A proteomics sample metadata representation for multiomics integration and big data analysis

Autor: Chengxin Dai, Anja Füllgrabe, Julianus Pfeuffer, Elizaveta M. Solovyeva, Jingwen Deng, Pablo Moreno, Selvakumar Kamatchinathan, Deepti Jaiswal Kundu, Nancy George, Silvie Fexova, Björn Grüning, Melanie Christine Föll, Johannes Griss, Marc Vaudel, Enrique Audain, Marie Locard-Paulet, Michael Turewicz, Martin Eisenacher, Julian Uszkoreit, Tim Van Den Bossche, Veit Schwämmle, Henry Webel, Stefan Schulze, David Bouyssié, Savita Jayaram, Vinay Kumar Duggineni, Patroklos Samaras, Mathias Wilhelm, Meena Choi, Mingxun Wang, Oliver Kohlbacher, Alvis Brazma, Irene Papatheodorou, Nuno Bandeira, Eric W. Deutsch, Juan Antonio Vizcaíno, Mingze Bai, Timo Sachsenberg, Lev I. Levitsky, Yasset Perez-Riverol

Publikováno v: Nature Communications, Vol 12, Iss 1, Pp 1-8 (2021)

The number of publicly available proteomics datasets is growing rapidly, but a standardized approach for describing the associated metadata is lacking. Here, the authors propose a format and a software pipeline to present and validate metadata, and i

Externí odkaz: https://doaj.org/article/33519ff7742042fb963af4bf5ef059fa

Common and distinct transcriptional signatures of mammalian embryonic lethality

Autor: John E. Collins, Richard J. White, Nicole Staudt, Ian M. Sealy, Ian Packham, Neha Wali, Catherine Tudor, Cecilia Mazzeo, Angela Green, Emma Siragher, Edward Ryder, Jacqueline K. White, Irene Papatheodoru, Amy Tang, Anja Füllgrabe, Konstantinos Billis, Stefan H. Geyer, Wolfgang J. Weninger, Antonella Galli, Myriam Hemberger, Derek L. Stemple, Elizabeth Robertson, James C. Smith, Timothy Mohun, David J. Adams, Elisabeth M. Busch-Nentwich

Publikováno v: Nature Communications, Vol 10, Iss 1, Pp 1-16 (2019)

The transcriptional signature of embryonic lethality has not been defined. Here, the authors, as part of the Deciphering the Mechanisms of Developmental Disorders programme, define genes causing murine embryonic lethality around E9.5 and identify dev

Externí odkaz: https://doaj.org/article/0cb4c8c4995e4b478eecfb999695d344

Ten quick tips for biocuration.

Autor: Y Amy Tang, Klemens Pichler, Anja Füllgrabe, Jane Lomax, James Malone, Monica C Munoz-Torres, Drashtti V Vasant, Eleanor Williams, Melissa Haendel

Publikováno v: PLoS Computational Biology, Vol 15, Iss 5, p e1006906 (2019)

Externí odkaz: https://doaj.org/article/c383af9e8d9943fcb3252192ba0235ad

A high-resolution mRNA expression time course of embryonic development in zebrafish

Autor: Richard J White, John E Collins, Ian M Sealy, Neha Wali, Christopher M Dooley, Zsofia Digby, Derek L Stemple, Daniel N Murphy, Konstantinos Billis, Thibaut Hourlier, Anja Füllgrabe, Matthew P Davis, Anton J Enright, Elisabeth M Busch-Nentwich

Publikováno v: eLife, Vol 6 (2017)

We have produced an mRNA expression time course of zebrafish development across 18 time points from 1 cell to 5 days post-fertilisation sampling individual and pools of embryos. Using poly(A) pulldown stranded RNA-seq and a 3′ end transcript counti

Externí odkaz: https://doaj.org/article/9bd40316a80c4e14af28a219f25761c8

Expression Atlas update: gene and protein expression in multiple species

Autor: John C. Marioni, Jana Eliasova, Alfonso Munoz-Pomer, Upendra Kumbham, David García-Seisdedos, Sunita Kumari, Zhichiao Miao, Doreen Ware, Marcela K. Tello-Ruiz, Anja Füllgrabe, Sarah A. Teichmann, Tony Burdett, Suhaib Mohammed, Mathias Walzer, David Osumi-Sutherland, Juan Antonio Vizcaíno, Kerstin B. Meyer, Natassja Bush, Jonathan R. Manning, Lingyun Zhao, Deepti J. Kundu, Laura Clarke, Irene Papatheodorou, Alvis Brazma, Pablo Moreno, Haider Iqbal, Nancy George, Ananth Prakash, Silvie Fexova, Shengbo Wang, Andrey Solovyev, Martijn C. Nawijn, Yalan Bi, Mark J. Arends

Publikováno v: Nucleic Acid Research
Nucleic Acids Research, 50(D1):gkab1030, 129-140. Oxford University Press
Moreno, P, Fexova, S, George, N, Manning, J R, Miao, Z, Mohammed, S, Muñoz-pomer, A, Fullgrabe, A, Bi, Y, Bush, N, Iqbal, H, Kumbham, U, Solovyev, A, Zhao, L, Prakash, A, García-seisdedos, D, Kundu, D, Wang, S, Walzer, M, Clarke, L, Osumi-sutherland, D, Tello-ruiz, M, Kumari, S, Ware, D, Eliasova, J, Arends, M, Nawijn, M, Meyer, K, Burdett, T, Marioni, J, Teichmann, S, Vizcaíno, J, Brazma, A & Papatheodorou, I 2021, ' Expression Atlas update : gene and protein expression in multiple species ', Nucleic Acids Research, vol. 50, no. D1, pp. D129-D140 . https://doi.org/10.1093/nar/gkab1030
Nucleic Acids Research

The EMBL-EBI Expression Atlas is an added value knowledge base that enables researchers to answer the question of where (tissue, organism part, developmental stage, cell type) and under which conditions (disease, treatment, gender, etc) a gene or pro

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::6df3657a122c18e66f9e4d8b29f9d492
https://www.repository.cam.ac.uk/handle/1810/333881