roys's biological_networks [39 articles] Export

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	Cross species analysis of microarray expression data [My Copy] Bioinformatics, Vol. 25, No. 12. (15 June 2009), pp. 1476-1483. by Yong Lu, Peter Huggins, Ziv Bar-Joseph posted to species_specific_nw comparative_genomics biological_networks by roys on 2009-10-16 22:39:39 as along with 12 people and 1 group jfr daveGerrard ptrobajo guhjy yaredo shikin dswan renatomilani rdiaz thomaskelder natstreet druvus Bioinformatics
	The Systems Biology Graphical Notation [My Copy] Nature Biotechnology, Vol. 27, No. 8. (07 August 2009), pp. 735-741. by Nicolas L. Novere, Michael Hucka, Huaiyu Mi, et al.Stuart Moodie, Falk Schreiber, Anatoly Sorokin, Emek Demir, Katja Wegner, Mirit I. Aladjem, Sarala M. Wimalaratne, Frank T. Bergman, Ralph Gauges, Peter Ghazal, Hideya Kawaji, Lu Li, Yukiko Matsuoka, Alice Villeger, Sarah E. Boyd, Laurence Calzone, Melanie Courtot, Ugur Dogrusoz, Tom C. Freeman, Akira Funahashi, Samik Ghosh, Akiya Jouraku, Sohyoung Kim, Fedor Kolpakov, Augustin Luna, Sven Sahle, Esther Schmidt, Steven Watterson, Guanming Wu, Igor Goryanin, Douglas B. Kell, Chris Sander, Herbert Sauro, Jacky L. Snoep, Kurt Kohn, Hiroaki Kitano posted to systems_biology network_representation biological_networks by roys on 2009-08-16 17:28:28 as along with 38 people and 3 groups singhsh greg tonamswish pablocarb josepe abc623 daforerog abhishek_tiwari robertrentzsch ngehlenborg pekrau thegoose bertelsen fgibson Borelli thomaskelder pmendes dullhunk polivares chasmand brianb torfinnnome guhjy Zephyrus lenov reyez allysonlister apocapoc renatomilani VGreiff druvus sjcockell jandot megraw leliavski frohike fpattyn jhyang Orengo Group Journal Picks Journal picks Neuroblastoma
	Spontaneous evolution of modularity and network motifs [My Copy] Proceedings of the National Academy of Sciences of the United States of America, Vol. 102, No. 39. (27 September 2005), pp. 13773-13778. by Nadav Kashtan, Uri Alon posted to biological_networks modularity by roys on 2009-08-11 05:36:18 as along with 22 people and 7 groups karthikraman rsantana vtraag anphony ocs saket mcphee marimo monod Borelli alexg i41m cmm Peterfine javierFellow rgb mattjb rebeccamancy cwr phreeza stefanoallesina carlk Modularity in evolutionary algorithms MathBio FAB-lab ComplexAdaptiveSystems pileWorks DSTO-CAS ColDyn
	Co-evolutionary networks of genes and cellular processes across fungal species [My Copy] Genome Biology, Vol. 10, No. 5. (2009), R48. by Tamir Tuller, Martin Kupiec, Eytan Ruppin posted to biological_networks evolution fungi by roys on 2009-06-12 17:59:01 as along with 5 people kiekyon inesdesantiago grahamc dokky michaelbarton
	Inferring cellular networks - a review [My Copy] BMC Bioinformatics, Vol. 8, No. Suppl 6. (2007), S5. by Florian Markowetz, Rainer Spang posted to biological_networks causality gene_expression network_inference by roys on 2009-05-24 18:02:13 as along with 15 people jaspervoskuilen antonkratz daforerog chica ocs cswinburne ndiaz edwardmorrissey guhjy tmmurali shigepong dejori heliopais bertelsen czeller
	Discovery of biological networks from diverse functional genomic data. [My Copy] Genome Biol, Vol. 6, No. 13. (2005) by C. L. Myers, D. Robson, A. Wible, et al.M. A. Hibbs, C. Chiriac, C. L. Theesfeld, K. Dolinski, O. G. Troyanskaya posted to bayesian_networks biological_networks data_integration functional_networks yeast by roys on 2009-04-23 05:02:15 as along with 5 people dragonrez cswinburne grahamc carlk AbnerCYH
	A genomewide functional network for the laboratory mouse. [My Copy] PLoS computational biology, Vol. 4, No. 9. (2008), e1000165. by Y. Guan, C. L. Myers, R. Lu, I. R. Lemischka, C. J. Bult, O. G. Troyanskaya posted to bayesian_networks biological_networks data_integration functional_networks gene_expression_nw mouse by roys on 2009-04-23 04:59:14 as along with 9 people dansullivanblk biomcgary cswinburne zwang pengchy ptrobajo guhjy grahamc tmmurali
	Bridging high-throughput genetic and transcriptional data reveals cellular responses to alpha-synuclein toxicity [My Copy] Nature Genetics, Vol. 41, No. 3. (22 February 2009), pp. 316-323. by Esti Yeger-Lotem, Laura Riva, Linhui J. Su, et al.Aaron D. Gitler, Anil G. Cashikar, Oliver D. King, Pavan K. Auluck, Melissa L. Geddie, Julie S. Valastyan, David R. Karger, Susan Lindquist, Ernest Fraenkel posted to biological_networks causality flow_networks qtl by roys on 2009-03-22 19:45:34 as along with 5 people tmmurali stasaki absterga provero psique
	Benchmarking regulatory network reconstruction with GRENDEL [My Copy] Bioinformatics, Vol. 25, No. 6. (15 March 2009), pp. 801-807. by Brian C. Haynes, Michael R. Brent posted to biological_networks network_inference nwsim regulatory_nw by roys on 2009-03-12 18:44:40 as along with 7 people dolchan tmarscha tonamswish TRHvidsten APRegier rdiaz imina
	Reverse engineering the genotype\|[ndash]\|phenotype map with natural genetic variation [My Copy] Nature, Vol. 456, No. 7223. (10 December 2008), pp. 738-744. by Matthew V. Rockman posted to biological_networks causality by roys on 2009-03-02 02:54:49 as along with 15 people and 1 group gdb carlk Keywan TRHvidsten jfr Zephyrus mjoach sg45653 natstreet druvus sriesenfeld lp2 pkonings stringertheory djkt Roswell Cancer Crosstalk
	Harnessing naturally randomized transcription to infer regulatory relationships among genes [My Copy] Genome Biology, Vol. 8 (11 October 2007), R219. by Lin S. Chen, Frank Emmert-Streib, John D. Storey posted to biological_networks causality tfnets by roys on 2009-03-01 18:28:05 as along with 1 person caseybrown
	Global networks of functional coupling in eukaryotes from comprehensive data integration. [My Copy] Genome research, Vol. 19, No. 6. (25 June 2009), pp. 1107-1116. by Andrey Alexeyenko, Erik L. Sonnhammer posted to biological_networks data_integration by roys on 2009-03-01 18:17:58 as along with 7 people and 1 group phoenixzxl ptrobajo kshameer rdiaz guhjy provero grahamc ParkinsonLab_at_MaRS
	SPINE: a framework for signaling-regulatory pathway inference from cause-effect experiments. [My Copy] Bioinformatics (Oxford, England), Vol. 23, No. 13. (1 July 2007) by Oved Ourfali, Tomer Shlomi, Trey Ideker, Eytan Ruppin, Roded Sharan posted to biological_networks causality signaling_nw by roys on 2009-02-28 19:46:21 as along with 2 people ptrobajo guhjy
	The human disease network [My Copy] Proceedings of the National Academy of Sciences, Vol. 104, No. 21. (22 May 2007), pp. 8685-8690. by Kwang-Il Goh, Michael E. Cusick, David Valle, Barton Childs, Marc Vidal, Albert-LÃ¡szlÃ³ BarabÃ¡si posted to biological_networks diseases human networks by roys on 2009-01-06 01:53:57 as along with 39 people and 9 groups robfsouza bertelsen smichan biomcgary pawelsobko CurAbility Scis0000002 qluo cbforrest daforerog nedwards Dulcinea saket kaarsinogen Yanno guhjy aalibes cannin kuhn jfr yas balicea neveaire bundschu raiyar grahamc joepickrell leSyl henning dejori xingxu winterschlaefer naegele shoshin shikin nolodie mingzhi carlk yaredo Network Analysis of Genes Regulated in Renal Diseases Biostatistics Computational-Genomics Bioinformatics Neuroscience steinmetzlab ic4 generif_paper GomezLab
	Predicting co-complexed protein pairs from heterogeneous data. [My Copy] PLoS computational biology, Vol. 4, No. 4. (April 2008) by J. Qiu, W. S. Noble posted to biological_networks networks protein_nw supervised_learning by roys on 2008-11-25 06:08:26 as along with 5 people guhjy bootsy carlk mingzhi penpen926
	Identification of functional modules using network topology and high-throughput data. [My Copy] BMC systems biology, Vol. 1, No. 1. (2007), 8. by Igor Ulitsky, Ron Shamir posted to biological_networks condition_specific_nw context_sensitive network_motifs by roys on 2008-11-12 05:15:55 as along with 18 people greg akshayk ptrobajo yaredo isimpson qluo aheilbut zufar frohike tmmurali dragonrez jfr wnpx Ao_Li2007 lyndon bertelsen ellakat carlk
	Network inference using informative priors [My Copy] Proceedings of the National Academy of Sciences, Vol. 105, No. 38. (2008), pp. 14313-14318. by Sach Mukherjee, Terence P. Speed posted to bayesian_networks biological_networks structure_learning structured_prior by roys on 2008-09-24 06:04:46 as along with 10 people and 1 group zufar bertelsen ggallone guhjy Borelli ptrobajo jfr markstoehr stringertheory tmmurali Jarman Lab
	Networking metabolites and diseases [My Copy] Proceedings of the National Academy of Sciences, Vol. 105, No. 29. (22 July 2008), pp. 9849-9850. by Pascal Braun, Edward Rietman, Marc Vidal posted to biological_networks diseases by roys on 2008-09-12 23:33:52 as along with 5 people mingzhi ptrobajo guhjy Borelli AbnerCYH
	Reconstruction of biological networks by supervised machine learning approaches [My Copy] (June 2008) by Jean-Philippe Vert posted to biological_networks network_inference supervised_learning by roys on 2008-09-12 23:06:08 as
	SIRENE: supervised inference of regulatory networks [My Copy] Bioinformatics, Vol. 24, No. 16. (15 August 2008), pp. i76-82. by Fantine Mordelet, Jean-Philippe Vert posted to biological_networks network_inference by roys on 2008-09-12 05:47:23 as along with 1 person hersh006
	Geometric interpretation of gene coexpression network analysis. [My Copy] PLoS computational biology, Vol. 4, No. 8. (15 August 2008), e1000117. by Steve Horvath, Jun Dong posted to biological_networks gene_expression_nw by roys on 2008-08-30 02:32:48 as along with 22 people jeremymiller zufar dolchan sficklin isimpson rdiaz guhjy cswinburne jfr ptrobajo pengchy nolodie druvus aramesh2 kengg Ema tmmurali Borelli Totobox AbnerCYH davidchavalarias caseybrown
	Large-Scale Mapping and Validation of Escherichia coli Transcriptional Regulation from a Compendium of Expression Profiles [My Copy] PLoS Biol, Vol. 5, No. 1. (9 January 2007), e8. by Jeremiah J. Faith, Boris Hayete, Joshua T. Thaden, et al.Ilaria Mogno, Jamey Wierzbowski, Guillaume Cottarel, Simon Kasif, James J. Collins, Timothy S. Gardner posted to biological_networks ecoli network_inference by roys on 2008-08-13 03:22:03 as along with 8 people and 2 groups frohike icases jfr teuder nickluscombe aswin heliopais austin EBI-regulation TNT
	Unraveling Protein Networks with Power Graph Analysis [My Copy] PLoS Comput Biol, Vol. 4, No. 7. (11 July 2008), e1000108. by Loïc Royer, Matthias Reimann, Bill Andreopoulos, Michael Schroeder posted to biological_networks network_motifs protein_nw by roys on 2008-07-26 21:04:28 as along with 24 people and 2 groups colmryan carlk saket diamantis yyby jfr jiny aramesh2 AbnerCYH jmuhlich MatthiasReimann royerloic Ema lptolik kengg reyez tmmurali nuin Borelli askrajiv renatomilani stajich sebk rsantana Mycology OPIG
	An Integrated Approach for the Analysis of Biological Pathways using Mixed Models [My Copy] PLoS Genet, Vol. 4, No. 7. (4 July 2008), e1000115. by Lily Wang, Bing Zhang, Russell D. Wolfinger, Xi Chen posted to annotation biological_networks ontology_similarity by roys on 2008-07-25 23:40:06 as along with 5 people jfr guhjy ptrobajo aviad_work inesdesantiago
	Direct targets of the TRP63 transcription factor revealed by a combination of gene expression profiling and reverse engineering [My Copy] Genome Res. (25 April 2008), gr.073601.107. by Giusy Della Gatta, Mukesh Bansal, Alberto Ambesi-Impiombato, Dario Antonini, Caterina Missero, Diego di Bernardo posted to biological_networks gene_expression mammals tfnet by roys on 2008-06-09 17:06:13 as along with 1 person tmmurali
	Dynamic Analysis of Integrated Signaling, Metabolic, and Regulatory Networks [My Copy] PLoS Comput Biol, Vol. 4, No. 5. (23 May 2008), e1000086. by Jong Min Lee, Erwin P. Gianchandani, James A. Eddy, Jason A. Papin posted to biological_networks data_integration metabolic_nw regulatory_nw signaling_nw by roys on 2008-06-08 02:57:39 as along with 9 people schwartzjmc abhishek_tiwari raik guhjy Borelli nolodie bootsy lymxz Ema
	Predictive Behavior Within Microbial Genetic Networks [My Copy] Science (8 May 2008), 1154456. by Ilias Tagkopoulos, Yir-Chung Liu, Saeed Tavazoie posted to biological_networks ecoli by roys on 2008-06-08 02:56:46 as along with 9 people and 1 group sugarexpletive rouault dbikard djkt skumagai brembs jjray deanmalmgren stringertheory Centre de Recherches Interdisciplinaires
	Modularization of biochemical networks based on classification of Petri net t-invariants [My Copy] BMC Bioinformatics, Vol. 9, No. 1. (2008) by Eva G. Belau, Falk Schreiber, Monika Heiner, et al.Andrea Sackmann, Bjorn Junker, Stefanie Grunwald, Astrid Speer, Katja Winder, Ina Koch posted to biological_networks petrinet by roys on 2008-06-08 02:23:05 as along with 5 people and 1 group reyez guhjy bootsy sobolevnrm maralena baker-group
	Reconstructing gene regulatory networks with bayesian networks by combining expression data with multiple sources of prior knowledge. [My Copy] Statistical applications in genetics and molecular biology, Vol. 6 (2007) by Adriano V. Werhli, Dirk Husmeier posted to bayesian_networks biological_networks data_integration by roys on 2008-05-17 01:55:56 as along with 2 people rdiaz edwardmorrissey
	Network properties of genes harboring inherited disease mutations. [My Copy] Proc Natl Acad Sci U S A (7 March 2008) by Igor Feldman, Andrey Rzhetsky, Dennis Vitkup posted to biological_networks tissue_specific_nw by roys on 2008-03-18 19:12:22 as along with 10 people daforerog frohike carlk saket yyby jeremymiller nolodie guhjy maralena ptrobajo
	High-confidence prediction of global interactomes based on genome-wide coevolutionary networks. [My Copy] Proceedings of the National Academy of Sciences of the United States of America, Vol. 105, No. 3. (22 January 2008), pp. 934-939. by David Juan, Florencio Pazos, Alfonso Valencia posted to biological_networks evolution by roys on 2008-01-24 19:51:34 as along with 18 people and 1 group dfdong ptrobajo biomcgary qluo winterschlaefer marti tmmurali brant balicea sebastien_vigneau bluto cjeans aconesa Katje friendpine huali mdstobbe paolomarcatili microbiology_nijmegen
	Learning module networks [My Copy] (2003) by E. Segal, D. Pe'er, A. Regev, D. Koller, N. Friedman posted to biological_networks bnet module_nw scalable_nw_learning by roys on 2008-01-23 22:47:10 as along with 2 people tvdbulck dimatura
	Modularized learning of genetic interaction networks from biological annotations and mRNA expression data [My Copy] Bioinformatics, Vol. 21, No. 11. (1 June 2005), pp. 2739-2747. by Phil H. Lee, Doheon Lee posted to bayesian_networks biological_networks network_inference scalable_nw_learning by roys on 2008-01-23 22:29:34 as along with 6 people verdicchio beete saman_vp patrycja_missiuro naegele tvdbulck
	Modularity and Dynamics of Cellular Networks [My Copy] PLoS Computational Biology, Vol. 2, No. 12. (1 December 2006), e174. by Yuan Qi, Hui Ge posted to biological_networks network_motifs networks nw_modularity by roys on 2008-01-11 17:32:52 as along with 8 people daforerog druvus giovenko joshuashen grahamc massivemayhem fishtank ccr
	Evolutionary plasticity of developmental gene regulatory network architecture [My Copy] Proceedings of the National Academy of Sciences (27 November 2007), 0709994104. by Veronica F. Hinman, Eric H. Davidson posted to biological_networks networks by roys on 2007-11-28 06:18:17 as along with 3 people tmmurali zwang maximilianh
	Inferring Genetic Networks and Identifying Compound Mode of Action via Expression Profiling [My Copy] Science, Vol. 301, No. 5629. (4 July 2003), pp. 102-105. by Timothy S. Gardner, Diego di Bernardo, David Lorenz, James J. Collins posted to biological_networks network_inference regression by roys on 2007-11-06 03:51:48 as along with 14 people and 9 groups Borelli edwardmorrissey myzhang mmcclean vertikalist rklancer kentsis dragonrez rhem1224 rubendrr adepace neveaire jayster4 heliopais BTS-PT-AS-CS Biostatistics Computational-Genomics Bioinformatics EisenLab Neuroscience TCR_Signaling cytoskeleton-and-afm SysbioMPI-TCells
	Linear Modeling of Genetic Networks from Experimental Data [My Copy] pp. 355-366. by E. P. van Someren, L. F. A. Wessels, M. J. T. Reinders posted to biological_networks network_inference regression by roys on 2007-11-06 03:49:52 as
	Boolean dynamics of genetic regulatory networks inferred from microarray time series data [My Copy] Bioinformatics, Vol. 23, No. 7. (1 April 2007), pp. 866-874. by Martin, Shawn, Zhang, et al. Zhaoduo, Martino, Anthony, Faulon, Jean-Loup posted to biological_networks boolean network_inference networks by roys on 2007-11-06 03:38:54 as
	A Probabilistic Methodology for Integrating Knowledge and Experiments on Biological Networks [My Copy] Journal of Computational Biology, Vol. 13, No. 2. (March 2006), pp. 165-181. by Irit Gat-Viks, Amos Tanay, Daniela Raijman, Ron Shamir posted to biological_networks factor_graphs transcription_modules by roys on 2007-11-06 03:28:53 as

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protein_nw	44
bayesian_networks	42
biological_networks	39
gene_expression	38
fly	32
network_inference	30
causality	28
neuroscience	27
networks	25
tfnets	24
regulatory_nw	23
yeast	21
eqtl	21
evolution	21
condition_specific_nw	19
metabolic_nw	18
data_integration	18
gene_expression_nw	17
tissue_specific_nw	17
clustering	17
comparative_genomics	17
cancer	14
markov_networks	14
condition_specific_response	14
human	13
statistical_relational_models	13
structure_learning	12
qtl	12
review	12
signaling_nw	12
diseases	12
tissue_specific_expression	11
genetic_nw	10
timeseries	10
regnet	10
species_specific_nw	10
network_motifs	9
development	9
protein_expression	9
graphical_models	9
combinatorial_control	8
tfprograms	8
mrf	8
differential_expression	8
tfnet	8
transcription_modules	8
systems_biology	8
tfbs	7
protein-dna_interaction_prediction	7
metabolic_flux	7
protein_domains	7
undirected_graphical_models	7
mental_diseases	7
mouse	7
hierarchical_models	6
gene_ontology	6
protein_nw_quality	6
subnw	6
module_nw	6
ca	6
information_theory	6
graph_theory	6
supervised_learning	5
quiescence	5
topic_models	5
mcmc	5
context_sensitive	5
worm	5
bnet	5
protein-dna	5
stress	5
multinet	5
nw_modularity	5
mixture_model	5
score_function	4
approximate_inference	4
protein_domain_sequences	4
glucose_response	4
nw_inference_method_comparison	4
dynamics	4
mrna_protein_correlation	4
nwsim	4
transcription_factor_binding_sites	4
context_specific_indep	4
protein_interaction_confidence	4
modularity	4
classification	4
lda	4
genome_wide_assoc	3
starvation	3
structural_em	3
rewiring	3
gene_regulation	3
regulatory_networks	3
mammals	3
stress_responses	3
higher_order_dependencies	3
graphical_gaussian	3
motif_discovery	3
scalable_nw_learning	3
graph_clustering	3
gaussian_processes	3
expression_correlation	3
dependency_networks	3
database	3
ecoli	3
worm_regulatory_nw	3
graphs	3
metabolite_expression	3
ncrna	3
mtl	3
regression	3
regulatory	3
hidden_vars	3
protein_dna_interactions	3
software	3
metagenomics	3
imp_aminoacids	3
factor_graphs	3
bde	2
fdr	2
inference	2
biclustering	2
maximum_likelihood	2
post_transcriptional	2
dirichlet_process	2
functional_networks	2
toolkits	2
prm	2
conditional_correlation	2
stationary_phase	2
sequence	2
param_est	2
data_pooling	2
dbn	2
modules	2
similarity_nw	2
loopy_belief_propogation	2
growth_control	2
fba	2
genome_complexity	2
protein_function_pred	2
decomposable	2
protein_complexity	2
noise_expression	2
mdl	2
expression_divergence	2
annotation	2
proteome_comparison	2
carbon_metabolism	2
crfs	2
ontology_similarity	2
hmms	2
flow_networks	2
nw_evolution	2
pseudolikelihood	2
markov_boundary	2
flow_cytometry	2
maximum_entropy	2
structured_prior	2
aging	2
celegans	2
snp	2
relational_markov_nw	2
mutual_information	2
nw	2
rnai	2
chipseqrev	1
laplacian	1
microrna	1
haplotype	1
partition_function	1
sam	1
genomes	1
ms	1
active	1
fungi	1
simulation	1
protein_interactions	1
sum_product	1
comparitive_analysis	1
multinets	1
petrinet	1
aminoacid_residues	1
dream	1
nutrient_limitation	1
imaging	1
forward_genetics	1
statistical_learning	1
rnaseqrev	1
proline	1
image_analysis	1
gene_duplication	1
spline	1
workshop	1
single_cell	1
drug_target_pred	1
synthetic_biology	1
alignments	1
canonical_correlation	1
omni	1
motif_libraries	1
moma	1
dna	1
experimental_conditions	1
cell_populations	1
sem	1
multitask_learning	1
osmotic_stress	1
crp	1
probability_distribution_spectral_method	1
motif_clustering	1
unsuperviselearning	1
high_resolution_network	1
gene_interactions	1
nmf	1
model_counting	1
motif_identification	1
bacteria	1
mt	1
imago	1
phenotype_correlation	1
boolean	1
tissue_specificity	1
protein_quantification	1
sparse_candidate	1
proteomics_data	1
pdags	1
nested_effect_models	1
protein_degradation	1
fold_prediction	1
phylogenetic_methods	1
mdags	1
interventions	1
evolution_complexity	1
species_data	1
tra	1
tor	1
bayesian_models	1
phenotypic_correlation	1
motifs	1
computational_biology	1
gene_expression_data	1
alcoholism	1
single_molecule	1
bounded_tree_width	1
lasso	1
modencode	1
logic_nw	1
perturbations	1
semantic_similarity	1
dnadamage	1
emap	1
svm	1
network_representation	1
rna_mrna_nw	1
schizophrenia	1
gene_ranking	1
edgetic	1
entropy	1
general	1
generalize_pseudo_likelihood	1
mixture_of_experts	1
kitano02	1
nextgen_sequencing	1
room	1
growth	1
learning	1
low_complexity_regions	1
gwa	1
drosophila	1
active_learning	1
phylogenetic_reconstruction	1
evolutionary_developmental_biology	1
mag	1
overlap_clustering	1
transfer_learning	1
intact	1
genomic_rearrangements	1
sequencing	1
robustness	1
structured_classification	1
glycine	1
multi_information	1
tree_distributions	1
gene_set_analysis	1
nucleosome	1
mrfs	1
tokha07	1
nw_alignment	1
nw_schema	1
community_structure	1
multiple_patient_data	1

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