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Tag system-biology [56 articles]

Recent papers classified by the tag system-biology.
  • Literature mining for the biologist: from information retrieval to biological discovery
    Nature Reviews Genetics, Vol. 7, No. 2. (2006), pp. 119-129.
    by Lars J Jensen, Jasmin Saric, Peer Bork
  • Text mining and its potential applications in systems biology.
    Trends in Biotechnology (11 October 2006)
    by Sophia Ananiadou, Douglas B Kell, Junichi Tsujii
  • Structural systems biology: modelling protein interactions
    Nature Reviews Molecular Cell Biology, Vol. 7, No. 3., pp. 188-197.
    by Patrick Aloy, Robert B Russell
  • Identification of an OCT4 and SRY regulatory module using integrated computational and experimental genomics approaches.
    Genome Res, Vol. 17, No. 6. (June 2007), pp. 807-817.
    by VX Jin, H O'geen, S Iyengar, R Green, PJ Farnham
  • The OBO Foundry: coordinated evolution of ontologies to support biomedical data integration
    Nat Biotech, Vol. 25, No. 11. (November 2007), pp. 1251-1255.
    by Barry Smith, Michael Ashburner, Cornelius Rosse, Jonathan Bard, William Bug, Werner Ceusters, Louis J Goldberg, Karen Eilbeck, Amelia Ireland, Christopher J Mungall, Neocles Leontis, Philippe Rocca-Serra, Alan Ruttenberg, Susanna-Assunta Sansone, Richard H Scheuermann, Nigam Shah, Patricia L Whetzel, Suzanna Lewis
  • The stability and robustness of metabolic states: identifying stabilizing sites in metabolic networks
    Mol Syst Biol, Vol. 3 (13 November 2007)
    by Sergio Grimbs, Joachim Selbig, Sascha Bulik, Hermann-Georg Holzhutter, Ralf Steuer
  • Noise in protein expression scales with natural protein abundance
    Nature Genetics, Vol. 38, No. 6. (21 May 2006), pp. 636-643.
    by Arren Bar-Even, Johan Paulsson, Narendra Maheshri, Miri Carmi, Erin O'Shea, Yitzhak Pilpel, Naama Barkai
  • Genome-wide transcriptional analysis of the human cell cycle identifies genes differentially regulated in normal and cancer cells
    Proceedings of the National Academy of Sciences (14 January 2008), 0704723105.
    by Ziv Bar-Joseph, Zahava Siegfried, Michael Brandeis, Benedikt Brors, Yong Lu, Roland Eils, Brian D Dynlacht, Itamar Simon
  • A map of human cancer signaling
    Mol Syst Biol, Vol. 3 (18 December 2007)
    by Qinghua Cui, Yun Ma, Maria Jaramillo, Hamza Bari, Arif Awan, Song Yang, Simo Zhang, Lixue Liu, Meng Lu, Maureen O'Connor-Mccourt, Enrico O Purisima, Edwin Wang
  • Network modeling links breast cancer susceptibility and centrosome dysfunction.
    Nat Genet (7 October 2007)
    by Miguel Angel A Pujana, Jing-Dong J D Han, Lea M M Starita, Kristen N N Stevens, Muneesh Tewari, Jin Sook S Ahn, Gad Rennert, Víctor Moreno, Tomas Kirchhoff, Bert Gold, Volker Assmann, Wael M M Elshamy, Jean-François F Rual, Douglas Levine, Laura S S Rozek, Rebecca S S Gelman, Kristin C C Gunsalus, Roger A A Greenberg, Bijan Sobhian, Nicolas Bertin, Kavitha Venkatesan, Nono Ayivi-Guedehoussou, Xavier Solé, Pilar Hernández, Conxi Lázaro, Katherine L L Nathanson, Barbara L L Weber, Michael E E Cusick, David E E Hill, Kenneth Offit, David M M Livingston, Stephen B B Gruber, Jeffrey D D Parvin, Marc Vidal
  • Systems metabolic engineering of Escherichia coli for L-threonine production
    Mol Syst Biol, Vol. 3 (4 December 2007)
    by Kwang H Lee, Jin H Park, Tae Y Kim, Hyun U Kim, Sang Y Lee
    posted to metabolic system-biology by cjeans on 2007-12-21 03:13:46 as ** along with 1 person westoll
  • Functional profiling of the Saccharomyces cerevisiae genome.
    Nature, Vol. 418, No. 6896. (25 July 2002), pp. 387-391.
  • Metabolic modeling of a mutualistic microbial community.
    Mol Syst Biol, Vol. 3 (2007)
    by S Stolyar, S Van Dien, KL Hillesland, N Pinel, TJ Lie, JA Leigh, DA Stahl
  • Variability and memory of protein levels in human cells
    Nature (19 November 2006)
    by Alex Sigal, Ron Milo, Ariel Cohen, Naama Geva-Zatorsky, Yael Klein, Yuvalal Liron, Nitzan Rosenfeld, Tamar Danon, Natalie Perzov, Uri Alon
  • Noise in transcription negative feedback loops: simulation and experimental analysis
    Mol Syst Biol, Vol. 2 (2006)
    by Yann Dublanche, Konstantinos Michalodimitrakis, Nico Kummerer, Mathilde Foglierini, Luis Serrano
  • A wiring of the human nucleolus.
    Mol Cell, Vol. 22, No. 2. (21 April 2006), pp. 285-295.
    by AM Hinsby, L Kiemer, EO Karlberg, K Lage, A Fausbøll, AS Juncker, JS Andersen, M Mann, S Brunak
    posted to integrative system-biology by cjeans on 2007-06-27 08:36:45 as **** along with 1 person arrak
  • Contributions of low molecule number and chromosomal positioning to stochastic gene expression
    Nature Genetics, Vol. 37, No. 9. (07 August 2005), pp. 937-944.
    by Attila Becskei, Benjamin B Kaufmann, Alexander van Oudenaarden
    posted to noise system-biology by cjeans on 2007-06-28 04:07:06 as *** along with 2 people rklancer margaritis
  • Co-evolution of transcriptional and post-translational cell-cycle regulation
    Nature (27 September 2006)
    by Lars J Jensen, Thomas S Jensen, Ulrik de Lichtenberg, Søren Brunak, Peer Bork
  • PhosphoPep[mdash]a phosphoproteome resource for systems biology research in Drosophila Kc167 cells
    Mol Syst Biol, Vol. 3 (16 October 2007)
    by Bernd Bodenmiller, Johan Malmstrom, Bertran Gerrits, David Campbell, Henry Lam, Alexander Schmidt, Oliver Rinner, Lukas N Mueller, Paul T Shannon, Patrick G Pedrioli, Christian Panse, Hoo-Keun Lee, Ralph Schlapbach, Ruedi Aebersold
    posted to dataset system-biology by cjeans on 2007-12-21 03:16:12 as ** along with 1 person zwang
  • High-dimensional and large-scale phenotyping of yeast mutants
    PNAS, Vol. 102, No. 52. (27 December 2005), pp. 19015-19020.
    by Yoshikazu Ohya, Jun Sese, Masashi Yukawa, Fumi Sano, Yoichiro Nakatani, Taro L Saito, Ayaka Saka, Tomoyuki Fukuda, Satoru Ishihara, Satomi Oka, Genjiro Suzuki, Machika Watanabe, Aiko Hirata, Miwaka Ohtani, Hiroshi Sawai, Nicolas Fraysse, Jean-Paul Latge, Jean M Francois, Markus Aebi, Seiji Tanaka, Sachiko Muramatsu, Hiroyuki Araki, Kintake Sonoike, Satoru Nogami, Shinichi Morishita
  • ASMPKS: an analysis system for modular polyketide synthases
    BMC Bioinformatics, Vol. 8 (03 September 2007), 327.
    by Hongseok Tae, Eun-Bae Kong, Kiejung Park
    posted to integrative system-biology by cjeans on 2007-11-10 01:53:39 as **
  • A network of multiple regulatory layers shapes gene expression in fission yeast.
    Mol Cell, Vol. 26, No. 1. (13 April 2007), pp. 145-155.
  • A human phenome-interactome network of protein complexes implicated in genetic disorders
    Nature Biotechnology, Vol. 25, No. 3. (07 March 2007), pp. 309-316.
    by Kasper Lage, Olof E Karlberg, Zenia M Størling, Páll, Anders G Pedersen, Olga Rigina, Anders M Hinsby, Zeynep Tümer, Flemming Pociot, Niels Tommerup, Yves Moreau, Søren Brunak
  • Systems biology: Many things from one
    Nature (19 November 2006)
    by John RS Newman, Jonathan S Weissman
    posted to noise system-biology by cjeans on 2007-06-30 08:06:03 as **** along with 2 people manduca totolee
  • Gene expression: Proteins in profile
    Nature Reviews Genetics, Vol. 8, No. 12., pp. 906-907.
    by Tanita Casci
    posted to experiment protein protein-abundance system-biology by cjeans on 2007-12-20 00:32:20 as **
  • Logic of the Yeast Metabolic Cycle: Temporal Compartmentalization of Cellular Processes
    Science, Vol. 310, No. 5751. (18 November 2005), pp. 1152-1158.
    by Benjamin P Tu, Andrzej Kudlicki, Maga Rowicka, Steven L Mcknight
  • Integrated analysis of regulatory and metabolic networks reveals novel regulatory mechanisms in Saccharomyces cerevisiae.
    Genome Res, Vol. 16, No. 5. (May 2006), pp. 627-635.
    by MJ Herrgård, BS Lee, V Portnoy, BØ Palsson
  • Integrated analysis of experimental data sets reveals many novel promoters in 1% of the human genome
    Genome Res., Vol. 17, No. 6. (1 June 2007), pp. 720-731.
    by Nathan D Trinklein, Ulas Karaoz, Jiaqian Wu, Anason Halees, Force, Patrick J Collins, Deyou Zheng, Zhengdong D Zhang, Mark B Gerstein, Michael Snyder, Richard M Myers, Zhiping Weng
  • A genome-scale metabolic reconstruction for Escherichia coli K-12 MG1655 that accounts for 1260 ORFs and thermodynamic information
    Mol Syst Biol, Vol. 3 (26 June 2007)
    by Adam M Feist, Christopher S Henry, Jennifer L Reed, Markus Krummenacker, Andrew R Joyce, Peter D Karp, Linda J Broadbelt, Vassily Hatzimanikatis, Bernhard O Palsson
  • Population level functional diversity in a microbial community revealed by comparative genomic and metagenomic analyses.
    ISME J, Vol. 1, No. 8. (December 2007), pp. 703-713.
    by D Bhaya, AR Grossman, AS Steunou, N Khuri, FM Cohan, N Hamamura, MC Melendrez, MM Bateson, DM Ward, JF Heidelberg
    posted to compare-genomics system-biology by cjeans on 2007-12-20 01:08:27 as ** along with 1 person evodeva
  • A Mass Conserved Reaction–Diffusion System Captures Properties of Cell Polarity
    PLoS Computational Biology, Vol. 3, No. 6. (1 June 2007), e108.
    by Mikiya Otsuji, Shuji Ishihara, Carl Co, Kozo Kaibuchi, Atsushi Mochizuki, Shinya Kuroda
    posted to model system-biology by cjeans on 2007-06-23 04:24:27 as **
  • The molecular sociology of the cell
    Nature, Vol. 450, No. 7172. (12 December 2007), pp. 973-982.
    by Carol V Robinson, Andrej Sali, Wolfgang Baumeister
  • Origins of extrinsic variability in eukaryotic gene expression
    Nature (21 December 2005)
    by Dmitri Volfson, Jennifer Marciniak, William J Blake, Natalie Ostroff, Lev S Tsimring, Jeff Hasty
  • Accurate prediction of gene feedback circuit behavior from component properties
    Mol Syst Biol, Vol. 3 (13 November 2007)
    by Nitzan Rosenfeld, Jonathan W Young, Uri Alon, Peter S Swain, Michael B Elowitz
  • Bacterial persistence as a phenotypic switch.
    Science, Vol. 305, No. 5690. (10 September 2004), pp. 1622-1625.
    by NQ Balaban, J Merrin, R Chait, L Kowalik, S Leibler
  • Single-cell quantification of molecules and rates using open-source microscope-based cytometry
    Nature Methods, Vol. 4, No. 2. (21 January 2007), pp. 175-181.
    by Andrew Gordon, Alejandro Colman-Lerner, Tina E Chin, Kirsten R Benjamin, Richard C Yu, Roger Brent
    posted to noise system-biology by cjeans on 2007-06-28 03:56:53 as ** along with 1 person jtaylor
  • Deriving structure from evolution: metazoan segmentation
    Mol Syst Biol, Vol. 3 (18 December 2007)
    by Paul Francois, Vincent Hakim, Eric D Siggia
  • Network-based classification of breast cancer metastasis
    Mol Syst Biol, Vol. 3 (16 October 2007)
    by Han-Yu Chuang, Eunjung Lee, Yu-Tsueng Liu, Doheon Lee, Trey Ideker
  • Functional characterization of the S. cerevisiae genome by gene deletion and parallel analysis.
    Science, Vol. 285, No. 5429. (6 August 1999), pp. 901-906.
  • Integration of Arabidopsis thaliana stress-related transcript profiles, promoter structures and cell-specific expression
    Genome Biology, Vol. 8 (04 April 2007), R49.
    by Shisong Ma, Hans J Bohnert
    posted to integrative system-biology by cjeans on 2007-06-27 10:29:58 as ***
  • Resources for integrative systems biology: from data through databases to networks and dynamic system models.
    Brief Bioinform, Vol. 7, No. 4. (December 2006), pp. 318-330.
    by A Ng, B Bursteinas, Q Gao, E Mollison, M Zvelebil
    posted to resources system-biology by cjeans on 2007-06-05 04:12:15 as read along with 4 people irenas jfr balajis daed
  • The Pathway Tools cellular overview diagram and Omics Viewer
    Nucl. Acids Res., Vol. 34, No. 13. (7 August 2006), pp. 3771-3778.
    by Suzanne M Paley, Peter D Karp
    posted to pathway software system-biology by cjeans on 2007-12-30 03:36:51 as ** along with 2 people jyuh JeremyZucker
  • Control of Yeast Filamentous-Form Growth by Modules in an Integrated Molecular Network
    Genome Res., Vol. 14, No. 3. (1 March 2004), pp. 380-390.
    by Susanne Prinz, Iliana Avila-Campillo, Christine Aldridge, Ajitha Srinivasan, Krassen Dimitrov, Andrew F Siegel, Timothy Galitski
  • The genetic design of signaling cascades to record receptor activation
    Proceedings of the National Academy of Sciences (28 December 2007), 0710487105.
    by Gilad Barnea, Walter Strapps, Gilles Herrada, Yemiliya Berman, Jane Ong, Brian Kloss, Richard Axel, Kevin J Lee
    posted to design experiment system-biology by cjeans on 2008-01-04 03:07:38 as ** along with 1 person jyuh
  • Modeling the regulatory network of histone acetylation in Saccharomyces cerevisiae
    Mol Syst Biol, Vol. 3 (18 December 2007)
    by Hung Pham, Roberto Ferrari, Shawn J Cokus, Siavash K Kurdistani, Matteo Pellegrini
    posted to network system-biology by cjeans on 2007-12-20 00:37:01 as ** along with 3 people epigenetics Ema maralena
  • The Frequency Dependence of Osmo-Adaptation in Saccharomyces cerevisiae
    Science, Vol. 319, No. 5862. (25 January 2008), pp. 482-484.
    by Jerome T Mettetal, Dale Muzzey, Carlos Gomez-Uribe, Alexander van Oudenaarden
  • Representing, storing and accessing molecular interaction data: a review of models and tools.
    Brief Bioinform, Vol. 7, No. 4. (December 2006), pp. 331-338.
  • Modeling Systems-Level Regulation of Host Immune Responses
    PLoS Computational Biology, Vol. 3, No. 6. (1 June 2007), e109.
    by Juilee Thakar, Mylisa Pilione, Girish Kirimanjeswara, Eric T Harvill, Réka Albert
    posted to model system-biology by cjeans on 2007-06-23 04:23:43 as **
  • Ligand-dependent responses of the ErbB signaling network: experimental and modeling analyses
    Mol Syst Biol, Vol. 3 (13 November 2007)
    by Marc R Birtwistle, Mariko Hatakeyama, Noriko Yumoto, Babatunde A Ogunnaike, Jan B Hoek, Boris N Kholodenko
    posted to network system-biology by cjeans on 2007-12-20 00:55:54 as ** along with 1 person Ema
  • AtPID: Arabidopsis thaliana protein interactome database an integrative platform for plant systems biology.
    Nucleic Acids Res (25 October 2007)
    by Jian Cui, Peng Li, Guang Li, Feng Xu, Chen Zhao, Yuhua Li, Zhongnan Yang, Guang Wang, Qingbo Yu, Yixue Li, Tieliu Shi
    posted to integrative system-biology by cjeans on 2007-11-10 01:54:05 as **
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