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Your search keyword '"Quackenbush, John"' showing total 880 results
Start Over Author "Quackenbush, John" Publication Type Academic Journals
880 results on '"Quackenbush, John"'

3. The Network Zoo: a multilingual package for the inference and analysis of gene regulatory networks

Author

Ben Guebila, Marouen, Wang, Tian, Lopes-Ramos, Camila M., Fanfani, Viola, Weighill, Des, Burkholz, Rebekka, Schlauch, Daniel, Paulson, Joseph N., Altenbuchinger, Michael, Shutta, Katherine H., Sonawane, Abhijeet R., Lim, James, Calderer, Genis, van IJzendoorn, David G.P., Morgan, Daniel, Marin, Alessandro, Chen, Cho-Yi, Song, Qi, Saha, Enakshi, DeMeo, Dawn L., Padi, Megha, Platig, John, Kuijjer, Marieke L., Glass, Kimberly, and Quackenbush, John

Published
2023
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4. MicroRNA-mRNA networks define translatable molecular outcome phenotypes in osteosarcoma.

Author

Lietz, Christopher E, Garbutt, Cassandra, Barry, William T, Deshpande, Vikram, Chen, Yen-Lin, Lozano-Calderon, Santiago A, Wang, Yaoyu, Lawney, Brian, Ebb, David, Cote, Gregory M, Duan, Zhenfeng, Hornicek, Francis J, Choy, Edwin, Petur Nielsen, G, Haibe-Kains, Benjamin, Quackenbush, John, and Spentzos, Dimitrios

Abstract

There is a lack of well validated prognostic biomarkers in osteosarcoma, a rare, recalcitrant disease for which treatment standards have not changed in over 20 years. We performed microRNA sequencing in 74 frozen osteosarcoma biopsy samples, constituting the largest single center translationally analyzed osteosarcoma cohort to date, and we separately analyzed a multi-omic dataset from a large NCI supported national cooperative group cohort. We validated the prognostic value of candidate microRNA signatures and contextualized them in relevant transcriptomic and epigenomic networks. Our results reveal the existence of molecularly defined phenotypes associated with outcome independent of clinicopathologic features. Through machine learning based integrative pharmacogenomic analysis, the microRNA biomarkers identify novel therapeutics for stratified application in osteosarcoma. The previously unrecognized osteosarcoma subtypes with distinct clinical courses and response to therapy could be translatable for discerning patients appropriate for more intensified, less intensified, or alternate therapeutic regimens.

Published
2020

5. Proceedings of the fifth international Molecular Pathological Epidemiology (MPE) meeting

Author

Yao, Song, Campbell, Peter T., Ugai, Tomotaka, Gierach, Gretchen, Abubakar, Mustapha, Adalsteinsson, Viktor, Almeida, Jonas, Brennan, Paul, Chanock, Stephen, Golub, Todd, Hanash, Samir, Harris, Curtis, Hathaway, Cassandra A., Kelsey, Karl, Landi, Maria Teresa, Mahmood, Faisal, Newton, Christina, Quackenbush, John, Rodig, Scott, Schultz, Nikolaus, Tearney, Guillermo, Tworoger, Shelley S., Wang, Molin, Zhang, Xuehong, Garcia-Closas, Montserrat, Rebbeck, Timothy R., Ambrosone, Christine B., and Ogino, Shuji

Published
2022
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10. Toward clinical genomics in everyday medicine: perspectives and recommendations

Author

Delaney, Susan K, Hultner, Michael L, Jacob, Howard J, Ledbetter, David H, McCarthy, Jeanette J, Ball, Michael, Beckman, Kenneth B, Belmont, John W, Bloss, Cinnamon S, Christman, Michael F, Cosgrove, Andy, Damiani, Stephen A, Danis, Timothy, Delledonne, Massimo, Dougherty, Michael J, Dudley, Joel T, Faucett, W Andrew, Friedman, Jennifer R, Haase, David H, Hays, Tom S, Heilsberg, Stu, Huber, Jeff, Kaminsky, Leah, Ledbetter, Nikki, Lee, Warren H, Levin, Elissa, Libiger, Ondrej, Linderman, Michael, Love, Richard L, Magnus, David C, Martland, AnneMarie, McClure, Susan L, Megill, Scott E, Messier, Helen, Nussbaum, Robert L, Palaniappan, Latha, Patay, Bradley A, Popovich, Bradley W, Quackenbush, John, Savant, Mark J, Su, Michael M, Terry, Sharon F, Tucker, Steven, Wong, William T, and Green, Robert C

Subjects
Genetics, Biotechnology, Clinical Research, Cancer, Human Genome, Generic health relevance, Good Health and Well Being, Delivery of Health Care, Genetic Testing, Genome, Human, Genomics, High-Throughput Nucleotide Sequencing, Humans, Precision Medicine, Reagent Kits, Diagnostic, Personalized medicine, precision medicine, clinical genomics, practice standards, genomic data, exome, genome, sequencing, genetic testing, Clinical Sciences
Abstract

Precision or personalized medicine through clinical genome and exome sequencing has been described by some as a revolution that could transform healthcare delivery, yet it is currently used in only a small fraction of patients, principally for the diagnosis of suspected Mendelian conditions and for targeting cancer treatments. Given the burden of illness in our society, it is of interest to ask how clinical genome and exome sequencing can be constructively integrated more broadly into the routine practice of medicine for the betterment of public health. In November 2014, 46 experts from academia, industry, policy and patient advocacy gathered in a conference sponsored by Illumina, Inc. to discuss this question, share viewpoints and propose recommendations. This perspective summarizes that work and identifies some of the obstacles and opportunities that must be considered in translating advances in genomics more widely into the practice of medicine.

Published
2016

11. Proceedings of the fourth international molecular pathological epidemiology (MPE) meeting

Author

Campbell, Peter T., Ambrosone, Christine B., Nishihara, Reiko, Aerts, Hugo J. W. L., Bondy, Melissa, Chatterjee, Nilanjan, Garcia-Closas, Montserrat, Giannakis, Marios, Golden, Jeffrey A., Heng, Yujing J., Kip, N. Sertac, Koshiol, Jill, Liu, X. Shirley, Lopes-Ramos, Camila M., Mucci, Lorelei A., Nowak, Jonathan A., Phipps, Amanda I., Quackenbush, John, Schoen, Robert E., Sholl, Lynette M., Tamimi, Rulla M., Wang, Molin, Weijenberg, Matty P., Wu, Catherine J., Wu, Kana, Yao, Song, Yu, Kun-Hsing, Zhang, Xuehong, Rebbeck, Timothy R., and Ogino, Shuji

Published
2019

14. CANCER : The march on malignancy

Author

Brody, Herb, May, Mike, GRAVITZ, LAUREN, EISENSTEIN, MICHAEL, WRIGHT, JESSICA, DEWEERDT, SARAH, KESSLER, REBECCA, BENDER, ERIC, SAVAGE, NEIL, Quackenbush, John, and BOURZAC, KATHERINE

Published
2014

22. Proceedings of the third international molecular pathological epidemiology (MPE) meeting

Author

Campbell, Peter T., Rebbeck, Timothy R., Nishihara, Reiko, Beck, Andrew H., Begg, Colin B., Bogdanov, Alexei A., Cao, Yin, Coleman, Helen G., Freeman, Gordon J., Heng, Yujing J., Huttenhower, Curtis, Irizarry, Rafael A., Kip, N. Sertac, Michor, Franziska, Nevo, Daniel, Peters, Ulrike, Phipps, Amanda I., Poole, Elizabeth M., Qian, Zhi Rong, Quackenbush, John, Robins, Harlan, Rogan, Peter K., Slattery, Martha L., Smith-Warner, Stephanie A., Song, Mingyang, VanderWeele, Tyler J., Xia, Daniel, Zabor, Emily C., Zhang, Xuehong, Wang, Molin, and Ogino, Shuji

Published
2017

24. Comparative Analyses of Potato Expressed Sequence Tag Libraries

Author

Ronning, Catherine M., White, Joseph A., Cho, Jennifer, Tsai, Jennifer, Quackenbush, John, Smart, Christine D., Fry, William E., Tanksley, Steve, Zhang, Peifen, Jin, Hailing, Yamamoto, Miki L., Baker, Barbara J., and Buell, C. Robin

Published
2003

25. Identification of conserved gene expression features between murine mammary carcinoma models and human breast tumors

Author

Herschkowitz, Jason I, Simin, Karl, Weigman, Victor J, Mikaelian, Igor, Usary, Jerry, Hu, Zhiyuan, Rasmussen, Karen E, Jones, Laundette P, Assefnia, Shahin, Chandrasekharan, Subhashini, Backlund, Michael G, Yin, Yuzhi, Khramtsov, Andrey I, Bastein, Roy, Quackenbush, John, Glazer, Robert I, Brown, Powel H, Green, Jeffrey E, Kopelovich, Levy, Furth, Priscilla A, Palazzo, Juan P, Olopade, Olufunmilayo I, Bernard, Philip S, Churchill, Gary A, Van Dyke, Terry, and Perou, Charles M

Subjects
Biological Sciences, Biomedical and Clinical Sciences, Genetics, Oncology and Carcinogenesis, Breast Cancer, Aging, Cancer, 2.1 Biological and endogenous factors, Aetiology, Animals, Breast Neoplasms, Cluster Analysis, Gene Expression Profiling, Gene Expression Regulation, Neoplastic, Humans, Mammary Neoplasms, Experimental, Mice, Neoplasm Proteins, Oligonucleotide Array Sequence Analysis, Species Specificity, Environmental Sciences, Information and Computing Sciences, Bioinformatics
Abstract

BackgroundAlthough numerous mouse models of breast carcinomas have been developed, we do not know the extent to which any faithfully represent clinically significant human phenotypes. To address this need, we characterized mammary tumor gene expression profiles from 13 different murine models using DNA microarrays and compared the resulting data to those from human breast tumors.ResultsUnsupervised hierarchical clustering analysis showed that six models (TgWAP-Myc, TgMMTV-Neu, TgMMTV-PyMT, TgWAP-Int3, TgWAP-Tag, and TgC3(1)-Tag) yielded tumors with distinctive and homogeneous expression patterns within each strain. However, in each of four other models (TgWAP-T121, TgMMTV-Wnt1, Brca1Co/Co;TgMMTV-Cre;p53+/- and DMBA-induced), tumors with a variety of histologies and expression profiles developed. In many models, similarities to human breast tumors were recognized, including proliferation and human breast tumor subtype signatures. Significantly, tumors of several models displayed characteristics of human basal-like breast tumors, including two models with induced Brca1 deficiencies. Tumors of other murine models shared features and trended towards significance of gene enrichment with human luminal tumors; however, these murine tumors lacked expression of estrogen receptor (ER) and ER-regulated genes. TgMMTV-Neu tumors did not have a significant gene overlap with the human HER2+/ER- subtype and were more similar to human luminal tumors.ConclusionMany of the defining characteristics of human subtypes were conserved among the mouse models. Although no single mouse model recapitulated all the expression features of a given human subtype, these shared expression features provide a common framework for an improved integration of murine mammary tumor models with human breast tumors.

Published
2007

32. Clinical and Molecular Analysis of Pathologic Fracture-associated Osteosarcoma: MicroRNA profile Is Different and Correlates with Prognosis

Author

Lozano Calderón, Santiago A., Garbutt, Cassandra, Kim, Jason, Lietz, Christopher E., Chen, Yen-Lin, Bernstein, Karen, Chebib, Ivan, Nielsen, G. Petur, Deshpande, Vikram, Rubio, Renee, Wang, Yaoyu E., Quackenbush, John, Delaney, Thomas, Raskin, Kevin, Schwab, Joseph, Cote, Gregory, and Spentzos, Dimitrios

Published
2019
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33. Supervised Risk Predictor of Breast Cancer Based on Intrinsic Subtypes.

Author

Parker, Joel S., Mullins, Michael, Cheang, Maggie C.U., Leung, Samuel, Voduc, David, Vickery, Tammi, Davies, Sherri, Fauron, Christiane, He, Xiaping, Hu, Zhiyuan, Quackenbush, John F., Stijleman, Inge J., Palazzo, Juan, Marron, J.S., Nobel, Andrew B., Mardis, Elaine, Nielsen, Torsten O., Ellis, Matthew J., Perou, Charles M., and Bernard, Philip S.

Published
2023
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36. NOTCH2 and FLT3 gene mis-splicings are common events in patients with acute myeloid leukemia (AML): new potential targets in AML

Author

Adamia, Sophia, Bar-Natan, Michal, Haibe-Kains, Benjamin, Pilarski, Patrick M., Bach, Christian, Pevzner, Samuel, Calimeri, Teresa, Avet-Loiseau, Herve, Lode, Laurence, Verselis, Sigitas, Fox, Edward A., Galinsky, Ilene, Mathews, Steven, Dagogo-Jack, Ibiayi, Wadleigh, Martha, Steensma, David P., Motyckova, Gabriela, Deangelo, Daniel J., Quackenbush, John, Tenen, Daniel G., Stone, Richard M., and Griffin, James D.

Published
2014
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38. CXCR4 pathway associated with family history of melanoma

Author

Li, Wen-Qing, Han, Jiali, Widlund, Hans R., Correll, Mick, Wang, Yaoyu E., Quackenbush, John, Mihm, Martin C., Canales, Alvaro Laga, Wu, Shaowei, Golub, Todd, Hoshida, Yujin, Hunter, David J., Murphy, George, Kupper, Thomas S., and Qureshi, Abrar A.

Published
2014

40. Mitochondrial iron chelation ameliorates cigarette smoke-induced bronchitis and emphysema in mice

Author

Cloonan, Suzanne M., Glass, Kimberly, Laucho-Contreras, Maria E., Bhashyam, Abhiram R., Cervo, Morgan, Pabon, Maria A., Konrad, Csaba, Polverino, Francesca, Siempos, Ilias I., Perez, Elizabeth, Mizumura, Kenji, Ghosh, Manik C., Parameswaran, Harikrishnan, Williams, Niamh C., Rooney, Kristen T., Chen, Zhi-Hua, Goldklang, Monica P., Yuan, Guo-Cheng, Moore, Stephen C., Demeo, Dawn L., Rouault, Tracey A., D'Armiento, Jeanine M., Schon, Eric A., Manfredi, Giovanni, Quackenbush, John, Mahmood, Ashfaq, Silverman, Edwin K., Owen, Caroline A., and Choi, &.Augustine M.K.

Subjects
Emphysema, Pulmonary -- Genetic aspects -- Care and treatment, Bronchitis -- Analysis -- Genetic aspects -- Care and treatment, Cigarette smoke -- Health aspects, Chelation therapy -- Methods -- Patient outcomes, Molecular targeted therapy -- Methods -- Patient outcomes, Biological sciences, Health
Abstract

Chronic obstructive pulmonary disease (COPD) is linked to both cigarette smoking and genetic determinants. We have previously identified iron-responsive element-binding protein 2 (IRP2) as an important COPD susceptibility gene and have shown that IRP2 protein is increased in the lungs of individuals with COPD. Here we demonstrate that mice deficient in Irp2 were protected from cigarette smoke (CS)-induced experimental COPD. By integrating RNA immunoprecipitation followed by sequencing (RIP-seq), RNA sequencing (RNA-seq), and gene expression and functional enrichment clustering analysis, we identified Irp2 as a regulator of mitochondrial function in the lungs of mice. Irp2 increased mitochondrial iron loading and levels of cytochrome c oxidase (COX), which led to mitochondrial dysfunction and subsequent experimental COPD. Frataxin-deficient mice, which had higher mitochondrial iron loading, showed impaired airway mucociliary clearance (MCC) and higher pulmonary inflammation at baseline, whereas mice deficient in the synthesis of cytochrome c oxidase, which have reduced COX, were protected from CS-induced pulmonary inflammation and impairment of MCC. Mice treated with a mitochondrial iron chelator or mice fed a low-iron diet were protected from CS-induced COPD. Mitochondrial iron chelation also alleviated CS-induced impairment of MCC, CS-induced pulmonary inflammation and CS-associated lung injury in mice with established COPD, suggesting a critical functional role and potential therapeuticition for the mitochondrial-iron axis in COPD., COPD presents as a complex, debilitating lung disease that encompasses a variety of clinical and pathologic phenotypes ranging from airway inflammation (chronic bronchitis) to destruction of lung tissue (emphysema) and [...]

Published
2016
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41. Safikhani et al. reply

Author

Safikhani, Zhaleh, El-Hachem, Nehme, Smirnov, Petr, Freeman, Mark, Goldenberg, Anna, Birkbak, Nicolai J., Beck, Andrew H., Aerts, Hugo J. W. L., Quackenbush, John, and Haibe-Kains, Benjamin

Published
2016
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45. Functional interactors of three genome-wide association study genes are differentially expressed in severe chronic obstructive pulmonary disease lung tissue

Author

Morrow, Jarrett D., Zhou, Xiaobo, Lao, Taotao, Jiang, Zhiqiang, DeMeo, Dawn L., Cho, Michael H., Qiu, Weiliang, Cloonan, Suzanne, Pinto-Plata, Victor, Celli, Bartholome, Marchetti, Nathaniel, Criner, Gerard J., Bueno, Raphael, Washko, George R., Glass, Kimberly, Quackenbush, John, Choi, Augustine M. K., Silverman, Edwin K., and Hersh, Craig P.

Published
2017
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48. Inconsistency in large pharmacogenomic studies

Author

Haibe-Kains, Benjamin, El-Hachem, Nehme, Birkbak, Nicolai Juul, Jin, Andrew C., Beck, Andrew H., Aerts, Hugo J. W. L., and Quackenbush, John

Subjects
Gene expression -- Research, Pharmacology, Experimental -- Research, Pharmacogenetics -- Research, Dose-response relationship (Biochemistry) -- Research, Environmental issues, Science and technology, Zoology and wildlife conservation
Abstract

This Analysis compares two large-scale pharmacogenomic data sets that catalogued the sensitivity of a large number of cancer cell lines to approved and potential drugs, and finds that whereas the gene expression data are largely concordant between the two studies, the reported drug sensitivity measures and subsequently their association with genomic features are highly discordant. Time to set a standard for drug responses Two large-scale data sets recently catalogued the sensitivity of a large number of cancer cell lines to pharmacological drugs, and integrated the drug-response data with genomic features, such as mutations and gene expression profiles. This Analysis by John Quackenbush and colleagues compares the two studies and finds that although the gene expression data are largely concordant between them, the reported drug-sensitivity measures and subsequently their association with genomic features are highly discordant. The authors call for standardization of drug-response measurements, to aid the discovery of robust biomarkers and mechanisms of drug response and hence progress in personalized cancer medicine. Two large-scale pharmacogenomic studies were published recently in this journal. Genomic data are well correlated between studies; however, the measured drug response data are highly discordant. Although the source of inconsistencies remains uncertain, it has potential implications for using these outcome measures to assess gene-drug associations or select potential anticancer drugs on the basis of their reported results., Author(s): Benjamin Haibe-Kains [sup.1] [sup.2] , Nehme El-Hachem [sup.1] , Nicolai Juul Birkbak [sup.3] , Andrew C. Jin [sup.4] , Andrew H. Beck [sup.4] , Hugo J. W. L. Aerts [...]

Published
2013
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49. Histone deacetylase 6-mediated selective autophagy regulates COPD-associated cilia dysfunction

Author

Lam, Hilaire C., Cloonan, Suzanne M., Bhashyam, Abhiram R., Haspel, Jeffery A., Singh, Anju, Sathirapongsasuti, J. Fah, Cervo, Morgan, Yao, Hongwei, Chung, Anna L., Mizumura, Kenji, An, Chang Hyeok, Shan, Bin, Franks, Jonathan M., Haley, Kathleen J., Owen, Caroline A., Tesfaigzi, Yohannes, Washko, George R., Quackenbush, John, Silverman, Edwin K., Rahman, Irfan, Kim, Hong Pyo, Mahmood, Ashfaq, Biswal, Shyam S., Ryter, Stefan W., and Choi, Augustine M.K.

Subjects
Lung diseases, Obstructive -- Research, Smoking -- Health aspects, Epithelial cells -- Physiological aspects, Health care industry
Abstract

Chronic obstructive pulmonary disease (COPD) involves aberrant airway inflammatory responses to cigarette smoke (CS) that are associated with epithelial cell dysfunction, cilia shortening, and mucociliary clearance disruption. Exposure to CS reduced cilia length and induced autophagy in vivo and in differentiated mouse tracheal epithelial cells (MTECs). Autophagy-impaired ([Becn1.sup.+/-] or [Map1lc3B.sup.-/-]) mice and MTECs resisted CS-induced cilia shortening. Furthermore, CS increased the autophagic turnover of ciliary proteins, indicating that autophagy may regulate cilia homeostasis. We identified cytosolic deacetylase HDAC6 as a critical regulator of autophagy-mediated cilia shortening during CS exposure. Mice bearing an X chromosome deletion of Hdac6 ([Hdac6.sup.-/Y]) and MTECs from these mice had reduced autophagy and were protected from CS-induced cilia shortening. Autophagy-impaired [Becn1.sup.+/-], [Map1lc3B.sup.-/-], and [Hdac6.sup.-/Y] mice or mice injected with an HDAC6 inhibitor were protected from CS-induced mucociliary clearance (MCC) disruption. MCC was preserved in mice given the chemical chaperone 4-phenylbutyric acid, but was disrupted in mice lacking the transcription factor NRF2, suggesting that oxidative stress and altered proteostasis contribute to the disruption of MCC. Analysis of human COPD specimens revealed epigenetic deregulation of HDAC6 by hypomethylation and increased protein expression in the airways. We conclude that an autophagy-dependent pathway regulates cilia length during CS exposure and has potential as a therapeutic target for COPD., doi:10.1172/JCI69636. Introduction Chronic obstructive pulmonary disease (COPD) contributes substantially to the global burden of disease as the fourth leading cause of morbidity and mortality worldwide (1). The pathogenesis of COPD [...]

Published
2013

50. Genetic control of gene expression at novel and established chronic obstructive pulmonary disease loci

Author

Castaldi, Peter J., Cho, Michael H., Zhou, Xiaobo, Qiu, Weiliang, Mcgeachie, Michael, Celli, Bartolome, Bakke, Per, Gulsvik, Amund, Lomas, David A., Crapo, James D., Beaty, Terri H., Rennard, Stephen, Harshfield, Benjamin, Lange, Christoph, Singh, Dave, Tal-Singer, Ruth, Riley, John H., Quackenbush, John, Raby, Benjamin A., Carey, Vincent J., Silverman, Edwin K., and Hersh, Craig P.

Published
2015
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