Beatrice S. Knudsen
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Beatrice S. Knudsen, MD, PhD

  • Over the last 10 years, I built a program that integrates histopathology, multiplex tissue staining, digital image analysis and computational pathology for biomarker development. Advances in machine learning and high-performance computing permit the extraction of quantitative data from images of cancer tissues form patients and mouse models and to use images as molecular datasets. I am applying this approach to close the gap between laboratory research and clinical care and to develop novel algorithms for diagnosis, prognostication and treatment of cancer patients.

    Specialties

    • Pathology, Anatomical

    Board Certification

    American Board of Anatomic Pathology

  • Over the last 10 years, I built a program that integrates histopathology, multiplex tissue staining, digital image analysis and computational pathology for biomarker development. Advances in machine learning and high-performance computing permit the extraction of quantitative data from images of cancer tissues form patients and mouse models and to use images as molecular datasets. I am applying this approach to close the gap between laboratory research and clinical care and to develop novel algorithms for diagnosis, prognostication and treatment of cancer patients.

    Board Certification and Academic Information

    Academic Departments Pathology -Professor (Clinical)
    Board Certification
    American Board of Anatomic Pathology

    Selected Publications

    Journal Article

    1. Guedes LB, Morais CL, Fedor H, Hicks J, Gurel B, Melamed J, Lee P, Gopalan A, Knudsen BS, True LD, Scher HI, Fine SW, Trock BJ, De Marzo AM, Lotan T (2019). Effect of Preanalytic Variables on an Automated PTEN Immunohistochemistry Assay for Prostate Cancer. Archives of pathology & laboratory medicine, 143(3), 338-348. (Read full publication)
    2. Pham H, Hui H, Morvaridi S, Cai J, Zhang S, Tan J, Wu V, Levin N, Knudsen B, Goddard WA 3rd, Pandol SJ, Abrol (2016). A bitter pill for type 2 diabetes? The activation of bitter taste receptor TAS2R38 can stimulate GLP-1 release from enteroendocrine L-cells. Biochemical and biophysical research communications, 475(3), 295-300. (Read full publication)
    3. Harryman WL, Hinton JP, Rubenstein CP, Singh P, Nagle RB, Parker SJ, Knudsen BS, Cress A (2016). The Cohesive Metastasis Phenotype in Human Prostate Cancer. Biochimica et biophysica acta, 1866(2), 221-231. (Read full publication)
    4. Wang M, Knudsen BS, Nagle RB, Rogers GC, Cress A (2019). A method of quantifying centrosomes at the single-cell level in human normal and cancer tissue. Molecular biology of the cell, 30(7), 811-819. (Read full publication)
    5. Wang M, Hinton JP, Gard JMC, Garcia JGN, Knudsen BS, Nagle RB, Cress A (2019). Integrin ¿6ß4E variant is associated with actin and CD9 structures and modifies the biophysical properties of cell-cell and cell-extracellular matrix interactions. Molecular biology of the cell, 30(7), 838-850. (Read full publication)
    6. Alvarez MJ, Subramaniam PS, Tang LH, Grunn A, Aburi M, Rieckhof G, Komissarova EV, Hagan EA, Bodei L, Clemons PA, Dela Cruz FS, Dhall D, Diolaiti D, Fraker DA, Ghavami A, Kaemmerer D, Karan C, Kidd M, Kim KM, Kim HC, Kunju LP, Langel Ü, Li Z, Lee J, Li H, LiVolsi V, Pfragner R, Rainey AR, Realubit RB, Remotti H, Regberg J, Roses R, Rustgi A, Sepulveda AR, Serra S, Shi C, Yuan X, Barberis M, Bergamaschi R, Chinnaiyan AM, Detre T, Ezzat S, Frilling A, Hommann M, Jaeger D, Kim MK, Knudsen BS, Kung AL, Leahy E, Metz DC, Milsom JW, Park YS, Reidy-Lagunes D, Schreiber S, Washington K, Wiedenmann B, Modlin I, Califano (2018). A precision oncology approach to the pharmacological targeting of mechanistic dependencies in neuroendocrine tumors. Nature genetics, 50(7), 979-989. (Read full publication)
    7. Li J, Speier W, Ho KC, Sarma KV, Gertych A, Knudsen BS, Arnold C (2018). An EM-based semi-supervised deep learning approach for semantic segmentation of histopathological images from radical prostatectomies. Computerized medical imaging and graphics, 69, 125-133. (Read full publication)
    8. Gertych A, Ing N, Ma Z, Fuchs TJ, Salman S, Mohanty S, Bhele S, Velásquez-Vacca A, Amin MB, Knudsen B (2015). Machine learning approaches to analyze histological images of tissues from radical prostatectomies. Computerized medical imaging and graphics, 46 Pt 2, 197-208. (Read full publication)
    9. Ogden A, Rida PC, Knudsen BS, Kucuk O, Aneja (2015). Docetaxel-induced polyploidization may underlie chemoresistance and disease relapse. Cancer letters, 367(2), 89-92. (Read full publication)
    10. Reis-Sobreiro M, Chen JF, Novitskaya T, You S, Morley S, Steadman K, Gill NK, Eskaros A, Rotinen M, Chu CY, Chung LWK, Tanaka H, Yang W, Knudsen BS, Tseng HR, Rowat AC, Posadas EM, Zijlstra A, Di Vizio D, Freeman M (2018). Emerin Deregulation Links Nuclear Shape Instability to Metastatic Potential. Cancer research, 78(21), 6086-6097. (Read full publication)
    11. You S, Knudsen BS, Erho N, Alshalalfa M, Takhar M, Al-Deen Ashab H, Davicioni E, Karnes RJ, Klein EA, Den RB, Ross AE, Schaeffer EM, Garraway IP, Kim J, Freeman M (2016). Integrated Classification of Prostate Cancer Reveals a Novel Luminal Subtype with Poor Outcome. Cancer research, 76(17), 4948-58. (Read full publication)
    12. Gertych A, Ma Z, Tajbakhsh J, Velásquez-Vacca A, Knudsen B (2016). Rapid 3-D delineation of cell nuclei for high-content screening platforms. Computers in biology and medicine, 69, 328-38. (Read full publication)
    13. Parikh NR, Kishan AU, Kane N, Diaz-Perez S, Ganapathy E, Nazarian R, Felix C, Mathis C, Bradley M, Sachdeva A, Wyatt B, Basehart V, Zomorodian N, Lin L, King CR, Kupelian PA, Rettig MB, Steinberg ML, Cao M, Knudsen BS, Elashoff D, Schaue D, Reiter RE, Nickols N (2020). Phase 1 Trial of Stereotactic Body Radiation Therapy Neoadjuvant to Radical Prostatectomy for Patients With High-Risk Prostate Cancer. International journal of radiation oncology, biology, physics, 108(4), 930-935. (Read full publication)
    14. Lai JP, Conley A, Knudsen BS, Guindi (2015). Hypoxia after transarterial chemoembolization may trigger a progenitor cell phenotype in hepatocellular carcinoma. Histopathology, 67(4), 442-50. (Read full publication)
    15. Das L, Anderson TA, Gard JM, Sroka IC, Strautman SR, Nagle RB, Morrissey C, Knudsen BS, Cress A (2017). Characterization of Laminin Binding Integrin Internalization in Prostate Cancer Cells. Journal of cellular biochemistry, 118(5), 1038-1049. (Read full publication)
    16. Wang M, Nagle RB, Knudsen BS, Rogers GC, Cress A (2017). A basal cell defect promotes budding of prostatic intraepithelial neoplasia. Journal of cell science, 130(1), 104-110. (Read full publication)
    17. Pollan SG, Huang F, Sperger JM, Lang JM, Morrissey C, Cress AE, Chu CY, Bhowmick NA, You S, Freeman MR, Spassov DS, Moasser MM, Carter WG, Satapathy SR, Shah K, Knudsen B (2018). Regulation of inside-out ß1-integrin activation by CDCP1. Oncogene, 37(21), 2817-2836. (Read full publication)
    18. Wang M, Nagle RB, Knudsen BS, Cress AE, Rogers G (2020). Centrosome loss results in an unstable genome and malignant prostate tumors. Oncogene, 39(2), 399-413. (Read full publication)
    19. Rotinen M, You S, Yang J, Coetzee SG, Reis-Sobreiro M, Huang WC, Huang F, Pan X, Yáñez A, Hazelett DJ, Chu CY, Steadman K, Morrissey CM, Nelson PS, Corey E, Chung LWK, Freedland SJ, Di Vizio D, Garraway IP, Murali R, Knudsen BS, Freeman M (2018). ONECUT2 is a targetable master regulator of lethal prostate cancer that suppresses the androgen axis. Nature medicine, 24(12), 1887-1898. (Read full publication)
    20. Li W, Li J, Sarma KV, Ho KC, Shen S, Knudsen BS, Gertych A, Arnold C (2019). Path R-CNN for Prostate Cancer Diagnosis and Gleason Grading of Histological Images. IEEE transactions on medical imaging, 38(4), 945-954. (Read full publication)
    21. Hahn NM, Knudsen BS, Daneshmand S, Koch MO, Bihrle R, Foster RS, Gardner TA, Cheng L, Liu Z, Breen T, Fleming MT, Lance R, Corless CL, Alva AS, Shen SS, Huang F, Gertych A, Gallick GE, Mallick J, Ryan C, Galsky MD, Lerner SP, Posadas EM, Sonpavde (2016). Neoadjuvant dasatinib for muscle-invasive bladder cancer with tissue analysis of biologic activity. Urologic oncology, 34(1), 4.e11-7. (Read full publication)
    22. Huang F, Tanaka H, Knudsen BS, Rutgers J (2020). Mutant POLQ and POLZ/REV3L DNA polymerases may contribute to the favorable survival of patients with tumors with POLE mutations outside the exonuclease domain. BMC medical genetics, 21(1), 167. (Read full publication)
    23. Miller ET, You S, Cadaneanu RM, Kim M, Yoon J, Liu ST, Li X, Kwan L, Hodge J, Quist MJ, Grasso CS, Lewis MS, Knudsen BS, Freeman MR, Garraway I (2020). Chromosomal instability in untreated primary prostate cancer as an indicator of metastatic potential. BMC cancer, 20(1), 398. (Read full publication)
    24. Knudsen BS, Kim HL, Erho N, Shin H, Alshalalfa M, Lam LLC, Tenggara I, Chadwich K, Van Der Kwast T, Fleshner N, Davicioni E, Carroll PR, Cooperberg MR, Chan JM, Simko J (2016). Application of a Clinical Whole-Transcriptome Assay for Staging and Prognosis of Prostate Cancer Diagnosed in Needle Core Biopsy Specimens. The Journal of molecular diagnostics, 18(3), 395-406. (Read full publication)
    25. Das L, Gard JMC, Prekeris R, Nagle RB, Morrissey C, Knudsen BS, Miranti CK, Cress A (2018). Novel Regulation of Integrin Trafficking by Rab11-FIP5 in Aggressive Prostate Cancer. Molecular cancer research, 16(8), 1319-1331. (Read full publication)
    26. Allott EH, Macias E, Sanders S, Knudsen BS, Thomas GV, Hursting SD, Freedland S (2017). Impact of carbohydrate restriction in the context of obesity on prostate tumor growth in the Hi-Myc transgenic mouse model. Prostate cancer and prostatic diseases, 20(2), 165-171. (Read full publication)
    27. Nickols NG, Ganapathy E, Nguyen C, Kane N, Lin L, Diaz-Perez S, Nazarian R, Mathis C, Felix C, Basehart V, Zomorodian N, Kwak J, Kishan AU, King CR, Kupelian PA, Rettig MB, Steinberg ML, Cao M, Knudsen BS, Chu FI, Romero T, Elashoff D, Reiter RE, Schaue (2020). The intraprostatic immune environment after stereotactic body radiotherapy is dominated by myeloid cells. Prostate cancer and prostatic diseases, 24, 135-139. (Read full publication)
    28. Li J, Sarma KV, Chung Ho K, Gertych A, Knudsen BS, Arnold C (2018). A Multi-scale U-Net for Semantic Segmentation of Histological Images from Radical Prostatectomies. AMIA ... Annual Symposium proceedings. AMIA Symposium, 2017, 1140-1148. (Read full publication)
    29. Qin Y, Walts AE, Knudsen BS, Gertych (2015). Computerized delineation of nuclei in liquid-based pap smears stained with immunohistochemical biomarkers. Cytometry. Part B, Clinical cytometry, 88(2), 110-9. (Read full publication)
    30. Ma Z, Shiao SL, Yoshida EJ, Swartwood S, Huang F, Doche ME, Chung AP, Knudsen BS, Gertych (2017). Data integration from pathology slides for quantitative imaging of multiple cell types within the tumor immune cell infiltrate. Diagnostic pathology, 12(1), 69. (Read full publication)
    31. Fassler DJ, Abousamra S, Gupta R, Chen C, Zhao M, Paredes D, Batool SA, Knudsen BS, Escobar-Hoyos L, Shroyer KR, Samaras D, Kurc T, Saltz (2020). Deep learning-based image analysis methods for brightfield-acquired multiplex immunohistochemistry images. Diagnostic pathology, 15(1), 100. (Read full publication)
    32. Conley A, Minciacchi VR, Lee DH, Knudsen BS, Karlan BY, Citrigno L, Viglietto G, Tewari M, Freeman MR, Demichelis F, Di Vizio (2017). High-throughput sequencing of two populations of extracellular vesicles provides an mRNA signature that can be detected in the circulation of breast cancer patients. RNA biology, 14(3), 305-316. (Read full publication)
    33. Liu S, Cadaneanu RM, Zhang B, Huo L, Lai K, Li X, Galet C, Grogan TR, Elashoff D, Freedland SJ, Rettig M, Aronson WJ, Knudsen BS, Lewis MS, Garraway I (2016). Keratin 13 Is Enriched in Prostate Tubule-Initiating Cells and May Identify Primary Prostate Tumors that Metastasize to the Bone. PloS one, 11(10), e0163232. (Read full publication)
    34. Kouspou MM, Fong JE, Brew N, Hsiao STF, Davidson SL, Choyke PL, Crispino T, Jain S, Jenster GW, Knudsen BS, Millar JL, Mittmann N, Ryan CJ, Tombal B, Buzza (2020). The Movember Prostate Cancer Landscape Analysis: an assessment of unmet research needs. Nature reviews. Urology, 17(9), 499-512. (Read full publication)
    35. Padilla-Rodriguez M, Parker SS, Adams DG, Westerling T, Puleo JI, Watson AW, Hill SM, Noon M, Gaudin R, Aaron J, Tong D, Roe DJ, Knudsen B, Mouneimne (2018). The actin cytoskeletal architecture of estrogen receptor positive breast cancer cells suppresses invasion. Nature communications, 9(1), 2980. (Read full publication)
    36. Edderkaoui M, Xu S, Chheda C, Morvaridi S, Hu RW, Grippo PJ, Mascariñas E, Principe DR, Knudsen B, Xue J, Habtezion A, Uyeminami D, Pinkerton KE, Pandol S (2016). HDAC3 mediates smoking-induced pancreatic cancer. Oncotarget, 7(7), 7747-60. (Read full publication)
    37. Vidal AC, Chen Z, Howard LE, Moreira DM, Castro-Santamaria R, Andriole GL, Taioli E, Fowke JH, Knudsen B, Drake CG, Nickel JC, Freedland S (2016). Racial differences in prostate inflammation: results from the REDUCE study. Oncotarget, 8(42), 71393-71399. (Read full publication)
    38. Jan YJ, Yoon J, Chen JF, Teng PC, Yao N, Cheng S, Lozano A, Chu GCY, Chung H, Lu YT, Chen PJ, Wang JJ, Lee YT, Kim M, Zhu Y, Knudsen BS, Feng FY, Garraway IP, Gao AC, Chung LWK, Freeman MR, You S, Tseng HR, Posadas E (2019). A Circulating Tumor Cell-RNA Assay for Assessment of Androgen Receptor Signaling Inhibitor Sensitivity in Metastatic Castration-Resistant Prostate Cancer. Theranostics, 9(10), 2812-2826. (Read full publication)
    39. Ing N, Huang F, Conley A, You S, Ma Z, Klimov S, Ohe C, Yuan X, Amin MB, Figlin R, Gertych A, Knudsen B (2017). A novel machine learning approach reveals latent vascular phenotypes predictive of renal cancer outcome. Scientific reports, 7(1), 13190. (Read full publication)
    40. Morley S, You S, Pollan S, Choi J, Zhou B, Hager MH, Steadman K, Spinelli C, Rajendran K, Gertych A, Kim J, Adam RM, Yang W, Krishnan R, Knudsen BS, Di Vizio D, Freeman M (2015). Regulation of microtubule dynamics by DIAPH3 influences amoeboid tumor cell mechanics and sensitivity to taxanes. Scientific reports, 5, 12136. (Read full publication)
    41. Gertych A, Swiderska-Chadaj Z, Ma Z, Ing N, Markiewicz T, Cierniak S, Salemi H, Guzman S, Walts AE, Knudsen B (2019). Convolutional neural networks can accurately distinguish four histologic growth patterns of lung adenocarcinoma in digital slides. Scientific reports, 9(1), 1483. (Read full publication)
    42. Miller ET, Chamie K, Kwan L, Lewis MS, Knudsen BS, Garraway I (2017). Impact of treatment on progression to castration-resistance, metastases, and death in men with localized high-grade prostate cancer. Cancer medicine, 6(1), 163-172. (Read full publication)
    43. Hu J, Schokrpur S, Archang M, Hermann K, Sharrow AC, Khanna P, Novak J, Signoretti S, Bhatt RS, Knudsen BS, Xu H, Wu (2018). A Non-integrating Lentiviral Approach Overcomes Cas9-Induced Immune Rejection to Establish an Immunocompetent Metastatic Renal Cancer Model. Molecular therapy. Methods & clinical development, 9, 203-210. (Read full publication)
    44. Huang F, Ma Z, Pollan S, Yuan X, Swartwood S, Gertych A, Rodriguez M, Mallick J, Bhele S, Guindi M, Dhall D, Walts AE, Bose S, de Peralta Venturina M, Marchevsky AM, Luthringer DJ, Feller SM, Berman B, Freeman MR, Alvord WG, Vande Woude G, Amin MB, Knudsen B (2016). Quantitative imaging for development of companion diagnostics to drugs targeting HGF/MET. The journal of pathology. Clinical research, 2(4), 210-222. (Read full publication)
    45. Kane N, Romero T, Diaz-Perez S, Rettig MB, Steinberg ML, Kishan AU, Schaue D, Reiter RE, Knudsen BS, Nickols N (2022). Significant changes in macrophage and CD8 T cell densities in primary prostate tumors 2 weeks after SBRT. Prostate cancer and prostatic diseases, (Read full publication)
    46. Pollan SG, Teng PC, Jan YJ, Livingstone J, Huang C, Kim M, Mariscal J, Rodriguez M, Chen JF, You S, DiVizio D, Boutros PC, Chan KS, Rasorenova O, Cress A, Spassov D, Moasser M, Posadas EM, Freedland SJ, Freeman MR, Zheng JJ, Knudsen B (2021). Loss of CDCP1 triggers FAK activation in detached prostate cancer cells. American journal of clinical and experimental urology, 9(4), 350-366. (Read full publication)
    47. Zhang W, Rhodes JS, Moon KR, Knudsen BS, Nokolova L, Zhou (2020). Imaging of PD-L1 in single cancer cells by SERS-based hyperspectral analysis. Biomedical optics express, 11(11), 6197-6210. (Read full publication)
    48. Liu Y, Wang J, Horton C, Yu C, Knudsen B, Stefanson J, Hu K, Stefanson O, Green J, Guo C, Xie Q, Wang Z (2022). Stromal AR inhibits prostate tumor progression by restraining secretory luminal epithelial cells. Cell reports, 39(8), 110848. (Read full publication)
    49. Marr KD, Gard JMC, Harryman WL, Keeswood EJ, Paxson AI, Wolgemuth C, Knudsen BS, Nagle RB, Hazlehurst L, Sorbellini M, Cress A (2023). Biophysical phenotype mixtures reveal advantages for tumor muscle invasion in vivo. Biophysical journal, 122(21), 4194-4206. (Read full publication)
    50. Ng AHC, Hu H, Wang K, Scherler K, Warren SE, Zollinger DR, McKay-Fleisch J, Sorg K, Beechem JM, Ragaglia E, Lacy JM, Smith KD, Marshall DA, Bundesmann MM, López de Castilla D, Corwin D, Yarid N, Knudsen BS, Lu Y, Goldman JD, Heath J (2023). Organ-specific immunity: A tissue analysis framework for investigating local immune responses to SARS-CoV-2. Cell reports, 42(10), 113212. (Read full publication)
    51. Kataria T, Rajamani S, Ayubi AB, Bronner M, Jedrzkiewicz J, Knudsen BS, Elhabian S (2023). Automating Ground Truth Annotations for Gland Segmentation Through Immunohistochemistry. Modern pathology, 36(12), 100331. (Read full publication)
    52. Zhang W, Koh MY, Sirohi D, Ying J, Brintz BJ, Knudsen B (2023). Predicting IHC staining classes of NF1 using features in the hematoxylin channel. Journal of pathology informatics, 14, 100196. (Read full publication)
    53. Qian C, Yang Q, Rotinen M, Huang R, Kim H, Gallent B, Yan Y, Cadaneanu RM, Zhang B, Kaochar S, Freedland SJ, Posadas EM, Ellis L, Vizio DD, Morrissey C, Nelson PS, Brady L, Murali R, Campbell MJ, Yang W, Knudsen BS, Mostaghel EA, Ye H, Garraway IP, You S, Freeman M (2023). ONECUT2 Activates Diverse Resistance Drivers of Androgen Receptor-Independent Heterogeneity in Prostate Cancer. (Read full publication)
    54. Gil J, Betancourt LH, Pla I, Sanchez A, Appelqvist R, Miliotis T, Kuras M, Oskolas H, Kim Y, Horvath Z, Eriksson J, Berge E, Burestedt E, Jönsson G, Baldetorp B, Ingvar C, Olsson H, Lundgren L, Horvatovich P, Murillo JR, Sugihara Y, Welinder C, Wieslander E, Lee B, Lindberg H, Paw'owski K, Kwon HJ, Doma V, Timar J, Karpati S, Szasz AM, Németh IB, Nishimura T, Corthals G, Rezeli M, Knudsen B, Malm J, Marko-Varga (2019). Clinical protein science in translational medicine targeting malignant melanoma. Cell biology and toxicology, 35(4), 293-332. (Read full publication)
    55. Schiewer MJ, Mandigo AC, Gordon N, Huang F, Gaur S, de Leeuw R, Zhao SG, Evans J, Han S, Parsons T, Birbe R, McCue P, McNair C, Chand SN, Cendon-Florez Y, Gallagher P, McCann JJ, Poudel Neupane N, Shafi AA, Dylgjeri E, Brand LJ, Visakorpi T, Raj GV, Lallas CD, Trabulsi EJ, Gomella LG, Dicker AP, Kelly WK, Leiby BE, Knudsen B, Feng FY, Knudsen K (2018). PARP-1 regulates DNA repair factor availability. EMBO molecular medicine, 10(12), (Read full publication)
    56. Samson SC, Rojas A, Zitnay RG, Carney KR, Hettinga W, Schaelling MC, Sicard D, Zhang W, Gilbert-Ross M, Dy GK, Cavnar MJ, Furqan M, Browning RF Jr, Naqash AR, Schneider BP, Tarhini A, Tschumperlin DJ, Venosa A, Marcus AI, Emerson LL, Spike BT, Knudsen BS, Mendoza M (2024). Tenascin-C in the early lung cancer tumor microenvironment promotes progression through integrin ¿vß1 and FAK. bioRxiv, (Read full publication)
    57. Qian C, Yang Q, Rotinen M, Huang R, Kim H, Gallent B, Yan Y, Cadaneanu RM, Zhang B, Kaochar S, Freedland SJ, Posadas EM, Ellis L, Di Vizio D, Morrissey C, Nelson PS, Brady L, Murali R, Campbell MJ, Yang W, Knudsen BS, Mostaghel EA, Ye H, Garraway IP, You S, Freeman M (2024). ONECUT2 acts as a lineage plasticity driver in adenocarcinoma as well as neuroendocrine variants of prostate cancer. Nucleic acids research, 52(13), 7740-7760. (Read full publication)
    58. Knudsen BS, Jadhav A, Perry LJ, Thagaard J, Deftereos G, Ying J, Brintz BJ, Zhang (2024). A Pipeline for Evaluation of Machine Learning/Artificial Intelligence Models to Quantify Programmed Death Ligand 1 Immunohistochemistry. Laboratory investigation; a journal of technical methods and pathology, 104(6), 102070. (Read full publication)
    59. Zamora I, Gutiérrez M, Pascual A, Pajares MJ, Barajas M, Perez LM, You S, Knudsen BS, Freeman MR, Encío IJ, Rotinen (2024). ONECUT2 is a druggable driver of luminal to basal breast cancer plasticity. Cellular oncology (Dordrecht, Netherlands), (Read full publication)
    60. Ferrero A, Ghelichkhan E, Manoochehri H, Ho MM, Albertson DJ, Brintz BJ, Tasdizen T, Whitaker RT, Knudsen B (2024). HistoEM: A Pathologist-Guided and Explainable Workflow Using Histogram Embedding for Gland Classification. Modern pathology, 37(4), 100447. (Read full publication)
    61. Wadhwa A, Roscoe C, Duran EA, Kwan L, Haroldsen CL, Shelton JB, Cullen J, Knudsen BS, Rettig MB, Pyarajan S, Nickols NG, Maxwell KN, Yamoah K, Rose BS, Rebbeck TR, Iyer HS, Garraway I (2024). Neighborhood Deprivation, Race and Ethnicity, and Prostate Cancer Outcomes Across California Health Care Systems. JAMA network open, 7(3), e242852. (Read full publication)
    62. Zhang W, Zhou Q, Nguyen JV, Egal E, Yang Q, Freeman MR, Hu-Lieskovan S, Suneja G, Coghill A, Knudsen B (2025). Comparison of QuPath and HALO Platforms for Analysis of the Tumor Microenvironment in Prostate Cancer. Laboratory investigation; a journal of technical methods and pathology, 105(12), 104246. (Read full publication)
    63. Zhang B, Manoochehri H, Ho MM, Fooladgar F, Chong Y, Knudsen BS, Sirohi D, Tasdizen (2025). CLASS-M: Adaptive stain separation-based contrastive learning with pseudo-labeling for histopathological image classification. Medical image analysis, 105, 103711. (Read full publication)
    64. Fenlon J, Van Bibber N, Mahlow J, Yamoah K, Soupir AC, Nguyen JV, Moran Segura C, Spivak AM, Knudsen BS, Zhou Q, Hu-Lieskovan S, Puri S, Zhang W, DeRose YS, Suneja G, Coghill A (2025). Human Immunodeficiency Virus-Associated Differences in the Tumor Immune Microenvironment of Lung, Breast, and Prostate Cancers. Cancer epidemiology, biomarkers & prevention, 34(6), 860-867. (Read full publication)
    65. Harryman WL, Hinton JP, Sainz R, Gard JMC, Ryniawec JM, Rogers GC, Warfel NA, Knudsen BS, Nagle RB, Chipollini JJ, Lee BR, Sun BL, Cress A (2024). Intermediate risk prostate tumors contain lethal subtypes. Frontiers in urology, 4, (Read full publication)
    66. Gutiérrez M, Zamora I, Iriarte R, Pajares MJ, Yang Q, Qian C, Otegui N, Fernández-Irigoyen J, Santamaría E, Alcala N, Sexton-Oates A, Fernández-Cuesta L, Barajas M, Calvo A, Montuenga LM, Knudsen B, You S, Freeman MR, Encío I, Rotinen (2025). ONECUT2 reprograms neuroendocrine fate and is an actionable therapeutic target in small cell lung cancer. Molecular medicine (Cambridge, Mass.), 31(1), 232. (Read full publication)
    67. Bialas P, Kobayashi T, Hellsten R, Krzyzanowska A, Persson M, Marginean F, Trudel D, Garraway IP, Trock BJ, Taimen P, Saad F, Mirtti T, Knudsen B, De Marzo AM, Bjartell (2025). pSTAT3 Expression is Increased in Advanced Prostate Cancer in Post-Initiation of Androgen Deprivation Therapy. The Prostate, 85(3), 252-264. (Read full publication)
    68. Qian C, Yang Q, Rotinen M, Huang R, Kim H, Gallent B, Yan Y, Cadaneanu RM, Zhang B, Kaochar S, Freedland SJ, Posadas EM, Ellis L, Di Vizio D, Morrissey C, Nelson PS, Brady L, Murali R, Campbell MJ, Yang W, Knudsen BS, Mostaghel EA, Ye H, Garraway IP, You S, Freeman M (2024). ONECUT2 acts as a lineage plasticity driver in adenocarcinoma as well as neuroendocrine variants of prostate cancer. Nucleic acids research, 52(13), 7740-7760. (Read full publication)
    69. Qian C, Yang Q, Rotinen M, Huang R, Kim H, Gallent B, Yan Y, Cadaneanu RM, Zhang B, Kaochar S, Freedland SJ, Posadas EM, Ellis L, Vizio DD, Morrissey C, Nelson PS, Brady L, Murali R, Campbell MJ, Yang W, Knudsen BS, Mostaghel EA, Ye H, Garraway IP, You S, Freeman M (2023). ONECUT2 Activates Diverse Resistance Drivers of Androgen Receptor-Independent Heterogeneity in Prostate Cancer. bioRxiv, (Read full publication)
    70. Ouellet V, Erickson A, GAP1 UTMAs Contributing Investigators, Wiley K, Morrissey C, Berge V, Moreno CS, Tasken KA, Trudel D, True LD, Lewis MS, Svindland A, Ertunc O, Vidal ID, Osunkoya AO, Jones T, Bova GS, Lamminen T, Achtman AH, Buzza M, Kouspou MM, Bigler SA, Zhou X, Freedland SJ, Mes-Masson AM, Garraway IP, Trock BJ, Taimen P, Saad F, Mirtti T, Knudsen BS, De Marzo A (2022). The Movember Global Action Plan 1 (GAP1): Unique Prostate Cancer Tissue Microarray Resource. Cancer epidemiology, biomarkers & prevention, 31(4), 715-727. (Read full publication)
    71. Sirohi D, Chipman J, Barry M, Albertson D, Mahlow J, Liu T, Raps E, Haaland B, Sayegh N, Li H, Rathi N, Sharma P, Agarwal N, Knudsen (2022). Histologic Growth Patterns in Clear Cell Renal Cell Carcinoma Stratify Patients into Survival Risk Groups. Clinical genitourinary cancer, 20(3), e233-e243. (Read full publication)

    Review

    1. Oskolas H, Nogueira FCN, Domont GB, Yu KH, Semenov YR, Sorger P, Steinfelder E, Corps L, Schulz L, Wieslander E, Fenyö D, Kárpáti S, Holló P, Kemény LV, Döme B, Megyesfalvi Z, Paw'owski K, Nishimura T, Kwon H, Encarnación-Guevara S, Szasz AM, Veréb Z, Gyulai R, Németh IB, Appelqvist R, Rezeli M, Baldetorp B, Horvatovich P, Malmström J, Pla I, Sanchez A, Knudsen B, Kiss A, Malm J, Marko-Varga G, Gil (2025). Comprehensive biobanking strategy with clinical impact at the European Cancer Moonshot Lund Center. Journal of proteomics, 316, 105442. (Read full publication)

    Editorial

    1. Delahunt B, Hammond E, Egevad L, Samaratunga H, Srigley JR, Humphrey PA, Rubin M, Epstein JI, Lin DW, Gore JL, Nacey JN, Klotz L, Sandler H, Zietman AL, Holden S, Montironi R, Evans AJ, McKenney JK, Berney D, Wheeler TM, Chinnaiyan AM, True L, Knudsen B, Amin M (2015). Active surveillance for prostate cancer: the role of the pathologist. Pathology, 47(1), 1-3. (Read full publication)

    Other

    1. Fassler DJ, Abousamra S, Gupta R, Chen C, Zhao M, Paredes D, Batool SA, Knudsen BS, Escobar-Hoyos L, Shroyer KR, Samaras D, Kurc T, Saltz (2020). Publisher Correction to: Deep learning-based image analysis methods for brightfield-acquired multiplex immunohistochemistry images. Diagnostic pathology, 15(1), 116. (Read full publication)
    2. Ouellet V, Erickson A, GAP1 UTMAs Contributing Investigators., Wiley K, Morrissey C, Berge V, Moreno CS, Tasken KA, Trudel D, True LD, Lewis MS, Svindland A, Ertunc O, Vidal ID, Osunkoya AO, Jones T, Bova GS, Lamminen T, Achtman AH, Buzza M, Kouspou MM, Bigler SA, Zhou X, Freedland SJ, Mes-Masson AM, Garraway IP, Trock BJ, Taimen P, Saad F, Mirtti T, Knudsen BS, De Marzo A (2022). The Movember Global Action Plan 1 (GAP1): Unique Prostate Cancer Tissue Microarray Resource. Cancer epidemiology, biomarkers & prevention, 31(4), 715-727. (Read full publication)
    3. Yan Y, Zhou B, Qian C, Vasquez A, Kamra M, Chatterjee A, Lee YJ, Yuan X, Ellis L, Di Vizio D, Posadas EM, Kyprianou N, Knudsen BS, Shah K, Murali R, Gertych A, You S, Freeman MR, Yang (2022). Receptor-interacting protein kinase 2 (RIPK2) stabilizes c-Myc and is a therapeutic target in prostate cancer metastasis. Nature communications, 13(1), 669. (Read full publication)
    4. Sirohi D, Chipman J, Barry M, Albertson D, Mahlow J, Liu T, Raps E, Haaland B, Sayegh N, Li H, Rathi N, Sharma P, Agarwal N, Knudsen (2022). Histologic Growth Patterns in Clear Cell Renal Cell Carcinoma Stratify Patients into Survival Risk Groups. Clinical genitourinary cancer, 20(3), e233-e243. (Read full publication)
    5. Betancourt LH, Gil J, Kim Y, Doma V, Çak'r U, Sanchez A, Murillo JR, Kuras M, Parada IP, Sugihara Y, Appelqvist R, Wieslander E, Welinder C, Velasquez E, de Almeida NP, Woldmar N, Marko-Varga M, Paw'owski K, Eriksson J, Szeitz B, Baldetorp B, Ingvar C, Olsson H, Lundgren L, Lindberg H, Oskolas H, Lee B, Berge E, Sjögren M, Eriksson C, Kim D, Kwon HJ, Knudsen B, Rezeli M, Hong R, Horvatovich P, Miliotis T, Nishimura T, Kato H, Steinfelder E, Oppermann M, Miller K, Florindi F, Zhou Q, Domont GB, Pizzatti L, Nogueira FCS, Horvath P, Szadai L, Tímár J, Kárpáti S, Szász AM, Malm J, Fenyö D, Ekedahl H, Németh IB, Marko-Varga (2021). The human melanoma proteome atlas-Defining the molecular pathology. Clinical and translational medicine, 11(7), e473. (Read full publication)
    6. Betancourt LH, Gil J, Sanchez A, Doma V, Kuras M, Murillo JR, Velasquez E, Çak'r U, Kim Y, Sugihara Y, Parada IP, Szeitz B, Appelqvist R, Wieslander E, Welinder C, de Almeida NP, Woldmar N, Marko-Varga M, Eriksson J, Paw'owski K, Baldetorp B, Ingvar C, Olsson H, Lundgren L, Lindberg H, Oskolas H, Lee B, Berge E, Sjögren M, Eriksson C, Kim D, Kwon HJ, Knudsen B, Rezeli M, Malm J, Hong R, Horvath P, Szász AM, Tímár J, Kárpáti S, Horvatovich P, Miliotis T, Nishimura T, Kato H, Steinfelder E, Oppermann M, Miller K, Florindi F, Zhou Q, Domont GB, Pizzatti L, Nogueira FCS, Szadai L, Németh IB, Ekedahl H, Fenyö D, Marko-Varga (2021). The Human Melanoma Proteome Atlas-Complementing the melanoma transcriptome. Clinical and translational medicine, 11(7), e451. (Read full publication)
    7. Saylor J, Ma Z, Goodridge HS, Huang F, Cress AE, Pandol SJ, Shiao SL, Vidal AC, Wu L, Nickols NG, Gertych A, Knudsen B (2018). Spatial Mapping of Myeloid Cells and Macrophages by Multiplexed Tissue Staining. Frontiers in immunology, 9, 2925. (Read full publication)

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