mdstobbe's library 63 articles Export

	Organization and integration of biomedical knowledge with concept maps for key peroxisomal pathways [My Copy] Bioinformatics, Vol. 24, No. 16. (15 August 2008), pp. i21-27. by A. M. Willemsen, G. A. Jansen, J. C. Komen, et al.S. van Hooff, H. R. Waterham, P. M. T. Brites, R. J. A. Wanders, A. H. C. van Kampen posted to bioexpert by mdstobbe on 2009-07-20 15:34:23 as along with 2 people guhjy ptrobajo
	Genome annotation errors in pathway databases due to semantic ambiguity in partial EC numbers [My Copy] Nucl. Acids Res., Vol. 33, No. 13. (20 July 2005), pp. 4035-4039. by M. L. Green, P. D. Karp posted to ec numbers by mdstobbe on 2009-07-20 15:28:46 as
	ConsensusPathDB--a database for integrating human functional interaction networks. [My Copy] Nucleic acids research, Vol. 37, No. Database issue. (21 January 2009), gkn698. by Atanas Kamburov, Christoph Wierling, Hans Lehrach, Ralf Herwig posted to consensus metabolic network by mdstobbe on 2009-07-20 14:57:09 as along with 7 people irenas ptrobajo lptolik guhjy barriot thomaskelder renatomilani
	Human metabolic network reconstruction and its impact on drug discovery and development☆ [My Copy] Drug Discovery Today, Vol. 13, No. 9-10. (May 2008), pp. 402-408. by H. Ma, I. Goryanin posted to metabolic network by mdstobbe on 2009-07-20 14:37:40 as along with 2 people mingzhi guhjy
	Technologies for integrating biological data. [My Copy] Brief Bioinform, Vol. 3, No. 4. (December 2002), pp. 389-404. by L. Wong posted to ar articleconsensus integration by mdstobbe on 2009-04-12 21:45:59 as along with 1 person and 1 group irenas dbk-lab
	Patikaweb: a Web interface for analyzing biological pathways through advanced querying and visualization [My Copy] Bioinformatics, Vol. 22, No. 3. (1 February 2006), pp. 374-375. by U. Dogrusoz, E. Z. Erson, E. Giral, et al.E. Demir, O. Babur, A. Cetintas, R. Colak posted to articleconsensus database pathway visualization by mdstobbe on 2009-04-12 21:31:00 as
	Systems Biology Metabolic Modeling Assistant (SBMM): An on-tology-based tool for the integration of metabolic data in kinetic modeling. [My Copy] Bioinformatics (Oxford, England) (2 February 2009) by Armando Reyes-Palomares, Raul Montañez, Alejando Del Real-Chicharro, et al.Othmane Chniber, Amine Kerzazi, Ismael Navas-Delgado, Miguel Ángel A. Medina, José Aldana A. Montes, Francisca Sánchez-Jiménez posted to flux kegg sbml by mdstobbe on 2009-03-25 12:29:45 as along with 6 people and 1 group sobolevnrm agomez imina dagmar allysonlister dullhunk baker-group
	Inferring pathways from gene lists using a literature-derived network of biological relationships [My Copy] Bioinformatics, Vol. 21, No. 6. (15 March 2005), pp. 788-793. by Rajagopalan Dilip, Agarwal Pankaj posted to humancyc by mdstobbe on 2009-03-24 10:52:52 as
	Pathway analysis in metabolic databases via differential metabolic display (DMD). [My Copy] Bioinformatics (Oxford, England), Vol. 16, No. 9. (September 2000), pp. 825-836. by R. Küffner, R. Zimmer, T. Lengauer posted to analysis differences kegg pathway by mdstobbe on 2009-03-20 07:30:37 as along with 4 people laurabertens reyez kabookie shung
	Supervised enzyme network inference from the integration of genomic data and chemical information. [My Copy] Bioinformatics, Vol. 21 Suppl 1 (1 June 2005) by Y. Yamanishi, J. P. Vert, M. Kanehisa posted to ec inference network numbers by mdstobbe on 2009-03-20 07:27:11 as along with 4 people rabbat rcraig bioinfo iris_2001
	ComPath: comparative enzyme analysis and annotation in pathway/subsystem contexts [My Copy] BMC Bioinformatics, Vol. 9 (06 March 2008), 145. by Kwangmin Choi, Sun Kim posted to kegg pathway by mdstobbe on 2009-03-19 09:28:09 as along with 2 people barriot guhjy
	Functional profiling of the Saccharomyces cerevisiae genome [My Copy] Nature, Vol. 418, No. 6896. (25 July 2002), pp. 387-391. by Guri Giaever, Angela M. Chu, Li Ni, et al.Carla Connelly, Linda Riles, Steeve Veronneau, Sally Dow, Ankuta Lucau-Danila, Keith Anderson, Bruno Andre, Adam P. Arkin, Anna Astromoff, Mohamed El Bakkoury, Rhonda Bangham, Rocio Benito, Sophie Brachat, Stefano Campanaro, Matt Curtiss, Karen Davis, Adam Deutschbauer, Karl-Dieter Entian, Patrick Flaherty, Francoise Foury, David J. Garfinkel, Mark Gerstein, Deanna Gotte, Ulrich Guldener, Johannes H. Hegemann, Svenja Hempel, Zelek Herman, Daniel F. Jaramillo, Diane E. Kelly, Steven L. Kelly, Peter Kotter, Darlene LaBonte, David C. Lamb, Ning Lan, Hong Liang, Hong Liao, Lucy Liu, Chuanyun Luo, Marc Lussier, Rong Mao, Patrice Menard, Siew L. Ooi, Jose L. Revuelta, Christopher J. Roberts, Matthias Rose, Petra Ross-Macdonald, Bart Scherens, Greg Schimmack, Brenda Shafer, Daniel D. Shoemaker, Sharon Sookhai-Mahadeo, Reginald K. Storms, Jeffrey N. Strathern, Giorgio Valle, Marleen Voet, Guido Volckaert, Ching-yun Wang, Teresa R. Ward, Julie Wilhelmy, Elizabeth A. Winzeler, Yonghong Yang, Grace Yen, Elaine Youngman, Kexin Yu, Howard Bussey, Jef D. Boeke, Michael Snyder, Peter Philippsen, Ronald W. Davis, Mark Johnston posted to kegg by mdstobbe on 2009-02-12 07:29:04 as along with 16 people and 3 groups michaelbarton myzhang thegoose2 tharris pcahan1 lfriedl balajis rebeccahainess nirfriedman koller raiyar cjeans jiny hplatero chasmand dylanwalker C. elegans / WormBase kdl steinmetzlab
	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 localization nucleus by mdstobbe on 2009-01-23 07:05:42 as along with 5 people firyarn84 mhamada grahamc druvus neils
	Incorporating pathway information into boosting estimation of high-dimensional risk prediction models [My Copy] BMC Bioinformatics, Vol. 10, No. 1. (2009), 18. by Harald Binder, Martin Schumacher posted to application kegg regulatory by mdstobbe on 2009-01-14 09:33:42 as along with 5 people and 1 group zufar ajbattle jfr rdiaz guhjy Bioinformatics
	Identifying differential correlation in gene/pathway combinations [My Copy] BMC Bioinformatics, Vol. 9, No. 1. (18 November 2008), 488. by Rosemary Braun, Leslie Cope, Giovanni Parmigiani posted to application kegg microarray by mdstobbe on 2008-11-24 07:14:22 as along with 11 people dolchan dipenps zufar jfr shikin imina rdiaz renatomilani lptolik barriot ptrobajo
	Can sugars be produced from fatty acids? A test case for pathway analysis tools [My Copy] Bioinformatics (19 September 2008), btn500. by Luis F. Figueiredo, Stefan Schuster, Christoph Kaleta, David A. Fell posted to application network pathway by mdstobbe on 2008-11-05 13:12:46 as along with 4 people guhjy sg45653 dullhunk renatomilani
	Assessing Systems Properties of Yeast Mitochondria through an Interaction Map of the Organelle [My Copy] PLoS Genetics, Vol. 2, No. 10. (1 October 2006), e170. by Fabiana Perocchi, Lars J. Jensen, Julien Gagneur, et al.Uwe Ahting, Christian von Mering, Peer Bork, Holger Prokisch, Lars M. Steinmetz posted to mitochondria by mdstobbe on 2008-11-04 14:33:25 as along with 3 people ptrobajo kristen larsjuhljensen
	The Rough Guide to In Silico Function Prediction, or How To Use Sequence and Structure Information To Predict Protein Function [My Copy] PLoS Comput Biol, Vol. 4, No. 10. (31 October 2008), e1000160. by Marco Punta, Yanay Ofran posted to function prediction protein by mdstobbe on 2008-11-03 07:42:31 as along with 20 people and 1 group ucbcjbm pansapiens kiekyon Thaverkamp niallhaslam daforerog Zalanszabo bpcusack Katje joseph_x_zhou taguchi sjcockell markchen ptrobajo chad_davis druvus giovenko nilanjanroy reyez GeeSharpMinor microbiology_nijmegen
	Support Vector Machines and Kernels for Computational Biology [My Copy] PLoS Comput Biol, Vol. 4, No. 10. (31 October 2008), e1000173. by Asa Ben-Hur, Cheng S. Ong, Sören Sonnenburg, Bernhard Schölkopf, Gunnar Rätsch posted to svm by mdstobbe on 2008-11-03 07:42:03 as along with 32 people and 3 groups guhjy VGreiff tomhebbron ucbcjbm thegoose Zephyrus phoenixzxl winterschlaefer kshameer svozil mmartin jfr MarcoAlvarez sobolevnrm Yanno Scis0000002 srp33 GustavoLacerda nuin rdiaz dakelley rschulz Borelli taguchi kristina bayesian chad_davis tny giovenko markchen druvus GeeSharpMinor Bioinformatics baker-group VisionLab
	Protein translocation into peroxisomes by ring-shaped import receptors [My Copy] FEBS Letters, Vol. 581, No. 25. (16 October 2007), pp. 4795-4802. by W. Stanley, K. Fodor, M. Martirenom, W. Schliebs, M. Wilmanns posted to peroxisome by mdstobbe on 2008-10-30 09:29:18 as
	Network-based prediction of human tissue-specific metabolism. [My Copy] Nature biotechnology, Vol. 26, No. 9. (17 September 2008), pp. 1003-1010. by Tomer Shlomi, Moran N. Cabili, Markus J. Herrgård, Bernhard Ø. Palsson, Eytan Ruppin posted to human network palsson tissue by mdstobbe on 2008-10-24 14:41:20 as along with 12 people phoenixzxl grahamc yaredo Sonix jfr roys klo peterli ptrobajo renatomilani zwang guhjy
	PathCase: Pathways Database System [My Copy] Bioinformatics (26 August 2008), btn459. by B. Elliott, M. Kirac, A. Cakmak, et al.G. Yavas, S. Mayes, E. Cheng, Y. Wang, C. Gupta, G. Ozsoyoglu, Z. M. Ozsoyoglu posted to articleconsensus pathcase pathway by mdstobbe on 2008-10-20 11:16:57 as along with 10 people and 2 groups AlexanderPico jfr Zephyrus ptrobajo druvus dullhunk guhjy aconesa renatomilani thomaskelder ConklinLab Roswell Cancer Crosstalk
	Analysis and comparison of metabolic pathway databases [My Copy] Brief Bioinform, Vol. 2, No. 2. (1 January 2001), pp. 126-142. by Ulrike Wittig, Ann De Beuckelaer posted to articleconsensus comparison pathway by mdstobbe on 2008-10-13 13:23:42 as along with 1 person renatomilani
	Structure-Guided Comparative Analysis of Proteins: Principles, Tools, and Applications for Predicting Function [My Copy] PLoS Comput Biol, Vol. 4, No. 9. (2008), e1000151. by Raja Mazumder, Sona Vasudevan posted to blast function prediction by mdstobbe on 2008-09-29 07:21:25 as along with 9 people and 2 groups i000 pengchy raik chad_davis zwang druvus reyez barry jameswasmuth structural_bioinformatics Bioinformatics
	Predicting Pathway Membership via Domain Signatures [My Copy] Bioinformatics (1 August 2008), btn403. by Holger Frohlich, Mark Fellmann, Holger Sultmann, Annemarie Poustka, Tim Beissbarth posted to kegg membership pathway prediction by mdstobbe on 2008-09-26 12:26:59 as along with 9 people le-gal druvus jameswasmuth kshameer jfr barriot ptrobajo phoenixzxl guhjy
	Genome-scale classification of metabolic reactions and assignment of EC numbers with self-organizing maps [My Copy] Bioinformatics, Vol. 24, No. 19. (1 October 2008), pp. 2236-2244. by Diogo A. Latino, Qing-You Zhang, Joao Aires-De-Sousa posted to ec kegg numbers reactions by mdstobbe on 2008-09-26 12:22:10 as along with 1 person shung
	Databases, data tombs and dust in the wind [My Copy] Bioinformatics, Vol. 24, No. 19. (1 October 2008), pp. 2127-2128. by Jonathan D. Wren, Alex Bateman posted to database by mdstobbe on 2008-09-26 12:19:32 as along with 16 people and 1 group applebyb thegoose Rosetta fgibson hpiwowar ajaymalik cisevol renatomilani sjcockell reyez Yanno druvus GeeSharpMinor neils dullhunk jandot BergmanLab
	Network inference algorithms elucidate Nrf2 regulation of mouse lung oxidative stress. [My Copy] PLoS computational biology, Vol. 4, No. 8. (2008), e1000166. by R. C. Taylor, G. Acquaah-Mensah, M. Singhal, D. Malhotra, S. Biswal posted to inference network svm by mdstobbe on 2008-09-01 07:19:04 as along with 2 people leemond31 ptrobajo
	Systematic identification of human mitochondrial disease genes through integrative genomics [My Copy] Nat Genet, Vol. 38, No. 5. (02 May 2006), pp. 576-582. by Sarah Calvo, Mohit Jain, Xiaohui Xie, et al.Sunil A. Sheth, Betty Chang, Olga A. Goldberger, Antonella Spinazzola, Massimo Zeviani, Steven A. Carr, Vamsi K. Mootha posted to genomic integrative mitochondrial nazanin by mdstobbe on 2008-08-21 11:07:45 as along with 6 people and 2 groups avilella kentsis balicea nirfriedman raiyar ptrobajo Ensembl Compara citations steinmetzlab
	In silico prediction of the peroxisomal proteome in fungi, plants and animals. [My Copy] Journal of molecular biology, Vol. 330, No. 2. (4 July 2003), pp. 443-456. by O. Emanuelsson, A. Elofsson, G. von Heijne, S. Cristóbal posted to in nazanin peroxisomes prediction silico by mdstobbe on 2008-08-21 11:07:21 as along with 1 person ptrobajo
	MultiLoc: prediction of protein subcellular localization using N-terminal targeting sequences, sequence motifs and amino acid composition. [My Copy] Bioinformatics (Oxford, England), Vol. 22, No. 10. (15 May 2006), pp. 1158-1165. by A. Höglund, P. Dönnes, T. Blum, H. W. Adolph, O. Kohlbacher posted to localization multiloc nazanin by mdstobbe on 2008-08-21 11:06:51 as along with 1 person ptrobajo
	Locating proteins in the cell using TargetP, SignalP and related tools. [My Copy] Nature protocols, Vol. 2, No. 4. (2007), pp. 953-971. by Olof Emanuelsson, Søren Brunak, Gunnar von Heijne, Henrik Nielsen posted to localization nazanin tools by mdstobbe on 2008-08-21 11:06:28 as along with 6 people azazello dandaman nlapalu raiyar guhjy ptrobajo
	PeroxisomeDB: a database for the peroxisomal proteome, functional genomics and disease [My Copy] Nucleic Acids Research, Vol. 35, No. Supplement 1. (January 2007), pp. D815-D822. by Schluter, Agatha, Fourcade, et al. Stephane, Domenech-Estevez, Enric, Gabaldon, Toni, Huerta-Cepas, Jaime, Berthommier, Guillaume, Ripp, Raymond, Wanders, J. A. Ronald, Poch, Olivier, Pujol, Aurora posted to articleconsensus nazanin peroxisomes by mdstobbe on 2008-08-21 11:06:05 as along with 1 person ptrobajo
	Peroxisome targeting signal 1: Is it really a simple tripeptide? [My Copy] Biochimica et Biophysica Acta (BBA) - Molecular Cell Research In Peroxisomes: Morphology, Function, Biogenesis and Disorders, Vol. 1763, No. 12. (December 2006), pp. 1565-1573. by Cecile Brocard, Andreas Hartig posted to nazanin pts1 by mdstobbe on 2008-08-21 11:05:45 as along with 3 people fhaenel viktor21614 ptrobajo
	Identifying novel peroxisomal proteins [My Copy] Proteins: Structure, Function, and Bioinformatics, Vol. 9999, No. 9999. (2007), NA. by John Hawkins, Donna Mahony, Stefan Maetschke, Mark Wakabayashi, Rohan D. Teasdale, Mikael Bodén posted to identifying nazanin peroxisomes by mdstobbe on 2008-08-21 11:05:30 as along with 2 people viktor21614 ptrobajo
	Proteomics Characterization of Mouse Kidney Peroxisomes by Tandem Mass Spectrometry and Protein Correlation Profiling [My Copy] Mol Cell Proteomics, Vol. 6, No. 12. (1 December 2007), pp. 2045-2057. by Sebastian Wiese, Thomas Gronemeyer, Rob Ofman, et al.Markus Kunze, Claudia P. Grou, Jose A. Almeida, Martin Eisenacher, Christian Stephan, Heiko Hayen, Lukas Schollenberger, Thomas Korosec, Hans R. Waterham, Wolfgang Schliebs, Ralf Erdmann, Johannes Berger, Helmut E. Meyer, Wilhelm Just, Jorge E. Azevedo, Ronald J. Wanders, Bettina Warscheid posted to mass nazanin peroxisomes spectrometry by mdstobbe on 2008-08-21 11:05:06 as along with 1 person ptrobajo
	A statistical framework for genomic data fusion. [My Copy] Bioinformatics, Vol. 20, No. 16. (1 November 2004), pp. 2626-2635. by G. R. Lanckriet, T. De Bie, N. Cristianini, M. I. Jordan, W. S. Noble posted to data fusion genomic nazanin by mdstobbe on 2008-08-21 11:04:34 as along with 8 people isimpson dragonrez tmmurali jfr mbeautru nedwards carlk ptrobajo
	A Mitochondrial Protein Compendium Elucidates Complex I Disease Biology [My Copy] Cell, Vol. 134, No. 1. (11 July 2008), pp. 112-123. by David J. Pagliarini, Sarah E. Calvo, Betty Chang, et al.Sunil A. Sheth, Scott B. Vafai, Shao-En Ong, Geoffrey A. Walford, Canny Sugiana, Avihu Boneh, William K. Chen, David E. Hill, Marc Vidal, James G. Evans, David R. Thorburn, Steven A. Carr, Vamsi K. Mootha posted to compendium mitochondrial nazanin by mdstobbe on 2008-08-21 11:04:11 as along with 4 people brianb neils ptrobajo raiyar
	Refining Protein Subcellular Localization [My Copy] PLoS Computational Biology, Vol. 1, No. 6. (1 November 2005), e66. by Michelle S. Scott, Sara J. Calafell, David Y. Thomas, Michael T. Hallett posted to localization nazanin scott by mdstobbe on 2008-08-21 11:03:16 as along with 4 people and 1 group dolhuis neils grahamc ptrobajo SNE
	SherLoc: high-accuracy prediction of protein subcellular localization by integrating text and protein sequence data. [My Copy] Bioinformatics, Vol. 23, No. 11. (1 June 2007), pp. 1410-1417. by H. Shatkay, A. Höglund, S. Brady, T. Blum, P. Dönnes, O. Kohlbacher posted to localization nazanin sherloc by mdstobbe on 2008-08-21 11:02:25 as along with 2 people raiyar ptrobajo
	IDconverter and IDClight: conversion and annotation of gene and protein IDs. [My Copy] BMC bioinformatics, Vol. 8, No. 1. (2007) by Andreu Alibés, Patricio Yankilevich, Andrés Cañada, Ramón Díaz-Uriarte posted to converter id by mdstobbe on 2008-06-30 15:47:07 as along with 10 people daforerog druvus operon dswan guhjy aalibes jfr grahamc cerami srp33
	Gene function prediction using labeled and unlabeled data [My Copy] BMC Bioinformatics, Vol. 9, No. 1. (2008), 57. by Xing M. Zhao, Yong Wang, Luonan Chen, Kazuyuki Aihara posted to function gene labeled nazanin prediction svm unlabeled by mdstobbe on 2008-06-27 12:39:47 as along with 4 people sdvillal ptrobajo tmmurali ironcamel
	Subcellular location prediction of proteins using support vector machines with alignment of block sequences utilizing amino acid composition [My Copy] BMC Bioinformatics, Vol. 8, No. 1. (2007) by Takeyuki Tamura, Tatsuya Akutsu posted to localization nazanin svm by mdstobbe on 2008-06-27 12:34:17 as along with 2 people neils grahamc
	'Unite and conquer': enhanced prediction of protein subcellular localization by integrating multiple specialized tools [My Copy] BMC Bioinformatics, Vol. 8 (29 October 2007), 420. by Yao-Qing Shen, Gertraud Burger posted to combination localization mitochondrial nazanin tools by mdstobbe on 2008-06-27 12:28:53 as along with 2 people ptrobajo iris_2001
	Combining classifiers to predict gene function in Arabidopsis thaliana using large-scale gene expression measurements [My Copy] BMC Bioinformatics, Vol. 8 (21 September 2007), 358. by Hui Lan, Rachel Carson, Nicholas J. Provart, Anthony J. Bonner posted to function gene learning machine nazanin prediction by mdstobbe on 2008-06-27 12:24:50 as along with 1 person sanchezbuelna
	Biological sequence classification utilizing positive and unlabeled data. [My Copy] Bioinformatics (14 March 2008) by Yuanyuan Xiao, Mark R R. Segal posted to classification nazanin sequence by mdstobbe on 2008-04-25 13:54:38 as along with 4 people eckart_bindewald djkt guhjy ptrobajo
	Pathways database system: an integrated system for biological pathways. [My Copy] Bioinformatics, Vol. 19, No. 8. (22 May 2003), pp. 930-937. by L. Krishnamurthy, J. Nadeau, G. Ozsoyoglu, et al.M. Ozsoyoglu, G. Schaeffer, M. Tasan, W. Xu posted to articleconsensus pathcase pathway by mdstobbe on 2008-04-25 13:08:43 as along with 3 people and 1 group Scis0000002 irenas kalvala dbk-lab
	Mining Biological Networks for Unknown Pathways. [My Copy] Bioinformatics (30 August 2007) by Ali Cakmak, Gultekin Ozsoyoglu posted to kegg pathway by mdstobbe on 2008-04-25 13:06:25 as along with 8 people cswinburne guhjy tmmurali bluto shigepong cabbagezs idonaldson acakmak
	The Edinburgh human metabolic network reconstruction and its functional analysis. [My Copy] Molecular systems biology, Vol. 3 (2007) by H. Ma, A. Sorokin, A. Mazein, et al.A. Selkov, E. Selkov, O. Demin, I. Goryanin posted to articleconsensus bigg comparison cyc network by mdstobbe on 2008-04-24 13:50:26 as along with 10 people JeremyZucker vpenelle peterli schwartzjmc Garamonfok dullhunk grahamc fishtank cjeans shung
	PLoS Computational Biology: Predicting Co-Complexed Protein Pairs from Heterogeneous Data [My Copy] posted to complexes kernel by mdstobbe on 2008-04-18 16:08:14 as

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mdstobbe's library 63 articles Export

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