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1. Universal DNA methylation age across mammalian tissues

Author

Lu, A. T., Fei, Z., Haghani, A., Robeck, T. R., Zoller, J. A., Li, C. Z., Lowe, R., Yan, Q., Zhang, J., Vu, H., Ablaeva, J., Acosta-Rodriguez, V. A., Adams, D. M., Almunia, J., Aloysius, A., Ardehali, R., Arneson, A., Baker, C. S., Banks, G., Belov, K., Bennett, N. C., Black, P., Blumstein, D. T., Bors, E. K., Breeze, C. E., Brooke, R. T., Brown, J. L., Carter, G. G., Caulton, A., Cavin, J. M., Chakrabarti, L., Chatzistamou, I., Chen, H., Cheng, K., Chiavellini, P., Choi, O. W., Clarke, S. M., Cooper, L. N., Cossette, M. L., Day, J., DeYoung, J., DiRocco, S., Dold, C., Ehmke, E. E., Emmons, C. K., Emmrich, S., Erbay, E., Erlacher-Reid, C., Faulkes, C. G., Ferguson, S. H., Finno, C. J., Flower, J. E., Gaillard, J. M., Garde, E., Gerber, L., Gladyshev, V. N., Gorbunova, V., Goya, R. G., Grant, M. J., Green, C. B., Hales, E. N., Hanson, M. B., Hart, D. W., Haulena, M., Herrick, K., Hogan, A. N., Hogg, C. J., Hore, T. A., Huang, T., Izpisua Belmonte, J. C., Jasinska, A. J., Jones, G., Jourdain, E., Kashpur, O., Katcher, H., Katsumata, E., Kaza, V., Kiaris, H., Kobor, M. S., Kordowitzki, P., Koski, W. R., Krützen, M., Kwon, S. B., Larison, B., Lee, S. G., Lehmann, M., Lemaitre, J. F., Levine, A. J., Li, C., Li, X., Lim, A. R., Lin, D. T. S., Lindemann, D. M., Little, T. J., Macoretta, N., Maddox, D., Matkin, C. O., Mattison, J. A., McClure, M., Mergl, J., Meudt, J. J., Montano, G. A., Mozhui, K., Munshi-South, J., Naderi, A., Nagy, M., Narayan, P., Nathanielsz, P. W., Nguyen, N. B., Niehrs, C., O’Brien, J. K., O’Tierney Ginn, P., Odom, D. T., Ophir, A. G., Osborn, S., Ostrander, E. A., Parsons, K. M., Paul, K. C., Pellegrini, M., Peters, K. J., Pedersen, A. B., Petersen, J. L., Pietersen, D. W., Pinho, G. M., Plassais, J., Poganik, J. R., Prado, N. A., Reddy, P., Rey, B., Ritz, B. R., Robbins, J., Rodriguez, M., Russell, J., Rydkina, E., Sailer, L. L., Salmon, A. B., Sanghavi, A., Schachtschneider, K. M., Schmitt, D., Schmitt, T., Schomacher, L., Schook, L. B., Sears, K. E., Seifert, A. W., Seluanov, A., Shafer, A. B. A., Shanmuganayagam, D., Shindyapina, A. V., Simmons, M., Singh, K., Sinha, I., Slone, J., Snell, R. G., Soltanmaohammadi, E., Spangler, M. L., Spriggs, M. C., Staggs, L., Stedman, N., Steinman, K. J., Stewart, D. T., Sugrue, V. J., Szladovits, B., Takahashi, J. S., Takasugi, M., Teeling, E. C., Thompson, M. J., Van Bonn, B., Vernes, S. C., Villar, D., Vinters, H. V., Wallingford, M. C., Wang, N., Wayne, R. K., Wilkinson, G. S., Williams, C. K., Williams, R. W., Yang, X. W., Yao, M., Young, B. G., Zhang, B., Zhang, Z., Zhao, P., Zhao, Y., Zhou, W., Zimmermann, J., Ernst, J., Raj, K., and Horvath, S.

Published
2023
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2. Author Correction: Universal DNA methylation age across mammalian tissues

Author

Lu, A. T., Fei, Z., Haghani, A., Robeck, T. R., Zoller, J. A., Li, C. Z., Lowe, R., Yan, Q., Zhang, J., Vu, H., Ablaeva, J., Acosta-Rodriguez, V. A., Adams, D. M., Almunia, J., Aloysius, A., Ardehali, R., Arneson, A., Baker, C. S., Banks, G., Belov, K., Bennett, N. C., Black, P., Blumstein, D. T., Bors, E. K., Breeze, C. E., Brooke, R. T., Brown, J. L., Carter, G. G., Caulton, A., Cavin, J. M., Chakrabarti, L., Chatzistamou, I., Chen, H., Cheng, K., Chiavellini, P., Choi, O. W., Clarke, S. M., Cooper, L. N., Cossette, M. L., Day, J., DeYoung, J., DiRocco, S., Dold, C., Ehmke, E. E., Emmons, C. K., Emmrich, S., Erbay, E., Erlacher-Reid, C., Faulkes, C. G., Ferguson, S. H., Finno, C. J., Flower, J. E., Gaillard, J. M., Garde, E., Gerber, L., Gladyshev, V. N., Gorbunova, V., Goya, R. G., Grant, M. J., Green, C. B., Hales, E. N., Hanson, M. B., Hart, D. W., Haulena, M., Herrick, K., Hogan, A. N., Hogg, C. J., Hore, T. A., Huang, T., Izpisua Belmonte, J. C., Jasinska, A. J., Jones, G., Jourdain, E., Kashpur, O., Katcher, H., Katsumata, E., Kaza, V., Kiaris, H., Kobor, M. S., Kordowitzki, P., Koski, W. R., Krützen, M., Kwon, S. B., Larison, B., Lee, S. G., Lehmann, M., Lemaitre, J. F., Levine, A. J., Li, C., Li, X., Lim, A. R., Lin, D. T. S., Lindemann, D. M., Little, T. J., Macoretta, N., Maddox, D., Matkin, C. O., Mattison, J. A., McClure, M., Mergl, J., Meudt, J. J., Montano, G. A., Mozhui, K., Munshi-South, J., Naderi, A., Nagy, M., Narayan, P., Nathanielsz, P. W., Nguyen, N. B., Niehrs, C., O’Brien, J. K., O’Tierney Ginn, P., Odom, D. T., Ophir, A. G., Osborn, S., Ostrander, E. A., Parsons, K. M., Paul, K. C., Pellegrini, M., Peters, K. J., Pedersen, A. B., Petersen, J. L., Pietersen, D. W., Pinho, G. M., Plassais, J., Poganik, J. R., Prado, N. A., Reddy, P., Rey, B., Ritz, B. R., Robbins, J., Rodriguez, M., Russell, J., Rydkina, E., Sailer, L. L., Salmon, A. B., Sanghavi, A., Schachtschneider, K. M., Schmitt, D., Schmitt, T., Schomacher, L., Schook, L. B., Sears, K. E., Seifert, A. W., Seluanov, A., Shafer, A. B. A., Shanmuganayagam, D., Shindyapina, A. V., Simmons, M., Singh, K., Sinha, I., Slone, J., Snell, R. G., Soltanmaohammadi, E., Spangler, M. L., Spriggs, M. C., Staggs, L., Stedman, N., Steinman, K. J., Stewart, D. T., Sugrue, V. J., Szladovits, B., Takahashi, J. S., Takasugi, M., Teeling, E. C., Thompson, M. J., Van Bonn, B., Vernes, S. C., Villar, D., Vinters, H. V., Wallingford, M. C., Wang, N., Wayne, R. K., Wilkinson, G. S., Williams, C. K., Williams, R. W., Yang, X. W., Yao, M., Young, B. G., Zhang, B., Zhang, Z., Zhao, P., Zhao, Y., Zhou, W., Zimmermann, J., Ernst, J., Raj, K., and Horvath, S.

Published
2023
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3. Proceedings to the Workshops 'What comes beyond the Standard model' 2000,2001, VOLUME 1: Festschrift dedicated to the 60th birthday of Holger Bech Nielsen

Author

Borstnik, N. S. Mankoc, Froggatt, C. D., Lukman, D., Axenides, M., Melikhov, D., Stech, B., Fairlie, D. B., Frampton, P. H., van Holten, J. W., Petersen, J. L., Laperashvili, L. V., Ryzhikh, D. A., Olesen, P., Susskind, L., Blinnikov, S. I., Okun, L. B., Vysotsky, M. I., and Greensite, Jeff

Subjects
High Energy Physics - Phenomenology
Abstract

The present volume is the collection of contributions by friends of Holger Bech Nielsen for his 60th birthday. Contents: 1.Unified internal space of spins and charges (N. Mankoc Borstnik) 2.Semitopological Q-Rings (M. Axenides) 3.Non-local axial anomalies in the Standard model (D. Melikhov, B. Stech) 4.Could there be a fourth generation? (C.D. Froggatt) 5.Another complex Bateman equation (D.B. Fairlie) 6.Non-associative loops for Holger Bech Nielsen (P.H. Frampton) 7.Particles, fluids and vortices (J.W. van Holten) 8.Results on 2D current algebras (J.L. Petersen) 9.Phase transition in gauge theories and the Planck scale physics (L.V. Laperashvili and D.A. Ryzhikh) 10.Some remarks on the 'classical' large N limit (P. Olesen) 11.String theory and the size of hadrons (L. Susskind) 12.Relativity and $c/sqrt3$ (S.I. Blinnikov, L.B. Okun and M.I. Vysotsky) 13.Vortices (Jeff Greensite), Comment: The proceedings includes 13 papers of different authors. Editors were N. S. Mankoc Borstnik, C. D. Froggatt, D. Lukman

Published
2002

4. Free Field Realizations of 2D Current Algebras, Screening Currents and Primary Fields

Author

Petersen, J. L., Rasmussen, J., and Yu, M.

Subjects
High Energy Physics - Theory
Abstract

In this paper we consider Wakimoto free field realizations of simple affine Lie algebras, a subject already much studied. We present three new sets of results. (i) Based on quantizing differential operator realizations of the corresponding Lie algebras we provide general universal very simple expressions for all currents, more compact than has been established so far. (ii) We supplement the treatment of screening currents of the first kind, known in the literature, by providing a direct proof of the properties for screening currents of the second kind. Finally (iii) we work out explicit free field realizations of primary fields with general non-integer weights. We use a formalism where the (generally infinite) multiplet is replaced by a generating function primary operator. These results taken together allow setting up integral representations for correlators of primary fields corresponding to non-integrable degenerate (in particular admissible) representations., Comment: 22 pages, LaTeX

Published
1997

5. Fusion, Crossing and Monodromy in Conformal Field Theory Based on $SL(2)$ Current Algebra with Fractional Level

Author

Petersen, J. L., Rasmussen, J., and Yu, M.

Subjects
High Energy Physics - Theory
Abstract

Based on our earlier work on free field realizations of conformal blocks for conformal field theories with $SL(2)$ current algebra and with fractional level and spins, we discuss in some detail the fusion rules which arise. By a careful analysis of the 4-point functions, we find that both the fusion rules previously found in the literature are realized in our formulation. Since this is somewhat contrary to our expectations in our first work based on 3-point functions, we reanalyse the 3-point functions and come to the same conclusion. We compare our results on 4-point conformal blocks in particular with a different realization of these found by O. Andreev, and we argue for the equivalence. We describe in detail how integration contours have to be chosen to obtain convenient bases for conformal blocks, both in his and in our own formulation. We then carry out the rather lengthy calculation to obtain the crossing matrix between s- and t-channel blocks, and we use that to determine the monodromy invariant 4-point greens functions. We use the monodromy coefficients to obtain the operator algebra coefficients for theories based on admissible representations., Comment: 42 Pages, LaTeX, uses pictex.sty, alternatively prepictex.tex, pictex.tex, postpictex.tex

Published
1996
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6. Free field realization of SL(2) correlators for admissible representations, and hamiltonian reduction for correlators

Author

Petersen, J. L., Rasmussen, J., and Yu, M.

Subjects
High Energy Physics - Theory
Abstract

Talk presented by J.L. Petersen at the 29th Symposium Ahrenshop, Buckow August 29-September 2, 1995. A presentation is given of the free field realization relevant to SL(2) WZW theories with a Hilbert space based on admissible representations. It is known that this implies the presence of two screening charges, one involving a fractional power of a free field. We develop the use of fractional calculus for treating in general such cases. We derive explicit integral representations of $N$-point conformal blocks. We show that they satisfy the Knizhnik-Zamolodchikov equations and we prove how they are related to minimal conformal blocks via a formulation of hamiltonian reduction advocated by Furlan, Ganchev, Paunov and Petkova., Comment: 8 pages, LaTeX, article.sty, espcrc2.sty

Published
1995
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7. Conformal blocks for admissible representations of $SL(2)$ current algebra

Author

Petersen, J. L., Rasmussen, J., and Yu, M.

Subjects
High Energy Physics - Theory
Abstract

A review is presented of the recently obtained expressions for conformal blocks for {\it admissible} representations in $SL(2)$ current algebra based on the Wakimoto free field construction. In this realization one needs to introduce a second screening charge, one which depends on fractional powers of free fields. The techniques necessary to deal with these complications are developed, and explicit general integral representations for conformal blocks on the sphere are provided. The fusion rules are discussed and as a check it is verified that the conformal blocks satisfy the Knizhnik-Zamolodchikov equations. (Talk presented by J. Rasmussen at the Leuven workshop, July 10-14 1995, to appear in the proceedings), Comment: 11 pages, LaTeX

Published
1995

8. Hamiltonian Reduction of $SL(2)$-theories at the Level of Correlators

Author

Petersen, J. L., Rasmussen, J., and Yu, M.

Subjects
High Energy Physics - Theory
Abstract

Since the work of Bershadsky and Ooguri and Feigin and Frenkel it is well known that correlators of $SL(2)$ current algebra for admissible representations should reduce to correlators for conformal minimal models. A precise proposal for this relation has been given at the level of correlators: When $SL(2)$ primary fields are expressed as $\phi_j(z_n,x_n)$ with $x_n$ being a variable to keep track of the $SL(2)$ representation multiplet (possibly infinitely dimensional for admissible representations), then the minimal model correlator is supposed to be obtained simply by putting all $x_n=z_n$. Although strong support for this has been presented, to the best of our understanding a direct, simple proof seems to be missing so in this paper we present one based on the free field Wakimoto construction and our previous study of that in the present context. We further verify that the explicit $SL(2)$ correlators we have published in a recent preprint reduce in the above way, up to a constant which we also calculate. We further discuss the relation to more standard formulations of hamiltonian reduction., Comment: 13 pages, LaTeX

Published
1995
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9. Conformal Blocks for admissible representations in SL(2) current algebra

Author

Petersen, J. L., Rasmussen, J., and Yu, M.

Subjects
High Energy Physics - Theory
Abstract

We show how to deal with screening charges involving fractional powers of free fields. This enables us to use the free field Wakimoto construction to obtain complete expressions for integral representations of conformal blocks for N-point functions on the sphere, also in the case of non-integrable representations, in particular for admissible representations. We verify several formal properties including the Knizhnik-Zamolodchikov equations. We discuss the fusion rules which result from our treatment, and compare with the literature., Comment: 30 pages, LaTeX

Published
1995
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10. Extended Superconformal Algebras and Free Field Realizations from Hamiltonian Reduction

Author

Ito, K., Madsen, J. O., and Petersen, J. L.

Subjects
High Energy Physics - Theory
Abstract

We develop the method of the hamiltonian reduction of affine Lie superalgebras to obtain explicit and general expressions both for the classical and the quantum extended superconformal algebras. By performing the gauge transformation which connects the diagonal gauge with the Drinfeld-Sokolov gauge and considering the quantum corrections, we get generic expressions for the classical and quantum free field realizations of the algebras., Comment: 10 pages, NBI-HE-93-18

Published
1993
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11. Coset Construction and Character Sumrules for the Doubly Extended $N=4$ Superconformal Algebras

Author

Petersen, J. L. and Taormina, A.

Subjects
High Energy Physics - Theory
Abstract

Character sumrules associated with the realization of the $N=4$ superconformal algebra $\At$ on manifolds corresponding to the group cosets $SU(3)_{\ktp }/U(1)$ are derived and developed as an important tool in obtaining the modular properties of $\At$ characters as well as information on certain extensions of that algebra. Their structure strongly suggests the existence of rational conformal field theories with central charges in the range $1 \le c\le 4$. The corresponding characters appear in the massive sector of the sumrules and are completely specified in terms of the characters for the parafermionic theory $SU(3)/(SU(2)\times U(1))$ and in terms of the branching functions of massless $\At$ characters into $SU(2)_{\ktp }\times SU(2)_1$ characters., Comment: 31 pages, DTP/92/49 NBI-HE-92-73 (latex file)

Published
1992
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12. Extended Superconformal Algebras from Classical and Quantum Hamiltonian Reduction

Author

Ito, K., Madsen, J. O., and Petersen, J. L.

Subjects
High Energy Physics - Theory
Abstract

We consider the extended superconformal algebras of the Knizhnik-Bershadsky type with $W$-algebra like composite operators occurring in the commutation relations, but with generators of conformal dimension 1,$\frac{3}{2}$ and 2, only. These have recently been neatly classified by several groups, and we emphasize the classification based on hamiltonian reduction of affine Lie superalgebras with even subalgebras $G\oplus sl(2)$. We reveiw the situation and improve on previous formulations by presenting generic and very compact expressions valid for all algebras, classical and quantum. Similarly generic and compact free field realizations are presented as are corresponding screening charges. Based on these a discussion of singular vectors is presented. (Based on talk by J.L. Petersen at the Int. Workshop on "String Theory, Quantum Gravity and the Unification of the Fundamental Interactions", Rome Sep. 21-26, 1992), Comment: 30 pages, NBI-HE-92-81

Published
1992

21. Genetic diversity and relationships among native Japanese horse breeds, the Japanese Thoroughbred and horses outside of Japan using genome‐wide SNP data

Author

Tozaki, T., primary, Kikuchi, M., additional, Kakoi, H., additional, Hirota, K., additional, Nagata, S., additional, Yamashita, D., additional, Ohnuma, T., additional, Takasu, M., additional, Kobayashi, I., additional, Hobo, S., additional, Manglai, D., additional, and Petersen, J. L., additional

Published
2019
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23. Generation of an equine biobank to be used for Functional Annotation of Animal Genomes project

Author

Burns, E. N., primary, Bordbari, M. H., additional, Mienaltowski, M. J., additional, Affolter, V. K., additional, Barro, M. V., additional, Gianino, F., additional, Gianino, G., additional, Giulotto, E., additional, Kalbfleisch, T. S., additional, Katzman, S. A., additional, Lassaline, M., additional, Leeb, T., additional, Mack, M., additional, Müller, E. J., additional, MacLeod, J. N., additional, Ming‐Whitfield, B., additional, Alanis, C. R., additional, Raudsepp, T., additional, Scott, E., additional, Vig, S., additional, Zhou, H., additional, Petersen, J. L., additional, Bellone, R. R., additional, and Finno, C. J., additional

Published
2018
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24. Generation of an equine biobank to be used for Functional Annotation of Animal Genomes project

Author

Burns, E. N., Bordbari, M. H., Mienaltowski, M. J., Affolter, V. K., Barro, M. V., Gianino, F., Gianino, G., Giulotto, E., Kalbfleisch, T. S., Katzman, S. A., Lassaline, M., Leeb, T., Mack, M., Muller, E. J., MacLeod, J. N., Ming-Whitfield, B., Alanis, C. R., Raudsepp, T., Scott, E., Vig, S., Zhou, H., Petersen, J. L., Bellone, R. R., Finno, C. J., Burns, E. N., Bordbari, M. H., Mienaltowski, M. J., Affolter, V. K., Barro, M. V., Gianino, F., Gianino, G., Giulotto, E., Kalbfleisch, T. S., Katzman, S. A., Lassaline, M., Leeb, T., Mack, M., Muller, E. J., MacLeod, J. N., Ming-Whitfield, B., Alanis, C. R., Raudsepp, T., Scott, E., Vig, S., Zhou, H., Petersen, J. L., Bellone, R. R., and Finno, C. J.

Abstract

The Functional Annotation of Animal Genomes (FAANG) project aims to identify genomic regulatory elements in both sexes across multiple stages of development in domesticated animals. This study represents the first stage of the FAANG project for the horse, Equus caballus. A biobank of 80 tissue samples, two cell lines and six body fluids was created from two adult Thoroughbred mares. Ante-mortem assessments included full physical examinations, lameness, ophthalmologic and neurologic evaluations. Complete blood counts and serum biochemistries were also performed. At necropsy, in addition to tissue samples, aliquots of serum, ethylenediaminetetraacetic acid (EDTA) plasma, heparinized plasma, cerebrospinal fluid, synovial fluid, urine and microbiome samples from all regions of the gastrointestinal and urogenital tracts were collected. Epidermal keratinocytes and dermal fibroblasts were cultured from skin samples. All tissues were grossly and histologically evaluated by a board-certified veterinary pathologist. The results of the clinical and pathological evaluations identified subclinical eosinophilic and lymphocytic infiltration throughout the length of the gastrointestinal tract as well as a mild clinical lameness in both animals. Each sample was cryo-preserved in multiple ways, and nuclei were extracted from selected tissues. These samples represent the first published systemically healthy equine-specific biobank with extensive clinical phenotyping ante- and post-mortem. The tissues in the biobank are intended for community-wide use in the functional annotation of the equine genome. The use of the biobank will improve the quality of the reference annotation and allow all equine researchers to elucidate unknown genomic and epigenomic causes of disease.

Published
2018

29. Identification of Ancestry Informative Markers in the Domestic Horse

Author

Petersen, J. L., Mickelson, J. R., Andersson, L. S., Bailey, E., Bannasch, D. L., Binns, M. M., Borges, A. S., Cothran, E. G., Câmara Machado, A., Distl, O., Felicetti, Michela, Graves, K. T., Guérin, G., Hasegawa, T., Haase, B., Hill, E. W., Leeb, T., Lopes, M. S., Lindgren, G., Lohi, H., Penedo, M. C. T., Piercy, R., Røed, K. H., Ryder, O. A., Silvestrelli, Maurizio, Swinburne, J. E., Tozaki, T., Vaudin, M., Wade, C. M., and Mccue, M. E.

Published
2012

30. The Equine Genetic Diversity Consortium: an international collaboration to describe genetic variation in modern horse breeds

Author

Petersen, J. L., Mickelson, J. R., Andersson, L. S., Bailey, E., Bannasch, D. L., Binns, M. M., Borges, A. S., Cothran, E. G., Câmara Machado, A., Distl, O., Felicetti, Michela, Graves, K. T., Guérin, G., Hasegawa, T., Haase, B., Hill, E. W., Leeb, T., Lopes, M. S., Lindgren, G., Lohi, H., Penedo, M. C. T., Piercy, R., Røed, K. H., Ryder, O. A., Silvestrelli, Maurizio, Swinburne, J. E., Tozaki, T., Vaudin, M., Wade, C. M., and Mccue, M. E.

Published
2011

35. Field theory

Author

Petersen, J L

Subjects
Particle Physics - Theory
Published
1998

46. N-Heterocyclic Carbene Palladium Complexes Bearing Carboxylate Ligands and Their Catalytic Activity in the Hydroarylation of Alkynes

Author

Viciu, M. S., Stevens, E. D., Petersen, J. L., Petersen, J. L., and Nolan, S. P.

Abstract

The synthesis and reactivity of palladium acetate/trifluoroacetate complexes stabilized by the presence of N-heterocyclic carbene (NHC) ligands are described. The structures and coordination characteristics of both (IPr)Pd(OAc)2 (1) and (IPr)Pd(OOCCF3)2(H2O) (2) were elucidated by spectroscopic and X-ray diffraction studies. The structure of 1 shows a novel coordination of the anions in a monomeric complex, with one acetate anion acting as a monodentate ligand while the second one coordinates through both oxygens. The NHC ligands in 1 and 2 are stable under acidic conditions. The complexes were used as precatalysts in the hydroarylation of alkynes. Using this simple protocol, a number of arenes react with various alkynes to produce stilbenes.

Published
2004

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