Computational approaches to cell cycle analysis: Current research topics (those I am allowed to talk...
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Transcript of Computational approaches to cell cycle analysis: Current research topics (those I am allowed to talk...
Current research topics(those I am allowed to talk about)
Lars Juhl JensenEMBL Heidelberg
literature mining
why?
too much to read
information retrieval
finding the papers
ad hoc retrieval
user-specified query
“yeast AND cell cycle”
stemming
yeast / yeasts
dynamic query expansion
yeast / S. cerevisiae
Mitotic cyclin (Clb2)-bound Cdc28 (Cdk1 homolog) directly phosphorylated Swe1 and this modification served as a priming step to promote subsequent Cdc5-dependent Swe1
hyperphosphorylation and degradation
no tool will find it
entity recognition
identifying the substance(s)
Mitotic cyclin (Clb2)-bound Cdc28 (Cdk1 homolog) directly phosphorylated Swe1 and this modification served as a priming step to promote subsequent Cdc5-dependent Swe1
hyperphosphorylation and degradation
good synonyms list
orthographic variation
CDC28
Cdc28p
disambiguation
hairy
SDS
APC
Cdc2
still too much to read
information extraction
formalizing the facts
co-mentioning
statistical methods
NLPNatural Language Processing
Gene and protein names
Cue words for entity recognition
Verbs for relation extraction
[nxexpr The expression of [nxgene the cytochrome genes [nxpg CYC1 and CYC7]]]is controlled by[nxpg HAP1]
Mitotic cyclin (Clb2)-bound Cdc28 (Cdk1 homolog) directly phosphorylated Swe1 and this modification served as a priming step to promote subsequent Cdc5-dependent Swe1
hyperphosphorylation and degradation
no new discoveries
text mining
undiscovered links
Raynaud’s syndrome
fish oil
temporal trends
buzzwords
association networks
information extraction
curated knowledge
experimental data
genomic context
variable reliability
raw quality scores
not comparable
benchmarking
calibrate vs. gold standard
probabilistic scores
spread over many species
transfer by orthology
combine all evidence
P = 1-(1-P1).(1-P2).(1-P3)…
signaling networks
phosphoproteomics
phosphorylation sites
kinases are unknown
computational methods
kinase families
overprediction
context
co-activators
scaffolders
association networks
NetworKIN
benchmarking
2.5-fold better accuracy
ATM signaling
experimental validation
ATM phosphorylates Rad50
Cdk1 phosphorylates 53BP1
multiple reaction monitoring
Acknowledgments
Reflect & NLP– Evangelos Pafilis– Jasmin Saric– Rossitza Ouzounova– Sean O’Donoghue– Isabel Rojas
STRING & STITCH– Christian von Mering– Michael Kuhn– Manuel Stark– Samuel Chaffron– Philippe Julien– Tobias Doerks– Jan Korbel– Berend Snel– Martijn Huynen– Peer Bork
NetworKIN & NetPhorest– Rune Linding– Martin Lee Miller– Gerard Ostheimer– Francesca Diella– Karen Colwill– Jing Jin– Pavel Metalnikov– Vivian Nguyen– Adrian Pasculescu– Jin Gyoon Park– Leona D. Samson– Nikolaj Blom– Rob Russell– Peer Bork– Søren Brunak– Michael Yaffe– Tony Pawson