Facilitating accessible, rapid, and appropriate processing of ancient metagenomic data with AMDirT [version 2; peer review: 1 approved, 2 approved with reservations]

Autor: Olivia S. Smith, Ophélie Lebrasseur, Nihan D. Dagtas, Nikolay Oskolkov, Miriam J. Bravo-Lopez, Mohamed S. Sarhan, Megan Michel, Meriam van Os, Maria Lopopolo, Markella Moraitou, Kelly E. Blevins, Kevin G. Daly, Julien Fumey, Kadir T. Özdoğan, Jasmin Frangenberg, Javier G. Serrano, James A. Fellows Yates, Valentina Vanghi, Christina Warinner, Sally Wasef, Shreya L. Ramachandran, Piotr Rozwalak, Raphael Eisenhofer, Maxime Borry, Irina M. Velsko, Iseult Jackson, I-Ting Huang, Ian Light, Gabriel Yaxal Ponce-Soto, Gunnar Neumann, Bjørn Peare Bartholdy, Diāna Spurīte, Arthur Kocher, Åshild J. Vågene‬, Andrea Quagliariello, Anna E. White, Alexander Hübner, Anan Ibrahim, Adrian Forsythe, Aida Andrades Valtueña

Publikováno v: F1000Research, Vol 12 (2024)

Background Access to sample-level metadata is important when selecting public metagenomic sequencing datasets for reuse in new biological analyses. The Standards, Precautions, and Advances in Ancient Metagenomics community (SPAAM, https://spaam-commu

Externí odkaz: https://doaj.org/article/7ebc1408c1734656935c58957d2eda4c

Accurate targeted long-read DNA methylation and hydroxymethylation sequencing with TAPS

Autor: Yibin Liu, Jingfei Cheng, Paulina Siejka-Zielińska, Carika Weldon, Hannah Roberts, Maria Lopopolo, Andrea Magri, Valentina D’Arienzo, James M. Harris, Jane A. McKeating, Chun-Xiao Song

Publikováno v: Genome Biology, Vol 21, Iss 1, Pp 1-9 (2020)

Abstract We present long-read Tet-assisted pyridine borane sequencing (lrTAPS) for targeted base-resolution sequencing of DNA methylation and hydroxymethylation in regions up to 10 kb from nanogram-level input. Compatible with both Oxford Nanopore an

Externí odkaz: https://doaj.org/article/51a16a1b45b7443391655c421790aeea

Constructing custom-made radiotranscriptomic signatures of vascular inflammation from routine CT angiograms: a prospective outcomes validation study in COVID-19

Autor: Christos P Kotanidis, Cheng Xie, Donna Alexander, Jonathan C L Rodrigues, Katie Burnham, Alexander Mentzer, Daniel O’Connor, Julian Knight, Muhammad Siddique, Helen Lockstone, Sheena Thomas, Rafail Kotronias, Evangelos K Oikonomou, Ileana Badi, Maria Lyasheva, Cheerag Shirodaria, Sheila F Lumley, Bede Constantinides, Nicholas Sanderson, Gillian Rodger, Kevin K Chau, Archie Lodge, Maria Tsakok, Fergus Gleeson, David Adlam, Praveen Rao, Das Indrajeet, Aparna Deshpande, Amrita Bajaj, Benjamin J Hudson, Vivek Srivastava, Shakil Farid, George Krasopoulos, Rana Sayeed, Ling-Pei Ho, Stefan Neubauer, David E Newby, Keith M Channon, John Deanfield, Charalambos Antoniades, David J Ahern, Zhichao Ai, Mark Ainsworth, Chris Allan, Alice Allcock, Brian Angus, M Azim Ansari, Carolina Arancibia-Cárcamo, Dominik Aschenbrenner, Moustafa Attar, J Kenneth Baillie, Eleanor Barnes, Rachael Bashford-Rogers, Archana Bashyal, Sally Beer, Georgina Berridge, Amy Beveridge, Sagida Bibi, Tihana Bicanic, Luke Blackwell, Paul Bowness, Andrew Brent, Andrew Brown, John Broxholme, David Buck, Helen Byrne, Susana Camara, Ivan Candido Ferreira, Philip Charles, Wentao Chen, Yi-Ling Chen, Amanda Chong, Elizabeth Clutterbuck, Mark Coles, Christopher Conlon, Richard Cornall, Adam Cribbs, Fabiola Curion, Emma Davenport, Neil Davidson, Simon Davis, Calliope Dendrou, Julie Dequaire, Lea Dib, James Docker, Christina Dold, Tao Dong, Damien Downes, Hal Drakesmith, Susanna Dunachie, David Duncan, Chris Eijsbouts, Robert Esnouf, Alexis Espinosa, Rachel Etherington, Benjamin Fairfax, Rory Fairhead, Hai Fang, Shayan Fassih, Sally Felle, Maria Fernandez Mendoza, Ricardo Ferreira, Roman Fischer, Thomas Foord, Aden Forrow, John Frater, Anastasia Fries, Veronica Gallardo Sanchez, Lucy Garner, Clementine Geeves, Dominique Georgiou, Leila Godfrey, Tanya Golubchik, Maria Gomez Vazquez, Angie Green, Hong Harper, Heather Harrington, Raphael Heilig, Svenja Hester, Jennifer Hill, Charles Hinds, Clare Hird, Renee Hoekzema, Benjamin Hollis, Jim Hughes, Paula Hutton, Matthew Jackson-Wood, Ashwin Jainarayanan, Anna James-Bott, Kathrin Jansen, Katie Jeffery, Elizabeth Jones, Luke Jostins, Georgina Kerr, David Kim, Paul Klenerman, Vinod Kumar, Piyush Kumar Sharma, Prathiba Kurupati, Andrew Kwok, Angela Lee, Aline Linder, Teresa Lockett, Lorne Lonie, Maria Lopopolo, Martyna Lukoseviciute, Jian Luo, Spyridoula Marinou, Brian Marsden, Jose Martinez, Philippa Matthews, Michalina Mazurczyk, Simon McGowan, Stuart McKechnie, Adam Mead, Yuxin Mi, Claudia Monaco, Ruddy Montadon, Giorgio Napolitani, Isar Nassiri, Alex Novak, Darragh O'Brien, Daniel O'Connor, Denise O'Donnell, Graham Ogg, Lauren Overend, Inhye Park, Ian Pavord, Yanchun Peng, Frank Penkava, Mariana Pereira Pinho, Elena Perez, Andrew Pollard, Fiona Powrie, Bethan Psaila, T Phuong Quan, Emmanouela Repapi, Santiago Revale, Laura Silva-Reyes, Jean-Baptiste Richard, Charlotte Rich-Griffin, Thomas Ritter, Christine Rollier, Matthew Rowland, Fabian Ruehle, Mariolina Salio, Stephen Nicholas Sansom, Raphael Sanches Peres, Alberto Santos Delgado, Tatjana Sauka-Spengler, Ron Schwessinger, Giuseppe Scozzafava, Gavin Screaton, Anna Seigal, Malcolm Semple, Martin Sergeant, Christina Simoglou Karali, David Sims, Donal Skelly, Hubert Slawinski, Alberto Sobrinodiaz, Nikolaos Sousos, Lizzie Stafford, Lisa Stockdale, Marie Strickland, Otto Sumray, Bo Sun, Chelsea Taylor, Stephen Taylor, Adan Taylor, Supat Thongjuea, Hannah Thraves, John Todd, Adriana Tomic, Orion Tong, Amy Trebes, Dominik Trzupek, Felicia Anna Tucci, Lance Turtle, Irina Udalova, Holm Uhlig, Erinke van Grinsven, Iolanda Vendrell, Marije Verheul, Alexandru Voda, Guanlin Wang, Lihui Wang, Dapeng Wang, Peter Watkinson, Robert Watson, Michael Weinberger, Justin Whalley, Lorna Witty, Katherine Wray, Luzheng Xue, Hing Yuen Yeung, Zixi Yin, Rebecca Young, Jonathan Youngs, Ping Zhang, Yasemin-Xiomara Zurke, Adrian Banning, Alexios Antonopoulos, Andrew Kelion, Attila Kardos, Benjamin Hudson, Bon-Kwon Koo, Christos Kotanidis, Ciara Mahon, Colin Berry, David Newby, Derek Connolly, Diane Scaletta, Ed Nicol, Elisa McAlindon, Evangelos Oikonomou, Francesca Pugliese, Gianluca Pontone, Giulia Benedetti, Guo-Wei He, Henry West, Hidekazu Kondo, Imre Benedek, Intrajeet Das, John Graby, John Greenwood, Jonathan Rodrigues, Junbo Ge, Keith Channon, Larissa Fabritz, Li-Juan Fan, Lucy Kingham, Marco Guglielmo, Matthias Schmitt, Meinrad Beer, Michelle Anderson, Milind Desai, Mohamed Marwan, Naohiko Takahashi, Nehal Mehta, Neng Dai, Nicholas Screaton, Nikant Sabharwal, Pál Maurovich-Horvat, Rajesh Kharbanda, Rebecca Preston, Richard Wood, Ron Blankstein, Ronak Rajani, Saeed Mirsadraee, Shahzad Munir, Steffen Klömpken, Steffen Petersen, Stephan Achenbach, Susan Anthony, Sze Mak, Tarun Mittal, Theodora Benedek, Vinoda Sharma, Wen-Hua Lin

Publikováno v: The Lancet. Digital Health, 4, 10, pp. e705-e716
The Lancet. Digital Health, 4, e705-e716

Contains fulltext : 286832.pdf (Publisher’s version ) (Open Access) BACKGROUND: Direct evaluation of vascular inflammation in patients with COVID-19 would facilitate more efficient trials of new treatments and identify patients at risk of long-term

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::667e9c3752db2a7c11d82a56de81ce50
https://ora.ox.ac.uk/objects/uuid:eae65b13-07e0-4f03-8fff-f05e44fa1bf9

A blood atlas of COVID-19 defines hallmarks of disease severity and specificity

Autor: David J. Ahern, Zhichao Ai, Mark Ainsworth, Chris Allan, Alice Allcock, Brian Angus, M. Azim Ansari, Carolina V. Arancibia-Cárcamo, Dominik Aschenbrenner, Moustafa Attar, J. Kenneth Baillie, Eleanor Barnes, Rachael Bashford-Rogers, Archana Bashyal, Sally Beer, Georgina Berridge, Amy Beveridge, Sagida Bibi, Tihana Bicanic, Luke Blackwell, Paul Bowness, Andrew Brent, Andrew Brown, John Broxholme, David Buck, Katie L. Burnham, Helen Byrne, Susana Camara, Ivan Candido Ferreira, Philip Charles, Wentao Chen, Yi-Ling Chen, Amanda Chong, Elizabeth A. Clutterbuck, Mark Coles, Christopher P. Conlon, Richard Cornall, Adam P. Cribbs, Fabiola Curion, Emma E. Davenport, Neil Davidson, Simon Davis, Calliope A. Dendrou, Julie Dequaire, Lea Dib, James Docker, Christina Dold, Tao Dong, Damien Downes, Hal Drakesmith, Susanna J. Dunachie, David A. Duncan, Chris Eijsbouts, Robert Esnouf, Alexis Espinosa, Rachel Etherington, Benjamin Fairfax, Rory Fairhead, Hai Fang, Shayan Fassih, Sally Felle, Maria Fernandez Mendoza, Ricardo Ferreira, Roman Fischer, Thomas Foord, Aden Forrow, John Frater, Anastasia Fries, Veronica Gallardo Sanchez, Lucy C. Garner, Clementine Geeves, Dominique Georgiou, Leila Godfrey, Tanya Golubchik, Maria Gomez Vazquez, Angie Green, Hong Harper, Heather A. Harrington, Raphael Heilig, Svenja Hester, Jennifer Hill, Charles Hinds, Clare Hird, Ling-Pei Ho, Renee Hoekzema, Benjamin Hollis, Jim Hughes, Paula Hutton, Matthew A. Jackson-Wood, Ashwin Jainarayanan, Anna James-Bott, Kathrin Jansen, Katie Jeffery, Elizabeth Jones, Luke Jostins, Georgina Kerr, David Kim, Paul Klenerman, Julian C. Knight, Vinod Kumar, Piyush Kumar Sharma, Prathiba Kurupati, Andrew Kwok, Angela Lee, Aline Linder, Teresa Lockett, Lorne Lonie, Maria Lopopolo, Martyna Lukoseviciute, Jian Luo, Spyridoula Marinou, Brian Marsden, Jose Martinez, Philippa C. Matthews, Michalina Mazurczyk, Simon McGowan, Stuart McKechnie, Adam Mead, Alexander J. Mentzer, Yuxin Mi, Claudia Monaco, Ruddy Montadon, Giorgio Napolitani, Isar Nassiri, Alex Novak, Darragh P. O'Brien, Daniel O'Connor, Denise O'Donnell, Graham Ogg, Lauren Overend, Inhye Park, Ian Pavord, Yanchun Peng, Frank Penkava, Mariana Pereira Pinho, Elena Perez, Andrew J. Pollard, Fiona Powrie, Bethan Psaila, T. Phuong Quan, Emmanouela Repapi, Santiago Revale, Laura Silva-Reyes, Jean-Baptiste Richard, Charlotte Rich-Griffin, Thomas Ritter, Christine S. Rollier, Matthew Rowland, Fabian Ruehle, Mariolina Salio, Stephen Nicholas Sansom, Raphael Sanches Peres, Alberto Santos Delgado, Tatjana Sauka-Spengler, Ron Schwessinger, Giuseppe Scozzafava, Gavin Screaton, Anna Seigal, Malcolm G. Semple, Martin Sergeant, Christina Simoglou Karali, David Sims, Donal Skelly, Hubert Slawinski, Alberto Sobrinodiaz, Nikolaos Sousos, Lizzie Stafford, Lisa Stockdale, Marie Strickland, Otto Sumray, Bo Sun, Chelsea Taylor, Stephen Taylor, Adan Taylor, Supat Thongjuea, Hannah Thraves, John A. Todd, Adriana Tomic, Orion Tong, Amy Trebes, Dominik Trzupek, Felicia Anna Tucci, Lance Turtle, Irina Udalova, Holm Uhlig, Erinke van Grinsven, Iolanda Vendrell, Marije Verheul, Alexandru Voda, Guanlin Wang, Lihui Wang, Dapeng Wang, Peter Watkinson, Robert Watson, Michael Weinberger, Justin Whalley, Lorna Witty, Katherine Wray, Luzheng Xue, Hing Yuen Yeung, Zixi Yin, Rebecca K. Young, Jonathan Youngs, Ping Zhang, Yasemin-Xiomara Zurke

Publikováno v: Cell
2022, ' A blood atlas of COVID-19 defines hallmarks of disease severity and specificity ', Cell, vol. 185, no. 5, pp. 916-938.e58 . https://doi.org/10.1016/j.cell.2022.01.012

Treatment of severe COVID-19 is currently limited by clinical heterogeneity and incomplete description of specific immune biomarkers. We present here a comprehensive multi-omic blood atlas for patients with varying COVID-19 severity in an integrated

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::c87a80bc978f9ac1dbe81c48b52553b3
https://pubmed.ncbi.nlm.nih.gov/35216673

A transcriptomic census reveals that Rbfox contributes to a broad but selective recapitulation of peripheral tissue splicing patterns in the thymus

Autor: Kathrin Jansen, Stefano Maio, Moustafa Attar, Noriko Shikama-Dorn, Stephen N. Sansom, David Buck, Georg A. Holländer, Maria Lopopolo

Thymic epithelial cells (TEC) control the selection of a T-cell repertoire reactive to pathogens but tolerant of self. While this process is known to involve the promiscuous expression of virtually the entire protein-coding gene repertoire the extent

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_________::aa0505972c4111e6769b563406e918c6
https://doi.org/10.1101/2020.03.06.980870