shikin's network [37 articles] Export

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	Network component analysis: reconstruction of regulatory signals in biological systems. [My Copy] Proceedings of the National Academy of Sciences of the United States of America, Vol. 100, No. 26. (23 December 2003), pp. 15522-15527. by James C. Liao, Riccardo Boscolo, Young-Lyeol L. Yang, Linh My M. Tran, Chiara Sabatti, Vwani P. Roychowdhury posted to transfac systems_biology network gene_expression by shikin on 2009-11-27 13:50:46 as along with 3 people davebridges arne bertelsen
	Protein networks in disease. [My Copy] Genome research, Vol. 18, No. 4. (1 April 2008), pp. 644-652. by Trey Ideker, Roded Sharan posted to network ideker by shikin on 2009-11-06 17:48:35 as along with 27 people carlk isimpson chica saket zufar kaarsinogen giovenko guhjy balicea tmmurali Borelli jwdietrich frohike bootsy nedwards roys mclarenv phoenixzxl brianb schuylrp jfr paolomarcatili gracio thomaskelder ptrobajo raiyar zwang
	Analysis of Gene Sets Based on the Underlying Regulatory Network [My Copy] Journal of Computational Biology, Vol. 16, No. 3. (March 2009), pp. 407-426. by Ali Shojaie, George Michailidis posted to pathway-analysis network by shikin on 2009-09-01 13:10:42 as along with 4 people and 1 group zufar guhjy jfr rdiaz Bioinformatics
	Hub genes with positive feedbacks function as master switches in developmental gene regulatory networks [My Copy] Bioinformatics, Vol. 25, No. 15. (1 August 2009), pp. 1898-1904. by Chang H. Seo, Jeong-Rae Kim, Man-Sun Kim, Kwang-Hyun Cho posted to network by shikin on 2009-07-20 10:28:54 as along with 3 people robfsouza GustavoLacerda jjray
	Filtering Genes for Cluster and Network Analysis [My Copy] BMC Bioinformatics, Vol. 10, No. 1. (2009), 193. by David Tritchler, Elena Parkhomenko, Joseph Beyene posted to gene_expression method network by shikin on 2009-07-06 11:51:34 as along with 6 people and 1 group zufar dswan lwaldron rdiaz bertelsen erexhepa Bioinformatics
	Computing paths and cycles in biological interaction graphs [My Copy] BMC Bioinformatics, Vol. 10, No. 1. (2009), 181. by Steffen Klamt, Axel von Kamp posted to network by shikin on 2009-06-22 11:36:11 as along with 4 people Scis0000002 rdiaz barriot imina
	Hypergraphs and Cellular Networks [My Copy] PLoS Comput Biol, Vol. 5, No. 5. (29 May 2009), e1000385. by Steffen Klamt, Utz-Uwe Haus, Fabian Theis posted to network by shikin on 2009-05-29 16:32:31 as along with 11 people rdiaz ptrobajo poirel apocapoc trfield uuh danmaclean fgibson dswan tmmurali Borelli
	A genomic strategy to elucidate modules of oncogenic pathway signaling networks. [My Copy] Molecular cell, Vol. 34, No. 1. (10 April 2009), pp. 104-114. by Jeffrey T. Chang, Carlos Carvalho, Seiichi Mori, et al.Andrea H. Bild, Michael L. Gatza, Quanli Wang, Joseph E. Lucas, Anil Potti, Phillip G. Febbo, Mike West, Joseph R. Nevins posted to cancer network by shikin on 2009-05-18 16:28:42 as along with 8 people and 1 group jfr bertelsen jmstat guhjy mspivako renatomilani fenghezi roys Journal picks
	The Importance of Bottlenecks in Protein Networks: Correlation with Gene Essentiality and Expression Dynamics [My Copy] PLoS Comput Biol, Vol. 3, No. 4. (20 April 2007), e59. by Haiyuan Yu, Philip M. Kim, Emmett Sprecher, Valery Trifonov, Mark Gerstein posted to interactome network by shikin on 2009-04-15 15:11:38 as along with 9 people lawraga flbarroso shung jiny jfr zwang Takayuki hryk carlk
	Information flow analysis of interactome networks. [My Copy] PLoS computational biology, Vol. 5, No. 4. (10 April 2009), e1000350. by Patrycja Vasilyev V. Missiuro, Kesheng Liu, Lihua Zou, et al.Brian C. Ross, Guoyan Zhao, Jun S. Liu, Hui Ge posted to interactome network by shikin on 2009-04-15 14:54:34 as along with 18 people and 1 group jfr freesci flbarroso peteruetz phoenixzxl robfsouza reyez VGreiff colmryan sobolevnrm hryk dswan fgibson coela ddahlem mstumpf zwang friendpine baker-group
	Identifying disease-specific genes based on their topological significance in protein networks [My Copy] BMC Systems Biology, Vol. 3, No. 1. (2009), 36. by Zoltan Dezso, Yuri Nikolsky, Tatiana Nikolskaya, et al.Jeremy Miller, David Cherba, Craig Webb, Andrej Bugrim posted to genego network by shikin on 2009-04-09 18:46:44 as along with 5 people idonaldson Keywan guhjy renatomilani kshameer
	Topological and organizational properties of the products of house-keeping and tissue-specific genes in protein-protein interaction networks [My Copy] BMC Systems Biology, Vol. 3, No. 1. (2009), 32. by Wen H. Lin, Wei C. Liu, Ming J. Hwang posted to network ppi systems_biology by shikin on 2009-03-25 20:01:56 as along with 1 person guhjy
	Cytoscape: a software environment for integrated models of biomolecular interaction networks. [My Copy] Genome research, Vol. 13, No. 11. (November 2003), pp. 2498-2504. by Paul Shannon, Andrew Markiel, Owen Ozier, et al.Nitin S. Baliga, Jonathan T. Wang, Daniel Ramage, Nada Amin, Benno Schwikowski, Trey Ideker posted to network pathway software temp by shikin on 2009-02-17 17:06:20 as along with 34 people and 3 groups JeremyZucker daveGerrard fastjoe23 badi stharward kentz tonamswish janani137 shung schwartzjmc APRegier panghouse robert85 capitall higueruelo daforerog cswinburne thomaskelder nolodie giovenko Stew dragonrez balajis tvdbulck frohike carmaus dagmar natstreet jlh64 Evangelia pmendes yggdrasil carlk Borelli dIEMoSIRIS MoSi-Rostock compneur
	Integrated network analysis platform for protein-protein interactions [My Copy] Nature Methods, Vol. 6, No. 1. (14 December 2008), pp. 75-77. by Jianmin Wu, Tea Vallenius, Kristian Ovaska, Jukka Westermarck, Tomi P. Makela, Sampsa Hautaniemi posted to network ppi software by shikin on 2008-12-30 18:58:04 as along with 6 people karthikraman Garamonfok renatomilani zwang guhjy Terkko
	A map of human cancer signaling [My Copy] Molecular Systems Biology, Vol. 3 (18 December 2007) by Qinghua Cui, Yun Ma, Maria Jaramillo, et al.Hamza Bari, Arif Awan, Song Yang, Simo Zhang, Lixue Liu, Meng Lu, Maureen O'Connor-McCourt, Enrico O. Purisima, Edwin Wang posted to cancer network by shikin on 2008-09-09 19:14:33 as along with 12 people and 1 group poojamaj tonamswish Zephyrus agomez jfr tmmurali ealloza cjeans Ema renatomilani srp33 frohike Roswell Cancer Crosstalk
	Why Do Hubs in the Yeast Protein Interaction Network Tend To Be Essential: Reexamining the Connection between the Network Topology and Essentiality [My Copy] PLoS Comput Biol, Vol. 4, No. 8. (1 August 2008), e1000140. by Elena Zotenko, Julian Mestre, Dianne P. O'Leary, Teresa M. Przytycka posted to network by shikin on 2008-09-01 10:00:47 as along with 12 people and 1 group lawraga marti chrisamiller kaarsinogen jfr aramata jmjimenez srp33 maralena cabbagesofdoom cerca tmmurali GeneGo
	Evidence for dynamically organized modularity in the yeast protein-protein interaction network. [My Copy] Nature, Vol. 430, No. 6995. (1 July 2004), pp. 88-93. by Jing-Dong D. Han, Nicolas Bertin, Tong Hao, et al.Debra S. Goldberg, Gabriel F. Berriz, Lan V. Zhang, Denis Dupuy, Albertha J. Walhout, Michael E. Cusick, Frederick P. Roth, Marc Vidal posted to network by shikin on 2008-05-20 14:57:26 as along with 29 people and 2 groups colmryan mgomes saket lawraga diamantis davidecellai dragonrez lfriedl balajis yoh j3xucite kintoki koller mikaelhuss ruvido gcalda grahamc iris_2001 lpfernandes winterschlaefer Evangelia cdeane shung phoenixzxl stefanoallesina ellakat frohike ksiek carlk kdl GeneGo
	Systems biology for cancer. [My Copy] Current opinion in oncology, Vol. 17, No. 1. (January 2005), pp. 44-48. by I. G. Khalil, C. Hill posted to network systems_biology by shikin on 2008-05-19 18:11:38 as along with 4 people and 1 group Borelli tonamswish vingron wnpx GeneGo
	Network Theory to Understand Microarray Studies of Complex Diseases [My Copy] Current Molecular Medicine, Vol. 6, No. 6. (September 2006), pp. 695-701. by Benson, Mikael, Breitling, Rainer posted to gene_expression network systems_biology by shikin on 2008-05-05 12:28:43 as along with 3 people iris_2001 karfunkel hedbag
	Network Motifs: Simple Building Blocks of Complex Networks [My Copy] Science, Vol. 298, No. 5594. (25 October 2002), pp. 824-827. by R. Milo, S. Shen-Orr, S. Itzkovitz, N. Kashtan, D. Chklovskii, U. Alon posted to network by shikin on 2008-05-04 17:45:59 as along with 72 people and 10 groups antonkratz jaspervoskuilen Sergey_gerbek nurban balabu ocs mjoach makrehchi schwartzjmc poirel tomhebbron arsyed vtraag sergiun fierykylin Akimasa operon dlobo daforerog chasmand wei_tang darian orahcio babakap brewbooks phoenixzxl Md_2007 mtagaya heliopais kaarsinogen galyardt cswinburne mullonc camster korakot aalibes ChaTo imouthesmp Borelli lfriedl alexg balicea tny ssb wnpx ddahlem cmm donade neveaire griota gurkanbebek jtaylor josepe iris_2001 michaelmampaey rebeccamancy karfunkel lenov Evangelia roys tfogal zibuyu maralena stefanoallesina pbull cmor renatomilani carlk applesnow subhacom i-stevenson ethkim complex networks GEB Philosophy_of_Information dbk-lab Blog_and_Wiki_Research kdl FAB-lab ColDyn ADMiRes GeneGo
	Genomic analysis of essentiality within protein networks. [My Copy] Trends Genet, Vol. 20, No. 6. (June 2004), pp. 227-231. by H. Yu, D. Greenbaum, H. Xin Lu, X. Zhu, M. Gerstein posted to network thesis by shikin on 2008-05-04 17:40:25 as along with 5 people and 1 group apaydin niolis nickluscombe grahamc dylanwalker EBI-regulation
	The large-scale organization of metabolic networks [My Copy] Nature, Vol. 407, No. 6804. (05 October 2000), pp. 651-654. by H. Jeong, B. Tombor, R. Albert, Z. N. Oltvai, A. L. Barabasi posted to metabolomics network systems_biology thesis by shikin on 2008-05-04 17:10:53 as along with 30 people and 3 groups jmenche tomhebbron asadrahman sergiun dlobo schwartzjmc muraken kentz camster snuppepuppan jpmague mague alexisgallagher bjorns Borelli shivaram lfriedl cmmorel alexg Shirakawa ddahlem gcalda grahamc jrbanga karfunkel Evangelia shung pmendes stefanoallesina dylanwalker GEB dbk-lab kdl
	Global properties of biological networks. [My Copy] Drug discovery today, Vol. 10, No. 5. (1 March 2005), pp. 365-372. by M. G. Grigorov posted to network systems_biology by shikin on 2008-05-04 13:22:48 as along with 1 group GeneGo
	A novel method for visualizing nuclear hormone receptor networks relevant to drug metabolism. [My Copy] Drug metabolism and disposition: the biological fate of chemicals, Vol. 33, No. 3. (March 2005), pp. 474-481. by S. Ekins, E. Kirillov, E. A. Rakhmatulin, T. Nikolskaya posted to genego network systems_biology toxicology by shikin on 2008-05-04 13:19:07 as along with 1 group GeneGo
	Algorithms for network analysis in systems-ADME/Tox using the MetaCore and MetaDrug platforms [My Copy] Xenobiotica, Vol. 36, No. 10-11. (8220), pp. 877-901. by Ekins, S., Bugrim, et al. A., Brovold, L., Kirillov, E., Nikolsky, Y., Rakhmatulin, E., Sorokina, S., Ryabov, A., Serebryiskaya, T., Melnikov, A., Metz, J., Nikolskaya, T. posted to genego method network systems_biology toxicology by shikin on 2008-05-04 13:08:06 as along with 1 group GeneGo
	The Structure and Function of Complex Networks [My Copy] SIAM Review, Vol. 45, No. 2. (2003), pp. 167-256. by M. E. J. Newman posted to network systems_biology by shikin on 2008-04-21 12:01:58 as along with 37 people and 4 groups Sergey_gerbek halukbingol jsaramak tomhebbron jotwin LaurentHD vmarceau qqwert mrkn ocs brihea chibatching davidecellai diamantis panisson spool deanmalmgren pcarbo matteodellamico eyliu afragop merazzle muraken lshaw jaspervoskuilen timflutre gcalda gi0rgi0ne rcrane nolodie stefanoallesina eustatic skumagai ilkert rrbarb ebalp Borelli complex networks Soslab Complex_Real_Networks EntrepreneurialRisks
	Protein interactions: two methods for assessment of the reliability of high throughput observations. [My Copy] Molecular & cellular proteomics : MCP, Vol. 1, No. 5. (May 2002), pp. 349-356. by Charlotte M. Deane, Łukasz Salwiński, Ioannis Xenarios, David Eisenberg posted to network ppi systems_biology by shikin on 2008-04-17 14:59:39 as along with 16 people and 1 group chica anf lawraga jimineep lptolik zdai tmmurali lfriedl bluto henschel ruvido iris_2001 cdeane Pao-Yang ras chasmand kdl
	How complete are current yeast and human protein-interaction networks? [My Copy] Genome Biology, Vol. 7, No. 11. (01 December 2006), 120. by G. Traver Hart, Arun Ramani, Edward Marcotte posted to network ppi systems_biology by shikin on 2008-04-17 14:25:58 as along with 7 people and 1 group jperkins suteedee waqaralikeble eukfn Pao-Yang carlk phoenixzxl GeneGo
	Genes2Networks: connecting lists of gene symbols using mammalian protein interactions databases [My Copy] BMC Bioinformatics, Vol. 8 (04 October 2007), 372. by Seth I. Berger, Jeremy M. Posner, Avi Ma'ayan posted to network systems_biology by shikin on 2008-04-15 08:14:04 as along with 6 people and 1 group turnersd fhalbrit balicea daforerog guhjy jfr GeneGo
	Identification of the Proliferation/Differentiation Switch in the Cellular Network of Multicellular Organisms [My Copy] PLoS Computational Biology, Vol. 2, No. 11. (1 November 2006), e145. by Kai Xia, Huiling Xue, Dong Dong, et al.Shanshan Zhu, Jiamu Wang, Qingpeng Zhang, Lei Hou, Hua Chen, Ran Tao, Zheng Huang, Zheng Fu, Ye-Guang Chen, Jing-Dong J. Han posted to gene_expression network systems_biology by shikin on 2008-04-15 07:49:08 as along with 3 people and 2 groups dolhuis mingzhi carlk SNE GeneGo
	Protein-protein interaction networks and biology--what's the connection? [My Copy] Nature biotechnology, Vol. 26, No. 1. (January 2008), pp. 69-72. by Luke Hakes, John W. Pinney, David L. Robertson, Simon C. Lovell posted to network systems_biology by shikin on 2008-04-15 07:31:04 as along with 19 people and 1 group ptrobajo colmryan lawraga flbarroso Yanno guhjy tmmurali jfr balicea dullhunk neils mikaelhuss cjeans nedwards biehl mclarenv Yumyai paolomarcatili zdai GeneGo
	Network biology: understanding the cell's functional organization. [My Copy] Nature reviews. Genetics, Vol. 5, No. 2. (February 2004), pp. 101-113. by Albert-László L. Barabási, Zoltán N. Oltvai posted to barabasi network systems_biology by shikin on 2008-04-14 17:00:49 as along with 40 people and 10 groups schwartzjmc daforerog fastjoe23 arsyed thepogoman mtagaya camster snuppepuppan dbk greg guhjy LeightonP hununu felciano mague kuhn textoris rhem1224 lfriedl balajis alexg wnpx jknabe adepace nickluscombe bundschu awooga jdiggans jeremymiller uprock timflutre mikaelhuss gcalda grahamc fishtank jayster4 naegele Evangelia heliopais hryk streptomyces dbk-lab kdl EisenLab TCR_Signaling EBI-regulation SysbioMPI-TCells GeschwindLab generif_paper GeneGo
	Comprehensive curation and analysis of global interaction networks in Saccharomyces cerevisiae [My Copy] Journal of Biology, Vol. 5, No. 4. (08 June 2006), 11. by Teresa Reguly, Ashton Breitkreutz, Lorrie Boucher, et al.Bobby J. Breitkreutz, Gary Hon, Chad Myers, Ainslie Parsons, Helena Friesen, Rose Oughtred, Amy Tong, Chris Stark, Yuen Ho, David Botstein, Brenda Andrews, Charles Boone, Olga Troyanskya, Trey Ideker, Kara Dolinski, Nizar Batada, Mike Tyers posted to ideker network systems_biology by shikin on 2008-04-10 14:12:53 as along with 18 people and 3 groups carlk snuppepuppan tmmurali lfriedl balajis wnpx nickluscombe egralla citecat noano koller grahamc iris_2001 sgoetz s041629 pmendes mtruksa chasmand kdl EBI-regulation GeneGo
	Integration of biological networks and gene expression data using Cytoscape. [My Copy] Nature protocols, Vol. 2, No. 10. (27 September 2007), pp. 2366-2382. by Melissa S. Cline, Michael Smoot, Ethan Cerami, et al.Allan Kuchinsky, Nerius Landys, Chris Workman, Rowan Christmas, Iliana Avila-Campilo, Michael Creech, Benjamin Gross, Kristina Hanspers, Ruth Isserlin, Ryan Kelley, Sarah Killcoyne, Samad Lotia, Steven Maere, John Morris, Keiichiro Ono, Vuk Pavlovic, Alexander R. Pico, Aditya Vailaya, Peng-Liang L. Wang, Annette Adler, Bruce R. Conklin, Leroy Hood, Martin Kuiper, Chris Sander, Ilya Schmulevich, Benno Schwikowski, Guy J. Warner, Trey Ideker, Gary D. Bader posted to ideker network systems_biology by shikin on 2008-04-10 14:10:43 as along with 19 people and 1 group daveGerrard greg badi ptrobajo tonamswish daforerog bertelsen Cortel cswinburne giovenko isimpson emmackinnon yaredo Stew guhjy jfr shung thomaskelder AlexanderPico GeneGo
	Network-based classification of breast cancer metastasis. [My Copy] Molecular systems biology, Vol. 3 (16 October 2007) by Han-Yu Y. Chuang, Eunjung Lee, Yu-Tsueng T. Liu, Doheon Lee, Trey Ideker posted to cancer ideker network systems_biology by shikin on 2008-04-10 10:44:58 as along with 29 people and 4 groups yaredo fesousa ipark-kaist aviad_work AbnerCYH zufar provero jmuhlich Zephyrus ggallone giovenko winterschlaefer isimpson ihpark bertelsen jfr kengg frohike mikaelhuss cjeans zwang cerami abhattac oelemento roys ptrobajo dap5087 saman_vp verdicchio Complex Networks Jarman Lab Bioinformatics GeneGo
	Variations in DNA elucidate molecular networks that cause disease. [My Copy] Nature, Vol. 452, No. 7186. (27 March 2008), pp. 429-435. by Yanqing Chen, Jun Zhu, Pek Yee Y. Lum, et al.Xia Yang, Shirly Pinto, Douglas J. MacNeil, Chunsheng Zhang, John Lamb, Stephen Edwards, Solveig K. Sieberts, Amy Leonardson, Lawrence W. Castellini, Susanna Wang, Marie-France F. Champy, Bin Zhang, Valur Emilsson, Sudheer Doss, Anatole Ghazalpour, Steve Horvath, Thomas A. Drake, Aldons J. Lusis, Eric E. Schadt posted to gene_association genomics network systems_biology by shikin on 2008-03-19 11:33:13 as along with 22 people and 2 groups mnishimu Zephyrus biomcgary daforerog roys druvus nicklynch semrich brianb jbsaltz djkt raiyar lp2 jo_davies caseybrown ptrobajo guhjy echinotrix natstreet sanchezbuelna jfr chrisamiller 4th_floor_JC GeneGo
	Understanding biological functions through molecular networks [My Copy] Cell Research, Vol. 18, No. 2. (01 February 2008), pp. 224-237. by Jing-Dong J. Han posted to network systems_biology by shikin on 2008-02-22 14:51:16 as along with 11 people and 1 group Katieleonard rdiaz aviad_work cmmorel cabbagezs jo_davies mingzhi giorgiofotia maralena phoenixzxl guhjy GeneGo

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gene_expression	97
systems_biology	93
microarray	79
genomics	78
statistics	74
cancer	52
meta-analysis	52
thesis	45
pathway-analysis	38
network	37
psoriasis	33
genego	29
proteomics	28
cnv	26
database	23
r	23
crohn	22
method	21
snp	21
affy	18
gwas	18
enrichment	17
breast	16
gene_association	16
toxicology	16
normalization	15
diabetes	12
illumina	12
integration	12
nephrotoxicity	11
gsea	10
rage	10
bayesian	9
qc	9
software	9
stem_cells	9
temp	9
annotation	8
immunology	8
methylation	8
nature_sysbio_08	8
evolution	7
ideker	7
mirna	6
ppi	6
sequencing	6
solexa	6
workflow	6
clustering	5
kinetics_modeling	5
metabolomics	4
pathway	4
permutation_test	4
synergy	4
classification	3
functional_analysis	3
gene_set	3
hood	3
pancreas	3
rank-aggregation	3
roc	3
rt-pcr	3
sage	3
ap1	2
barabasi	2
coexpression	2
differential_expression	2
history	2
iconix	2
interactome	2
mged	2
signature	2
background_correction	1
batch-correction	1
bg_correction	1
comparison	1
copynumber	1
development	1
genome_browser	1
hgp	1
hmm	1
linguistics	1
maqc	1
misc	1
onthology	1
prostate	1
sample-size	1
transfac	1

shikin's network [37 articles] Export

shikin's tags