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Hyb: a bioinformatics pipeline for the analysis of CLASH (crosslinking, ligation and sequencing of hybrids) data

pipeline programs

Travis AJ, Tollervey D, Kudla G.
GSID: PlXOsjXzh38J
AJ Travis, J Moody, A Helwak, D Tollervey, G Kudla - Methods, 2014 - Elsevier

… Whilst primarily designed for the analysis of AGO CLASH data, our programs can also be used to identify chimeric reads in other applications of CLASH, as well as for the analysis of CRAC, CLIP, and RNA-Seq data. The...

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Travis, A. J., Moody, J., Helwak, A., Tollervey, D., & Kudla, G. (2014). Hyb: a bioinformatics pipeline for the analysis of CLASH (crosslinking, ligation and sequencing of hybrids) data. Methods, 65(3), 263-273.
Travis, Anthony J., et al. "Hyb: a bioinformatics pipeline for the analysis of CLASH (crosslinking, ligation and sequencing of hybrids) data." Methods 65.3 (2014): 263-273.
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Development and characterization of microsatellite primers in Geranium carolinianum (Geraniaceae) with 454 sequencing.

Applications in plant sciences

Shirk RY, Glenn TC, Chang SM, Hamrick JL.
PMID: 25202576
Appl Plant Sci. 2013 Jul 22;1(8). doi: 10.3732/apps.1300006. eCollection 2013 Aug.

PREMISE OF THE STUDY: Microsatellite primers were developed for Geranium carolinanum, a North American winter annual herb, for use in population genetic analyses. •METHODS AND RESULTS: Genomic DNA enriched for repeat-containing fragments was sequenced on the Roche 454 Titanium...

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Shirk RY, Glenn TC, Chang SM, et al. Development and characterization of microsatellite primers in Geranium carolinianum (Geraniaceae) with 454 sequencing. Appl Plant Sci. 2013;1(8)doi: 10.3732/apps.1300006.
Shirk, R. Y., Glenn, T. C., Chang, S. M., & Hamrick, J. L. (2013). Development and characterization of microsatellite primers in Geranium carolinianum (Geraniaceae) with 454 sequencing. Applications in plant sciences, 1(8), . https://doi.org/10.3732/apps.1300006
Shirk, Rebecca Y, et al. "Development and characterization of microsatellite primers in Geranium carolinianum (Geraniaceae) with 454 sequencing." Applications in plant sciences vol. 1,8 (2013). doi: https://doi.org/10.3732/apps.1300006
Shirk RY, Glenn TC, Chang SM, Hamrick JL. Development and characterization of microsatellite primers in Geranium carolinianum (Geraniaceae) with 454 sequencing. Appl Plant Sci. 2013 Jul 22;1(8). doi: 10.3732/apps.1300006. eCollection 2013 Aug. PMID: 25202576; PMCID: PMC4103449.
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Habitat predictors of genetic diversity for two sympatric wetland-breeding amphibian species.

Ecology and evolution

McKee AM, Maerz JC, Smith LL, Glenn TC.
PMID: 28861231
Ecol Evol. 2017 Jul 03;7(16):6271-6283. doi: 10.1002/ece3.3203. eCollection 2017 Aug.

Population genetic diversity is widely accepted as important to the conservation and management of wildlife. However, habitat features may differentially affect evolutionary processes that facilitate population genetic diversity among sympatric species. We measured genetic diversity for two pond-breeding amphibian...

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McKee AM, Maerz JC, Smith LL, et al. Habitat predictors of genetic diversity for two sympatric wetland-breeding amphibian species. Ecol Evol. 2017;7(16):6271-6283doi: 10.1002/ece3.3203.
McKee, A. M., Maerz, J. C., Smith, L. L., & Glenn, T. C. (2017). Habitat predictors of genetic diversity for two sympatric wetland-breeding amphibian species. Ecology and evolution, 7(16), 6271-6283. https://doi.org/10.1002/ece3.3203
McKee, Anna M, et al. "Habitat predictors of genetic diversity for two sympatric wetland-breeding amphibian species." Ecology and evolution vol. 7,16 (2017): 6271-6283. doi: https://doi.org/10.1002/ece3.3203
McKee AM, Maerz JC, Smith LL, Glenn TC. Habitat predictors of genetic diversity for two sympatric wetland-breeding amphibian species. Ecol Evol. 2017 Jul 03;7(16):6271-6283. doi: 10.1002/ece3.3203. eCollection 2017 Aug. PMID: 28861231; PMCID: PMC5574763.
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A Common Purpose: Reducing Bias in the Curriculum.

Academic medicine : journal of the Association of American Medical Colleges

Gowda D, Benoit LJ, Travis CI.
PMID: 28221223
Acad Med. 2017 Mar;92(3):274-275. doi: 10.1097/ACM.0000000000001548.

No abstract available.

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Gowda D, Benoit LJ, Travis CI. A Common Purpose: Reducing Bias in the Curriculum. Acad Med. 2017;92(3):274-275doi: 10.1097/ACM.0000000000001548.
Gowda, D., Benoit, L. J., & Travis, C. I. (2017). A Common Purpose: Reducing Bias in the Curriculum. Academic medicine : journal of the Association of American Medical Colleges, 92(3), 274-275. https://doi.org/10.1097/ACM.0000000000001548
Gowda, Deepthiman, et al. "A Common Purpose: Reducing Bias in the Curriculum." Academic medicine : journal of the Association of American Medical Colleges vol. 92,3 (2017): 274-275. doi: https://doi.org/10.1097/ACM.0000000000001548
Gowda D, Benoit LJ, Travis CI. A Common Purpose: Reducing Bias in the Curriculum. Acad Med. 2017 Mar;92(3):274-275. doi: 10.1097/ACM.0000000000001548. PMID: 28221223.
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A technique for pediatric chest wall reconstruction using custom-designed titanium implants: description of technique and report of two cases.

Journal of children's orthopaedics

Anderson CJ, Spruiell MD, Wylie EF, McGowan CM, Deleyiannis FW, Donaldson NJ, Heare TC.
PMID: 26782367
J Child Orthop. 2016 Feb;10(1):49-55. doi: 10.1007/s11832-015-0709-1. Epub 2016 Jan 18.

PURPOSE: We present a surgical technique for chest wall reconstruction using custom-designed titanium implants developed for two female patients to provide both chest wall symmetry and adequate stability for staged breast reconstruction.METHODS: A retrospective review was performed for two...

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Anderson CJ, Spruiell MD, Wylie EF, et al. A technique for pediatric chest wall reconstruction using custom-designed titanium implants: description of technique and report of two cases. J Child Orthop. 2016;10(1):49-55doi: 10.1007/s11832-015-0709-1.
Anderson, C. J., Spruiell, M. D., Wylie, E. F., McGowan, C. M., Deleyiannis, F. W., Donaldson, N. J., & Heare, T. C. (2016). A technique for pediatric chest wall reconstruction using custom-designed titanium implants: description of technique and report of two cases. Journal of children's orthopaedics, 10(1), 49-55. https://doi.org/10.1007/s11832-015-0709-1
Anderson, Colin J, et al. "A technique for pediatric chest wall reconstruction using custom-designed titanium implants: description of technique and report of two cases." Journal of children's orthopaedics vol. 10,1 (2016): 49-55. doi: https://doi.org/10.1007/s11832-015-0709-1
Anderson CJ, Spruiell MD, Wylie EF, McGowan CM, Deleyiannis FW, Donaldson NJ, Heare TC. A technique for pediatric chest wall reconstruction using custom-designed titanium implants: description of technique and report of two cases. J Child Orthop. 2016 Feb;10(1):49-55. doi: 10.1007/s11832-015-0709-1. Epub 2016 Jan 18. PMID: 26782367; PMCID: PMC4763153.
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Height drift correction in non-raster atomic force microscopy.

Ultramicroscopy

Meyer TR, Ziegler D, Brune C, Chen A, Farnham R, Huynh N, Chang JM, Bertozzi AL, Ashby PD.
PMID: 24295799
Ultramicroscopy. 2014 Feb;137:48-54. doi: 10.1016/j.ultramic.2013.10.014. Epub 2013 Nov 04.

We propose a novel method to detect and correct drift in non-raster scanning probe microscopy. In conventional raster scanning drift is usually corrected by subtracting a fitted polynomial from each scan line, but sample tilt or large topographic features...

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Meyer TR, Ziegler D, Brune C, et al. Height drift correction in non-raster atomic force microscopy. Ultramicroscopy. 2013;137:48-54doi: 10.1016/j.ultramic.2013.10.014.
Meyer, T. R., Ziegler, D., Brune, C., Chen, A., Farnham, R., Huynh, N., Chang, J. M., Bertozzi, A. L., & Ashby, P. D. (2014). Height drift correction in non-raster atomic force microscopy. Ultramicroscopy, 13748-54. https://doi.org/10.1016/j.ultramic.2013.10.014
Meyer, Travis R, et al. "Height drift correction in non-raster atomic force microscopy." Ultramicroscopy vol. 137 (2014): 48-54. doi: https://doi.org/10.1016/j.ultramic.2013.10.014
Meyer TR, Ziegler D, Brune C, Chen A, Farnham R, Huynh N, Chang JM, Bertozzi AL, Ashby PD. Height drift correction in non-raster atomic force microscopy. Ultramicroscopy. 2014 Feb;137:48-54. doi: 10.1016/j.ultramic.2013.10.014. Epub 2013 Nov 04. PMID: 24295799.
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Preference of a native beetle for "exoticism," characteristics that contribute to invasive success of Costelytra zealandica (Scarabaeidae: Melolonthinae).

PeerJ

Lefort MC, Boyer S, Vereijssen J, Sprague R, Glare TR, Worner SP.
PMID: 26644985
PeerJ. 2015 Nov 30;3:e1454. doi: 10.7717/peerj.1454. eCollection 2015.

Widespread replacement of native ecosystems by productive land sometimes results in the outbreak of a native species. In New Zealand, the introduction of exotic pastoral plants has resulted in diet alteration of the native coleopteran species, Costelytra zealandica (White)...

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Lefort MC, Boyer S, Vereijssen J, et al. Preference of a native beetle for "exoticism," characteristics that contribute to invasive success of Costelytra zealandica (Scarabaeidae: Melolonthinae). PeerJ. 2015;3:e1454doi: 10.7717/peerj.1454.
Lefort, M. C., Boyer, S., Vereijssen, J., Sprague, R., Glare, T. R., & Worner, S. P. (2015). Preference of a native beetle for "exoticism," characteristics that contribute to invasive success of Costelytra zealandica (Scarabaeidae: Melolonthinae). PeerJ, 3e1454. https://doi.org/10.7717/peerj.1454
Lefort, Marie-Caroline, et al. "Preference of a native beetle for "exoticism," characteristics that contribute to invasive success of Costelytra zealandica (Scarabaeidae: Melolonthinae)." PeerJ vol. 3 (2015): e1454. doi: https://doi.org/10.7717/peerj.1454
Lefort MC, Boyer S, Vereijssen J, Sprague R, Glare TR, Worner SP. Preference of a native beetle for "exoticism," characteristics that contribute to invasive success of Costelytra zealandica (Scarabaeidae: Melolonthinae). PeerJ. 2015 Nov 30;3:e1454. doi: 10.7717/peerj.1454. eCollection 2015. PMID: 26644985; PMCID: PMC4671192.
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Correction: The Influence of Hormonal Factors on the Risk of Developing Cervical Cancer and Pre-Cancer: Results from the EPIC Cohort.

PloS one

Roura E, Travier N, Waterboer T, de Sanjosé S, Bosch FX, Pawlita M, Pala V, Weiderpass E, Margall N, Dillner J, Gram IT, Tjønneland A, Munk C, Palli D, Khaw KT, Overvad K, Clavel-Chapelon F, Mesrine S, Fournier A, Fortner RT, Ose J, Steffen A, Trichopoulou A, Lagiou P, Orfanos P, Masala G, Tumino R, Sacerdote C, Polidoro S, Mattiello A, Lund E, Peeters PH, Bueno-de-Mesquita HB, Ramón Quirós J, Sánchez MJ, Navarro C, Barricarte A, Larrañaga N, Ekström J, Lindquist D, Idahl A, Travis RC, Merritt MA, Gunter MJ, Rinaldi S, Tommasino M, Franceschi S, Riboli E, Castellsagué X.
PMID: 26954296
PLoS One. 2016 Mar 08;11(3):e0151427. doi: 10.1371/journal.pone.0151427. eCollection 2016.

No abstract available.

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Roura E, Travier N, Waterboer T, et al. Correction: The Influence of Hormonal Factors on the Risk of Developing Cervical Cancer and Pre-Cancer: Results from the EPIC Cohort. PLoS One. 2016;11(3):e0151427doi: 10.1371/journal.pone.0151427.
Roura, E., Travier, N., Waterboer, T., de Sanjosé, S., Bosch, F. X., Pawlita, M., Pala, V., Weiderpass, E., Margall, N., Dillner, J., Gram, I. T., Tjønneland, A., Munk, C., Palli, D., Khaw, K. T., Overvad, K., Clavel-Chapelon, F., Mesrine, S., Fournier, A., Fortner, R. T., Ose, J., Steffen, A., Trichopoulou, A., Lagiou, P., Orfanos, P., Masala, G., Tumino, R., Sacerdote, C., Polidoro, S., Mattiello, A., Lund, E., Peeters, P. H., Bueno-de-Mesquita, H. B., Ramón Quirós, J., Sánchez, M. J., Navarro, C., Barricarte, A., Larrañaga, N., Ekström, J., Lindquist, D., Idahl, A., Travis, R. C., Merritt, M. A., Gunter, M. J., Rinaldi, S., Tommasino, M., Franceschi, S., Riboli, E., & Castellsagué, X. (2016). Correction: The Influence of Hormonal Factors on the Risk of Developing Cervical Cancer and Pre-Cancer: Results from the EPIC Cohort. PloS one, 11(3), e0151427. https://doi.org/10.1371/journal.pone.0151427
Roura, Esther, et al. "Correction: The Influence of Hormonal Factors on the Risk of Developing Cervical Cancer and Pre-Cancer: Results from the EPIC Cohort." PloS one vol. 11,3 (2016): e0151427. doi: https://doi.org/10.1371/journal.pone.0151427
Roura E, Travier N, Waterboer T, de Sanjosé S, Bosch FX, Pawlita M, Pala V, Weiderpass E, Margall N, Dillner J, Gram IT, Tjønneland A, Munk C, Palli D, Khaw KT, Overvad K, Clavel-Chapelon F, Mesrine S, Fournier A, Fortner RT, Ose J, Steffen A, Trichopoulou A, Lagiou P, Orfanos P, Masala G, Tumino R, Sacerdote C, Polidoro S, Mattiello A, Lund E, Peeters PH, Bueno-de-Mesquita HB, Ramón Quirós J, Sánchez MJ, Navarro C, Barricarte A, Larrañaga N, Ekström J, Lindquist D, Idahl A, Travis RC, Merritt MA, Gunter MJ, Rinaldi S, Tommasino M, Franceschi S, Riboli E, Castellsagué X. Correction: The Influence of Hormonal Factors on the Risk of Developing Cervical Cancer and Pre-Cancer: Results from the EPIC Cohort. PLoS One. 2016 Mar 08;11(3):e0151427. doi: 10.1371/journal.pone.0151427. eCollection 2016. PMID: 26954296; PMCID: PMC4783099.
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Three-dimensional reconstruction of microstructures in gibbsite using charge contrast images.

Scanning

Baroni TC, Griffin BJ, Cornell JB, Roach GI, Lincoln FJ.
PMID: 11871361
Scanning. 2002 Jan-Feb;24(1):18-24. doi: 10.1002/sca.4950240103.

An iterative process of serial sectioning and charge contrast imaging has been applied to gibbsite particles embedded in epoxy resin. The features observed in the two-dimensional sections have been reconstructed into three-dimensional (3-D) objects, so that the volumetric relationships...

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Baroni TC, Griffin BJ, Cornell JB, et al. Three-dimensional reconstruction of microstructures in gibbsite using charge contrast images. Scanning. 2002;24(1):18-24doi: 10.1002/sca.4950240103.
Baroni, T. C., Griffin, B. J., Cornell, J. B., Roach, G. I., & Lincoln, F. J. (2002). Three-dimensional reconstruction of microstructures in gibbsite using charge contrast images. Scanning, 24(1), 18-24. https://doi.org/10.1002/sca.4950240103
Baroni, Travis C, et al. "Three-dimensional reconstruction of microstructures in gibbsite using charge contrast images." Scanning vol. 24,1 (2002): 18-24. doi: https://doi.org/10.1002/sca.4950240103
Baroni TC, Griffin BJ, Cornell JB, Roach GI, Lincoln FJ. Three-dimensional reconstruction of microstructures in gibbsite using charge contrast images. Scanning. 2002 Jan-Feb;24(1):18-24. doi: 10.1002/sca.4950240103. PMID: 11871361.
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Facile oxidation of aldehydes to acids and esters with Oxone.

Organic letters

Travis BR, Sivakumar M, Hollist GO, Borhan B.
PMID: 12659566
Org Lett. 2003 Apr 03;5(7):1031-4. doi: 10.1021/ol0340078.

[reaction: see text] A highly efficient, mild, and simple protocol is presented for the oxidation of aldehydes to carboxylic acids utilizing Oxone as the sole oxidant. Direct conversion of aldehydes in alcoholic solvents to their corresponding ester products is...

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Travis BR, Sivakumar M, Hollist GO, et al. Facile oxidation of aldehydes to acids and esters with Oxone. Org Lett. 2003;5(7):1031-4doi: 10.1021/ol0340078.
Travis, B. R., Sivakumar, M., Hollist, G. O., & Borhan, B. (2003). Facile oxidation of aldehydes to acids and esters with Oxone. Organic letters, 5(7), 1031-4. https://doi.org/10.1021/ol0340078
Travis, Benjamin R, et al. "Facile oxidation of aldehydes to acids and esters with Oxone." Organic letters vol. 5,7 (2003): 1031-4. doi: https://doi.org/10.1021/ol0340078
Travis BR, Sivakumar M, Hollist GO, Borhan B. Facile oxidation of aldehydes to acids and esters with Oxone. Org Lett. 2003 Apr 03;5(7):1031-4. doi: 10.1021/ol0340078. PMID: 12659566.
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An international evaluation of holmium oxide solution reference materials for wavelength calibration in molecular absorption spectrophotometry.

Analytical chemistry

Travis JC, Zwinkels JC, Mercader F, Ruíz A, Early EA, Smith MV, Noël M, Maley M, Kramer GW, Eckerle KL, Duewer DL.
PMID: 12139047
Anal Chem. 2002 Jul 15;74(14):3408-15. doi: 10.1021/ac0255680.

Commercial spectrophotometers typically use absorption-based wavelength calibration reference materials to provide wavelength accuracy for their applications. Low-mass fractions of holmium oxide (Ho2O3) in dilute acidic aqueous solution and in glass matrixes have been favored for use as wavelength calibration...

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Travis JC, Zwinkels JC, Mercader F, et al. An international evaluation of holmium oxide solution reference materials for wavelength calibration in molecular absorption spectrophotometry. Anal Chem. 2002;74(14):3408-15doi: 10.1021/ac0255680.
Travis, J. C., Zwinkels, J. C., Mercader, F., Ruíz, A., Early, E. A., Smith, M. V., Noël, M., Maley, M., Kramer, G. W., Eckerle, K. L., & Duewer, D. L. (2002). An international evaluation of holmium oxide solution reference materials for wavelength calibration in molecular absorption spectrophotometry. Analytical chemistry, 74(14), 3408-15. https://doi.org/10.1021/ac0255680
Travis, John C, et al. "An international evaluation of holmium oxide solution reference materials for wavelength calibration in molecular absorption spectrophotometry." Analytical chemistry vol. 74,14 (2002): 3408-15. doi: https://doi.org/10.1021/ac0255680
Travis JC, Zwinkels JC, Mercader F, Ruíz A, Early EA, Smith MV, Noël M, Maley M, Kramer GW, Eckerle KL, Duewer DL. An international evaluation of holmium oxide solution reference materials for wavelength calibration in molecular absorption spectrophotometry. Anal Chem. 2002 Jul 15;74(14):3408-15. doi: 10.1021/ac0255680. PMID: 12139047.
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Surface Electrodes for Recording Bioelectric Potentials.

Science (New York, N.Y.)

Kennedy JL, Travis RC.
PMID: 17821145
Science. 1948 Aug 20;108(2799):183. doi: 10.1126/science.108.2799.183-a.

No abstract available.

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Kennedy JL, Travis RC. Surface Electrodes for Recording Bioelectric Potentials. Science. 1948;108(2799):183doi: 10.1126/science.108.2799.183-a.
Kennedy, J. L., & Travis, R. C. (1948). Surface Electrodes for Recording Bioelectric Potentials. Science (New York, N.Y.), 108(2799), 183. https://doi.org/10.1126/science.108.2799.183-a
Kennedy, J L, and Travis, R C. "Surface Electrodes for Recording Bioelectric Potentials." Science (New York, N.Y.) vol. 108,2799 (1948): 183. doi: https://doi.org/10.1126/science.108.2799.183-a
Kennedy JL, Travis RC. Surface Electrodes for Recording Bioelectric Potentials. Science. 1948 Aug 20;108(2799):183. doi: 10.1126/science.108.2799.183-a. PMID: 17821145.
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Showing 1 to 12 of 408 entries