Publications

Martini R, Delpe P, Chu TR, Arora K, Lord B, Verma A, Bedi D, Karanam B, Elhussin I, Chen Y et al..  2022.  African Ancestry-Associated Gene Expression Profiles in Triple-Negative Breast Cancer Underlie Altered Tumor Biology and Clinical Outcome in Women of African Descent.. Cancer Discov. 12(11):2530-2551.

Ciani Y, Fedrizzi T, Prandi D, Lorenzin F, Locallo A, Gasperini P, Franceschini GMarco, Benelli M, Elemento O, Fava LL et al..  2022.  Allele-specific genomic data elucidate the role of somatic gain and copy-number neutral loss of heterozygosity in cancer.. Cell Syst. 13(2):183-193.e7.

Doane AS, Elemento O.  2022.  Alterations in transcriptional networks in cancer: the role of noncoding somatic driver mutations.. Curr Opin Genet Dev. 75:101919.

Meggendorfer M, Jobanputra V, Wrzeszczynski KO, Roepman P, de Bruijn E, Cuppen E, Buttner R, Caldas C, Grimmond S, Mullighan CG et al..  2022.  Analytical demands to use whole-genome sequencing in precision oncology.. Semin Cancer Biol. 84:16-22.

Brendel M, Su C, Bai Z, Zhang H, Elemento O, Wang F.  2022.  Application of Deep Learning on Single-cell RNA Sequencing Data Analysis: A Review.. Genomics Proteomics Bioinformatics. 20(5):814-835.

Elkhader J, Elemento O.  2022.  Artificial intelligence in oncology: From bench to clinic.. Semin Cancer Biol. 84:113-128.

Kim J, Rustam S, Mosquera JMiguel, Randell SH, Shaykhiev R, Rendeiro AF, Elemento O.  2022.  Author Correction: Unsupervised discovery of tissue architecture in multiplexed imaging.. Nat Methods. 19(12):1662.

Yao P, Witte D, Gimonet H, German A, Andreadis K, Cheng M, Sulica L, Elemento O, Barnes J, Rameau A.  2022.  Automatic classification of informative laryngoscopic images using deep learning.. Laryngoscope Investig Otolaryngol. 7(2):460-466.

Sternberg CN, Shin N, Chernyshov K, Calabro F, Cerbone L, Procopio G, Miheecheva N, Sagaradze G, Zaichikova A, Samarina N et al..  2022.  Case report: Metastatic urothelial cancer with an exceptional response to immunotherapy and comprehensive understanding of the tumor and the tumor microenvironment.. Front Oncol. 12:1006017.

Napoli S, Cascione L, Rinaldi A, Spriano F, Guidetti F, Zhang F, Cacciapuoti MTeresa, Mensah AAdjeiwaa, Sartori G, Munz N et al..  2022.  Characterization of GECPAR, a noncoding RNA that regulates the transcriptional program of diffuse large B-cell lymphoma.. Haematologica. 107(5):1131-1143.

Kulm S, Kolin DA, Langhans MT, Kaidi AC, Elemento O, Bostrom MP, Shen TS.  2022.  Characterization of Genetic Risk of End-Stage Knee Osteoarthritis Treated with Total Knee Arthroplasty: A Genome-Wide Association Study.. J Bone Joint Surg Am. 104(20):1814-1820.

Jobanputra V, Wrzeszczynski KO, Buttner R, Caldas C, Cuppen E, Grimmond S, Haferlach T, Mullighan C, Schuh A, Elemento O.  2022.  Clinical interpretation of whole-genome and whole-transcriptome sequencing for precision oncology.. Semin Cancer Biol. 84:23-31.

Rosenquist R, Cuppen E, Buettner R, Caldas C, Dreau H, Elemento O, Frederix G, Grimmond S, Haferlach T, Jobanputra V et al..  2022.  Clinical utility of whole-genome sequencing in precision oncology.. Semin Cancer Biol. 84:32-39.

Fontugne J, Cai PY, Alnajar H, Bhinder B, Park K, Ye H, Beg S, Sailer V, Siddiqui J, Blattner-Johnson M et al..  2022.  Collision tumors revealed by prospectively assessing subtype-defining molecular alterations in 904 individual prostate cancer foci.. JCI Insight. 7(4)

Berchuck JE, Baca SC, McClure HM, Korthauer K, Tsai HK, Nuzzo PVitale, Kelleher KM, He M, Steinharter JA, Zacharia S et al..  2022.  Detecting Neuroendocrine Prostate Cancer Through Tissue-Informed Cell-Free DNA Methylation Analysis.. Clin Cancer Res. 28(5):928-938.

Mosquera MJ, Kim S, Bareja R, Fang Z, Cai S, Pan H, Asad M, Martin MLaura, Sigouros M, Rowdo FM et al..  2022.  Extracellular Matrix in Synthetic Hydrogel-Based Prostate Cancer Organoids Regulate Therapeutic Response to EZH2 and DRD2 Inhibitors.. Adv Mater. 34(2):e2100096.

Jang J-Y, Hwang I, Pan H, Yao J, Alinari L, Imada E, Zanettini C, Kluk MJ, Wang Y, Lee Y et al..  2022.  A FOXO1-dependent transcription network is a targetable vulnerability of mantle cell lymphomas.. J Clin Invest. 132(24)

Jacobsen JOB, Baudis M, Baynam GS, Beckmann JS, Beltran S, Buske OJ, Callahan TJ, Chute CG, Courtot M, Danis D et al..  2022.  The GA4GH Phenopacket schema defines a computable representation of clinical data.. Nat Biotechnol. 40(6):817-820.

Xu X, Wang K, Vera O, Verma A, Jasani N, Bok I, Elemento O, Du D, Yu X, Karreth FA.  2022.  Gain of Chromosome 1q Perturbs a Competitive Endogenous RNA Network to Promote Melanoma Metastasis.. Cancer Res. 82(17):3016-3031.

Tang CP, Clark O, Ferrarone JR, Campos C, Lalani AS, Chodera JD, Intlekofer AM, Elemento O, Mellinghoff IK.  2022.  GCN2 kinase activation by ATP-competitive kinase inhibitors.. Nat Chem Biol. 18(2):207-215.

Kulm S, Langhans MT, Shen TS, Kolin DA, Elemento O, Rodeo SA.  2022.  Genome-Wide Association Study of Adhesive Capsulitis Suggests Significant Genetic Risk Factors.. J Bone Joint Surg Am. 104(21):1869-1876.

van der Mijn JC, Eng KW, Chandra P, Fernandez E, Ramazanoglu S, Sigaras A, Oromendia C, Gudas LJ, Tagawa ST, Nanus DM et al..  2022.  The genomic landscape of metastatic clear cell renal cell carcinoma after systemic therapy.. Mol Oncol. 16(12):2384-2395.

Altorki NK, Borczuk AC, Harrison S, Groner LK, Bhinder B, Mittal V, Elemento O, McGraw TE.  2022.  Global evolution of the tumor microenvironment associated with progression from preinvasive invasive to invasive human lung adenocarcinoma.. Cell Rep. 39(1):110639.

DiNapoli SE, Martinez-McFaline R, Shen H, Doane AS, Perez AR, Verma A, Simon A, Nelson I, Balgobin CA, Bourque CT et al..  2022.  Histone 3 Methyltransferases Alter Melanoma Initiation and Progression Through Discrete Mechanisms.. Front Cell Dev Biol. 10:814216.

Yaron TM, Heaton BE, Levy TM, Johnson JL, Jordan TX, Cohen BM, Kerelsky A, Lin T-Y, Liberatore KM, Bulaon DK et al..  2022.  Host protein kinases required for SARS-CoV-2 nucleocapsid phosphorylation and viral replication.. Sci Signal. 15(757):eabm0808.