Functionomics journal club / Group meetings
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Method: 1. Book room. 2. Announce to sonnhammer-at-sbc.su.se@lists.su.se, unit@compmed.se. 3. Add to calendar
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Suggested papers:
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Proteomics. Tissue-based map of the human proteome.Uhlén M, ..., Pontén F.Science. 2015 Jan 23;347(6220):1260419
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Complex archaea that bridge the gap between prokaryotes and eukaryotes.
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Genome-Wide Scale-Free Network Inference for Candida albicans.Altwasser R, Linde J, Buyko E, Hahn U, Guthke R.Front Microbiol. 2012 Feb 16;3:51
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In silico model-based inference: an emerging approach for inverse problems in engineering better medicines
Christoph
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Systematic humanization of yeast genes reveals conserved functions and genetic modularity
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NET-GE: a novel NETwork-based Gene Enrichment for detecting biological processes associated to Mendelian diseases.
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Distinctive Behaviors of Druggable Proteins in Cellular Networks
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Understanding multicellular function and disease with human tissue-specific networks
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Sequence Similarity Network Reveals Common Ancestry of Multidomain Proteins
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PyPanda: a Python package for gene regulatory network reconstruction.
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DatePresenterPaperVotes...
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150218ErikGene expression analysis identifies global gene dosage sensitivity in cancer.
Fehrmann et al., Nat Genet. 2015 47:115-25.
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150318MobashirTumour evolution inferred by single-cell sequencing. Navin N et al., Nature. 2011, 472(7341):90--94
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150401MateuszSpeeding up all-against-all protein comparisons while maintaining sensitivity by considering subsequence-level homology. Lucas D. Wittwer​, Ivana Piližota​, Adrian M. Altenhoff, Christophe DessimozMateusz
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MORPHIN: a web tool for human disease research by projecting model organism biology onto a human integrated gene network.Hwang S, Kim E, Yang S, Marcotte EM, Lee I.Christoph
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150417DimitriPan-cancer network analysis identifies combinations of rare somatic mutations across pathways and protein complexes.Leiserson et al.Dimitri
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150521AndreasBioPreDyn-bench: a suite of benchmark problems for dynamic modelling in systems biologyAndreas
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150923DanielEnabling network inference methods to handle missing data and outliersDimitri,Mateusz
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151008StefanieAnalysis of the genetic phylogeny of multifocal prostate cancer identifies multiple independent clonal expansions in neoplastic and morphologically normal prostate tissue
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160212Christoph/Sam
LEGO: a novel method for gene set over-representation analysis by incorporating network-based gene weights
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160314ErikAn experimentally supported model of the Bacillus subtilis global transcriptional regulatory network
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160323MateuszRooted phylogeny of the three superkingdoms.Harish A, Tunlid A, Kurland CG.Biochimie. 2013 Aug;95(8):1593-604
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160503Dimitriown benchmark paper
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160519DanielUniversal resilience patterns in complex networks
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160602StefanieSubclonal diversification of primary breast cancer revealed by multiregion sequencing
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161101ChristophDown-weighting overlapping genes improves gene set analysis
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161111DimitriProtein interaction networks from yeast to human
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161209ErikNetwork-based stratification of tumor mutations.
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170323MiguelNEAT: an efficient network enrichment analysis test
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170406MateuszDomain similarity based orthology detection
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Daniel
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171201StefanieA spatial model predicts that dispersal and cell turnover limit intratumour heterogeneity
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Christoph
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Dimitri
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Erik
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Miguel
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Mateusz
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Deniz
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Journal Club
Group meetings