TY  - GEN
A1  - Van Bel, Michiel
A1  - Proost, Sebastian
A1  - Van  Neste, Christophe
A1  - Deforce, Dieter
A1  - Van de Peer, Yves
A1  - Vandepoele, Klaas
T1  - TRAPID
BT  - an efficient online tool for the functional and comparative analysis of de novo RNA-Seq transcriptomes
T2  - Postprints der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe
N2  - Transcriptome analysis through next-generation sequencing technologies allows the generation of detailed gene catalogs for non-model species, at the cost of new challenges with regards to computational requirements and bioinformatics expertise. Here, we present TRAPID, an online tool for the fast and efficient processing of assembled RNA-Seq transcriptome data, developed to mitigate these challenges. TRAPID offers high-throughput open reading frame detection, frameshift correction and includes a functional, comparative and phylogenetic toolbox, making use of 175 reference proteomes. Benchmarking and comparison against state-of-the-art transcript analysis tools reveals the efficiency and unique features of the TRAPID system. TRAPID is freely available at http://bioinformatics.psb.ugent.be/webtools/trapid/.
T3  - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe - 900 
KW  - gene ontology
KW  - gene family
KW  - functional annotation
KW  - reference database
KW  - reference proteomes
Y1  - 2020
U6  - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus4-436409
SN  - 1866-8372
IS  - 900
ER  - 
TY  - GEN
A1  - Powell, Anahid E.
A1  - Lenhard, Michael
T1  - Control of organ size in plants
T2  - Postprints der Universität Potsdam : Mathematisch Naturwissenschaftliche Reihe
N2  - The size of plant organs, such as leaves and flowers, is determined by an interaction of genotype and environmental influences. Organ growth occurs through the two successive processes of cell proliferation followed by cell expansion. A number of genes influencing either or both of these processes and thus contributing to the control of final organ size have been identified in the last decade. Although the overall picture of the genetic regulation of organ size remains fragmentary, two transcription factor/microRNA-based genetic pathways are emerging in the control of cell proliferation. However, despite this progress, fundamental questions remain unanswered, such as the problem of how the size of a growing organ could be monitored to determine the appropriate time for terminating growth. While genetic analysis will undoubtedly continue to advance our knowledge about size control in plants, a deeper understanding of this and other basic questions will require including advanced live-imaging and mathematical modeling, as impressively demonstrated by some recent examples. This should ultimately allow the comparison of the mechanisms underlying size control in plants and in animals to extract common principles and lineage-specific solutions.
T3  - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe - 898 
KW  - BHLH transcription factor
KW  - genome-wide association
KW  - arabidopsis-thaliana
KW  - cell-proliferation
KW  - leaf development
KW  - developing leaves
KW  - petal growth
KW  - gene family
KW  - tor kinase
KW  - auxin
Y1  - 2020
U6  - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus4-438029
SN  - 1866-8372
IS  - 898
ER  -