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 Q. Naiman; Donald Geman (BMC Bioinform., 2009)

switchBox: an R package for k-Top Scoring Pairs classifier development. - Bahman Afsari; Elana J. Fertig; Donald Geman; Luigi Marchionni (Bioinform., 2015)

A multi-omic analysis of human naïve CD4+ T cells. - Christopher J. Mitchell; Derese Getnet; Min Sik Kim; Srinivas Manda Srikanth; Praveen Kumar; Tai-Chung Huang; Sneha M. Pinto; Nirujogi Raja Sekhar; Mio Iwasaki; Patrick G. Shaw; Xinyan Wu; Jun Zhong; et al. (BMC Syst. Biol., 2015)

PatternMarkers & GWCoGAPS for novel data-driven biomarkers via whole transcriptome NMF. - Genevieve L. Stein-O'Brien; Jacob L. Carey; Waishing Lee; Michael Considine; Alexander V. Favorov; Emily Flam; Theresa Guo; Sijia Li; Luigi Marchionni; Thomas Sherman; Shawn Sivy; Daria A. Gaykalova; et al. (Bioinform., 2017)

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 J. Biol. Databases Curation, 2021)

A field guide to cultivating computational biology. - Anne E. Carpenter; Casey S. Greene; Piero Carnici; Benilton S. Carvalho; Michiel de Hoon; Stacey D. Finley; Kim-Anh Lê Cao; Jerry S. H. Lee; Luigi Marchionni; Suzanne Sindi; Fabian J. Theis; Gregory P. Way; et al. (CoRR, 2021)

Efficient representations of tumor diversity with paired DNA-RNA aberrations. - Qian Ke; Wikum Dinalankara; Laurent Younes; Donald Geman; Luigi Marchionni (PLoS Comput. Biol., 2021)

Whole Slide Image to DICOM Conversion as Event-Driven Cloud Infrastructure. - David Brundage; Jacob Rosenthal; Ryan Carelli; Sophie Rand; Renato Umeton; Massimo Loda; Luigi Marchionni (CoRR, 2022)

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; Eddie Luidy Imada; Luigi Marchionni; Luiz-Eduardo Del-Bem; Anderson Vieira Chaves; Gabriel Magno de Freitas Almeida; Felipe Campelo; Francisco Pereira Lobo (Patterns, 2023)

Federated benchmarking of medical artificial intelligence with MedPerf. - Alexandros Karargyris; Renato Umeton; Micah J. Sheller; Alejandro Aristizabal; Johnu George; Anna Wuest; Sarthak Pati; Hasan Kassem; Maximilian Zenk; Ujjwal Baid; Prakash Narayana Moorthy; Alexander Chowdhury; et al. (Nat. Mac. Intell., 2023)

Multiplex Imaging Analysis in Pathology: a Comprehensive Review on Analytical Approaches and Digital Toolkits. - Mohamed Omar; Giuseppe Nicoló Fanelli; Fabio Socciarelli; Varun Ullanat; Sreekar Reddy Puchala; James Wen; Alexander Chowdhury; Itzel Valencia; Cristian Scatena; Luigi Marchionni; Renato Umeton; Massimo Loda (CoRR, 2024)