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9. Whole-genome sequencing reveals new Alzheimer's disease-associated rare variants in loci related to synaptic function and neuronal development

Author

Prokopenko, D., Morgan, S.L., Mullin, K., Hofmann, O., Chapman, B., Kirchner, R., Amberkar, S., Wohlers, I., Lange, C., Hide, W., Bertram, L., and Tanzi, R.E.

Abstract

Introduction\ud \ud Genome-wide association studies have led to numerous genetic loci associated with Alzheimer's disease (AD). Whole-genome sequencing (WGS) now permits genome-wide analyses to identify rare variants contributing to AD risk.\ud \ud \ud \ud Methods\ud \ud We performed single-variant and spatial clustering–based testing on rare variants (minor allele frequency [MAF] ≤1%) in a family-based WGS-based association study of 2247 subjects from 605 multiplex AD families, followed by replication in 1669 unrelated individuals.\ud \ud \ud \ud Results\ud \ud We identified 13 new AD candidate loci that yielded consistent rare-variant signals in discovery and replication cohorts (4 from single-variant, 9 from spatial-clustering), implicating these genes: FNBP1L, SEL1L, LINC00298, PRKCH, C15ORF41, C2CD3, KIF2A, APC, LHX9, NALCN, CTNNA2, SYTL3, and CLSTN2.\ud \ud \ud \ud Discussion\ud \ud Downstream analyses of these novel loci highlight synaptic function, in contrast to common AD-associated variants, which implicate innate immunity and amyloid processing. These loci have not been associated previously with AD, emphasizing the ability of WGS to identify AD-associated rare variants, particularly outside of the exome.

Published
2021

10. Folding of laser-cut templates with plasmonic functionalized surfaces into micro cubes

Author

Lorenz, P., Yu, Y., Franz, R., Petersen, C., Zajadacz, J., Ehrhardt, M., Lecrivain, G., Kirchner, R., and Zimmer, K.

Abstract

Functional 3D microstructures offer enhanced functionalities but need specific fabrication schemas. One approach is (self) folding of planar structures that enable to apply traditional microelectronic-based fabrication schemas and allows the cost-effective fabrication of such 3D microstructures. Following this approach we combined templating lithographic techniques for plasmonic gold patterns with laser patterning and subsequent folding of the planar structures. Hence, the nanopattern design and the cut out shape can be separated and optimized independently. The micro cubes were realized in polyimide foil which was attached to a wafer for patterning the plasmonic structures. Thereafter the laser patterning and the folding procedure follows. Two different folding concepts was studied: suction and water droplet supported folding.

Published
2021

13. Beta decay of 101Sn

Author

Kavatsyuk, O., Mazzocchi, C., Janas, Z., Banu, A., Batist, L., Becker, F., Blazhev, A., Brüchle, W., Döring, J., Faestermann, T., Górska, M., Grawe, H., Jungclaus, A., Karny, M., Kavatsyuk, M., Klepper, O., Kirchner, R., La Commara, M., Miernik, K., Mukha, I., Plettner, C., Płochocki, A., Roeckl, E., Romoli, M., Rykaczewski, K., Schädel, M., Schmidt, K., Schwengner, R., and Żylicz, J.

Published
2007
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15. Gamow-Teller beta decay of 105Sn

Author

Kavatsyuk, M., Batist, L., Becker, F., Blazhev, A., Brüchle, W., Döring, J., Faestermann, T., Górska, M., Grawe, H., Janas, Z., Jungclaus, A., Karny, M., Kavatsyuk, O., Kirchner, R., La Commara, M., Mandal, S., Mazzocchi, C., Mukha, I., Muralithar, S., Plettner, C., Płochocki, A., Roeckl, E., Romoli, M., Schädel, M., and Żylicz, J.

Published
2006
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16. Beta decay of the proton-rich nuclei 102Sn and 104Sn

Author

Karny, M., Batist, L., Banu, A., Becker, F., Blazhev, A., Brown, B. A., Brüchle, W., Döring, J., Faestermann, T., Górska, M., Grawe, H., Janas, Z., Jungclaus, A., Kavatsyuk, M., Kavatsyuk, O., Kirchner, R., La Commara, M., Mandal, S., Mazzocchi, C., Miernik, K., Mukha, I., Muralithar, S., Plettner, C., Płochocki, A., Roeckl, E., Romoli, M., Rykaczewski, K., Schädel, M., Schmidt, K., Schwengner, R., and Żylicz, J.

Published
2006
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17. Beta-decay studies near 100Sn

Author

Karny, M., Batist, L., Banu, A., Becker, F., Blazhev, A., Burkard, K., Brüchle, W., Döring, J., Faestermann, T., Górska, M., Grawe, H., Janas, Z., Jungclaus, A., Kavatsyuk, M., Kavatsyuk, O., Kirchner, R., La Commara, M., Mandal, S., Mazzocchi, C., Miernik, K., Mukha, I., Muralithar, S., Plettner, C., Płochocki, A., Roeckl, E., Romoli, M., Rykaczewski, K., Schädel, M., Schmidt, K., Schwengner, R., and Żylicz, J.

Published
2005
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19. Beta decay of 103Sn

Author

Kavatsyuk, O., Kavatsyuk, M., Batist, L., Banu, A., Becker, F., Blazhev, A., Brüchle, W., Döring, J., Faestermann, T., Górska, M., Grawe, H., Janas, Z., Jungclaus, A., Karny, M., Kirchner, R., La Commara, M., Mandal, S., Mazzocchi, C., Mukha, I., Muralithar, S., Plettner, C., Płochocki, A., Roeckl, E., Romoli, M., Schädel, M., Schwengner, R., and Żylicz, J.

Published
2005
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24. Beta-decay studies using total absorption spectroscopy

Author

Algora, A., Batist, L., Borge, M. J. G., Cano-Ott, D., Collatz, R., Courtin, S., Dessagne, Ph, Fraile, L. M., Gadea, A., Gelletly, W., Hellström, M., Janas, Z., Jungclaus, A., Kirchner, R., Karny, M., Le Scornet, G., Miehé, Ch, Maréchal, F., Moroz, F., Nácher, E., Poirier, E., Roeckl, E., Rubio, B., Rykaczewski, K., Tain, J. L., Tengblad, O., Wittmann, V., GSI-TAS Collaboration, and LUCRECIA-TAgS Collaboration

Published
2003
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25. Beta decay of 57Zn*

Author

Jokinen, A., Nieminen, A., Äystö, J., Borcea, R., Caurier, E., Dendooven, P., Gierlik, M., Górska, M., Grawe, H., Hellström, M., Karny, M., Janas, Z., Kirchner, R., Commara, M. La, Martinez-Pinedo, G., Mayet, P., Penttilä, H., Plochocki, A., Rejmund, M., Roeckl, E., Sawicka, M., Schlegel, C., Schmidt, K., and Schwengner, R.

Published
2002
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27. First measurement of β-decay properties of the proton drip-line nucleus 60Ga

Author

Mazzocchi, C., Janas, Z., Döring, J., Axiotis, M., Batist, L., Borcea, R., Cano-Ott, D., Caurier, E., de Angelis, G., Farnea, E., Faßbender, A., Gadea, A., Grawe, H., Jungclaus, A., Kapica, M., Kirchner, R., Kurcewicz, J., Lenzi, S.M., Martínez, T., Mukha, I., Nácher, E., Napoli, D.R., Roeckl, E., Rubio, B., Schwengner, R., Tain, J.L., and Ur, C.A.

Published
2001
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29. Beta decay of 93Pd

Author

Schmidt, K., Mazzocchi, C., Borcea, R., Döring, J., Galanopoulos, S., Górska, M., Grawe, H., Harissopulos, S., Hellström, M., Janas, Z., Kirchner, R., Kriembardis, G., La Commara, M., Ostrowski, A. N., Rainovski, G., and Roeckl, E.

Published
2000
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31. A molecular oyster: a neutral anion receptor containing two cyclopeptide subunits with a remarkable sulfate affinity in aqueous solution

Author

Kubik, Stefan, Kirchner, R., Nolting, D., and Seide, J.

Subjects
Amino acids -- Structure, Amino acids -- Chemical properties, Peptide hormones -- Chemical properties, Anions -- Chemical properties, Anions -- Structure, Chemistry
Abstract

An artificial anion receptor is presented, in which two cyclohexapeptide subunits containing l-proline and 6-aminopicolinic acid subunits in an alternating sequence are connected via an adipinic acid spacer. Covalently linking two cyclopeptide molecules derived from 6-aminopicolinic acid subunits with a suitable spacer, an artificial receptor is accessible that strongly binds anions in 50% water/methanol.

Published
2002

32. Beta decay of 61Ga

Author

Oinonen, M., Baumann, P., Dendooven, P., Fujita, Y., Górska, M., Grawe, H., Hu, Z., Janas, Z., Jokinen, A., Kirchner, R., Klepper, O., Knipper, A., Liu, W., Penttilä, H., Plochocki, A., Ramdhane, M., Roeckl, E., Walter, G., and Äystö, J.

Published
1999
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34. Bioconda: sustainable and comprehensive software distribution for the life sciences

Author

Dale R., Gruning B., Sjodin A., Rowe J., Chapman B. A., Tomkins-Tinch C. H., Valieris R., Batut B., Caprez A., Cokelaer T., Yusuf D., Beauchamp K. A., Brinda K., Wollmann T., Corguille G. L., Ryan D., Bretaudeau A., Hoogstrate Y., Pedersen B. S., Heeringen S., Raden M., Luna-Valero S., Soranzo N., Smet M. D., Kuster G. V., Kirchner R., Pantano L., Charlop-Powers Z., Thornton K., Martin M., Beek M. D., Maticzka D., Miladi M., Will S., Gravouil K., Unneberg P., Brueffer C., Blank C., Piro V. C., Wolff J., Antao T., Gladman S., Shlyakhter I., Hollander M., Mabon P., Shen W., Boekel J., Holtgrewe M., Bouvier D., de Ruiter J. R., Cabral J., Choudhary S., Harding N., Kleinkauf R., Enns E., Eggenhofer F., Brown J., Cock P. J. A., Timm H., Thomas C., Zhang X. -O., Chambers M., Turaga N., Seiler E., Brislawn C., Pruesse E., Fallmann J., Kelleher J., Nguyen H., Parsons L., Fang Z., Stovner E. B., Stoler N., Ye S., Wohlers I., Farouni R., Freeberg M., Johnson J. E., Bargull M., Kensche P. R., Webster T. H., Eppley J. M., Stahl C., Rose A. S., Reynolds A., Wang L. -B., Garnier X., Dirmeier S., Knudsen M., Taylor J., Srivastava A., Rai V., Agren R., Junge A., Guimera R. V., Khan A., Schmeier S., He G., Pinello L., Hagglund E., Mikheyev A. S., Preussner J., Waters N. R., Li W., Capellades J., Chande A. T., Pirola Y., Hiltemann S., Bendall M. L., Singh S., Dunn W. A., Drouin A., Domenico T. D., Bruijn I., Larson D. E., Chicco D., Grassi E., Gonnella G., B J., Wang L., Giacomoni F., Clarke E., Blankenberg D., Tran C., Patro R., Laurent S., Gopez M., Sennblad B., Baaijens J. A., Ewels P., Wright P. R., Enache O. M., Roger P., Dampier W., Koppstein D., Devisetty U. K., Rausch T., Cornwell M., Salatino A. E., Seiler J., Jung M., Kornobis E., Cumbo F., Stocker B. K., Moskalenko O., Bogema D. R., Workentine M. L., Newhouse S. J., Leprevost F. D. V., Arvai K., Koster J., Albert-Ludwigs-Universität Freiburg, National Institutes of Health [Bethesda] (NIH), Swedish Defence Research Agency [Stockholm] (FOI), Umeå University, Harvard T.H. Chan School of Public Health, New York University [Abu Dhabi], NYU System (NYU), Harvard University [Cambridge], Hospital Camargo Sao Paulo, Partenaires INRAE, University of Duisburg-Essen, This work was supported by the Intramural Program of the National Institute of Diabetes and Digestive and Kidney Diseases, US National Institutes of Health (R.D.), the Netherlands Organisation for Scientific Research (NWO) (VENI grant 016.Veni.173.076 to J.K.), the German Research Foundation (SFB 876 to J.K.), and the NYU Abu Dhabi Research Institute for the NYU Abu Dhabi Center for Genomics and Systems Biology, program number CGSB1 (grant to J.R. and A. Yousif)., We thank all contributors, the conda-forge team, and Anaconda Inc. for excellent cooperation. Further, we thank Travis CI (https://travis-ci.com) and Circle CI (https://circleci.com) for providing free Linux and macOS computing capacity. Finally, we thank ELIXIR (https://www.elixir-europe.org) for constant support and donation of staff., Etienne Kornobis (Epigenetic Regulation Unit, Institut Pasteur, Paris, France) fait partie de Bioconda Team, Bioinformatics Group, Department ​ ​ of ​ ​ Computer ​ ​ Science, University of Freiburg [Freiburg], Laboratory of Cellular and Developmental Biology (LCDB), NIDDK, NIH, Department of Organismic and Evolutionary Biology, Broad Institute of MIT and Harvard (BROAD INSTITUTE), Harvard Medical School [Boston] (HMS)-Massachusetts Institute of Technology (MIT)-Massachusetts General Hospital [Boston], Microbiologie Environnement Digestif Santé (MEDIS), INRA Clermont-Ferrand-Theix-Université Clermont Auvergne [2017-2020] (UCA [2017-2020]), Umea Plant Science Center (UPSC), Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences (SLU)-Swedish University of Agricultural Sciences (SLU), Laboratoire Microorganismes : Génome et Environnement (LMGE), Université Clermont Auvergne [2017-2020] (UCA [2017-2020])-Centre National de la Recherche Scientifique (CNRS), Harvard University, Universität Duisburg-Essen = University of Duisburg-Essen [Essen], Dale, R, Gruning, B, Sjodin, A, Rowe, J, Chapman, B, Tomkins-Tinch, C, Valieris, R, Batut, B, Caprez, A, Cokelaer, T, Yusuf, D, Beauchamp, K, Brinda, K, Wollmann, T, Corguille, G, Ryan, D, Bretaudeau, A, Hoogstrate, Y, Pedersen, B, Heeringen, S, Raden, M, Luna-Valero, S, Soranzo, N, Smet, M, Kuster, G, Kirchner, R, Pantano, L, Charlop-Powers, Z, Thornton, K, Martin, M, Beek, M, Maticzka, D, Miladi, M, Will, S, Gravouil, K, Unneberg, P, Brueffer, C, Blank, C, Piro, V, Wolff, J, Antao, T, Gladman, S, Shlyakhter, I, Hollander, M, Mabon, P, Shen, W, Boekel, J, Holtgrewe, M, Bouvier, D, de Ruiter, J, Cabral, J, Choudhary, S, Harding, N, Kleinkauf, R, Enns, E, Eggenhofer, F, Brown, J, Cock, P, Timm, H, Thomas, C, Zhang, X, Chambers, M, Turaga, N, Seiler, E, Brislawn, C, Pruesse, E, Fallmann, J, Kelleher, J, Nguyen, H, Parsons, L, Fang, Z, Stovner, E, Stoler, N, Ye, S, Wohlers, I, Farouni, R, Freeberg, M, Johnson, J, Bargull, M, Kensche, P, Webster, T, Eppley, J, Stahl, C, Rose, A, Reynolds, A, Wang, L, Garnier, X, Dirmeier, S, Knudsen, M, Taylor, J, Srivastava, A, Rai, V, Agren, R, Junge, A, Guimera, R, Khan, A, Schmeier, S, He, G, Pinello, L, Hagglund, E, Mikheyev, A, Preussner, J, Waters, N, Li, W, Capellades, J, Chande, A, Pirola, Y, Hiltemann, S, Bendall, M, Singh, S, Dunn, W, Drouin, A, Domenico, T, Bruijn, I, Larson, D, Chicco, D, Grassi, E, Gonnella, G, B, J, Giacomoni, F, Clarke, E, Blankenberg, D, Tran, C, Patro, R, Laurent, S, Gopez, M, Sennblad, B, Baaijens, J, Ewels, P, Wright, P, Enache, O, Roger, P, Dampier, W, Koppstein, D, Devisetty, U, Rausch, T, Cornwell, M, Salatino, A, Seiler, J, Jung, M, Kornobis, E, Cumbo, F, Stocker, B, Moskalenko, O, Bogema, D, Workentine, M, Newhouse, S, Leprevost, F, Arvai, K, Koster, J, Urology, and Pathology

Subjects
0301 basic medicine, Computer science, [SDV]Life Sciences [q-bio], Medizin, computer.software_genre, Biochemistry, User-Computer Interface, 03 medical and health sciences, 0302 clinical medicine, Software system, Molecular Biology, ComputingMilieux_MISCELLANEOUS, Social software engineering, Database, business.industry, Software development, INF/01 - INFORMATICA, Computational Biology, Cell Biology, Software distribution, 030104 developmental biology, Software construction, [SDE]Environmental Sciences, Package development process, Backporting, [INFO.INFO-BI]Computer Science [cs]/Bioinformatics [q-bio.QM], business, computer, Software, 030217 neurology & neurosurgery, Biotechnology
Abstract

International audience; We present Bioconda (https://bioconda.github.io), a distribution of bioinformatics software for the lightweight, multi- platform and language-agnostic package manager Conda. Currently, Bioconda o ers a collection of over 3000 software packages, which is continuously maintained, updated, and extended by a growing global community of more than 200 contributors. Bio- conda improves analysis reproducibility by allowing users to de ne isolated environments with de ned software versions, all of which are easily installed and managed without administrative privileges.

Published
2018

36. Decay properties of ground-state and isomer of 103In

Author

Szerypo, J., Grzywacz, R., Janas, Z., Karny, M., Pfützner, M., Plochocki, A., Rykaczewski, K., Żylicz, J., Huyse, M., Reusen, G., Schwarzenberg, J., Van Duppen, P., Woehr, A., Keller, H., Kirchner, R., Klepper, O., Piechaczek, A., Roeckl, E., Schmidt, K., Batist, L., Bykov, A., Wittman, V., and Brown, B. A.

Published
1997
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39. Beta-decay spectroscopy of 103, 105Sn

Author

Kavatsyuk, M., Kavatsyuk, O., Batist, L., Banu, A., Becker, F., Blazhev, A., Brüchle, W., Burkard, K., Döring, J., Faestermann, T., Górska, M., Grawe, H., Janas, Z., Jungclaus, A., Karny, M., Kirchner, R., La Commara, M., Mandal, S., Mazzocchi, C., Mukha, I., Muralithar, S., Plettner, C., Płochocki, A., Roeckl, E., Romoli, M., Schädel, M., Schwengner, R., and Żylicz, J.

Published
2005
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40. Study of the ( 21+) isomer in 94Ag

Author

Mukha, I., Roeckl, E., Grawe, H., Döring, J., Batist, L., Blazhev, A., Hoffman, C. R., Janas, Z., Kirchner, R., La Commara, M., Dean, S., Mazzocchi, C., Plettner, C., Tabor, S. L., and Wiedeking, M.

Published
2005
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45. Studies of β-delayed proton decays of N≃Z nuclei around 100Sn at the GSI-ISOL facility

Author

Mukha, I., Batist, L., Becker, F., Blazhev, A., Brüchle, A., Döring, J., Górska, M., Grawe, H., Faestermann, T., Hoffman, C., Janas, Z., Jungclaus, A., Karny, M., Kavatsyuk, M., Kavatsyuk, O., Kirchner, R., La Commara, M., Mazzocchi, C., Plettner, C., Płochocki, A., Roeckl, E., Romoli, M., Schädel, M., Schwengner, R., Tabor, S.L., and Wiedeking, M.

Published
2004
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50. Total absorption spectroscopy of 58Cu decay

Author

Janas, Z., Karny, M., Fujita, Y., Batist, L., Cano-Ott, D., Collatz, R., Dendooven, P., Gadea, A., Gierlik, M., Hellström, M., Hu, Z., Jokinen, A., Kirchner, R., Klepper, O., Moroz, F., Oinonen, M., Penttilä, H., Płochocki, A., Roeckl, E., Rubio, B., Shibata, M., Tain, J.L., and Wittman, V.

Published
2001
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