brianb's modeling [41 articles] Export

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	Genomic analysis reveals a tight link between transcription factor dynamics and regulatory network architecture [My Copy] Molecular Systems Biology, Vol. 5 (18 August 2009) by Raja Jothi, S. Balaji, Arthur Wuster, et al.Joshua A. Grochow, Jorg Gsponer, Teresa M. Przytycka, L. Aravind, Madan M. Babu posted to network modeling genomics by brianb on 2009-10-09 15:20:14 as along with 12 people ashishanand apocapoc dswan sjcockell zwang fenghezi rdiaz megraw poirel TRHvidsten jjray biomcgary
	Determining Protein Complex Connectivity Using a Probabilistic Deletion Network Derived from Quantitative Proteomics [My Copy] PLoS ONE, Vol. 4, No. 10. (6 October 2009), e7310. by Mihaela E. Sardiu, Joshua M. Gilmore, Michael J. Carrozza, et al.Bing Li, Jerry L. Workman, Laurence Florens, Michael P. Washburn posted to quantitation proteomics modeling interaction by brianb on 2009-10-07 17:37:24 as along with 1 person poirel
	Fast and accurate alignment of multiple protein networks. [My Copy] Journal of computational biology : a journal of computational molecular cell biology, Vol. 16, No. 8. (22 August 2009), pp. 989-999. by Maxim Kalaev, Vineet Bafna, Roded Sharan posted to proteomics network modeling by brianb on 2009-10-06 20:16:53 as along with 4 people balajis Balou nuin chica
	Transforming Boolean models to continuous models: methodology and application to T-cell receptor signaling [My Copy] BMC Systems Biology, Vol. 3, No. 1. (28 September 2009), 98. by Dominik Wittmann, Jan Krumsiek, Julio S. Rodriguez, Douglas Lauffenburger, Steffen Klamt, Fabian Theis posted to sysbio signaling quantitation network modeling by brianb on 2009-10-02 19:09:14 as along with 5 people colinveal perkeo cmzmasek rdiaz peterhilbers
	Proteome-wide Prediction of Signal Flow Direction in Protein Interaction Networks Based on Interacting Domains [My Copy] Mol Cell Proteomics, Vol. 8, No. 9. (1 September 2009), pp. 2063-2070. by Wei Liu, Dong Li, Jian Wang, Hongwei Xie, Yunping Zhu, Fuchu He posted to signaling proteomics modeling interaction by brianb on 2009-09-11 01:27:52 as along with 1 person hryk
	A novel algorithm for detecting differentially regulated paths based on gene set enrichment analysis [My Copy] Bioinformatics, Vol. 25, No. 21. (1 November 2009), pp. 2787-2794. by Andreas Keller, Christina Backes, Andreas Gerasch, et al.Michael Kaufmann, Oliver Kohlbacher, Eckart Meese, Hans-Peter Lenhof posted to network modeling genomics bioinformatics algorithm by brianb on 2009-08-28 19:05:22 as along with 9 people and 1 group bertelsen jperkins tonamswish heliopais dolchan greg zufar rdiaz ptrobajo Orengo Group Journal Picks
	SubpathwayMiner: a software package for flexible identification of pathways. [My Copy] Nucleic acids research, Vol. 37, No. 19. (25 October 2009), gkp667. by Chunquan Li, Xia Li, Yingbo Miao, et al.Qianghu Wang, Wei Jiang, Chun Xu, Jing Li, Junwei Han, Fan Zhang, Binsheng Gong, Liangde Xu posted to network modeling bioinformatics algorithm by brianb on 2009-08-28 19:03:38 as along with 6 people and 1 group davidalee Vincent_Rouilly ptrobajo irenas renatomilani neils Orengo Group Journal Picks
	A survey of visualization tools for biological network analysis. [My Copy] Biodata mining, Vol. 1, No. 1. (28 November 2008), 12. by Georgios A. Pavlopoulos, Anna-Lynn L. Wegener, Reinhard Schneider posted to bioinformatics modeling network by brianb on 2009-07-25 18:45:53 as along with 13 people and 2 groups nolodie abhishek_tiwari eesruiz daforerog lptolik guhjy renatomilani hersh006 behindtherabbit dswan fgibson allysonlister sjcockell ImagCom - Biomedical Text Computing Complex Networks
	Multi-tissue coexpression networks reveal unexpected subnetworks associated with disease [My Copy] Genome Biology, Vol. 10, No. 5. (22 May 2009), R55. by Radu Dobrin, Jun Zhu, Cliona Molony, et al.Carmen Argman, Mark Parrish, Sonia Carlson, Mark Allan, Daniel Pomp, Eric Schadt posted to disease modeling network by brianb on 2009-05-26 17:56:12 as along with 6 people greg winterstream grahamc ptrobajo lp2 roys
	Fuzzy Logic Analysis of Kinase Pathway Crosstalk in TNF/EGF/Insulin-Induced Signaling [My Copy] PLoS Comput Biol, Vol. 5, No. 4. (3 April 2009), e1000340. by Bree B. Aldridge, Julio Saez-Rodriguez, Jeremy L. Muhlich, Peter K. Sorger, Douglas A. Lauffenburger posted to bioinformatics modeling network proteomics by brianb on 2009-04-06 18:11:23 as along with 4 people ptrobajo abhishek_tiwari renatomilani agonzale
	A network biology approach to aging in yeast [My Copy] Proceedings of the National Academy of Sciences, Vol. 106, No. 4. (27 January 2009), pp. 1145-1150. by David R. Lorenz, Charles R. Cantor, James J. Collins posted to modeling network by brianb on 2009-02-04 22:35:23 as along with 4 people TRHvidsten cactus rdiaz bcondon
	InSilicoSpectro: an open-source proteomics library. [My Copy] Journal of proteome research, Vol. 5, No. 3. (March 2006), pp. 619-624. by J. Colinge, A. Masselot, P. Carbonell, R. D. Appel posted to bioinformatics chromatography modeling proteomics by brianb on 2009-01-31 22:45:28 as along with 1 person pablocarb
	Prediction of the isoelectric point of an amino acid based on GA-PLS and SVMs. [My Copy] Journal of chemical information and computer sciences, Vol. 44, No. 1. (b 2004), pp. 161-167. by H. X. Liu, R. S. Zhang, X. J. Yao, M. C. Liu, Z. D. Hu, B. T. Fan posted to bioinformatics electrophoresis modeling by brianb on 2009-01-31 22:43:34 as
	Input-output behavior of ErbB signaling pathways as revealed by a mass action model trained against dynamic data [My Copy] Mol Syst Biol, Vol. 5 (20 January 2009) by William W. Chen, Birgit Schoeberl, Paul J. Jasper, et al.Mario Niepel, Ulrik B. Nielsen, Douglas A. Lauffenburger, Peter K. Sorger posted to modeling network proteomics signaling by brianb on 2009-01-21 17:27:22 as along with 5 people mhellmann agomez agonzale cjryan stringertheory
	An integrated workflow for charting the human interaction proteome: insights into the PP2A system [My Copy] Mol Syst Biol, Vol. 5 (20 January 2009) by Timo Glatter, Alexander Wepf, Ruedi Aebersold, Matthias Gstaiger posted to interaction modeling network proteomics by brianb on 2009-01-21 17:26:03 as along with 2 people phoenixzxl guhjy
	Dynamic map of protein interactions in the Escherichia coli chemotaxis pathway [My Copy] Mol Syst Biol, Vol. 5 (20 January 2009) by David Kentner, Victor Sourjik posted to interaction modeling network proteomics signaling by brianb on 2009-01-21 17:25:08 as along with 1 person jjray
	How to deal with large models[quest] [My Copy] Mol Syst Biol, Vol. 5 (20 January 2009) by William S. Hlavacek posted to modeling network proteomics signaling by brianb on 2009-01-21 17:23:20 as along with 3 people and 1 group sobolevnrm lptolik agonzale baker-group
	Dynamic Proteomics of Individual Cancer Cells in Response to a Drug [My Copy] Science, Vol. 322, No. 5907. (5 December 2008), pp. 1511-1516. by A. A. Cohen, N. Geva-Zatorsky, E. Eden, et al.M. Frenkel-Morgenstern, I. Issaeva, A. Sigal, R. Milo, C. Cohen-Saidon, Y. Liron, Z. Kam, L. Cohen, T. Danon, N. Perzov, U. Alon posted to modeling proteomics quantitation by brianb on 2009-01-20 22:48:53 as along with 15 people tienholin agonzale VGreiff tjchen myzhang Borelli lflorez jessopher reyez jbhiatt caseybrown winterschlaefer sjcockell renatomilani pengchy
	Prion Disease Diagnosis by Proteomic Profiling [My Copy] Journal of Proteome Research, Vol. 0, No. 0. (0000) by Allen Herbst, Sean Mcilwain, Joshua J. Schmidt, Judd M. Aiken, David C. Page, Lingjun Li posted to disease modeling proteomics by brianb on 2009-01-10 19:32:33 as
	Use of high-throughput mass spectrometry to elucidate host-pathogen interactions in Salmonella. [My Copy] Future microbiology, Vol. 3 (December 2008), pp. 625-634. by K. D. Rodland, J. N. Adkins, C. Ansong, et al.S. Chowdhury, N. P. Manes, L. Shi, H. Yoon, R. D. Smith, F. Heffron posted to interaction modeling proteomics by brianb on 2008-12-23 14:56:48 as
	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 localization modeling network proteomics by brianb on 2008-11-13 14:36:02 as along with 6 people tienholin carlk neils grahamc giovenko ptrobajo
	Data-driven modelling of signal-transduction networks [My Copy] Nature Reviews Molecular Cell Biology, Vol. 7, No. 11., pp. 820-828. by Kevin A. Janes, Michael B. Yaffe posted to modeling network signaling by brianb on 2008-10-20 18:20:20 as along with 8 people and 2 groups windman83 babakap cryptochrome guhjy cdppublications winterschlaefer cdpwebadmin shikin CDP GeneGo
	Modelling and analysis of gene regulatory networks [My Copy] Nat Rev Mol Cell Biol, Vol. 9, No. 10. (October 2008), pp. 770-780. by Guy Karlebach, Ron Shamir posted to gene modeling network by brianb on 2008-09-30 21:06:53 as along with 14 people antonkratz agonzale cannin tklee aviad_work kaarsinogen thomaskelder fgibson druvus balicea nedwards dakelley guhjy tmmurali
	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 modeling network by brianb on 2008-09-16 21:22:02 as along with 22 people and 2 groups mnishimu Zephyrus biomcgary daforerog roys druvus nicklynch semrich jbsaltz djkt raiyar lp2 jo_davies shikin caseybrown ptrobajo guhjy echinotrix natstreet sanchezbuelna jfr chrisamiller 4th_floor_JC GeneGo
	Quantitative analysis of HER2-mediated effects on HER2 and epidermal growth factor receptor endocytosis: distribution of homo- and heterodimers depends on relative HER2 levels. [My Copy] The Journal of biological chemistry, Vol. 278, No. 26. (27 June 2003), pp. 23343-23351. by B. S. Hendriks, L. K. Opresko, H. S. Wiley, D. Lauffenburger posted to cancer interaction modeling by brianb on 2008-08-17 22:53:55 as
	Systems biology: On the cell cycle and its switches [My Copy] Nature, Vol. 454, No. 7202. (16 July 2008), pp. 288-289. by Silvia D. M. Santos, James E. Ferrell posted to modeling network sysbio by brianb on 2008-08-08 14:58:53 as along with 2 people reyez cabbagesofdoom
	Improving the success rate of proteome analysis by modeling protein-abundance distributions and experimental designs [My Copy] Nature Biotechnology, Vol. 25, No. 6., pp. 651-655. by Jan Eriksson, David Fenyö posted to chromatography modeling proteomics by brianb on 2008-07-30 15:56:00 as along with 3 people guhjy grahamc nedwards
	Protein Interaction Data Set Highlighted with Human Ras-MAPK/PI3K Signaling Pathways [My Copy] J. Proteome Res. (15 July 2008) by Jian Wang, Yanzhi Yuan, Ying Zhou, et al.Longhua Guo, Lingqiang Zhang, Xuezhang Kuai, Binwei Deng, Zhi Pan, Dong Li, Fuchu He posted to interaction modeling proteomics y2h by brianb on 2008-07-16 02:04:59 as
	Calculation of the isoelectric point of tryptic peptides in the pH 3.5-4.5 range based on adjacent amino acid effects. [My Copy] Electrophoresis, Vol. 29, No. 13. (10 July 2008), pp. 2768-2778. by Benjamin J J. Cargile, Joel R R. Sevinsky, Amal S S. Essader, Jerry P P. Eu, James L L. Stephenson posted to bioinformatics electrophoresis modeling proteomics by brianb on 2008-07-13 01:07:20 as along with 1 person fishtank
	Deducing topology of protein-protein interaction networks from experimentally measured sub-networks [My Copy] BMC Bioinformatics, Vol. 9, No. 1. (2008) by Ling Yang, Thomas Vondriska, Zhangang Han, Robb Maclellan, James Weiss, Zhilin Qu posted to interaction modeling network proteomics by brianb on 2008-07-04 21:01:16 as along with 6 people sergiun cerca satre dolchan renatomilani neils
	Protein microarrays for multiplex analysis of signal transduction pathways. [My Copy] Nat Med, Vol. 10, No. 12. (December 2004), pp. 1390-1396. by S. M. Chan, J. Ermann, L. Su, C. G. Fathman, P. J. Utz posted to arrays modeling proteomics signaling by brianb on 2008-07-03 16:05:26 as along with 2 people and 2 groups kentsis breden FAB-lab SFUAntibodyResearch
	An Immuno-Chemo-Proteomics Method for Drug Target Deconvolution [My Copy] J. Proteome Res. (1 July 2008) by Chaitanya Saxena, Eugene Zhen, Richard E. Higgs, John E. Hale posted to modeling proteomics by brianb on 2008-07-03 15:57:32 as
	Assessing the limits of genomic data integration for predicting protein networks [My Copy] Genome Research, Vol. 15, No. 7. (July 2005), pp. 945-953. by Long J. Lu, Yu Xia, Alberto Paccanaro, Haiyuan Yu, Mark Gerstein posted to bioinformatics genomics modeling network by brianb on 2008-06-05 05:08:41 as along with 17 people and 3 groups ashishanand paccanarolab jaimie aelef okarsligil lfriedl balajis maryee opheliav wnpx mbeautru eukfn grahamc nedwards iris_2001 carlk phoenixzxl Paccanaro Lab kdl Bioinformatics
	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 bioinformatics modeling network proteomics by brianb on 2008-06-05 05:07:23 as along with 27 people shikin carlk isimpson chica saket zufar kaarsinogen giovenko guhjy balicea tmmurali Borelli jwdietrich frohike bootsy nedwards roys mclarenv phoenixzxl schuylrp jfr paolomarcatili gracio thomaskelder ptrobajo raiyar zwang
	NeAT: a toolbox for the analysis of biological networks, clusters, classes and pathways [My Copy] Nucl. Acids Res. (4 June 2008), gkn336. by Sylvain Brohee, Karoline Faust, Gipsi Lima-Mendez, et al.Olivier Sand, Rekin's Janky, Gilles Vanderstocken, Yves Deville, Jacques van Helden posted to bioinformatics modeling network proteomics by brianb on 2008-06-05 04:57:45 as along with 2 people neils balicea
	Probabilistic assembly of human protein interaction networks from label-free quantitative proteomics. [My Copy] Proc Natl Acad Sci U S A (24 January 2008) by Mihaela E E. Sardiu, Yong Cai, Jingji Jin, et al.Selene K K. Swanson, Ronald C C. Conaway, Joan W W. Conaway, Laurence Florens, Michael P P. Washburn posted to bioinformatics interaction modeling network proteomics by brianb on 2008-05-30 04:40:18 as along with 2 people guhjy renatomilani
	Statistics of cellular signal transduction as a race to the nucleus by multiple random walkers in compartment/phosphorylation space [My Copy] Proceedings of the National Academy of Sciences, Vol. 103, No. 45. (7 November 2006), pp. 16752-16757. by Ting Lu, Tongye Shen, Chenghang Zong, Jeff Hasty, Peter G. Wolynes posted to modeling network phosphorylation proteomics signaling by brianb on 2008-05-28 15:10:39 as along with 1 person neils
	Transient heterogeneity in extracellular protease production by Bacillus subtilis [My Copy] Mol Syst Biol, Vol. 4 (15 April 2008) by Jan-Willem Veening, Oleg A. Igoshin, Robyn T. Eijlander, Reindert Nijland, Leendert W. Hamoen, Oscar P. Kuipers posted to modeling quantitation subtilis by brianb on 2008-05-08 19:13:29 as along with 4 people Winzer jjray balabu margaritis
	Quantitative Analysis of Pathways Controlling Extrinsic Apoptosis in Single Cells [My Copy] Molecular Cell, Vol. 30, No. 1. (11 April 2008), pp. 11-25. by John G. Albeck, John M. Burke, Bree B. Aldridge, Mingsheng Zhang, Douglas A. Lauffenburger, Peter K. Sorger posted to apoptosis modeling proteomics quantitation signaling by brianb on 2008-05-08 19:09:55 as along with 3 people and 1 group emiko jaycopeland burkey SorgerLab
	MULTI-PATHWAY MODEL ENABLES PREDICTION OF KINASE INHIBITOR CROSS-TALK EFFECTS ON MIGRATION OF HER2-OVEREXPRESSING MAMMARY EPITHELIAL CELLS [My Copy] Mol Pharmacol (18 March 2008), mol.107.043794. by Neil Kumar, Raffi Afeyan, Hyung-Do Kim, Douglas A. Lauffenburger posted to modeling proteomics quantitation by brianb on 2008-04-28 01:39:33 as
	A connector of two-component regulatory systems promotes signal amplification and persistence of expression. [My Copy] Proc Natl Acad Sci U S A (5 July 2007) by Akinori Kato, Alexander Y Y. Mitrophanov, Eduardo A A. Groisman posted to matlab modeling signaling by brianb on 2008-04-24 15:43:27 as along with 3 people sebastien_vigneau lilith jjray

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proteomics	673
electrophoresis	145
quantitation	144
bioinformatics	137
interaction	78
disease	73
cancer	70
chromatography	61
diganostic	60
phosphorylation	55
network	55
fdr	43
expression	42
modeling	41
gene	40
tissue	37
formaldehyde	37
genomics	34
statistics	33
ptm	33
pathology	32
signaling	31
fragmentation	31
plasma	22
antibody	22
arrays	21
review	20
fluid	19
sample_prep	19
repository	16
topdown	16
bias	15
lcm	15
algorithm	15
silac	13
sysbio	10
mapping	10
isoform	9
xlink	9
itraq	8
sle	8
localization	7
dige	7
prokaryote	5
diabetes	5
ionization	5
time-course	4
imaging	4
annotation	4
hdx	3
structure	3
food	3
ar	3
apoptosis	3
metabolomics	3
standard	3
population	3
rnai	3
csc	3
glycosylation	3
chip	2
snp	2
splicing	2
subtilis	2
autophagy	2
mrm	2
noise	2
metrics	2
y2h	1
immunology	1
mirna	1
visualization	1
spr	1
db	1
toxicity	1
faims	1
fret	1
antimicrobial	1
matlab	1
opinion	1
circulating	1

brianb's modeling [41 articles] Export

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