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| 1 | FunGeneClusterS: Predicting fungal gene clusters from genome and transcriptome data显示文摘Introduction:Secondary metabolites of fungi are receiving an increasing amount of interest due to their prolific bioactivities and the fact that fungal biosynthesis of secondary metabolites often occurs from co-regulated and co-located gene clusters.This makes the gene clusters attractive for synthetic biology and industrial biotechnology applications.We have previously published a method for accurate prediction of clusters from genome and transcriptome data,which could also suggest cross-chemistry,however,this method was limited both in the number of parameters which could be adjusted as well as in userfriendliness.Furthermore,sensitivity to the transcriptome data required manual curation of the predictions.In the present work,we have aimed at improving these features.Results:FunGeneClusterS is an improved implementation of our previous method with a graphical user interface for off-and on-line use.The new method adds options to adjust the size of the gene cluster(s)being sought as well as an option for the algorithm to be flexible with genes in the cluster which may not seem to be co-regulated with the remainder of the cluster.We have benchmarked the method using data from the well-studied Aspergillus nidulans and found that the method is an improvement over the previous one.In particular,it makes it possible to predict clusters with more than 10 genes more accurately,and allows identification of co-regulated gene clusters irrespective of the function of the genes.It also greatly reduces the need for manual curation of the prediction results.We furthermore applied the method to transcriptome data from A.niger.Using the identified best set of parameters,we were able to identify clusters for 31 out of 76 previously predicted secondary metabolite synthases/synthetases.Furthermore,we identified additional putative secondary metabolite gene clusters.In total,we predicted 432 co-transcribed gene clusters in A.niger(spanning 1.323 genes,12%of the genome).Some of these had functions related to primary metabolism,e.g.we have identified a cluster for biosynthesis of biotin,as well as several for degradation of aromatic compounds.The data identifies that suggests that larger parts of the fungal genome than previously anticipated operates as gene clusters.This includes both primary and secondary metabolism as well as other cellular maintenance functions.Conclusion:We have developed FunGeneClusterS in a graphical implementation and made the method capable of adjustments to different datasets and target clusters.The method is versatile in that it can predict co-regulated clusters not limited to secondary metabolism.Our analysis of data has shown not only the validity of the method,but also strongly suggests that large parts of fungal primary metabolism and cellular functions are both co-regulated and co-located. | Tammi C.Vesth Julian Brandl Mikael Rodam Andersen | 2016 | Synthetic and Systems Biotechnology2016，1，2： | 2 |
| 2 | Bisphosphonates: mechanisms of action 显示文摘 | Rodam GA F|eisch HA | 1996 | J Clin Invest1996，97，12： | 1 |
| 3 | Pharmacokinetic variability in the adolescent: implications of body size and organ function for dosage regimen design 显示文摘 | RODAM J H | 1994 | J Adolese Health1994，15，8： | 1 |
| 4 | Bisphosphonates:mechanisms of action显示文摘 | Rodam G A Fleisch H A | 1996 | J Clin Invest1996，97，12： | 1 |
| 5 | A Localization Technique for Linear Preserver Problems 显示文摘 | Rodam L Semrl P | 2010 | Linear Algebra and Its Application2010，433，1112： | 1 |
| 6 | Proof - of - concept trails for lung stem cell therpy 显示文摘 | Rodam DM | 2008 | Proc Am Thorac Soc2008，5，6： | 1 |
| 7 | Development and validation of a liquid chromatography/tandem mass spectrometry procedure for the quantification of sunitinib(SU11248) and its active metaholite,N-desethyl sunitinib (SU12662),in human plasma:application to an explorative study显示文摘 | Rodamer M Elsinghorst PW Kinzig M | | 0，，： | 1 |
| 8 | Time Allocation Patterns of Lowland Woolly Monkeys (Lagothrix lagotricha poeppigii) in a Neotropi- c al Terra Firma Forest 显示文摘 | DI FIORE A RODAM S | 2001 | International Journal of Primatology2001，22，： | 1 |
| 9 | 丹麦国家海事博物馆显示文摘丹麦海事博物馆位于独特的历史和空间环境中:在丹麦最重要和最著名的建筑之一克伦堡城堡和文化庭院——一个新的、雄心勃勃的文化中心之间。BIG建议将博物馆放在地下,就在船坞的墙壁外侧,以便将船坞保留为开放的户外展示空间,保存其强有力的结构作为海事博物馆中心。将博物馆这样设置,使它在成为与克伦堡城堡和邻近的文化庭院相联系的文化环境的一部分的同时,彰显自身. | John Pries Jensen Henrik Kania Ariel Joy Norback Wallner Rasmus Pedersen Annette Jensen Dennis Rasmussen Jan Magasanik Jeppe Ecklon Karsten Hammer Hansen Rasmus Rodam Rune Hansen Alina Tamosiunaite Alysen Hiller Ana Merino Armen Menendian Andy Yu Andreas Johansen Baptiste Blot Christian Alvarez Christin Svensson Claudia Hertrich Claudio Moretti Cory Mattheis Eskild Nordbud Felicia Guldberg Finn N■rkj■r Gül Ertekin Jan Borgstr■m James Schrader Johan Cool Jonas M■nster Kirstine Ragnhild Malte Kloe Michael Andersen Michal Kristof Marc Jay Maria Mavriku Masatoshi Oka Oana Simionescu Pablo Labra Peter Rieff Qianyi Lim Sara Sosio Sebastian Latz Tina Lund H■jgaard Tina Troster Todd Bennet Xi Chen Xing Xiong Xu Li Zoltan Kalaszi Iwan Baan Rasmus Hjortshoj Luca Santiago Mora Dragoer Luftfoto Jens Lindhe Lorenzon Boddi Thiks Wolzak 陈子钰(译) | 2019 | 城市环境设计2019，0，2： | 0 |
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