jperkins's library 133 articles Export

	Predicting homologous signaling pathways using machine learning [My Copy] Bioinformatics, Vol. 25, No. 22. (15 November 2009), pp. 2913-2920. by Babak Bostan, Russell Greiner, Duane Szafron, Paul Lu posted to 13-nov-09 by jperkins on 2009-11-13 11:31:50 as along with 1 group Orengo Group Journal Picks
	Simultaneous inference of biological networks of multiple species from genome-wide data and evolutionary information: a semi-supervised approach [My Copy] Bioinformatics, Vol. 25, No. 22. (15 November 2009), pp. 2962-2968. by Hisashi Kashima, Yoshihiro Yamanishi, Tsuyoshi Kato, Masashi Sugiyama, Koji Tsuda posted to 13-nov-09 by jperkins on 2009-11-13 11:28:15 as along with 3 people and 1 group roys phoenixzxl druvus Orengo Group Journal Picks
	Next generation software for functional trend analysis [My Copy] Bioinformatics, Vol. 25, No. 22. (15 November 2009), pp. 3043-3044. by Gabriel F. Berriz, John E. Beaver, Can Cenik, Murat Tasan, Frederick P. Roth posted to 13-nov-09 by jperkins on 2009-11-13 11:27:41 as along with 4 people and 1 group tmmurali kmdaily VGreiff guhjy Orengo Group Journal Picks
	Statistical methods for gene set co-expression analysis [My Copy] Bioinformatics, Vol. 25, No. 21. (1 November 2009), pp. 2780-2786. by YounJeong Choi, Christina Kendziorski posted to 13-nov-09 by jperkins on 2009-11-13 11:27:06 as along with 7 people and 1 group ptrobajo natstreet heliopais dolchan zufar rdiaz neils Orengo Group Journal Picks
	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 13-nov-09 by jperkins on 2009-11-13 11:26:20 as along with 8 people and 1 group tonamswish heliopais dolchan greg zufar rdiaz ptrobajo brianb Orengo Group Journal Picks
	integrOmics: an R package to unravel relationships between two omics datasets [My Copy] Bioinformatics, Vol. 25, No. 21. (1 November 2009), pp. 2855-2856. by Kim-Anh Le Cao, Ignacio Gonzalez, Sebastien Dejean posted to 13-nov-09 by jperkins on 2009-11-13 11:24:21 as along with 17 people and 1 group molnet-mna tonamswish dswan mayercd operon kshameer heliopais dolchan nuin ptrobajo sebastien_vigneau rdiaz cassj brianb neils natstreet druvus Orengo Group Journal Picks
	Conserved Expression Patterns Predict microRNA Targets [My Copy] PLoS Comput Biol, Vol. 5, No. 9. (25 September 2009), e1000513. by William Ritchie, Megha Rajasekhar, Stephane Flamant, John E. J. Rasko posted to 23-oct-09 by jperkins on 2009-10-22 17:17:40 as along with 11 people and 1 group heliopais gdb samgj ealloza toni_marco neils ptrobajo al2na TRHvidsten djkt cisevol microRNA
	NETGEN: generating phylogenetic networks with diploid hybrids [My Copy] Bioinformatics, Vol. 22, No. 15. (1 August 2006), pp. 1921-1923. by M. M. Morin, B. M. E. Moret posted to introduction by jperkins on 2009-10-12 11:21:19 as
	Physical protein-protein interactions predicted from microarrays [My Copy] Bioinformatics, Vol. 24, No. 22. (15 November 2008), pp. 2608-2614. by Ta-tsen Soong, Kazimierz O. Wrzeszczynski, Burkhard Rost posted to introduction by jperkins on 2009-10-12 11:11:48 as along with 12 people kiekyon jfr cgaugain guhjy saket iris_2001 pengchy natstreet grahamc phoenixzxl neils renatomilani
	Structural genomics of membrane proteins [My Copy] Genome Biology, Vol. 5, No. 4. (2004), 215. by Peter Walian, Timothy Cross, Bing Jap posted to introduction by jperkins on 2009-10-12 11:06:44 as
	PRISM: protein interactions by structural matching [My Copy] Nucl. Acids Res., Vol. 33, No. suppl_2. (1 July 2005), pp. W331-336. by Utkan Ogmen, Ozlem Keskin, A. Selim Aytuna, Ruth Nussinov, Attila Gursoy posted to introduction by jperkins on 2009-10-12 11:05:51 as
	Detecting distant homology with Meta-BASIC [My Copy] Nucl. Acids Res., Vol. 32, No. suppl_2. (1 July 2004), pp. W576-581. by Krzysztof Ginalski, Marcin von Grotthuss, Nick V. Grishin, Leszek Rychlewski posted to introduction by jperkins on 2009-10-12 11:04:55 as along with 2 people rabio schuylrp
	Exploring Expression Data: Identification and Analysis of Coexpressed Genes [My Copy] Genome Research, Vol. 9, No. 11. (1 November 1999), pp. 1106-1115. by Laurie J. Heyer, Semyon Kruglyak, Shibu Yooseph posted to introduction by jperkins on 2009-10-12 10:58:42 as along with 2 people daveGerrard aswin
	Progress and challenges in protein structure prediction [My Copy] Current Opinion in Structural Biology In Nucleic acids / Sequences and topology, Vol. 18, No. 3. (June 2008), pp. 342-348. by Y. Zhang posted to introduction by jperkins on 2009-10-09 10:58:54 as along with 11 people saunders ameetsoni rodrigofaccioli newton1234 hadesnumb kgutwin chad_davis barry phoenixzxl marck zwang
	GenTHREADER: an efficient and reliable protein fold recognition method for genomic sequences. [My Copy] Journal of molecular biology, Vol. 287, No. 4. (9 April 1999), pp. 797-815. by D. T. Jones posted to introduction by jperkins on 2009-10-09 10:52:46 as along with 5 people pjcite j3xucite dgront schuylrp janasont
	Bioinformatics : genes, proteins, and computers [My Copy] (29 July 2003) by Christine Orengo, David Jones, Janet M. Thornton posted to introduction by jperkins on 2009-10-09 10:44:34 as along with 1 person npt11tpn
	Comparative protein structure modeling of genes and genomes. [My Copy] Annual review of biophysics and biomolecular structure, Vol. 29 (2000), pp. 291-325. by M. A. Martí-Renom, A. C. Stuart, A. Fiser, R. Sánchez, F. Melo, A. Sali posted to introduction by jperkins on 2009-10-09 10:33:09 as along with 15 people and 2 groups tjimenez fautore aalibes nigham chad_davis ttjoseph marcius ffranca duartemolha dgront ruvido insectopalo min013 IrinaMoreira granujilla BioinfoCIPF SGU-CIPF
	Computational approaches to predict protein-protein and domain-domain interactions [My Copy] In Bioinformatics Algorithms: Techniques and Applications (2008), pp. 465-490. by Raja Jothi, Teresa M. Przytycka posted to introduction by jperkins on 2009-10-09 10:29:20 as along with 1 person ethkim
	Conserved network motifs allow protein-protein interaction prediction [My Copy] Bioinformatics, Vol. 20, No. 18. (12 December 2004), pp. 3346-3352. by Istvan Albert, Reka Albert posted to introduction by jperkins on 2009-10-09 10:22:45 as along with 4 people nurban cjeans Evangelia iris_2001
	IntAct--open source resource for molecular interaction data. [My Copy] Nucleic acids research, Vol. 35, No. Database issue. (12 January 2007), pp. D561-565. by S. Kerrien, Y. Alam-Faruque, B. Aranda, et al.I. Bancarz, A. Bridge, C. Derow, E. Dimmer, M. Feuermann, A. Friedrichsen, R. Huntley, C. Kohler, J. Khadake, C. Leroy, A. Liban, C. Lieftink, L. Montecchi-Palazzi, S. Orchard, J. Risse, K. Robbe, B. Roechert, D. Thorneycroft, Y. Zhang, R. Apweiler, H. Hermjakob posted to introduction by jperkins on 2009-10-09 10:19:41 as along with 11 people and 3 groups dullhunk chica robert85 mbehbah1 diamantis guhjy chad_davis joergkurtwegner lpfernandes carlk bicko Molecular-Modelling Drug-Design Cheminformatics
	The Database of Interacting Proteins: 2004 update [My Copy] Nucl. Acids Res., Vol. 32, No. suppl_1. (1 January 2004), pp. D449-451. by Lukasz Salwinski, Christopher S. Miller, Adam J. Smith, Frank K. Pettit, James U. Bowie, David Eisenberg posted to introduction by jperkins on 2009-10-09 10:18:08 as along with 4 people npozo minostro chad_davis bicko
	MINT: the Molecular INTeraction database. [My Copy] Nucleic acids research, Vol. 35, No. Database issue. (12 January 2007), pp. D572-574. by Andrew Chatr-aryamontri, Arnaud Ceol, Luisa Montecchi M. Palazzi, et al.Giuliano Nardelli, Maria Victoria V. Schneider, Luisa Castagnoli, Gianni Cesareni posted to introduction by jperkins on 2009-10-09 10:16:39 as along with 4 people aceol swp09 guhjy cerca
	How does gene expression clustering work? [My Copy] Nature Biotechnology, Vol. 23, No. 12. (01 December 2005), pp. 1499-1501. by Patrik D'haeseleer posted to introduction by jperkins on 2009-10-09 10:06:04 as along with 6 people and 1 group bozdagd Yanno okarsligil sesejun tabu renatomilani Bioinformatics
	Conserved clusters of functionally related genes in two bacterial genomes. [My Copy] Journal of molecular evolution, Vol. 44, No. 1. (January 1997), pp. 66-73. by J. Tamames, G. Casari, C. Ouzounis, A. Valencia posted to introduction by jperkins on 2009-10-09 10:04:40 as
	An efficient algorithm for large-scale detection of protein families [My Copy] Nucl. Acids Res., Vol. 30, No. 7. (1 April 2002), pp. 1575-1584. by A. J. Enright, S. Van Dongen, C. A. Ouzounis posted to introduction by jperkins on 2009-10-09 10:00:27 as along with 22 people and 2 groups calderonv nedwards dakelley druvus treangen carlk cgaugain johanviklund chad_davis camster operon knaseanka indigoviolet skhadar nirfriedman dgront entropy gcalda GustavoLacerda hpaces RebeccaHamer Borelli dbk-lab EisenLab
	Protein interaction maps for complete genomes based on gene fusion events [My Copy] Nature, Vol. 402, No. 6757. (04 November 1999), pp. 86-90. by Anton J. Enright, Ioannis Iliopoulos, Nikos C. Kyrpides, Christos A. Ouzounis posted to introduction by jperkins on 2009-10-09 09:56:56 as along with 6 people swp09 balajis ruvido selrac carlk iris_2001
	A combined algorithm for genome-wide prediction of protein function. [My Copy] Nature, Vol. 402, No. 6757. (4 November 1999), pp. 83-86. by E. M. Marcotte, M. Pellegrini, M. J. Thompson, T. O. Yeates, D. Eisenberg posted to introduction by jperkins on 2009-10-09 09:54:32 as along with 7 people and 1 group dragonrez Robinder shivaram lfriedl ruvido cjeans carlk kdl
	Use of Logic Relationships to Decipher Protein Network Organization [My Copy] Science, Vol. 306, No. 5705. (24 December 2004), pp. 2246-2249. by Peter M. Bowers, Shawn J. Cokus, David Eisenberg, Todd O. Yeates posted to introduction by jperkins on 2009-10-09 09:51:51 as along with 4 people and 1 group mdimmic lfriedl opheliav wnpx kdl
	Phylogenetic Networks: Modeling, Reconstructibility, and Accuracy [My Copy] IEEE/ACM Transactions on Computational Biology and Bioinformatics, Vol. 1, No. 1. (2004), pp. 13-23. by Bernard M. E. Moret, Luay Nakhleh, Tandy Warnow, et al.C. Randal Linder, Anna Tholse, Anneke Padolina, Jerry Sun, Ruth Timme posted to introduction by jperkins on 2009-10-09 09:50:20 as
	Predicting Functional Gene Links from Phylogenetic-Statistical Analyses of Whole Genomes [My Copy] PLoS Comput Biol, Vol. 1, No. 1. (24 June 2005), e3. by Daniel Barker, Mark Pagel posted to introduction by jperkins on 2009-10-09 09:47:56 as along with 10 people and 1 group biomcgary skembel Robinder rw294 balajis maryee arunyan bartleby pradiptaray rvosa iSEEM
	Assigning protein functions by comparative genome analysis: Protein phylogenetic profiles [My Copy] Proceedings of the National Academy of Sciences of the United States of America, Vol. 96, No. 8. (13 April 1999), pp. 4285-4288. by Matteo Pellegrini, Edward M. Marcotte, Michael J. Thompson, David Eisenberg, Todd O. Yeates posted to introduction by jperkins on 2009-10-09 09:46:45 as along with 15 people and 1 group calderonv pablocarb chica skembel Robinder dragonrez bicko lfriedl balajis opheliav tny ruvido winterschlaefer shung carlk kdl
	The inference of protein-protein interactions by co-evolutionary analysis is improved by excluding the information about the phylogenetic relationships [My Copy] Bioinformatics, Vol. 21, No. 17. (30 June 2005), pp. bti564-3489. by Tetsuya Sato, Yoshihiro Yamanishi, Minoru Kanehisa, Hiroyuki Toh posted to introduction by jperkins on 2009-10-05 16:51:24 as along with 2 people biomcgary cjeans
	The human protein coevolution network. [My Copy] Genome research, Vol. 19, No. 10. (20 October 2009), pp. 1861-1871. by Elisabeth R. Tillier, Robert L. Charlebois posted to introduction by jperkins on 2009-10-05 16:43:07 as along with 7 people dfdong Garamonfok venancio TRHvidsten djkt phoenixzxl tmmurali
	Assessing protein co-evolution in the context of the tree of life assists in the prediction of the interactome. [My Copy] Journal of molecular biology, Vol. 352, No. 4. (30 September 2005), pp. 1002-1015. by Florencio Pazos, Juan A. Ranea, David Juan, Michael J. Sternberg posted to introduction by jperkins on 2009-10-05 16:39:50 as along with 5 people chica biomcgary Robinder balajis cjeans
	In silico two-hybrid system for the selection of physically interacting protein pairs. [My Copy] Proteins, Vol. 47, No. 2. (1 May 2002), pp. 219-227. by Florencio Pazos, Alfonso Valencia posted to introduction by jperkins on 2009-10-05 16:36:43 as along with 4 people and 1 group bicko lfriedl balajis dgront kdl
	Co-evolution of proteins with their interaction partners1 [My Copy] Journal of Molecular Biology, Vol. 299, No. 2. (02 June 2000), pp. 283-293. by Chern-Sing Goh, Andrew A. Bogan, Marcin Joachimiak, Dirk Walther, Fred E. Cohen posted to introduction by jperkins on 2009-10-05 16:34:08 as along with 6 people stharward chica druvus Robinder opheliav cjeans
	Similarity of phylogenetic trees as indicator of protein-protein interaction [My Copy] Protein Eng., Vol. 14, No. 9. (1 September 2001), pp. 609-614. by Florencio Pazos, Alfonso Valencia posted to introduction by jperkins on 2009-10-05 16:32:42 as along with 8 people Robinder marti balajis IbnBio tale selrac ca3295 bicko
	Targeting and tinkering with interaction networks [My Copy] Nature Chemical Biology, Vol. 4, No. 11. (20 October 2008), pp. 666-673. by Robert B. Russell, Patrick Aloy posted to introduction by jperkins on 2009-10-05 16:31:26 as along with 3 people and 1 group lees zwang chad_davis Orengo Group Journal Picks
	Diversity of protein\|[ndash]\|protein interactions [My Copy] The EMBO Journal, Vol. 22, No. 14. (15 July 2003), pp. 3486-3492. by Irene M. A. Nooren, Janet M. Thornton posted to introduction by jperkins on 2009-10-05 16:29:17 as
	The biological effects of endogenous nerve growth factor on adult sensory neurons revealed by a trkA-IgG fusion molecule [My Copy] Nature Medicine, Vol. 1, No. 8. (01 August 1995), pp. 774-780. by Stephen B. Mcmahon, David L. H. Bennett, John V. Priestley, David L. Shelton posted to introduction by jperkins on 2009-10-05 16:26:01 as
	Functions and mechanisms of retrograde neurotrophin signalling [My Copy] Nat Rev Neurosci, Vol. 6, No. 8. (01 August 2005), pp. 615-625. by Larry S. Zweifel, Rejji Kuruvilla, David D. Ginty posted to introduction by jperkins on 2009-10-05 16:24:56 as
	Molecular biology of the cell [My Copy] (20 November 2008) by Bruce Alberts posted to introduction by jperkins on 2009-10-05 16:22:41 as along with 2 people heliopais ilyashl
	Ontologies of Cellular Networks [My Copy] Sci. Signal., Vol. 1, No. 50. (16 December 2008), mr2. by Robert Arp, Barry Smith posted to introduction by jperkins on 2009-10-05 16:14:31 as along with 4 people guhjy renatomilani balicea reyez
	Cluster analysis. [My Copy] (01 May 2001) by Brian Everitt, Sabine Landau, Morven Leese posted to introduction by jperkins on 2009-10-05 16:11:31 as along with 5 people akastrin lwilliams ingo ykuoka quianominorleo
	Machine learning in bioinformatics [My Copy] Brief Bioinform, Vol. 7, No. 1. (27 February 2006), pp. bbk007-112. by Pedro Larranaga, Borja Calvo, Roberto Santana, et al.Concha Bielza, Josu Galdiano, Inaki Inza, Jose A. Lozano, Ruben Armananzas, Guzman Santafe, Aritz Perez, Victor Robles posted to introduction by jperkins on 2009-10-05 16:10:17 as along with 8 people and 2 groups akastrin svozil jfr yas caporaso rsantana dimatura xili03 T_lab biomedical-nlp
	Discovering molecular functions significantly related to phenotypes by combining gene expression data and biological information [My Copy] Bioinformatics, Vol. 21, No. 13. (19 April 2005), pp. bti457-2993. by Fatima Al-Shahrour, Ramon Diaz-Uriarte, Joaquin Dopazo posted to introduction by jperkins on 2009-10-05 14:54:38 as
	Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources [My Copy] Nature Protocols, Vol. 4, No. 1. (18 December 2008), pp. 44-57. by Da W. Huang, Brad T. Sherman, Richard A. Lempicki posted to introduction by jperkins on 2009-10-05 14:45:21 as along with 16 people and 2 groups darian rschulz tonamswish operon VGreiff jfr Stew bertelsen Sonix dswan guhjy wimufi brianb idonaldson mrochman daforerog Bioinformatics - CRUK Bioinformatics
	CLENCH: a program for calculating CLuster ENriCHment using the Gene Ontology [My Copy] Bioinformatics, Vol. 20, No. 7. (5 February 2004), pp. bth056-1197. by N. H. Shah, N. V. Fedoroff posted to introduction by jperkins on 2009-10-05 14:43:06 as along with 1 person dragonrez
	FatiGO: a web tool for finding significant associations of Gene Ontology terms with groups of genes. [My Copy] Bioinformatics (Oxford, England), Vol. 20, No. 4. (1 March 2004), pp. 578-580. by Fátima Al-Shahrour, Ramón Díaz-Uriarte, Joaquín Dopazo posted to introduction by jperkins on 2009-10-05 14:41:03 as along with 8 people vkwn diamantis aalibes RMGraze macavity1g Garamonfok ellakat sgoetz
	GOTree Machine (GOTM): a web-based platform for interpreting sets of interesting genes using Gene Ontology hierarchies [My Copy] BMC Bioinformatics, Vol. 5, No. 1. (2004), 16. by Bing Zhang, Denise Schmoyer, Stefan Kirov, Jay Snoddy posted to introduction by jperkins on 2009-10-05 14:30:38 as

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jperkins's library 133 articles Export

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