agonzale's library 773 articles Export

	cPath: open source software for collecting, storing, and querying biological pathways [My Copy] BMC Bioinformatics, Vol. 7, No. 1. (13 November 2006), 497. by Ethan Cerami, Gary Bader, Benjamin Gross, Chris Sander posted to modeling by agonzale on 2009-10-26 05:25:57 as along with 10 people and 2 groups irenas fgibson shikin jfr dquest carmaus bootsy cerami AlexanderPico srp33 dIEMoSIRIS MoSi-Rostock
	Expression of the oscillating gene <I>her1</I> is directly regulated by hairy/enhancer of split, T-box, and suppressor of hairless proteins in the zebrafish segmentation clock [My Copy] Developmental Dynamics, Vol. 238, No. 11. (2009), pp. 2745-2759. by Tim Brend, Scott A. Holley posted to zebrafish segmentation by agonzale on 2009-10-20 02:46:32 as
	Xenopus Rnd1 and Rnd3 GTP-binding proteins are expressed under the control of segmentation clock and required for somite formation. [My Copy] Developmental dynamics : an official publication of the American Association of Anatomists (30 September 2009) by Tadahiro Goda, Chiyo Takagi, Naoto Ueno posted to xenopus segmentation by agonzale on 2009-10-20 02:45:51 as
	Downstream of FGF during mesoderm formation in Xenopus: The roles of Elk-1 and Egr-1 [My Copy] Developmental Biology (30 September 2009) by Oliver Nentwich, Kevin S. Dingwell, A. Nordheim, J. C. Smith posted to xenopus segmentation mapk by agonzale on 2009-10-09 11:00:00 as
	Unbiased Reconstruction of a Mammalian Transcriptional Network Mediating Pathogen Responses [My Copy] Science, Vol. 326, No. 5950. (9 October 2009), pp. 257-263. by Ido Amit, Manuel Garber, Nicolas Chevrier, et al.Ana P. Leite, Yoni Donner, Thomas Eisenhaure, Mitchell Guttman, Jennifer K. Grenier, Weibo Li, Or Zuk, Lisa A. Schubert, Brian Birditt, Tal Shay, Alon Goren, Xiaolan Zhang, Zachary Smith, Raquel Deering, Rebecca C. McDonald, Moran Cabili, Bradley E. Bernstein, John L. Rinn, Alex Meissner, David E. Root, Nir Hacohen, Aviv Regev posted to reconstruction network by agonzale on 2009-10-09 10:57:32 as along with 9 people xianjun inesdesantiago leliavski TRHvidsten gbloeb roys ptrobajo natgoodman tmmurali
	Expression of sprouty2 inhibits B-cell proliferation and is epigenetically silenced in mouse and human B-cell lymphomas [My Copy] Blood, Vol. 113, No. 11. (12 March 2009), pp. 2478-2487. by Matthew J. Frank, David W. Dawson, Steven J. Bensinger, et al.Jason S. Hong, Wendy M. Knosp, Lizhong Xu, Cynthia E. Balatoni, Eric L. Allen, Rhine R. Shen, Dafna Bar-Sagi, Gail R. Martin, Michael A. Teitell posted to segmentation mouse mapk by agonzale on 2009-10-06 01:28:33 as
	Negative-feedback regulation of FGF signalling by DUSP6/MKP-3 is driven by ERK1/2 and mediated by Ets factor binding to a conserved site within the DUSP6/MKP-3 gene promoter. [My Copy] The Biochemical journal, Vol. 412, No. 2. (1 June 2008), pp. 287-298. by Maria Ekerot, Marios P. Stavridis, Laurent Delavaine, et al.Michael P. Mitchell, Christopher Staples, David M. Owens, Iain D. Keenan, Robin J. Dickinson, Kate G. Storey, Stephen M. Keyse posted to segmentation mouse mapk by agonzale on 2009-10-06 01:15:07 as
	A familial 593-kb microdeletion of 16p11.2 associated with mental retardation and hemivertebrae. [My Copy] European journal of medical genetics (19 September 2009) by Keiko Shimojima, Takehiko Inoue, Yuji Fujii, Kousaku Ohno, Toshiyuki Yamamoto posted to segmentation human by agonzale on 2009-10-05 01:40:31 as
	Genetic interaction between <I>Lrp6</I> and <I>Wnt5a</I> during mouse development [My Copy] Developmental Dynamics, Vol. 9999, No. 9999. (2009), NA. by Emma Andersson, Lenka Bryjova, Kristin Biris, Terry P. Yamaguchi, Ernest Arenas, Vít&ecaron;zslav Bryja posted to segmentation mouse by agonzale on 2009-10-05 01:36:50 as
	A module of negative feedback regulators defines growth factor signaling [My Copy] Nature Genetics, Vol. 39, No. 4. (25 February 2007), pp. 503-512. by Ido Amit, Ami Citri, Tal Shay, et al.Yiling Lu, Menachem Katz, Fan Zhang, Gabi Tarcic, Doris Siwak, John Lahad, Jasmine Jacob-Hirsch, Ninette Amariglio, Nora Vaisman, Eran Segal, Gideon Rechavi, Uri Alon, Gordon B. Mills, Eytan Domany, Yosef Yarden posted to mapk by agonzale on 2009-09-28 03:19:00 as along with 5 people ptrobajo guhjy jfr pjasper klu
	Diverse two-dimensional input functions control bacterial sugar genes. [My Copy] Molecular cell, Vol. 29, No. 6. (28 March 2008), pp. 786-792. by Shai Kaplan, Anat Bren, Alon Zaslaver, Erez Dekel, Uri Alon posted to hill fluorescence by agonzale on 2009-09-28 03:08:00 as along with 3 people kentz siebert kentsis
	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 dynamics by agonzale on 2009-09-28 02:24:05 as along with 14 people VGreiff tjchen myzhang brianb Borelli lflorez jessopher reyez jbhiatt caseybrown winterschlaefer sjcockell renatomilani pengchy
	Executing multicellular differentiation: quantitative predictive modelling of C.elegans vulval development [My Copy] Bioinformatics, Vol. 25, No. 19. (1 October 2009), 2624. by Nicola Bonzanni, Elzbieta Krepska, K. Anton Feenstra, et al.Wan Fokkink, Thilo Kielmann, Henri Bal, Jaap Heringa posted to network multicellular modeling by agonzale on 2009-09-28 02:07:44 as along with 1 person laurabertens
	Fgf8 morphogen gradient forms by a source-sink mechanism with freely diffusing molecules [My Copy] Nature, Vol. 461, No. 7263. (09 September 2009), pp. 533-536. by Shuizi R. Yu, Markus Burkhardt, Matthias Nowak, et al.Jonas Ries, Zdenek Petrasek, Steffen Scholpp, Petra Schwille, Michael Brand posted to parameter modeling diffusion by agonzale on 2009-09-24 08:39:38 as along with 3 people chigle davidcsterratt paulschlesinger
	Automated seeding of specialised wiki knowledgebases with BioKb [My Copy] BMC Bioinformatics, Vol. 10, No. 1. (2009), 291. by Jonathan Manning, Ann Hedley, John Mullins, Donald Dunbar posted to wiki by agonzale on 2009-09-23 09:33:12 as along with 7 people perkeo kshameer ptrobajo neils dullhunk barriot druvus
	Logical modelling of cell cycle control in eukaryotes: a comparative study [My Copy] Mol. BioSyst. (2009) by Adrien Faure, Denis Thieffry posted to oscillations logical_models by agonzale on 2009-09-23 09:29:04 as
	A Method for determining the dobustness of bio-molecular oscillator models [My Copy] BMC Systems Biology, Vol. 3, No. 1. (2009), 95. by Reza Ghaemi, Jing Sun, Pablo Iglesias, Domitilla Del Vecchio posted to robustness_analysis oscillations modeling by agonzale on 2009-09-23 09:27:35 as along with 1 person abhishek_tiwari
	Requirement of mesodermal retinoic acid generated by Raldh2 for posterior neural transformation [My Copy] Mechanisms of Development, Vol. 122, No. 2. (February 2005), pp. 145-155. by Natalia Molotkova, Andrei Molotkov, I. Ovidiu Sirbu, Gregg Duester posted to neural_tube mouse by agonzale on 2009-09-15 03:57:39 as
	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 review network modeling by agonzale on 2009-09-03 07:28:30 as along with 14 people antonkratz cannin tklee aviad_work kaarsinogen thomaskelder fgibson druvus balicea brianb nedwards dakelley guhjy tmmurali
	Scaling of the BMP activation gradient in Xenopus embryos [My Copy] Nature, Vol. 453, No. 7199. (26 June 2008), pp. 1205-1211. by Danny Ben-Zvi, Ben-Zion Shilo, Abraham Fainsod, Naama Barkai posted to modeling gradient by agonzale on 2009-09-03 04:39:10 as along with 1 person alhufton
	Probing the Limits to Positional Information [My Copy] Vol. 130, No. 1. (13 July 2007), pp. 153-164. by Thomas Gregor, David W. Tank, Eric F. Wieschaus, William Bialek posted to modeling drosophila by agonzale on 2009-09-01 06:06:43 as
	Stable, Precise, and Reproducible Patterning of Bicoid and Hunchback Molecules in the Early Drosophila Embryo [My Copy] PLoS Comput Biol, Vol. 5, No. 8. (28 August 2009), e1000486. by Yurie Okabe-Oho, Hiroki Murakami, Suguru Oho, Masaki Sasai posted to modeling drosophila by agonzale on 2009-08-31 03:31:24 as along with 1 person keigoi
	hunchback Functions as a Segmentation Gene in the Spider Achaearanea tepidariorum [My Copy] Vol. 19, No. 16. (25 August 2009), pp. 1333-1340. by Evelyn E. Schwager, Matthias Pechmann, Natàlia M. Feitosa, Alistair P. Mcgregor, Wim G. M. Damen posted to segmentation insect by agonzale on 2009-08-26 08:04:37 as
	Monte Carlo analysis of an ODE Model of the Sea Urchin Endomesoderm Network. [My Copy] BMC systems biology, Vol. 3, No. 1. (2009), 83. by Clemens Kühn, Christoph Wierling, Alexander Kühn, et al.Edda Klipp, Georgia Panopoulou, Hans Lehrach, Albert J. Poustka posted to parameter_estimation ode by agonzale on 2009-08-24 11:16:45 as along with 3 people reyez mjoach abhishek_tiwari
	A mass action model of a Fibroblast Growth Factor signaling pathway and its simplification. [My Copy] Bulletin of mathematical biology, Vol. 70, No. 8. (1 November 2008), pp. 2229-2263. by E. A. Gaffney, J. K. Heath, M. Z. Kwiatkowska posted to ode modeling fgf by agonzale on 2009-08-24 10:46:07 as
	Computational approaches to parameter estimation and model selection in immunology [My Copy] Journal of Computational and Applied Mathematics, Vol. 184, No. 1. (01 December 2005), pp. 50-76. by C. Baker, G. Bocharov, J. Ford, et al.P. Lumb, S. Norton, C. Paul, T. Junt, P. Krebs, B. Ludewig posted to parameter_estimation delay dde by agonzale on 2009-08-21 06:57:33 as
	Biological pathways as communicating computer systems. [My Copy] Journal of cell science, Vol. 122, No. Pt 16. (15 August 2009), pp. 2793-2800. by Marta Z. Kwiatkowska, John K. Heath posted to reconstruction network inference by agonzale on 2009-08-21 04:31:56 as along with 4 people and 1 group daforerog cmura grahamc barry McCammon
	Retroposition and evolution of the DNA-binding motifs of YY1, YY2 and REX1. [My Copy] Nucleic acids research, Vol. 35, No. 10. (2007), pp. 3442-3452. by Jeong Do D. Kim, Christopher Faulk, Joomyeong Kim posted to yy1 mouse by agonzale on 2009-08-18 04:30:12 as
	An analysis of genes regulated by the multi-functional transcriptional regulator Yin Yang-1. [My Copy] Nucleic acids research, Vol. 22, No. 24. (11 December 1994), pp. 5151-5155. by A. Shrivastava, K. Calame posted to yy1 mouse by agonzale on 2009-08-18 04:14:04 as along with 1 person aalibes
	YY1's longer DNA-binding motifs. [My Copy] Genomics, Vol. 93, No. 2. (February 2009), pp. 152-158. by Jeong do Kim, Joomyeong Kim posted to yy1 mouse by agonzale on 2009-08-18 04:09:39 as along with 2 people and 3 groups absterga sebastien_vigneau X-chromosome inactivation Imprinting Epigenetics
	Comparing different ODE modelling approaches for gene regulatory networks [My Copy] Journal of Theoretical Biology, Vol. 261, No. 4. (21 December 2009), pp. 511-530. by A. Polynikis, S. J. Hogan, M. di Bernardo posted to review ode modeling by agonzale on 2009-08-14 06:06:47 as along with 1 person joseph_x_zhou
	Modular logical modelling of the budding yeast cell cycle [My Copy] Mol. BioSyst. (2009) by Adrien Faure, Aurelien Naldi, Fabrice Lopez, Claudine Chaouiya, Andrea Ciliberto, Denis Thieffry posted to logical by agonzale on 2009-08-03 08:43:31 as along with 1 person karthikraman
	Stem cells, signals and vertebrate body axis extension [My Copy] Development, Vol. 136, No. 10. (15 May 2009), pp. 1591-1604. by Valerie Wilson, Isabel Olivera-Martinez, Kate G. Storey posted to mouse segmentation stem_cells by agonzale on 2009-07-16 10:59:24 as
	Two distinct sources for a population of maturing axial progenitors [My Copy] Development, Vol. 134, No. 15. (1 August 2007), pp. 2829-2840. by Noemi Cambray, Valerie Wilson posted to mouse segmentation stem_cells by agonzale on 2009-07-16 10:58:44 as
	Increased Cdx protein dose effects upon axial patterning in transgenic lines of mice [My Copy] Development, Vol. 135, No. 15. (1 August 2008), pp. 2511-2520. by Stephen J. Gaunt, Deborah Drage, Richard C. Trubshaw posted to cdx mouse segmentation by agonzale on 2009-07-16 10:58:10 as
	Systems biology: Table of suppliers [My Copy] Nature, Vol. 460, No. 7253. (16 July 2009), pp. 419-420. posted to review systems_biology by agonzale on 2009-07-16 02:17:26 as
	Systems biology: Playing by the rules [My Copy] Nature, Vol. 460, No. 7253. (16 July 2009), pp. 417-417. posted to reviews systems_biology by agonzale on 2009-07-16 02:16:06 as along with 2 people leemond31 dswan
	Systems biology: Untangling the protein web [My Copy] Nature, Vol. 460, No. 7253. (15 July 2009), pp. 415-418. by Nathan Blow posted to review systems_biology by agonzale on 2009-07-16 02:13:58 as along with 14 people and 1 group robertrentzsch pekrau apocapoc psique leemond31 colmryan reyez carlk guhjy saket tmmurali dswan dullhunk renatomilani Orengo Group Journal Picks
	Wnt-3a is required for somite specification along the anteroposterior axis of the mouse embryo and for regulation of cdx-1 expression [My Copy] Mechanisms of Development, Vol. 103, No. 1-2. (May 2001), pp. 27-33. by M. Ikeya posted to mouse segmentation wnt by agonzale on 2009-07-09 02:44:28 as
	Multiple joint and skeletal patterning defects caused by single and double mutations in the mouse Gdf6 and Gdf5 genes [My Copy] Developmental Biology, Vol. 254, No. 1. (01 February 2003), pp. 116-130. by S. Settlejr, R. Rountree, A. Sinha, A. Thacker, K. Higgins, D. Kingsley posted to human segmentation by agonzale on 2009-07-09 02:13:22 as
	Lack of evidence of WNT3A as a candidate gene for congenital vertebral malformations [My Copy] Scoliosis, Vol. 2, No. 1. (23 September 2007), 13. by Nader Ghebranious, Cathleen Raggio, Robert Blank, et al.Elizabeth Mcpherson, James Burmester, Lynn Ivacic, Kristen Rasmussen, Jennifer Kislow, Ingrid Glurich, F. Stig Jacobsen, Thomas Faciszewski, Richard Pauli, Oheneba B. Adjei, Philip Giampietro posted to human segmentation by agonzale on 2009-07-09 02:11:50 as
	Incomplete penetrance and phenotypic variability characterize Gdf6-attributable oculo-skeletal phenotypes [My Copy] Hum. Mol. Genet., Vol. 18, No. 6. (15 March 2009), pp. 1110-1121. by Mika Asai-Coakwell, Curtis R. French, Ming Ye, et al.Kamal Garcha, Karin Bigot, Anoja G. Perera, Karen Staehling-Hampton, Silvina C. Mema, Bhaskar Chanda, Arcady Mushegian, Steven Bamforth, Michael R. Doschak, Guang Li, Matthew B. Dobbs, Philip F. Giampietro, Brian P. Brooks, Perumalsamy Vijayalakshmi, Yves Sauve, Marc Abitbol, Periasamy Sundaresan, Veronica van Heyningen, Olivier Pourquie, T. Michael Underhill, Andrew J. Waskiewicz, Ordan J. Lehmann posted to human segmentation by agonzale on 2009-07-09 02:11:08 as
	Evaluation of SLC35A3 as a candidate gene for human vertebral malformations. [My Copy] American journal of medical genetics. Part A, Vol. 140, No. 12. (15 June 2006), pp. 1346-1348. by N. Ghebranious, J. K. Burmester, I. Glurich, et al.E. McPherson, L. Ivacic, J. Kislow, K. Rasmussen, V. Kumar, C. L. Raggio, R. D. Blank, F. S. Jacobsen, T. Faciszewski, J. Womack, P. F. Giampietro posted to cow segmentation by agonzale on 2009-07-09 02:10:00 as
	A missense mutation in the bovine SLC35A3 gene, encoding a UDP-N-acetylglucosamine transporter, causes complex vertebral malformation [My Copy] Genome Research, Vol. 16, No. 1. (January 2006), pp. 97-105. by Bo Thomsen, Per Horn, Frank Panitz, et al.Emøke Bendixen, Anette H. Petersen, Lars-Erik Holm, Vivi H. Nielsen, Jørgen S. Agerholm, Jens Arnbjerg, Christian Bendixen posted to cow segmentation by agonzale on 2009-07-09 02:08:50 as
	<I>DLL3</I> as a candidate gene for vertebral malformations [My Copy] American Journal of Medical Genetics Part A, Vol. 140A, No. 22. (2006), pp. 2447-2453. by Philip F. Giampietro, Cathleen L. Raggio, Cory Reynolds, et al.Nader Ghebranious, James K. Burmester, Ingrid Glurich, Kristen Rasmussen, Elizabeth Mcpherson, Richard M. Pauli, Sanjay K. Shukla, Sajid Merchant, F. Stig Jacobsen, Thomas Faciszewski, Robert D. Blank posted to human segmentation by agonzale on 2009-07-09 02:02:06 as
	Cdx1 and Cdx2 are functionally equivalent in vertebral patterning [My Copy] Developmental Biology, Vol. 330, No. 1. (01 June 2009), pp. 114-122. by Joanne G. A. Savory, Nicolas Pilon, Stephanie Grainger, et al.Jean-René Sylvestre, Mélanie Béland, Martin Houle, Karen Oh, David Lohnes posted to mouse segmentation by agonzale on 2009-07-09 02:00:53 as along with 1 person rk
	Notch signalling in the paraxial mesoderm is most sensitive to reduced Pofut1 levels during early mouse development. [My Copy] BMC developmental biology, Vol. 9 (22 January 2009), 6. by K. Schuster-Gossler, B. Harris, K. R. Johnson, J. Serth, A. Gossler posted to mouse segmentation by agonzale on 2009-07-07 04:05:47 as
	Smad6 inhibits the transcriptional activity of Tbx6 through mediating its degradation. [My Copy] The Journal of biological chemistry (26 June 2009) by Yue-Lei L. Chen, Bin Liu, Zhen-Ning N. Zhou, et al.Rui-Ying Y. Hu, Cong Fei, Zhi-Hui H. Xie, Xiaoyan Ding posted to mouse segmentation by agonzale on 2009-07-07 01:21:00 as
	Morphological features of tail bud development in truncate mouse mutants. [My Copy] Cells, tissues, organs, Vol. 178, No. 1. (2004), pp. 23-32. by D. Mitrecić, L. Kostović-Knezević, S. Gajović posted to mouse segmentation by agonzale on 2009-06-30 09:48:37 as
	Effect of retinoic acid signaling on Wnt/β-catenin and FGF signaling during body axis extension [My Copy] Gene Expression Patterns (17 June 2009) by Xianling Zhao, Gregg Duester posted to mouse segmentation by agonzale on 2009-06-30 01:12:16 as

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segmentation	252
drosophila	249
ap_boundary	178
mouse	158
experimental	156
dv_boundary	70
tfbs	63
thermodynamic_model	59
modeling	55
network	26
dde	21
parameter_estimation	21
logical	16
oscillations	16
mapk	13
human	12
zebrafish	11
fgf	10
inference	9
chick	8
hedgehog	8
plde	8
reviews	8
synchronization	8
xenopus	8
gene	7
parameter	7
retinoic	6
review	6
values	6
wing_disc	6
equation	5
mackey-glass	5
notch	5
ode	5
circadian	3
delay	3
erk	3
kuramoto	3
mek1	3
reconstruction	3
snail	3
systems_biology	3
visualization	3
wing	3
wnt	3
yy1	3
boolean	2
cow	2
dynamics	2
insect	2
methylation	2
promoter	2
psm	2
software	2
stem_cells	2
stochastic	2
synthetic_biology	2
cdx	1
continuation	1
cyclinb1	1
development	1
diffusion	1
fluorescence	1
follicle	1
fuzzy_logic	1
gradient	1
hes7	1
hill	1
kinase	1
logic	1
logical_models	1
medaka	1
metabolic	1
multicellular	1
neural_tube	1
numerical	1
pde	1
physics	1
robustness_analysis	1
self-repressed	1
self-repressed-gene	1
simulation	1
stability	1
tbox	1
topology	1
translation	1
wiki	1

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