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Systems Biology Papers

Selected Scientific Papers on Systems Biology

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Author(s) Title Journal Year Volume Pages Links Free Article Subscription Required Times Cited (Google Scholar) Date of Analysis Comments
Kandel ER, Dudai Y, Mayford MR. The molecular and systems biology of memory. Cell. 2014 157(1) 163-86 PUBMED JOURNAL + 232 15/08/2017
Ghosh S, Matsuoka Y, Asai Y, Hsin KY, Kitano H. Software for systems biology: From tools to integrated platforms. Nat Rev Genet. 2011 12(12) 821-32 PUBMED JOURNAL + 189 15/08/2017
Loscalzo J, Barabasi AL. Systems biology and the future of medicine. Wiley Interdiscip Rev Syst Biol Med. 2011 3(6) 619-27 PUBMED JOURNAL + 143 15/08/2017
Chuang HY, Hofree M, Ideker T. A decade of systems biology. Annu Rev Cell Dev Biol. 2010 26 721-44 PUBMED JOURNAL + 210 15/08/2017
Gehlenborg N, O‘Donoghue SI, Baliga NS, Goesmann A, Hibbs MA, Kitano H, Kohlbacher O, Neuweger H, Schneider R, Tenenbaum D, Gavin AC. Visualization of omics data for systems biology. Nat Methods. 2010 7(3 Suppl.) S56-68 PUBMED JOURNAL + 443 15/08/2017
Huang da W, Sherman BT, Lempicki RA. Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources. Nat Protoc. 2009 4(1) 44-57 PUBMED JOURNAL PDF 7641 15/08/2017
Wang Z, Gerstein M, Snyder M. RNA-Seq: A revolutionary tool for transcriptomics. Nat Rev Genet. 2009 10(1) 57-63 PUBMED JOURNAL + 6709 16/08/2017
Goh KI, Cusick ME, Valle D, Childs B, Vidal M, BarabÃsi AL. The human disease network. Proc Natl Acad Sci U S A. 2007 104(21) 8685-90 PUBMED JOURNAL PDF 2225 16/08/2017
Boccaletti S, Latora V, Moreno Y, Chavez M, Hwang DU. Complex networks: Structure and dynamics. Physics Reports. 2006 424(4-5) 175-308 JOURNAL + 7503 16/08/2017
Krogan NJ, Cagney G, Yu H, Zhong G, Guo X, Ignatchenko A, Li J, Pu S, Datta N, Tikuisis AP, Punna T, PeregrÃn-Alvarez JM, Shales M, Zhang X, Davey M, Robinson MD, Paccanaro A, Bray JE, Sheung A, Beattie B, Richards DP, Canadien V, Lalev A, Mena F, Wong P, Starostine A, Canete MM, Vlasblom J, Wu S, Orsi C, Collins SR, Chandran S, Haw R, Rilstone JJ, Gandi K, Thompson NJ, Musso G, St Onge P, Ghanny S, Lam MH, Butland G, Altaf-Ul AM, Kanaya S, Shilatifard A, O‘Shea E, Weissman JS, Ingles CJ, Hughes TR, Parkinson J, Gerstein M, Wodak SJ, Emili A, Greenblatt JF. Global landscape of protein complexes in the yeast Saccharomyces cerevisiae. Nature. 2006 440(7084) 637-43 PUBMED JOURNAL PDF 2570 16/08/2017
Stelzl U, Worm U, Lalowski M, Haenig C, Brembeck FH, Goehler H, Stroedicke M, Zenkner M, Schoenherr A, Koeppen S, Timm J, Mintzlaff S, Abraham C, Bock N, Kietzmann S, Goedde A, ToksÃz E, Droege A, Krobitsch S, Korn B, Birchmeier W, Lehrach H, Wanker EE. A human protein-protein interaction network: A resource for annotating the proteome. Cell. 2005 122(6) 957-68 PUBMED JOURNAL PDF 2020 16/08/2017
Subramanian A, Tamayo P, Mootha VK, Mukherjee S, Ebert BL, Gillette MA,
Paulovich A, Pomeroy SL, Golub TR, Lander ES, Mesirov JP.
Gene set enrichment
analysis: a knowledge-based approach for interpreting genome-wide expression
profiles.
Proc Natl Acad Sci U S A. 2005 102(43) 15545-50 PUBMED JOURNAL + 12063 16/08/2017
Blagoev B, Ong SE, Kratchmarova I, Mann M. Temporal analysis of phosphotyrosine-dependent signaling networks by quantitative proteomics. Nat Biotechnol. 2004 22(9) 1139-45 PUBMED JOURNAL + 717 16/08/2017
Dujon B, Sherman D, Fischer G, Durrens P, Casaregola S, Lafontaine I, De Montigny J, Marck C, Neuvéglise C, Talla E, Goffard N, Frangeul L, Aigle M, Anthouard V, Babour A, Barbe V, Barnay S, Blanchin S, Beckerich JM, Beyne E, Bleykasten C, Boisramé A, Boyer J, Cattolico L, Confanioleri F, De Daruvar A, Despons L, Fabre E, Fairhead C, Ferry-Dumazet H, Groppi A, Hantraye F, Hennequin C, Jauniaux N, Joyet P, Kachouri R, Kerrest A, Koszul R, Lemaire M, Lesur I, Ma L, Muller H, Nicaud JM, Nikolski M, Oztas S, Ozier-Kalogeropoulos O, Pellenz S, Potier S, Richard GF, Straub ML, Suleau A, Swennen D, Tekaia F, Wésolowski-Louvel M, Westhof E, Wirth B, Zeniou-Meyer M, Zivanovic I, Bolotin-Fukuhara M, Thierry A, Bouchier C, Caudron B, Scarpelli C, Gaillardin C, Weissenbach J, Wincker P, Souciet JL. Genome evolution in yeasts. Nature 2004 430(6995) 35-44 PUBMED JOURNAL + 1357 16/08/2017
Hood L, Heath JR, Phelps ME, Lin B. Systems biology and new technologies enable predictive and preventative medicine. Science. 2004 306(5696) 640-3 PUBMED JOURNAL + 1068 16/08/2017
Aebersold R, Mann M. Mass spectrometry-based proteomics. Nature. 2003 422(6928) 198-207 PUBMED JOURNAL + 6673 16/08/2017
Giot L, Bader JS, Brouwer C, Chaudhuri A, Kuang B, Li Y, Hao YL, Ooi CE, Godwin B, Vitols E, Vijayadamodar G, Pochart P, Machineni H, Welsh M, Kong Y, Zerhusen B, Malcolm R, Varrone Z, Collis A, Minto M, Burgess S, McDaniel L, Stimpson E, Spriggs F, Williams J, Neurath K, Ioime N, Agee M, Voss E, Furtak K, Renzulli R, Aanensen N, Carrolla S, Bickelhaupt E, Lazovatsky Y, DaSilva A, Zhong J, Stanyon CA, Finley RL Jr, White KP, Braverman M, Jarvie T, Gold S, Leach M, Knight J, Shimkets RA, McKenna MP, Chant J, Rothberg JM. A protein interaction map of Drosophila melanogaster. Science. 2003 302(5651) 1727-36 PUBMED JOURNAL + 2411 16/08/2017
Hucka M, Finney A, Sauro HM, Bolouri H, Doyle JC, Kitano H, Arkin AP, Bornstein BJ, Bray D, Cornish-Bowden A, Cuellar AA, Dronov S, Gilles ED, Ginkel M, Gor V, Goryanin II, Hedley WJ, Hodgman TC, Hofmeyr JH, Hunter PJ, Juty NS, Kasberger JL, Kremling A, Kummer U, Le NovÃre N, Loew LM, Lucio D, Mendes P, Minch E, Mjolsness ED, Nakayama Y, Nelson MR, Nielsen PF, Sakurada T, Schaff JC, Shapiro BE, Shimizu TS, Spence HD, Stelling J, Takahashi K, Tomita M, Wagner J, Wang J; SBML Forum. The systems biology markup language (SBML): A medium for representation and exchange of biochemical network models. Bioinformatics. 2003 19(4) 524-31 PUBMED JOURNAL PDF 2720 16/08/2017
Newman MEJ The structure and function of complex networks. SIAM Rev. 2003 45 167-256 JOURNAL PDF 16204 16/08/2017
Shannon P, Markiel A, Ozier O, Baliga NS, Wang JT, Ramage D, Amin N,
Schwikowski B, Ideker T.
Cytoscape: a software environment for integrated models of biomolecular interaction networks. Genome Res. 2003 13(11) 2498-2504 PUBMED JOURNAL + 8979 16/08/2017
Kitano H. Computational systems biology. Nature. 2002 420(6912) 206-10 PUBMED JOURNAL + 2137 16/08/2017
Kitano H. Systems biology: A brief overview. Science. 2002 295(5560) 1662-4 PUBMED JOURNAL + 3958 16/08/2017
Stelling J, Klamt S, Bettenbrock K, Schuster S, Gilles ED. Metabolic network structure determines key aspects of functionality and regulation. Nature. 2002 420(6912) 190-3 PUBMED JOURNAL + 803 16/08/2017
Ideker T, Galitski T, Hood L A new approach to decoding life: Systems biology. Annu Rev Genomics Hum Genet. 2001 2 343-72 PUBMED JOURNAL PDF 1725 16/08/2017
Jeong H, Tombor B, Albert R, Oltvai ZN, Barabasi AL. The large scale organization of metabolic networks. Nature. 2000 407(6804) 651-4 PUBMED JOURNAL PDF 5003 16/08/2017
Barabasi AL, Albert R. Emergence of scaling in random networks. Science 1999 286(5439) 509-12

PUBMED JOURNAL

+ 29014 16/08/2017
Tavazoie S, Hughes JD, Campbell MJ, Cho RJ, Church GM. Systematic determination of genetic network architecture. Nat Genet. 1999 22(3) 281-5 PUBMED JOURNAL + 2710 16/08/2017
Watts DJ, Strogatz SH. Collective dynamics of ‘small-world‘ networks. Nature. 1998 393(6684) 440-42 PUBMED JOURNAL + 33670 16/08/2017