Integrative genomic analyses in adipocytes implicate DNA methylation in human obesity and diabetes

Autor: Liam McAllan, Damir Baranasic, Sergio Villicaña, Scarlett Brown, Weihua Zhang, Benjamin Lehne, Marco Adamo, Andrew Jenkinson, Mohamed Elkalaawy, Borzoueh Mohammadi, Majid Hashemi, Nadia Fernandes, Nathalie Lambie, Richard Williams, Colette Christiansen, Youwen Yang, Liudmila Zudina, Vasiliki Lagou, Sili Tan, Juan Castillo-Fernandez, James W. D. King, Richie Soong, Paul Elliott, James Scott, Inga Prokopenko, Inês Cebola, Marie Loh, Boris Lenhard, Rachel L. Batterham, Jordana T. Bell, John C. Chambers, Jaspal S. Kooner, William R. Scott

Publikováno v: Nature Communications, Vol 14, Iss 1, Pp 1-20 (2023)

Abstract DNA methylation variations are prevalent in human obesity but evidence of a causative role in disease pathogenesis is limited. Here, we combine epigenome-wide association and integrative genomics to investigate the impact of adipocyte DNA me

Externí odkaz: https://doaj.org/article/ea82019d0abe4ca49fb6dbbbe87cd979

Reference-Grade Genome and Large Linear Plasmid of Streptomyces rimosus: Pushing the Limits of Nanopore Sequencing

Autor: Lucija Slemc, Jernej Jakše, Alessandro Filisetti, Damir Baranasic, Antonio Rodríguez-García, Francesco Del Carratore, Stefano Maria Marino, Jurica Zucko, Antonio Starcevic, Martin Šala, Mercedes Pérez-Bonilla, Marina Sánchez-Hidalgo, Ignacio González, Fernando Reyes, Olga Genilloud, Vicki Springthorpe, Dušan Goranovič, Gregor Kosec, Gavin H. Thomas, Davide De Lucrezia, Hrvoje Petković, Miha Tome

Publikováno v: Microbiology Spectrum, Vol 10, Iss 2 (2022)

ABSTRACT Streptomyces rimosus ATCC 10970 is the parental strain of industrial strains used for the commercial production of the important antibiotic oxytetracycline. As an actinobacterium with a large linear chromosome containing numerous long repeat

Externí odkaz: https://doaj.org/article/121744588d984f3da64c26eae0840f83

Synthetic Biology: A Novel Approach for the Construction of Industrial Microorganisms

Autor: Antonio Starcevic, Jurica Zucko, Juan Diego Rojas, Janko Diminic, Damir Baranasic, Ranko Gacesa, Gabriel Padilla, Paul F. Long, John Cullum, Daslav Hranueli

Publikováno v: Food Technology and Biotechnology, Vol 51, Iss 1, Pp 3-11 (2013)

The recent achievement of synthesising a functioning bacterial chromosome marks a coming of age for engineering living organisms. In the future this should allow the construction of novel organisms to help solve the problems facing the human race, in

Externí odkaz: https://doaj.org/article/ca002933408a4464a5b3ae36a1455d68

Multiomic atlas with functional stratification and developmental dynamics of zebrafish cis-regulatory elements

Autor: Damir Baranasic, Matthias Hörtenhuber, Piotr J. Balwierz, Tobias Zehnder, Abdul Kadir Mukarram, Chirag Nepal, Csilla Várnai, Yavor Hadzhiev, Ada Jimenez-Gonzalez, Nan Li, Joseph Wragg, Fabio M. D’Orazio, Dorde Relic, Mikhail Pachkov, Noelia Díaz, Benjamín Hernández-Rodríguez, Zelin Chen, Marcus Stoiber, Michaël Dong, Irene Stevens, Samuel E. Ross, Anne Eagle, Ryan Martin, Oluwapelumi Obasaju, Sepand Rastegar, Alison C. McGarvey, Wolfgang Kopp, Emily Chambers, Dennis Wang, Hyejeong R. Kim, Rafael D. Acemel, Silvia Naranjo, Maciej Łapiński, Vanessa Chong, Sinnakaruppan Mathavan, Bernard Peers, Tatjana Sauka-Spengler, Martin Vingron, Piero Carninci, Uwe Ohler, Scott Allen Lacadie, Shawn M. Burgess, Cecilia Winata, Freek van Eeden, Juan M. Vaquerizas, José Luis Gómez-Skarmeta, Daria Onichtchouk, Ben James Brown, Ozren Bogdanovic, Erik van Nimwegen, Monte Westerfield, Fiona C. Wardle, Carsten O. Daub, Boris Lenhard, Ferenc Müller

Publikováno v: Baranasic, D, Hörtenhuber, M, Balwierz, P J, Zehnder, T, Mukarram, A K, Nepal, C, Várnai, C, Hadzhiev, Y, Jimenez-Gonzalez, A, Li, N, Wragg, J, D’Orazio, F M, Relic, D, Pachkov, M, Díaz, N, Hernández-Rodríguez, B, Chen, Z, Stoiber, M, Dong, M, Stevens, I, Ross, S E, Eagle, A, Martin, R, Obasaju, O, Rastegar, S, McGarvey, A C, Kopp, W, Chambers, E, Wang, D, Kim, H R, Acemel, R D, Naranjo, S, Łapiński, M, Chong, V, Mathavan, S, Peers, B, Sauka-Spengler, T, Vingron, M, Carninci, P, Ohler, U, Lacadie, S A, Burgess, S M, Winata, C, van Eeden, F, Vaquerizas, J M, Gómez-Skarmeta, J L, Onichtchouk, D, Brown, B J, Bogdanovic, O, van Nimwegen, E, Westerfield, M, Wardle, F C, Daub, C O, Lenhard, B & Müller, F 2022, ' Multiomic atlas with functional stratification and developmental dynamics of zebrafish cis-regulatory elements ', Nature Genetics, vol. 54, no. 7, pp. 1037-1050 . https://doi.org/10.1038/s41588-022-01089-w
Nature Genetics, 54, 1037–1050
Digital.CSIC. Repositorio Institucional del CSIC
instname

14 pages, 8 figures, supplementary information https://doi.org/10.1038/s41588-022-01089-w.-- Data availability: Raw and aligned sequencing data are available at https://danio-code.zfin.org/dataExport/. The raw sequencing data produced for this study

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::a5c9b0ff730aa047c825365d177a9878
https://edoc.unibas.ch/89500/

JASPAR 2020: update of the open-access database of transcription factor binding profiles

Autor: Albin Sandelin, Solenne Correard, Xi Zhang, Aziz Khan, Boris Lenhard, Oriol Fornes, Ge Tan, Robin van der Lee, François Parcy, Phillip A. Richmond, Anthony Mathelier, Benoit Ballester, Bhavi P. Modi, Wyeth W. Wasserman, Jaime A. Castro-Mondragon, Walter Santana-Garcia, Jeanne Chèneby, Marius Gheorghe, Damir Baranasic

Publikováno v: Nucleic Acids Research
Nucleic Acids Research, Oxford University Press, 2020, 48 (D1), pp.D87-D92. ⟨10.1093/nar/gkz1001⟩
Fornes, O, Castro-Mondragon, J A, Khan, A, van der Lee, R, Zhang, X, Richmond, P A, Modi, B P, Correard, S, Gheorghe, M, Baranašić, D, Santana-Garcia, W, Tan, G, Chèneby, J, Ballester, B, Parcy, F, Sandelin, A, Lenhard, B, Wasserman, W W & Mathelier, A 2020, ' JASPAR 2020 : update of the open-access database of transcription factor binding profiles ', Nucleic Acids Research, vol. 48, no. D1, pp. D87-D92 . https://doi.org/10.1093/nar/gkz1001
Nucleic Acids Research, 48 (D1)
Nucleic Acids Research, 2020, 48 (D1), pp.D87-D92. ⟨10.1093/nar/gkz1001⟩

JASPAR (http://jaspar.genereg.net) is an open-access database of curated, non-redundant transcription factor (TF)-binding profiles stored as position frequency matrices (PFMs) for TFs across multiple species in six taxonomic groups. In this 8th relea

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::19ef818b7e58418944efd4e2a867268c
https://hal.archives-ouvertes.fr/hal-02365013/file/gkz1001.pdf