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alexg's library [264 articles]

Recent papers added to alexg's library ordered by importance.
  • Global metabolic changes following loss of a feedback loop reveal dynamic steady states of the yeast metabolome.
    Metab Eng, Vol. 9, No. 1. (30 June 2006), pp. 8-20.
    by Peng Lu, Anupama Rangan, Sherwin YY Chan, Dean RR Appling, David WW Hoffman, Edward MM Marcotte
    posted to allostery regulation by alexg on 2007-08-09 06:35:01 as ***** along with 1 person dbikard
  • Systems biology, metabolic modelling and metabolomics in drug discovery and development
    Drug Discovery Today, Vol. 11, No. 23-24. (December 2006), pp. 1085-1092.
    by Douglas B Kell
    posted to metabolism systems_biology by alexg on 2007-08-06 06:27:02 as ***** along with 8 people and 2 groups alanrw shikin irenas nicklynch dullhunk mhucka raiyar fishtank GeneGo steinmetzlab
  • Underground metabolism
    BioEssays, Vol. 20, No. 2. (1998), pp. 181-186.
    by Richard D'Ari, Josep Casadesús
    posted to metabolism by alexg on 2007-08-06 06:20:02 as *****
  • 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), 121.
    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
    posted to flux_balance_analysis systems_biology by alexg on 2007-07-31 07:08:42 as ***** along with 4 people JeremyZucker michaelbarton hryk cjeans
  • Life and reference.
    Biosystems, Vol. 60, No. 1-3. (y 2001), pp. 123-130.
    by J Hoffmeyer
    posted to biosemiotics by alexg on 2007-07-30 08:58:37 as *****
  • Protein interactions from complexes: a structural perspective.
    Comp Funct Genomics (2007)
    by L Hakes, DL Robertson, SG Oliver, SC Lovell
    posted to networks ppi protein_structure by alexg on 2007-07-30 07:33:04 as *****
  • Repression of the human dihydrofolate reductase gene by a non-coding interfering transcript
    Nature (21 January 2007)
    by Igor Martianov, Aroul Ramadass, Ana S Barros, Natalie Chow, Alexandre Akoulitchev
    posted to metabolism ncrna by alexg on 2007-07-30 06:52:18 as ***** along with 1 person and 2 groups dchughes G4ID Genetics-of-Gambling
  • From genomes to in silico cells via metabolic networks.
    Curr Opin Biotechnol, Vol. 16, No. 3. (June 2005), pp. 350-355.
    by I Borodina, J Nielsen
    posted to metabolism systems_biology by alexg on 2007-07-30 06:47:35 as ***** along with 1 person Ema
  • Comparative Analysis of Structured RNAs in S. cerevisiae Indicates a Multitude of Different Functions
    BMC Biology, Vol. 5 (18 June 2007), 25.
    by Stephan Steigele, Wolfgang Huber, Claudia Stocsits, Peter F Stadler, Kay Nieselt
    posted to ncrna yeast by alexg on 2007-07-30 06:22:20 as ***** along with 2 people and 2 groups dpollard andersbj EisenLab microRNA
  • The expanding universe of noncoding RNAs.
    Cold Spring Harb Symp Quant Biol, Vol. 71 (2006), pp. 551-564.
    by GJ Hannon, FV Rivas, EP Murchison, JA Steitz
    posted to ncrna review by alexg on 2007-07-30 05:44:12 as ***** along with 1 person and 1 group andersbj microRNA
  • Noncoding RNAs and Gene Silencing
    Cell, Vol. 128, No. 4. (23 February 2007), pp. 763-776.
    by Mikel Zaratiegui, Danielle V Irvine, Robert A Martienssen
    posted to ncrna by alexg on 2007-07-30 05:43:25 as ***** along with 4 people and 2 groups jyuh dchughes sebastien_vigneau N0131826 G4ID Genetics-of-Gambling
  • A noncoding RNA in Saccharomyces cerevisiae is an RNase P substrate.
    RNA, Vol. 13, No. 5. (May 2007), pp. 682-690.
    by L Yang, S Altman
    posted to ncrna yeast by alexg on 2007-07-30 05:42:47 as ***** along with 1 person zwang
  • Functionality or transcriptional noise? Evidence for selection within long noncoding RNAs
    Genome Res., Vol. 17, No. 5. (1 May 2007), pp. 556-565.
    by Jasmina Ponjavic, Chris P Ponting, Gerton Lunter
    posted to evolution ncrna by alexg on 2007-07-30 05:42:14 as ***** along with 5 people and 4 groups aprasad dchughes djkt Stew elfar Bioinformatics EisenLab G4ID Genetics-of-Gambling
  • Genomics: The amazing complexity of the human transcriptome
    European Journal of Human Genetics, Vol. aop, No. current.
    by Martin C Frith, Michael Pheasant, John S Mattick, John S Mattick
    posted to ncrna by alexg on 2007-07-30 05:37:01 as ***** along with 1 person cassj
  • Accelerating, hyperaccelerating, and decelerating networks.
    Phys Rev E Stat Nonlin Soft Matter Phys, Vol. 72, No. 1 Pt 2. (July 2005)
    by MJ Gagen, JS Mattick
    posted to networks by alexg on 2007-07-30 05:36:29 as *****
  • The Functional Genomics of Noncoding RNA
    Science, Vol. 309, No. 5740. (02 September 2005), pp. 1527-1528.
    by John S Mattick
    posted to ncrna by alexg on 2007-07-30 05:35:51 as ***** along with 10 people and 8 groups biozhang2001 lyongu marcius eckart_bindewald dchughes mtagaya cmm neveaire bsmagic jayster4 Biostatistics Computational-Genomics Bioinformatics Neuroscience FAB-lab BioinfoCIPF bioinplant SGU-CIPF
  • Rapid evolution of noncoding RNAs: lack of conservation does not mean lack of function
    Trends in Genetics, Vol. 22, No. 1. (January 2006), pp. 1-5.
    by Ken C Pang, Martin C Frith, John S Mattick
    posted to evolution ncrna by alexg on 2007-07-30 05:35:10 as ***** along with 6 people and 5 groups cassj marcius eckart_bindewald andersbj dchughes mtagaya microRNA G4ID BioinfoCIPF SGU-CIPF Genetics-of-Gambling
  • Experimental validation of the regulated expression of large numbers of non-coding RNAs from the mouse genome.
    Genome Res, Vol. 16, No. 1. (January 2006), pp. 11-19.
    by T Ravasi, H Suzuki, KC Pang, S Katayama, M Furuno, R Okunishi, S Fukuda, K Ru, MC Frith, MM Gongora, SM Grimmond, DA Hume, Y Hayashizaki, JS Mattick
    posted to ncrna by alexg on 2007-07-30 05:34:43 as ***** along with 2 people mtagaya raylim
  • RNA: Networks & Imaging.
    Mol Syst Biol, Vol. 2 (2006)
    by M Kenzelmann, K Rippe, JS Mattick
    posted to ncrna networks by alexg on 2007-07-30 05:34:10 as *****
  • The relationship between non-protein-coding DNA and eukaryotic complexity
    BioEssays, Vol. 29, No. 3. (2007), pp. 288-299.
    by Ryan J Taft, Michael Pheasant, John S Mattick
    posted to ncrna by alexg on 2007-07-30 05:32:24 as ***** along with 4 people and 2 groups aprasad dchughes cas heliopais G4ID Genetics-of-Gambling
  • A new paradigm for developmental biology.
    J Exp Biol, Vol. 210, No. Pt 9. (May 2007), pp. 1526-1547.
    by JS Mattick
    posted to development by alexg on 2007-07-30 05:31:39 as ***** along with 3 people braingrind dullhunk BioNica
  • Noncoding RNAs and RNA Editing in Brain Development, Functional Diversification, and Neurological Disease.
    Physiol Rev, Vol. 87, No. 3. (July 2007), pp. 799-823.
    by MF Mehler, JS Mattick
    posted to development ncrna by alexg on 2007-07-30 05:30:49 as ***** along with 2 people and 2 groups dchughes cas G4ID Genetics-of-Gambling
  • Evaluation of predicted network modules in yeast metabolism using NMR-based metabolite profiling.
    Genome Res, Vol. 17, No. 4. (April 2007), pp. 510-519.
    by JG Bundy, B Papp, R Harmston, RA Browne, EM Clayson, N Burton, RJ Reece, SG Oliver, KM Brindle
    posted to metabolism nmr systems_biology by alexg on 2007-07-30 05:25:38 as ***** along with 1 person and 1 group raiyar steinmetzlab
  • Metabolic footprinting and systems biology: the medium is the message
    Nature Reviews Microbiology, Vol. 3, No. 7. (01 July 2005), pp. 557-565.
    by Douglas B Kell, Marie Brown, Hazel M Davey, Warwick B Dunn, Irena Spasic, Stephen G Oliver
    posted to metabolism systems_biology by alexg on 2007-07-30 05:20:18 as ***** along with 4 people and 1 group bayesian irenas andytseng Borelli dbk-lab
  • From genomes to systems: the path with yeast.
    Philos Trans R Soc Lond B Biol Sci, Vol. 361, No. 1467. (29 March 2006), pp. 477-482.
    by SG Oliver
    posted to review systems_biology by alexg on 2007-07-30 05:19:08 as ***** along with 1 person dullhunk
  • Growth control of the eukaryote cell: a systems biology study in yeast
    Journal of Biology, Vol. 6 (30 April 2007), 4.
    by Juan I Castrillo, Leo A Zeef, David C Hoyle, Nianshu Zhang, Andrew Hayes, David CJ Gardner, Michael J Cornell, June Petty, Luke Hakes, Leanne Wardleworth, Bharat Rash, Marie Brown, Warwick B Dunn, David Broadhurst, Kerry O'Donoghue, Svenja S Hester, Tom PJ Dunkley, Sarah R Hart, Neil Swainston, Peter Li, Simon J Gaskell, Norman W Paton, Kathryn S Lilley, Douglas B Kell, Stephen G Oliver
    posted to systems_biology by alexg on 2007-07-30 05:16:34 as ***** along with 8 people and 1 group alanrw aalibes dullhunk balabu dylan77 cabbagezs Stew roys EisenLab
  • How enzymes work: analysis by modern rate theory and computer simulations.
    Science, Vol. 303, No. 5655. (9 January 2004), pp. 186-195.
    by M Garcia-Viloca, J Gao, M Karplus, DG Truhlar
    posted to catalysis enzyme by alexg on 2006-01-05 02:12:42 as ***** along with 3 people BragilMassoud baaden tny
  • Qualitative modelling of regulated metabolic pathways: application to the tryptophan biosynthesis in E.Coli.
    Bioinformatics, Vol. 21, No. Suppl 2. (1 September 2005), pp. 190-196.
    by E Simão, E Remy, D Thieffry, C Chaouiya
    posted to metabolism net_paper networks pathways by alexg on 2005-12-07 02:14:54 as *****
  • A systems biology perspective on protein structural dynamics and signal transduction.
    Curr Opin Struct Biol, Vol. 15, No. 1. (February 2005), pp. 23-30.
    by F Rousseau, J Schymkowitz
    posted to allostery protein_structure systems_biology by alexg on 2005-11-28 09:48:47 as ***** along with 6 people lna eweaver dgront choonpeng ruvido jlh64
  • Transition state stabilization by general acid catalysis, water expulsion, and enzyme reorganization in Medicago savita chalcone isomerase.
    Proc Natl Acad Sci U S A, Vol. 101, No. 9. (2 March 2004), pp. 2730-2735.
    by S Hur, ZE Newby, TC Bruice
    posted to catalysis enzyme protein_structure by alexg on 2005-11-01 17:18:30 as *****
  • Control theory of regulatory cascades.
    J Theor Biol, Vol. 153, No. 2. (21 November 1991), pp. 255-285.
    by D Kahn, HV Westerhoff
    posted to metabolism by alexg on 2007-09-14 03:20:32 as ****
  • Systems biology. Tracing life's circuitry.
    Science, Vol. 302, No. 5651. (5 December 2003), pp. 1646-1649.
    by E Pennisi
    posted to systems_biology by alexg on 2007-08-31 05:05:47 as **** along with 1 person wnpx
  • Bow ties, metabolism and disease
    Trends in Biotechnology, Vol. 22, No. 9. (September 2004), pp. 446-450.
    by Marie Csete, John Doyle
    posted to metabolism systems_biology by alexg on 2007-08-24 06:10:59 as **** along with 1 person and 2 groups rhem1224 TCR_Signaling SysbioMPI-TCells
  • An excitable gene regulatory circuit induces transient cellular differentiation
    Nature, Vol. 440, No. 7083., pp. 545-550.
    by Gã¼rol M Sã¼el, Jordi Garcia-Ojalvo, Louisa M Liberman, Michael B Elowitz
    posted to synthetic_biology by alexg on 2007-08-23 07:19:20 as **** along with 10 people and 1 group jjray rklancer madhadron balabu nickluscombe comb dbikard mhucka margaritis paurue EBI-regulation
  • A synthetic gene–metabolic oscillator
    Nature, Vol. 435, No. 7038., pp. 118-122.
    by Eileen Fung, Wilson W Wong, Jason K Suen, Thomas Bulter, Sun-Gu Lee, James C Liao
    posted to synthetic_biology by alexg on 2007-08-23 07:19:09 as **** along with 4 people rklancer bayesian balabu johncumbers
  • Modular approaches to expanding the functions of living matter
    Nat Chem Biol, Vol. 2, No. 6. (June 2006), pp. 304-311.
    by Jason W Chin
    posted to synthetic_biology by alexg on 2007-08-23 07:09:49 as ****
  • Integration of metabolome data with metabolic networks reveals reporter reactions.
    Mol Syst Biol, Vol. 2 (2006)
    by T Cakir, KR Patil, Z Onsan, KO Ulgen, B Kirdar, J Nielsen
    posted to metabolism systems_biology by alexg on 2007-08-15 09:08:12 as ****
  • Uncovering transcriptional regulation of metabolism by using metabolic network topology.
    Proc Natl Acad Sci U S A, Vol. 102, No. 8. (22 February 2005), pp. 2685-2689.
    by KR Patil, J Nielsen
    posted to metabolism systems_biology by alexg on 2007-08-15 09:07:09 as **** along with 1 person and 1 group raiyar steinmetzlab
  • Current Progress in computational metabolomics.
    Brief Bioinform (11 July 2007)
    by David S S Wishart
    posted to metabolism systems_biology by alexg on 2007-08-06 06:24:46 as **** along with 1 person and 1 group jyuh Bioinformatics
  • Intergenic transcription is required to repress the Saccharomyces cerevisiae SER3 gene.
    Nature, Vol. 429, No. 6991. (3 June 2004), pp. 571-574.
    by JA Martens, L Laprade, F Winston
    posted to ncrna yeast by alexg on 2007-07-30 09:13:02 as **** along with 2 people and 1 group dpollard maralena EisenLab
  • A high-resolution map of transcription in the yeast genome
    PNAS, Vol. 103, No. 14. (4 April 2006), pp. 5320-5325.
    by Lior David, Wolfgang Huber, Marina Granovskaia, Joern Toedling, Curtis J Palm, Lee Bofkin, Ted Jones, Ronald W Davis, Lars M Steinmetz
    posted to ncrna transcription yeast by alexg on 2007-07-30 06:27:53 as **** along with 7 people and 2 groups chasmand tuck eckart_bindewald dpollard entropy raiyar xingxu EisenLab steinmetzlab
  • Global identification of noncoding RNAs in Saccharomyces cerevisiae by modulating an essential RNA processing pathway.
    Proc Natl Acad Sci U S A, Vol. 103, No. 11. (14 March 2006), pp. 4192-4197.
    by MP Samanta, W Tongprasit, H Sethi, CS Chin, V Stolc
    posted to ncrna yeast by alexg on 2007-07-30 06:26:32 as **** along with 1 person eckart_bindewald
  • Detection of non-coding RNAs on the basis of predicted secondary structure formation free energy change.
    BMC Bioinformatics, Vol. 7, No. 1. (27 March 2006)
    by Andrew V Uzilov, Joshua M Keegan, David H Mathews
    posted to ncrna by alexg on 2007-07-30 06:26:05 as **** along with 2 people and 2 groups marcius eckart_bindewald BioinfoCIPF SGU-CIPF
  • RNA Maps Reveal New RNA Classes and a Possible Function for Pervasive Transcription
    Science (17 May 2007), 1138341.
    by Philipp Kapranov, Jill Cheng, Sujit Dike, David A Nix, Radharani Duttagupta, Aarron T Willingham, Peter F Stadler, Jana Hertel, Joerg Hackermueller, Ivo L Hofacker, Ian Bell, Evelyn Cheung, Jorg Drenkow, Erica Dumais, Sandeep Patel, Gregg Helt, Madhavan Ganesh, Srinka Ghosh, Antonio Piccolboni, Victor Sementchenko, Hari Tammana, Thomas R Gingeras
    posted to ncrna by alexg on 2007-07-30 05:43:43 as **** along with 11 people and 4 groups xingxu marcius dpollard xico mtagaya rdiaz djkt stajich mathijsv asddd elfar EisenLab WetBiology BioinfoCIPF SGU-CIPF
  • RNAdb 2.0--an expanded database of mammalian non-coding RNAs.
    Nucleic Acids Res (1 December 2006)
    by Ken C C Pang, Stuart Stephen, Marcel E E Dinger, Pär G G Engström, Boris Lenhard, John S S Mattick
    posted to ncrna by alexg on 2007-07-30 05:33:22 as **** along with 4 people and 1 group jfr balajis andersbj mtagaya microRNA
  • Quantitative prediction of cellular metabolism with constraint-based models: the COBRA Toolbox.
    Nat Protoc, Vol. 2, No. 3. (2007), pp. 727-738.
    by SA Becker, AM Feist, ML Mo, G Hannum, BØ Palsson, MJ Herrgard
    posted to flux_balance_analysis metabolism by alexg on 2007-04-24 07:47:56 as **** along with 2 people jyuh edwardmorrissey
  • Robustness in simple biochemical networks.
    Nature, Vol. 387 (1997), pp. 913-917.
    by N Barkal, S Leibler
    posted to networks by alexg on 2006-04-13 06:18:02 as ****
  • Comparative assessment of large-scale data sets of protein-protein interactions.
    Nature, Vol. 417, No. 6887. (23 May 2002), pp. 399-403.
    by C von Mering, R Krause, B Snel, M Cornell, SG Oliver, S Fields, P Bork
    posted to networks by alexg on 2006-01-24 02:01:41 as **** along with 19 people and 6 groups carlk camster barry dragonrez bicko lfriedl chad_davis j3xucite bundschu yeastyboy ruvido raiyar grahamc iris_2001 cmor shu Evangelia shikin Pao-Yang dbk-lab structural_bioinformatics kdl Bioinformatics generif_paper GeneGo
  • Theory for the systemic definition of metabolic pathways and their use in interpreting metabolic function from a pathway-oriented perspective.
    J Theor Biol, Vol. 203, No. 3. (7 April 2000), pp. 229-248.
    by CH Schilling, D Letscher, BO Palsson
    posted to metabolism pathways by alexg on 2005-10-24 14:32:23 as ****
  • Fragnostic: walking through protein structure space.
    Nucleic Acids Res, Vol. 33, No. Web Server issue. (1 July 2005)
    by I Friedberg, A Godzik
    posted to protein_structure by alexg on 2005-10-24 11:11:19 as **** along with 7 people and 4 groups ana barry pansapiens aalibes Einat marcius eweaver structural_bioinformatics Bioinformatics BioinfoCIPF SGU-CIPF
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