, Isabella Taylor, Luigi Marchionni, Eric Raabe, Charles G. Eberhart, Fausto J. Rodriguez
Journal of Neuropathology & Experimental Neurology  ·  01 Feb 2015  ·  doi:10.1097/NEN.0000000000000155
Identification of miR-145 targets through an integrated omics analysis
Identification of miR-145 targets through an integrated omics analysis
Tai-Chung Huang, Santosh Renuse, Sneha Pinto, Praveen Kumar, Yi Yang, …, Joshua T. Mendell, Marc K. Halushka, Curt I. Civin, Luigi Marchionni, Akhilesh Pandey
Molecular BioSystems  ·  01 Jan 2015  ·  doi:10.1039/c4mb00585f

2014

Only three driver gene mutations are required for the development of lung and colorectal cancers.
Only three driver gene mutations are required for the development of lung and colorectal cancers.
Cristian Tomasetti, Luigi Marchionni, Martin A Nowak, Giovanni Parmigiani, Bert Vogelstein
Proceedings of the National Academy of Sciences of the United States of America  ·  22 Dec 2014  ·  pubmed:25535351
Only three driver gene mutations are required for the development of lung and colorectal cancers
Only three driver gene mutations are required for the development of lung and colorectal cancers
Cristian Tomasetti, Luigi Marchionni, Martin A. Nowak, Giovanni Parmigiani, Bert Vogelstein
Proceedings of the National Academy of Sciences  ·  22 Dec 2014  ·  doi:10.1073/pnas.1421839112
Identification of miR-145 targets through an integrated omics analysis.
Identification of miR-145 targets through an integrated omics analysis.
Tai-Chung Huang, Santosh Renuse, Sneha Pinto, Praveen Kumar, Yi Yang, …, Joshua T Mendell, Marc K Halushka, Curt I Civin, Luigi Marchionni, Akhilesh Pandey
Molecular bioSystems  ·  30 Oct 2014  ·  pubmed:25354783
switchBox: an R package for k-Top Scoring Pairs classifier development.
switchBox: an R package for k-Top Scoring Pairs classifier development.
Bahman Afsari, Elana J Fertig, Donald Geman, Luigi Marchionni
Bioinformatics (Oxford, England)  ·  26 Sep 2014  ·  pubmed:25262153
switchBox: an R package for k Top Scoring Pairs classifier development
switchBox: an R package for k–Top Scoring Pairs classifier development
Bahman Afsari, Elana J. Fertig, Donald Geman, Luigi Marchionni
Bioinformatics  ·  26 Sep 2014  ·  doi:10.1093/bioinformatics/btu622
Clear cell papillary renal cell carcinoma: micro-RNA expression profiling and comparison with clear cell renal cell carcinoma and papillary renal cell carcinoma
Clear cell papillary renal cell carcinoma: micro-RNA expression profiling and comparison with clear cell renal cell carcinoma and papillary renal cell carcinoma
Enrico Munari, Luigi Marchionni, Apurva Chitre, Masamichi Hayashi, Guido Martignoni, …, Stefano Gobbo, Pedram Argani, Mohamad Allaf, Mohammad O. Hoque, George J. Netto
Human Pathology  ·  01 Jun 2014  ·  doi:10.1016/j.humpath.2014.01.013
Key tumor suppressor genes inactivated by greater promoter methylation and somatic mutations in head and neck cancer.
Key tumor suppressor genes inactivated by "greater promoter" methylation and somatic mutations in head and neck cancer.
Rafael Guerrero-Preston, Christina Michailidi, Luigi Marchionni, Curtis R Pickering, Mitchell J Frederick, …, William Westra, Wayne Koch, Joseph Califano, Victor E Velculescu, David Sidransky
Epigenetics  ·  01 May 2014  ·  pubmed:24786473
Key tumor suppressor genes inactivated by greater promoter methylation and somatic mutations in head and neck cancer
Key tumor suppressor genes inactivated by “greater promoter” methylation and somatic mutations in head and neck cancer
Rafael Guerrero-Preston, Christina Michailidi, Luigi Marchionni, Curtis R Pickering, Mitchell J Frederick, …, William Westra, Wayne Koch, Joseph Califano, Victor E Velculescu, David Sidransky
Epigenetics  ·  01 May 2014  ·  doi:10.4161/epi.29025
Correction: H2S Increases Survival During Sepsis: Protective Effect of CHOP Inhibition
Correction: H2S Increases Survival During Sepsis: Protective Effect of CHOP Inhibition
Marcella Ferlito, Qihong Wang, William B. Fulton, Paul M. Colombani, Luigi Marchionni, Karen Fox-Talbot, Nazareno Paolocci, Charles Steenbergen
The Journal of Immunology  ·  15 Apr 2014  ·  doi:10.4049/jimmunol.1490009
Integrative Analysis of 1q23.3 Copy-Number Gain in Metastatic Urothelial Carcinoma
Integrative Analysis of 1q23.3 Copy-Number Gain in Metastatic Urothelial Carcinoma
Markus Riester, Lillian Werner, Joaquim Bellmunt, Shamini Selvarajah, Elizabeth A. Guancial, …, Massimo Loda, David M. Berman, Philip W. Kantoff, Franziska Michor, Jonathan E. Rosenberg
Clinical Cancer Research  ·  31 Mar 2014  ·  doi:10.1158/1078-0432.CCR-13-0759
H2S Increases Survival during Sepsis: Protective Effect of CHOP Inhibition
H2S Increases Survival during Sepsis: Protective Effect of CHOP Inhibition
Marcella Ferlito, Qihong Wang, William B. Fulton, Paul M. Colombani, Luigi Marchionni, Karen Fox-Talbot, Nazareno Paolocci, Charles Steenbergen
The Journal of Immunology  ·  15 Feb 2014  ·  doi:10.4049/jimmunol.1300835
Clear cell papillary renal cell carcinoma: micro-RNA expression profiling and comparison with clear cell renal cell carcinoma and papillary renal cell carcinoma.
Clear cell papillary renal cell carcinoma: micro-RNA expression profiling and comparison with clear cell renal cell carcinoma and papillary renal cell carcinoma.
Enrico Munari, Luigi Marchionni, Apurva Chitre, Masamichi Hayashi, Guido Martignoni, …, Stefano Gobbo, Pedram Argani, Mohamad Allaf, Mohammad O Hoque, George J Netto
Human pathology  ·  31 Jan 2014  ·  pubmed:24703100
Integrative analysis of 1q23.3 copy-number gain in metastatic urothelial carcinoma.
Integrative analysis of 1q23.3 copy-number gain in metastatic urothelial carcinoma.
Markus Riester, Lillian Werner, Joaquim Bellmunt, Shamini Selvarajah, Elizabeth A Guancial, …, Massimo Loda, David M Berman, Philip W Kantoff, Franziska Michor, Jonathan E Rosenberg
Clinical cancer research : an official journal of the American Association for Cancer Research  ·  31 Jan 2014  ·  pubmed:24486590
Hydrogen sulfide corrected increases survival during sepsis: protective effect of CHOP inhibition.
Hydrogen sulfide [corrected] increases survival during sepsis: protective effect of CHOP inhibition.
Marcella Ferlito, Qihong Wang, William B Fulton, Paul M Colombani, Luigi Marchionni, Karen Fox-Talbot, Nazareno Paolocci, Charles Steenbergen
Journal of immunology (Baltimore, Md. : 1950)  ·  08 Jan 2014  ·  pubmed:24403532

2013

Association of promoter methylation of VGF and PGP9.5 with ovarian cancer progression.
Association of promoter methylation of VGF and PGP9.5 with ovarian cancer progression.
Mariana Brait, Leonel Maldonado, Maartje G Noordhuis, Shahnaz Begum, Myriam Loyo, …, Pauline de Graeff, Ate G J van der Zee, G Bea A Wisman, David Sidransky, Mohammad O Hoque
PloS one  ·  27 Sep 2013  ·  pubmed:24086249
Association of Promoter Methylation of VGF and PGP9.5 with Ovarian Cancer Progression
Association of Promoter Methylation of VGF and PGP9.5 with Ovarian Cancer Progression
Mariana Brait, Leonel Maldonado, Maartje Noordhuis, Shahnaz Begum, Myriam Loyo, …, Pauline de Graeff, Ate G. J. van der Zee, G. Bea A. Wisman, David Sidransky, Mohammad O. Hoque
PLoS ONE  ·  27 Sep 2013  ·  doi:10.1371/journal.pone.0070878
Next-generation sequence analysis of cancer xenograft models.
Next-generation sequence analysis of cancer xenograft models.
Fernando J Rossello, Richard W Tothill, Kara Britt, Kieren D Marini, Jeanette Falzon, …, Erwin Tantoso, Tracey Brown, Philip Chan, Luciano G Martelotto, D Neil Watkins
PloS one  ·  26 Sep 2013  ·  pubmed:24086345
Next-Generation Sequence Analysis of Cancer Xenograft Models
Next-Generation Sequence Analysis of Cancer Xenograft Models
Fernando J. Rossello, Richard W. Tothill, Kara Britt, Kieren D. Marini, Jeanette Falzon, …, Erwin Tantoso, Tracey Brown, Philip Chan, Luciano G. Martelotto, D. Neil Watkins
PLoS ONE  ·  26 Sep 2013  ·  doi:10.1371/journal.pone.0074432
Analysis of the genomic response of human prostate cancer cells to histone deacetylase inhibitors
Analysis of the genomic response of human prostate cancer cells to histone deacetylase inhibitors
Madeleine SQ Kortenhorst, Michel D Wissing, Ronald Rodriguez, Sushant K Kachhap, Judith JM Jans, …, Paul O Aiyetan, Elsken van der Wall, Michael A Carducci, Paul J Van Diest, Luigi Marchionni
Epigenetics  ·  01 Sep 2013  ·  doi:10.4161/epi.25574
High Levels of CD2 Expression Identify HIV-1 Latently Infected Resting Memory CD4 sup sup T Cells in Virally Suppressed Subjects
High Levels of CD2 Expression Identify HIV-1 Latently Infected Resting Memory CD4+T Cells in Virally Suppressed Subjects
Maria Iglesias-Ussel, Claire Vandergeeten, Luigi Marchionni, Nicolas Chomont, Fabio Romerio
Journal of Virology  ·  15 Aug 2013  ·  doi:10.1128/JVI.01297-13
Analysis of the genomic response of human prostate cancer cells to histone deacetylase inhibitors.
Analysis of the genomic response of human prostate cancer cells to histone deacetylase inhibitors.
Madeleine S Q Kortenhorst, Michel D Wissing, Ronald Rodríguez, Sushant K Kachhap, Judith J M Jans, …, Paul O Aiyetan, Elsken van der Wall, Michael A Carducci, Paul J Van Diest, Luigi Marchionni
Epigenetics  ·  19 Jul 2013  ·  pubmed:23880963
prostate-cancer epigenetics combination-therapy gene-expression
High levels of CD2 expression identify HIV-1 latently infected resting memory CD4 T cells in virally suppressed subjects.
High levels of CD2 expression identify HIV-1 latently infected resting memory CD4+ T cells in virally suppressed subjects.
Maria Iglesias-Ussel, Claire Vandergeeten, Luigi Marchionni, Nicolas Chomont, Fabio Romerio
Journal of virology  ·  12 Jun 2013  ·  pubmed:23760244
ERK Phosphorylation Is Predictive of Resistance to IGF-1R Inhibition in Small Cell Lung Cancer
ERK Phosphorylation Is Predictive of Resistance to IGF-1R Inhibition in Small Cell Lung Cancer
Rebekah L. Zinn, Eric E. Gardner, Luigi Marchionni, Sara C. Murphy, Irina Dobromilskaya, Christine L. Hann, Charles M. Rudin
Molecular Cancer Therapeutics  ·  01 Jun 2013  ·  doi:10.1158/1535-7163.MCT-12-0618
A simple and reproducible breast cancer prognostic test.
A simple and reproducible breast cancer prognostic test.
Luigi Marchionni, Bahman Afsari, Donald Geman, Jeffrey T Leek
BMC genomics  ·  17 May 2013  ·  pubmed:23682826
breast-cancer classification single-cell gene-expression-signature statistical-method
A simple and reproducible breast cancer prognostic test
A simple and reproducible breast cancer prognostic test
Luigi Marchionni, Bahman Afsari, Donald Geman, Jeffrey T Leek
BMC Genomics  ·  17 May 2013  ·  doi:10.1186/1471-2164-14-336
Isolation of microarray-quality RNA from primary human cells after intracellular immunostaining and fluorescence-activated cell sorting
Isolation of microarray-quality RNA from primary human cells after intracellular immunostaining and fluorescence-activated cell sorting
Maria Iglesias-Ussel, Luigi Marchionni, Fabio Romerio
Journal of Immunological Methods  ·  01 May 2013  ·  doi:10.1016/j.jim.2013.02.003
ERK phosphorylation is predictive of resistance to IGF-1R inhibition in small cell lung cancer.
ERK phosphorylation is predictive of resistance to IGF-1R inhibition in small cell lung cancer.
Rebekah L Zinn, Eric E Gardner, Luigi Marchionni, Sara C Murphy, Irina Dobromilskaya, Christine L Hann, Charles M Rudin
Molecular cancer therapeutics  ·  20 Mar 2013  ·  pubmed:23515613
Combination treatment with ABT-737 and chloroquine in preclinical models of small cell lung cancer.
Combination treatment with ABT-737 and chloroquine in preclinical models of small cell lung cancer.
Rebekah L Zinn, Eric E Gardner, Irina Dobromilskaya, Sara Murphy, Luigi Marchionni, Christine L Hann, Charles M Rudin
Molecular cancer  ·  02 Mar 2013  ·  pubmed:23452820
Combination treatment with ABT-737 and chloroquine in preclinical models of small cell lung cancer
Combination treatment with ABT-737 and chloroquine in preclinical models of small cell lung cancer
Rebekah L Zinn, Eric E Gardner, Irina Dobromilskaya, Sara Murphy, Luigi Marchionni, Christine L Hann, Charles M Rudin
Molecular Cancer  ·  02 Mar 2013  ·  doi:10.1186/1476-4598-12-16
Isolation of microarray-quality RNA from primary human cells after intracellular immunostaining and fluorescence-activated cell sorting.
Isolation of microarray-quality RNA from primary human cells after intracellular immunostaining and fluorescence-activated cell sorting.
Maria Iglesias-Ussel, Luigi Marchionni, Fabio Romerio
Journal of immunological methods  ·  20 Feb 2013  ·  pubmed:23434645

2012

MicroRNA profiling in pediatric pilocytic astrocytoma reveals biologically relevant targets, including PBX3, NFIB, and METAP2.
MicroRNA profiling in pediatric pilocytic astrocytoma reveals biologically relevant targets, including PBX3, NFIB, and METAP2.
Cheng-Ying Ho, Eli Bar, Caterina Giannini, Luigi Marchionni, Matthias A Karajannis, David Zagzag, David H Gutmann, Charles G Eberhart, Fausto J Rodriguez
Neuro-oncology  ·  15 Nov 2012  ·  pubmed:23161775
MicroRNA profiling in pediatric pilocytic astrocytoma reveals biologically relevant targets, including PBX3, NFIB, and METAP2
MicroRNA profiling in pediatric pilocytic astrocytoma reveals biologically relevant targets, including PBX3, NFIB, and METAP2
Cheng-Ying Ho, Eli Bar, Caterina Giannini, Luigi Marchionni, Matthias A. Karajannis, David Zagzag, David H. Gutmann, Charles G. Eberhart, Fausto J. Rodriguez
Neuro-Oncology  ·  15 Nov 2012  ·  doi:10.1093/neuonc/nos269
Wnt signaling though beta-catenin is required for prostate lineage specification
Wnt signaling though beta-catenin is required for prostate lineage specification
Brian W. Simons, Paula J. Hurley, Zhenhua Huang, Ashley E. Ross, Rebecca Miller, Luigi Marchionni, David M. Berman, Edward M. Schaeffer
Developmental Biology  ·  01 Nov 2012  ·  doi:10.1016/j.ydbio.2012.08.016
Wnt signaling though beta-catenin is required for prostate lineage specification.
Wnt signaling though beta-catenin is required for prostate lineage specification.
Brian W Simons, Paula J Hurley, Zhenhua Huang, Ashley E Ross, Rebecca Miller, Luigi Marchionni, David M Berman, Edward M Schaeffer
Developmental biology  ·  30 Aug 2012  ·  pubmed:22960283
Secreted protein, acidic and rich in cysteine-like 1 SPARCL1 is down regulated in aggressive prostate cancers and is prognostic for poor clinical outcome.
Secreted protein, acidic and rich in cysteine-like 1 (SPARCL1) is down regulated in aggressive prostate cancers and is prognostic for poor clinical outcome.
Paula J Hurley, Luigi Marchionni, Brian W Simons, Ashley E Ross, Sarah B Peskoe, …, Elai Davicioni, Robert B Jenkins, Elizabeth A Platz, David M Berman, Edward M Schaeffer
Proceedings of the National Academy of Sciences of the United States of America  ·  27 Aug 2012  ·  pubmed:22927397
Secreted protein, acidic and rich in cysteine-like 1 SPARCL1 is down regulated in aggressive prostate cancers and is prognostic for poor clinical outcome
Secreted protein, acidic and rich in cysteine-like 1 (SPARCL1) is down regulated in aggressive prostate cancers and is prognostic for poor clinical outcome
Paula J. Hurley, Luigi Marchionni, Brian W. Simons, Ashley E. Ross, Sarah B. Peskoe, …, Elai Davicioni, Robert B. Jenkins, Elizabeth A. Platz, David M. Berman, Edward M. Schaeffer
Proceedings of the National Academy of Sciences  ·  27 Aug 2012  ·  doi:10.1073/pnas.1203525109
Sox9 is required for prostate development and prostate cancer initiation
Sox9 is required for prostate development and prostate cancer initiation
Zhenhua Huang, Paula J Hurley, Brian W Simons, Luigi Marchionni, David M Berman, Ashley E Ross, Edward M Schaeffer
Oncotarget  ·  30 Jun 2012  ·  doi:10.18632/oncotarget.531
Sox9 is required for prostate development and prostate cancer initiation.
Sox9 is required for prostate development and prostate cancer initiation.
Zhenhua Huang, Paula J Hurley, Brian W Simons, Luigi Marchionni, David M Berman, Ashley E Ross, Edward M Schaeffer
Oncotarget  ·  01 Jun 2012  ·  pubmed:22761195
Oncogene amplification in male breast cancer: analysis by multiplex ligation-dependent probe amplification.
Oncogene amplification in male breast cancer: analysis by multiplex ligation-dependent probe amplification.
Robert Kornegoor, Cathy B Moelans, Anoek H J Verschuur-Maes, Marieke C H Hogenes, Peter C de Bruin, Joost J Oudejans, Luigi Marchionni, Paul J van Diest
Breast cancer research and treatment  ·  13 Apr 2012  ·  pubmed:22527098
Oncogene amplification in male breast cancer: analysis by multiplex ligation-dependent probe amplification
Oncogene amplification in male breast cancer: analysis by multiplex ligation-dependent probe amplification
Robert Kornegoor, Cathy B. Moelans, Anoek H. J. Verschuur-Maes, Marieke C. H. Hogenes, Peter C. de Bruin, Joost J. Oudejans, Luigi Marchionni, Paul J. van Diest
Breast Cancer Research and Treatment  ·  13 Apr 2012  ·  doi:10.1007/s10549-012-2051-3
MYC Is Activated by USP2a-Mediated Modulation of MicroRNAs in Prostate Cancer
MYC Is Activated by USP2a-Mediated Modulation of MicroRNAs in Prostate Cancer
Barbara Benassi, Richard Flavin, Luigi Marchionni, Silvio Zanata, Yunfeng Pan, …, Marina Marani, Sabrina Strano, Paola Muti, Giovanni Blandino, Massimo Loda
Cancer Discovery  ·  01 Mar 2012  ·  doi:10.1158/2159-8290.CD-11-0219
Regulation of lipid metabolism by Dicer revealed through SILAC mice.
Regulation of lipid metabolism by Dicer revealed through SILAC mice.
Tai-Chung Huang, Nandini A Sahasrabuddhe, Min-Sik Kim, Derese Getnet, Yi Yang, …, Raghothama Chaerkady, Steven D Leach, Luigi Marchionni, G William Wong, Akhilesh Pandey
Journal of proteome research  ·  28 Feb 2012  ·  pubmed:22313051
Regulation of Lipid Metabolism by Dicer Revealed through SILAC Mice
Regulation of Lipid Metabolism by Dicer Revealed through SILAC Mice
Tai-Chung Huang, Nandini A. Sahasrabuddhe, Min-Sik Kim, Derese Getnet, Yi Yang, …, Raghothama Chaerkady, Steven D. Leach, Luigi Marchionni, G. William Wong, Akhilesh Pandey
Journal of Proteome Research  ·  28 Feb 2012  ·  doi:10.1021/pr2009884
MYC is activated by USP2a-mediated modulation of microRNAs in prostate cancer.
MYC is activated by USP2a-mediated modulation of microRNAs in prostate cancer.
Barbara Benassi, Richard Flavin, Luigi Marchionni, Silvio Zanata, Yunfeng Pan, …, Marina Marani, Sabrina Strano, Paola Muti, Giovanni Blandino, Massimo Loda
Cancer discovery  ·  05 Jan 2012  ·  pubmed:22585994

2011

Integrating diverse genomic data using gene sets.
Integrating diverse genomic data using gene sets.
Svitlana Tyekucheva, Luigi Marchionni, Rachel Karchin, Giovanni Parmigiani
Genome biology  ·  21 Oct 2011  ·  pubmed:22018358
Integrating diverse genomic data using gene sets
Integrating diverse genomic data using gene sets
Svitlana Tyekucheva, Luigi Marchionni, Rachel Karchin, Giovanni Parmigiani
Genome Biology  ·  21 Oct 2011  ·  doi:10.1186/gb-2011-12-10-r105
Effects of Age and Heart Failure on Human Cardiac Stem Cell Function
Effects of Age and Heart Failure on Human Cardiac Stem Cell Function
Daniela Cesselli, Antonio P. Beltrami, Federica D’Aurizio, Patrizia Marcon, Natascha Bergamin, …, Marcello Rota, Jan Kajstura, Piero Anversa, Carlo A. Beltrami, Annarosa Leri
The American Journal of Pathology  ·  01 Jul 2011  ·  doi:10.1016/j.ajpath.2011.03.036
An EGFR-ERK-SOX9 Signaling Cascade Links Urothelial Development and Regeneration to Cancer
An EGFR-ERK-SOX9 Signaling Cascade Links Urothelial Development and Regeneration to Cancer
Shizhang Ling, Xiaofei Chang, Luciana Schultz, Thomas K. Lee, Alcides Chaux, Luigi Marchionni, George J. Netto, David Sidransky, David M. Berman
Cancer Research  ·  31 May 2011  ·  doi:10.1158/0008-5472.CAN-10-3072
Effects of age and heart failure on human cardiac stem cell function.
Effects of age and heart failure on human cardiac stem cell function.
Daniela Cesselli, Antonio P Beltrami, Federica D’Aurizio, Patrizia Marcon, Natascha Bergamin, …, Marcello Rota, Jan Kajstura, Piero Anversa, Carlo A Beltrami, Annarosa Leri
The American journal of pathology  ·  19 May 2011  ·  pubmed:21703415
In vivo liver regeneration potential of human induced pluripotent stem cells from diverse origins.
In vivo liver regeneration potential of human induced pluripotent stem cells from diverse origins.
Hua Liu, Yonghak Kim, Saul Sharkis, Luigi Marchionni, Yoon-Young Jang
Science translational medicine  ·  11 May 2011  ·  pubmed:21562231
In Vivo Liver Regeneration Potential of Human Induced Pluripotent Stem Cells from Diverse Origins
In Vivo Liver Regeneration Potential of Human Induced Pluripotent Stem Cells from Diverse Origins
Hua Liu, Yonghak Kim, Saul Sharkis, Luigi Marchionni, Yoon-Young Jang
Science Translational Medicine  ·  11 May 2011  ·  doi:10.1126/scitranslmed.3002376
Molecular Effects of Genistein on Male Urethral Development
Molecular Effects of Genistein on Male Urethral Development
Ashley E. Ross, Luigi Marchionni, Timothy M. Phillips, Rebecca M. Miller, Paula J. Hurley, Brian W. Simons, Amirali H. Salmasi, Anthony J. Schaeffer, John P. Gearhart, Edward M. Schaeffer
Journal of Urology  ·  01 May 2011  ·  doi:10.1016/j.juro.2010.12.095
An EGFR-ERK-SOX9 signaling cascade links urothelial development and regeneration to cancer.
An EGFR-ERK-SOX9 signaling cascade links urothelial development and regeneration to cancer.
Shizhang Ling, Xiaofei Chang, Luciana Schultz, Thomas K Lee, Alcides Chaux, Luigi Marchionni, George J Netto, David Sidransky, David M Berman
Cancer research  ·  21 Apr 2011  ·  pubmed:21512138
Molecular effects of genistein on male urethral development.
Molecular effects of genistein on male urethral development.
Ashley E Ross, Luigi Marchionni, Timothy M Phillips, Rebecca M Miller, Paula J Hurley, Brian W Simons, Amirali H Salmasi, Anthony J Schaeffer, John P Gearhart, Edward M Schaeffer
The Journal of urology  ·  21 Mar 2011  ·  pubmed:21421236
Gene expression pathways of high grade localized prostate cancer.
Gene expression pathways of high grade localized prostate cancer.
Ashley E Ross, Luigi Marchionni, Milena Vuica-Ross, Chris Cheadle, Jinshui Fan, David M Berman, Edward M Schaeffer
The Prostate  ·  25 Feb 2011  ·  pubmed:21360566
Gene expression pathways of high grade localized prostate cancer
Gene expression pathways of high grade localized prostate cancer
Ashley E. Ross, Luigi Marchionni, Milena Vuica‐Ross, Chris Cheadle, Jinshui Fan, David M. Berman, Edward M. Schaeffer
The Prostate  ·  25 Feb 2011  ·  doi:10.1002/pros.21373

2010

Dimeric naphthoquinones, a novel class of compounds with prostate cancer cytotoxicity.
Dimeric naphthoquinones, a novel class of compounds with prostate cancer cytotoxicity.
Ashley E Ross, Ashkan Emadi, Luigi Marchionni, Paula J Hurley, Brian W Simons, Edward M Schaeffer, Milena Vuica-Ross
BJU international  ·  22 Dec 2010  ·  pubmed:21176082
Dimeric naphthoquinones, a novel class of compounds with prostate cancer cytotoxicity
Dimeric naphthoquinones, a novel class of compounds with prostate cancer cytotoxicity
Ashley E. Ross, Ashkan Emadi, Luigi Marchionni, Paula J. Hurley, Brian W. Simons, Edward M. Schaeffer, Milena Vuica‐Ross
BJU International  ·  22 Dec 2010  ·  doi:10.1111/j.1464-410X.2010.09907.x
The Notch target Hes1 directly modulates Gli1 expression and Hedgehog signaling: a potential mechanism of therapeutic resistance.
The Notch target Hes1 directly modulates Gli1 expression and Hedgehog signaling: a potential mechanism of therapeutic resistance.
Karisa C Schreck, Pete Taylor, Luigi Marchionni, Vidya Gopalakrishnan, Eli E Bar, Nicholas Gaiano, Charles G Eberhart
Clinical cancer research : an official journal of the American Association for Cancer Research  ·  15 Dec 2010  ·  pubmed:21169257
The Notch Target Hes1 Directly Modulates Gli1 Expression and Hedgehog Signaling: A Potential Mechanism of Therapeutic Resistance
The Notch Target Hes1 Directly Modulates Gli1 Expression and Hedgehog Signaling: A Potential Mechanism of Therapeutic Resistance
Karisa C. Schreck, Pete Taylor, Luigi Marchionni, Vidya Gopalakrishnan, Eli E. Bar, Nicholas Gaiano, Charles G. Eberhart
Clinical Cancer Research  ·  15 Dec 2010  ·  doi:10.1158/1078-0432.CCR-10-1624
A novel role of IL-17 producing lymphocytes in mediating lytic bone disease in multiple myeloma
A novel role of IL-17–producing lymphocytes in mediating lytic bone disease in multiple myeloma
Kimberly Noonan, Luigi Marchionni, Judy Anderson, Drew Pardoll, G. David Roodman, Ivan Borrello
Blood  ·  04 Nov 2010  ·  doi:10.1182/blood-2010-05-283895
Methylation profiles of endometrioid and serous endometrial cancers
Methylation profiles of endometrioid and serous endometrial cancers
Laura M S Seeber, Ronald P Zweemer, Luigi Marchionni, Leon F A G Massuger, Vincent T H B M Smit, W Marchien van Baal, René H M Verheijen, Paul J van Diest
Endocrine-Related Cancer  ·  01 Sep 2010  ·  doi:10.1677/ERC-10-0014
A novel role of IL-17-producing lymphocytes in mediating lytic bone disease in multiple myeloma.
A novel role of IL-17-producing lymphocytes in mediating lytic bone disease in multiple myeloma.
Kimberly Noonan, Luigi Marchionni, Judy Anderson, Drew Pardoll, G David Roodman, Ivan Borrello
Blood  ·  27 Jul 2010  ·  pubmed:20664052
Methylation profiles of endometrioid and serous endometrial cancers.
Methylation profiles of endometrioid and serous endometrial cancers.
Laura M S Seeber, Ronald P Zweemer, Luigi Marchionni, Leon F A G Massuger, Vincent T H B M Smit, W Marchien van Baal, René H M Verheijen, Paul J van Diest
Endocrine-related cancer  ·  25 Jun 2010  ·  pubmed:20488783
Downregulation of homologous recombination DNA repair genes by HDAC inhibition in prostate cancer is mediated through the E2F1 transcription factor.
Downregulation of homologous recombination DNA repair genes by HDAC inhibition in prostate cancer is mediated through the E2F1 transcription factor.
Sushant K Kachhap, Nadine Rosmus, Spencer J Collis, Madeleine S Q Kortenhorst, Michel D Wissing, …, Naseruddin Höti, Johan W R Nortier, Theodore L DeWeese, Hans Hammers, Michael A Carducci
PloS one  ·  18 Jun 2010  ·  pubmed:20585447
Downregulation of Homologous Recombination DNA Repair Genes by HDAC Inhibition in Prostate Cancer Is Mediated through the E2F1 Transcription Factor
Downregulation of Homologous Recombination DNA Repair Genes by HDAC Inhibition in Prostate Cancer Is Mediated through the E2F1 Transcription Factor
Sushant K. Kachhap, Nadine Rosmus, Spencer J. Collis, Madeleine S. Q. Kortenhorst, Michel D. Wissing, …, Naseruddin Höti, Johan W. R. Nortier, Theodore L. DeWeese, Hans Hammers, Michael A. Carducci
PLoS ONE  ·  18 Jun 2010  ·  doi:10.1371/journal.pone.0011208

2009

The ordering of expression among a few genes can provide simple cancer biomarkers and signal BRCA1 mutations.
The ordering of expression among a few genes can provide simple cancer biomarkers and signal BRCA1 mutations.
Xue Lin, Bahman Afsari, Luigi Marchionni, Leslie Cope, Giovanni Parmigiani, Daniel Naiman, Donald Geman
BMC bioinformatics  ·  20 Aug 2009  ·  pubmed:19695104
The ordering of expression among a few genes can provide simple cancer biomarkers and signal BRCA1 mutations
The ordering of expression among a few genes can provide simple cancer biomarkers and signal BRCA1 mutations
Xue Lin, Bahman Afsari, Luigi Marchionni, Leslie Cope, Giovanni Parmigiani, Daniel Naiman, Donald Geman
BMC Bioinformatics  ·  20 Aug 2009  ·  doi:10.1186/1471-2105-10-256
Differentiation of a highly tumorigenic basal cell compartment in urothelial carcinoma.
Differentiation of a highly tumorigenic basal cell compartment in urothelial carcinoma.
Xiaobing He, Luigi Marchionni, Donna E Hansel, Wayne Yu, Akshay Sood, Jie Yang, Giovanni Parmigiani, William Matsui, David M Berman
Stem cells (Dayton, Ohio)  ·  01 Jul 2009  ·  pubmed:19544456
A primary xenograft model of small-cell lung cancer reveals irreversible changes in gene expression imposed by culture in vitro
A primary xenograft model of small-cell lung cancer reveals irreversible changes in gene expression imposed by culture in vitro
Vincent C Daniel, Luigi Marchionni, Jared S Hierman, Jonathan T Rhodes, Wendy L Devereux, …, Rex Yung, Giovanni Parmigiani, Marion Dorsch, Craig D Peacock, D Neil Watkins
Cancer research  ·  15 Apr 2009  ·  pmc:PMC2821899
A Primary Xenograft Model of Small-Cell Lung Cancer Reveals Irreversible Changes in Gene Expression Imposed by Culture i In vitro i
A Primary Xenograft Model of Small-Cell Lung Cancer Reveals Irreversible Changes in Gene Expression Imposed by CultureIn vitro
Vincent C. Daniel, Luigi Marchionni, Jared S. Hierman, Jonathan T. Rhodes, Wendy L. Devereux, …, Rex Yung, Giovanni Parmigiani, Marion Dorsch, Craig D. Peacock, D. Neil Watkins
Cancer Research  ·  15 Apr 2009  ·  doi:10.1158/0008-5472.CAN-08-4210
Differentiation of a Highly Tumorigenic Basal Cell Compartment in Urothelial Carcinoma
Differentiation of a Highly Tumorigenic Basal Cell Compartment in Urothelial Carcinoma
Xiaobing He, Luigi Marchionni, Donna E. Hansel, Wayne Yu, Akshay Sood, Jie Yang, Giovanni Parmigiani, William Matsui, David M. Berman
Stem Cells  ·  09 Apr 2009  ·  doi:10.1002/stem.92

2008

Androgen-induced programs for prostate epithelial growth and invasion arise in embryogenesis and are reactivated in cancer
Androgen-induced programs for prostate epithelial growth and invasion arise in embryogenesis and are reactivated in cancer
E M Schaeffer, L Marchionni, Z Huang, B Simons, A Blackman, W Yu, G Parmigiani, D M Berman
Oncogene  ·  15 Sep 2008  ·  doi:10.1038/onc.2008.327
Systematic review: gene expression profiling assays in early-stage breast cancer.
Systematic review: gene expression profiling assays in early-stage breast cancer.
Luigi Marchionni, Renee F Wilson, Antonio C Wolff, Spyridon Marinopoulos, Giovanni Parmigiani, Eric B Bass, Steven N Goodman
Annals of internal medicine  ·  04 Feb 2008  ·  pubmed:18252678
review breast-cancer gene-expression prediction

2007

Impact of gene expression profiling tests on breast cancer outcomes.
Impact of gene expression profiling tests on breast cancer outcomes.
Luigi Marchionni, Renee F Wilson, Spyridon S Marinopoulos, Antonio C Wolff, Giovanni Parmigiani, Eric B Bass, Steven N Goodman
Evidence report/technology assessment  ·  01 Dec 2007  ·  pubmed:18457476
review gene-expression breast-cancer prediction

2005

Discovery of 342 putative new genes from the analysis of 5 -end-sequenced full-length-enriched cDNA human transcripts
Discovery of 342 putative new genes from the analysis of 5′-end-sequenced full-length-enriched cDNA human transcripts
E. Dalla, F. Mignone, R. Verardo, L. Marchionni, S. Marzinotto, …, G. Marcuzzi, R. Gambetta, M.A. Pierotti, G. Pesole, C. Schneider
Genomics  ·  01 Jun 2005  ·  doi:10.1016/j.ygeno.2005.02.009

2004

Gene expression profiling of advanced ovarian cancer: characterization of a molecular signature involving fibroblast growth factor 2.
Gene expression profiling of advanced ovarian cancer: characterization of a molecular signature involving fibroblast growth factor 2.
Loris De Cecco, Luigi Marchionni, Manuela Gariboldi, James F Reid, M Stefania Lagonigro, …, Francesco Raspagliesi, Silvana Pilotti, Marco A Pierotti, Silvana Canevari, Claudio Schneider
Oncogene  ·  21 Oct 2004  ·  pubmed:15377994
Gene expression profiling of advanced ovarian cancer: characterization of a molecular signature involving fibroblast growth factor 2
Gene expression profiling of advanced ovarian cancer: characterization of a molecular signature involving fibroblast growth factor 2
Loris De Cecco, Luigi Marchionni, Manuela Gariboldi, James F Reid, M Stefania Lagonigro, …, Francesco Raspagliesi, Silvana Pilotti, Marco A Pierotti, Silvana Canevari, Claudio Schneider
Oncogene  ·  20 Sep 2004  ·  doi:10.1038/sj.onc.1207979
hGTSE-1 Expression Stimulates Cytoplasmic Localization of p53
hGTSE-1 Expression Stimulates Cytoplasmic Localization of p53
Martin Monte, Roberta Benetti, Licio Collavin, Luigi Marchionni, Giannino Del Sal, Claudio Schneider
Journal of Biological Chemistry  ·  01 Mar 2004  ·  doi:10.1074/jbc.M311123200
hGTSE-1 expression stimulates cytoplasmic localization of p53.
hGTSE-1 expression stimulates cytoplasmic localization of p53.
Martin Monte, Roberta Benetti, Licio Collavin, Luigi Marchionni, Giannino Del Sal, Claudio Schneider
The Journal of biological chemistry  ·  05 Jan 2004  ·  pubmed:14707141

2003

LNCIB human full-length cDNAs collection: towards a better comprehension of the human transcriptome
LNCIB human full-length cDNAs collection: towards a better comprehension of the human transcriptome
Emiliano Dalla, Roberto Verardo, Dejan Lazarević, Luigi Marchionni, James F. Reid, …, Giacomo Marcuzzi, Riccardo Marzio, Anna Belgrano, Danilo Licastro, Claudio Schneider
Comptes Rendus. Biologies  ·  01 Oct 2003  ·  doi:10.1016/j.crvi.2003.09.029
LNCIB human full-length cDNAs collection: towards a better comprehension of the human transcriptome.
LNCIB human full-length cDNAs collection: towards a better comprehension of the human transcriptome.
Emiliano Dalla, Roberto Verardo, Dejan Lazarević, Luigi Marchionni, James F Reid, …, Giacomo Marcuzzi, Riccardo Marzio, Anna Belgrano, Danilo Licastro, Claudio Schneider
Comptes rendus biologies  ·  01 Jan 2003  ·  pubmed:14744102

2002

Analysis of the mouse transcriptome based on functional annotation of 60,770 full-length cDNAs
Analysis of the mouse transcriptome based on functional annotation of 60,770 full-length cDNAs
Nature  ·  01 Dec 2002  ·  doi:10.1038/nature01266

2001

Functional annotation of a full-length mouse cDNA collection
Functional annotation of a full-length mouse cDNA collection
J. Kawai, A. Shinagawa, K. Shibata, M. Yoshino, M. Itoh, …, K. Yoshida, Y. Hasegawa, H. Kawaji, S. Kohtsuki, Y. Hayashizaki
Nature  ·  08 Feb 2001  ·  doi:10.1038/35055500

The citations on this page were generated automatically from just identifiers using the Manubot cite utility developed by the Greene Lab!