PUBLICATIONS

Original Research in Google Scholar and PubMed

2018

Pea A*, Yu J*, Marchionni L*, Noe M, Luchini C, Pulvirenti A, de Wilde RF, Brosens LA, Rezaee N, Javed A, Gobbo S, Regi P, Salvia R, Bassi C, He J, Weiss MJ, Cameron JL, Offerhaus GJA, Hruban RH, Lawlor RT, Scarpa A, Heaphy CM, Wood LD, Wolfgang CL. Genetic Analysis of Small Well-differentiated Pancreatic Neuroendocrine Tumors Identifies Subgroups With Differing Risks of Liver Metastases. Ann Surg. 2018 Oct 17. doi: 10.1097/SLA.0000000000003022. [Epub ahead of print] PubMed PMID: 30339629
*Equally contributing first authorr
Kumar B, Rosenberg AZ, Choi SM, Fox-Talbot K, De Marzo AM, Nonn L, Brennen WN, Marchionni L, Halushka MK, Lupold SE. Cell-type specific expression of oncogenic and tumor suppressive microRNAs in the human prostate and prostate cancer. Sci Rep. 2018 May 8;8(1):7189. doi:10.1038/s41598-018-25320-z. PMID: 29739972; PMCID: PMC5940660.
Munari E, Zamboni G, Lunardi G, Marchionni L, Marconi M, Sommaggio M, Brunelli M, Martignoni G, Netto GJ, Hoque MO, Moretta F, Mingari MC, Pegoraro MC, Inno A, Paiano S, Terzi A, Cavazza A, Rossi G, Mariotti FR, Vacca P, Moretta L, Bogina G. PD-L1 Expression Heterogeneity in Non-Small Cell Lung Cancer: Defining Criteria for Harmonization between Biopsy Specimens and Whole Sections. J Thorac Oncol. 2018 Aug;13(8):1113-1120. doi:10.1016/j.jtho.2018.04.017. Epub 2018 Apr 25. PMID: 29704674.
Hata T, Suenaga M, Marchionni L, Macgregor-Das A, Yu J, Shindo K, Tamura K, Hruban RH, Goggins M. Genome-Wide Somatic Copy Number Alterations and Mutations in High-Grade Pancreatic Intraepithelial Neoplasia. Am J Pathol. 2018 Jul;188(7):1723-1733. doi:10.1016/j.ajpath.2018.03.012. Epub 2018 Apr 22. PMID: 29684357; PMCID: PMC6024190.
Dinalankara W, Ke Q, Xu Y, Ji L, Pagane N, Lien A, Matam T, Fertig EJ, Price ND, Younes L, Marchionni L*§, Geman D*. Digitizing omics profiles by divergence from a baseline. Proc Natl Acad Sci U S A. 2018 May 1;115(18):4545-4552. doi:10.1073/pnas.1721628115. Epub 2018 Apr 16. PMID: 29666255; PMCID: PMC5939095.
*Equally contributing senior author and §Co-corresponding author
Lau BW, Huh K, Madero-Marroquin R, De Marchi F, Lim Y, Wang Q, Lobo F, Marchionni L, Smith DB, DeZern A, Levis MJ, Aplan PD, Matsui W, Gondek LP. Hedgehog/GLI1 activation leads to leukemic transformation of myelodysplastic syndrome in vivo and GLI1 inhibition results in antitumor activity. Oncogene. 2018 Aug 31. doi:10.1038/s41388-018-0431-9. [Epub ahead of print] PMID: 30171262.
Haffner MC, Taheri D, Luidy-Imada E, Palsgrove DN, Eich ML, Netto GJ, Matoso A, Nirschl TR, Zheng Q, Hicks JL, Nelson WG, De Marzo AM, Marchionni L, Drake CG, Yegnasubramanian S. Hypomethylation, endogenous retrovirus expression, and interferon signaling in testicular germ cell tumors. Proc Natl Acad Sci U S A. 2018 Sep 11;115(37):E8580-E8582. doi:10.1073/pnas.1803292115. Epub 2018 Sep 4. PMID: 30181298; PMCID: PMC6140483.
Ooki A, Dinalankara W, Marchionni L, Tsay JJ, Goparaju C, Maleki Z, Rom WN, Pass HI, Hoque MO. Epigenetically regulated PAX6 drives cancer cells toward a stem-like state via GLI-SOX2 signaling axis in lung adenocarcinoma. Oncogene. 2018 Jul 6. doi:10.1038/s41388-018-0373-2. [Epub ahead of print] PMID:29980786.
Ooki A, Del Carmen Rodriguez Pena M, Marchionni L, Dinalankara W, Begum A, Hahn NM, VandenBussche CJ, Rasheed ZA, Mao S, Netto GJ, Sidransky D, Hoque MO. YAP1 and COX2 Coordinately Regulate Urothelial Cancer Stem-like Cells. Cancer research. 2018; 78(1):168-181. NIHMSID: NIHMS919734 PMID: 29180467; PMCID: PMC5754245.
Ooki A, Begum A, Marchionni L, Vanden-Bussche CJ, Mao S, Kates M, Hoque MO. Arsenic promotes the COX2/PGE2-SOX2 axis to increase the malignant stemness properties of urothelial cells. Int J Cancer. 2018 Jul 1;143(1):113-126. doi:10.1002/ijc.31290. PMID: 29396848; PMCID: PMC5938132
The names of my mentees are underlined.
Ravi R, Noonan KA, Pham V, Bedi R, Zhavoronkov A, Ozerov IV, Makarev E, V Artemov A, Wysocki PT, Mehra R, Nimmagadda S, Marchionni L, Sidransky D, Borrello IM, Izumchenko E, Bedi A. Bifunctional immune checkpoint- targeted antibody-ligand traps that simultaneously disable TGFβ enhance the efficacy of cancer immunotherapy. Nature communications. 2018; 9(1):741. PMID: 29467463; PMCID: PMC5821872
Bellazzo A, Di Minin G, Valentino E, Sicari D, Torre D, Marchionni L, Serpi F, Stadler MB, Taverna D, Zuccolotto G, Montagner IM, Rosato A, Tonon F, Zennaro C, Agostinis C, Bulla R, Mano M, Del Sal G, Collavin L. Cell- autonomous and cell non-autonomous downregulation of tumor suppressor DAB2IP by microRNA-149-3p promotes aggressiveness of cancer cells. Cell death and differentiation. 2018; PMID: 29568059

2017

De Robertis M, Loiacono L, Fusilli C, Poeta ML, Mazza T, Sanchez M, Marchionni L, Signori E, Lamorte G, Vescovi AL, Garcia-Foncillas J, Fazio VM. Dysregulation of EGFR Pathway in EphA2 Cell Subpopulation Significantly Associates with Poor Prognosis in Colorectal Cancer. Clinical cancer research. 2017; 23(1):159-170, PMID: 27401248; PMCID: PMC5822042
Stein-O'Brien GL, Carey JL, Lee WS, Considine M, Favorov AV, Flam E, Guo T, Li S, Marchionni L, Sherman T, Sivy S, Gaykalova DA, McKay RD, Ochs MF, Colantuoni C, Fertig EJ. PatternMarkers & GWCoGAPS for novel data-driven biomarkers via whole transcriptome NMF. Bioinformatics. 2017 Jun 15;33(12):1892-1894. doi:10.1093/bioinformatics/btx058, PMID: 28174896; PMCID: PMC5860188.
Marchionni L*§, Hayashi M*, Guida E, Ooki A, Munari E, Jabboure FJ, Dinalankara W, Raza A, Netto GJ, Hoque MO, and Argani P§. MicroRNA expression profiling of Xp11 renal cell carcinoma. Human pathology. 2017; 67:18-29. NIHMSID: NIHMS902381, PMID: 28411178; PMCID: PMC5628161
*Equally contributing first author and §Co-corresponding author; The names of my mentees are underlined.
Isella C, Brundu F, Bellomo SE, Galimi F, Zanella E, Porporato R, Petti C, Fiori A, Orzan F, Senetta R, Boccaccio R, Ficarra E, Marchionni L, Trusolino L, Medico E, and Bertotti A. Selective analysis of cancer-cell intrinsic transcriptional traits defines novel clinically relevant subtypes of colorectal cancer. Nature communications. 2017; 8:15107, PMID: 28561063; PMCID: PMC5499209
Gandy L, Gumm J, Fertig B, Kennish MJ, Chavan S, Thessen A, Marchionni L, Xia X, Shankrit S, Fertig EJ. Synthesizer: Expediting synthesis studies from context-free data with natural language processing. PloS one. 2017; 12(4):e0175860, PMID: 28437440; PMCID: PMC5402950
The names of my mentees are underlined.
Marchionni L§, Netto GJ, Hoque MO, Argani P. MicroRNAs, promising biomarkers in the diagnosis of Xp11 translocation RCC-reply. Hum Pathol. 2017 Oct;68:206-207. ; PMID: 28811253
§Corresponding author; The names of my mentees are underlined.
Begum A, Ewachiw T, Jung C, Huang A, Norberg KJ, Marchionni L, McMillan R, Penchev V, Rajeshkumar NV, Maitra A, Wood L, Wang C, Wolfgang C, DeJesus-Acosta A, Laheru D, Shapiro IM, Padval M, Pachter JA, Weaver DT, Rasheed ZA, Matsui W. The extracellular matrix and focal adhesion kinase signaling regulate cancer stem cell function in pancreatic ductal adenocarcinoma. PloS one. 2017; 12(7):e0180181, PMID: 28692661; PMCID: PMC5503247
Ross ER, Hughes RM, Glavaris S, Ghabili K, He P, Anders NM, Harb R, Tosoian JJ, Marchionni L, Schaeffer EM, Partin AW, Allaf ME, Bivalacqua TJ, Chapman C, O’Neal T, DeMarzo AM, Hurley PJ, Rudek MA, and Antonarakis ES. Pharmacodynamic and pharmacokinetic neoadjuvant study of hedgehog pathway inhibitor Sonidegib (LDE-225) in men with high-risk localized prostate cancer undergoing prostatectomy. Oncotarget. 2017 Oct 26;8(61):104182-104192. doi:10.18632/oncotarget.22115. PMID: 29262631; PMCID: PMC5732797.
Guerrero-Preston R, White JR, Godoy-Vitorino F, Rodríguez-Hilario A, Navarro K, González H, Michailidi C, Jedlicka A, Canapp S, Bondy J, Dziedzic A, Mora-Lagos B, Rivera-Alvarez G, Ili-Gangas C, Brebi-Mieville P, Westra W, Koch W, Kang H, Marchionni L, Kim Y, and Sidransky D. High-resolution microbiome pro ling uncovers Fusobacterium nucleatum, Lactobacillus gasseri/johnsonii, and Lactobacillus vaginalis associated to oral and oropharyngeal cancer in saliva from HPV positive and HPV negative patients treated with surgery and chemo-radiation. Oncotarget. 2017 Sep 7;8(67):110931-110948. doi:10.18632/oncotarget.20677. PMID: 29340028; PMCID: PMC5762296.

2016

Ross AE, Johnson MH, Yousefi K, Davicioni E, Netto GJ, Marchionni L, Fedor HL, Glavaris S, Choeurng V, Buerki C, Erho N, Lam LL, Humphreys EB, Faraj S, Bezerra SM, Han M, Partin AW, Trock BJ, Schaeffer EM. Tissue-based Genomics Augments Post-prostatectomy Risk Stratification in a Natural History Cohort of Intermediate- and High-Risk Men. European urology. 2016; 69(1):157-65, PMID: 26058959
Hurley PJ, Sundi D, Shinder B, Simons BW, Hughes RM, Miller RM, Benzon B, Faraj SF, Netto GJ, Vergara IA, Erho N, Davicioni E, Karnes RJ, Yan G, Ewing C, Isaacs SD, Berman DM, Rider JR, Jordahl KM, Mucci LA, Huang J, An SS, Park BH, Isaacs WB, Marchionni L, Ross AE, Schaeffer EM. Germline Variants in Asporin Vary by Race, Modulate the Tumor Microenvironment, and Are Differentially Associated with Metastatic Prostate Cancer. Clinical cancer research. 2016; 22(2):448-58. NIHMSID: NIHMS729650, PMID: 26446945; PMCID: PMC4715968
Kahlert UD, Cheng M, Koch K, Marchionni L, Fan X, Raabe EH, Maciaczyk J, Glunde K, Eberhart CG. Alterations in cellular metabolome after pharmacological inhibition of Notch in glioblastoma cells. International journal of cancer. 2016; 138(5):1246-55. NIHMSID: NIHMS759533, PMID: 26422827; PMCID: PMC4772139
Rettig EM, Talbot CC Jr, Sausen M, Jones S, Bishop JA, Wood LD, Tokheim C, Niknafs N, Karchin R, Fertig EJ, Wheelan SJ, Marchionni L, Considine M, Fakhry C, Papadopoulos N, Kinzler KW, Vogelstein B, Ha PK, Agrawal N. Whole-Genome Sequencing of Salivary Gland Adenoid Cystic Carcinoma. Cancer prevention research (Philadelphia, Pa.). 2016; 9(4):265-74. NIHMSID: NIHMS759794, PMID: 26862087; PMCID: PMC4818686
Christensen-Quick A, Lafferty M, Sun L, Marchionni L, DeVico A, Garzino-Demo A. Human Th17 Cells Lack HIV-Inhibitory RNases and Are Highly Permissive to Productive HIV Infection. Journal of virology. 2016; 90(17):7833-47, PMID: 27334595; PMCID: PMC4988157
Kumar B, Khaleghzadegan S, Mears B, Hatano K, Kudrolli TA, Chowdhury WH, Yeater DB, Ewing CM, Luo J, Isaacs WB, Marchionni L, Lupold SE. 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. Oncotarget. 2016; 7(45):72593-72607, PMID: 27683042
Carroll VA, Lafferty MK, Marchionni L, Bryant JL, Gallo RC, Garzino-Demo A. Expression of HIV-1 matrix protein p17 and association with B-cell lymphoma in HIV-1 transgenic mice. Proceedings of the National Academy of Sciences of the United States of America. 2016; 113(46):13168-13173, PMID: 27799525; PMCID: PMC5135339
Lee BJ*, Marchionni L*, Andrews CE, Norris AL, Nucifora LG, Wu YC, Wright RA, Pevsner J, Ross CA, Margolis RL, Sawa A, Nucifora FC Jr. Analysis of differential gene expression mediated by clozapine in human postmortem brains. Schizophr Res. 2017 Jul;185:58-66. doi:10.1016/j.schres.2016.12.017. Epub 2016 Dec 27, PMID: 28038920
*Equally contributing first author.

2015

Guerrero-Preston R, Michailidi C, Marchionni L, Pickering CR, Frederick MJ, Myers JN, Yegnasubramanian S, Hadar T, Noordhuis MG, Zizkova V, Fertig E, Agrawal N, Westra W, Koch W, Califano J, Velculescu VE, Sidransky D. Key tumor suppressor genes inactivated by "greater promoter" methylation and somatic mutations in head and neck cancer. Epigenetics. 2014; 9(7):1031-46, PMID: 24786473; PMCID: PMC4143405
Huang TC, Renuse S, Pinto S, Kumar P, Yang Y, Chaerkady R, Godsey B, Mendell JT, Halushka MK, Civin CI, Marchionni L§, Pandey A§. Identification of miR-145 targets through an integrated omics analysis. Molecular bioSystems. 2015; 11(1):197-207. NIHMSID: NIHMS659355, PMID: 25354783; PMCID: PMC4352311
§ Co-corresponding last author; The names of my mentees are underlined.
Tomasetti C, Marchionni L, Nowak MA, Parmigiani G, Vogelstein B. Only three driver gene mutations are required for the development of lung and colorectal cancers. Proceedings of the National Academy of Sciences of the United States of America. 2015; 112(1):118-23, PMID: 25535351; PMCID: PMC4291633
Afsari B, Fertig EJ, Geman D, Marchionni L§. switchBox: an R package for k-Top Scoring Pairs classifier development. Bioinformatics (Oxford, England). 2015; 31(2):273-4, PMID: 25262153; PMCID: PMC4287945
§ Corresponding author; The names of my mentees are underlined.
Brandt WD, Schreck KC, Bar EE, Taylor I, Marchionni L, Raabe E, Eberhart CG, Rodriguez FJ. Notch signaling activation in pediatric low-grade astrocytoma. Journal of neuropathology and experimental neurology. 2015; 74(2):121-31. NIHMSID: NIHMS642970, PMID: 25575134; PMCID: PMC4357229
Lim Y, Gondek L, Li L, Wang Q, Ma H, Chang E, Huso DL, Foerster S, Marchionni L, McGovern K, Watkins DN, Peacock CD, Levis M, Smith BD, Merchant AA, Small D, Matsui W. Integration of Hedgehog and mutant FLT3 signaling in myeloid leukemia. Science translational medicine. 2015; 7(291):291ra96. NIHMSID: NIHMS733757, PMID: 26062848; PMCID: PMC4644635
Carvalho FL, Marchionni L,Gupta A, Kummangal BA, Schaeffer EM, Ross AE, Berman DM. HES6 promotes prostate cancer aggressiveness independently of Notch signalling. Journal of cellular and molecular medicine. 2015; 19(7):1624-36, PMID: 25864518; PMCID: PMC4511360
Baras AS, Gandhi N, Munari E, Faraj S, Shultz L, Marchionni L, Schoenberg M, Hahn N, Hoque MO, Berman D, Bivalacqua TJ, Netto G. Identification and Validation of Protein Biomarkers of Response to Neoadjuvant Platinum Chemotherapy in Muscle Invasive Urothelial Carcinoma. PloS one. 2015; 10(7):e0131245, PMID: 26230923; PMCID: PMC4521868
Izumchenko E, Chang X, Brait M, Fertig E, Kagohara LT, Bedi A, Marchionni L, Agrawal N, Ravi R, Jones S, Hoque MO, Westra WH, Sidransky D. Targeted sequencing reveals clonal genetic changes in the progression of early lung neoplasms and paired circulating DNA. Nature communications. 2015; 6:8258. NIHMSID: NIHMS713162, PMID: 26374070; PMCID: PMC4595648
Ramirez-Correa GA, Ma J, Slawson C, Zeidan Q, Lugo-Fagundo NS, Xu M, Shen X, Gao WD, Caceres V, Chakir K, DeVine L, Cole RN, Marchionni L, Paolocci N, Hart GW, Murphy AM. Removal of Abnormal Myofilament O-GlcNAcylation Restores Ca2+ Sensitivity in Diabetic Cardiac Muscle. Diabetes. 2015; 64(10):3573-87, PMID: 26109417; PMCID: PMC4587639
Romano A, Parrinello NL, Consoli ML, Marchionni L, Forte S, Conticello C, Pompa A, Corso A, Milone G, Di Raimondo F, Borrello I. Neutrophil to lymphocyte ratio (NLR) improves the risk assessment of ISS staging in newly diagnosed MM patients treated upfront with novel agents. Annals of hematology. 2015; 94(11):1875-83. NIHMSID: NIHMS737797, PMID: 26223359; PMCID: PMC4695982
Mitchell CJ, Getnet D, Kim MS, Manda SS, Kumar P, Huang TC, Pinto SM, Nirujogi RS, Iwasaki M, Shaw PG, Wu X, Zhong J, Chaerkady R, Marimuthu A, Muthusamy B, Sahasrabuddhe NA, Raju R, Bowman C, Danilova L, Cutler J, Kelkar DS, Drake CG, Prasad TS, Marchionni L, Murakami PN, Scott AF, Shi L, Thierry-Mieg J, Thierry-Mieg D, Irizarry R, Cope L, Ishihama Y, Wang C, Gowda H, Pandey A. A multi-omic analysis of human naïve CD4+ T cells. BMC systems biology. 2015; 9:75, PMID: 26542228; PMCID: PMC4636073
The names of my mentees are underlined.

2013 - 2014

Ferlito M, Wang Q, Fulton WB, Colombani PM, Marchionni L, Fox-Talbot K, Paolocci N, Steenbergen C. Hydrogen sulfide [corrected] increases survival during sepsis: protective effect of CHOP inhibition. Journal of immunology (Baltimore, Md.: 1950). 2014; 192(4):1806-14. NIHMSID: NIHMS547372, PMID: 24403532; PMCID: PMC3946246
Riester M, Werner L, Bellmunt J, Selvarajah S, Guancial EA, Weir BA, Stack EC, Park RS, O'Brien R, Schutz FA, Choueiri TK, Signoretti S, Lloreta J, Marchionni L, Gallardo E, Rojo F, Garcia DI, Chekaluk Y, Kwiatkowski DJ, Bochner BH, Hahn WC, Ligon AH, Barletta JA, Loda M, Berman DM, Kantoff PW, Michor F, Rosenberg JE. Integrative analysis of 1q23.3 copy-number gain in metastatic urothelial carcinoma. Clinical cancer research. 2014; 20(7):1873-83. NIHMSID: NIHMS562563, PMID: 24486590; PMCID: PMC3975677
Munari E*, Marchionni L*, Chitre A, Hayashi M, Martignoni G, Brunelli M, Gobbo S, Argani P, Allaf M, Hoque MO, Netto GJ. Clear cell papillary renal cell carcinoma: micro-RNA expression profiling and comparison with clear cell renal cell carcinoma and papillary renal cell carcinoma. Human pathology. 2014; 45(6):1130-8. NIHMSID: NIHMS662126, PMID: 24703100; PMCID: PMC4332813
*Equally contributing first author; The names of my mentees are underlined.
Ho CY, Bar E, Giannini C, Marchionni L, Karajannis MA, Zagzag D, Gutmann DH, Eberhart CG, Rodriguez FJ. MicroRNA profiling in pediatric pilocytic astrocytoma reveals biologically relevant targets, including PBX3, NFIB, and METAP2. Neuro-oncology. 2013; 15(1):69-82, PMID: 23161775; PMCID: PMC3534421

Zinn RL, Gardner EE, Dobromilskaya I, Murphy S, Marchionni L, Hann CL, Rudin CM. Combination treatment with ABT-737 and chloroquine in preclinical models of small cell lung cancer. Molecular cancer. 2013; 12:16, PMID: 23452820; PMCID: PMC3599053
Marchionni L, Afsari B, Geman D, Leek JT. A simple and reproducible breast cancer prognostic test. BMC genomics. 2013; 14:336, PMID: 23682826; PMCID: PMC3662649
The names of my mentees are underlined.
Iglesias-Ussel M, Marchionni L, Romerio F. Isolation of microarray-quality RNA from primary human cells after intracellular immunostaining and fluorescence-activated cell sorting. Journal of immunological methods. 2013; 391(1-2):22-30. NIHMSID: NIHMS454380, PMID: 23434645; PMCID: PMC3627819
Zinn RL, Gardner EE, Marchionni L, Murphy SC, Dobromilskaya I, Hann CL, Rudin CM. ERK phosphorylation is predictive of resistance to IGF-1R inhibition in small cell lung cancer. Molecular cancer therapeutics. 2013; 12(6):1131-9. NIHMSID: NIHMS457979, PMID: 23515613; PMCID: PMC3681842
Iglesias-Ussel M, Vandergeeten C, Marchionni L, Chomont N, Romerio F. High levels of CD2 expression identify HIV-1 latently infected resting memory CD4+ T cells in virally suppressed subjects. Journal of virology. 2013; 87(16):9148-58, PMID: 23760244; PMCID: PMC3754042
Kortenhorst MS, Wissing MD, Rodríguez R, Kachhap SK, Jans JJ, Van der Groep P, Verheul HM, Gupta A, Aiyetan PO, van der Wall E, Carducci MA, Van Diest PJ, Marchionni L§. Analysis of the genomic response of human prostate cancer cells to histone deacetylase inhibitors. Epigenetics. 2013; 8(9):907-20, PMID: 23880963; PMCID: PMC3883768
§ Corresponding author; The names of my mentees are underlined.
Rossello FJ, Tothill RW, Britt K, Marini KD, Falzon J, Thomas DM, Peacock CD, Marchionni L, Li J, Bennett S, Tantoso E, Brown T, Chan P, Martelotto LG, Watkins DN. Next-generation sequence analysis of cancer xenograft models. PloS one. 2013; 8(9):e74432, PMID: 24086345; PMCID: PMC3784448
Brait M, Maldonado L, Noordhuis MG, Begum S, Loyo M, Poeta ML, Barbosa A, Fazio VM, Angioli R, Rabitti C, Marchionni L, de Graeff P, van der Zee AG, Wisman GB, Sidransky D, Hoque MO. Association of promoter methylation of VGF and PGP9.5 with ovarian cancer progression. PloS one. 2013; 8(9):e70878, PMID: 24086249; PMCID: PMC3785492

2011 - 2012

Benassi B, Flavin R, Marchionni L, Zanata S, Pan Y, Chowdhury D, Marani M, Strano S, Muti P, Blandino G, Loda M. MYC is activated by USP2a-mediated modulation of microRNAs in prostate cancer. Cancer discovery. 2012; 2(3):236-47. NIHMSID: NIHMS379659, PMID: 22585994; PMCID: PMC3523361
Huang TC, Sahasrabuddhe NA, Kim MS, Getnet D, Yang Y, Peterson JM, Ghosh B, Chaerkady R, Leach SD, Marchionni L, Wong GW, Pandey A. Regulation of lipid metabolism by Dicer revealed through SILAC mice. Journal of proteome research. 2012; 11(4):2193-205. NIHMSID: NIHMS360335, PMID: 22313051; PMCID: PMC3612551
Huang Z, Hurley PJ, Simons BW, Marchionni L, Berman DM, Ross AE, Schaeffer EM. Sox9 is required for prostate development and prostate cancer initiation. Oncotarget. 2012; 3(6):651-63, PMID: 22761195; PMCID: PMC3442290
Kornegoor R, Moelans CB, Verschuur-Maes AH, Hogenes MC, de Bruin PC, Oudejans JJ, Marchionni L, van Diest PJ. Oncogene amplification in male breast cancer: analysis by multiplex ligation-dependent probe amplification. Breast cancer research and treatment. 2012; 135(1):49-58, PMID: 22527098; PMCID: PMC3413821
Hurley PJ, Marchionni L, Simons BW, Ross AE, Peskoe SB, Miller RM, Erho N, Vergara IA, Ghadessi M, Huang Z, Gurel B, Park BH, Davicioni E, Jenkins RB, Platz EA, Berman DM, Schaeffer EM. Secreted protein, acidic and rich in cysteine-like 1 (SPARCL1) is down regulated in aggressive prostate cancers and is prognostic for poor clinical outcome. Proceedings of the National Academy of Sciences of the United States of America. 2012; 109(37):14977-82, PMID: 22927397; PMCID: PMC3443123
Simons BW, Hurley PJ, Huang Z, Ross AE, Miller R, Marchionni L, Berman DM, Schaeffer EM. Wnt signaling though beta-catenin is required for prostate lineage specification. Developmental biology. 2012; 371(2):246-55. NIHMSID: NIHMS404765, PMID: 22960283; PMCID: PMC3472417
Ross AE, Marchionni L, Phillips TM, Miller RM, Hurley PJ, Simons BW, Salmasi AH, Schaeffer AJ, Gearhart JP, Schaeffer EM. Molecular effects of genistein on male urethral development. The Journal of urology. 2011; 185(5):1894-8, PMID: 21421236

Liu H, Kim Y, Sharkis S, Marchionni L, Jang YY. In vivo liver regeneration potential of human induced pluripotent stem cells from diverse origins. Science translational medicine. 2011; 3(82):82ra39. NIHMSID: NIHMS358406, PMID: 21562231; PMCID: PMC3305909
Ling S, Chang X, Schultz L, Lee TK, Chaux A, Marchionni L, Netto GJ, Sidransky D, Berman DM. An EGFR-ERK-SOX9 signaling cascade links urothelial development and regeneration to cancer. Cancer research. 2011; 71(11):3812-21. NIHMSID: NIHMS283473, PMID: 21512138; PMCID: PMC3107391
Ross AE, Emadi A, Marchionni L, Hurley PJ, Simons BW, Schaeffer EM, Vuica-Ross M. Dimeric naphthoquinones, a novel class of compounds with prostate cancer cytotoxicity. BJU international. 2011; 108(3):447-54. NIHMSID: NIHMS403303, PMID: 21176082; PMCID: PMC3700341
Ross AE, Marchionni L, Vuica-Ross M, Cheadle C, Fan J, Berman DM, Schaeffer EM. Gene expression pathways of high grade localized prostate cancer. The Prostate. 2011; 71(14):1568-77, PMID: 21360566
Tyekucheva S, Marchionni L, Karchin R, Parmigiani G. Integrating diverse genomic data using gene sets. Genome biology. 2011; 12(10):R105, PMID: 22018358; PMCID: PMC3333775

2009 - 2010

Kachhap SK, Rosmus N, Collis SJ, Kortenhorst MS, Wissing MD, Hedayati M, Shabbeer S, Mendonca J, Deangelis J, Marchionni L, Lin J, Höti N, Nortier JW, DeWeese TL, Hammers H, Carducci MA. Downregulation of homologous recombination DNA repair genes by HDAC inhibition in prostate cancer is mediated through the E2F1 transcription factor. PloS one. 2010; 5(6):e11208, PMID: 20585447; PMCID: PMC2887841
Seeber LM, Zweemer RP, Marchionni L, Massuger LF, Smit VT, van Baal WM, Verheijen RH, van Diest PJ. Methylation profiles of endometrioid and serous endometrial cancers. Endocrine-related cancer. 2010; 17(3):663-73, PMID: 20488783
Noonan K, Marchionni L, Anderson J, Pardoll D, Roodman GD, Borrello I. A novel role of IL-17-producing lymphocytes in mediating lytic bone disease in multiple myeloma. Blood. 2010; 116(18):3554-63, PMID: 20664052; PMCID: PMC4017298
Schreck KC, Taylor P, Marchionni L, Gopalakrishnan V, Bar EE, Gaiano N, Eberhart CG. The Notch target Hes1 directly modulates Gli1 expression and Hedgehog signaling: a potential mechanism of therapeutic resistance. Clinical cancer research. 2010; 16(24):6060-70. NIHMSID: NIHMS247142, PMID: 21169257; PMCID: PMC3059501
Daniel VC*, Marchionni L*, Hierman JS, Rhodes JT, Devereux WL, Rudin CM, Yung R, Parmigiani G, Dorsch M, Peacock CD, Watkins DN. A primary xenograft model of small-cell lung cancer reveals irreversible changes in gene expression imposed by culture in vitro. Cancer research. 2009; 69(8):3364-73. NIHMSID: NIHMS97707, PMID: 19351829; PMCID: PMC2821899
*Equally contributing first author.

He X, Marchionni L, Hansel DE, Yu W, Sood A, Yang J, Parmigiani G, Matsui W, Berman DM. Differentiation of a highly tumorigenic basal cell compartment in urothelial carcinoma. Stem cells (Dayton, Ohio). 2009; 27(7):1487-95. NIHMSID: NIHMS236727, PMID: 19544456; PMCID: PMC3060766
Lin X, Afsari B, Marchionni L, Cope L, Parmigiani G, Naiman D, Geman D. The ordering of expression among a few genes can provide simple cancer biomarkers and signal BRCA1 mutations. BMC Bioinformatics. 2009 Aug 20;10:256. doi:10.1186/1471-2105-10-256. PMID: 19695104; PMCID: PMC2745389

2001 - 2008

Schaeffer EM*, Marchionni L*, Huang Z, Simons B, Blackman A, Yu W, Parmigiani G, Berman DM. Androgen-induced programs for prostate epithelial growth and invasion arise in embryogenesis and are reactivated in cancer. Oncogene. 2008; 27(57):7180-91. NIHMSID: NIHMS84639, PMID: 18794802; PMCID: PMC2676849
*Equally contributing first author.
Carninci P, Kasukawa T, Katayama S, Gough J, Frith MC, Maeda N, Oyama R, Ravasi T, Lenhard B, Wells C, Kodzius R, Shimokawa K, Bajic VB, Brenner SE, Batalov S, Forrest AR, Zavolan M, Davis MJ, Wilming LG, Aidinis V, Allen JE, Ambesi-Impiombato A, Apweiler R, Aturaliya RN, Bailey TL, Bansal M, Baxter L, Beisel KW, Bersano T, Bono H, Chalk AM, Chiu KP, Choudhary V, Christoffels A, Clutterbuck DR, Crowe ML, Dalla E, Dalrymple BP, de Bono B, Della Gatta G, di Bernardo D, Down T, Engstrom P, Fagiolini M, Faulkner G, Fletcher CF, Fukushima T, Furuno M, Futaki S, Gariboldi M, Georgii-Hemming P, Gingeras TR, Gojobori T, Green RE, Gustincich S, Harbers M, Hayashi Y, Hensch TK, Hirokawa N, Hill D, Huminiecki L, Iacono M, Ikeo K, Iwama A, Ishikawa T, Jakt M, Kanapin A, Katoh M, Kawasawa Y, Kelso J, Kitamura H, Kitano H, Kollias G, Krishnan SP, Kruger A, Kummerfeld SK, Kurochkin IV, Lareau LF, Lazarevic D, Lipovich L, Liu J, Liuni S, McWilliam S, Madan Babu M, Madera M, Marchionni L, Matsuda H, Matsuzawa S, Miki H, Mignone F, Miyake S, Morris K, Mottagui-Tabar S, Mulder N, Nakano N, Nakauchi H, Ng P, Nilsson R, Nishiguchi S, Nishikawa S, Nori F, Ohara O, Okazaki Y, Orlando V, Pang KC, Pavan WJ, Pavesi G, Pesole G, Petrovsky N, Piazza S, Reed J, Reid JF, Ring BZ, Ringwald M, Rost B, Ruan Y, Salzberg SL, Sandelin A, Schneider C, Schönbach C, Sekiguchi K, Semple CA, Seno S, Sessa L, Sheng Y, Shibata Y, Shimada H, Shimada K, Silva D, Sinclair B, Sperling S, Stupka E, Sugiura K, Sultana R, Takenaka Y, Taki K, Tammoja K, Tan SL, Tang S, Taylor MS, Tegner J, Teichmann SA, Ueda HR, van Nimwegen E, Verardo R, Wei CL, Yagi K, Yamanishi H, Zabarovsky E, Zhu S, Zimmer A, Hide W, Bult C, Grimmond SM, Teasdale RD, Liu ET, Brusic V, Quackenbush J, Wahlestedt C, Mattick JS, Hume DA, Kai C, Sasaki D, Tomaru Y, Fukuda S, Kanamori-Katayama M, Suzuki M, Aoki J, Arakawa T, Iida J, Imamura K, Itoh M, Kato T, Kawaji H, Kawagashira N, Kawashima T, Kojima M, Kondo S, Konno H, Nakano K, Ninomiya N, Nishio T, Okada M, Plessy C, Shibata K, Shiraki T, Suzuki S, Tagami M, Waki K, Watahiki A, Okamura-Oho Y, Suzuki H, Kawai J, Hayashizaki Y. The transcriptional landscape of the mammalian genome. Science (New York, N.Y.). 2005; 309(5740):1559-63, PMID: 16141072
Dalla E, Mignone F, Verardo R, Marchionni L, Marzinotto S, Lazarević D, Reid JF, Marzio R, Klarić E, Licastro D, Marcuzzi G, Gambetta R, Pierotti MA, Pesole G, Schneider C. Discovery of 342 putative new genes from the analysis of 5'-end-sequenced full-length-enriched cDNA human transcripts. Genomics. 2005; 85(6):739-51, PMID: 15885500
De Cecco L*, Marchionni L*, Gariboldi M, Reid JF, Lagonigro MS, Caramuta S, Ferrario C, Bussani E, Mezzanzanica D, Turatti F, Delia D, Daidone MG, Oggionni M, Bertuletti N, Ditto A, Raspagliesi F, Pilotti S, Pierotti MA, Canevari S, Schneider C. Gene expression profiling of advanced ovarian cancer: characterization of a molecular signature involving fibroblast growth factor 2. Oncogene. 2004; 23(49):8171-83, PMID: 15377994
*Equally contributing first author.
Monte M, Benetti R, Collavin L, Marchionni L, Del Sal G, Schneider C. hGTSE-1 expression stimulates cytoplasmic localization of p53. The Journal of Biological Chemistry. 2004; 279(12):11744-52, PMID: 14707141
Dalla E, Verardo R, Lazarević D, Marchionni L, Reid JF, Bahar N, Klarić E, Marcuzzi G, Marzio R, Belgrano A, Licastro D, Schneider C. LNCIB human full-length cDNAs collection: towards a better comprehension of the human transcriptome. Comptes Rendus Biologies. 2003; 326(10-11):967-70, PMID: 14744102
Okazaki Y, Furuno M, Kasukawa T, Adachi J, Bono H, Kondo S, Nikaido I, Osato N, Saito R, Suzuki H, Yamanaka I, Kiyosawa H, Yagi K, Tomaru Y, Hasegawa Y, Nogami A, Schönbach C, Gojobori T, Baldarelli R, Hill DP, Bult C, Hume DA, Quackenbush J, Schriml LM, Kanapin A, Matsuda H, Batalov S, Beisel KW, Blake JA, Bradt D, Brusic V, Chothia C, Corbani LE, Cousins S, Dalla E, Dragani TA, Fletcher CF, Forrest A, Frazer KS, Gaasterland T, Gariboldi M, Gissi C, Godzik A, Gough J, Grimmond S, Gustincich S, Hirokawa N, Jackson IJ, Jarvis ED, Kanai A, Kawaji H, Kawasawa Y, Kedzierski RM, King BL, Konagaya A, Kurochkin IV, Lee Y, Lenhard B, Lyons PA, Maglott DR, Maltais L, Marchionni L, McKenzie L, Miki H, Nagashima T, Numata K, Okido T, Pavan WJ, Pertea G, Pesole G, Petrovsky N, Pillai R, Pontius JU, Qi D, Ramachandran S, Ravasi T, Reed JC, Reed DJ, Reid J, Ring BZ, Ringwald M, Sandelin A, Schneider C, Semple CA, Setou M, Shimada K, Sultana R, Takenaka Y, Taylor MS, Teasdale RD, Tomita M, Verardo R, Wagner L, Wahlestedt C, Wang Y, Watanabe Y, Wells C, Wilming LG, Wynshaw-Boris A, Yanagisawa M, Yang I, Yang L, Yuan Z, Zavolan M, Zhu Y, Zimmer A, Carninci P, Hayatsu N, Hirozane-Kishikawa T, Konno H, Nakamura M, Sakazume N, Sato K, Shiraki T, Waki K, Kawai J, Aizawa K, Arakawa T, Fukuda S, Hara A, Hashizume W, Imotani K, Ishii Y, Itoh M, Kagawa I, Miyazaki A, Sakai K, Sasaki D, Shibata K, Shinagawa A, Yasunishi A, Yoshino M, Waterston R, Lander ES, Rogers J, Birney E, Hayashizaki Y. Analysis of the mouse transcriptome based on functional annotation of 60,770 full-length cDNAs. Nature. 2002; 420(6915):563-73, PMID: 12466851
Kawai J, Shinagawa A, Shibata K, Yoshino M, Itoh M, Ishii Y, Arakawa T, Hara A, Fukunishi Y, Konno H, Adachi J, Fukuda S, Aizawa K, Izawa M, Nishi K, Kiyosawa H, Kondo S, Yamanaka I, Saito T, Okazaki Y, Gojobori T, Bono H, Kasukawa T, Saito R, Kadota K, Matsuda H, Ashburner M, Batalov S, Casavant T, Fleischmann W, Gaasterland T, Gissi C, King B, Kochiwa H, Kuehl P, Lewis S, Matsuo Y, Nikaido I, Pesole G, Quackenbush J, Schriml LM, Staubli F, Suzuki R, Tomita M, Wagner L, Washio T, Sakai K, Okido T, Furuno M, Aono H, Baldarelli R, Barsh G, Blake J, Boffelli D, Bojunga N, Carninci P, de Bonaldo MF, Brownstein MJ, Bult C, Fletcher C, Fujita M, Gariboldi M, Gustincich S, Hill D, Hofmann M, Hume DA, Kamiya M, Lee NH, Lyons P, Marchionni L, Mashima J, Mazzarelli J, Mombaerts P, Nordone P, Ring B, Ringwald M, Rodriguez I, Sakamoto N, Sasaki H, Sato K, Schönbach C, Seya T, Shibata Y, Storch KF, Suzuki H, Toyo-oka K, Wang KH, Weitz C, Whittaker C, Wilming L, Wynshaw-Boris A, Yoshida K, Hasegawa Y, Kawaji H, Kohtsuki S, Hayashizaki Y. Functional annotation of a full-length mouse cDNA collection. Nature. 2001; 409(6821):685-90, PMID: 11217851

PUBLICATIONS – Review Articles

Marchionni L, Wilson RF, Wolff AC, Marinopoulos S, Parmigiani G, Bass EB, Goodman SN. Systematic review: gene expression profiling assays in early-stage breast cancer. Annals of internal medicine. 2008; 148(5):358-69, PMID: 18252678
Lerner SP, Bajorin DF, Dinney CP, Efstathiou JA, Groshen S, Hahn NM, Hansel D, Kwiatkowski D, O'Donnell M, Rosenberg J, Svatek R, Abrams JS, Al-Ahmadie H, Apolo AB, Bellmunt J, Callahan M, Cha EK, Drake C, Jarow J, Kamat A, Kim W, Knowles M, Mann B, Marchionni L, McConkey D, McShane L, Ramirez N, Sharabi A, Sharpe AH, Solit D, Tangen CM, Amiri AT, Van Allen E, West PJ, Witjes JA, Quale DZ. Summary and Recommendations from the National Cancer Institute's Clinical Trials Planning Meeting on Novel Therapeutics for Non-Muscle Invasive Bladder Cancer. Bladder cancer (Amsterdam, Netherlands). 2016; 2(2):165-202, PMID: 27376138; PMCID: PMC4927845

PUBLICATIONS – Book Chapters and Monographs

Zhong X, Marchionni L, Cope L, Iversen ES, Garrett-Mayer ES, Gabrielson E, and Parmigiani G. “Optimized cross-study analysis of microarray-based predictors”. Editors: Kim-Anh Do, Zhaohui Steve Qin, and Marina Vannucci. Cambridge University Press.
Marchionni L and Theodorescu D. “Chapter 18: Molecular Pathogenesis of Bladder Cancer - The Urinary Tract - A Comprehensive Guide to Patient Diagnosis and Management“. Editors: Donna E. Hansel, Jesse K. McKenney, Andrew J. Stephenson, and Sam S. Chang. 2012, Springer, New York.
Marchionni L, Wilson RF, Marinopoulos SS, Wolff AC, Parmigiani G, Bass EB, Goodman SN. Impact of gene expression profiling tests on breast cancer outcomes. Evid Rep Technol Assess (Full Rep). 2007 Dec;(160):1-105. PMID: 18457476; PMCID: PMC4781418. Download the book here.

PUBLICATIONS – Pre-prints

Kumar B, Rosenberg AZ, Choi SM, Fox-Talbot K, DeMarzo AM, Nonn L, Brennen WN, Marchionni L, Halushka MK, Lupold SE. Cell-type specific expression of oncogenic and tumor suppressive microRNAs in the human prostate and prostate cancer. 2018, biorXiv; doi: https://doi.org/10.1101/251090
Gandy L, Gumm J, Fertig B, Kennish MJ, Chavan S, Thessen A, Marchionni L, Xia X, Shankrit S, Fertig EJ. Synthesizer: Expediting synthesis studies from context-free data with natural language processing. bioRxiv: 053629. doi:http://dx.doi.org/10.1101/053629
The names of my mentees are underlined