Eleven grand challenges in single-cell data science

Autor: David Lähnemann, Johannes Köster, Ewa Szczurek, Davis J. McCarthy, Stephanie C. Hicks, Mark D. Robinson, Catalina A. Vallejos, Kieran R. Campbell, Niko Beerenwinkel, Ahmed Mahfouz, Luca Pinello, Pavel Skums, Alexandros Stamatakis, Camille Stephan-Otto Attolini, Samuel Aparicio, Jasmijn Baaijens, Marleen Balvert, Buys de Barbanson, Antonio Cappuccio, Giacomo Corleone, Bas E. Dutilh, Maria Florescu, Victor Guryev, Rens Holmer, Katharina Jahn, Thamar Jessurun Lobo, Emma M. Keizer, Indu Khatri, Szymon M. Kielbasa, Jan O. Korbel, Alexey M. Kozlov, Tzu-Hao Kuo, Boudewijn P.F. Lelieveldt, Ion I. Mandoiu, John C. Marioni, Tobias Marschall, Felix Mölder, Amir Niknejad, Alicja Rączkowska, Marcel Reinders, Jeroen de Ridder, Antoine-Emmanuel Saliba, Antonios Somarakis, Oliver Stegle, Fabian J. Theis, Huan Yang, Alex Zelikovsky, Alice C. McHardy, Benjamin J. Raphael, Sohrab P. Shah, Alexander Schönhuth

Publikováno v: Genome Biology, Vol 21, Iss 1, Pp 1-35 (2020)

Abstract The recent boom in microfluidics and combinatorial indexing strategies, combined with low sequencing costs, has empowered single-cell sequencing technology. Thousands—or even millions—of cells analyzed in a single experiment amount to a

Externí odkaz: https://doaj.org/article/9368dc7f34b5489abc7fc8743d7a022d

The genome sequence of Hirschfeldia incana, a species with high photosynthetic light-use efficiency

Autor: Francesco Garassino, Raúl Y. Wijfjes, René Boesten, Frank F. M. Becker, Vittoria Clapero, Iris van den Hatert, Rens Holmer, M. Eric Schranz, Jeremy Harbinson, Dick de Ridder, Sandra Smit, Mark G. M. Aarts

Photosynthesis is a biophysical and biochemical process that plays a key role in sustaining plant and human life, being the first step in the production of energy-rich molecules and oxygen in the biosphere. Improving the photosynthetic capacity of ag

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_________::afd12cb2293c87245e537188a3ccb4f4
https://doi.org/10.1101/2022.01.29.478283

Comparative and functional genomics of nitrogen-fixing rhizobium symbiosis in plants

Autor: Rens Holmer

Given that nodulating plants do not require exogenous nitrogen fertilizer, engineering nodulation in non-nodulating crops has been a longstanding ambition. From an evolutionary perspective, identifying the genetic changes that led to nodulation can p

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::f0af031f2c5215dc3ef9dfdfb116f24b
https://doi.org/10.18174/545827

GeneNoteBook, a collaborative notebook for comparative genomics

Autor: Ton Bisseling, Sandra Smit, Rens Holmer, René Geurts, Robin van Velzen, Dick de Ridder

Publikováno v: Bioinformatics (Oxford, England), 35(22), 4779-4781
Bioinformatics (Oxford, England) 35 (2019) 22
Bioinformatics

Summary Analysis and comparison of genomic and transcriptomic datasets have become standard procedures in biological research. However, for non-model organisms no efficient tools exist to visually work with multiple genomes and their metadata, and to

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::5da690449b2ad7473016287ee8a651ea
https://doi.org/10.1093/bioinformatics/btz491

Comparative genomics of the nonlegume Parasponia reveals insights into evolution of nitrogen-fixing rhizobium symbioses

Autor: M. Eric Schranz, Luuk Rutten, Rimi Repin, J.G.J. Hontelez, Elio Schijlen, Wei Liu, Defeng Shen, Robin van Velzen, Kana Miyata, Luca Santuari, Fengjiao Bu, Arjan van Zeijl, Sandra Smit, Trupti Sharma, Renze Heidstra, Rens Holmer, Yuda Purwana Roswanjaya, Titis A. K. Wardhani, Wouter Kohlen, J. Verver, René Geurts, Menno Schilthuizen, Marijke Hartog, Qingqin Cao, Ton Bisseling, Berivan Gungor, Joelle Jansen, Wei-Cai Yang, Johan van den Hoogen, Maryam Seifi Kalhor, Elena Fedorova

Publikováno v: Proceedings of the National Academy of Sciences of the United States of America
Proceedings of the National Academy of Sciences of the United States of America 115 (2018) 20
Proceedings of the National Academy of Sciences of the United States of America, 115(20), E4700-E4709

Significance Fixed nitrogen is essential for plant growth. Some plants, such as legumes, can host nitrogen-fixing bacteria within cells in root organs called nodules. Nodules are considered to have evolved in parallel in different lineages, but the g

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::f03136c9a702ec73257e365a026b10f8
https://doi.org/10.1073/pnas.1721395115