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

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

2024

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
Cold Spring Harbor Laboratory  ·  31 Aug 2024  ·  doi:10.1101/2024.08.30.24312735
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
Artificial intelligence applications in histopathology
Artificial intelligence applications in histopathology
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
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 spatial-transcriptomics

2023

Supplementary Vignette 3 from Building Tools for Machine Learning and Artificial Intelligence in Cancer Research: Best Practices and a Case Study with the PathML Toolkit for Computational Pathology
Supplementary Vignette 3 from 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
American Association for Cancer Research (AACR)  ·  15 Dec 2023  ·  doi:10.1158/1541-7786.24833350.v1
Supplementary Vignette 3 from Building Tools for Machine Learning and Artificial Intelligence in Cancer Research: Best Practices and a Case Study with the PathML Toolkit for Computational Pathology
Supplementary Vignette 3 from 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
American Association for Cancer Research (AACR)  ·  15 Dec 2023  ·  doi:10.1158/1541-7786.24833350
Supplementary Vignette 2 from Building Tools for Machine Learning and Artificial Intelligence in Cancer Research: Best Practices and a Case Study with the PathML Toolkit for Computational Pathology
Supplementary Vignette 2 from 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
American Association for Cancer Research (AACR)  ·  15 Dec 2023  ·  doi:10.1158/1541-7786.24833353
Supplementary Vignette 2 from Building Tools for Machine Learning and Artificial Intelligence in Cancer Research: Best Practices and a Case Study with the PathML Toolkit for Computational Pathology
Supplementary Vignette 2 from 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
American Association for Cancer Research (AACR)  ·  15 Dec 2023  ·  doi:10.1158/1541-7786.24833353.v1
Supplementary Vignette 1 from Building Tools for Machine Learning and Artificial Intelligence in Cancer Research: Best Practices and a Case Study with the PathML Toolkit for Computational Pathology
Supplementary Vignette 1 from 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
American Association for Cancer Research (AACR)  ·  15 Dec 2023  ·  doi:10.1158/1541-7786.24833356
Supplementary Vignette 1 from Building Tools for Machine Learning and Artificial Intelligence in Cancer Research: Best Practices and a Case Study with the PathML Toolkit for Computational Pathology
Supplementary Vignette 1 from 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
American Association for Cancer Research (AACR)  ·  15 Dec 2023  ·  doi:10.1158/1541-7786.24833356.v1
Supplementary Table 1 from Building Tools for Machine Learning and Artificial Intelligence in Cancer Research: Best Practices and a Case Study with the PathML Toolkit for Computational Pathology
Supplementary Table 1 from 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
American Association for Cancer Research (AACR)  ·  15 Dec 2023  ·  doi:10.1158/1541-7786.24833359
Supplementary Table 1 from Building Tools for Machine Learning and Artificial Intelligence in Cancer Research: Best Practices and a Case Study with the PathML Toolkit for Computational Pathology
Supplementary Table 1 from 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
American Association for Cancer Research (AACR)  ·  15 Dec 2023  ·  doi:10.1158/1541-7786.24833359.v1
Supplementary Figure 1 from Building Tools for Machine Learning and Artificial Intelligence in Cancer Research: Best Practices and a Case Study with the PathML Toolkit for Computational Pathology
Supplementary Figure 1 from 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
American Association for Cancer Research (AACR)  ·  15 Dec 2023  ·  doi:10.1158/1541-7786.24833362
Supplementary Figure 1 from Building Tools for Machine Learning and Artificial Intelligence in Cancer Research: Best Practices and a Case Study with the PathML Toolkit for Computational Pathology
Supplementary Figure 1 from 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
American Association for Cancer Research (AACR)  ·  15 Dec 2023  ·  doi:10.1158/1541-7786.24833362.v1
Data from Building Tools for Machine Learning and Artificial Intelligence in Cancer Research: Best Practices and a Case Study with the PathML Toolkit for Computational Pathology
Data from 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
American Association for Cancer Research (AACR)  ·  15 Dec 2023  ·  doi:10.1158/1541-7786.c.6983057.v1
Data from Building Tools for Machine Learning and Artificial Intelligence in Cancer Research: Best Practices and a Case Study with the PathML Toolkit for Computational Pathology
Data from 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
American Association for Cancer Research (AACR)  ·  15 Dec 2023  ·  doi:10.1158/1541-7786.c.6983057
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 structural-variants
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
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
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
Supplementary Tables S1-S2, Supplementary Figures S1-S5 from PDCD4 Is an Androgen-Repressed Tumor Suppressor that Regulates Prostate Cancer Growth and Castration Resistance
Supplementary Tables S1-S2, Supplementary Figures S1-S5 from 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
American Association for Cancer Research (AACR)  ·  03 Apr 2023  ·  doi:10.1158/1541-7786.22512904.v1
Supplementary Tables S1-S2, Supplementary Figures S1-S5 from PDCD4 Is an Androgen-Repressed Tumor Suppressor that Regulates Prostate Cancer Growth and Castration Resistance
Supplementary Tables S1-S2, Supplementary Figures S1-S5 from 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
American Association for Cancer Research (AACR)  ·  03 Apr 2023  ·  doi:10.1158/1541-7786.22512904
Supplemental Figures 1 - 6 from Ezrin Promotes Stem Cell Properties in Pancreatic Ductal Adenocarcinoma
Supplemental Figures 1 - 6 from 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
American Association for Cancer Research (AACR)  ·  03 Apr 2023  ·  doi:10.1158/1541-7786.22513348
Supplemental Figures 1 - 6 from Ezrin Promotes Stem Cell Properties in Pancreatic Ductal Adenocarcinoma
Supplemental Figures 1 - 6 from 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
American Association for Cancer Research (AACR)  ·  03 Apr 2023  ·  doi:10.1158/1541-7786.22513348.v1
Data from PDCD4 Is an Androgen-Repressed Tumor Suppressor that Regulates Prostate Cancer Growth and Castration Resistance
Data from 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
American Association for Cancer Research (AACR)  ·  03 Apr 2023  ·  doi:10.1158/1541-7786.c.6540367
Data from PDCD4 Is an Androgen-Repressed Tumor Suppressor that Regulates Prostate Cancer Growth and Castration Resistance
Data from 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
American Association for Cancer Research (AACR)  ·  03 Apr 2023  ·  doi:10.1158/1541-7786.c.6540367.v1
Data from Ezrin Promotes Stem Cell Properties in Pancreatic Ductal Adenocarcinoma
Data from 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
American Association for Cancer Research (AACR)  ·  03 Apr 2023  ·  doi:10.1158/1541-7786.c.6540496
Data from Ezrin Promotes Stem Cell Properties in Pancreatic Ductal Adenocarcinoma
Data from 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
American Association for Cancer Research (AACR)  ·  03 Apr 2023  ·  doi:10.1158/1541-7786.c.6540496.v1
Supplementary Data from Newly Identified Members of FGFR1 Splice Variants Engage in Cross-talk with AXL AKT Axis in Salivary Adenoid Cystic Carcinoma
Supplementary Data from 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
American Association for Cancer Research (AACR)  ·  31 Mar 2023  ·  doi:10.1158/0008-5472.22426882.v1
Supplementary Data from Newly Identified Members of FGFR1 Splice Variants Engage in Cross-talk with AXL AKT Axis in Salivary Adenoid Cystic Carcinoma
Supplementary Data from 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
American Association for Cancer Research (AACR)  ·  31 Mar 2023  ·  doi:10.1158/0008-5472.22426882
Data from Newly Identified Members of FGFR1 Splice Variants Engage in Cross-talk with AXL AKT Axis in Salivary Adenoid Cystic Carcinoma
Data from 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
American Association for Cancer Research (AACR)  ·  31 Mar 2023  ·  doi:10.1158/0008-5472.c.6512485
Data from Newly Identified Members of FGFR1 Splice Variants Engage in Cross-talk with AXL AKT Axis in Salivary Adenoid Cystic Carcinoma
Data from 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
American Association for Cancer Research (AACR)  ·  31 Mar 2023  ·  doi:10.1158/0008-5472.c.6512485.v1
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

2022

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
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
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

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  ·  08 Dec 2021  ·  doi:10.1158/1541-7786.MCR-21-0665
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
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
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
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
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
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
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
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
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

2020

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
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
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

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
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
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

2018

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
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 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

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 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
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
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  ·  doi:10.1371/journal.pone.0175860
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

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
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
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  ·  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  ·  doi:10.1186/s12918-015-0225-4
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
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
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 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  ·  doi:10.1126/scitranslmed.aaa5731
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 & 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  ·  22 Dec 2014  ·  doi:10.1073/pnas.1421839112
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  ·  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

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 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  ·  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
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
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

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  ·  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
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
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  ·  doi:10.1021/pr2009884

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  ·  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
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
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  ·  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  ·  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
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  ·  doi:10.1186/1471-2105-10-256
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

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  ·  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

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

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!