Date
Presenter
Article
2010
8 December
Dave Messina
Kelley DR, Salzberg SL. Clustering metagenomic sequences with interpolated Markov models. BMC Bioinformatics. 2010 Nov 2;11:544.
24 November
Kristoffer Forslund
Parfrey LW, Grant J, Tekle YI, Lasek-Nesselquist E, Morrison HG, Sogin ML, Patterson DJ, Katz LA. Broadly sampled multigene analyses yield a well-resolved eukaryotic tree of life. Syst Biol. 2010 Oct;59(5):518-33.
10 November
Dimitri Guala
Zhang M, Lu LJ. Investigating the validity of current network analysis on static conglomerate networks by protein network stratification. BMC Bioinformatics. 2010 Sep 16;11:466.
27 October
Gabriel Östlund
Vogel C, Abreu Rde S, Ko D, Le SY, Shapiro BA, Burns SC, Sandhu D, Boutz DR, Marcotte EM, Penalva LO. Sequence signatures and mRNA concentration can explain two-thirds of protein abundance variation in a human cell line. Mol Syst Biol. 2010 Aug 24;6:400.
13 October
Erik Sonnhammer
29 September
Thomas Schmitt
Pandey G, Zhang B, Chang AN, Myers CL, Zhu J, Kumar V, Schadt EE. An integrative multi-network and multi-classifier approach to predict genetic interactions. PLoS Comput Biol. 2010 Sep 9;6(9).
15 September
Oliver Frings
Agarwal S, Deane CM, Porter MA, Jones NS. Revisiting date and party hubs: novel approaches to role assignment in protein interaction networks. PLoS Comput Biol. 2010 Jun 17;6(6):e1000817.
26 May
Dave Messina
Stefan Washietli, Sven Findeiß, Stephan Mueller, Stefan Kalkhof, Martin von Bergen, Ivo L. Hofacker, Peter F. Stadler, Nick Goldman. RNAcode: robust prediction of protein coding regions in comparative genomics data.
12 May
Thomas Schmitt
Taylor IW, Linding R, Warde-Farley D, Liu Y, Pesquita C, Faria D, Bull S, Pawson T, Morris Q, Wrana JL. Dynamic modularity in protein interaction networks predicts breast cancer outcome. Nat Biotechnol. 2009 Feb;27(2):199-204.
28 Apr
Erik Sonnhammer
Salichos et al.
07 Apr
Gabriel Östlund
Hannum G, Srivas R, Guénolé A, van Attikum H, Krogan NJ, Karp RM, Ideker T. Genome-wide association data reveal a global map of genetic interactions among protein complexes. PLoS Genet. 2009 Dec;5(12).
17 Mar
Kristoffer Forslund
Buljan M, Bateman A. The evolution of protein domain families. Biochem Soc Trans. 2009 Aug;37(Pt 4):751-5.
17 Feb
Sanjit Roopra
Meng-Ru Ho, Chun-houh Chen and Wen-chang Lin. Gene-oriented ortholog database: a functional comparison platform for orthologous loci. Database (2010) Vol. 2010: February 10, 2010.
3 Feb
Oliver Frings
Vanunu O, Magger O, Ruppin E, Shlomi T, Sharan R. Associating genes and protein complexes with disease via network propagation. PLoS Comput Biol. 2010 Jan 15;6(1):e1000641.
2009
16 Dec
Thomas Schmitt
C. Huttenhower, E.M. Haley, M.A. Hibbs, V. Dumeaux, D.R. Barrett, H.A. Coller, and O.G. Troyanskaya. Exploring the human genome with functional maps. Genome Research, vol. 19, Jun. 2009, pp. 1093-1106.
4 Dec
Dave Messina
Jaroszewski L, Li Z, Krishna SS, Bakolitsa C, Wooley J, Deacon AM, Wilson IA, Godzik A. Exploration of uncharted regions of the protein universe. PLoS Biol. 2009 Sep;7(9):e1000205.
18 Nov
Erik Sonnhammer
Lee et al.
4 Nov
Gabriel Östlund
Montaner D, Minguez P, Al-Shahrour F, Dopazo J. Gene set internal coherence in the context of functional profiling. BMC Genomics. 2009 Apr 27;10:197.
21 Oct
Kristoffer Forslund
Dudley JT, Tibshirani R, Deshpande T, Butte AJ. Disease signatures are robust across tissues and experiments. Mol Syst Biol. 2009;5:307.
7 Oct
Sanjit Roopra
Yip KY, Kim PM, McDermott D, Gerstein M. Multi-level learning: improving the prediction of protein, domain and residue interactions by allowing information flow between levels. BMC Bioinformatics. 2009 Aug 5;10:241.
23 Sep
Oliver Frings
Liu G, Wong L, Chua HN. Complex discovery from weighted PPI networks. Bioinformatics. 2009 Aug 1;25(15):1891-7.
9 Sep
Anna Henricson
Weiner J 3rd, Moore AD, Bornberg-Bauer E. Just how versatile are domains? BMC Evol Biol. 2008 Oct 14;8:285.
10 Jun
Dave Messina
Biegert A, Söding J. Sequence context-specific profiles for homology searching. Proc Natl Acad Sci U S A. 2009 Mar 10;106(10):3770-5.
13 May
Gabriel Östlund
Moxley JF, Jewett MC, Antoniewicz MR, Villas-Boas SG, Alper H, Wheeler RT, Tong L, Hinnebusch AG, Ideker T, Nielsen J, Stephanopoulos G. Linking high-resolution metabolic flux phenotypes and transcriptional regulation in yeast modulated by the global regulator Gcn4p. Proc Natl Acad Sci U S A. 2009 Apr 21;106(16):6477-82.
29 Apr
Erik Sonnhammer
Cosgrove EJ, Zhou Y, Gardner TS, Kolaczyk ED. Predicting gene targets of perturbations via network-based filtering of mRNA expression compendia. Bioinformatics. 2008 Nov 1;24(21):2482-90.
7 Apr
Sanjit Roopra
Marbach D, Schaffter T, Mattiussi C, Floreano D. Generating realistic in silico gene networks for performance assessment of reverse engineering methods. J Comput Biol. 2009 Feb;16(2):229-39.
25 Mar
Thomas Schmitt
Clauset A, Moore C, Newman ME. Hierarchical structure and the prediction of missing links in networks. Nature. 2008 May 1;453(7191):98-101.
4 Mar
Kristoffer Forslund
Sven Nelander, Weiqing Wang, Björn Nilsson, Qing-Bai She, Christine Pratilas, Neal Rosen, Peter Gennemark & Chris Sander. Models from experiments: combinatorial drug perturbations of cancer cells. Molecular Systems Biology 4:216 (2008).
18 Feb
Oliver Frings
Hwang W, Cho YR, Zhang A, Ramanathan M. A novel functional module detection algorithm for protein-protein interaction networks. Algorithms Mol Biol. 2006 Dec 5;1:24.
4 Feb
Andrey Alexeyenko
Yu H, Braun P, Yildirim MA, Lemmens I, Venkatesan K, Sahalie J, Hirozane-Kishikawa T, Gebreab F, Li N, Simonis N, Hao T, Rual JF, Dricot A, Vazquez A, Murray RR, Simon C, Tardivo L, Tam S, Svrzikapa N, Fan C, de Smet AS, Motyl A, Hudson ME, Park J, Xin X,. High-quality binary protein interaction map of the yeast interactome network. Science. 2008 Oct 3;322(5898):104-10.
2008
17 Dec
Dave Messina
Wu M, Eisen JA. A simple, fast, and accurate method of phylogenomic inference. Genome Biol. 2008 Oct 13;9(10):R151.
4 Dec
Gabriel Östlund
Zhu J, Zhang B, Smith EN, Drees B, Brem RB, Kruglyak L, Bumgarner RE, Schadt EE. Integrating large-scale functional genomic data to dissect the complexity of yeast regulatory networks. Nat Genet. 2008 Jul;40(7):854-61.
20 Nov
Patrik Björkholm
Sun FJ, Caetano-Anollés G, Evolutionary patterns in the sequence and structure of transfer RNA: early origins of archaea and viruses, PLoS Comput Biol. 2008 Mar 7;4(3):e1000018
5 Nov
Erik Sonnhammer
Pujana MA, Han JD, Starita LM, Stevens KN, Tewari M, Ahn JS, Rennert G, Moreno V, Kirchhoff T, Gold B, Assmann V, Elshamy WM, Rual JF, Levine D, Rozek LS, Gelman RS, Gunsalus KC, Greenberg RA, Sobhian B, Bertin N, Venkatesan K, Ayivi-Guedehoussou N, Solé X, Hernández P, Lázaro C, Nathanson KL, Weber BL, Cusick ME, Hill DE, Offit K, Livingston DM, Gruber SB, Parvin JD, Vidal M. Network modeling links breast cancer susceptibility and centrosome dysfunction, Nat Genet. 2007 Nov;39(11):1338-49. Epub 2007 Oct 7
22 Oct
Andrey Alexeyenko
Ergün A, Lawrence CA, Kohanski MA, Brennan TA, Collins JJ. A network biology approach to prostate cancer. Mol Syst Biol. 2007;3:82. Epub 2007 Feb 13.
8 Oct
Kristoffer Forslund
Fröhlich H, Fellmann M, Sültmann H, Poustka A, Beissbarth T. Predicting pathway membership via domain signatures. Bioinformatics. 2008 Oct 1;24(19):2137-42.
24 Sep
Oliver Frings
Katoh K, Toh H. Improved accuracy of multiple ncRNA alignment by incorporating structural information into a MAFFT-based framework. BMC Bioinformatics. 2008 Apr 25;9:212.
23 Apr
Gabriel Östlund
Xu M, Kao MC, Nunez-Iglesias J, Nevins JR, West M, Zhou XJ. An integrative approach to characterize disease-specific pathways and their coordination: a case study in cancer. BMC Genomics. 2008;9 Suppl 1:S12.
2 Apr
Kristoffer Forslund
Tetko IV, Rodchenkov IV, Walter MC, Rattei T, Mewes HW. Beyond the 'best' match: machine learning annotation of protein sequences by integration of different sources of information. Bioinformatics. 2008 Mar 1;24(5):621-8. Epub 2008 Jan 3.
12 Mar
Dave Messina
Bushell KM, Söllner C, Schuster-Boeckler B, Bateman A, Wright GJ. Large-scale screening for novel low-affinity extracellular protein interactions. Genome Res. 2008 Feb 22;
27 Feb
Thomas Schmitt
Lu ZJ, Mathews DH. Efficient siRNA selection using hybridization thermodynamics. Nucleic Acids Res. 2008 Feb;36(2):640-7. Epub 2007 Dec 10.
13 Feb
Erik Sonnhammer
Lee I, Lehner B, Crombie C, Wong W, Fraser AG, Marcotte EM. A single gene network accurately predicts phenotypic effects of gene perturbation in Caenorhabditis elegans. Nat Genet. 2008 Feb;40(2):181-8. Epub 2008 Jan 27.
30 Jan
Andrey Alexeyenko
Rokhlenko O, Shlomi T, Sharan R, Ruppin E, Pinter RY. Constraint-based functional similarity of metabolic genes: going beyond network topology. Bioinformatics. 2007 Aug 15;23(16):2139-46. Epub 2007 Jun 22.
2007
19 Dec
Kristoffer Forslund
Yi G, Sze SH, Thon MR. Identifying clusters of functionally related genes in genomes. Bioinformatics. 2007 May 1;23(9):1053-60.
5 Dec
Cristina Al-Khalili Szigyarto
Josefine Sprenger, J. Lynn Fink, Seetha Karunaratne, Kelly Hanson, Nicholas A. Hamilton and Rohan D. Teasdale LOCATE: a mammalian protein subcellular localization database (2007) Nucleic Acids Research 1-4.
28 Nov
Gabriel Östlund
Jensen LJ, Julien P, Kuhn M, von Mering C, Muller J, Doerks T, Bork P. eggNOG: automated construction and annotation of orthologous groups of genes. Nucleic Acids Res. 2007 Oct 16.
7 Nov
Anna Henricson
Carmel L, Wolf YI, Rogozin IB, Koonin EV. Three distinct modes of intron dynamics in the evolution of eukaryotes. Genome Res. 2007 Jul;17(7):1034-44. Epub 2007 May 10.
24 Oct
Andrey Alexeyenko
Yildirim
MA, Goh KI, Cusick ME, Barabasi AL, Vidal M. Drug-target
network. Nat Biotechnol. 2007 Oct;25(10):1119-1126.
10 Oct
Dave Messina
Wapinski I, Pfeffer A, Friedman N, Regev A. Natural history and evolutionary principles of gene duplication in fungi. Nature. 2007 Sep 6;449(7158):54-61.
26 Sep
Vincent Devloo
Kwang-Il Goh, Michael E. Cusick, David Valle, Barton Childs, Marc Vidal,and Albert-László Barabási The human disease network PNAS, May 22, 2007, 104:21 8685-8690.
12 Sep
Erik Sonnhammer
Chen F, Mackey AJ, Vermunt JK, Roos DS. Assessing performance of orthology detection strategies applied to eukaryotic genomes. PLoS ONE. 2007 Apr 18;2:e383.
20 Jun
Kristoffer Forslund
Komurov K, White M. Revealing static and dynamic modular architecture of the eukaryotic protein interaction network. Mol Syst Biol. 2007;3:110. Epub 2007 Apr 24.
6 Jun Sveriges nationaldag
23 May
Cristina Al-Khalili Szigyarto
Saeys Y, Rouze P, Van de Peer Y. In search of the small ones: improved prediction of short exons in vertebrates, plants, fungi and protists. Bioinformatics. 2007 Feb 15;23(4):414-20. Epub 2007 Jan 4.
9 May
Olof Karlberg
Schlicker A, Huthmacher C, Ramirez F, Lengauer T, and Albrecht M Functional evaluation of domain-domain interactions and human protein interaction networks, Bioinformatics 23(7):859, 2007.
25 Apr
Linn Fagerberg
Krissinel E. On the relationship between sequence and structure similarities in proteomics. Bioinformatics, 2007, Mar 15; 23(6):717-723.
11 Apr
Mats Lindskog
Futschik ME, Chaurasia G, Herzel H. Comparison of human protein-protein interaction maps, Bioinformatics, 2007, Mar 1;23(5): 605-11
Påsk, Easter, IIacxa
14 Mar
Lisa Berglund
Sasson, O., Kaplan, N. and Linial, M. Functional annotation prediction: All for one and one for all. Protein Sci. 2006 15:1557-1562
28 Feb
Gabriel Östlund
Roger A Craig and Li Liao. Phylogenetic tree information aids supervised learning for predicting protein-protein interaction based on distance matrices. BMC Bioinformatics 2007, 8:6
14 Feb
Anna Henricson
Bashton M and Chothia C. The generation of new protein functions by the combination of domains. Structure 2007 Jan; 15(1):85-99.
31 Jan
Andrey Alexeyenko
Ceulemans H, Beke L, Bollen M. Approaches to defining the ancestral eukaryotic protein complexome. Bioessays. 2006 Mar;28(3):316-24.
2006
18 Dec
Tomten
Xia K., Dong D., Han J. IntNetDB v1.0: an integrated protein-protein interaction network database generated by a probabilistic model BMC Bioinformatics, 2006 7:508 (18 November 2006).
13 Dec
Kristoffer Forslund
Richard A. George, Jason Y. Liu, Lina L. Feng, Robert J. Bryson-Richardson, Diane Fatkin and Merridee A. Wouters Analysis of protein sequence and interaction data for candidate disease gene prediction. Nucleic Acids Research. 2006 34(19)
22 Nov
Cristina Al-Khalili Szigyarto
Milanesi L, Petrillo M, Sepe L, Boccia A, D'Agostino N, Passamano M, Di Nardo S, Tasco G, Casadio R, Paolella G. Systematic analysis of human kinase genes: a large number of genes and alternative splicing events result in functional and structural diversity. BMC Bioinformatics. 2005 Dec 1;6 Suppl 4:S20.
8 Nov
Olof Karlberg
Mika S, Rost B. Protein-protein interactions more conserved within species than across species. PLoS Comput Biol. 2006 Jul 21;2(7):e79. Epub 2006 M
18 Oct
Mats Lindskog
Jonsson PF, Bates PA. Global topological features of cancer proteins in the human interactome. Bioinformatics. 2006 Sep 15;22(18):2291-7. Epub 2006 Jul 14
4 Oct
Erik Sonnhammer
Rhodes DR, Tomlins SA, Varambally S, Mahavisno V, Barrette T, Kalyana-Sundaram S, Ghosh D, Pandey A, Chinnaiyan AM. (2005) Probabilistic model of the human protein-protein interaction network. Nat Biotechnol. Aug;23(8):951-9.
6 Sep
Lisa Berglund
Myhre, S., Tveit, H., Mollestad, T. and Laegreid, A. (2006). Additional Gene Ontology structure for improved biological reasoning. Bioinformatics. 22:2020-2027
10 May
Thomas Ohlson
Qi
Y, Bar-Joseph Z, Klein-Seetharaman J. Evaluation of different
biological data and computational classification methods for use
in protein interaction prediction.
Proteins. 2006 May
15;63(3):490-500.
4 May
Abhiman Saraswahti
Aerts S, Lambrechts D, Maity S, Van Loo P, Coessens B, De Smet F, Tranchevent LC, De Moor B, Marynen P, Hassan B, Carmeliet P, Moreau Y. Gene prioritization through genomic data fusion. Nat Biotechnol. 2006 May;24(5):537-544.
26 Apr
Timo Lassmann
Ciccarelli FD, Doerks T, von Mering C, Creevey CJ, Snel B, Bork P. Toward automatic reconstruction of a highly resolved tree of life. Science. 2006 Mar 3;311(5765):1283-7.
12 Apr
Påsk, Easter, IIacxa
29 Mar
Julia Lindberg
Bandyopadhyay S, Sharan R, Ideker T. Systematic identification of functional orthologs based on protein network comparison. Genome Res. 2006 Mar;16(3):428-35.
15 Mar
Jinghong Wan
Sato S, Tomomori-Sato C, Parmely TJ, Florens L, Zybailov B, Swanson SK, Banks CA, Jin J, Cai Y, Washburn MP, Conaway JW, Conaway RC. A set of consensus mammalian mediator subunits identified by multidimensional protein identification technology. Mol Cell. 2004 Jun 4;14(5):685-91.
1 Mar
Åsa Pérez-Bercoff
Li H, Coghlan A, Ruan J, Coin LJ, Heriche JK, Osmotherly L, Li R, Liu T, Zhang Z, Bolund L, Wong GK, Zheng W, Dehal P, Wang J, Durbin R. TreeFam: a curated database of phylogenetic trees of animal gene families. Nucleic Acids Res. 2006 Jan 1;34(Database issue):D572-80.
15 Feb
Cristina Al-Khalili Szigyarto
Hoglund A, Donnes P, Blum T, Adolph HW, Kohlbacher O. MultiLoc: prediction of protein subcellular localization using N-terminal targeting sequences, sequence motifs, and amino acid composition. Bioinformatics. 2006 Jan 20; [Epub ahead of print]
1 Feb
Andrey Alexeyenko
Antonov AV, Tetko IV, Mewes HW. A systematic approach to infer biological relevance and biases of gene network structures. Nucleic Acids Res. 2006 Jan 10;34(1):e6.
2005
8 Dec
Lukas Käll
Kahsay RY, Gao G, Liao L. An improved hidden Markov model for transmembrane protein detection and topology prediction and its applications to complete genomes. Bioinformatics. 2005 May 1;21(9):1853-8. Epub 2005 Feb 2.
24 Nov
Erik Sonnhammer
R.Riley, C.Lee, C.Sabatti and D.Eisenberg Inferring protein domain interactions from databases of interacting proteins Genome Biology 2005, 6:R89
10 Nov
Abhiman Saraswahti
Lu LJ et al Assessing the limits of genomic data integration for predicting protein networks
27 Oct
Carsten Daub
Ihmels J. et al Comparative Gene Expression Analysis by a Differential Clustering Approach: Application to the Candida albicans Transcription Program.
3 June
Andrey Alexeyenko
Tirosh I et al. Computational verification of protein-protein interactions by orthologous co-expression BMC Bioinformatics. 2005 Mar 2;6(1):40.
12 May
Anna Henriksson
Sverdlov AV et al. Conservation versus parallel gains in intron evolution Nucleic Acids Res. 2005 Mar 23;33(6):1741-8.
5 May
Kristi himmelsfärdsdag (no journal club)
21 April
Timo Lassmann
Qian et al. Detecting distant homologs using phylogenetic tree-based HMMs Proteins: Structure, Function, and Genetics. July 2003, Volume 52, Issue 3 , Pages 446 - 453
31 March
Markus Wistrand
Coin et al. Improved techniques for the identification of pseudogenes Bioinformatics. 2004 Aug 4;20 Suppl 1:I94-I100
10 March
Lukas Käll
Jordan IK et al. A universal trend of amino acid gain and loss in protein evolution Nature 433, 633 - 638 (10 February 2005)
24 Feb
Carsten Daub
Gat-Viks I, Sharan R, Shamir R. Scoring clustering solutions by their biological relevance. Bioinformatics. 2003 Dec 12;19(18):2381-9
10 Feb
Abhiman Saraswathi
Ovcharenko I et al. Evolution and functional classification of vertebrate gene deserts. Genome Res. 2005 Jan;15(1):137-45. Epub 2004 Dec 08
27 Jan
Erik Sonnhammer
von Mering et al. STRING: known and predicted protein-protein associations, integrated and transferred across organisms. Nucleic Acids Research 2005 33(Database issue):D433-D437
13 Jan
Volker Hollich
Söding J. Protein homology detection by HMM-HMM comparison. Bioinformatics Advance Access published online on November 5, 2004
2004
16 Dec
Timo Lassmann
Protein ranking: from local to global structure in the protein similarity network. Proc Natl Acad Sci U S A. 2004 Apr 27;101(17):6559-63.
2 Dec
Andrey Alexeyenko
King AD. et al. Protein complex prediction via cost-based clustering. Bioinformatics. 2004 Nov 22;20(17):3013-20.
18 Nov
Timo Lassmann
8 Nov
Markus Wistrand
Coin L. et al. Enhanced protein domain discovery using taxonomy. BMC Bioinformatics. 2004, May 11;5(1):56.
25 Oct
Lukas Käll
Bendtsen JD. et al. Improved prediction of signal peptides: SignalP 3.0. J Mol Biol. 2004 Jul 16;340(4):783-95.
7 Oct
Abhiman Saraswathi
Jordan IK. et al. Co-Evolution in the Scale-Free Human Gene Coexpression Network. Mol Biol Evol. 2004 Jul 28
23 Sept . Obs at 14.00
Carsten Daub
Snel B. et al. Gene co-regulation is highly conserved in the evolution of eukaryotes and prokaryotes NAR,2004 32(16):4725-4731
9 Sept
Erik Sonnhammer
Sandberg R. et al. Quantifying the species-specificity in genomic signatures, synonymous codon choice, amino acid usage and G+C content. Gene. 2003 Jun 5;311:35-42.
13 May
Andrey Alexeyenko
Grigoryev D.N. et al. Orthologous gene-expression profiling in multi-species models: search for candidate genes Genome Biology 2004, 5:R34
29 April
Timo Lassmann
Koonin E et al. A comprehensive evolutionary classification of proteins encoded in complete eukaryotic genomes. Genome Biology, Jan, 2004
15 April
Markus Wistrand
Liu Y et al. Genomic analysis of membrane protein families: abundance and conserved motifs. Genome Biology 3(10), 2002
31 March
Lukas Käll
Kuhlman B. et al. Design of a novel globular protein fold with atomic-level accuracy. Science, Nov. 2003.
17 March
Abhiman Saraswathi
Torrents D. et al. A genome-wide survey of human pseudogenes. Genome Research 13:2559-2567, 2003.
3 March
Kevin O'Brien
18 Feb
Andrey Alexeyenko
Kim WK. et al. Large-scale co-evolution analysis of protein structural interlogues using the global protein structural interactome map (PSIMAP).
4 Feb
Erik Sonnhammer
Kuo et al. Analysis of matched mRNA measurements from two different microarray technologies.
21 Jan
Volker Hollich
Otu HH et al. A new sequence distance measure for phylogenetic tree construction.
2003
10 Dec
Rajani Vangali
Fraser HB et al. A simple dependence between protein evolution rate and the number of protein-protein interactions
26 Nov
Timo Lassmann
12 Nov
Markus Wistrand
Jansen R. et al. A Bayesian networks approach for predicting protein-protein interactions from genomic data.
29 Oct
Lukas Käll
Krylow et al. Gene Loss, Protein Sequence Divergence, Expression Level, and Interactivity Are Correlated in Eukaryotic Evolution