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A machine learning approach to optimizing cell-free DNA sequencing panels: with an application to prostate cancer.
Published in:
2020
By:
- Cario, Clinton L.;
- Chen, Emmalyn;
- Leong, Lancelote;
- Emami, Nima C.;
- Lopez, Karen;
- Tenggara, Imelda;
- Simko, Jeffry P.;
- Friedlander, Terence W.;
- Li, Patricia S.;
- Paris, Pamela L.;
- Carroll, Peter R.;
- Witte, John S.
Publication type:
journal article
Characterization and stratification of prostate lesions based on comprehensive multiparametric MRI using detailed whole-mount histopathology as a reference standard.
Published in:
NMR in Biomedicine, 2017, v. 30, n. 12, p. n/a, doi. 10.1002/nbm.3796
By:
- Starobinets, Olga;
- Simko, Jeffry P.;
- Kuchinsky, Kyle;
- Kornak, John;
- Carroll, Peter R.;
- Greene, Kirsten L.;
- Kurhanewicz, John;
- Noworolski, Susan M.
Publication type:
Article
Metabolic, pathologic, and genetic analysis of prostate tissues: quantitative evaluation of histopathologic and mRNA integrity after HR-MAS spectroscopy.
Published in:
NMR in Biomedicine, 2010, v. 23, n. 4, p. 391, doi. 10.1002/nbm.1474
By:
- Santos, Carissa F.;
- Kurhanewicz, John;
- Tabatabai, Z. Laura;
- Simko, Jeffry P.;
- Keshari, Kayvan R.;
- Gbegnon, Akpene;
- Santos, Romelyn DeLos;
- Federman, Scot;
- Shinohara, Katsuto;
- Carroll, Peter R.;
- Haqq, Christopher M.;
- Swanson, Mark G.
Publication type:
Article
Clinical utility of endorectal MRI-guided prostate biopsy: Preliminary experience.
Published in:
Journal of Magnetic Resonance Imaging, 2014, v. 40, n. 2, p. 314, doi. 10.1002/jmri.24383
By:
- Jung, Adam J.;
- Westphalen, Antonio C.;
- Kurhanewicz, John;
- Wang, Zhen J.;
- Carroll, Peter R.;
- Simko, Jeffry P.;
- Coakley, Fergus V.
Publication type:
Article
Semiautomatic registration of digital histopathology images to in vivo MR images in molded and unmolded prostates.
Published in:
Journal of Magnetic Resonance Imaging, 2014, v. 39, n. 5, p. 1223, doi. 10.1002/jmri.24287
By:
- Starobinets, Olga;
- Guo, Richard;
- Simko, Jeffry P.;
- Kuchinsky, Kyle;
- Kurhanewicz, John;
- Carroll, Peter R.;
- Greene, Kirsten L.;
- Noworolski, Susan M.
Publication type:
Article
Integration of high-resolution array comparative genomic hybridization analysis of chromosome 16q with expression array data refines common regions of loss at 16q23-qter and identifies underlying candidate tumor suppressor genes in prostate cancer.
Published in:
Oncogene, 2004, v. 23, n. 19, p. 3487, doi. 10.1038/sj.onc.1207474
By:
- Doggett, Norman A.;
- Albertson, Donna G.;
- Andaya, Armann;
- Chinnaiyan, Arul;
- van Dekken, Herman;
- Ginzinger, David;
- Haqq, Christopher;
- James, Karen;
- Kamkar, Sherwin;
- Kowbel, David;
- Pinkel, Daniel;
- Schmitt, Lars;
- Simko, Jeffry P.;
- Volik, Stanislav;
- Weinberg, Vivian K.;
- Paris, Pamela L.;
- Collins, Colin;
- Watson, J. E. Vivienne
Publication type:
Article
Development and pilot evaluation of a personalized decision support intervention for low risk prostate cancer patients.
Published in:
Cancer Medicine, 2020, v. 9, n. 1, p. 125, doi. 10.1002/cam4.2685
By:
- Belkora, Jeffrey;
- Chan, June M.;
- Cooperberg, Matthew R.;
- Neuhaus, John;
- Stupar, Lauren;
- Weinberg, Tia;
- Broering, Jeanette M.;
- Tenggara, Imelda;
- Cowan, Janet E.;
- Rosenfeld, Stan;
- Kenfield, Stacey A.;
- Van Blarigan, Erin L.;
- Simko, Jeffry P.;
- Witte, John;
- Carroll, Peter R.
Publication type:
Article
Large cribriform glands (> 0.25 mm diameter) as a predictor of adverse pathology in men with Grade Group 2 prostate cancer.
Published in:
Histopathology, 2024, v. 84, n. 4, p. 614, doi. 10.1111/his.15102
By:
- Greenland, Nancy Y;
- Cowan, Janet E;
- Stohr, Bradley A;
- Simko, Jeffry P;
- Carroll, Peter R;
- Chan, Emily
Publication type:
Article
Positive NKX3.1 as a diagnostic pitfall for prostate cancer in extramammary Paget's disease of genitourinary sites.
Published in:
Histopathology, 2024, v. 84, n. 3, p. 565, doi. 10.1111/his.15061
By:
- Chen, Constance V;
- Francois, Rony A;
- Mully, Thaddeus W;
- Sangoi, Ankur;
- LeBoit, Philip E;
- Simko, Jeffry P;
- Chan, Emily
Publication type:
Article
An exploration in pitfalls in interpreting SDHB immunohistochemistry.
Published in:
Histopathology, 2022, v. 81, n. 2, p. 264, doi. 10.1111/his.14681
By:
- Ding, Chien‐Kuang Cornelia;
- Chan, Salina;
- Mak, Julie;
- Umetsu, Sarah E;
- Simko, Jeffry P;
- Ruiz‐Cordero, Roberto;
- Saunders, Tara;
- Chan, Emily
Publication type:
Article
Renal NUT carcinoma: a case report.
Published in:
2018
By:
- Sirohi, Deepika;
- Garg, Karuna;
- Simko, Jeffry P.;
- Grenert, James P.
Publication type:
Case Study
Phase I Study of CTT1057, an 18F-Labeled Imaging Agent with Phosphoramidate Core Targeting Prostate-Specific Membrane Antigen in Prostate Cancer.
Published in:
Journal of Nuclear Medicine, 2019, v. 60, n. 7, p. 910, doi. 10.2967/jnumed.118.220715
By:
- Behr, Spencer C.;
- Aggarwal, Rahul;
- VanBrocklin, Henry F.;
- Flavell, Robert R.;
- Gao, Kenneth;
- Small, Eric J.;
- Blecha, Joseph;
- Jivan, Salma;
- Hope, Thomas A.;
- Simko, Jeffry P.;
- Kurhanewicz, John;
- Noworolski, Susan M.;
- Korn, Natalie J.;
- De Los Santos, Romelyn;
- Cooperberg, Matthew R.;
- Carroll, Peter R.;
- Nguyen, Hao G.;
- Greene, Kirsten L.;
- Langton-Webster, Beatrice;
- Berkman, Clifford E.
Publication type:
Article
Expansile cribriform Gleason pattern 4 has histopathologic and molecular features of aggressiveness and greater risk of biochemical failure compared to glomerulation Gleason pattern 4.
Published in:
Prostate, 2020, v. 80, n. 8, p. 653, doi. 10.1002/pros.23977
By:
- Greenland, Nancy Y.;
- Cowan, Janet E.;
- Zhang, Li;
- Carroll, Peter R.;
- Chan, Emily;
- Stohr, Bradley A.;
- Simko, Jeffry P.
Publication type:
Article
Tissue Sources for Accurate Measurement of Germline DNA Genotypes in Prostate Cancer Patients Treated With Radical Prostatectomy.
Published in:
Prostate, 2017, v. 77, n. 4, p. 425, doi. 10.1002/pros.23283
By:
- Emami, Nima C.;
- Leong, Lancelote;
- Wan, Eunice;
- Van Blarigan, Erin L.;
- Cooperberg, Matthew R.;
- Tenggara, Imelda;
- Carroll, Peter R.;
- Chan, June M.;
- Witte, John S.;
- Simko, Jeffry P.
Publication type:
Article
US lesion visibility predicts clinically significant upgrade of prostate cancer by systematic biopsy.
Published in:
Abdominal Radiology, 2022, v. 47, n. 3, p. 1133, doi. 10.1007/s00261-021-03389-x
By:
- Velarde, Nathan;
- Westphalen, Antonio C.;
- Nguyen, Hao G.;
- Neuhaus, John;
- Shinohara, Katsuto;
- Simko, Jeffry P.;
- Larson, Peder E.;
- Magudia, Kirti
Publication type:
Article
Cell-free DNA concentration and fragment size as a biomarker for prostate cancer.
Published in:
Scientific Reports, 2021, v. 11, n. 1, p. 1, doi. 10.1038/s41598-021-84507-z
By:
- Chen, Emmalyn;
- Cario, Clinton L.;
- Leong, Lancelote;
- Lopez, Karen;
- Márquez, César P.;
- Chu, Carissa;
- Li, Patricia S.;
- Oropeza, Erica;
- Tenggara, Imelda;
- Cowan, Janet;
- Simko, Jeffry P.;
- Chan, June M.;
- Friedlander, Terence;
- Wyatt, Alexander W.;
- Aggarwal, Rahul;
- Paris, Pamela L.;
- Carroll, Peter R.;
- Feng, Felix;
- Witte, John S.
Publication type:
Article
Expression of the DNA repair gene MLH1 correlates with survival in patients who have resected pancreatic cancer and have received adjuvant chemoradiation: NRG Oncology RTOG Study 9704.
Published in:
2018
By:
- Lawrence, Yaacov R.;
- Moughan, Jennifer;
- Magliocco, Anthony M.;
- Klimowicz, Alexander C.;
- Regine, William F.;
- Mowat, Rex B.;
- DiPetrillo, Thomas A.;
- Small, Jr, William;
- Simko, Jeffry P.;
- Golan, Talia;
- Winter, Kathryn A.;
- Guha, Chandan;
- Crane, Christopher H.;
- Dicker, Adam P.;
- Small, William Jr
Publication type:
journal article
Morphologic patterns observed in prostate biopsy cases with discrepant grade group and molecular risk classification.
Published in:
Prostate, 2024, v. 84, n. 11, p. 1076, doi. 10.1002/pros.24725
By:
- Greenland, Nancy Y.;
- Cooperberg, Matthew R.;
- Carroll, Peter R.;
- Cowan, Janet E.;
- Simko, Jeffry P.;
- Stohr, Bradley A.;
- Chan, Emily
Publication type:
Article
Prostate biopsy histopathologic features correlate with a commercial gene expression assay's reclassification of patient NCCN risk category.
Published in:
Prostate, 2020, v. 80, n. 16, p. 1421, doi. 10.1002/pros.24072
By:
- Greenland, Nancy Y.;
- Cowan, Janet E.;
- Chan, Emily;
- Carroll, Peter R.;
- Stohr, Bradley A.;
- Simko, Jeffry P.
Publication type:
Article
Evaluation of lactate and alanine as metabolic biomarkers of prostate cancer using 1H HR-MAS spectroscopy of biopsy tissues.
Published in:
Magnetic Resonance in Medicine, 2008, v. 60, n. 3, p. 510, doi. 10.1002/mrm.21694
By:
- Tessem, May-Britt;
- Swanson, Mark G.;
- Keshari, Kayvan R.;
- Albers, Mark J.;
- Joun, David;
- Tabatabai, Z. Laura;
- Simko, Jeffry P.;
- Shinohara, Katsuto;
- Nelson, Sarah J.;
- Vigneron, Daniel B.;
- Gribbestad, Ingrid S.;
- Kurhanewicz, John
Publication type:
Article
Quantification of choline- and ethanolamine-containing metabolites in human prostate tissues using 1H HR-MAS total correlation spectroscopy.
Published in:
Magnetic Resonance in Medicine, 2008, v. 60, n. 1, p. 33, doi. 10.1002/mrm.21647
By:
- Swanson, Mark G.;
- Keshari, Kayvan R.;
- Tabatabai, Z. Laura;
- Simko, Jeffry P.;
- Shinohara, Katsuto;
- Carroll, Peter R.;
- Zektzer, Andrew S.;
- Kurhanewicz, John
Publication type:
Article
Author Correction: Prostate cancer therapy personalization via multi-modal deep learning on randomized phase III clinical trials.
Published in:
2023
By:
- Esteva, Andre;
- Feng, Jean;
- van der Wal, Douwe;
- Huang, Shih-Cheng;
- Simko, Jeffry P.;
- DeVries, Sandy;
- Chen, Emmalyn;
- Schaeffer, Edward M.;
- Morgan, Todd M.;
- Sun, Yilun;
- Ghorbani, Amirata;
- Naik, Nikhil;
- Nathawani, Dhruv;
- Socher, Richard;
- Michalski, Jeff M.;
- Roach III, Mack;
- Pisansky, Thomas M.;
- Monson, Jedidiah M.;
- Naz, Farah;
- Wallace, James
Publication type:
Correction Notice
Prostate cancer therapy personalization via multi-modal deep learning on randomized phase III clinical trials.
Published in:
NPJ Digital Medicine, 2022, v. 5, n. 1, p. 1, doi. 10.1038/s41746-022-00613-w
By:
- Esteva, Andre;
- Feng, Jean;
- van der Wal, Douwe;
- Huang, Shih-Cheng;
- Simko, Jeffry P.;
- DeVries, Sandy;
- Chen, Emmalyn;
- Schaeffer, Edward M.;
- Morgan, Todd M.;
- Sun, Yilun;
- Ghorbani, Amirata;
- Naik, Nikhil;
- Nathawani, Dhruv;
- Socher, Richard;
- Michalski, Jeff M.;
- Roach III, Mack;
- Pisansky, Thomas M.;
- Monson, Jedidiah M.;
- Naz, Farah;
- Wallace, James
Publication type:
Article
Molecular risk classifier score and biochemical recurrence risk are associated with cribriform pattern type in Gleason 3+4=7 prostate cancer.
Published in:
Investigative & Clinical Urology, 2022, v. 63, n. 1, p. 27, doi. 10.4111/icu.20210262
By:
- Greenland, Nancy Y.;
- Cooperberg, Matthew R.;
- Wong, Anthony C.;
- Chan, Emily;
- Carroll, Peter R.;
- Simko, Jeffry P.;
- Stohr, Bradley A.
Publication type:
Article
TP53 structural variants in metastatic prostatic carcinoma.
Published in:
PLoS ONE, 2019, v. 14, n. 6, p. 1, doi. 10.1371/journal.pone.0218618
By:
- Sirohi, Deepika;
- Devine, Patrick;
- Grenert, James P.;
- van Ziffle, Jessica;
- Simko, Jeffry P.;
- Stohr, Bradley A.
Publication type:
Article
Differences in Laboratory Findings for Cerebrospinal Fluid Specimens Obtained from Patients with Meningitis or Encephalitis Due to Herpes Simplex Virus (HSV) Documented by Detection of HSV DNA.
Published in:
Clinical Infectious Diseases, 2002, v. 35, n. 4, p. 414, doi. 10.1086/341979
By:
- Simko, Jeffry P.;
- Caliendo, Angela M.;
- Hogle, Kay;
- Versalovic, James
Publication type:
Article
The impact of genomic biomarkers on a clinical risk prediction model for upgrading/upstaging among men with favorable-risk prostate cancer.
Published in:
Cancer (0008543X), 2024, v. 130, n. 10, p. 1766, doi. 10.1002/cncr.35215
By:
- Braun, Avery E.;
- Chan, June M.;
- Neuhaus, John;
- Cowan, Janet E.;
- Kenfield, Stacey A.;
- Van Blarigan, Erin L.;
- Tenggara, Imelda;
- Broering, Jeanette M.;
- Simko, Jeffry P.;
- Carroll, Peter R.;
- Cooperberg, Matthew R.
Publication type:
Article

Found: 27

A machine learning approach to optimizing cell-free DNA sequencing panels: with an application to prostate cancer.

Characterization and stratification of prostate lesions based on comprehensive multiparametric MRI using detailed whole-mount histopathology as a reference standard.

Metabolic, pathologic, and genetic analysis of prostate tissues: quantitative evaluation of histopathologic and mRNA integrity after HR-MAS spectroscopy.

Clinical utility of endorectal MRI-guided prostate biopsy: Preliminary experience.

Semiautomatic registration of digital histopathology images to in vivo MR images in molded and unmolded prostates.

Integration of high-resolution array comparative genomic hybridization analysis of chromosome 16q with expression array data refines common regions of loss at 16q23-qter and identifies underlying candidate tumor suppressor genes in prostate cancer.

Development and pilot evaluation of a personalized decision support intervention for low risk prostate cancer patients.

Large cribriform glands (> 0.25 mm diameter) as a predictor of adverse pathology in men with Grade Group 2 prostate cancer.

Positive NKX3.1 as a diagnostic pitfall for prostate cancer in extramammary Paget's disease of genitourinary sites.

An exploration in pitfalls in interpreting SDHB immunohistochemistry.

Renal NUT carcinoma: a case report.

Phase I Study of CTT1057, an <sup>18</sup>F-Labeled Imaging Agent with Phosphoramidate Core Targeting Prostate-Specific Membrane Antigen in Prostate Cancer.

Expansile cribriform Gleason pattern 4 has histopathologic and molecular features of aggressiveness and greater risk of biochemical failure compared to glomerulation Gleason pattern 4.

Tissue Sources for Accurate Measurement of Germline DNA Genotypes in Prostate Cancer Patients Treated With Radical Prostatectomy.

US lesion visibility predicts clinically significant upgrade of prostate cancer by systematic biopsy.

Cell-free DNA concentration and fragment size as a biomarker for prostate cancer.

Expression of the DNA repair gene MLH1 correlates with survival in patients who have resected pancreatic cancer and have received adjuvant chemoradiation: NRG Oncology RTOG Study 9704.

Morphologic patterns observed in prostate biopsy cases with discrepant grade group and molecular risk classification.

Prostate biopsy histopathologic features correlate with a commercial gene expression assay's reclassification of patient NCCN risk category.

Evaluation of lactate and alanine as metabolic biomarkers of prostate cancer using <sup>1</sup>H HR-MAS spectroscopy of biopsy tissues.

Quantification of choline- and ethanolamine-containing metabolites in human prostate tissues using <sup>1</sup>H HR-MAS total correlation spectroscopy.

Author Correction: Prostate cancer therapy personalization via multi-modal deep learning on randomized phase III clinical trials.

Prostate cancer therapy personalization via multi-modal deep learning on randomized phase III clinical trials.

Molecular risk classifier score and biochemical recurrence risk are associated with cribriform pattern type in Gleason 3+4=7 prostate cancer.

TP53 structural variants in metastatic prostatic carcinoma.

Differences in Laboratory Findings for Cerebrospinal Fluid Specimens Obtained from Patients with Meningitis or Encephalitis Due to Herpes Simplex Virus (HSV) Documented by Detection of HSV DNA.

The impact of genomic biomarkers on a clinical risk prediction model for upgrading/upstaging among men with favorable-risk prostate cancer.