Publications

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.

Jaiswal A, Verma A, Dannenfelser R, Melssen M, Tirosh I, Izar B, Kim T-G, Nirschl CJ, K Devi SP, Olson WC et al..  2022.  An activation to memory differentiation trajectory of tumor-infiltrating lymphocytes informs metastatic melanoma outcomes.. Cancer Cell. 40(5):524-544.e5.

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)

Jessurun J, Orr C, McNulty SN, Hagen CE, Alnajar H, Wilkes D, Kudman S, Assaad MAl, Dorsaint P, Ohara K et al..  2023.  GLI1 -Rearranged Enteric Tumor : Expanding the Spectrum of Gastrointestinal Neoplasms With GLI1 Gene Fusions.. Am J Surg Pathol. 47(1):65-73.

Jiang Y, Ortega-Molina A, Geng H, Ying H-Y, Hatzi K, Parsa S, McNally D, Wang L, Doane AS, Agirre X et al..  2017.  CREBBP Inactivation Promotes the Development of HDAC3-Dependent Lymphomas.. Cancer Discov. 7(1):38-53.

Jiang Y, Nie K, Redmond D, Melnick AM, Tam W, Elemento O.  2015.  VDJ-Seq: Deep Sequencing Analysis of Rearranged Immunoglobulin Heavy Chain Gene to Reveal Clonal Evolution Patterns of B Cell Lymphoma.. J Vis Exp. (106):e53215.

Jiang Y, T Soong D, Wang L, Melnick AM, Elemento O.  2012.  Genome-wide detection of genes targeted by non-Ig somatic hypermutation in lymphoma.. PLoS One. 7(7):e40332.

Jiang Y, Redmond D, Nie K, Eng KW, Clozel T, Martin P, Tan LHc, Melnick AM, Tam W, Elemento O.  2014.  Deep sequencing reveals clonal evolution patterns and mutation events associated with relapse in B-cell lymphomas.. Genome Biol. 15(8):432.

Jiang Y, Elemento O.  2014.  Tracing the roots of cancer evolution.. Cancer Discov. 4(9):995-7.

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.

Johnson M, Bell A, Lauing KL, Ladomersky E, Zhai L, Penco-Campillo M, Shah Y, Mauer E, Xiu J, Nicolaides T et al..  2023.  Advanced Age in Humans and Mouse Models of Glioblastoma Show Decreased Survival from Extratumoral Influence.. Clin Cancer Res. 29(23):4973-4989.

Johnson JL, Yaron TM, Huntsman EM, Kerelsky A, Song J, Regev A, Lin T-Y, Liberatore K, Cizin DM, Cohen BM et al..  2023.  An atlas of substrate specificities for the human serine/threonine kinome.. Nature. 613(7945):759-766.

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.

Kandola MS, Kulm S, Kim LK, Markowitz SM, Liu CF, Thomas G, Ip JE, Lerman BB, Elemento O, Cheung JW.  2023.  Population-Level Prevalence of Rare Variants Associated With Atrial Fibrillation and its Impact on Patient Outcomes.. JACC Clin Electrophysiol. 9(7 Pt 2):1137-1146.

Kansler ER, Verma A, Langdon EM, Simon-Vermot T, Yin A, Lee W, Attiyeh M, Elemento O, White RM.  2017.  Melanoma genome evolution across species.. BMC Genomics. 18(1):136.

Karass M, Bareja R, Shelkey E, Vlachostergios PJ, Robinson BD, Khani F, Mosquera JMiguel, Scherr DS, Sboner A, Tagawa ST et al..  2019.  Oncogenic Addiction to ERBB2 Signaling Predicts Response to Trastuzumab in Urothelial Cancer.. J Natl Compr Canc Netw. 17(3):194-200.

Karimzadeh M, Momen-Roknabadi A, Cavazos TB, Fang Y, Chen N-C, Multhaup M, Yen J, Ku J, Wang J, Zhao X et al..  2024.  Deep generative AI models analyzing circulating orphan non-coding RNAs enable detection of early-stage lung cancer.. Nat Commun. 15(1):10090.

Kasap C, Elemento O, Kapoor TM.  2014.  DrugTargetSeqR: a genomics- and CRISPR-Cas9-based method to analyze drug targets.. Nat Chem Biol. 10(8):626-8.

Kassambara A, Jourdan M, Bruyer A, Robert N, Pantesco V, Elemento O, Klein B, Moreaux J.  2017.  Global miRNA expression analysis identifies novel key regulators of plasma cell differentiation and malignant plasma cell.. Nucleic Acids Res. 45(10):5639-5652.

Kassambara A, Herviou L, Ovejero S, Jourdan M, Thibaut C, Vikova V, Pasero P, Elemento O, Moreaux J.  2021.  RNA-sequencing data-driven dissection of human plasma cell differentiation reveals new potential transcription regulators.. Leukemia. 35(5):1451-1462.

Kaya C, Dorsaint P, Mercurio S, Campbell AM, Eng KWha, Nikiforova MN, Elemento O, Nikiforov YE, Sboner A.  2021.  Limitations of Detecting Genetic Variants from the RNA Sequencing Data in Tissue and Fine-Needle Aspiration Samples.. Thyroid. 31(4):589-595.

Kaza S, Mohanty AS, Serpedin A, Yau J, Kim YEun, Kutler RB, Elemento O, Sulica L, Khosravi P, Rameau A.  2026.  Exploring Real-Time Tracking of Vocal Fold Polyps in Video-Stroboscopy Using Deep Learning.. Laryngoscope.

Keutgen XM, Buitrago D, Filicori F, Kundel A, Elemento O, Fahey TJ, Zarnegar R.  2012.  Calcimimetics versus parathyroidectomy for treatment of primary hyperparathyroidism: retrospective chart analysis of a prospective database.. Ann Surg. 255(5):981-5.

Keutgen XM, Filicori F, Crowley MJ, Wang Y, Scognamiglio T, Hoda R, Buitrago D, Cooper D, Zeiger MA, Zarnegar R et al..  2012.  A panel of four miRNAs accurately differentiates malignant from benign indeterminate thyroid lesions on fine needle aspiration.. Clin Cancer Res. 18(7):2032-8.

Khani F, Hooper WF, Wang X, Chu TR, Shah M, Winterkorn L, Sigouros M, Conteduca V, Pisapia D, Wobker S et al..  2023.  Author Correction: Evolution of structural rearrangements in prostate cancer intracranial metastases.. NPJ Precis Oncol. 7(1):113.