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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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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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Crystal structure of tetra-aqua-(di-methyl-formamide)-tetra-kis-(μ-N,2-dioxido-benzene-1-carboximidato)tetra-kis-(μ-tri-methyl-acetato)-tetra-manganese(III)sodiumyttrium-di-methyl-formamide-water (1/8.04/0.62).

Acta crystallographica. Section E, Crystallographic communications

Travis JR, Zeller M, Zaleski CM.
PMID: 26594496
Acta Crystallogr E Crystallogr Commun. 2015 Oct 10;71:1300-6. doi: 10.1107/S2056989015018216. eCollection 2015 Nov 01.

The synthesis and crystal structure for the title compound, [YNaMn4(C7H4NO3)4(C5H9O2)4(H2O)3.76(C3H7NO)0.24]·8.04C3H7NO·0.62H2O or [Y(III)Na(OTMA)4[12-MCMn(III)N(shi)-4](H2O)3.76(DMF)0.24·8.04DMF·0.62H2O, where OTMA is tri-methyl-acetate, MC is metallacrown, shi(3-) is salicyl-hydroximate, and DMF is N,N-di-methyl-formamide, is reported. The macrocyclic metallacrown consists of an -[Mn(III)-N-O]4- ring repeat unit, and...

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Travis JR, Zeller M, Zaleski CM. Crystal structure of tetra-aqua-(di-methyl-formamide)-tetra-kis-(μ-N,2-dioxido-benzene-1-carboximidato)tetra-kis-(μ-tri-methyl-acetato)-tetra-manganese(III)sodiumyttrium-di-methyl-formamide-water (1/8.04/0.62). Acta Crystallogr E Crystallogr Commun. 2015;71:1300-6doi: 10.1107/S2056989015018216.
Travis, J. R., Zeller, M., & Zaleski, C. M. (2015). Crystal structure of tetra-aqua-(di-methyl-formamide)-tetra-kis-(μ-N,2-dioxido-benzene-1-carboximidato)tetra-kis-(μ-tri-methyl-acetato)-tetra-manganese(III)sodiumyttrium-di-methyl-formamide-water (1/8.04/0.62). Acta crystallographica. Section E, Crystallographic communications, 711300-6. https://doi.org/10.1107/S2056989015018216
Travis, Jordan R, et al. "Crystal structure of tetra-aqua-(di-methyl-formamide)-tetra-kis-(μ-N,2-dioxido-benzene-1-carboximidato)tetra-kis-(μ-tri-methyl-acetato)-tetra-manganese(III)sodiumyttrium-di-methyl-formamide-water (1/8.04/0.62)." Acta crystallographica. Section E, Crystallographic communications vol. 71 (2015): 1300-6. doi: https://doi.org/10.1107/S2056989015018216
Travis JR, Zeller M, Zaleski CM. Crystal structure of tetra-aqua-(di-methyl-formamide)-tetra-kis-(μ-N,2-dioxido-benzene-1-carboximidato)tetra-kis-(μ-tri-methyl-acetato)-tetra-manganese(III)sodiumyttrium-di-methyl-formamide-water (1/8.04/0.62). Acta Crystallogr E Crystallogr Commun. 2015 Oct 10;71:1300-6. doi: 10.1107/S2056989015018216. eCollection 2015 Nov 01. PMID: 26594496; PMCID: PMC4645067.
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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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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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Adrenaline Release by Chromaffin Cells: Constrained Swelling of the Vesicle Matrix Leads to Full Fusion At the ENS, this work has been supported in part by the CNRS (UMR 8640, Ultimatech and the program "Physique et Chimie du Vivant"), by the ENS, and by the French Ministry of Research and Education (MENESR). At the UNC, this work was supported by the NIH.

Angewandte Chemie (International ed. in English)

Amatore C, Bouret Y, Travis ER, Wightman RM.
PMID: 10940992
Angew Chem Int Ed Engl. 2000 Jun 02;39(11):1952-1955. doi: 10.1002/1521-3773(20000602)39:11<1952::aid-anie1952>3.0.co;2-3.

No abstract available.

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Amatore C, Bouret Y, Travis ER, et al. Adrenaline Release by Chromaffin Cells: Constrained Swelling of the Vesicle Matrix Leads to Full Fusion At the ENS, this work has been supported in part by the CNRS (UMR 8640, Ultimatech and the program "Physique et Chimie du Vivant"), by the ENS, and by the French Ministry of Research and Education (MENESR). At the UNC, this work was supported by the NIH. Angew Chem Int Ed Engl. 2000;39(11):1952-1955doi: 10.1002/1521-3773(20000602)39:11<1952::aid-anie1952>3.0.co;2-3.
Amatore, C., Bouret, Y., Travis, E. R., & Wightman, R. M. (2000). Adrenaline Release by Chromaffin Cells: Constrained Swelling of the Vesicle Matrix Leads to Full Fusion At the ENS, this work has been supported in part by the CNRS (UMR 8640, Ultimatech and the program "Physique et Chimie du Vivant"), by the ENS, and by the French Ministry of Research and Education (MENESR). At the UNC, this work was supported by the NIH. Angewandte Chemie (International ed. in English), 39(11), 1952-1955. https://doi.org/10.1002/1521-3773(20000602)39:11<1952::aid-anie1952>3.0.co;2-3
Amatore, et al. "Adrenaline Release by Chromaffin Cells: Constrained Swelling of the Vesicle Matrix Leads to Full Fusion At the ENS, this work has been supported in part by the CNRS (UMR 8640, Ultimatech and the program "Physique et Chimie du Vivant"), by the ENS, and by the French Ministry of Research and Education (MENESR). At the UNC, this work was supported by the NIH." Angewandte Chemie (International ed. in English) vol. 39,11 (2000): 1952-1955. doi: https://doi.org/10.1002/1521-3773(20000602)39:11<1952::aid-anie1952>3.0.co;2-3
Amatore C, Bouret Y, Travis ER, Wightman RM. Adrenaline Release by Chromaffin Cells: Constrained Swelling of the Vesicle Matrix Leads to Full Fusion At the ENS, this work has been supported in part by the CNRS (UMR 8640, Ultimatech and the program "Physique et Chimie du Vivant"), by the ENS, and by the French Ministry of Research and Education (MENESR). At the UNC, this work was supported by the NIH. Angew Chem Int Ed Engl. 2000 Jun 02;39(11):1952-1955. doi: 10.1002/1521-3773(20000602)39:11<1952::aid-anie1952>3.0.co;2-3. PMID: 10940992.
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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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Image capture via a wedge light-guide with no margins.

Optics express

Travis AR, Large T, Emerton N, Zhu Z, Bathiche S.
PMID: 20588691
Opt Express. 2010 Apr 12;18(8):8453-8. doi: 10.1364/OE.18.008453.

We report the capture of images via a wedge light-guide without the margin for fan-in needed heretofore. While this lets one look out of a slim panel as if it were a periscope, half the power is lost and...

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Travis AR, Large T, Emerton N, et al. Image capture via a wedge light-guide with no margins. Opt Express. 2010;18(8):8453-8doi: 10.1364/OE.18.008453.
Travis, A. R., Large, T., Emerton, N., Zhu, Z., & Bathiche, S. (2010). Image capture via a wedge light-guide with no margins. Optics express, 18(8), 8453-8. https://doi.org/10.1364/OE.18.008453
Travis, Adrian R L, et al. "Image capture via a wedge light-guide with no margins." Optics express vol. 18,8 (2010): 8453-8. doi: https://doi.org/10.1364/OE.18.008453
Travis AR, Large T, Emerton N, Zhu Z, Bathiche S. Image capture via a wedge light-guide with no margins. Opt Express. 2010 Apr 12;18(8):8453-8. doi: 10.1364/OE.18.008453. PMID: 20588691.
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Titanium(IV) halide mediated coupling of alkoxides and alkynes: an efficient and stereoselective route to trisubstituted (E)-alkenyl halides.

Organic letters

Yao ML, Quick TR, Wu Z, Quinn MP, Kabalka GW.
PMID: 19445487
Org Lett. 2009 Jun 18;11(12):2647-9. doi: 10.1021/ol900669t.

Alkoxide C-O bond cleavage occurs readily at room temperature in the presence of titanium(IV) halide. Capture of the resultant carbocation by alkynes provides an efficient route to trisubstituted (E)-alkenyl halides with high stereoselectivity.

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Yao ML, Quick TR, Wu Z, et al. Titanium(IV) halide mediated coupling of alkoxides and alkynes: an efficient and stereoselective route to trisubstituted (E)-alkenyl halides. Org Lett. 2009;11(12):2647-9doi: 10.1021/ol900669t.
Yao, M. L., Quick, T. R., Wu, Z., Quinn, M. P., & Kabalka, G. W. (2009). Titanium(IV) halide mediated coupling of alkoxides and alkynes: an efficient and stereoselective route to trisubstituted (E)-alkenyl halides. Organic letters, 11(12), 2647-9. https://doi.org/10.1021/ol900669t
Yao, Min-Liang, et al. "Titanium(IV) halide mediated coupling of alkoxides and alkynes: an efficient and stereoselective route to trisubstituted (E)-alkenyl halides." Organic letters vol. 11,12 (2009): 2647-9. doi: https://doi.org/10.1021/ol900669t
Yao ML, Quick TR, Wu Z, Quinn MP, Kabalka GW. Titanium(IV) halide mediated coupling of alkoxides and alkynes: an efficient and stereoselective route to trisubstituted (E)-alkenyl halides. Org Lett. 2009 Jun 18;11(12):2647-9. doi: 10.1021/ol900669t. PMID: 19445487.
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Owner controlled data exchange in nutrigenomic collaborations: the NuGO information network.

Genes & nutrition

Harttig U, Travis AJ, Rocca-Serra P, Renkema M, van Ommen B, Boeing H.
PMID: 19408032
Genes Nutr. 2009 Jun;4(2):113-22. doi: 10.1007/s12263-009-0123-8. Epub 2009 Apr 30.

New 'omics' technologies are changing nutritional sciences research. They enable to tackle increasingly complex questions but also increase the need for collaboration between research groups. An important challenge for successful collaboration is the management and structured exchange of information...

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Harttig U, Travis AJ, Rocca-Serra P, et al. Owner controlled data exchange in nutrigenomic collaborations: the NuGO information network. Genes Nutr. 2009;4(2):113-22doi: 10.1007/s12263-009-0123-8.
Harttig, U., Travis, A. J., Rocca-Serra, P., Renkema, M., van Ommen, B., & Boeing, H. (2009). Owner controlled data exchange in nutrigenomic collaborations: the NuGO information network. Genes & nutrition, 4(2), 113-22. https://doi.org/10.1007/s12263-009-0123-8
Harttig, Ulrich, et al. "Owner controlled data exchange in nutrigenomic collaborations: the NuGO information network." Genes & nutrition vol. 4,2 (2009): 113-22. doi: https://doi.org/10.1007/s12263-009-0123-8
Harttig U, Travis AJ, Rocca-Serra P, Renkema M, van Ommen B, Boeing H. Owner controlled data exchange in nutrigenomic collaborations: the NuGO information network. Genes Nutr. 2009 Jun;4(2):113-22. doi: 10.1007/s12263-009-0123-8. Epub 2009 Apr 30. PMID: 19408032; PMCID: PMC2690731.
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