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Transposable elements are major contributors to the origin, diversification, and regulation of vertebrate long noncoding RNAs

STEM and diversification

Kapusta A, Kronenberg Z, Lynch VJ, Zhuo X.
GSID: BRdtna0155cJ
A Kapusta, Z Kronenberg, VJ Lynch, X Zhuo… - PLoS …, 2013 - journals.plos.org

… the potential to form a stable stem-loop structure at the RNA … potential to form a long stem-loop structure by intramolecular … in one of the arms of the predicted stem-loop structure were …

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Kapusta, A., Kronenberg, Z., Lynch, V. J., Zhuo, X., Ramsay, L., Bourque, G., ... & Feschotte, C. (2013). Transposable elements are major contributors to the origin, diversification, and regulation of vertebrate long noncoding RNAs. PLoS genetics, 9(4), e1003470.
Kapusta, Aurélie, et al. "Transposable elements are major contributors to the origin, diversification, and regulation of vertebrate long noncoding RNAs." PLoS genetics 9.4 (2013): e1003470.
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Reliability of reporting on life-style and agricultural factors by a sample of participants in the Agricultural Health Study from Iowa

field stations

Blair A, Lynch CF, Rowland A, Sandler D.
GSID: zpfy4vQkFLgJ
A Blair, R Tarone, D Sandler, CF Lynch, A Rowland… - Epidemiology, 2002 - JSTOR

Repeat interviews from 4,088 Iowa pesticide applicators participating in the Agricultural Health Study provided the opportunity to evaluate the reliability of self-reported information …

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Blair, A., Tarone, R., Sandler, D., Lynch, C. F., Rowland, A., Wintersteen, W., ... & Alavanja, M. C. (2002). Reliability of reporting on life-style and agricultural factors by a sample of participants in the Agricultural Health Study from Iowa. Epidemiology, 94-99.
Blair, Aaron, et al. "Reliability of reporting on life-style and agricultural factors by a sample of participants in the Agricultural Health Study from Iowa." Epidemiology (2002): 94-99.
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A comparison of parental views of their pre-school children's 'healthy'versus 'unhealthy'diets. A qualitative study

Pre-school

Parletta N, Lynch J.
GSID: Ytb2PsUy3cUJ
J Peters, N Parletta, J Lynch, K Campbell - Appetite, 2014 - Elsevier

Despite recommended dietary guidelines, recent population surveys have recorded low fruit and vegetable and high non-core food consumption by Australian children. Young children rely on parents or primary carers to provide their diets; therefore pre-school age is an optimal...

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Peters, J., Parletta, N., Lynch, J., & Campbell, K. (2014). A comparison of parental views of their pre-school children’s ‘healthy’versus ‘unhealthy’diets. A qualitative study. Appetite, 76, 129-136.
Peters, Jacqueline, et al. "A comparison of parental views of their pre-school children’s ‘healthy’versus ‘unhealthy’diets. A qualitative study." Appetite 76 (2014): 129-136.
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Inventing an arsenal: adaptive evolution and neofunctionalization of snake venom phospholipase A2 genes

STEM and diversify

Lynch VJ.
GSID: GARAU2ivG58J
VJ Lynch - BMC evolutionary biology, 2007 - bmcecolevol.biomedcentral.com

… novel functions emerge and continues as gene families diversify and are refined. Surprisingly, … For example, amino acid changes that occurred in the stem-lineage of neurotoxic genes (…

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Lynch, V. J. (2007). Inventing an arsenal: adaptive evolution and neofunctionalization of snake venom phospholipase A2 genes. BMC evolutionary biology, 7(1), 1-14.
Lynch, Vincent J. "Inventing an arsenal: adaptive evolution and neofunctionalization of snake venom phospholipase A2 genes." BMC evolutionary biology 7.1 (2007): 1-14.
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Glucocorticoid receptor expression in 20 solid tumor types using immunohistochemistry assay.

Cancer management and research

Block TS, Murphy TI, Munster PN, Nguyen DP, Lynch FJ.
PMID: 28293120
Cancer Manag Res. 2017 Mar 06;9:65-72. doi: 10.2147/CMAR.S124475. eCollection 2017.

BACKGROUND: Glucocorticoid receptor (GR) activity plays a role in many aspects of human physiology and may play a crucial role in chemotherapy resistance in a wide variety of solid tumors. A novel immunohistochemistry (IHC) based assay has been previously...

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Block TS, Murphy TI, Munster PN, et al. Glucocorticoid receptor expression in 20 solid tumor types using immunohistochemistry assay. Cancer Manag Res. 2017;9:65-72doi: 10.2147/CMAR.S124475.
Block, T. S., Murphy, T. I., Munster, P. N., Nguyen, D. P., & Lynch, F. J. (2017). Glucocorticoid receptor expression in 20 solid tumor types using immunohistochemistry assay. Cancer management and research, 965-72. https://doi.org/10.2147/CMAR.S124475
Block, Thaddeus S, et al. "Glucocorticoid receptor expression in 20 solid tumor types using immunohistochemistry assay." Cancer management and research vol. 9 (2017): 65-72. doi: https://doi.org/10.2147/CMAR.S124475
Block TS, Murphy TI, Munster PN, Nguyen DP, Lynch FJ. Glucocorticoid receptor expression in 20 solid tumor types using immunohistochemistry assay. Cancer Manag Res. 2017 Mar 06;9:65-72. doi: 10.2147/CMAR.S124475. eCollection 2017. PMID: 28293120; PMCID: PMC5345989.
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A radio counterpart to a neutron star merger.

Science (New York, N.Y.)

Hallinan G, Corsi A, Mooley KP, Hotokezaka K, Nakar E, Kasliwal MM, Kaplan DL, Frail DA, Myers ST, Murphy T, De K, Dobie D, Allison JR, Bannister KW, Bhalerao V, Chandra P, Clarke TE, Giacintucci S, Ho AYQ, Horesh A, Kassim NE, Kulkarni SR, Lenc E, Lockman FJ, Lynch C, Nichols D, Nissanke S, Palliyaguru N, Peters WM, Piran T, Rana J, Sadler EM, Singer LP.
PMID: 29038372
Science. 2017 Dec 22;358(6370):1579-1583. doi: 10.1126/science.aap9855. Epub 2017 Oct 16.

Gravitational waves have been detected from a binary neutron star merger event, GW170817. The detection of electromagnetic radiation from the same source has shown that the merger occurred in the outskirts of the galaxy NGC 4993, at a distance...

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Hallinan G, Corsi A, Mooley KP, et al. A radio counterpart to a neutron star merger. Science. 2017;358(6370):1579-1583doi: 10.1126/science.aap9855.
Hallinan, G., Corsi, A., Mooley, K. P., Hotokezaka, K., Nakar, E., Kasliwal, M. M., Kaplan, D. L., Frail, D. A., Myers, S. T., Murphy, T., De, K., Dobie, D., Allison, J. R., Bannister, K. W., Bhalerao, V., Chandra, P., Clarke, T. E., Giacintucci, S., Ho, A. Y. Q., Horesh, A., Kassim, N. E., Kulkarni, S. R., Lenc, E., Lockman, F. J., Lynch, C., Nichols, D., Nissanke, S., Palliyaguru, N., Peters, W. M., Piran, T., Rana, J., Sadler, E. M., & Singer, L. P. (2017). A radio counterpart to a neutron star merger. Science (New York, N.Y.), 358(6370), 1579-1583. https://doi.org/10.1126/science.aap9855
Hallinan, G, et al. "A radio counterpart to a neutron star merger." Science (New York, N.Y.) vol. 358,6370 (2017): 1579-1583. doi: https://doi.org/10.1126/science.aap9855
Hallinan G, Corsi A, Mooley KP, Hotokezaka K, Nakar E, Kasliwal MM, Kaplan DL, Frail DA, Myers ST, Murphy T, De K, Dobie D, Allison JR, Bannister KW, Bhalerao V, Chandra P, Clarke TE, Giacintucci S, Ho AYQ, Horesh A, Kassim NE, Kulkarni SR, Lenc E, Lockman FJ, Lynch C, Nichols D, Nissanke S, Palliyaguru N, Peters WM, Piran T, Rana J, Sadler EM, Singer LP. A radio counterpart to a neutron star merger. Science. 2017 Dec 22;358(6370):1579-1583. doi: 10.1126/science.aap9855. Epub 2017 Oct 16. PMID: 29038372.
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Illuminating gravitational waves: A concordant picture of photons from a neutron star merger.

Science (New York, N.Y.)

Kasliwal MM, Nakar E, Singer LP, Kaplan DL, Cook DO, Van Sistine A, Lau RM, Fremling C, Gottlieb O, Jencson JE, Adams SM, Feindt U, Hotokezaka K, Ghosh S, Perley DA, Yu PC, Piran T, Allison JR, Anupama GC, Balasubramanian A, Bannister KW, Bally J, Barnes J, Barway S, Bellm E, Bhalerao V, Bhattacharya D, Blagorodnova N, Bloom JS, Brady PR, Cannella C, Chatterjee D, Cenko SB, Cobb BE, Copperwheat C, Corsi A, De K, Dobie D, Emery SWK, Evans PA, Fox OD, Frail DA, Frohmaier C, Goobar A, Hallinan G, Harrison F, Helou G, Hinderer T, Ho AYQ, Horesh A, Ip WH, Itoh R, Kasen D, Kim H, Kuin NPM, Kupfer T, Lynch C, Madsen K, Mazzali PA, Miller AA, Mooley K, Murphy T, Ngeow CC, Nichols D, Nissanke S, Nugent P, Ofek EO, Qi H, Quimby RM, Rosswog S, Rusu F, Sadler EM, Schmidt P, Sollerman J, Steele I, Williamson AR, Xu Y, Yan L, Yatsu Y, Zhang C, Zhao W.
PMID: 29038373
Science. 2017 Dec 22;358(6370):1559-1565. doi: 10.1126/science.aap9455. Epub 2017 Oct 16.

Merging neutron stars offer an excellent laboratory for simultaneously studying strong-field gravity and matter in extreme environments. We establish the physical association of an electromagnetic counterpart (EM170817) with gravitational waves (GW170817) detected from merging neutron stars. By synthesizing a...

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Kasliwal MM, Nakar E, Singer LP, et al. Illuminating gravitational waves: A concordant picture of photons from a neutron star merger. Science. 2017;358(6370):1559-1565doi: 10.1126/science.aap9455.
Kasliwal, M. M., Nakar, E., Singer, L. P., Kaplan, D. L., Cook, D. O., Van Sistine, A., Lau, R. M., Fremling, C., Gottlieb, O., Jencson, J. E., Adams, S. M., Feindt, U., Hotokezaka, K., Ghosh, S., Perley, D. A., Yu, P. C., Piran, T., Allison, J. R., Anupama, G. C., Balasubramanian, A., Bannister, K. W., Bally, J., Barnes, J., Barway, S., Bellm, E., Bhalerao, V., Bhattacharya, D., Blagorodnova, N., Bloom, J. S., Brady, P. R., Cannella, C., Chatterjee, D., Cenko, S. B., Cobb, B. E., Copperwheat, C., Corsi, A., De, K., Dobie, D., Emery, S. W. K., Evans, P. A., Fox, O. D., Frail, D. A., Frohmaier, C., Goobar, A., Hallinan, G., Harrison, F., Helou, G., Hinderer, T., Ho, A. Y. Q., Horesh, A., Ip, W. H., Itoh, R., Kasen, D., Kim, H., Kuin, N. P. M., Kupfer, T., Lynch, C., Madsen, K., Mazzali, P. A., Miller, A. A., Mooley, K., Murphy, T., Ngeow, C. C., Nichols, D., Nissanke, S., Nugent, P., Ofek, E. O., Qi, H., Quimby, R. M., Rosswog, S., Rusu, F., Sadler, E. M., Schmidt, P., Sollerman, J., Steele, I., Williamson, A. R., Xu, Y., Yan, L., Yatsu, Y., Zhang, C., & Zhao, W. (2017). Illuminating gravitational waves: A concordant picture of photons from a neutron star merger. Science (New York, N.Y.), 358(6370), 1559-1565. https://doi.org/10.1126/science.aap9455
Kasliwal, M M, et al. "Illuminating gravitational waves: A concordant picture of photons from a neutron star merger." Science (New York, N.Y.) vol. 358,6370 (2017): 1559-1565. doi: https://doi.org/10.1126/science.aap9455
Kasliwal MM, Nakar E, Singer LP, Kaplan DL, Cook DO, Van Sistine A, Lau RM, Fremling C, Gottlieb O, Jencson JE, Adams SM, Feindt U, Hotokezaka K, Ghosh S, Perley DA, Yu PC, Piran T, Allison JR, Anupama GC, Balasubramanian A, Bannister KW, Bally J, Barnes J, Barway S, Bellm E, Bhalerao V, Bhattacharya D, Blagorodnova N, Bloom JS, Brady PR, Cannella C, Chatterjee D, Cenko SB, Cobb BE, Copperwheat C, Corsi A, De K, Dobie D, Emery SWK, Evans PA, Fox OD, Frail DA, Frohmaier C, Goobar A, Hallinan G, Harrison F, Helou G, Hinderer T, Ho AYQ, Horesh A, Ip WH, Itoh R, Kasen D, Kim H, Kuin NPM, Kupfer T, Lynch C, Madsen K, Mazzali PA, Miller AA, Mooley K, Murphy T, Ngeow CC, Nichols D, Nissanke S, Nugent P, Ofek EO, Qi H, Quimby RM, Rosswog S, Rusu F, Sadler EM, Schmidt P, Sollerman J, Steele I, Williamson AR, Xu Y, Yan L, Yatsu Y, Zhang C, Zhao W. Illuminating gravitational waves: A concordant picture of photons from a neutron star merger. Science. 2017 Dec 22;358(6370):1559-1565. doi: 10.1126/science.aap9455. Epub 2017 Oct 16. PMID: 29038373.
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Correction: TP53 copy number expansion is associated with the evolution of increased body size and an enhanced DNA damage response in elephants.

eLife

Sulak M, Fong L, Mika K, Chigurupati S, Yon L, Mongan NP, Emes RD, Lynch VJ.
PMID: 27997337
Elife. 2016 Dec 20;5. doi: 10.7554/eLife.24307.

No abstract available.

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Sulak M, Fong L, Mika K, et al. Correction: TP53 copy number expansion is associated with the evolution of increased body size and an enhanced DNA damage response in elephants. Elife. 2016;5doi: 10.7554/eLife.24307.
Sulak, M., Fong, L., Mika, K., Chigurupati, S., Yon, L., Mongan, N. P., Emes, R. D., & Lynch, V. J. (2016). Correction: TP53 copy number expansion is associated with the evolution of increased body size and an enhanced DNA damage response in elephants. eLife, 5. https://doi.org/10.7554/eLife.24307
Sulak, Michael, et al. "Correction: TP53 copy number expansion is associated with the evolution of increased body size and an enhanced DNA damage response in elephants." eLife vol. 5 (2016). doi: https://doi.org/10.7554/eLife.24307
Sulak M, Fong L, Mika K, Chigurupati S, Yon L, Mongan NP, Emes RD, Lynch VJ. Correction: TP53 copy number expansion is associated with the evolution of increased body size and an enhanced DNA damage response in elephants. Elife. 2016 Dec 20;5. doi: 10.7554/eLife.24307. PMID: 27997337; PMCID: PMC5173317.
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Conversion of nitroalkanes into carboxylic acids via iodide catalysis in water.

Chemical communications (Cambridge, England)

Marcé P, Lynch J, Blacker AJ, Williams JM.
PMID: 26593690
Chem Commun (Camb). 2016 Jan 18;52(5):1013-6. doi: 10.1039/c5cc08681g.

We report a new method for the conversion of nitroalkanes into carboxylic acids that achieves this transformation under very mild conditions. Catalytic amounts of iodide in combination with a simple zinc catalyst are needed to give good conversions into...

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Marcé P, Lynch J, Blacker AJ, et al. Conversion of nitroalkanes into carboxylic acids via iodide catalysis in water. Chem Commun (Camb). 2016;52(5):1013-6doi: 10.1039/c5cc08681g.
Marcé, P., Lynch, J., Blacker, A. J., & Williams, J. M. (2016). Conversion of nitroalkanes into carboxylic acids via iodide catalysis in water. Chemical communications (Cambridge, England), 52(5), 1013-6. https://doi.org/10.1039/c5cc08681g
Marcé, Patricia, et al. "Conversion of nitroalkanes into carboxylic acids via iodide catalysis in water." Chemical communications (Cambridge, England) vol. 52,5 (2016): 1013-6. doi: https://doi.org/10.1039/c5cc08681g
Marcé P, Lynch J, Blacker AJ, Williams JM. Conversion of nitroalkanes into carboxylic acids via iodide catalysis in water. Chem Commun (Camb). 2016 Jan 18;52(5):1013-6. doi: 10.1039/c5cc08681g. PMID: 26593690.
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Quantifying the impact of inter-site heterogeneity on the distribution of ChIP-seq data.

Frontiers in genetics

Cairns J, Lynch AG, Tavaré S.
PMID: 25452765
Front Genet. 2014 Nov 14;5:399. doi: 10.3389/fgene.2014.00399. eCollection 2014.

Chromatin Immunoprecipitation followed by sequencing (ChIP-seq) is a valuable tool for epigenetic studies. Analysis of the data arising from ChIP-seq experiments often requires implicit or explicit statistical modeling of the read counts. The simple Poisson model is attractive, but...

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Cairns J, Lynch AG, Tavaré S. Quantifying the impact of inter-site heterogeneity on the distribution of ChIP-seq data. Front Genet. 2014;5:399doi: 10.3389/fgene.2014.00399.
Cairns, J., Lynch, A. G., & Tavaré, S. (2014). Quantifying the impact of inter-site heterogeneity on the distribution of ChIP-seq data. Frontiers in genetics, 5399. https://doi.org/10.3389/fgene.2014.00399
Cairns, Jonathan, et al. "Quantifying the impact of inter-site heterogeneity on the distribution of ChIP-seq data." Frontiers in genetics vol. 5 (2014): 399. doi: https://doi.org/10.3389/fgene.2014.00399
Cairns J, Lynch AG, Tavaré S. Quantifying the impact of inter-site heterogeneity on the distribution of ChIP-seq data. Front Genet. 2014 Nov 14;5:399. doi: 10.3389/fgene.2014.00399. eCollection 2014. PMID: 25452765; PMCID: PMC4231950.
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Surgical strategy for intracranial dermoid and epidermoid tumors: An experience with 33 Patients.

Surgical neurology international

Lynch JC, Aversa A, Pereira C, Nogueira J, Gonçalves M, Lopes H.
PMID: 25558422
Surg Neurol Int. 2014 Nov 28;5:163. doi: 10.4103/2152-7806.145764. eCollection 2014.

BACKGROUND: The aim of this paper is to report on our surgical strategy and technique and to identify the best management for intracranial dermoids and epidermoids tumors (IDETs).METHODS: We retrospectively reviewed 33 consecutive patients (14 males and 19 females;...

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Lynch JC, Aversa A, Pereira C, et al. Surgical strategy for intracranial dermoid and epidermoid tumors: An experience with 33 Patients. Surg Neurol Int. 2014;5:163doi: 10.4103/2152-7806.145764.
Lynch, J. C., Aversa, A., Pereira, C., Nogueira, J., Gonçalves, M., & Lopes, H. (2014). Surgical strategy for intracranial dermoid and epidermoid tumors: An experience with 33 Patients. Surgical neurology international, 5163. https://doi.org/10.4103/2152-7806.145764
Lynch, Jose Carlos, et al. "Surgical strategy for intracranial dermoid and epidermoid tumors: An experience with 33 Patients." Surgical neurology international vol. 5 (2014): 163. doi: https://doi.org/10.4103/2152-7806.145764
Lynch JC, Aversa A, Pereira C, Nogueira J, Gonçalves M, Lopes H. Surgical strategy for intracranial dermoid and epidermoid tumors: An experience with 33 Patients. Surg Neurol Int. 2014 Nov 28;5:163. doi: 10.4103/2152-7806.145764. eCollection 2014. PMID: 25558422; PMCID: PMC4278097.
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The importance of scientific peer review at SETAC.

Environmental toxicology and chemistry

Wenning RJ, Burton GA, Ward H, Lynch J.
PMID: 24357029
Environ Toxicol Chem. 2014 Jan;33(1):2-3. doi: 10.1002/etc.2449.

No abstract available.

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Wenning RJ, Burton GA, Ward H, et al. The importance of scientific peer review at SETAC. Environ Toxicol Chem. 2014;33(1):2-3doi: 10.1002/etc.2449.
Wenning, R. J., Burton, G. A., Ward, H., & Lynch, J. (2014). The importance of scientific peer review at SETAC. Environmental toxicology and chemistry, 33(1), 2-3. https://doi.org/10.1002/etc.2449
Wenning, Richard J, et al. "The importance of scientific peer review at SETAC." Environmental toxicology and chemistry vol. 33,1 (2014): 2-3. doi: https://doi.org/10.1002/etc.2449
Wenning RJ, Burton GA, Ward H, Lynch J. The importance of scientific peer review at SETAC. Environ Toxicol Chem. 2014 Jan;33(1):2-3. doi: 10.1002/etc.2449. PMID: 24357029.
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Showing 1 to 12 of 677 entries