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balicea's systems-biology [93 articles]

Recent papers added to balicea's library classified by the tag systems-biology. You can also see everyone's systems-biology.
  • A network-based method for target selection in metabolic networks
    Bioinformatics, Vol. 23, No. 13. (1 July 2007), pp. 1616-1622.
    by R Guimera, M Sales-Pardo, LAN Amaral
    posted to systems-biology networks metabolomics by balicea on 2008-07-25 16:21:28 as ** along with 2 people jiny AbnerCYH
  • Uncertainty, Neuromodulation, and Attention
    Neuron, Vol. 46, No. 4. (19 May 2005), pp. 681-692.
    by Angela J Yu, Peter Dayan
    posted to systems-biology neuro-computation neuro-coding neuro-chem control-theory attention by balicea on 2008-07-20 02:50:21 as ** along with 7 people and 1 group nishiokov fbaroni oamg jmc rchava sbarthelme awooga Glimcher_Lab
  • A Global View of Gene Activity and Alternative Splicing by Deep Sequencing of the Human Transcriptome
    Science (3 July 2008), 1160342.
    by Marc Sultan, Marcel H Schulz, Hugues Richard, Alon Magen, Andreas Klingenhoff, Matthias Scherf, Martin Seifert, Tatjana Borodina, Aleksey Soldatov, Dmitri Parkhomchuk, Dominic Schmidt, Sean O'Keeffe, Stefan Haas, Martin Vingron, Hans Lehrach, Marie-Laure Yaspo
    posted to systems-biology genome-variation genome-transcriptome genome-splicings genome-sequencing gene-expression by balicea on 2008-07-12 05:49:09 as ** along with 7 people Ema kjglennie GeeSharpMinor dh0000 caseybrown reyez oelemento
  • Optimization in computational systems biology
    BMC Systems Biology, Vol. 2, No. 1. (2008)
    by Julio Banga
    posted to systems-biology modeling-and-simulation informatics by balicea on 2008-06-30 02:09:50 as ** along with 5 people phoenixzxl biehl reyez jrbanga tmmurali
  • An in Vivo Map of the Yeast Protein Interactome
    Science, Vol. 320, No. 5882. (13 June 2008), pp. 1465-1470.
    by Kirill Tarassov, Vincent Messier, Christian R Landry, Stevo Radinovic, Mercedes M Molina, Igor Shames, Yelena Malitskaya, Jackie Vogel, Howard Bussey, Stephen W Michnick
    posted to systems-biology informatics genome-interactome evolutionary-proteomics animal-model by balicea on 2008-06-27 05:09:07 as ** along with 3 people zwang renatomilani Petersarkies
  • Predicting Movement from Multiunit Activity
    J. Neurosci., Vol. 27, No. 31. (1 August 2007), pp. 8387-8394.
    by Eran Stark, Moshe Abeles
    posted to systems-biology neuro-spike neuro-computation neuro-coding musculoskeletal_systems movement-science machine-learning brain-machine-interface by balicea on 2008-06-19 17:04:39 as ** along with 1 person erk
  • EagleView: a genome assembly viewer for next-generation sequencing technologies.
    Genome research (11 June 2008)
    by Weichun Huang, Gabor T T Marth
    posted to systems-biology informatics genome-sequencing functional-genome evo-tech by balicea on 2008-06-19 17:00:25 as ** along with 5 people GustavoLacerda Neeperando APRegier fpattyn bcondon
  • The immune system, adaptation, and machine learning
    Phys. D, Vol. 2, No. 1-3. (1986), pp. 187-204.
    by JD Farmer, NH Packard, AS Perelson
    posted to systems-biology machine-learning immunity general-physiology functional-genome ecophysiology diseaseomics adaptive-systems by balicea on 2008-06-19 16:31:05 as ** along with 1 person tomhebbron
  • The biological principles of swarm intelligence
    Swarm Intelligence, Vol. 1, No. 1. (18 June 2007), pp. 3-31.
    by Simon Garnier, Jacques Gautrais, Guy Theraulaz
    posted to time-dynamics systems-biology modeling-and-simulation informatics cultural-evolution complexity applied-math animal-model alife adaptive-systems by balicea on 2008-06-16 04:07:11 as ** along with 4 people and 1 group nojhan sviscido cwr SimonGarnier Social Aggregation
  • Disease Gene Explorer: Display Disease Gene Dependency by Combining Bayesian Networks with Clustering
    (2004), pp. 574-575.
    by Qian Diao, We Hu, Hao Zhong, Juntao Li, Feng Xue, Tao Wang, Yimin Zhang
    posted to systems-biology informatics genome-structure evolutionary-genomics diseaseomics bio-stat applied-math by balicea on 2008-06-16 03:29:47 as ** along with 1 person and 2 groups mattjb DSTO-CAS ComplexAdaptiveSystems
  • Predicting failure rate of PCR in large genomes
    Nucl. Acids Res. (20 May 2008), gkn290.
    by Reidar Andreson, Tonu Mols, Maido Remm
    posted to systems-biology methods informatics genome-sequencing genome-prediction functional-genome by balicea on 2008-06-15 04:36:47 as ** along with 3 people jyuh niallhaslam wisdom_love
  • 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
    posted to systems-biology switching-examples robustness genotype-to-phenotype animal-model by balicea on 2008-06-13 19:27:23 as ** along with 4 people kentsis lingchong mhucka cjeans
  • Microarrays--planning your experiment.
    Methods in molecular medicine, Vol. 141 (2008), pp. 71-85.
    by JY Yang
    posted to systems-biology reviews microarray methods gene-expression by balicea on 2008-06-13 16:43:47 as ** along with 1 person jfr
  • The effects of running and of inhibiting adult neurogenesis on learning and memory in rats
    European Journal of Neuroscience, Vol. 27, No. 6. (March 2008), pp. 1494-1502.
    by Wojtowicz, J Martin, Askew, L Michele, Winocur, Gordon
    posted to systems-biology physiological-remodeling neuroplasticity exercise ecophysiology cell-models brain-anatomy animal-model adaptive-systems by balicea on 2008-06-10 19:54:06 as ** along with 1 person sen_cheng
  • Dynamics of neuronal firing correlation: modulation of "effective connectivity"
    J Neurophysiol, Vol. 61, No. 5. (1 May 1989), pp. 900-917.
    by AM Aertsen, GL Gerstein, MK Habib, G Palm
    posted to systems-biology neuro-spike neuro-connectivity networks cog-neuro brain-anatomy by balicea on 2008-06-10 19:29:19 as *** along with 2 people sam1001 dcoates
  • SNPbox: web-based high-throughput primer design from gene to genome.
    Nucleic Acids Res, Vol. 32, No. Web Server issue. (1 July 2004)
    by S Weckx, P De Rijk, C Van Broeckhoven, J Del-Favero
    posted to systems-biology informatics genome-variation by balicea on 2008-06-06 03:37:30 as ** along with 2 people sebastien_vigneau jyuh
  • NeAT: a toolbox for the analysis of biological networks, clusters, classes and pathways
    Nucl. Acids Res. (4 June 2008), gkn336.
    by Sylvain Brohee, Karoline Faust, Gipsi Lima-Mendez, Olivier Sand, Rekin's Janky, Gilles Vanderstocken, Yves Deville, Jacques van Helden
    posted to systems-biology networks informatics by balicea on 2008-06-05 05:30:48 as ** along with 2 people brianb neils
  • Can a biologist fix a radio?--Or, what I learned while studying apoptosis.
    Cancer Cell, Vol. 2, No. 3. (September 2002), pp. 179-182.
    by Y Lazebnik
    posted to systems-biology reviews cell-models by balicea on 2008-06-03 03:19:53 as ** along with 15 people and 6 groups bayesian leilaperie Tominator dbikard mattjb tvdbulck quianominorleo rklancer dbk irenas manduca monod chihchun_chen massivemayhem gisle SynBioSys Centre de Recherches Interdisciplinaires DSTO-CAS ComplexAdaptiveSystems streptomyces dbk-lab
  • Long-term evolution of transposable elements
    Proceedings of the National Academy of Sciences (26 November 2007), 0705238104.
    by Arnaud Le Rouzic, Thibaud S Boutin, Pierre Capy
    posted to systems-biology genome-transposon functional-genome evolutionary-genomics evolution by balicea on 2008-06-02 17:44:15 as ** along with 5 people smbe2008 operon sebastien_vigneau saru hpaces
  • Estimating the size of the human interactome
    Proceedings of the National Academy of Sciences (12 May 2008), 0708078105.
    by Michael P Stumpf, Thomas Thorne, Eric de Silva, Ronald Stewart, Hyeong J An, Michael Lappe, Carsten Wiuf
    posted to systems-biology informatics genome-interactome gene-gene bio-stat applied-math by balicea on 2008-06-01 06:55:29 as *** along with 19 people dragonrez chad_davis Evangelia marck paolomarcatili sanchezbuelna cabbagesofdoom xingxu mjoach jyuh chrissp100 zwang roys brianb friendpine Ema neils tmmurali phoenixzxl
  • Response delays and the structure of transcription networks.
    J Mol Biol, Vol. 329, No. 4. (13 June 2003), pp. 645-654.
    by N Rosenfeld, U Alon
    posted to systems-biology networks graph-theory gene-gene by balicea on 2008-05-28 19:19:14 as *** along with 1 person madhadron
  • Cross-species microarray hybridizations: a developing tool for studying species diversity
    Trends in Genetics, Vol. 23, No. 4. (April 2007), pp. 200-207.
    by Carmiya Bar-Or, Henryk Czosnek, Hinanit Koltai
    posted to systems-biology reviews evo-tech comparative-neuro animal-model by balicea on 2008-05-07 16:13:54 as **** along with 4 people ptrobajo jyuh dchughes TaqSys
  • 'Deep phenotyping': characterizing populations in the era of genomics and systems biology.
    Current opinion in lipidology, Vol. 19, No. 2. (April 2008), pp. 151-157.
    by RP Tracy
    posted to systems-biology reviews genotype-to-phenotype genome-variation genome-interactome by balicea on 2008-05-06 16:58:39 as *** along with 1 person jyuh
  • Structure and function of the feed-forward loop network motif.
    Proc Natl Acad Sci U S A, Vol. 100, No. 21. (14 October 2003), pp. 11980-11985.
    by S Mangan, U Alon
    posted to adaptive-systems biological-inspired-modeling control-theory networks regulatory-cascades robustness systems-biology by balicea on 2008-02-18 02:37:22 as *** along with 12 people and 3 groups hannahrajasingh marck camster rklancer korakot zqshen jstajic jjray alexg ddahlem jtaylor gcalda Philosophy_of_Information dbk-lab Blog_and_Wiki_Research
  • The Human Connectome: A Structural Description of the Human Brain
    PLoS Computational Biology, Vol. 1, No. 4. (1 September 2005), e42.
    by Olaf Sporns, Giulio Tononi, Rolf Kötter
    posted to brain-anatomy general-physiology genome-interactome informatics neuro-connectivity neuro-tech systems-biology by balicea on 2008-01-25 05:43:26 as *** along with 5 people and 1 group jotwin bandrewfox dolhuis josepe suizan SNE
  • Emergence is coupled to scope, not level
    Complexity, Vol. 13, No. 2. (2007), pp. 67-77.
    by Alex J Ryan
    posted to adaptive-systems applied-math complexity reviews systems-biology by balicea on 2008-01-22 19:48:02 as *** along with 2 people and 2 groups mattjb livingthingdan ComplexAdaptiveSystems DSTO-CAS
  • High-confidence prediction of global interactomes based on genome-wide coevolutionary networks
    Proceedings of the National Academy of Sciences (16 January 2008), 0709671105.
    by David Juan, Florencio Pazos, Alfonso Valencia
    posted to coevolution evolutionary-genomics genome-interactome informatics networks systems-biology whole-genomic by balicea on 2008-01-22 19:41:32 as *** along with 12 people and 1 group paolomarcatili tmmurali brant sebastien_vigneau bluto cjeans aconesa Katje roys friendpine huali mdstobbe microbiology_nijmegen
  • Survivin, cancer networks and pathway-directed drug discovery
    Nature Reviews Cancer, Vol. 8, No. 1., pp. 61-70.
    by Dario C Altieri
    posted to diseaseomics molecular-signaling networks regulatory-cascades systems-biology by balicea on 2008-01-22 17:08:19 as *** along with 4 people jyuh cjeans jdiezperezj renatomilani
  • Extensive low-affinity transcriptional interactions in the yeast genome.
    Genome Res (29 June 2006)
    by Amos Tanay
    posted to animal-model evo-computation evolutionary-proteomics gene-expression gene-gene genome-association genome-sequencing genome-structure genome-variation genotype-to-phenotype informatics systems-biology by balicea on 2008-01-22 00:21:45 as *** along with 6 people and 1 group devin indigoviolet dpollard koller lusk emptyhb EisenLab
  • Vienna RNA secondary structure server.
    Nucleic Acids Res, Vol. 31, No. 13. (1 July 2003), pp. 3429-3431.
    by IL Hofacker
    posted to evolutionary-proteomics informatics machine-learning systems-biology by balicea on 2008-01-22 00:15:05 as *** along with 10 people reyez evaf dayjm eckart_bindewald arcticrasta mtagaya dquest ilh onufriev maralena
  • Combining docking, scoring and molecular field analyses to probe influenza neuraminidase-ligand interactions.
    J Mol Graph Model, Vol. 26, No. 2. (September 2007), pp. 443-456.
    by AM Abu Hammad, FU Afifi, MO Taha
    posted to biological-mechanics cell-models diseaseomics evolutionary-proteomics gene-gene informatics modeling-and-simulation systems-biology by balicea on 2008-01-21 20:01:52 as *** along with 1 person apostola
  • Practical Strategies for Discovering Regulatory DNA Sequence Motifs
    PLoS Computational Biology, Vol. 2, No. 4. (1 April 2006), e36.
    by Kenzie D Macisaac, Ernest Fraenkel
    posted to evolutionary-genomics genome-sequencing genome-structure genome-variation genotype-to-phenotype growth-regulation homeotic-theory informatics systems-biology by balicea on 2008-01-21 19:51:16 as *** along with 6 people and 2 groups kristallreiner ana chad_davis hggr GustavoLacerda svdate structural_bioinformatics Bioinformatics
  • The Many Roles of Computation in Drug Discovery
    Science, Vol. 303, No. 5665. (19 March 2004), pp. 1813-1818.
    by William L Jorgensen
    posted to diseaseomics informatics methods modeling-and-simulation reviews systems-biology by balicea on 2008-01-21 03:57:54 as *** along with 8 people dgruiz kuhn blackbart ramensky euan junehlee onufriev ashaytan
  • An integrative genomics approach to the reconstruction of gene networks in segregating populations.
    Cytogenet Genome Res, Vol. 105, No. 2-4. (2004), pp. 363-374.
    by J Zhu, PY Lum, J Lamb, D GuhaThakurta, SW Edwards, R Thieringer, JP Berger, MS Wu, J Thompson, AB Sachs, EE Schadt
    posted to genome-association genome-structure genotype-to-phenotype heredity networks systems-biology by balicea on 2008-01-20 23:03:59 as *** along with 3 people maryee brant jo_davies
  • Integrated approaches to uncovering transcription regulatory networks in mammalian cells.
    Genomics (7 January 2008)
    by Kai Tan, Jesper Tegner, Timothy Ravasi
    posted to animal-model gene-expression gene-gene genotype-to-phenotype graph-theory networks systems-biology by balicea on 2008-01-18 03:54:40 as *** along with 3 people brant jyuh lp2
  • On the relation between promoter divergence and gene expression evolution
    Mol Syst Biol, Vol. 4 (15 January 2008)
    by Itay Tirosh, Adina Weinberger, Dana Bezalel, Mark Kaganovich, Naama Barkai
    posted to evolution evolutionary-genomics gene-expression systems-biology by balicea on 2008-01-16 17:36:17 as *** along with 8 people and 2 groups Jporci kengg zwang biomcgary cisevol caseybrown renatomilani mclarenv cis-regulatory-evolution BergmanLab
  • Global survey of organ and organelle protein expression in mouse: combined proteomic and transcriptomic profiling.
    Cell, Vol. 125, No. 1. (7 April 2006), pp. 173-186.
    by T Kislinger, B Cox, A Kannan, C Chung, P Hu, A Ignatchenko, MS Scott, AO Gramolini, Q Morris, MT Hallett, J Rossant, TR Hughes, B Frey, A Emili
    posted to animal-model evolutionary-proteomics evo-tech gene-expression informatics systems-biology by balicea on 2008-01-14 19:13:25 as *** along with 1 person kristen
  • AGEMAP: A Gene Expression Database for Aging in Mice
    PLoS Genetics, Vol. 3, No. 11. (1 November 2007), e201.
    by Jacob M Zahn, Suresh Poosala, Art B Owen, Donald K Ingram, Ana Lustig, Arnell Carter, Ashani T Weeraratna, Dennis D Taub, Myriam Gorospe, Krystyna Mazan-Mamczarz, Edward G Lakatta, Kenneth R Boheler, Xiangru Xu, Mark P Mattson, Geppino Falco, Minoru S Ko, David Schlessinger, Jeffrey Firman, Sarah K Kummerfeld, William H Wood, Alan B Zonderman, Stuart K Kim, Kevin G Becker
    posted to animal-model development gene-expression informatics systems-biology by balicea on 2008-01-14 19:12:05 as *** along with 3 people tmmurali johncumbers kristen
  • STITCH: interaction networks of chemicals and proteins.
    Nucleic Acids Res (15 December 2007)
    by Michael Kuhn, Christian von Mering, Monica Campillos, Lars Juhl J Jensen, Peer Bork
    posted to evolutionary-proteomics informatics networks systems-biology by balicea on 2008-01-13 20:10:34 as *** along with 6 people and 1 group higueruelo jyuh massivemayhem bootsy sobolevnrm larsjuhljensen baker-group
  • A more complete, complexed and structured interactome.
    Curr Opin Struct Biol (14 June 2007)
    by Damien Devos, Robert B B Russell
    posted to complexity evolutionary-genomics evolutionary-proteomics gene-gene genome-structure genotype-to-phenotype networks systems-biology by balicea on 2008-01-13 19:36:36 as *** along with 4 people chad_davis skhadar choonpeng ruvido
  • Shaping the future of interactome networks
    Genome Biology, Vol. 8 (01 November 2007), 316.
    by Patrick Aloy
    posted to evolution evolutionary-genomics evolutionary-proteomics gene-gene genotype-to-phenotype molecular-signaling networks regulatory-cascades systems-biology by balicea on 2008-01-13 19:34:35 as *** along with 1 person ruvido
  • A forest-based approach to identifying gene and gene gene interactions
    Proceedings of the National Academy of Sciences (28 November 2007), 0709868104.
    by Xiang Chen, Ching-Ti Liu, Meizhuo Zhang, Heping Zhang
    posted to gene-gene genome-structure informatics systems-biology by balicea on 2008-01-11 19:14:18 as *** along with 5 people jyuh cjeans zwang xingxu hpaces
  • A highly sensitive and specific system for large-scale gene expression profiling
    BMC Genomics, Vol. 9, No. 1. (2008)
    by Guohong Hu, Qifeng Yang, Xiangfeng Cui, Gang Yue, Marco Azaro, Hui Y Wang, Honghua Li
    posted to evolutionary-genomics gene-expression general-physiology genome-variation informatics modeling-and-simulation systems-biology whole-genomic by balicea on 2008-01-11 04:56:04 as *** along with 2 people jyuh GeeSharpMinor
  • DAISY: a new software tool to test global identifiability of biological and physiological systems.
    Comput Methods Programs Biomed, Vol. 88, No. 1. (October 2007), pp. 52-61.
    by G Bellu, MP Saccomani, S Audoly, L D'Angiò
    posted to general-physiology informatics reviews systems-biology by balicea on 2008-01-11 04:54:10 as *** along with 1 person jyuh
  • Computational approaches to identify promoters and cis-regulatory elements in plant genomes.
    Plant Physiol, Vol. 132, No. 3. (July 2003), pp. 1162-1176.
    by S Rombauts, K Florquin, M Lescot, K Marchal, P Rouzé, Y van de Peer
    posted to evo-computation gene-expression genome-structure homeotic-theory informatics regulatory-cascades systems-biology by balicea on 2008-01-10 04:39:30 as *** along with 2 people saru xili03
  • RNA-mediated epigenetic programming of a genome-rearrangement pathway
    Nature (28 November 2007)
    by Mariusz Nowacki, Vikram Vijayan, Yi Zhou, Klaas Schotanus, Thomas G Doak, Laura F Landweber
    posted to epigenetics evo-computation molecular-signaling regulatory-cascades rna systems-biology by balicea on 2008-01-10 04:36:46 as *** along with 6 people mtagaya sebastien_vigneau margaritis zwang rebeccamancy rschulz
  • Transcriptional regulatory code of a eukaryotic genome
    Nature, Vol. 431, No. 7004. (2004), pp. 99-104.
    by Christopher T Harbison, Benjamin D Gordon, Tong I Lee, Nicola J Rinaldi, Kenzie D Macisaac, Timothy W Danford, Nancy M Hannett, Jean-Bosco Tagne, David B Reynolds, Jane Yoo, Ezra G Jennings, Julia Zeitlinger, Dmitry K Pokholok, Manolis Kellis, Alex P Rolfe, Ken T Takusagawa, Eric S Lander, David K Gifford, Ernest Fraenkel, Richard A Young
    posted to evo-computation evo-devo evolutionary-genomics gene-expression genome-structure regulatory-cascades systems-biology whole-genomic by balicea on 2008-01-10 04:31:42 as *** along with 22 people and 8 groups kristallreiner mariakmejia brant alokm tuck chad_davis lyongu kaspermunch dpollard kt dchughes nirfriedman cmm nickluscombe kengg gespim koller lusk nklee cisevol njcitulike xili03 Bioinformatics EisenLab FAB-lab G4ID EBI-regulation Plantandetc Genetics-of-Gambling BergmanLab
  • Engineering and applications of genetic circuits.
    Mol Biosyst, Vol. 3, No. 12. (December 2007), pp. 835-840.
    by DJ Sayut, PK Kambam, L Sun
    posted to control-theory evo-computation evolution systems-biology by balicea on 2008-01-10 04:27:26 as *** along with 1 person austin
  • Protein-protein interaction networks and biology—what's the connection?
    Nature Biotechnology, Vol. 26, No. 1., pp. 69-72.
    by Luke Hakes, John W Pinney, David L Robertson, Simon C Lovell
    posted to evolutionary-proteomics gene-gene networks systems-biology by balicea on 2008-01-09 18:40:15 as *** along with 14 people and 1 group paolomarcatili Yanno jyuh tmmurali jfr dullhunk neils mikaelhuss cjeans nedwards biehl shikin mclarenv Yumyai GeneGo
  • Interactions between calcium release pathways: multiple messengers and multiple stores
    Cell Calcium, Vol. 32, No. 5-6. ( 2002), pp. 343-354.
    by A Galione, GC Churchill
    posted to control-theory evolvability molecular-signaling networks regulatory-cascades systems-biology by balicea on 2008-01-09 18:19:01 as *** along with 1 person CharlesM
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