@article{gong2021cross-oncopanel,

title = {Cross-oncopanel study reveals high sensitivity and accuracy with overall analytical performance depending on genomic regions},

author = {Binsheng Gong and Dan Li and Rebecca Kusko and Natalia Novoradovskaya and Yifan Zhang and Shangzi Wang and Carlos Pabón-Pe na and Zhihong Zhang and Kevin Lai and Wanshi Cai and Jennifer S. LoCoco and Eric Lader and Todd A. Richmond and Vinay K. Mittal and Liang-Chun Liu and Donald J. Johann and James C. Willey and Pierre R. Bushel and Ying Yu and Chang Xu and Guangchun Chen and Daniel Burgess and Simon Cawley and Kristina Giorda and Nathan Haseley and Fujun Qiu and Katherine Wilkins and Hanane Arib and Claire Attwooll and Kevin Babson and Longlong Bao and Wenjun Bao and Anne Bergstrom Lucas and Hunter Best and Ambica Bhandari and Halil Bisgin and James Blackburn and Thomas M. Blomquist and Lisa Boardman and Blake Burgher and Daniel J. Butler and Chia-Jung Chang and Alka Chaubey and Tao Chen and Marco Chierici and Christopher R. Chin and Devin Close and Jeffrey Conroy and Jessica Cooley Coleman and Daniel J. Craig and Erin Crawford and Angela Pozo and Ira W. Deveson and Daniel Duncan and Agda Karina Eterovic and Xiaohui Fan and Jonathan Foox and Cesare Furlanello and Abhisek Ghosal and Sean Glenn and Meijian Guan and Christine Haag and Xinyi Hang and Scott Happe and Brittany Hennigan and Jennifer Hipp and Huixiao Hong and Kyle Horvath and Jianhong Hu and Li-Yuan Hung and Mirna Jarosz and Jennifer Kerkhof and Benjamin Kipp and David Philip Kreil and Paweł Łabaj and Pablo Lapunzina and Peng Li and Quan-Zhen Li and Weihua Li and Zhiguang Li and Yu Liang and Shaoqing Liu and Zhichao Liu and Charles Ma and Narasimha Marella and Rubén Mart'in-Arenas and Dalila B. Megherbi and Qingchang Meng and Piotr A. Mieczkowski and Tom Morrison and Donna Muzny and Baitang Ning and Barbara L. Parsons and Cloud P. Paweletz and Mehdi Pirooznia and Wubin Qu and Amelia Raymond and Paul Rindler and Rebecca Ringler and Bekim Sadikovic and Andreas Scherer and Egbert Schulze and Robert Sebra and Rita Shaknovich and Qiang Shi and Tieliu Shi and Juan Carlos Silla-Castro and Melissa Smith and Mario Sol'is López and Ping Song and Daniel Stetson and Maya Strahl and Alan Stuart and Julianna Supplee and Philippe Szankasi and Haowen Tan and Lin-ya Tang and Yonghui Tao and Shraddha Thakkar and Danielle Thierry-Mieg and Jean Thierry-Mieg and Venkat J. Thodima and David Thomas and Boris Tich'y and Nikola Tom and Elena Vallespin Garcia and Suman Verma and Kimbley Walker and Charles Wang and Junwen Wang and Yexun Wang and Zhining Wen and Valtteri Wirta and Leihong Wu and Chunlin Xiao and Wenzhong Xiao and Shibei Xu and Mary Yang and Jianming Ying and Shun H. Yip and Guangliang Zhang and Sa Zhang and Meiru Zhao and Yuanting Zheng and Xiaoyan Zhou and Christopher E. Mason and Timothy Mercer and Weida Tong and Leming Shi and Wendell Jones and Joshua Xu},

year  = {2021},

date = {2021-01-01},

journal = {Genome Biology},

volume = {22},

number = {1},

pages = {109},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{jones2021verified,

title = {A verified genomic reference sample for assessing performance of cancer panels detecting small variants of low allele frequency},

author = {Wendell Jones and Binsheng Gong and Natalia Novoradovskaya and Dan Li and Rebecca Kusko and Todd A. Richmond and Donald J. Johann and Halil Bisgin and Sayed Mohammad Ebrahim Sahraeian and Pierre R. Bushel and Mehdi Pirooznia and Katherine Wilkins and Marco Chierici and Wenjun Bao and Lee Scott Basehore and Anne Bergstrom Lucas and Daniel Burgess and Daniel J. Butler and Simon Cawley and Chia-Jung Chang and Guangchun Chen and Tao Chen and Yun-Ching Chen and Daniel J. Craig and Angela Pozo and Jonathan Foox and Margherita Francescatto and Yutao Fu and Cesare Furlanello and Kristina Giorda and Kira P. Grist and Meijian Guan and Yingyi Hao and Scott Happe and Gunjan Hariani and Nathan Haseley and Jeff Jasper and Giuseppe Jurman and David Philip Kreil and Paweł Łabaj and Kevin Lai and Jianying Li and Quan-Zhen Li and Yulong Li and Zhiguang Li and Zhichao Liu and Mario Sol'is López and Kelci Miclaus and Raymond Miller and Vinay K. Mittal and Marghoob Mohiyuddin and Carlos Pabón-Pe na and Barbara L. Parsons and Fujun Qiu and Andreas Scherer and Tieliu Shi and Suzy Stiegelmeyer and Chen Suo and Nikola Tom and Dong Wang and Zhining Wen and Leihong Wu and Wenzhong Xiao and Chang Xu and Ying Yu and Jiyang Zhang and Yifan Zhang and Zhihong Zhang and Yuanting Zheng and Christopher E. Mason and James C. Willey and Weida Tong and Leming Shi and Joshua Xu},

year  = {2021},

date = {2021-01-01},

journal = {Genome Biology},

volume = {22},

number = {1},

pages = {1--38},

publisher = {BioMed Central},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{melaiu2020cellular,

title = {Cellular and gene signatures of tumor-infiltrating dendritic cells and natural-killer cells predict prognosis of neuroblastoma},

author = {Ombretta Melaiu and Marco Chierici and Valeria Lucarini and Giuseppe Jurman and Libenzio Adrian Conti and Rita De Vito and Renata Boldrini and Loredana Cifaldi and Aurora Castellano and Cesare Furlanello and Vincenzo Barnaba and Franco Locatelli and Doriana Fruci},

year  = {2020},

date = {2020-01-01},

journal = {Nature Communications},

volume = {11},

number = {1},

pages = {5992},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{chierici2020integrative,

title = {Integrative Network Fusion: A Multi-Omics Approach in Molecular Profiling},

author = {Marco Chierici and Nicole Bussola and Alessia Marcolini and Margherita Francescatto and Alessandro Zandon`a and Lucia Trastulla and Claudio Agostinelli and Giuseppe Jurman and Cesare Furlanello},

year  = {2020},

date = {2020-01-01},

journal = {Frontiers in Oncology},

volume = {10},

pages = {1065},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{chierici2020predictability,

title = {Predictability of drug-induced liver injury by machine learning},

author = {Marco Chierici and Margherita Francescatto and Nicole Bussola and Giuseppe Jurman and Cesare Furlanello},

year  = {2020},

date = {2020-01-01},

journal = {Biology Direct},

volume = {15},

number = {1},

pages = {3},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{polano2019pan,

title = {A Pan-Cancer Approach to Predict Responsiveness to Immune Checkpoint Inhibitors by Machine Learning},

author = {Maurizio Polano and Marco Chierici and Michele Dal Bo and Davide Gentilini and Federica Di Cintio and Lorena Baboci and David L Gibbs and Cesare Furlanello and Giuseppe Toffoli},

year  = {2019},

date = {2019-01-01},

journal = {Cancers},

volume = {11},

number = {10},

pages = {1562},

publisher = {Multidisciplinary Digital Publishing Institute},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{bizzego2019evaluating,

title = {Evaluating reproducibility of AI algorithms in digital pathology with DAPPER},

author = {Andrea Bizzego and Nicole Bussola and Marco Chierici and Valerio Maggio and Margherita Francescatto and Luca Cima and Marco Cristoforetti and Giuseppe Jurman and Cesare Furlanello},

year  = {2019},

date = {2019-01-01},

journal = {PLoS computational biology},

volume = {15},

number = {3},

pages = {e1006269},

publisher = {Public Library of Science},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{boldrini2019tumor,

title = {Tumor-infiltrating T cells and PD-L1 expression in childhood malignant extracranial germ-cell tumors},

author = {Renata Boldrini and Maria Debora De Pasquale and Ombretta Melaiu and Marco Chierici and Giuseppe Jurman and Maria Chiara Benedetti and Nunzio C Salfi and Aurora Castellano and Paola Collini and Cesare Furlanello and others},

year  = {2019},

date = {2019-01-01},

journal = {OncoImmunology},

volume = {8},

number = {2},

pages = {e1542245},

publisher = {Taylor & Francis},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{chierici2018machine,

title = {Machine learning models for predicting endocrine disruption potential of environmental chemicals},

author = {Marco Chierici and Marco Giulini and Nicole Bussola and Giuseppe Jurman and Cesare Furlanello},

year  = {2018},

date = {2018-01-01},

journal = {Journal of Environmental Science and Health, Part C},

pages = {1--15},

publisher = {Taylor & Francis},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{maggio2018distillation,

title = {Distillation of the clinical algorithm improves prognosis by multi-task deep learning in high-risk Neuroblastoma},

author = {Valerio Maggio and Marco Chierici and Giuseppe Jurman and Cesare Furlanello},

year  = {2018},

date = {2018-01-01},

journal = {PloS ONE},

volume = {13},

number = {12},

pages = {e0208924},

publisher = {Public Library of Science},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{fioravanti2018phylogenetic,

title = {Phylogenetic convolutional neural networks in metagenomics},

author = {Diego Fioravanti and Ylenia Giarratano and Valerio Maggio and Claudio Agostinelli and Marco Chierici and Giuseppe Jurman and Cesare Furlanello},

year  = {2018},

date = {2018-01-01},

journal = {BMC bioinformatics},

volume = {19},

number = {2},

pages = {49},

publisher = {BioMed Central},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{francescatto2018multi,

title = {Multi-omics integration for neuroblastoma clinical endpoint prediction},

author = {Margherita Francescatto and Marco Chierici and Setareh Rezvan Dezfooli and Alessandro Zandon`a and Giuseppe Jurman and Cesare Furlanello},

year  = {2018},

date = {2018-01-01},

journal = {Biology direct},

volume = {13},

number = {1},

pages = {5},

publisher = {BioMed Central},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{melaiu2017pd,

title = {PD-L1 is a therapeutic target of the bromodomain inhibitor JQ1 and, combined with HLA class I, a promising prognostic biomarker in neuroblastoma},

author = {Ombretta Melaiu and Marco Mina and Marco Chierici and Renata Boldrini and Giuseppe Jurman and Paolo Romania and Valerio D'Alicandro and Maria C Benedetti and Aurora Castellano and Tao Liu and others},

year  = {2017},

date = {2017-01-01},

journal = {Clinical Cancer Research},

volume = {23},

number = {15},

pages = {4462--4472},

publisher = {AACR},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{gnani2017focal,

title = {Focal adhesion kinase depletion reduces human hepatocellular carcinoma growth by repressing enhancer of zeste homolog},

author = {Daniela Gnani and Ilaria Romito and Simona Artuso and Marco Chierici and Cristiano De Stefanis and Nadia Panera and Annalisa Crudele and Sara Ceccarelli and Elena Carcarino and Valentina D'Oria and Manuela Porru and Ezio Giorda and Karin Ferrari and Luca Miele and Erica Villa and Clara Balsano and Diego Pasini and Cesare Furlanello and Franco Locatelli and Valerio Nobili and Rossella Rota and Carlo Leonetti and Anna Alisi},

year  = {2017},

date = {2017-01-01},

journal = {Cell Death and Differentiation},

volume = {24},

pages = {889--902},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{mortera2016monitoring,

title = {Monitoring perinatal gut microbiota in mouse models by mass spectrometry approaches: parental genetic background and breastfeeding effects},

author = {Stefano Levi Mortera and Federica Del Chierico and Pamela Vernocchi and Maria M Rosado and Agnese Cavola and Marco Chierici and Luisa Pieroni and Andrea Urbani and Rita Carsetti and Isabella Lante and others},

year  = {2016},

date = {2016-01-01},

journal = {Frontiers in Microbiology},

volume = {7},

publisher = {Frontiers Media SA},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{hurst2015constrained,

title = {The constrained maximal expression level owing to haploidy shapes gene content on the mammalian X chromosome},

author = {Laurence D Hurst and Avazeh T Ghanbarian and Alistair RR Forrest and FANTOM consortium and Lukasz Huminiecki},

year  = {2015},

date = {2015-01-01},

journal = {PLoS biology},

volume = {13},

number = {12},

pages = {e1002315},

publisher = {Public Library of Science San Francisco, CA USA},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{zhang2015comparison,

title = {Comparison of RNA-seq and microarray-based models for clinical endpoint prediction},

author = {Wenqian Zhang and Ying Yu and Falk Hertwig and Jean Thierry-Mieg and Wenwei Zhang and Danielle Thierry-Mieg and Jian Wang and Cesare Furlanello and Viswanath Devanarayan and Jie Cheng and others},

year  = {2015},

date = {2015-01-01},

journal = {Genome biology},

volume = {16},

number = {1},

pages = {133},

publisher = {BioMed Central},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{demariano2015identification,

title = {Identification of GALNT14 as a novel neuroblastoma predisposition gene},

author = {Marilena De Mariano and Roberta Gallesio and Marco Chierici and Cesare Furlanello and Massimo Conte and Alberto Garaventa and Michela Croce and Silvano Ferrini and Gian Paolo Tonini and Luca Longo},

year  = {2015},

date = {2015-01-01},

journal = {Oncotarget},

volume = {6},

number = {28},

pages = {26335},

publisher = {Impact Journals, LLC},

keywords = {},

pubstate = {published},

tppubtype = {article}

}