Publications

Kim YE, Dobko M, Li H, Shao T, Periyakoil P, Tipton C, Colasacco C, Serpedin A, Elemento O, Sabuncu M et al..  2025.  A Deep-Learning Model for Multi-class Audio Classification of Vocal Fold Pathologies in Office Stroboscopy.. Laryngoscope. 135(7):2428-2436.

Ohara K, Assaad MAl, McNulty SN, Alnajar H, Sboner A, Wilkes DC, He F, Xiang JZhaoying, Mathew S, Elemento O et al..  2025.  Detection of rare and novel gene fusions in patients with diffuse glioma: An institutional retrospective study.. J Neuropathol Exp Neurol. 84(3):269-271.

Windon A, Assaad MAl, Hadi K, Mendelson N, Hissong E, Deshpande A, Tranquille M, Mclee J, Levine MF, Patel M et al..  2025.  Emerging molecular phenotypes and potential therapeutic targets in esophageal and gastric adenocarcinoma unearthed by whole genome and transcriptome analyses.. Pathol Res Pract. 266:155788.

Assaad MAl, Hadi K, Tu J, Levine MF, Patel M, Deshpande A, Manohar J, Sigouros M, Sboner A, Chapman-Davis E et al..  2025.  Enhancing the detection of clinically relevant biomarkers in advanced uterine and tubo-ovarian carcinomas through genome-wide analysis.. Pathol Res Pract. 266:155773.

Cheng APellan, Widman AJ, Arora A, Rusinek I, Sossin A, Rajagopalan S, Midler N, Hooper WF, Murray RM, Halmos D et al..  2025.  Error-corrected flow-based sequencing at whole-genome scale and its application to circulating cell-free DNA profiling.. Nat Methods. 22(5):973-981.

Phipps W, Bhinder B, Towlerton A, Mooka P, Kafeero J, Fitzgibbon M, Elemento O, Cesarman E.  2025.  Exome Sequencing Reveals a Sparse Genomic Landscape in Kaposi Sarcoma.. Mol Cancer Res. 23(5):438-449.

Rajendran S, Rehani E, Phu W, Zhan Q, Malmsten JE, Meseguer M, Miller KA, Rosenwaks Z, Elemento O, Zaninovic N et al..  2025.  A foundational model for in vitro fertilization trained on 18 million time-lapse images.. Nat Commun. 16(1):6235.

Claridge SE, Nath S, Baum A, Farias R, Cavallo J-A, Rizvi NM, De Boni L, Park E, Granados GLara, Hauesgen M et al..  2025.  Functional genomics pipeline identifies CRL4 inhibition for the treatment of ovarian cancer.. Clin Transl Med. 15(2):e70078.

Ranti D, Yu H, Salomé B, Bang S, Duquesne I, Wang YA, Bieber C, Strandgaard T, Merritt E, Doherty G et al..  2025.  HLA-E and NKG2A Mediate Resistance to BCG Immunotherapy in Non-Muscle-Invasive Bladder Cancer.. bioRxiv.

Buqué A, Bloy N, Petroni G, Jiménez-Cortegana C, Sato A, Iribarren C, Yamazaki T, Galassi C, Hensler M, Bhinder B et al..  2025.  Impact of radiation therapy dose, fractionation, and immunotherapeutic partner in a mouse model of hormone receptor-positive mammary carcinogenesis.. J Natl Cancer Inst. 117(5):934-947.

Hissong E, Bhinder B, Kim J, Ohara K, Ravichandran H, Assaad MAl, Elsoukkary S, Shusterman M, Khan U, Eng KWha et al..  2025.  Integrative transcriptomic and single-cell protein characterization of colorectal carcinoma delineates distinct tumor immune microenvironments associated with overall survival.. Pathol Res Pract. 273:156150.

Barton BM, Son F, Verma A, Bal SKumar, Tang Q, Wang R, Umphred-Wilson K, Khan R, Trichka J, Dong H et al..  2025.  IRE1α-XBP1 safeguards hematopoietic stem and progenitor cells by restricting pro-leukemogenic gene programs.. Nat Immunol. 26(2):200-214.

Rowdo FPMadorsky, Martini R, Ackermann SE, Tang CP, Tranquille M, Irizarry A, Us I, Alawa O, Moyer JE, Sigouros M et al..  2025.  Kinome-Focused CRISPR-Cas9 Screens in African Ancestry Patient-Derived Breast Cancer Organoids Identify Essential Kinases and Synergy of EGFR and FGFR1 Inhibition.. Cancer Res. 85(3):551-566.

He Y, Waltman P, Kane T, Sigouros M, Chandra P, Gorski K, Zhang C, Proietti A, Singh A, Mittal V et al..  2025.  Longitudinal Genomic Analysis of Five Cases of Recurrent Thymomas.. J Thorac Oncol.

Guevara D, Shin N, Boiko A, Valiev I, Elsaeed AG, Mosquera JMiguel, Assaad MAl, Manohar J, Sigouros M, Zaichikova A et al..  2025.  Mesonephric Adenocarcinoma in a Young Male Patient.. Anticancer Res. 45(2):619-623.

Chen HJoyce, Gardner EE, Shah Y, Zhang K, Thakur A, Zhang C, Elemento O, Varmus H.  2025.  Metastatic small cell lung cancer arises from TP53/RB1-deficient and MYC overproduction hESC-derived PNECs.. Elife. 13

Vicario R, Fragkogianni S, Weber L, Lazarov T, Hu Y, Hayashi SY, Craddock B, Socci ND, Alberdi A, Baako A et al..  2025.  A microglia clonal inflammatory disorder in Alzheimer's disease.. Elife. 13

Ruan J, Bond DA, Shah BD, Allan JN, Rutherford SC, Gribbin C, Chen Z, Bhinder B, Tam W, Rossi D et al..  2025.  MRD-driven Initial Therapy of Acalabrutinib and Lenalidomide plus Rituximab (ALR) or Obinutuzumab (ALO) for Mantle Cell Lymphoma.. Blood Adv.

de la Mora JDelgado-, Assaad MAl, Quitian S, Levine MF, Deshpande A, Sigouros M, Manohar J, Medina-Martínez JS, Sboner A, Elemento O et al..  2025.  Novel structural variants that impact cell cycle genes are elucidated in metastatic gastrointestinal stromal tumors.. Pathol Res Pract. 266:155782.

Kyei I, Bea VJ, Gyan KK, Adjei E, Stonaker B, Bekele M, Abebe E, Davis M, Boakye A, Boateng R et al..  2025.  Oncologic Anthropology and the African Diaspora: Twenty-Year Anniversary Report, International Center for the Study of Breast Cancer Subtypes (ICSBCS).. Ann Surg Oncol.

Hanif SZ, Au CMCherie, Torregroza I, Kutz C, Jannath SY, Fabiha T, Bhinder B, Washburn MP, Devost D, Liu S et al..  2025.  The Orphan G Protein-Coupled Receptor GPR52 is a Novel Regulator of Breast Cancer Multicellular Organization.. bioRxiv.

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.