grahamc's methods [78 articles] Export

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	Functionally guided alignment of protein interaction networks for module detection [My Copy] Bioinformatics, Vol. 25, No. 23. (1 December 2009), pp. 3166-3173. by Waqar Ali, Charlotte M. Deane posted to tools network_alignment methods by grahamc on 2009-10-19 03:29:35 as along with 1 person druvus
	A novel scoring approach for protein co-purification data reveals high interaction specificity. [My Copy] PLoS computational biology, Vol. 5, No. 9. (September 2009) by Xueping Yu, Joseph Ivanic, Anders Wallqvist, Jaques Reifman posted to protein_protein_interactions network_confidence modularity methods mass_spec by grahamc on 2009-10-11 15:50:35 as along with 2 people snow_dragon carlk
	Geometric De-noising of Protein-Protein Interaction Networks [My Copy] PLoS Comput Biol, Vol. 5, No. 8. (7 August 2009), e1000454. by Oleksii Kuchaiev, Marija Rašajski, Desmond J. Higham, Nataša Pržulj posted to protein-protein prediction methods interaction human assessment by grahamc on 2009-08-16 03:23:32 as along with 8 people and 1 group CorinYeats klexa tmmurali roys zwang robfsouza phoenixzxl kiekyon Orengo Group Journal Picks
	Semi-automated curation of protein subcellular localization: a text mining-based approach to Gene Ontology (GO) Cellular Component curation. [My Copy] BMC bioinformatics, Vol. 10, No. 1. (21 July 2009), 228. by Kimberly Van Auken, Joshua Jaffery, Juancarlos Chan, Hans-Michael M. Müller, Paul W. Sternberg posted to subcellular_location prediction methods gene_ontology curation by grahamc on 2009-08-16 02:55:05 as along with 3 people and 2 groups kshameer tharris jvb C. elegans / WormBase Journal picks
	PhyloBayes 3: a Bayesian software package for phylogenetic reconstruction and molecular dating [My Copy] Bioinformatics, Vol. 25, No. 17. (1 September 2009), pp. 2286-2288. by Nicolas Lartillot, Thomas Lepage, Samuel Blanquart posted to bioinformatics methods phylogenetic_analysis tools by grahamc on 2009-06-23 04:18:50 as along with 6 people and 1 group nesnidal djkt leemond31 operon nuin phoenixzxl iSEEM
	Quantum dots go large. [My Copy] Nature, Vol. 459, No. 7248. (11 June 2009), pp. 760-761. by K. Sanderson posted to imaging methods microscopy by grahamc on 2009-06-16 19:15:59 as
	Domain-oriented edge-based alignment of protein interaction networks [My Copy] Bioinformatics, Vol. 25, No. 12. (15 June 2009), pp. i240-1246. by Xin Guo, Alexander J. Hartemink posted to methods network_alignment tools by grahamc on 2009-06-15 05:19:21 as along with 4 people megraw yaredo guhjy roys
	Network-based prediction of metabolic enzymes' subcellular localization [My Copy] Bioinformatics, Vol. 25, No. 12. (15 June 2009), pp. i247-1252. by Shira Mintz-Oron, Asaph Aharoni, Eytan Ruppin, Tomer Shlomi posted to metabolism methods prediction subcellular_location by grahamc on 2009-06-15 05:18:12 as along with 1 person kshameer
	Protein-protein interaction based on pairwise similarity [My Copy] BMC Bioinformatics, Vol. 10 (17 May 2009), 150. by Nazar, Piers Campbell posted to interactions methods prediction protein-protein by grahamc on 2009-05-26 03:07:42 as along with 4 people chocolate2009 renatomilani reyez barriot
	Complex discovery from weighted PPI networks. [My Copy] Bioinformatics (Oxford, England), Vol. 25, No. 15. (1 August 2009), pp. 1891-1897. by Guimei Liu, Limsoon Wong, Hon Nian N. Chua posted to algorithm bioinformatics methods network_topology tools by grahamc on 2009-05-26 03:00:04 as along with 7 people kgutwin kiekyon zwang friendpine poirel neils tmmurali
	Identification of differentially expressed subnetworks based on multivariate ANOVA [My Copy] BMC Bioinformatics, Vol. 10, No. 1. (30 April 2009), 128. by Taeyoung Hwang, Taesung Park posted to bioinformatics human interaction methods network_biology protein-protein by grahamc on 2009-05-05 03:08:04 as along with 6 people and 1 group rdiaz guhjy lwaldron TRHvidsten renatomilani erexhepa Bioinformatics
	Uncovering the rules for protein-protein interactions from yeast genomic data. [My Copy] Proceedings of the National Academy of Sciences of the United States of America, Vol. 106, No. 10. (10 March 2009), pp. 3752-3757. by Jin Wang, Chunhe Li, Erkang Wang, Xidi Wang posted to bioinformatics interactions methods network_properties protein-protein yeast by grahamc on 2009-03-01 20:29:35 as along with 8 people and 1 group carlk guhjy AbnerCYH sobolevnrm mariap3636 mstumpf zwang phoenixzxl baker-group
	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 bioinformatics methods network_biology network_confidence network_visualization tools by grahamc on 2009-03-01 17:46:08 as along with 7 people and 1 group phoenixzxl ptrobajo kshameer rdiaz guhjy provero roys ParkinsonLab_at_MaRS
	Disease candidate gene identification and prioritization using protein interaction networks [My Copy] BMC Bioinformatics, Vol. 10, No. 1. (2009), 73. by Jing Chen, Bruce Aronow, Anil Jegga posted to bioinformatics disease interactions methods prediction protein-protein by grahamc on 2009-03-01 17:27:47 as along with 12 people and 1 group carlk zufar guhjy jfr daforerog saket provero mitko neils barriot renatomilani rjazwiec Bioinformatics
	Enumeration of condition-dependent dense modules in protein interaction networks [My Copy] Bioinformatics, Vol. 25, No. 7. (1 April 2009), pp. 933-940. by Elisabeth Georgii, Sabine Dietmann, Takeaki Uno, Philipp Pagel, Koji Tsuda posted to functional_modules methods network_topology prediction tools by grahamc on 2009-02-23 18:40:01 as along with 5 people carlk hryk eesruiz imina mhamada
	Homogeneous decomposition of protein interaction networks: refining the description of intra-modular interactions. [My Copy] Bioinformatics (Oxford, England) (17 February 2009) by Géraldine Del Mondo, Damien Eveillard, Irena Rusu posted to bioinformatics methods network_biology network_properties network_topology tools by grahamc on 2009-02-23 18:34:54 as
	A factor graph nested effects model to identify networks from genetic perturbations. [My Copy] PLoS computational biology, Vol. 5, No. 1. (January 2009) by Charles J. Vaske, Carrie House, Truong Luu, et al.Bryan Frank, Chen-Hsiang H. Yeang, Norman H. Lee, Joshua M. Stuart posted to disease human methods network_biology prediction by grahamc on 2009-02-02 18:33:46 as along with 2 people ptrobajo psychorav
	Prediction of protein-protein interaction types using association rule based classification [My Copy] BMC Bioinformatics, Vol. 10, No. 1. (2009) by Sung H. Park, Jose Reyes, David Gilbert, Ji W. Kim, Sangsoo Kim posted to interaction methods prediction protein-protein by grahamc on 2009-02-02 18:07:27 as along with 4 people anf renatomilani higueruelo neils
	Detecting Gene Clusters under Evolutionary Constraint in a Large Number of Genomes [My Copy] Bioinformatics (21 January 2009), btp027. by Xu Ling, Xin He, Dong Xin posted to bioinformatics genome_evolution methods by grahamc on 2009-02-02 18:01:40 as along with 6 people nuin idoerg malcook druvus djkt Neeperando
	Ortholog-based protein-protein interaction prediction and its application to inter-species interactions. [My Copy] BMC bioinformatics, Vol. 9 Suppl 12 (2008) by S. A. Lee, C. H. Chan, C. H. Tsai, et al.J. M. Lai, F. S. Wang, C. Y. Kao, C. Y. Huang posted to interaction methods prediction protein-protein by grahamc on 2009-01-26 18:25:15 as along with 2 people cerca guhjy
	BFL: a node and edge betweenness based fast layout algorithm for large scale networks [My Copy] BMC Bioinformatics, Vol. 10 (15 January 2009), 19. by Tatsunori, Satoru Miyano posted to methods network_properties network_visualization by grahamc on 2009-01-26 18:20:48 as along with 1 person robert85
	Improved homology-driven computational validation of protein-protein interactions motivated by the evolutionary gene duplication and divergence hypothesis [My Copy] BMC Bioinformatics, Vol. 10, No. 1. (2009) by Christian Frech, Michael Kommenda, Viktoria Dorfer, et al.Thomas Kern, Helmut Hintner, Johann Bauer, Kamil Oender posted to interactions methods prediction protein-protein validation by grahamc on 2009-01-26 18:19:28 as along with 3 people guhjy timg barriot
	Prediction of Nuclear Proteins using SVM and HMM Models [My Copy] BMC Bioinformatics, Vol. 10, No. 1. (2009) by Manish Kumar, Gajendra Raghava posted to methods prediction subcellular_location by grahamc on 2009-01-26 18:18:12 as along with 5 people firyarn84 mhamada mdstobbe druvus neils
	Sequence-based Prediction of Protein Interaction Sites with an Integrative Method. [My Copy] Bioinformatics (Oxford, England) (19 January 2009) by Xue-Wen W. Chen, Jong Cheol C. Jeong posted to interactions methods prediction protein-protein by grahamc on 2009-01-26 18:09:07 as along with 2 people iaolier carlosjavierna
	Precision and recall estimates for two-hybrid screens. [My Copy] Bioinformatics (Oxford, England), Vol. 25, No. 3. (1 February 2009), pp. 372-378. by Hailiang Huang, Joel S. Bader posted to accuracy evaluation interactions methods two-hybrid by grahamc on 2009-01-13 02:33:13 as along with 8 people anf guhjy mariap3636 roys phoenixzxl mstumpf tmmurali sjcockell
	Evaluating contributions of natural language parsers to protein-protein interaction extraction [My Copy] Bioinformatics, Vol. 25, No. 3. (1 February 2009), pp. 394-400. by Yusuke Miyao, Kenji Sagae, Rune Saetre, Takuya Matsuzaki, Jun'ichi Tsujii posted to interactions methods protein-protein text_mining by grahamc on 2009-01-12 18:22:19 as along with 6 people and 2 groups RNawaz liblab Effie mstumpf behindtherabbit henk-cul NaCTeM dbmi-nlp
	Algorithm of OMA for large-scale orthology inference [My Copy] BMC Bioinformatics, Vol. 9 (04 December 2008), 518. by Alexander, Christophe Dessimoz posted to comparative_genomics methods orthologues prediction by grahamc on 2008-12-08 14:36:27 as along with 5 people AaronDarling alpae cgaugain barriot druvus
	ESLpred2: improved method for predicting subcellular localization of eukaryotic proteins [My Copy] BMC Bioinformatics, Vol. 9 (28 November 2008), 503. by Aarti Garg, Gajendra P. S. Raghava posted to methods prediction subcellular_location by grahamc on 2008-12-01 14:52:09 as
	Combining multiple positive training sets to generate confidence scores for protein-protein interactions. [My Copy] Bioinformatics (Oxford, England) (14 November 2008) by Jingkai Yu, Russell L L. Finley posted to human interactions methods protein-protein scoring by grahamc on 2008-11-20 22:42:40 as along with 2 people anf cerca
	Training set expansion: an approach to improving the reconstruction of biological networks from limited and uneven reliable interactions [My Copy] Bioinformatics, Vol. 25, No. 2. (15 January 2009), pp. 243-250. by Kevin Y. Yip, Mark Gerstein posted to interactions methods network_biology prediction protein-protein by grahamc on 2008-11-20 22:32:55 as along with 6 people ptrobajo anf guhjy mstumpf imina kgutwin
	Transmembrane topology and signal peptide prediction using dynamic bayesian networks. [My Copy] PLoS computational biology, Vol. 4, No. 11. (November 2008) by S. M. Reynolds, L. Käll, M. E. Riffle, J. A. Bilmes, W. S. Noble posted to methods prediction signal_peptide tools transmembrane_prediction by grahamc on 2008-11-10 00:47:38 as along with 1 person cabbagesofdoom
	Protein networks markedly improve prediction of subcellular localization in multiple eukaryotic species [My Copy] Nucl. Acids Res. (4 October 2008), gkn619. by Kiyoung Lee, Han-Yu Chuang, Andreas Beyer, et al.Min-Kyung Sung, Won-Ki Huh, Bonghee Lee, Trey Ideker posted to interactions methods prediction protein-protein subcellular_location by grahamc on 2008-11-03 19:20:16 as along with 6 people tienholin carlk brianb neils giovenko ptrobajo
	An incremental approach to automated protein localisation [My Copy] BMC Bioinformatics, Vol. 9 (20 October 2008), 445. by Marko Tscherepanow, Nickels Jensen, Franz Kummert posted to methods subcellular_location by grahamc on 2008-10-27 15:50:49 as
	Improving Subcellular Localization Prediction using Text Classification and the Gene Ontology [My Copy] Bioinformatics (26 August 2008), btn463. by Alona Fyshe, Yifeng Liu, Duane Szafron, Russ Greiner, Paul Lu posted to gene_ontology methods prediction subcellular_location by grahamc on 2008-10-27 15:25:39 as along with 3 people guhjy ptrobajo phoenixzxl
	Evaluation and comparison of mammalian subcellular localization prediction methods. [My Copy] BMC bioinformatics, Vol. 7 Suppl 5 (2006) by J. Sprenger, J. L. Fink, R. D. Teasdale posted to methods prediction subcellular_location by grahamc on 2008-09-09 16:39:41 as
	Transcriptome-based systematic identification of extracellular matrix proteins [My Copy] Proceedings of the National Academy of Sciences, Vol. 105, No. 35. (2008), pp. 12849-12854. by Ri-Ichiroh Manabe, Ko Tsutsui, Tomiko Yamada, et al.Mina Kimura, Itsuko Nakano, Chisei Shimono, Noriko Sanzen, Yutaka Furutani, Tomohiko Fukuda, Yasuko Oguri, Keiko Shimamoto, Daiji Kiyozumi, Yuya Sato, Yoshikazu Sado, Haruki Senoo, Shohei Yamashina, Shiro Fukuda, Jun Kawai, Nobuo Sugiura, Koji Kimata, Yoshihide Hayashizaki, Kiyotoshi Sekiguchi posted to bioinformatics ecm methods tools by grahamc on 2008-09-04 15:43:17 as along with 2 people guhjy sg45653
	Identification and correction of abnormal, incomplete and mispredicted proteins in public databases [My Copy] BMC Bioinformatics, Vol. 9, No. 1. (2008) by Alinda Nagy, Hedi Hegyi, Krisztina Farkas, et al.Hedvig Tordai, Evelin Kozma, Laszlo Banyai, Laszlo Patthy posted to genome_annotation genomes methods tools by grahamc on 2008-09-03 21:25:49 as along with 2 people neils piergiorgioduca
	SynBlast: Assisting the analysis of conserved synteny information [My Copy] BMC Bioinformatics, Vol. 9, No. 1. (24 August 2008), 351. by Jorg Lehmann, Peter Stadler, Sonja Prohaska posted to bioinformatics homologue_detection methods synteny tools by grahamc on 2008-09-03 21:20:54 as along with 6 people and 1 group avilella natstreet druvus maximilianh nuin Neeperando Ensembl Compara citations
	Improved network-based identification of protein orthologs. [My Copy] Bioinformatics (Oxford, England), Vol. 24, No. 16. (15 August 2008) by N. Yosef, R. Sharan, W. S. Noble posted to methods orthologues by grahamc on 2008-08-28 00:50:12 as along with 1 person chad_davis
	Predicting sub-Golgi localization of type II membrane proteins. [My Copy] Bioinformatics (Oxford, England), Vol. 24, No. 16. (15 August 2008), pp. 1779-1786. by A. D. van Dijk, D. Bosch, C. J. ter Braak, A. R. van der Krol, R. C. van Ham posted to methods prediction subcellular_location by grahamc on 2008-08-28 00:43:45 as
	High Performance Signal Peptide Prediction Based on Sequence Alignment Techniques. [My Copy] Bioinformatics (Oxford, England) (12 August 2008) by Karl Frank, Manfred J J. Sippl posted to methods prediction secretome signal_peptide by grahamc on 2008-08-28 00:40:35 as
	Computational Prediction of Human Proteins That Can Be Secreted into the Bloodstream [My Copy] Bioinformatics (12 August 2008), btn418. by Juan Cui, Qi Liu, David Puett, Ying Xu posted to machine_learning methods prediction proteomics secretome by grahamc on 2008-08-28 00:37:24 as along with 2 people guhjy sg45653
	Discovery of a Cytokine and Its Receptor by Functional Screening of the Extracellular Proteome [My Copy] Science, Vol. 320, No. 5877. (9 May 2008), pp. 807-811. by Haishan Lin, Ernestine Lee, Kevin Hestir, et al.Cindy Leo, Minmei Huang, Elizabeth Bosch, Robert Halenbeck, Ge Wu, Aileen Zhou, Dirk Behrens, Diane Hollenbaugh, Thomas Linnemann, Minmin Qin, Justin Wong, Keting Chu, Stephen K. Doberstein, Lewis T. Williams posted to ecm methods by grahamc on 2008-05-28 03:22:17 as along with 1 person guhjy
	A new way to explore the world of extracellular protein interactions [My Copy] Genome Res., Vol. 18, No. 4. (1 April 2008), pp. 517-520. by Christopher M. Sanderson posted to interactions methods protein-protein by grahamc on 2008-04-23 17:34:40 as along with 1 person carlk
	Insights into Protein–Protein Interfaces using a Bayesian Network Prediction Method [My Copy] Journal of Molecular Biology, Vol. 362, No. 2. (15 September 2006), pp. 365-386. by James R. Bradford, Chris J. Needham, Andrew J. Bulpitt, David R. Westhead posted to methods network_biology prediction by grahamc on 2008-03-28 20:46:28 as along with 8 people and 2 groups dfdong barry conkymacro ameetsoni massivemayhem phoenixzxl marti paolomarcatili structural_bioinformatics Bioinformatics
	Functional discrimination of membrane proteins using machine learning techniques [My Copy] BMC Bioinformatics, Vol. 9 (03 March 2008), 135. by Michael M. Gromiha, Yukimitsu Yabuki posted to methods transmembrane_prediction by grahamc on 2008-03-25 23:48:33 as
	From pull-down data to protein interaction networks and com-plexes with biological relevance. [My Copy] Bioinformatics (26 February 2008) by Bing Zhang, Byung-Hoon H. Park, Tatiana Karpinets, Nagiza F F. Samatova posted to interactions mass_spec methods protein-protein by grahamc on 2008-03-23 02:49:45 as along with 4 people guhjy chad_davis kluck carlk
	An assessment of the uses of homologous interactions [My Copy] Bioinformatics, Vol. 24, No. 5. (1 March 2008), pp. 689-695. by Ramazan Saeed, Charlotte Deane posted to gold_standards interactions methods protein-protein by grahamc on 2008-03-23 02:40:55 as along with 11 people snow_dragon carlk lawraga winterschlaefer chad_davis cjeans laughcry mingzhi cdeane Pao-Yang samesense
	Accurate prediction of protein\|[ndash]\|protein interactions from sequence alignments using a Bayesian method [My Copy] Molecular Systems Biology, Vol. 4 (12 February 2008) by Lukas Burger, Erik van Nimwegen posted to interactions methods prediction protein-protein by grahamc on 2008-02-28 04:53:44 as along with 14 people iaolier robfsouza raik sjcockell kengg laughcry zwang biomcgary cabbagezs roys cdeane gjuggler phoenixzxl pansapiens
	Reconstruction of ancestral protein interaction networks for the bZIP transcription factors. [My Copy] Proceedings of the National Academy of Sciences of the United States of America, Vol. 104, No. 51. (18 December 2007), pp. 20449-20453. by John W. Pinney, Grigoris D. Amoutzias, Magnus Rattray, David L. Robertson posted to evolution interactions interologues methods protein-protein by grahamc on 2008-01-05 04:31:11 as along with 7 people carlk biomcgary saket tmmurali cjeans Pao-Yang hplatero

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interactions	169
protein-protein	143
methods	78
synthetic_biology	72
tools	67
evolution	64
ecm	56
network_biology	53
prediction	46
network_topology	33
human	32
bioinformatics	29
data_integration	26
domains	25
network_properties	25
disease	21
genomics	21
elastin	20
igem	20
database	19
subcellular_location	19
proteomics	18
metabolism	17
motifs	17
comparative_genomics	16
systems_biology	16
algorithm	15
elastomer	15
function_prediction	15
statistics	15
network_statistics	14
sequencing	14
domain	13
gene_ontology	13
review	13
yeast	13
model_organisms	10
self-assembly	10
collagen	9
modeling	9
network_confidence	9
clustering_methods	8
tissue_specific_gene_expression	8
algorithms	7
cytoscape	7
matrix_architecture	7
network_alignment	7
protein_evolution	7
annotation	6
clustering	6
pattern_recognition	6
phenotype	6
protein_complexes	6
transmembrane_prediction	6
bio_fuel	5
functional_modules	5
interaction	5
network_comparison	5
post_translational_modification	5
alignment	4
biological_networks	4
ecm_remodeling	4
ecoli	4
expression	4
gene_expression	4
genomes	4
go_terms	4
graph_theory	4
matrix_remodeling	4
metabolic_channeling	4
minimal_cell	4
protein_protein_interactions	4
signaling	4
signal_peptide	4
two-hybrid	4
visualization	4
wound_repair	4
angiogenesis	3
betweenness	3
biology	3
bone_homeostasis	3
choanoflagellates	3
co-expression	3
development	3
function	3
functional_annotation	3
gene_identifiers	3
genome_evolution	3
mass_spec	3
microarray	3
network_visualization	3
orthologues	3
pathway_modeling	3
phylogenetic_analysis	3
protein	3
scientific_communication	3
simulation	3
structure	3
vertebrate_genomics	3
accuracy	2
aging	2
assembly	2
binding_domains	2
cancer	2
cardiac	2
centrality	2
co-localization	2
epigenetics	2
evaluation	2
fibroblast	2
hydra	2
integrin	2
interologues	2
long_pcr	2
matrix_mmp	2
metazoa	2
morphology	2
pattern_development	2
publishing	2
scoring	2
search	2
secretome	2
selection	2
sequence_conservation	2
sequenced_organisms	2
software	2
specialty-network	2
sponges	2
standards	2
synteny	2
text_mining	2
transcription_factors	2
translation	2
aging_network	1
alternative_splicing	1
ancestral_genomes	1
ancient_dna	1
aorta	1
api	1
assessment	1
bacteria	1
biofuels	1
biological_computation	1
bladder	1
bone_mineralization	1
bone_regulatory_network	1
capillary_formation	1
carbohydrate	1
career_science	1
cell_migration	1
cell_wall	1
cloning	1
cnidaria	1
curation	1
cysteine-labeling	1
cytoskeleton	1
decorin	1
diatoms	1
disease_classification	1
domain-domain	1
early_life	1
e_coli	1
encode_project	1
engineered_proteins	1
enrichment	1
ethics	1
exobiology	1
extracellular	1
extracellular_proteins	1
fibrillin	1
fibrin	1
fibulin	1
functional_maps	1
fuzzy_logic	1
gene	1
gene_environment	1
gene_families	1
gene_loss	1
genome_annotation	1
glycomics	1
gold_standards	1
hemostasis	1
hexapoda	1
homologue_detection	1
hydrophobic_polymerization	1
imaging	1
induction	1
interaction_site	1
introns	1
java	1
kidney_development	1
learning	1
lumier	1
machine_learning	1
mammalian	1
mars	1
memory	1
mesh_terms	1
metadata	1
micro_rna	1
microscopy	1
modularity	1
molecular_dynamics	1
mouse	1
mouse_development	1
multicellularity	1
net	1
network_analysis	1
neuroplasticity	1
normal_vs_disease	1
ontologies	1
organogenesis	1
orthologous	1
phage_display	1
plasmodium	1
poster	1
protein_dynamics	1
protein_features	1
protein_folding	1
protein_function	1
protein_interactions	1
protein_scaffolds	1
quality	1
reliability	1
scale-free	1
secondary_structure	1
silkworm	1
systems	1
tension	1
tissue	1
uniprot	1
validation	1
vasculogenesis	1
visualization_system	1
zebrafish	1

grahamc's methods [78 articles] Export

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