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Showing 1 to 12 of 204 entries
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Widespread intron retention diversifies most cancer transcriptomes.

Genome medicine

Dvinge H, Bradley RK.
PMID: 26113877
Genome Med. 2015 May 15;7(1):45. doi: 10.1186/s13073-015-0168-9. eCollection 2015.

BACKGROUND: Somatic mutations affecting components of the RNA splicing machinery occur with high frequencies across many tumor types. These mutations give rise to distinct alterations in normal splice site and exon recognition, such as unusual 3' splice site preferences,...

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Dvinge H, Bradley RK. Widespread intron retention diversifies most cancer transcriptomes. Genome Med. 2015;7(1):45doi: 10.1186/s13073-015-0168-9.
Dvinge, H., & Bradley, R. K. (2015). Widespread intron retention diversifies most cancer transcriptomes. Genome medicine, 7(1), 45. https://doi.org/10.1186/s13073-015-0168-9
Dvinge, Heidi, and Bradley, Robert K. "Widespread intron retention diversifies most cancer transcriptomes." Genome medicine vol. 7,1 (2015): 45. doi: https://doi.org/10.1186/s13073-015-0168-9
Dvinge H, Bradley RK. Widespread intron retention diversifies most cancer transcriptomes. Genome Med. 2015 May 15;7(1):45. doi: 10.1186/s13073-015-0168-9. eCollection 2015. PMID: 26113877; PMCID: PMC4480902.
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The conserved HDAC Rpd3 drives transcriptional quiescence in S. cerevisiae.

Genomics data

McKnight JN, Tsukiyama T.
PMID: 26697386
Genom Data. 2015 Oct 17;6:245-8. doi: 10.1016/j.gdata.2015.10.008. eCollection 2015 Dec.

Quiescence is a ubiquitous cell cycle stage conserved from microbes through humans and is essential to normal cellular function and response to changing environmental conditions. We recently reported a massive repressive event associated with quiescence in Saccharomyces cerevisiae, where...

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McKnight JN, Tsukiyama T. The conserved HDAC Rpd3 drives transcriptional quiescence in S. cerevisiae. Genom Data. 2015;6:245-8doi: 10.1016/j.gdata.2015.10.008.
McKnight, J. N., & Tsukiyama, T. (2015). The conserved HDAC Rpd3 drives transcriptional quiescence in S. cerevisiae. Genomics data, 6245-8. https://doi.org/10.1016/j.gdata.2015.10.008
McKnight, Jeffrey N, and Tsukiyama, Toshio. "The conserved HDAC Rpd3 drives transcriptional quiescence in S. cerevisiae." Genomics data vol. 6 (2015): 245-8. doi: https://doi.org/10.1016/j.gdata.2015.10.008
McKnight JN, Tsukiyama T. The conserved HDAC Rpd3 drives transcriptional quiescence in S. cerevisiae. Genom Data. 2015 Oct 17;6:245-8. doi: 10.1016/j.gdata.2015.10.008. eCollection 2015 Dec. PMID: 26697386; PMCID: PMC4664762.
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Obesity and inflammation markers in relation to leukocyte telomere length in a cross-sectional study of persons with Barrett's esophagus.

BMC obesity

Hardikar S, Song X, Risques RA, Montine TJ, Duggan C, Blount PL, Reid BJ, Anderson GL, Kratz M, White E, Vaughan TL.
PMID: 26380096
BMC Obes. 2015 Sep 10;2:32. doi: 10.1186/s40608-015-0063-3. eCollection 2015.

BACKGROUND: Telomere shortening is associated with increasing age, male gender and lifestyle factors such as obesity and smoking. Inflammation has also been implicated in cellular senescence and may promote telomere shortening in chronic conditions such as obesity and diabetes....

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Hardikar S, Song X, Risques RA, et al. Obesity and inflammation markers in relation to leukocyte telomere length in a cross-sectional study of persons with Barrett's esophagus. BMC Obes. 2015;2:32doi: 10.1186/s40608-015-0063-3.
Hardikar, S., Song, X., Risques, R. A., Montine, T. J., Duggan, C., Blount, P. L., Reid, B. J., Anderson, G. L., Kratz, M., White, E., & Vaughan, T. L. (2015). Obesity and inflammation markers in relation to leukocyte telomere length in a cross-sectional study of persons with Barrett's esophagus. BMC obesity, 232. https://doi.org/10.1186/s40608-015-0063-3
Hardikar, Sheetal, et al. "Obesity and inflammation markers in relation to leukocyte telomere length in a cross-sectional study of persons with Barrett's esophagus." BMC obesity vol. 2 (2015): 32. doi: https://doi.org/10.1186/s40608-015-0063-3
Hardikar S, Song X, Risques RA, Montine TJ, Duggan C, Blount PL, Reid BJ, Anderson GL, Kratz M, White E, Vaughan TL. Obesity and inflammation markers in relation to leukocyte telomere length in a cross-sectional study of persons with Barrett's esophagus. BMC Obes. 2015 Sep 10;2:32. doi: 10.1186/s40608-015-0063-3. eCollection 2015. PMID: 26380096; PMCID: PMC4566310.
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Regression Models For Multivariate Count Data.

Journal of computational and graphical statistics : a joint publication of American Statistical Association, Institute of Mathematical Statistics, Interface Foundation of North America

Zhang Y, Zhou H, Zhou J, Sun W.
PMID: 28348500
J Comput Graph Stat. 2017;26(1):1-13. doi: 10.1080/10618600.2016.1154063. Epub 2017 Feb 16.

Data with multivariate count responses frequently occur in modern applications. The commonly used multinomial-logit model is limiting due to its restrictive mean-variance structure. For instance, analyzing count data from the recent RNA-seq technology by the multinomial-logit model leads to...

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Zhang Y, Zhou H, Zhou J, et al. Regression Models For Multivariate Count Data. J Comput Graph Stat. 2017;26(1):1-13doi: 10.1080/10618600.2016.1154063.
Zhang, Y., Zhou, H., Zhou, J., & Sun, W. (2017). Regression Models For Multivariate Count Data. Journal of computational and graphical statistics : a joint publication of American Statistical Association, Institute of Mathematical Statistics, Interface Foundation of North America, 26(1), 1-13. https://doi.org/10.1080/10618600.2016.1154063
Zhang, Yiwen, et al. "Regression Models For Multivariate Count Data." Journal of computational and graphical statistics : a joint publication of American Statistical Association, Institute of Mathematical Statistics, Interface Foundation of North America vol. 26,1 (2017): 1-13. doi: https://doi.org/10.1080/10618600.2016.1154063
Zhang Y, Zhou H, Zhou J, Sun W. Regression Models For Multivariate Count Data. J Comput Graph Stat. 2017;26(1):1-13. doi: 10.1080/10618600.2016.1154063. Epub 2017 Feb 16. PMID: 28348500; PMCID: PMC5365157.
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Students' Consumption of Beverages and Snacks at School and Away from School: A Case Study in the North East of Italy.

Frontiers in nutrition

Losasso C, Cappa V, Neuhouser ML, Giaccone V, Andrighetto I, Ricci A.
PMID: 26501063
Front Nutr. 2015 Oct 07;2:30. doi: 10.3389/fnut.2015.00030. eCollection 2015.

In North-East Italy (the Veneto region), several public school nutrition policies have been developed to reduce the consumption of high-caloric snacks and beverages. However, little is known about whether the policies actually influence students' dietary behaviors. In order to...

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Losasso C, Cappa V, Neuhouser ML, et al. Students' Consumption of Beverages and Snacks at School and Away from School: A Case Study in the North East of Italy. Front Nutr. 2015;2:30doi: 10.3389/fnut.2015.00030.
Losasso, C., Cappa, V., Neuhouser, M. L., Giaccone, V., Andrighetto, I., & Ricci, A. (2015). Students' Consumption of Beverages and Snacks at School and Away from School: A Case Study in the North East of Italy. Frontiers in nutrition, 230. https://doi.org/10.3389/fnut.2015.00030
Losasso, Carmen, et al. "Students' Consumption of Beverages and Snacks at School and Away from School: A Case Study in the North East of Italy." Frontiers in nutrition vol. 2 (2015): 30. doi: https://doi.org/10.3389/fnut.2015.00030
Losasso C, Cappa V, Neuhouser ML, Giaccone V, Andrighetto I, Ricci A. Students' Consumption of Beverages and Snacks at School and Away from School: A Case Study in the North East of Italy. Front Nutr. 2015 Oct 07;2:30. doi: 10.3389/fnut.2015.00030. eCollection 2015. PMID: 26501063; PMCID: PMC4595772.
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Hematopoietic Cell Transplantation for Older Patients with MDS.

Mediterranean journal of hematology and infectious diseases

Shadman M, Deeg HJ.
PMID: 25237469
Mediterr J Hematol Infect Dis. 2014 Sep 01;6(1):e2014056. doi: 10.4084/MJHID.2014.056. eCollection 2014.

The incidence of myeloid malignancies, including myelodysplastic syndromes (MDS) increases with age. While several therapeutic modalities have been developed, for most of these patients the only treatment with curative potential is allogeneic hematopoietic cell transplantation (HCT). The development of...

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Shadman M, Deeg HJ. Hematopoietic Cell Transplantation for Older Patients with MDS. Mediterr J Hematol Infect Dis. 2014;6(1):e2014056doi: 10.4084/MJHID.2014.056.
Shadman, M., & Deeg, H. J. (2014). Hematopoietic Cell Transplantation for Older Patients with MDS. Mediterranean journal of hematology and infectious diseases, 6(1), e2014056. https://doi.org/10.4084/MJHID.2014.056
Shadman, Mazyar, and Deeg, H Joachim. "Hematopoietic Cell Transplantation for Older Patients with MDS." Mediterranean journal of hematology and infectious diseases vol. 6,1 (2014): e2014056. doi: https://doi.org/10.4084/MJHID.2014.056
Shadman M, Deeg HJ. Hematopoietic Cell Transplantation for Older Patients with MDS. Mediterr J Hematol Infect Dis. 2014 Sep 01;6(1):e2014056. doi: 10.4084/MJHID.2014.056. eCollection 2014. PMID: 25237469; PMCID: PMC4165501.
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Tetramer guided, cell sorter assisted production of clinical grade autologous NY-ESO-1 specific CD8(+) T cells.

Journal for immunotherapy of cancer

Pollack SM, Jones RL, Farrar EA, Lai IP, Lee SM, Cao J, Pillarisetty VG, Hoch BL, Gullett A, Bleakley M, Conrad EU, Eary JF, Shibuya KC, Warren EH, Carstens JN, Heimfeld S, Riddell SR, Yee C.
PMID: 25317334
J Immunother Cancer. 2014 Oct 14;2(1):36. doi: 10.1186/s40425-014-0036-y. eCollection 2014.

BACKGROUND: Adoptive T cell therapy represents an attractive modality for the treatment of patients with cancer. Peripheral blood mononuclear cells have been used as a source of antigen specific T cells but the very low frequency of T cells...

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Pollack SM, Jones RL, Farrar EA, et al. Tetramer guided, cell sorter assisted production of clinical grade autologous NY-ESO-1 specific CD8(+) T cells. J Immunother Cancer. 2014;2(1):36doi: 10.1186/s40425-014-0036-y.
Pollack, S. M., Jones, R. L., Farrar, E. A., Lai, I. P., Lee, S. M., Cao, J., Pillarisetty, V. G., Hoch, B. L., Gullett, A., Bleakley, M., Conrad, E. U., Eary, J. F., Shibuya, K. C., Warren, E. H., Carstens, J. N., Heimfeld, S., Riddell, S. R., & Yee, C. (2014). Tetramer guided, cell sorter assisted production of clinical grade autologous NY-ESO-1 specific CD8(+) T cells. Journal for immunotherapy of cancer, 2(1), 36. https://doi.org/10.1186/s40425-014-0036-y
Pollack, Seth M, et al. "Tetramer guided, cell sorter assisted production of clinical grade autologous NY-ESO-1 specific CD8(+) T cells." Journal for immunotherapy of cancer vol. 2,1 (2014): 36. doi: https://doi.org/10.1186/s40425-014-0036-y
Pollack SM, Jones RL, Farrar EA, Lai IP, Lee SM, Cao J, Pillarisetty VG, Hoch BL, Gullett A, Bleakley M, Conrad EU, Eary JF, Shibuya KC, Warren EH, Carstens JN, Heimfeld S, Riddell SR, Yee C. Tetramer guided, cell sorter assisted production of clinical grade autologous NY-ESO-1 specific CD8(+) T cells. J Immunother Cancer. 2014 Oct 14;2(1):36. doi: 10.1186/s40425-014-0036-y. eCollection 2014. PMID: 25317334; PMCID: PMC4196009.
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Feasibility study of FDG PET as an indicator of early response to aromatase inhibitors and trastuzumab in a heterogeneous group of breast cancer patients.

EJNMMI research

Kurland BF, Gadi VK, Specht JM, Allison KH, Livingston RB, Rodler ET, Peterson LM, Schubert EK, Chai X, Mankoff DA, Linden HM.
PMID: 22731662
EJNMMI Res. 2012 Jun 25;2(1):34. doi: 10.1186/2191-219X-2-34.

BACKGROUND: In breast cancer endocrine therapy, post-therapy Ki-67 assay of biopsy material predicts recurrence-free survival but is invasive and prone to sampling error. [18F]Fluorodeoxyglucose (FDG) positron emission tomography (PET) has shown an early agonist or 'flare' response to tamoxifen...

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Kurland BF, Gadi VK, Specht JM, et al. Feasibility study of FDG PET as an indicator of early response to aromatase inhibitors and trastuzumab in a heterogeneous group of breast cancer patients. EJNMMI Res. 2012;2(1):34doi: 10.1186/2191-219X-2-34.
Kurland, B. F., Gadi, V. K., Specht, J. M., Allison, K. H., Livingston, R. B., Rodler, E. T., Peterson, L. M., Schubert, E. K., Chai, X., Mankoff, D. A., & Linden, H. M. (2012). Feasibility study of FDG PET as an indicator of early response to aromatase inhibitors and trastuzumab in a heterogeneous group of breast cancer patients. EJNMMI research, 2(1), 34. https://doi.org/10.1186/2191-219X-2-34
Kurland, Brenda F, et al. "Feasibility study of FDG PET as an indicator of early response to aromatase inhibitors and trastuzumab in a heterogeneous group of breast cancer patients." EJNMMI research vol. 2,1 (2012): 34. doi: https://doi.org/10.1186/2191-219X-2-34
Kurland BF, Gadi VK, Specht JM, Allison KH, Livingston RB, Rodler ET, Peterson LM, Schubert EK, Chai X, Mankoff DA, Linden HM. Feasibility study of FDG PET as an indicator of early response to aromatase inhibitors and trastuzumab in a heterogeneous group of breast cancer patients. EJNMMI Res. 2012 Jun 25;2(1):34. doi: 10.1186/2191-219X-2-34. PMID: 22731662; PMCID: PMC3444390.
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B16 melanoma tumor growth is delayed in mice in an age-dependent manner.

Pathobiology of aging & age related diseases

Pettan-Brewer C, Morton J, Coil R, Hopkins H, Fatemie S, Ladiges W.
PMID: 22953040
Pathobiol Aging Age Relat Dis. 2012;2. doi: 10.3402/pba.v2i0.19182. Epub 2012 Aug 20.

A major risk factor for cancer is increasing age, which suggests that syngeneic tumor implants in old mice would grow more rapidly. However, various reports have suggested that old mice are not as permissive to implanted tumor cells as...

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Pettan-Brewer C, Morton J, Coil R, et al. B16 melanoma tumor growth is delayed in mice in an age-dependent manner. Pathobiol Aging Age Relat Dis. 2012;2doi: 10.3402/pba.v2i0.19182.
Pettan-Brewer, C., Morton, J., Coil, R., Hopkins, H., Fatemie, S., & Ladiges, W. (2012). B16 melanoma tumor growth is delayed in mice in an age-dependent manner. Pathobiology of aging & age related diseases, 2. https://doi.org/10.3402/pba.v2i0.19182
Pettan-Brewer, Christina, et al. "B16 melanoma tumor growth is delayed in mice in an age-dependent manner." Pathobiology of aging & age related diseases vol. 2 (2012). doi: https://doi.org/10.3402/pba.v2i0.19182
Pettan-Brewer C, Morton J, Coil R, Hopkins H, Fatemie S, Ladiges W. B16 melanoma tumor growth is delayed in mice in an age-dependent manner. Pathobiol Aging Age Relat Dis. 2012;2. doi: 10.3402/pba.v2i0.19182. Epub 2012 Aug 20. PMID: 22953040; PMCID: PMC3424493.
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Light-sheet microscopy for slide-free non-destructive pathology of large clinical specimens.

Nature biomedical engineering

Glaser AK, Reder NP, Chen Y, McCarty EF, Yin C, Wei L, Wang Y, True LD, Liu JTC.
PMID: 29750130
Nat Biomed Eng. 2017 Jul;1(7). doi: 10.1038/s41551-017-0084. Epub 2017 Jun 26.

For the 1.7 million patients per year in the U.S. who receive a new cancer diagnosis, treatment decisions are largely made after a histopathology exam. Unfortunately, the gold standard of slide-based microscopic pathology suffers from high inter-observer variability and...

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Glaser AK, Reder NP, Chen Y, et al. Light-sheet microscopy for slide-free non-destructive pathology of large clinical specimens. Nat Biomed Eng. 2017;1(7)doi: 10.1038/s41551-017-0084.
Glaser, A. K., Reder, N. P., Chen, Y., McCarty, E. F., Yin, C., Wei, L., Wang, Y., True, L. D., & Liu, J. T. C. (2017). Light-sheet microscopy for slide-free non-destructive pathology of large clinical specimens. Nature biomedical engineering, 1(7), . https://doi.org/10.1038/s41551-017-0084
Glaser, Adam K, et al. "Light-sheet microscopy for slide-free non-destructive pathology of large clinical specimens." Nature biomedical engineering vol. 1,7 (2017). doi: https://doi.org/10.1038/s41551-017-0084
Glaser AK, Reder NP, Chen Y, McCarty EF, Yin C, Wei L, Wang Y, True LD, Liu JTC. Light-sheet microscopy for slide-free non-destructive pathology of large clinical specimens. Nat Biomed Eng. 2017 Jul;1(7). doi: 10.1038/s41551-017-0084. Epub 2017 Jun 26. PMID: 29750130; PMCID: PMC5940348.
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Structured detection of interactions with the directed lasso.

Statistics in biosciences

Pashova H, LeBlanc M, Kooperberg C.
PMID: 29292402
Stat Biosci. 2017 Dec;9(2):676-691. doi: 10.1007/s12561-016-9184-6. Epub 2016 Nov 29.

When considering low-dimensional gene-treatment or gene-environment interactions we might suspect groups of genes to interact with treatment or environment in a similar way. For example, genes associated with related biological processes might interact with an environmental factor or a...

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Pashova H, LeBlanc M, Kooperberg C. Structured detection of interactions with the directed lasso. Stat Biosci. 2016;9(2):676-691doi: 10.1007/s12561-016-9184-6.
Pashova, H., LeBlanc, M., & Kooperberg, C. (2017). Structured detection of interactions with the directed lasso. Statistics in biosciences, 9(2), 676-691. https://doi.org/10.1007/s12561-016-9184-6
Pashova, Hristina, et al. "Structured detection of interactions with the directed lasso." Statistics in biosciences vol. 9,2 (2017): 676-691. doi: https://doi.org/10.1007/s12561-016-9184-6
Pashova H, LeBlanc M, Kooperberg C. Structured detection of interactions with the directed lasso. Stat Biosci. 2017 Dec;9(2):676-691. doi: 10.1007/s12561-016-9184-6. Epub 2016 Nov 29. PMID: 29292402; PMCID: PMC5747322.
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Breast-cancer-specific mortality in patients treated based on the 21-gene assay: a SEER population-based study.

NPJ breast cancer

Petkov VI, Miller DP, Howlader N, Gliner N, Howe W, Schussler N, Cronin K, Baehner FL, Cress R, Deapen D, Glaser SL, Hernandez BY, Lynch CF, Mueller L, Schwartz AG, Schwartz SM, Stroup A, Sweeney C, Tucker TC, Ward KC, Wiggins C, Wu XC, Penberthy L, Shak S.
PMID: 28721379
NPJ Breast Cancer. 2016 Jun 08;2:16017. doi: 10.1038/npjbcancer.2016.17. eCollection 2016.

The 21-gene Recurrence Score assay is validated to predict recurrence risk and chemotherapy benefit in hormone-receptor-positive (HR+) invasive breast cancer. To determine prospective breast-cancer-specific mortality (BCSM) outcomes by baseline Recurrence Score results and clinical covariates, the National Cancer Institute...

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Petkov VI, Miller DP, Howlader N, et al. Breast-cancer-specific mortality in patients treated based on the 21-gene assay: a SEER population-based study. NPJ Breast Cancer. 2016;2:16017doi: 10.1038/npjbcancer.2016.17.
Petkov, V. I., Miller, D. P., Howlader, N., Gliner, N., Howe, W., Schussler, N., Cronin, K., Baehner, F. L., Cress, R., Deapen, D., Glaser, S. L., Hernandez, B. Y., Lynch, C. F., Mueller, L., Schwartz, A. G., Schwartz, S. M., Stroup, A., Sweeney, C., Tucker, T. C., Ward, K. C., Wiggins, C., Wu, X. C., Penberthy, L., & Shak, S. (2016). Breast-cancer-specific mortality in patients treated based on the 21-gene assay: a SEER population-based study. NPJ breast cancer, 216017. https://doi.org/10.1038/npjbcancer.2016.17
Petkov, Valentina I, et al. "Breast-cancer-specific mortality in patients treated based on the 21-gene assay: a SEER population-based study." NPJ breast cancer vol. 2 (2016): 16017. doi: https://doi.org/10.1038/npjbcancer.2016.17
Petkov VI, Miller DP, Howlader N, Gliner N, Howe W, Schussler N, Cronin K, Baehner FL, Cress R, Deapen D, Glaser SL, Hernandez BY, Lynch CF, Mueller L, Schwartz AG, Schwartz SM, Stroup A, Sweeney C, Tucker TC, Ward KC, Wiggins C, Wu XC, Penberthy L, Shak S. Breast-cancer-specific mortality in patients treated based on the 21-gene assay: a SEER population-based study. NPJ Breast Cancer. 2016 Jun 08;2:16017. doi: 10.1038/npjbcancer.2016.17. eCollection 2016. PMID: 28721379; PMCID: PMC5515329.
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Showing 1 to 12 of 204 entries