Growing a circular economy with fungal biotechnology: a white paper

Autor: Vera Meyer, Evelina Y. Basenko, J. Philipp Benz, Gerhard H. Braus, Mark X. Caddick, Michael Csukai, Ronald P. de Vries, Drew Endy, Jens C. Frisvad, Nina Gunde-Cimerman, Thomas Haarmann, Yitzhak Hadar, Kim Hansen, Robert I. Johnson, Nancy P. Keller, Nada Kraševec, Uffe H. Mortensen, Rolando Perez, Arthur F. J. Ram, Eric Record, Phil Ross, Volha Shapaval, Charlotte Steiniger, Hans van den Brink, Jolanda van Munster, Oded Yarden, Han A. B. Wösten

Publikováno v: Fungal Biology and Biotechnology, Vol 7, Iss 1, Pp 1-23 (2020)

Abstract Fungi have the ability to transform organic materials into a rich and diverse set of useful products and provide distinct opportunities for tackling the urgent challenges before all humans. Fungal biotechnology can advance the transition fro

Externí odkaz: https://doaj.org/article/79587d4d7bd94545823f6e23e6f66477

VEuPathDB: the eukaryotic pathogen, vector and host bioinformatics resource center

Autor: Jamie Long, Sheena Shah Tomko, Susanne Warrenfeltz, Kristopher Lamoureux, Mary Ann McDowell, Brett Fox, Ulrike Böhme, Mark J Hickman, Steve Fisher, David Starns, George K. Christophides, Ana Barreto, Ann Sizemore Blevins, David S. Roos, Daniel Lawson, Lin Xu, Jie Zheng, John Judkins, Kristina Davis, Ryan Doherty, Jeremy D. DeBarry, Jaroslaw Nabrzyski, Lahcen I. Campbell, Samuel S. C. Rund, Evelina Y. Basenko, Beatrice Amos, Dave Falke, Mikkel B. Christensen, Stephanie Wever Schulman, Robert Wieck, Michael J. Dunn, Gareth Maslen, Mark X. Caddick, Haiming Wang, Robert Belnap, Wei Li, Christiane Hertz-Fowler, Achchuthan Shanmugasundram, Kathryn Crouch, Sarah A. Kelly, Wojciech Bażant, Sufen Hu, Bindu Gajria, Christian J. Stoeckert, Elizabeth Harper, Jay C. Humphrey, Jessica C. Kissinger, Paul A Wilkinson, Yikun Duan, Brian P. Brunk, John Brestelli, Matthieu Barba, Robert M. MacCallum, Kallie Lies, Omar S. Harb, Vasily Sitnik, Paul Flicek, Andrew M. Jones, Disha Lodha, Gloria I. Giraldo-Calderón, John Iodice, Danielle Callan, Drew Spruill, Cristina Aurrecoechea, Connor Howington, Dae Kun Kwon

Publikováno v: NUCLEIC ACIDS RESEARCH
Nucleic Acids Research
Amos, B, Aurrecoechea, C, Barba, M, Barreto, A, Basenko, E Y, Bażant, W, Belnap, R, Blevins, A S, Böhme, U, Brestelli, J, Brunk, B P, Caddick, M, Callan, D, Campbell, L, Christensen, M B, Christophides, G K, Crouch, K, Davis, K, Debarry, J, Doherty, R, Duan, Y, Dunn, M, Falke, D, Fisher, S, Flicek, P, Fox, B, Gajria, B, Giraldo-Calderón, G I, Harb, O S, Harper, E, Hertz-Fowler, C, Hickman, M J, Howington, C, Hu, S, Humphrey, J, Iodice, J, Jones, A, Judkins, J, Kelly, S A, Kissinger, J C, Kwon, D K, Lamoureux, K, Lawson, D, Li, W, Lies, K, Lodha, D, Long, J, MacCallum, R M, Maslen, G, McDowell, M A, Nabrzyski, J, Roos, D S, Rund, S S C, Schulman, S W, Shanmugasundram, A, Sitnik, V, Spruill, D, Starns, D, Stoeckert, C J, Tomko, S S, Wang, H, Warrenfeltz, S, Wieck, R, Wilkinson, P A, Xu, L & Zheng, J 2022, ' VEuPathDB : The eukaryotic pathogen, vector and host bioinformatics resource center ', Nucleic Acids Research, vol. 50, no. D1 . https://doi.org/10.1093/nar/gkab929

The Eukaryotic Pathogen, Vector and Host Informatics Resource (VEuPathDB, https://veupathdb.org) represents the 2019 merger of VectorBase with the EuPathDB projects. As a Bioinformatics Resource Center funded by the National Institutes of Health, wit

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::3e18d51670b3121a959cb0e4c2478f0b
http://livrepository.liverpool.ac.uk/3142948/1/gkab929.pdf

High-Quality Draft Genome Sequence and Annotation of the Basidiomycete Yeast

Autor: Stefany, Solano-González, Alistair C, Darby, Doug, Cossar, Mark X, Caddick

Publikováno v: Microbiology Resource Announcements

The basidiomycete Sporisorium graminicola (formally Pseudozyma graminicola) strain CBS10092 was originally isolated from an herbaceous plant in Russia. It is a known producer of mannosylerythritol lipids (MELs), the main component being MEL-C. Here,

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=pmid________::dbe9ea0b9760566b717447363969bd8a
https://pubmed.ncbi.nlm.nih.gov/31624158

Building a global alliance of biofoundries

Autor: Evelyn Travnik, Susan J. Rosser, Nicola J. Patron, Douglas C. Friedman, Vincent J. J. Martin, Jose A. Carrasco, Akihiko Kondo, Nathan J. Hillson, Filippo Menolascina, Hille Tekotte, Richard I. Kitney, David J. Bell, Maciej B. Holowko, Wen Shan Yew, N Curach, Jay D. Keasling, Rosalind Le Feuvre, Claudia E. Vickers, Chenli Liu, Yizhi Cai, Ying-Jin Yuan, Xiongfei Fu, Mark X. Caddick, Marilene Pavan, Matthew Wook Chang, Nicholas D. Gold, James R. Johnson, Huimin Zhao, Isak S. Pretorius, Chiaki Ogino, Richard A. Johnson, Paul S. Freemont, Chueh Loo Poh, Marko Storch, Nigel S. Scrutton, Markus J. Herrgård

Publikováno v: Hillson, Nathan; Caddick, Mark; Cai, Yizhi; Carrasco, Jose A; Chang, Matthew Wook; Curach, Natalie C; et al.(2019). Building a global alliance of biofoundries.. Nature communications, 10(1), 2040. doi: 10.1038/s41467-019-10079-2. Lawrence Berkeley National Laboratory: Retrieved from: http://www.escholarship.org/uc/item/0x93g6g7
Hillson, N, Caddick, M, Cai, Y, Carrasco, J A, Chang, M W, Curach, N C, Bell, D J, Le Feuvre, R, Friedman, D C, Fu, X, Gold, N D, Herrgård, M J, Holowko, M B, Johnson, J R, Johnson, R A, Keasling, J D, Kitney, R I, Kondo, A, Liu, C, Martin, V J J, Menolascina, F, Ogino, C, Patron, N J, Pavan, M, Poh, C L, Pretorius, I S, Rosser, S J, Scrutton, N S, Storch, M, Tekotte, H, Travnik, E, Vickers, C E, Yew, W S, Yuan, Y, Zhao, H & Freemont, P S 2019, ' Building a global alliance of biofoundries ', Nature Communications, vol. 10, 2040 . https://doi.org/10.1038/s41467-019-10079-2
Nature Communications
Nature communications, vol 10, iss 1
Hillson, N, Caddick, M, Cai, Y, Carrasco, J A, Chang, M W, Curach, N C, Bell, D J, Le Feuvre, R, Friedman, D C, Fu, X, Gold, N D, Herrgård, M J, Holowko, M B, Johnson, J R, Johnson, R A, Keasling, J D, Kitney, R I, Kondo, A, Liu, C, Martin, V J J, Menolascina, F, Ogino, C, Patron, N J, Pavan, M, Poh, C L, Pretorius, I S, Rosser, S J, Scrutton, N S, Storch, M, Tekotte, H, Travnik, E, Vickers, C E, Yew, W S, Yuan, Y, Zhao, H & Freemont, P S 2019, ' Building a global alliance of biofoundries ', Nature Communications, vol. 10, no. 1, pp. 2040 . https://doi.org/10.1038/s41467-019-10079-2, https://doi.org/10.1038/s41467-019-10079-2
Nature Communications, Vol 10, Iss 1, Pp 1-4 (2019)

Biofoundries provide an integrated infrastructure to enable the rapid design,construction, and testing of genetically reprogrammed organisms for biotechnologyapplications and research. Many biofoundries are being built and aGlobal Biofoundry Alliance

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::8452de3fa823d2195fcd3f3d0192fcfb
http://www.escholarship.org/uc/item/0x93g6g7

Similarity regression predicts evolution of transcription factor sequence specificity

Autor: Matthew T. Weirauch, Quaid Morris, Mark X. Caddick, Timothy P. Hughes, Ally Yang, Alexander Sasse, Gwendolyn Cowley, Mihai Albu, Samuel A. Lambert

Publikováno v: Nature Genetics

Transcription factor (TF) binding specificities (motifs) are essential for the analysis of gene regulation. Accurate prediction of TF motifs is critical, because it is infeasible to assay all TFs in all sequenced eukaryotic genomes. There is ongoing

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::d303131fd4e8084b659d24c181bffe1f
https://pubmed.ncbi.nlm.nih.gov/31133749