Publications

Cheng APellan, Rusinek I, Sossin A, Widman AJ, Meiri E, Krieger G, Hirschberg O, Tov DShem, Gilad S, Jaimovich A et al..  2025.  Paired plus-minus sequencing is an ultra-high throughput and accurate method for dual strand sequencing of DNA molecules.. bioRxiv.

Bhinder B, Friedl V, Sethuraman S, Risso D, Chiotti KE, R Mashl J, Ellrott KP, Lee JA, Wong CK, Gyan K et al..  2025.  Pan-cancer immune and stromal deconvolution predicts clinical outcomes and mutation profiles.. Sci Rep. 15(1):23921.

Fiore D, Cappelli LVincenzo, Zhaoqi L, Kotlov N, Sorokina M, Phillip J, Zumbo P, Yoffe L, Ghione P, Wang A et al..  2025.  A patient-derived T cell lymphoma biorepository uncovers pathogenetic mechanisms and host-related therapeutic vulnerabilities.. Cell Rep Med. 6(4):102029.

K Devi SP, Wang E, Jaiswal A, Konieczny P, Kim T-G, Nirschl CJ, Verma A, Liu Y, Milczanowski J, Christo SN et al..  2025.  PD-1 is requisite for skin T cell formation and specification by TGFβ.. Nat Immunol. 26(8):1339-1351.

Bai Z, Osman M, Brendel M, Tangen CM, Flaig TW, Thompson IM, Plets M, M Lucia S, Theodorescu D, Gustafson D et al..  2025.  Predicting response to neoadjuvant chemotherapy in muscle-invasive bladder cancer via interpretable multimodal deep learning.. NPJ Digit Med. 8(1):174.

Bayou N, Henretta S, Munoz-Arcos L, Molteni E, Gianni C, Serafini MSerena, Nicolò E, Pontolillo L, Pasto B, Gaudio HAndrew et al..  2025.  Quantitative HER2 profiling on circulating tumor cells using an EpCAM-independent platform in metastatic breast cancer.. Cancer Cell Int. 25(1):439.

Akinsanya K, AlQuraishi M, Boija A, Chodera J, Cichońska A, Ghassemi M, Head M, Jin W, Kibbe WA, Krogan N et al..  2025.  Redefining druggable targets with artificial intelligence.. Nat Biotechnol. 43(9):1416-1418.

Vicario R, Fragkogianni S, Pokrovskii M, Meyer C, Lopez-Rodrigo E, Hu Y, Ogishi M, Alberdi A, Baako A, Ay O et al..  2025.  Role of clonal inflammatory microglia in histiocytosis-associated neurodegeneration.. Neuron. 113(7):1065-1081.e13.

Kim J, Ravichandran H, Yoffe L, Bhinder B, Finos K, Singh A, Pua BB, Bates S, Huang BEmma, Rendeiro AF et al..  2025.  Simultaneous immunomodulation and epithelial-to-mesenchymal transition drives lung adenocarcinoma progression.. bioRxiv.

Park J, De Gregorio R, Hissong E, Ozcelik E, Bartelo N, Dezem FSegato, Zhang L, Marção M, Chasteen H, Zheng Y et al..  2025.  The Spatial Atlas of Human Anatomy (SAHA): A Multimodal Subcellular-Resolution Reference Across Human Organs.. bioRxiv.

Rubinelli L, Manzo OLaura, Sungho J, Del Gaudio I, Bareja R, Marino A, Palikhe S, Di Mauro V, Bucci M, Falcone DJ et al..  2025.  Suppression of endothelial ceramide de novo biosynthesis by Nogo-B contributes to cardiometabolic diseases.. Nat Commun. 16(1):1968.

Ovejero S, Devin J, Alibert L, Soun C, Lin Y-L, Dutrieux L, Abouladze M, de Paco EGarcia, Gadacha OKarmous, Constantinou A et al..  2025.  Synthetic Lethal Combinations of DNA Repair Inhibitors and Genotoxic Agents to Target High-Risk Diffuse Large B Cell Lymphoma.. Hematol Oncol. 43(5):e70131.

Roshal M, Kong IY, Dinalankara W, Reichel JB, Teater M, Binder B, Zairis S, Brody JD, Park SI, Kovach AE et al..  2025.  Transcriptome sequencing of Hodgkin lymphoma Hodgkin and Reed-Sternberg cells reveals escape from NK cell recognition and an unfolded protein response.. bioRxiv.

Honigsberg R, Cruz T, Yoffe L, Tang MStephanie, Dicle O, Markowitz G, Michael M, Singh A, Altorki NK, Elemento O et al..  2025.  Tumor-specific draining lymph node CD8 T cells orchestrate an anti-tumor response to neoadjuvant PD-1 immune checkpoint blockade.. bioRxiv.

Nath S, Claridge S, Granados GLara, Assaad MAl, Park E, Cavallo J-A, Nuwere U, Ackon MEsi, De Boni L, Baker S et al..  2025.  Unlocking the therapeutic potential of rigosertib as a selective therapy for ovarian cancer.. Cell Rep Med. 6(7):102218.

Guevara D, Shin N, Boiko A, Valiev I, Elsaeed AG, Mosquera JMiguel, Assaad MAl, Manohar J, Sigouros M, Zaichikova A et al..  2025.  Unusual Presentation of Advanced Urothelial Cancer in a Young Patient.. Anticancer Res. 45(2):613-618.

Elemento O, Khozin S, Sternberg CN.  2025.  The use of artificial intelligence for cancer therapeutic decision-making.. NEJM AI. 2(5)

de la Mora JDelgado-, Assaad MAl, Karaaslan S, Hadi K, Halima A, Deshpande A, Manohar J, Sigouros M, Medina-Martínez JS, Lieberman MD et al..  2025.  Whole genome and transcriptome analysis of pancreatic acinar cell carcinoma elucidates mechanisms of homologous recombination deficiency and unravels novel relevant fusion events.. Pathol Res Pract. 266:155798.

Kalomeris T, Assaad MAl, de la Mora JDelgado-, Gundem G, Levine MF, Boyraz B, Manohar J, Sigouros M, Medina-Martínez JS, Sboner A et al..  2025.  Whole genome profiling of primary and metastatic adrenocortical carcinoma unravels significant molecular events.. Pathol Res Pract. 266:155725.

El-Deiry WS, Bresson C, Wunder F, Carneiro BA, Dizon DS, Warner JL, Graff SL, Azzoli CG, Wong ET, Cheng L et al..  2025.  Worldwide Innovative Network (WIN) Consortium in Personalized Cancer Medicine: Bringing next-generation precision oncology to patients.. Oncotarget. 16:140-162.

Guillet S, Lazarov T, Jordan N, Boisson B, Tello M, Craddock B, Zhou T, Nishi C, Bareja R, Yang H et al..  2024.  ACK1 and BRK non-receptor tyrosine kinase deficiencies are associated with familial systemic lupus and involved in efferocytosis.. Elife. 13

Guillet S, Lazarov T, Jordan N, Boisson B, Tello M, Craddock B, Zhou T, Nishi C, Bareja R, Yang H et al..  2024.  ACK1 and BRK non-receptor tyrosine kinase deficiencies are associated with familial systemic lupus and involved in efferocytosis.. medRxiv.

Altorki NK, Walsh ZH, Melms JC, Port JL, Lee BE, Nasar A, Spinelli C, Caprio L, Rogava M, Ho P et al..  2024.  Author Correction: Neoadjuvant durvalumab plus radiation versus durvalumab alone in stages I-III non-small cell lung cancer: survival outcomes and molecular correlates of a randomized phase II trial.. Nat Commun. 15(1):225.

Rajendran S, Brendel M, Barnes J, Zhan Q, Malmsten JE, Zisimopoulos P, Sigaras A, Ofori-Atta K, Meseguer M, Miller KA et al..  2024.  Automatic ploidy prediction and quality assessment of human blastocysts using time-lapse imaging.. Nat Commun. 15(1):7756.

Shah Y, Kulm S, Nauseef JT, Chen Z, Elemento O, Kensler KH, Sharaf RN.  2024.  Benchmarking multi-ancestry prostate cancer polygenic risk scores in a real-world cohort.. PLoS Comput Biol. 20(4):e1011990.