Publications

Boehm KMichael, Bhinder B, Raja VJoseph, Dephoure N, Elemento O.  2019.  Predicting peptide presentation by major histocompatibility complex class I: an improved machine learning approach to the immunopeptidome.. BMC Bioinformatics. 20(1):7.

Li JJ, Shen MM.  2019.  Prostate Stem Cells and Cancer Stem Cells.. Cold Spring Harb Perspect Med. 9(6)

Choudhury AD, Beltran H.  2019.  Retinoblastoma Loss in Cancer: Casting a Wider Net.. Clin Cancer Res. 25(14):4199-4201.

Locallo A, Prandi D, Fedrizzi T, Demichelis F.  2019.  TPES: tumor purity estimation from SNVs.. Bioinformatics. 35(21):4433-4435.

Beltran H, Nanus DM, Sboner A, Mosquera JMiguel, Elemento O, Tagawa ST, Demichelis F, Romanel A, Conteduca V, Casiraghi N et al..  2020.  Circulating tumor DNA profile recognizes transformation to castration-resistant neuroendocrine prostate cancer.. J Clin Invest. 130(4):1653-1668.

Kolin DA, Kulm S, Elemento O.  2020.  Clinical and Genetic Characteristics of Covid-19 Patients from UK Biobank.. medRxiv.

Barbieri CE, Sboner A, Liu D, Ben-Salem S, Hu Q, Liu Y, Alshalalfa M, Zhao X, Wang I, Venkadakrishnan VBalaji et al..  2020.  Diversity in Androgen Receptor Action Among Treatment-naïve Prostate Cancers Is Reflected in Treatment Response Predictions and Molecular Subtypes.. Eur Urol Open Sci. 22:34-44.

Loda M, Bastos DC, Ribeiro CF, Ahearn T, Nascimento J, Pakula H, Clohessy J, Mucci L, Roberts T, Zanata SM et al..  2020.  Genetic ablation of FASN attenuates the invasive potential of prostate cancer driven by Pten loss.. J Pathol.

Liu D, Barbieri CE, Rubin MA, Demichelis F, Mosquera JMiguel, Elemento O, Sboner A, Shoag JE, Poliak D, Goueli RS et al..  2020.  Integrative multiplatform molecular profiling of benign prostatic hyperplasia identifies distinct subtypes.. Nat Commun. 11(1):1987.

Butler LM, Perone Y, Dehairs J, Lupien LE, de Laat V, Loda M, Talebi A, Kinlaw WB, Swinnen JV.  2020.  Lipids and cancer: Emerging roles in pathogenesis, diagnosis and therapeutic intervention.. Adv Drug Deliv Rev. 159:245-293.

Gilvary C, Elkhader J, Madhukar N, Henchcliffe C, Goncalves MD, Elemento O.  2020.  A machine learning and network framework to discover new indications for small molecules.. PLoS Comput Biol. 16(8):e1008098.

Stopsack KH, Huang Y, Tyekucheva S, Gerke TA, Bango C, Elfandy H, Bowden M, Penney KL, Roberts TM, Parmigiani G et al..  2020.  Multiplex Immunofluorescence in Formalin-Fixed Paraffin-Embedded Tumor Tissue to Identify Single-Cell-Level PI3K Pathway Activation.. Clin Cancer Res. 26(22):5903-5913.

Park K, Rubin MA, Sboner A, Mosquera JMiguel, Elemento O, Tran H, Eng KW, Ramazanoglu S, Rolon RMMarrero, Scognamiglio T et al..  2020.  Performance Characteristics of a Targeted Sequencing Platform for Simultaneous Detection of Single Nucleotide Variants, Insertions/Deletions, Copy Number Alterations, and Gene Fusions in Cancer Genome.. Arch Pathol Lab Med. 144(12):1535-1546.

Rubin MA, Beltran H, Ballman KV, Sboner A, Cyrta J, Demichelis F, Augspach A, De Filippo MRosaria, Prandi D, Thienger P et al..  2020.  Role of specialized composition of SWI/SNF complexes in prostate cancer lineage plasticity.. Nat Commun. 11(1):5549.

Ricker E, Verma A, Marullo R, Gupta S, Ye C, Pannellini T, Manni M, Tam W, Inghirami G, Elemento O et al..  2020.  Selective dysregulation of ROCK2 activity promotes aberrant transcriptional networks in ABC diffuse large B-cell lymphoma.. Sci Rep. 10(1):13094.

Thienger P, Rubin MA.  2020.  SETting Up for Epigenetic Regulation of Advanced Prostate Cancer.. Cancer Cell. 38(3):309-311.

Robinson BD, Shen MM, Crowley L, Cambuli F, Aparicio L, Shibata M, Xuan S, Loda M, Li W, Hibshoosh H et al..  2020.  A single-cell atlas of the mouse and human prostate reveals heterogeneity and conservation of epithelial progenitors.. Elife. 9

Lehmann GL, Hanke-Gogokhia C, Hu Y, Bareja R, Salfati Z, Ginsberg M, Nolan DJ, Mendez-Huergo SP, Dalotto-Moreno T, Wojcinski A et al..  2020.  Single-cell profiling reveals an endothelium-mediated immunomodulatory pathway in the eye choroid.. J Exp Med. 217(6)

Conteduca V, Beltran H, Nanus DM, Tagawa ST, Mosquera JMiguel, Sboner A, Elemento O, Ku S-Y, Puca L, Slade M et al..  2020.  SLFN11 Expression in Advanced Prostate Cancer and Response to Platinum-based Chemotherapy.. Mol Cancer Ther. 19(5):1157-1164.

Gjyrezi A, Xie F, Voznesensky O, Khanna P, Calagua C, Bai Y, Kung J, Wu J, Corey E, Montgomery B et al..  2020.  Taxane resistance in prostate cancer is mediated by decreased drug-target engagement.. J Clin Invest. 130(6):3287-3298.

Conteduca V, Ku S-Y, Fernandez L, Dago-Rodriquez A, Lee J, Jendrisak A, Slade M, Gilbertson C, Manohar J, Sigouros M et al..  2021.  Circulating tumor cell heterogeneity in neuroendocrine prostate cancer by single cell copy number analysis.. NPJ Precis Oncol. 5(1):76.

Berchuck JE, Viscuse PV, Beltran H, Aparicio A.  2021.  Clinical considerations for the management of androgen indifferent prostate cancer.. Prostate Cancer Prostatic Dis. 24(3):623-637.

Cotter KA, Gallon J, Uebersax N, Rubin P, Meyer KD, Piscuoglio S, Jaffrey SR, Rubin MA.  2021.  Mapping of m6A and Its Regulatory Targets in Prostate Cancer Reveals a METTL3-Low Induction of Therapy Resistance.. Mol Cancer Res. 19(8):1398-1411.

Penney KL, Tyekucheva S, Rosenthal J, Fandy HEl, Carelli R, Borgstein S, Zadra G, Fanelli GNicolò, Stefanizzi L, Giunchi F et al..  2021.  Metabolomics of Prostate Cancer Gleason Score in Tumor Tissue and Serum.. Mol Cancer Res. 19(3):475-484.

Grbesa I, Augello MA, Liu D, McNally DR, Gaffney CD, Huang D, Lin K, Ivenitsky D, Goueli R, Robinson BD et al..  2021.  Reshaping of the androgen-driven chromatin landscape in normal prostate cells by early cancer drivers and effect on therapeutic sensitivity.. Cell Rep. 36(10):109625.