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Deep Feature Transfer Learning in Combination with Traditional Features Predicts Survival Among Patients with Lung Adenocarcinoma.

Tomography (Ann Arbor, Mich.)

Paul R, Hawkins SH, Balagurunathan Y, Schabath MB, Gillies RJ, Hall LO, Goldgof DB.
PMID: 28066809
Tomography. 2016 Dec;2(4):388-395. doi: 10.18383/j.tom.2016.00211.

Lung cancer is the most common cause of cancer-related deaths in the USA. It can be detected and diagnosed using computed tomography images. For an automated classifier, identifying predictive features from medical images is a key concern. Deep feature...

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Paul R, Hawkins SH, Balagurunathan Y, et al. Deep Feature Transfer Learning in Combination with Traditional Features Predicts Survival Among Patients with Lung Adenocarcinoma. Tomography. 2016;2(4):388-395doi: 10.18383/j.tom.2016.00211.
Paul, R., Hawkins, S. H., Balagurunathan, Y., Schabath, M. B., Gillies, R. J., Hall, L. O., & Goldgof, D. B. (2016). Deep Feature Transfer Learning in Combination with Traditional Features Predicts Survival Among Patients with Lung Adenocarcinoma. Tomography (Ann Arbor, Mich.), 2(4), 388-395. https://doi.org/10.18383/j.tom.2016.00211
Paul, Rahul, et al. "Deep Feature Transfer Learning in Combination with Traditional Features Predicts Survival Among Patients with Lung Adenocarcinoma." Tomography (Ann Arbor, Mich.) vol. 2,4 (2016): 388-395. doi: https://doi.org/10.18383/j.tom.2016.00211
Paul R, Hawkins SH, Balagurunathan Y, Schabath MB, Gillies RJ, Hall LO, Goldgof DB. Deep Feature Transfer Learning in Combination with Traditional Features Predicts Survival Among Patients with Lung Adenocarcinoma. Tomography. 2016 Dec;2(4):388-395. doi: 10.18383/j.tom.2016.00211. PMID: 28066809; PMCID: PMC5218828.
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Representation of Deep Features using Radiologist defined Semantic Features.

Proceedings of ... International Joint Conference on Neural Networks. International Joint Conference on Neural Networks

Paul R, Liu Y, Li Q, Hall L, Goldgof D, Balagurunathan Y, Schabath M, Gillies R.
PMID: 30443437
Proc Int Jt Conf Neural Netw. 2018 Jul;2018. doi: 10.1109/IJCNN.2018.8489440. Epub 2018 Sep 15.

Semantic features are common radiological traits used to characterize a lesion by a trained radiologist. These features have been recently formulated, quantified on a point scale in the context of lung nodules by our group. Certain radiological semantic traits...

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Paul R, Liu Y, Li Q, et al. Representation of Deep Features using Radiologist defined Semantic Features. Proc Int Jt Conf Neural Netw. 2018;2018doi: 10.1109/IJCNN.2018.8489440.
Paul, R., Liu, Y., Li, Q., Hall, L., Goldgof, D., Balagurunathan, Y., Schabath, M., & Gillies, R. (2018). Representation of Deep Features using Radiologist defined Semantic Features. Proceedings of ... International Joint Conference on Neural Networks. International Joint Conference on Neural Networks, 2018. https://doi.org/10.1109/IJCNN.2018.8489440
Paul, Rahul, et al. "Representation of Deep Features using Radiologist defined Semantic Features." Proceedings of ... International Joint Conference on Neural Networks. International Joint Conference on Neural Networks vol. 2018 (2018). doi: https://doi.org/10.1109/IJCNN.2018.8489440
Paul R, Liu Y, Li Q, Hall L, Goldgof D, Balagurunathan Y, Schabath M, Gillies R. Representation of Deep Features using Radiologist defined Semantic Features. Proc Int Jt Conf Neural Netw. 2018 Jul;2018. doi: 10.1109/IJCNN.2018.8489440. Epub 2018 Sep 15. PMID: 30443437; PMCID: PMC6233304.
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Lesbian, Gay, Bisexual, Transgender, Queer/Questioning (LGBTQ) Perceptions and Health Care Experiences.

Journal of gay & lesbian social services

Quinn GP, Sutton SK, Winfield B, Breen S, Canales J, Shetty G, Sehovic I, Green BL, Schabath MB.
PMID: 30996583
J Gay Lesbian Soc Serv. 2015;27(2):246-261. doi: 10.1080/10538720.2015.1022273. Epub 2015 Jun 10.

BACKGROUND: The goal study of this was to explore attitudes, health knowledge, and experiences with healthcare setting and providers among gay, lesbian, bisexual, transgender, queer/questioning (GLBTQ) individuals and to identify areas for improvement.METHODS: Members of Equality Florida™ residing in...

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Quinn GP, Sutton SK, Winfield B, et al. Lesbian, Gay, Bisexual, Transgender, Queer/Questioning (LGBTQ) Perceptions and Health Care Experiences. J Gay Lesbian Soc Serv. 2015;27(2):246-261doi: 10.1080/10538720.2015.1022273.
Quinn, G. P., Sutton, S. K., Winfield, B., Breen, S., Canales, J., Shetty, G., Sehovic, I., Green, B. L., & Schabath, M. B. (2015). Lesbian, Gay, Bisexual, Transgender, Queer/Questioning (LGBTQ) Perceptions and Health Care Experiences. Journal of gay & lesbian social services, 27(2), 246-261. https://doi.org/10.1080/10538720.2015.1022273
Quinn, Gwendolyn P, et al. "Lesbian, Gay, Bisexual, Transgender, Queer/Questioning (LGBTQ) Perceptions and Health Care Experiences." Journal of gay & lesbian social services vol. 27,2 (2015): 246-261. doi: https://doi.org/10.1080/10538720.2015.1022273
Quinn GP, Sutton SK, Winfield B, Breen S, Canales J, Shetty G, Sehovic I, Green BL, Schabath MB. Lesbian, Gay, Bisexual, Transgender, Queer/Questioning (LGBTQ) Perceptions and Health Care Experiences. J Gay Lesbian Soc Serv. 2015;27(2):246-261. doi: 10.1080/10538720.2015.1022273. Epub 2015 Jun 10. PMID: 30996583; PMCID: PMC6464116.
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Genome-wide association study of INDELs identified four novel susceptibility loci associated with lung cancer risk.

International journal of cancer

Dai J, Huang M, Amos CI, Hung RJ, Tardon A, Andrew A, Chen C, Christiani DC, Albanes D, Rennert G, Fan J, Goodman G, Liu G, Field JK, Grankvist K, Kiemeney LA, Le Marchand L, Schabath MB, Johansson M, Aldrich MC, Johansson M, Caporaso N, Lazarus P, Lam S, Bojesen SE, Arnold S, Landi MT, Risch A, Wichmann HE, Bickeboller H, Brennan P, Shete S, Melander O, Brunnstrom H, Zienolddiny S, Woll P, Stevens V, Hu Z, Shen H.
PMID: 31577861
Int J Cancer. 2020 May 15;146(10):2855-2864. doi: 10.1002/ijc.32698. Epub 2019 Oct 31.

Genome-wide association studies (GWAS) have identified 45 susceptibility loci associated with lung cancer. Only less than SNPs, small insertions and deletions (INDELs) are the second most abundant genetic polymorphisms in the human genome. INDELs are highly associated with multiple...

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Dai J, Huang M, Amos CI, et al. Genome-wide association study of INDELs identified four novel susceptibility loci associated with lung cancer risk. Int J Cancer. 2019;146(10):2855-2864doi: 10.1002/ijc.32698.
Dai, J., Huang, M., Amos, C. I., Hung, R. J., Tardon, A., Andrew, A., Chen, C., Christiani, D. C., Albanes, D., Rennert, G., Fan, J., Goodman, G., Liu, G., Field, J. K., Grankvist, K., Kiemeney, L. A., Le Marchand, L., Schabath, M. B., Johansson, M., Aldrich, M. C., Johansson, M., Caporaso, N., Lazarus, P., Lam, S., Bojesen, S. E., Arnold, S., Landi, M. T., Risch, A., Wichmann, H. E., Bickeboller, H., Brennan, P., Shete, S., Melander, O., Brunnstrom, H., Zienolddiny, S., Woll, P., Stevens, V., Hu, Z., & Shen, H. (2020). Genome-wide association study of INDELs identified four novel susceptibility loci associated with lung cancer risk. International journal of cancer, 146(10), 2855-2864. https://doi.org/10.1002/ijc.32698
Dai, Juncheng, et al. "Genome-wide association study of INDELs identified four novel susceptibility loci associated with lung cancer risk." International journal of cancer vol. 146,10 (2020): 2855-2864. doi: https://doi.org/10.1002/ijc.32698
Dai J, Huang M, Amos CI, Hung RJ, Tardon A, Andrew A, Chen C, Christiani DC, Albanes D, Rennert G, Fan J, Goodman G, Liu G, Field JK, Grankvist K, Kiemeney LA, Le Marchand L, Schabath MB, Johansson M, Aldrich MC, Johansson M, Caporaso N, Lazarus P, Lam S, Bojesen SE, Arnold S, Landi MT, Risch A, Wichmann HE, Bickeboller H, Brennan P, Shete S, Melander O, Brunnstrom H, Zienolddiny S, Woll P, Stevens V, Hu Z, Shen H. Genome-wide association study of INDELs identified four novel susceptibility loci associated with lung cancer risk. Int J Cancer. 2020 May 15;146(10):2855-2864. doi: 10.1002/ijc.32698. Epub 2019 Oct 31. PMID: 31577861; PMCID: PMC7101262.
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Together-Equitable-Accessible-Meaningful (TEAM) Training to Improve Cancer Care for Sexual and Gender Minorities (SGM): Outcomes from a Pilot Study.

Journal of cancer education : the official journal of the American Association for Cancer Education

Pratt-Chapman ML, Wang Y, Eckstrand K, Radix A, Quinn GP, Schabath MB, Lopez AM.
PMID: 35013901
J Cancer Educ. 2022 Jan 10; doi: 10.1007/s13187-022-02134-2. Epub 2022 Jan 10.

To alleviate health disparities experienced by sexual and gender minority (SGM) patients, cancer care professionals need further education on the needs of SGM cancer patients and their loved ones and caregivers. The Together-Equitable-Accessible-Meaningful (TEAM) Training to Improve Cancer Care...

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Pratt-Chapman ML, Wang Y, Eckstrand K, et al. Together-Equitable-Accessible-Meaningful (TEAM) Training to Improve Cancer Care for Sexual and Gender Minorities (SGM): Outcomes from a Pilot Study. J Cancer Educ. 2022;doi: 10.1007/s13187-022-02134-2.
Pratt-Chapman, M. L., Wang, Y., Eckstrand, K., Radix, A., Quinn, G. P., Schabath, M. B., & Lopez, A. M. (2022). Together-Equitable-Accessible-Meaningful (TEAM) Training to Improve Cancer Care for Sexual and Gender Minorities (SGM): Outcomes from a Pilot Study. Journal of cancer education : the official journal of the American Association for Cancer Education, . https://doi.org/10.1007/s13187-022-02134-2
Pratt-Chapman, Mandi L, et al. "Together-Equitable-Accessible-Meaningful (TEAM) Training to Improve Cancer Care for Sexual and Gender Minorities (SGM): Outcomes from a Pilot Study." Journal of cancer education : the official journal of the American Association for Cancer Education vol. (2022). doi: https://doi.org/10.1007/s13187-022-02134-2
Pratt-Chapman ML, Wang Y, Eckstrand K, Radix A, Quinn GP, Schabath MB, Lopez AM. Together-Equitable-Accessible-Meaningful (TEAM) Training to Improve Cancer Care for Sexual and Gender Minorities (SGM): Outcomes from a Pilot Study. J Cancer Educ. 2022 Jan 10; doi: 10.1007/s13187-022-02134-2. Epub 2022 Jan 10. PMID: 35013901.
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Counterfactual time series analysis of short-term change in air pollution following the COVID-19 state of emergency in the United States.

Scientific reports

Dey T, Tyagi P, Sabath MB, Kamareddine L, Henneman L, Braun D, Dominici F.
PMID: 34876601
Sci Rep. 2021 Dec 07;11(1):23517. doi: 10.1038/s41598-021-02776-0.

Lockdown measures implemented in response to the COVID-19 pandemic produced sudden behavioral changes. We implement counterfactual time series analysis based on seasonal autoregressive integrated moving average models (SARIMA), to examine the extent of air pollution reduction attained following state-level...

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Dey T, Tyagi P, Sabath MB, et al. Counterfactual time series analysis of short-term change in air pollution following the COVID-19 state of emergency in the United States. Sci Rep. 2021;11(1):23517doi: 10.1038/s41598-021-02776-0.
Dey, T., Tyagi, P., Sabath, M. B., Kamareddine, L., Henneman, L., Braun, D., & Dominici, F. (2021). Counterfactual time series analysis of short-term change in air pollution following the COVID-19 state of emergency in the United States. Scientific reports, 11(1), 23517. https://doi.org/10.1038/s41598-021-02776-0
Dey, Tanujit, et al. "Counterfactual time series analysis of short-term change in air pollution following the COVID-19 state of emergency in the United States." Scientific reports vol. 11,1 (2021): 23517. doi: https://doi.org/10.1038/s41598-021-02776-0
Dey T, Tyagi P, Sabath MB, Kamareddine L, Henneman L, Braun D, Dominici F. Counterfactual time series analysis of short-term change in air pollution following the COVID-19 state of emergency in the United States. Sci Rep. 2021 Dec 07;11(1):23517. doi: 10.1038/s41598-021-02776-0. PMID: 34876601; PMCID: PMC8651777.
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Radiomics of .

Radiology. Artificial intelligence

Mu W, Tunali I, Qi J, Schabath MB, Gillies RJ.
PMID: 33937811
Radiol Artif Intell. 2020 Jan 29;2(1):e190063. doi: 10.1148/ryai.2019190063. eCollection 2020 Jan.

PURPOSE: To investigate the performance of pretreatment fluorine 18 (MATERIALS AND METHODS: The retrospective arm of this study included 146 patients with histologically confirmed stage IIIB-IV NSCLC who were treated with immune checkpoint blockade between June 2011 and December...

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Mu W, Tunali I, Qi J, et al. Radiomics of . Radiol Artif Intell. 2020;2(1):e190063doi: 10.1148/ryai.2019190063.
Mu, W., Tunali, I., Qi, J., Schabath, M. B., & Gillies, R. J. (2020). Radiomics of . Radiology. Artificial intelligence, 2(1), e190063. https://doi.org/10.1148/ryai.2019190063
Mu, Wei, et al. "Radiomics of ." Radiology. Artificial intelligence vol. 2,1 (2020): e190063. doi: https://doi.org/10.1148/ryai.2019190063
Mu W, Tunali I, Qi J, Schabath MB, Gillies RJ. Radiomics of . Radiol Artif Intell. 2020 Jan 29;2(1):e190063. doi: 10.1148/ryai.2019190063. eCollection 2020 Jan. PMID: 33937811; PMCID: PMC8074998.
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County-level exposures to greenness and associations with COVID-19 incidence and mortality in the United States.

medRxiv : the preprint server for health sciences

Klompmaker JO, Hart JE, Holland I, Sabath MB, Wu X, Laden F, Dominici F, James P.
PMID: 32908990
medRxiv. 2020 Nov 16; doi: 10.1101/2020.08.26.20181644.

BACKGROUND: COVID-19 is an infectious disease that has killed more than 246,000 people in the US. During a time of social distancing measures and increasing social isolation, green spaces may be a crucial factor to maintain a physically and...

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Klompmaker JO, Hart JE, Holland I, et al. County-level exposures to greenness and associations with COVID-19 incidence and mortality in the United States. medRxiv. 2020;doi: 10.1101/2020.08.26.20181644.
Klompmaker, J. O., Hart, J. E., Holland, I., Sabath, M. B., Wu, X., Laden, F., Dominici, F., & James, P. (2020). County-level exposures to greenness and associations with COVID-19 incidence and mortality in the United States. medRxiv : the preprint server for health sciences, . https://doi.org/10.1101/2020.08.26.20181644
Klompmaker, Jochem O, et al. "County-level exposures to greenness and associations with COVID-19 incidence and mortality in the United States." medRxiv : the preprint server for health sciences vol. (2020). doi: https://doi.org/10.1101/2020.08.26.20181644
Klompmaker JO, Hart JE, Holland I, Sabath MB, Wu X, Laden F, Dominici F, James P. County-level exposures to greenness and associations with COVID-19 incidence and mortality in the United States. medRxiv. 2020 Nov 16; doi: 10.1101/2020.08.26.20181644. PMID: 32908990; PMCID: PMC7480038.
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Developing a web-based LGBT cultural competency training for oncologists: The COLORS training.

Patient education and counseling

Seay J, Hicks A, Markham MJ, Schlumbrecht M, Bowman M, Woodard J, Kollefrath A, Diego D, Quinn GP, Schabath MB.
PMID: 30642714
Patient Educ Couns. 2019 May;102(5):984-989. doi: 10.1016/j.pec.2019.01.006. Epub 2019 Jan 07.

OBJECTIVE: Despite substantial LGBT cancer health disparities, there are no LGBT cultural competency trainings tailored for oncologists. Here we describe the systematic development of a web-based, oncology-focused LGBT cultural competency training.METHODS: A literature review regarding LGBT cancer outcomes and...

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Seay J, Hicks A, Markham MJ, et al. Developing a web-based LGBT cultural competency training for oncologists: The COLORS training. Patient Educ Couns. 2019;102(5):984-989doi: 10.1016/j.pec.2019.01.006.
Seay, J., Hicks, A., Markham, M. J., Schlumbrecht, M., Bowman, M., Woodard, J., Kollefrath, A., Diego, D., Quinn, G. P., & Schabath, M. B. (2019). Developing a web-based LGBT cultural competency training for oncologists: The COLORS training. Patient education and counseling, 102(5), 984-989. https://doi.org/10.1016/j.pec.2019.01.006
Seay, Julia, et al. "Developing a web-based LGBT cultural competency training for oncologists: The COLORS training." Patient education and counseling vol. 102,5 (2019): 984-989. doi: https://doi.org/10.1016/j.pec.2019.01.006
Seay J, Hicks A, Markham MJ, Schlumbrecht M, Bowman M, Woodard J, Kollefrath A, Diego D, Quinn GP, Schabath MB. Developing a web-based LGBT cultural competency training for oncologists: The COLORS training. Patient Educ Couns. 2019 May;102(5):984-989. doi: 10.1016/j.pec.2019.01.006. Epub 2019 Jan 07. PMID: 30642714.
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Radiomics predicts risk of cachexia in advanced NSCLC patients treated with immune checkpoint inhibitors.

British journal of cancer

Mu W, Katsoulakis E, Whelan CJ, Gage KL, Schabath MB, Gillies RJ.
PMID: 33828255
Br J Cancer. 2021 Jul;125(2):229-239. doi: 10.1038/s41416-021-01375-0. Epub 2021 Apr 07.

BACKGROUND: Approximately 50% of cancer patients eventually develop a syndrome of prolonged weight loss (cachexia), which may contribute to primary resistance to immune checkpoint inhibitors (ICI). This study utilised radiomics analysis of METHODS: Baseline (pre-therapy) PET/CT images and clinical...

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Mu W, Katsoulakis E, Whelan CJ, et al. Radiomics predicts risk of cachexia in advanced NSCLC patients treated with immune checkpoint inhibitors. Br J Cancer. 2021;125(2):229-239doi: 10.1038/s41416-021-01375-0.
Mu, W., Katsoulakis, E., Whelan, C. J., Gage, K. L., Schabath, M. B., & Gillies, R. J. (2021). Radiomics predicts risk of cachexia in advanced NSCLC patients treated with immune checkpoint inhibitors. British journal of cancer, 125(2), 229-239. https://doi.org/10.1038/s41416-021-01375-0
Mu, Wei, et al. "Radiomics predicts risk of cachexia in advanced NSCLC patients treated with immune checkpoint inhibitors." British journal of cancer vol. 125,2 (2021): 229-239. doi: https://doi.org/10.1038/s41416-021-01375-0
Mu W, Katsoulakis E, Whelan CJ, Gage KL, Schabath MB, Gillies RJ. Radiomics predicts risk of cachexia in advanced NSCLC patients treated with immune checkpoint inhibitors. Br J Cancer. 2021 Jul;125(2):229-239. doi: 10.1038/s41416-021-01375-0. Epub 2021 Apr 07. PMID: 33828255; PMCID: PMC8292339.
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County-level exposures to greenness and associations with COVID-19 incidence and mortality in the United States.

medRxiv : the preprint server for health sciences

Klompmaker JO, Hart JE, Holland I, Sabath MB, Wu X, Laden F, Dominici F, James P.
PMID: 32908990
medRxiv. 2020 Nov 16; doi: 10.1101/2020.08.26.20181644.

BACKGROUND: COVID-19 is an infectious disease that has killed more than 246,000 people in the US. During a time of social distancing measures and increasing social isolation, green spaces may be a crucial factor to maintain a physically and...

Cite
Klompmaker JO, Hart JE, Holland I, et al. County-level exposures to greenness and associations with COVID-19 incidence and mortality in the United States. medRxiv. 2020;doi: 10.1101/2020.08.26.20181644.
Klompmaker, J. O., Hart, J. E., Holland, I., Sabath, M. B., Wu, X., Laden, F., Dominici, F., & James, P. (2020). County-level exposures to greenness and associations with COVID-19 incidence and mortality in the United States. medRxiv : the preprint server for health sciences, . https://doi.org/10.1101/2020.08.26.20181644
Klompmaker, Jochem O, et al. "County-level exposures to greenness and associations with COVID-19 incidence and mortality in the United States." medRxiv : the preprint server for health sciences vol. (2020). doi: https://doi.org/10.1101/2020.08.26.20181644
Klompmaker JO, Hart JE, Holland I, Sabath MB, Wu X, Laden F, Dominici F, James P. County-level exposures to greenness and associations with COVID-19 incidence and mortality in the United States. medRxiv. 2020 Nov 16; doi: 10.1101/2020.08.26.20181644. PMID: 32908990; PMCID: PMC7480038.
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An analysis of HPV infection incidence and clearance by genotype and age in men: The HPV Infection in Men (HIM) Study.

Papillomavirus research (Amsterdam, Netherlands)

Ingles DJ, Lin HY, Fulp WJ, Sudenga SL, Lu B, Schabath MB, Papenfuss MR, Abrahamsen ME, Salmeron J, Villa LL, Ponce EL, Giuliano AR.
PMID: 27547836
Papillomavirus Res. 2015 Dec;1:126-135. doi: 10.1016/j.pvr.2015.09.001. Epub 2015 Oct 08.

OBJECTIVES: Genital HPV infection in men causes benign and cancerous lesions, the incidence of which differs by age. The goal of this work was to comprehensively evaluate incidence and clearance of individual HPV genotypes among men by age group.METHODS:...

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Ingles DJ, Lin HY, Fulp WJ, et al. An analysis of HPV infection incidence and clearance by genotype and age in men: The HPV Infection in Men (HIM) Study. Papillomavirus Res. 2015;1:126-135doi: 10.1016/j.pvr.2015.09.001.
Ingles, D. J., Lin, H. Y., Fulp, W. J., Sudenga, S. L., Lu, B., Schabath, M. B., Papenfuss, M. R., Abrahamsen, M. E., Salmeron, J., Villa, L. L., Ponce, E. L., & Giuliano, A. R. (2015). An analysis of HPV infection incidence and clearance by genotype and age in men: The HPV Infection in Men (HIM) Study. Papillomavirus research (Amsterdam, Netherlands), 1126-135. https://doi.org/10.1016/j.pvr.2015.09.001
Ingles, Donna J, et al. "An analysis of HPV infection incidence and clearance by genotype and age in men: The HPV Infection in Men (HIM) Study." Papillomavirus research (Amsterdam, Netherlands) vol. 1 (2015): 126-135. doi: https://doi.org/10.1016/j.pvr.2015.09.001
Ingles DJ, Lin HY, Fulp WJ, Sudenga SL, Lu B, Schabath MB, Papenfuss MR, Abrahamsen ME, Salmeron J, Villa LL, Ponce EL, Giuliano AR. An analysis of HPV infection incidence and clearance by genotype and age in men: The HPV Infection in Men (HIM) Study. Papillomavirus Res. 2015 Dec;1:126-135. doi: 10.1016/j.pvr.2015.09.001. Epub 2015 Oct 08. PMID: 27547836; PMCID: PMC4986989.
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